library.bib

### A ###
@article{Aerts2023,
    author = {Aerts, Peter and Mielke, Falk and Vanden Hole, Charlotte and Van Gorp, Merel J.W. and Van Ginneken, Chris},
    year = {2023},
    title = {{Early development of locomotion in the term piglet model: does size matter?}},
    doi = {10.1093/icb/icad054},
    pages = {icad054},
    journal = {Integrative and Comparative Biology},
}

@article{Aerts2023b,
    author = {Aerts, Peter and Goyens, Jana and Berillon, Gilles and D'Août, Kristiaan and Druelle, François},
    year = {2023},
    title = {{From quadrupedal to bipedal walking ‘on the fly’: the mechanics of dynamical mode transition in primates}},
    doi = {10.1242/jeb.244792},
    journal = {Journal of Experimental Biology},
    volume = {226},
    number = {2},
    pages = {jeb244792},
    month = {01},
    abstract = {{We investigated how baboons transition from quadrupedal to bipedal walking without any significant interruption in their forward movement (i.e. transition ‘on the fly’). Building on basic mechanical principles (momentum only changes when external forces/moments act on the body), insights into possible strategies for such a dynamical mode transition are provided and applied first to the recorded planar kinematics of an example walking sequence (including several continuous quadrupedal, transition and subsequent bipedal steps). Body dynamics are calculated from the kinematics. The strategy used in this worked example boils down to: crouch the hind parts and sprint them underneath the rising body centre of mass. Forward accelerations are not in play. Key characteristics of this transition strategy were extracted: progression speed, hip height, step duration (frequency), foot positioning at touchdown with respect to the hip and the body centre of mass (BCoM), and congruity between the moments of the ground reaction force about the BCoM and the rate of change of the total angular moment. Statistical analyses across the full sample (15 transitions of 10 individuals) confirm this strategy is always used and is shared across individuals. Finally, the costs (in J kg−1 m−1) linked to on the fly transitions were estimated. The costs are approximately double those of both the preceding quadrupedal and subsequent bipedal walking. Given the short duration of the transition as such (\\<1 s), it is argued that the energetic costs to change walking posture on the fly are negligible when considered in the context of the locomotor repertoire.}},
    issn = {0022-0949},
}

@book{Alexander2003,
    author = {Alexander, R McNeill},
    year = {2003},
    title = {Principles of animal locomotion},
    publisher = {Princeton University Press},
}

@incollection{Alexander2003Energy,
    author = {Alexander, R McNeill},
    title = {Energy Requirements for Locomotion},
    year = {2003},
    booktitle = {Principles of animal locomotion},
    publisher = {Princeton University Press},
    chapter = 3,
}

@article{Alvarenga2013,
    author = {Alvarenga, A.L.N. and Chiarini-Garcia, H. and Cardeal, P.C. and Moreira, L.P. and Foxcroft, G.R. and Fontes, D.O. and Almeida, F.R.C.L.},
    year = {2013},
    title = {{Intra-uterine growth retardation affects birthweight and postnatal development in pigs, impairing muscle accretion, duodenal mucosa morphology and carcass traits}},
    doi = {10.1071/RD12021},
    journal = {Reproduction, Fertility and Development},
    volume = {25},
    number = {2},
    pages = {387--395},
    publisher = {CSIRO Publishing}
}

### B ###
@article{Benjamin2019,
    author = {Benjamin, Madonna and Yik, Steven},
    year = {2019},
    title = {{Precision Livestock Farming in Swine Welfare: A Review for Swine Practitioners}},
    doi = {10.3390/ani9040133},
    journal = {Animals},
    volume = {9},
    number = {4},
    article-number = {133},
    url = {https://www.mdpi.com/2076-2615/9/4/133},
    pubmedid = {30935123},
    issn = {2076-2615},
    abstract = {The burgeoning research and applications of technological advances are launching the development of precision livestock farming. Through sensors (cameras, microphones and accelerometers), images, sounds and movements are combined with algorithms to non-invasively monitor animals to detect their welfare and predict productivity. In turn, this remote monitoring of livestock can provide quantitative and early alerts to situations of poor welfare requiring the stockperson’s attention. While swine practitioners’ skills include translation of pig data entry into pig health and well-being indices, many do not yet have enough familiarity to advise their clients on the adoption of precision livestock farming practices. This review, intended for swine veterinarians and specialists, (1) includes an introduction to algorithms and machine learning, (2) summarizes current literature on relevant sensors and sensor network systems, and drawing from industry pig welfare audit criteria, (3) explains how these applications can be used to improve swine welfare and meet current pork production stakeholder expectations. Swine practitioners, by virtue of their animal and client advocacy roles, interpretation of benchmarking data, and stewardship in regulatory and traceability programs, can play a broader role as advisors in the transfer of precision livestock farming technology, and its implications to their clients.},
}

@article{Bernstein1927a,
    author = {Bernstein, Nikolai A.},
    year = {1927},
    title = {{Analyse aperiodischer trigonometrischer Reihen}},
    doi = {10.1002/ZAMM.19270070606},
    journal = {ZAMM-Journal of Applied Mathematics and Mechanics/Zeitschrift f{\"u}r Angewandte Mathematik und Mechanik},
    volume = {7},
    number = {6},
    pages = {476--485},
    publisher = {Wiley Online Library},
}

@article{Bernstein1927b,
    author   = {Bernstein, Nikolai A.},
    year     = {1927},
    title    = {Kymozyklographion, ein neuer {A}pparat f{\"u}r {B}ewegungsstudium},
    doi      = {10.1007/BF01723725},
    journal  = {{Pfl{\"u}ger's Archiv f{\"u}r die gesamte Physiologie des Menschen und der Tiere}},
    volume   = {217},
    number   = {1},
    pages    = {782--792},
    month    = {Dec},
    issn     = {1432-2013},
    abstract = {Der vom Verf. zu besonders exakten Untersuchungen im Bereiche normaler und pathologischer Bewegungen konstruierte Apparat, Kymozyklographion (K.-Z.) benannt, basiert auf dem Prinzip des Chronophotographierens einer Reihe von Leuchtpunkten, die an den Gelenken des Versuchsorgans angebracht sind, (Chronozyklographie), auf einem gleichm{\"a}{\ss}ig beweglichen Film. Dieses Verfahren vereinigt die Vorz{\"u}ge der chronozyklographischen Methode der Bewegungsregistration mit einer M{\"o}glichkeit beliebig lange dauernde und komplizierte Bewegungsfolgerungen aufzuzeichnen und zu analysieren. Die Methode ist zum Studium verschiedenster normaler und pathologischer Bewegungen anwendbar, wobei die Dechiffrierung der Aufzeichnungen der K.-Z.-Kamera mittels der zyklogrammetrischen Methodik des Verfassers besonders bequem und exakt erscheint.},
    day      = {01},
}

@incollection{Bernstein1935,
    author = {Bernstein, Nikolai A.},
    year = {1935},
    title = {{The Problem of the Interrelation of Co-Ordination and Localization}},
    doi = {10.1016/S0166-4115(08)61370-9},
    chapter = {2},
    editor = {Whiting, H.T.A.},
    series = {Advances in Psychology},
    publisher = {North-Holland},
    volume = {17},
    pages = {77-119},
    booktitle = {{Human Motor Actions: Bernstein Reassessed (1984)}},
    issn = {0166-4115},
    url = {https://www.sciencedirect.com/science/article/pii/S0166411508613709},
}

@book{Biewener2018,
    author={Biewener, Andrew and Patek, Sheila},
    year={2018},
    title={Animal locomotion},
    publisher={Oxford University Press},
}

@incollection{Biewener2018Energy,
    author={Biewener, Andrew and Patek, Sheila},
    year={2018},
    title = {Energetics of Locomotion},
    booktitle={Animal locomotion},
    publisher={Oxford University Press},
    chapter = 3,
}

@article {Black1996,
    title = {Human energy expenditure in affluent societies: an analysis of 574 doubly-labelled water measurements},
    author = {Black, AE and Coward, WA and Cole, TJ and Prentice, AM},
    number = {2},
    volume = {50},
    month = {February},
    year = {1996},
    journal = {European journal of clinical nutrition},
    issn = {0954-3007},
    pages = {72—92},
    abstract = {To describe average levels of free-living energy expenditure in people from affluent societies and to determine the influence of body weight, height, age and sex. Analysis of 574 measurements of total energy expenditure (TEE, assessed by the doubly-labelled water method); basal metabolic rate (BMR, directly measured or derived from similar directly measured proxy measures such as during sleep); activity energy expenditure (AEE, derived as TEE-BMR); and physical activity level (PAL, derived as TEE/BMR) from people aged 2-95 years. The dataset was extracted from 1614 published and unpublished measurements in 1156 subjects after exclusion of repeat estimates and subjects in special physiological or behavioural states (eg pregnancy, athletic or military training etc). A separate analysis of data from non-ambulant subjects, and from elite endurance athletes (all excluded from the main dataset) established the limits of human daily energy expenditure at around 1.2 x BMR and 4.5 x BMR. In the main analysis, the validity of PAL as an index of TEE adjusted for BMR was tested and confirmed. Regression equations were then derived to describe TEE, BMR, AEE and PAL in terms of body weight, height, age and sex. As anticipated, TEE, BMR and AEE were all positively related to weight and height, while age was a negative predictor, especially of activity. The influence of weight disappeared when TEE was expressed as PAL, but height and age remained as highly significant predictors. For all three components, females expended 11\% less energy on average than males after adjustment for weight, height and age. Average levels of energy expenditure in different age and sex groups are tabulated. There now exists a large and robust database of energy expenditure measurements obtained by the doubly-labelled water method. Analysis of the data from affluent societies shows that, in general, levels of energy expenditure are similar to the recommendations for energy requirements adopted by FAO/WHO/UNU (1985) and UK Department of Health (1991). PAL values for active subjects tend to be higher than is currently assumed. The current analysis provides a substantial body of normal data against which other estimates can be compared.},
    url = {http://europepmc.org/abstract/MED/8641250}
}

@article{Bongaardt2000,
    author    = {Bongaardt, Rob and Meijer, Onno G.},
    journal   = {Journal of Motor Behavior},
    title     = {{Bernstein's Theory of Movement Behavior: Historical Development and Contemporary Relevance}},
    year      = {2000},
    number    = {1},
    pages     = {57--71},
    volume    = {32},
    abstract  = {In present-day movement science, N. A. Bernstein's formulation of the problems of motor control is often taken as the starting point. The reliance on Bernstein has not brought agreement among his followers, however. In this article, the authors pose the following question: Does the disagreement arise from the structure of his work itself or from incomplete exploitation of his thinking? By using, inter alia, Bernstein's 24 English and German articles, the authors present an analysis of the development of Bernstein's theory of movement behavior, against the backdrop of the scientific progress in the Soviet Union in Bernstein's time and the clashes between Soviet politics and science. Bernstein addressed in his early articles the measurement and biomechanical analysis of movements. His experimental data soon indicated the need for a new understanding of the organization of movements, which he formulated in terms of coordination. Because of political problems, his work was interrupted; but after being “rehabilitated” and again allowed to work. Bernstein aimed to explain how animals find and optimize the solutions to motor problems. The structure of the theory that ensued was comprehensive exactly by virtue of his repeatedly shifting focus between the different aspects of the organization of movement: More important than the answers he gave were the questions he asked. Moreover, the way he approached those questions may help scientists solve pressing problems in present-day movement science.},
    doi       = {10.1080/00222890009601360},
    publisher = {Routledge},
}

@article{Borghese1996,
    author = {Borghese, N A and Bianchi, L and Lacquaniti, F},
    year = {1996},
    title = {{Kinematic determinants of human locomotion.}},
    doi = {10.1113/jphysiol.1996.sp021539},
    journal = {The Journal of Physiology},
    volume = {494},
    number = {3},
    pages = {863-879},
    url = {https://physoc.onlinelibrary.wiley.com/doi/abs/10.1113/jphysiol.1996.sp021539},
    abstract = {1. The aim of this study was to find kinematic patterns that are invariant across the normal range of locomotion speeds. Subjects walked at different, freely chosen speeds ranging from 0.9 to 2.1 m s-1, while motion and ground reaction forces on the right side of the body were recorded in three-dimensional space. 2. The time course of the anatomical angles of flexion-extension at the hip and ankle was variable not only across subjects, but even from trial to trial in the same subject. By contrast, the time course of the changes in the angles of elevation of each limb segment (pelvis, thigh, shank and foot) relative to the vertical was stereotyped across subjects. 3. To compare the waveforms across speeds, data were scaled in time relative to gait cycle duration. The pattern of ground reaction forces was highly speed dependent. Several distinct families of curves could be recognized in the flexion-extension angles at the hip and ankle. Instead, the waveforms of global length and elevation of the limb, elevation angles of all limb segments and flexion-extension at the knee were invariant with speed. 4. When gait trajectories at all speeds are plotted in the position space defined by the elevation angles of the limb segments, they describe regular loops on a plane. The statistical characteristics of these angular covariations were quantified by means of principal component analysis. The first two principal components accounted together for > 99\% of the total experimental variance, and were quantitatively comparable in all subjects. 5. This constraint of planar covariation of the elevation angles is closely reminiscent of that previously described for the control of posture. The existence of laws of intersegmental co-ordination, common to the control of posture and locomotion, presumably assures the maintenance of dynamic equilibrium during forward progression, and the anticipatory adaptation to potentially destabilizing factors by means of co-ordinated kinematic synergies of the whole body.},
}


### C ###

@article{Chamberlin1890,
    author  = {Chamberlin, T. C.},
    journal = {Science},
    title   = {{The Method of Multiple Working Hypotheses}},
    year    = {1890},
    number  = {366},
    pages   = {92-96},
    volume  = {ns-15},
    doi     = {10.1126/science.ns-15.366.92},
    url     = {https://www.science.org/doi/abs/10.1126/science.ns-15.366.92},
}

@article{Che2010,
    author = {Che, Lianqiang and Thymann, Thomas and Bering, Stine B and Hu{\"e}rou-Luron, Le and D'inca, Romain and Zhang, Keying and Sangild, Per T and others},
    year = {2010},
    title = {{IUGR does not predispose to necrotizing enterocolitis or compromise postnatal intestinal adaptation in preterm pigs}},
    doi = {10.1203/PDR.0b013e3181c1b15e},
    journal = {Pediatric research},
    volume = {67},
    number = {1},
    pages = {54--59},
    publisher = {Nature Publishing Group},
}

@article{Cilieborg2011,
    author = {Cilieborg, Malene S and Boye, Mette and M{\o}lbak, Lars and Thymann, Thomas and Sangild, Per T},
    year = {2011},
    title = {{Preterm birth and necrotizing enterocolitis alter gut colonization in pigs}},
    doi = {10.1203/PDR.0b013e3181ff2a89},
    journal = {Pediatric research},
    volume = {69},
    number = {1},
    pages = {10--16},
    publisher = {Nature Publishing Group},
}


### D ###
@book{Darwin1859,
    author = {Darwin, Charles},
    year = {1859},
    title  = {On the Origin of Species by Means of Natural Selection},
    publisher = {Murray},
    address = {London},
    keywords = {evolution},
}

@incollection{Darwin1859cpt3,
    author = {Darwin, Charles},
    year = {1859},
    title = {Chapter III. Struggle for Existence},
    booktitle = {On the Origin of Species by Means of Natural Selection},
    publisher = {Murray},
    chapter = 3,
    address = {London},
    keywords = {evolution},
}

@article{Demuth2023,
    author = {Demuth, Oliver E. and Herbst, Eva and Polet, Delyle T. and Wiseman, Ashleigh L. A. and Hutchinson, John R.},
    year = {2023},
    title = {{Modern three-dimensional digital methods for studying locomotor biomechanics in tetrapods}},
    doi = {10.1242/jeb.245132},
    journal = {Journal of Experimental Biology},
    volume = {226},
    number = {Suppl1},
    pages = {jeb245132},
    month = {02},
    abstract = {{Here, we review the modern interface of three-dimensional (3D) empirical (e.g. motion capture) and theoretical (e.g. modelling and simulation) approaches to the study of terrestrial locomotion using appendages in tetrapod vertebrates. These tools span a spectrum from more empirical approaches such as XROMM, to potentially more intermediate approaches such as finite element analysis, to more theoretical approaches such as dynamic musculoskeletal simulations or conceptual models. These methods have much in common beyond the importance of 3D digital technologies, and are powerfully synergistic when integrated, opening a wide range of hypotheses that can be tested. We discuss the pitfalls and challenges of these 3D methods, leading to consideration of the problems and potential in their current and future usage. The tools (hardware and software) and approaches (e.g. methods for using hardware and software) in the 3D analysis of tetrapod locomotion have matured to the point where now we can use this integration to answer questions we could never have tackled 20 years ago, and apply insights gleaned from them to other fields.}},
    issn = {0022-0949},
}


### G ###
@article{Grandinson2002,
    author = {Grandinson, Katja and Lund, Mogens Sand{\o} and Rydhmer, Lotta and Strandberg, Erling},
    year = {2002},
    title = {{Genetic Parameters for the Piglet Mortality Traits Crushing, Stillbirth and Total Mortality, and their Relation to Birth Weight}},
    doi = {10.1080/090647002762381041},
    journal = {Acta Agriculturae Scandinavica, Section A - Animal Science},
    volume = {52},
    number = {4},
    pages = {167-173},
    publisher = {Taylor \& Francis},
}

### H ###

@article{Hildebrand1989,
    author    = {Hildebrand, Milton},
    journal   = {BioScience},
    title     = {{The Quadrupedal Gaits of Vertebrates}},
    year      = {1989},
    issn      = {00063568, 15253244},
    number    = {11},
    pages     = {766--775},
    volume    = {39},
    doi       = {10.2307/1311182},
    publisher = {[American Institute of Biological Sciences, Oxford University Press]},
    url       = {http://www.jstor.org/stable/1311182},
    urldate   = {2023-03-09},
}


### I ###

@article{Ivanenko2008,
    author   = {Ivanenko, Y. P. and d'Avella, A. and Poppele, R. E. and Lacquaniti, F.},
    journal  = {Journal of Neurophysiology},
    title    = {On the Origin of Planar Covariation of Elevation Angles During Human Locomotion},
    year     = {2008},
    number   = {4},
    pages    = {1890-1898},
    volume   = {99},
    abstract = {Leg segment rotations in human walking covary, so that the three-dimensional trajectory of temporal changes in the elevation angles lies close to a plane. Recently the role of central versus biomechanical constraints on the kinematics control of human locomotion has been questioned. Here we show, based on both modeling and experimental data, that the planar law of intersegmental coordination is not a simple consequence of biomechanics. First, the full limb behavior in various locomotion modes (walking on inclined surface, staircase stepping, air-stepping, crouched walking, hopping) can be expressed as 2 degrees of freedom planar motion even though the orientation of the plane and pairwise segment angle correlations may differ substantially. Second, planar covariation is not an inevitable outcome of any locomotor movement. It can be systematically violated in some conditions (e.g., when stooping and grasping an object on the floor during walking or in toddlers at the onset of independent walking) or transferred into a simple linear relationship in others (e.g., during stepping in place). Finally, all three major limb segments contribute importantly to planar covariation and its characteristics resulting in a certain endpoint trajectory defined by the limb axis length and orientation. Recent advances in the neural control of movement support the hypothesis about central representation of kinematics components.},
    doi      = {10.1152/jn.01308.2007},
}




### L ###
@book{Lewin2012,
    title={{For the Love of Physics: From the End of the Rainbow to the Edge of Time-A Journey through the Wonders of Physics}},
    author={Lewin, Walter and Goldstein, Warren},
    year={2012},
    publisher={Simon and Schuster}
}


### M ###
@article{Mielke2019,
    author = {Mielke, Falk and Van Ginneken, Chris and Aerts, Peter},
    year = {2019},
    title = {{Quantifying intralimb coordination of terrestrial ungulates with Fourier Coefficient Affine Superimposition}},
    doi = {10.1093/zoolinnean/zlz135},
    journal = {Zoological Journal of the Linnean Society},
    volume = {189},
    number = {3},
    pages = {1067-1083},
    month = {11},
    issn = {0024-4082},
    abstract = {Many phenomena related to motor behaviour in animals are spatially and temporally periodic, making them accessible for transformation to the frequency domain via Fourier Series. Although this has been applied previously, it had not been noticed that the characteristic arrangement of Fourier coefficients in their complex-valued representation resembles landmarks in geometric morphometrics. We define a superimposition procedure in the frequency domain, which removes affine differences (mean, amplitude, phase) to reveal and compare the shape of periodic kinematic measures. This procedure is conceptually linked to dynamic similarity, which can thereby be assessed on the level of individual limb elements. We demonstrate how to make intralimb coordination accessible for large-scale, quantitative analyses. By applying this to a dataset from terrestrial ungulates, dominant patterns in forelimb coordination during walking are identified. This analysis shows that typical strides of these animals differ mostly in how much the limbs are lifted in the presence or absence of obstructive substrate features. This is shown to be independent of morphological features. Besides revealing fundamental characteristics of ungulate locomotion, we argue that the suggested method is generally suitable for the large-scale quantitative assessment of coordination and dynamics in periodic locomotor phenomena.},
}

@article{Mielke2023,
    author   = {Mielke, Falk and Van Ginneken, Chris and Aerts, Peter},
    journal  = {{Frontiers in Veterinary Science}},
    title    = {{A Workflow for Automatic, High Precision Livestock Diagnostic Screening of Locomotor Kinematics}},
    year     = {2023},
    volume   = {10},
    doi      = {10.3389/fvets.2023.1111140},
    keywords = {Locomotion, kinematics, Probabilistic Modeling, Fourier series, precision livestock farming, diagnostics, piglets, low birth weight},
    url      = {https://www.frontiersin.org/articles/10.3389/fvets.2023.1111140},
}



### N ###
@article{Nornberg2021,
    author = {Norberg, Rolf \AA ke},
    year = {2021},
    title = {Test of theory of foraging mode: Goldcrests, Regulus regulus, forage by high-yield, energy-expensive hovering flight when food is abundant but use low-yield, low-cost methods when food is scarce},
    doi = {10.1002/ece3.8205},
    journal = {Ecology and Evolution},
    volume = {11},
    number = {23},
    pages = {16547-16561},
    url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.8205},
    abstract = {{Here, I describe foraging behavior of goldcrests, Regulus regulus, based on eight years of field observation in a coniferous forest dominated by Norway spruce Picea abies in southwestern Sweden. The aim was to test predictions from theory on the choice of optimal foraging modes in relation to food availability. Mortality from early November to early March amounts to 70–86\% among goldcrests in the resident population, suggesting they are food-limited in winter. Food-limitation manifests itself as a shortage of time for foraging. It promotes the use of foraging methods that minimize the daily foraging time by maximizing the rate of net energy gain. It increases both individual survival and competitiveness. Elimination of competitors by exploitation occurs when an individual is able to support itself, while food density in the habitat is reduced to levels at which others cannot. Theory shows that when food is abundant, high-efficiency energy-expensive search and capture methods give shorter daily foraging times than low-efficiency low-cost methods, whereas the latter gives shorter daily foraging times at food shortages (Norberg 2021). Hovering flight is extremely expensive in energy but results in high foraging efficiency. Hover-foraging should therefore be used when food is abundant. In autumn, there were 85.3 arthropods per kilogram of branch mass, as opposed to 12.9 in spring. The numerical decline of arthropods, their fat metabolism, and size-biased predation by birds reduced the spring density of food for goldcrests to less than 15.1\% of the autumn density. Hover-foraging occurred 5.29 times per minute in autumn but only 0.23 times per minute in spring, which is 4.4\% of the autumn frequency. Foraging conditions are favorable at midsummer because of long days, high temperatures, and an abundance of arthropod prey. Parent birds that were feeding fledglings gathered food at a high rate and hovered 5.42 times per minute. But adults with no young to feed were not compelled to maximize the rate of net energy gain and only hover-foraged 0.52 times per minute, which is 10\% of that of providers. These results are highly consistent from year to year and in qualitative agreement with theory.}},
}

### P ###
@article{Pike2002,
    author = {Pike, A. V. L. and Alexander, R. McN.},
    year = {2002},
    title = {{The relationship between limb-segment proportions and joint kinematics for the hind limbs of quadrupedal mammals}},
    DOI = {10.1017/S0952836902001577},
    journal = {Journal of Zoology},
    volume = {258},
    number = {4},
    publisher = {Cambridge University Press},
    pages = {427–433}
}

@article{Platt1964,
    author  = {Platt, John R.},
    journal = {Science},
    title   = {Strong Inference},
    year    = {1964},
    number  = {3642},
    pages   = {347-353},
    volume  = {146},
    doi     = {10.1126/science.146.3642.347},
    url     = {https://www.science.org/doi/abs/10.1126/science.146.3642.347},
}

@article{Plocek2023,
    author = {Plocek, Maura R. and Dunham, Noah T.},
    year = {2023},
    title = {{Spatiotemporal walking gait kinematics of semi-arboreal red pandas (\textit{Ailurus fulgens})}},
    journal = {{Journal of Experimental Zoology Part A: Ecological and Integrative Physiology}},
    keywords = {Ailuridae, arboreal, gait kinematics, red panda, terrestrial},
    doi = {10.1002/jez.2725},
    url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/jez.2725},
    abstract = {Abstract Semi-arboreal mammals must routinely cope with the differing biomechanical challenges of terrestrial versus arboreal locomotion; however, it is not clear to what extent semi-arboreal mammals adjust footfall patterns when moving on different substrates. We opportunistically filmed quadrupedal locomotion (n = 132 walking strides) of semi-arboreal red pandas (Ailurus fulgens; n = 3) housed at Cleveland Metroparks Zoo and examined the effects of substrate type on spatiotemporal gait kinematic variables using linear mixed models. We further investigated the effects of substrate diameter and orientation on arboreal gait kinematics. Red pandas exclusively used lateral sequence (LS) gaits and most frequently utilized LS lateral couplet gaits across terrestrial and arboreal substrates. Red pandas moved significantly slower (p < 0.001), and controlling for speed, had significantly greater relative stride length (p < 0.001), mean stride duration (p = 0.002), mean duty factor (p < 0.001), and mean number of supporting limbs (p < 0.001) during arboreal locomotion. Arboreal strides on inclined substrates were characterized by significantly faster relative speeds and increased limb phase values compared with those horizontal and declined substrates. These kinematics adjustments help to reduce substrate oscillations thereby promoting stability on potentially precarious arboreal substrates. Red panda limb phase values are similar to those of (primarily terrestrial) Carnivora examined to date. Despite the similarity in footfall patterns during arboreal and terrestrial locomotion, flexibility in other kinematic variables is important for semi-arboreal red pandas that must navigate disparate biomechanical challenges inherent to arboreal versus terrestrial locomotion.},
}

@book{Popper2002,
    author = {Popper, Karl},
    year = {2002},
    title = {The logic of scientific discovery},
    doi = {10.4324/9780203994627},
    edition = {2},
    publisher = {Routledge},
}


### Q ###
@article{Quiniou2002,
    author = {Quiniou, N. and Dagorn, J. and Gaudr\'{e}, D.},
    year = {2002},
    title = {{Variation of piglets’ birth weight and consequences on subsequent performance}},
    doi = {10.1016/S0301-6226(02)00181-1},
    journal = {Livestock Production Science},
    volume = {78},
    number = {1},
    pages = {63--70},
    issn = {0301-6226},
    abstract = {Data collected from 965 litters from the start of the Pig Research Station of ITP in July 1998 until October 2000 (12,041 piglets born) were used to evaluate the variation of piglets’ birth weight and its consequences on post-weaning performance. All piglets were individually weighed at birth and at 27 days of age (weaning) but only some of them were studied after weaning. Increasing litter size from ≤11 to ≥16 piglets results in a reduced mean birth weight from 1.59 to 1.26 kg, which corresponds to a mean decrease of 35 g per each additional piglet born. Concomitantly, the proportion of small piglets, i.e. weighing less than 1 kg, increases from 7 to 23% of total born in these litters. Below 1.0 kg BW, more than 11% of piglets are stillbirths and thereafter more than 17% die within the first 24 h. The corresponding values above 1.0 kg average 4 and 3%, respectively. Despite a low number of small animals still alive at weaning, our data indicate that the higher is the birth weight the higher is the average daily gain both over the sucking, the post-weaning and the growing–finishing periods.},
    comment = {Peri- and Post-Natal Mortality in the Pig},
    keywords = {Piglet, Birth weight, Survival, Growth performance},
    url = {http://www.sciencedirect.com/science/article/pii/S0301622602001811},
}


### R ###
@article{Rubenson2007,
    author = {Rubenson, Jonas and Heliams, Denham B. and Maloney, Shane K. and Withers, Philip C. and Lloyd, David G. and Fournier, Paul A.},
    year = {2007},
    title = {Reappraisal of the comparative cost of human locomotion using gait-specific allometric analyses},
    journal = {Journal of Experimental Biology},
    doi = {10.1242/jeb.000992},
    volume = {210},
    number = {20},
    pages = {3513-3524},
    month = {10},
    abstract = {{The alleged high net energy cost of running and low net energy cost of walking in humans have played an important role in the interpretation of the evolution of human bipedalism and the biomechanical determinants of the metabolic cost of locomotion. This study re-explores how the net metabolic energy cost of running and walking (J kg–1m–1) in humans compares to that of animals of similar mass using new allometric analyses of previously published data. Firstly, this study shows that the use of the slope of the regression between the rate of energy expenditure and speed to calculate the net energy cost of locomotion overestimates the net cost of human running. Also, the net energy cost of human running is only 17\% higher than that predicted based on their mass. This value is not exceptional given that over a quarter of the previously examined mammals and birds have a net energy cost of running that is 17\% or more above their allometrically predicted value. Using a new allometric equation for the net energy cost of walking, this study also shows that human walking is 20\%less expensive than predicted for their mass. Of the animals used to generate this equation, 25\% have a relatively lower net cost of walking compared with their allometrically predicted value. This new walking allometric analysis also indicates that the scaling of the net energy cost of locomotion with body mass is gait dependent. In conclusion, the net costs of running and walking in humans are moderately different from those predicted from allometry and are not remarkable for an animal of its size.}},
    issn = {0022-0949},
}


### S ###
@article{Sangild2006,
    author = {Sangild, Per T. and Siggers, Richard H. and Schmidt, Mette and Elnif, Jan and Bjornvad, Charlotte R. and Thymann, Thomas and Grondahl, Marie L. and Hansen, Axel K. and Jensen, Soeren K. and Boye, Mette and Moelbak, Lars and Buddington, Randal K. and Weström, Björn R. and Holst, Jens J. and Burrin, Douglas G.},
    year = {2006},
    title = {{Diet- and Colonization-Dependent Intestinal Dysfunction Predisposes to Necrotizing Enterocolitis in Preterm Pigs}},
    doi = {10.1053/j.gastro.2006.02.026},
    journal = {Gastroenterology},
    volume = {130},
    number = {6},
    pages = {1776-1792},
    issn = {0016-5085},
    url = {https://www.sciencedirect.com/science/article/pii/S0016508506003374},
    abstract = {{Background \& Aims: Preterm birth and formula feeding are key risk factors associated with necrotizing enterocolitis (NEC) in infants, but little is known about intestinal conditions that predispose to disease. Thus, structural, functional, and microbiologic indices were used to investigate the etiology of spontaneous NEC development in preterm pigs. Methods: Piglets were delivered by cesarean section at 92\% gestation, reared in infant incubators, and fed infant formula or colostrum every 3 hours (n = 120) until tissue collection at 1–2 days of age. Results: Clinical and histopathologic signs of NEC were observed in 57\% of pigs fed FORMULA (26/46) and in 5\% of pigs fed COLOSTRUM (2/38) (P < .05). Relative to COLOSTRUM, both healthy and sick FORMULA pigs had reduced intestinal villous heights, enzyme activities, nutrient absorption, and antioxidant levels and higher inducible nitric oxide synthetase activity (P < .05). In healthy pigs, mucosal microbial diversity remained low and diet independent. NEC pigs showed bacterial overgrowth, and a high mucosal density of Clostridium perfringens was detected in some but not all pigs. Germ-free conditions and antiserum against Clostridium perfringens toxin prevented intestinal dysfunction and NEC in formula-fed pigs, whereas the gut trophic factors, epidermal growth factor, and glucagon-like peptide 2 had limited effects. Conclusions: A subclinical, formula-induced mucosal atrophy and dysfunction predispose to NEC and bacterial overgrowth. The adverse feeding effects are colonization dependent and may be reduced by factors in colostrum that include antibodies against aggressive toxins such as those of Clostridium perfringens.}},
}


### T ###
@article{Taylor1982,
    author = {Taylor, C. R. and Heglund, N. C. and Maloiy, G. M.},
    year = {1982},
    title = {{Energetics and mechanics of terrestrial locomotion. I. Metabolic energy consumption as a function of speed and body size in birds and mammals}},
    doi = {10.1242/jeb.97.1.1},
    journal = {Journal of Experimental Biology},
    volume = {97},
    number = {1},
    pages = {1-21},
    month = {04},
    abstract = {{This series of four papers investigates the link between the energetics and the mechanics of terrestrial locomotion. Two experimental variables are used throughout the study: speed and body size. Mass-specific metabolic rates of running animals can be varied by about tenfold using either variable. This first paper considers metabolic energy consumed during terrestrial locomotion. New data relating rate of oxygen consumption and speed are reported for: eight species of wild and domestic artiodactyls; seven species of carnivores; four species of primates; and one species of rodent. These are combined with previously published data to formulate a new allometric equation relating mass-specific rates of oxygen consumed (VO2/Mb) during locomotion at a constant speed to speed and body mass (based on data from 62 avian and mammalian species): VO2/Mb = 0.533 Mb-0.316.vg + 0.300 Mb-0.303 where VO2/Mb has the units ml O2 s-1 kg-1; Mb is in kg; and vg is in m s-1. This equation can be expressed in terms of mass-specific rates of energy consumption (Emetab/Mb) using the energetic equivalent of 1 ml O2 = 20.1 J because the contribution of anaerobic glycolysis was negligible: Emetab/Mb = 10.7 Mb-0.316.vg + 6.03 Mb-0.303 where Emetab/Mb has the units watts/kg. This new relationship applies equally well to bipeds and quadrupeds and differs little from the allometric equation reported 12 years ago by Taylor, Schmid-Nielsen; Raab (1970). Ninety per cent of the values calculated from this genera equation for the diverse assortment of avian and mammalian species included in this regression fall within 25\% of the observed values at the middle of the speed range where measurements were made. This agreement is impressive when one considers that mass-specific rates of oxygen consumption differed by more than 1400\% over this size range of animals.}},
    issn = {0022-0949},
}


### V ###
@article{VandenHole2017,
    author = {Vanden Hole, Charlotte and Goyens, Jana and Prims, Sara and Fransen, Erik and Ayuso Hernando, Miriam and Van Cruchten, Steven and Aerts, Peter and Van Ginneken, Chris},
    year = {2017},
    title = {{How innate is locomotion in precocial animals? A study on the early development of spatio-temporal gait variables and gait symmetry in piglets}},
    doi = {10.1242/jeb.157693},
    journal = {Journal of Experimental Biology},
    volume = {220},
    number = {15},
    pages = {2706-2716},
    month = {08},
    issn = {0022-0949},
    abstract = {Locomotion is one of the most important ecological functions in animals. Precocial animals, such as pigs, are capable of independent locomotion shortly after birth. This raises the question whether coordinated movement patterns and the underlying muscular control in these animals is fully innate or whether there still exists a rapid maturation. We addressed this question by studying gait development in neonatal pigs through the analysis of spatio-temporal gait characteristics during locomotion at self-selected speed. To this end, we made video recordings of piglets walking along a corridor at several time points (from 0 h to 96 h). After digitization of the footfalls, we analysed self-selected speed and spatio-temporal characteristics (e.g. stride and step lengths, stride frequency and duty factor) to study dynamic similarity, intralimb coordination and interlimb coordination. To assess the variability of the gait pattern, left–right asymmetry was studied. To distinguish neuromotor maturation from effects caused by growth, both absolute and normalized data (according to the dynamic similarity concept) were included in the analysis. All normalized spatio-temporal variables reached stable values within 4 h of birth, with most of them showing little change after the age of 2 h. Most asymmetry indices showed stable values, hovering around 10\%, within 8 h of birth. These results indicate that coordinated movement patterns are not entirely innate, but that a rapid neuromotor maturation, potentially also the result of the rearrangement or recombination of existing motor modules, takes place in these precocial animals.},
}

@article{VandenHole2019thesis,
    author = {Vanden Hole, Charlotte},
    year = {2019},
    title = {{Locomotor Development in the Newborn Pig}},
    journal = {PhD Thesis},
    publisher = {University of Antwerp},
    url = {https://medialibrary.uantwerpen.be/oldcontent/container2699/files/PhD\%20thesis_Charlotte\%20Vanden\%20Hole.pdf},
}




### W ###
@article{Webb2007,
    author = {Webb, David and Sparrow, William Anthony},
    year = {2007},
    title = {{Description of joint movements in human and non-human primate locomotion using {Fourier} analysis}},
    doi = {10.1007/s10329-007-0043-4},
    journal = {Primates},
    volume = {48},
    number = {4},
    pages = {277--292},
    month = {Oct},
    issn = {1610-7365},
    day = {01},
    abstract = {To describe and help interpret joint movements in various forms of primate locomotion, we explored the use of Fourier analysis to represent changing joint angles as a series of sine and cosine curves added together to approximate the raw angular data. Results are presented for four joints (shoulder, elbow, hip and knee) with emphasis on the shoulder, and for five types of locomotion (catarhine primate quadrupedal walking, human hands-and-feet creeping and hands-and-knees creeping, and human walking and running). Fourier analysis facilitates functional interpretation of the angles of all four joints, by providing average joint angles and an indication of the number of peaks and troughs in the angular data. The description of limb movements also afforded us the opportunity to compare human and other catarhine joint angles, and we interpret the Fourier results in terms of locomotor posture and type. In addition, the shoulder data are useful for determination of some aspects of interlimb coordination. Non-human primates walking quadrupedally and humans creeping on hands and knees generally evince diagonal couplets interlimb coordination, in which the hand on one side strikes the substrate at about the same time as the contralateral foot or knee. Furthermore, human walking and running seem to follow a similar pattern, as indicated by Fourier analysis. From our data it is concluded that human bipedal gaits are qualitatively similar to diagonal couplets gaits in other primates, but quite different from the lateral couplets gaits used by many non-primate mammals. A number of other benefits of Fourier analysis in primate locomotion studies are also discussed. These include the ability to make statistical comparisons among various types of limb movements in a wide variety of species, a simple archival technique for limb movement data, and a greater understanding of the variability of locomotor movements.},
}

@article{Westerterp2004,
    author = {Westerterp, Klaas R and Plasqui, Guy},
    year = {2004},
    title = {Physical activity and human energy expenditure},
    doi = {10.1097/00075197-200411000-00004},
    journal = {Current Opinion in Clinical Nutrition \& Metabolic Care},
    volume = {7},
    number = {6},
    pages = {607--613},
    publisher = {Lippincott Williams \& Wilkins, Inc.},
}

@article{Westerterp2008,
    author = {Westerterp, Klaas R and Speakman, John R},
    year = {2008},
    title = {Physical activity energy expenditure has not declined since the 1980s and matches energy expenditures of wild mammals},
    journal = {International journal of obesity},
    volume = {32},
    number = {8},
    pages = {1256--1263},
    doi = {10.1038/ijo.2008.74},
    publisher = {Nature Publishing Group},
}

@article{Wischner2009,
    author = {Wischner, Diane and Kemper, Nicole and Krieter, Joachim},
    year = {2009},
    title = {{Nest-building behaviour in sows and consequences for pig husbandry}},
    journal = {Livestock Science},
    volume = {124},
    number = {1},
    pages = {1-8},
    issn = {1871-1413},
    doi = {10.1016/j.livsci.2009.01.015},
    url = {https://www.sciencedirect.com/science/article/pii/S1871141309000328},
    keywords = {Reproduction, Crates, Maternal behaviour, Piglets, Pens},
    abstract = {Patterns of maternal behaviour are strongly related to reproductive abilities in sows. Prepartal behaviour of sows is mainly characterised by nest-building activities, resulting in a nest that provides shelter for the piglets. In the course of domestication, sows have not lost their instinctive behaviour to nest-build, but perform at least elements of it when appropriate space and materials are available. The onset and performance of nest-building is both stimulated internally via hormones and externally via feedback from the environment. With this environmental influence, the possibilities to perform nest-building can be restricted to different extents in commercially farmed pigs. The aim of the present review is to point out the sow's need for nest-building performance as part of the natural behaviour pattern, although they are kept in different modern housing systems. With regard to increased demands for animal welfare and following changes in the legislation for pig husbandry, possible consequences for different housing systems are discussed.},
}


### Z ###
@article{Zeki2001,
    author = {Semir Zeki},
    year = {2001},
    title = {{Artistic Creativity and the Brain}},
    journal = {Science},
    volume = {293},
    number = {5527},
    pages = {51-52},
    doi = {10.1126/science.1062331},
    url = {https://www.science.org/doi/abs/10.1126/science.1062331},
}


% ### CHAPTER 2 ###
% #### A ####
@article{Alexander1980,
    author = {Alexander, R.McN. and Jayes, A.S.},
    year = {1980},
    title = {{Fourier analysis of forces exerted in walking and running}},
    doi = {10.1016/0021-9290(80)90019-6},
    journal = {Journal of Biomechanics},
    volume = {13},
    number = {4},
    pages = {383-390},
    issn = {0021-9290},
    url = {https://www.sciencedirect.com/science/article/pii/0021929080900196},
    abstract = {{The forces exerted on the ground by men walking and running have been recorded by means of a force platform. A simple method of Fourier analysis has been used to analyse the records. It shows differences between walking and running, between slow and fast walking, between accelerated and decelerated walking and between different individuals walking at the same speed.}},
}

@article{Audigie1999,
    author = {Audigié, F. and Pourcelot, P. and Degueurce, C. and Denoix, J. M. and Geiger, D.},
    year = {1999},
    title = {{Kinematics of the equine back: flexion-extension movements in sound trotting horses}},
    doi = {10.1111/j.2042-3306.1999.tb05219.x},
    journal = {Equine Veterinary Journal},
    volume = {31},
    number = {S30},
    pages = {210-213},
    keywords = {horse, back, locomotion, repeatability, trunk muscles},
    url = {https://beva.onlinelibrary.wiley.com/doi/abs/10.1111/j.2042-3306.1999.tb05219.x},
    abstract = {Summary This study was undertaken to evaluate the flexion-extension movements of the back in a group of sound trotting horses. Using a 3-D kinematic analysis system, 13 clinically sound horses fitted with 5 skin markers placed on the dorsal midline of their trunk were recorded while trotting on a track in the conditions of the routine lameness examination. These markers were used to calculate 3 back angles (thoracic, thoracolumbar and lumbosacral angle). These back angles were then filtered using Fourier series. To evaluate the repeatability of flexion-extension movements, the intra- and inter-individual variabilities were studied. The angle-time diagrams showed that the equine back extended during the first part of each diagonal stance phase and flexed during the second part of each diagonal stance phase. The ranges of motion were less than 4° for the 3 back angles. The intra- and inter-individual variability values of maximal extension and maximal flexion time points were similar and extremely low. This demonstrates the high repeatability of the temporal pattern of flexion-extension movements of the back. Intra-and inter-individual variabilities of the range of motion showed that the back mobility varies more in-between horses than between trials of the same horse. Compared with electromyographic activities of back muscles reported in the literature, flexion-extension movements described in this study tend to show that, at a slow trot, trunk muscles act mainly to limit flexion-extension movements of the back rather than to induce movements.},
}

@book{Braune1895,
    author = {Fischer, Otto and Braune, Christian Wilhelm},
    year = {1895-1904},
    title = {{Der Gang des Menschen}},
    publisher = {BG Teubner}
}

@article{Brown2010,
    author = {Brown, Robert A. and Lauzon, M. Louis and Frayne, Richard},
    year = {2010},
    title = {{A General Description of Linear Time-Frequency Transforms and Formulation of a Fast, Invertible Transform That Samples the Continuous S-Transform Spectrum Nonredundantly}},
    doi = {10.1109/TSP.2009.2028972},
    journal = {IEEE Transactions on Signal Processing},
    volume = {58},
    number = {1},
    pages = {281-290},
    abstract = {{Examining the frequency content of signals is critical in many applications, from neuroscience to astronomy. Many techniques have been proposed to accomplish this. One of these, the S-transform, provides simultaneous time and frequency information similar to the wavelet transform, but uses sinusoidal basis functions to produce frequency and globally referenced phase measurements. It has shown promise in many medical imaging applications but has high computational requirements. This paper presents a general transform that describes Fourier-family transforms, including the Fourier, short-time Fourier, and S- transforms. A discrete, nonredundant formulation of this transform, as well as algorithms for calculating the forward and inverse transforms are also developed. These utilize efficient sampling of the time-frequency plane and have the same computational complexity as the fast Fourier transform. When configured appropriately, this new algorithm samples the continuous S-transform spectrum efficiently and nonredundantly, allowing signals to be transformed in milliseconds rather than days, as compared to the original S-transform algorithm. The new and efficient algorithms make practical many existing signal and image processing techniques, both in biomedical and other applications.}},
    issn = {1941-0476},
    month = {Jan},
}

@article{Broyden1970,
    author = {Broyden, C. G.},
    year = {1970},
    title = {{The Convergence of a Class of Double-rank Minimization Algorithms 1. General Considerations}},
    doi = {10.1093/imamat/6.1.76},
    journal = {IMA Journal of Applied Mathematics},
    volume = {6},
    number = {1},
    pages = {76-90},
    month = {03},
    abstract = {{This paper presents a more detailed analysis of a class of minimization algorithms, which includes as a special case the DFP (Davidon-Fletcher-Powell) method, than has previously appeared. Only quadratic functions are considered but particular attention is paid to the magnitude of successive errors and their dependence upon the initial matrix. On the basis of this a possible explanation of some of the observed characteristics of the class is tentatively suggested.}},
    issn = {0272-4960},
}


% #### C ####
@article{Crall2015,
    author = {Crall, James D. and Gravish, Nick and Mountcastle, Andrew M. and Combes, Stacey A.},
    year = {2015},
    title = {{BEEtag: A Low-Cost, Image-Based Tracking System for the Study of Animal Behavior and Locomotion}},
    doi = {10.1371/journal.pone.0136487},
    journal = {PLOS ONE},
    publisher = {Public Library of Science},
    month = {09},
    volume = {10},
    pages = {1-13},
    number = {9},
    abstract = {{A fundamental challenge common to studies of animal movement, behavior, and ecology is the collection of high-quality datasets on spatial positions of animals as they change through space and time. Recent innovations in tracking technology have allowed researchers to collect large and highly accurate datasets on animal spatiotemporal position while vastly decreasing the time and cost of collecting such data. One technique that is of particular relevance to the study of behavioral ecology involves tracking visual tags that can be uniquely identified in separate images or movie frames. These tags can be located within images that are visually complex, making them particularly well suited for longitudinal studies of animal behavior and movement in naturalistic environments. While several software packages have been developed that use computer vision to identify visual tags, these software packages are either (a) not optimized for identification of single tags, which is generally of the most interest for biologists, or (b) suffer from licensing issues, and therefore their use in the study of animal behavior has been limited. Here, we present BEEtag, an open-source, image-based tracking system in Matlab that allows for unique identification of individual animals or anatomical markers. The primary advantages of this system are that it (a) independently identifies animals or marked points in each frame of a video, limiting error propagation, (b) performs well in images with complex backgrounds, and (c) is low-cost. To validate the use of this tracking system in animal behavior, we mark and track individual bumblebees (Bombus impatiens) and recover individual patterns of space use and activity within the nest. Finally, we discuss the advantages and limitations of this software package and its application to the study of animal movement, behavior, and ecology.}},
}

% #### D ####
@article{DiBerardinoIII2010,
    author = {DiBerardino {III}, Louis A. and Polk, John D. and Rosengren, Karl S. and Spencer-Smith, Jesse B. and Hsiao-Wecksler,  Elizabeth T.},
    year = {2010},
    title = {{Quantifying complexity and variability in phase portraits of gait}},
    doi = {10.1016/j.clinbiomech.2010.03.007},
    journal = {Clinical Biomechanics},
    volume = {25},
    number = {6},
    pages = {552-556},
    issn = {0268-0033},
    url = {https://www.sciencedirect.com/science/article/pii/S0268003310000926},
    keywords = {Asymmetric gait, Treadmill walking, Orthotic brace, Elliptical Fourier Analysis},
    abstract = {Background: Injuries to the lower extremity often cause limitations to joint motion and alter movement patterns of limb segments during gait. We hypothesized that complexity and variability of limb segment motion during gait would increase in both limbs due to unilateral injury. Using simulated injury to generate asymmetric gait, we developed new methods to quantify changes in the complexity and variability of limb segment angular phase portraits. ; Methods: To simulate reduced range of motion associated with knee injury, the right knee was constrained to full extension by an external brace. Thigh, shank and foot segment angular phase portraits were generated from 20 healthy male subjects walking for 3-minute trials with and without the brace. Using Fourier-based methods, complexity was quantified by the number of harmonic frequencies suitable for fitting the phase-portrait shape — with a larger number of harmonics indicating greater complexity. Variability was characterized by the drift and confidence area generated by the inter-cycle excursion of the phase-portrait centroid. ; Findings: Significant differences were found in complexity and variability measures due to bracing. Phase-portrait shape complexity and variability increased in the right (braced) limb, compared to the unbraced condition; while only variability increased for the left (contralateral) limb during bracing. ; Interpretation: These new methods proved successful at quantifying changes in the complexity and variability that have been visually observed in phase portraits during asymmetric gait. This work provides a method that can be incorporated into clinical assessments to provide quantifiable measures of more precise differences in gait dynamics.},
}

@article{Druelle2021,
    author = {Druelle, François and Özçelebi, Jonathan and Marchal, François and Berillon, Gilles},
    year = {2021},
    title = {{Development of bipedal walking in olive baboons, \textit{Papio anubis}: A kinematic analysis}},
    doi = {10.1002/ajpa.24454},
    journal = {American Journal of Biological Anthropology},
    keywords = {balance, bipedalism, coordination, evolution, ontogeny},
    url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ajpa.24454},
    abstract = {Objective Although extant nonhuman primates are not habitual bipeds, they are able to walk bipedally from an early age. In humans, children improve their walking skills through developmental processes and learning experience. In nonhuman primates, infants do not routinely experience bipedalism and their musculoskeletal system gradually specializes for other locomotor modes. The aim of this study is to explore the development of occasional bipedal walking in olive baboon and to test whether the postural adjustments change with age. Materials and Methods We collected kinematics and spatiotemporal parameters of bipedal gait in an ontogenetic sample of 24 baboons. Data were collected at the primatology station of the CNRS (France) and a total of 47 bipedal strides were extracted for the present analysis. Results Adults and adolescents walk bipedally in the same way, and the average kinematic pattern is similar across the age-classes. Infants walk bipedally with longer duty factor, they present larger movement amplitude of the thigh and the amplitude of the knee joint decreases with speed. In contrast, older baboons increase the amplitude of the knee and ankle joints with speed. Discussion In a non-adapted biped, the postural adjustments of bipedal walking vary with age. In infant baboons, the balance requirements are likely to be higher and these are solved by adopting a “blocking strategy”. In older baboons, the postural adjustments are focused on the lower limb and the movements increase with speed. These results may echo, in some respects, the developmental sequence of the intersegmental coordination described in the ontogeny of human locomotion.}
}

@article{Dunn2021,
    author = {Dunn, Timothy W. and Marshall, Jesse D. and Severson, Kyle S. and Aldarondo, Diego E. and Hildebrand, David GC. and Chettih, Selmaan N. and Wang, William L. and Gellis, Amanda J. and Carlson, David E. and Aronov, Dmitriy and Freiwald, Winrich A. and Wang, Fan and Ölveczky, Bence P.},
    year = {2021},
    title = {{Geometric deep learning enables 3D kinematic profiling across species and environments}},
    doi = {10.1038/s41592-021-01106-6},
    journal = {Nature methods},
    volume = {18},
    number = {5},
    pages = {564--573},
    publisher = {Nature Publishing Group},
}

% #### E ####
@article{Ekhator2023,
    author = {Ekhator, Chukwuyem and Varshney, Arnavi and Young, Melody W. and Tanis, Daniel and Granatosky, Michael C. and Diaz, Raul E. and Molnar, Julia L.},
    year = {2023},
    title = {{Locomotor characteristics of the ground-walking chameleon \textit{Brookesia superciliaris}}},
    journal = {{Journal of Experimental Zoology Part A: Ecological and Integrative Physiology}},
    volume = {339},
    number = {6},
    pages = {602-614},
    keywords = {arboreal, biomechanics, Brookesia, gait, leaf chameleons, terrestrial},
    doi = {10.1002/jez.2703},
    url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/jez.2703},
    abstract = {{Understanding the locomotor characteristics of early diverging ground-walking chameleons (members of the genera Brookesia, Rhampholeon, Palleon, and Rieppeleon) can help to explain how their unique morphology is adapted to fit their environment and mode of life. However, nearly all quantitative studies of chameleon locomotion thus far have focused on the larger “true arboreal” chameleons. We investigated kinematics and spatiotemporal gait characteristics of the Brown Leaf Chameleon (Brookesia superciliaris) on different substrates and compared them with true arboreal chameleons, nonchameleon lizards, and other small arboreal animals. Brookesia exhibits a combination of locomotor traits, some of which are traditionally arboreal, others more terrestrial, and a few that are very unusual. Like other chameleons, Brookesia moved more slowly on narrow dowels than on broad planks (simulating arboreal and terrestrial substrates, respectively), and its speed was primarily regulated by stride frequency rather than stride length. While Brookesia exhibits the traditionally arboreal trait of a high degree of humeral protraction at the beginning of stance, unlike most arboreal tetrapods, it uses smaller shoulder and hip excursions on narrower substrates, possibly reflecting its more terrestrial habits. When moving at very slow speeds, Brookesia often adopts an unusual footfall pattern, lateral-sequence lateral-couplets. Because Brookesia is a member of one of the earliest-diverging groups of chameleons, its locomotion may provide a good model for an intermediate stage in the evolution of arboreal chameleons. Thus, the transition to a fully arboreal way of life in “true arboreal” chameleons may have involved changes in spatiotemporal and kinematic characteristics as well as morphology.}},
}

% #### F ####
@article{Fischer2006,
    author = {Fischer, Martin S. and Blickhan, Reinhard},
    year = {2006},
    title = {The tri-segmented limbs of therian mammals: kinematics, dynamics, and self-stabilization—a review},
    doi = {10.1002/jez.a.333},
    journal = {Journal of Experimental Zoology Part A: Comparative Experimental Biology},
    volume = {305A},
    number = {11},
    pages = {935-952},
    url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/jez.a.333},
    abstract = {Abstract The evolution of therian mammals is to a large degree marked by changes in their motion systems. One of the decisive transitions has been from the sprawled, bi-segmented to the parasagittal, tri-segmented limb. Here, we review aspects of the tri-segmented limb in locomotion which have been elucidated in our research groups in the last 10 years. First, we report the kinematics of the tri-segmented therian limb from mouse to elephant in order to explore general principles of the therian limb configuration and locomotion. Torques will be reported from a previous paper (Witte et al., 2002. J Exp Biol 205:1339–1353) for a better understanding of the anti-gravity work of all limb joints. The stability of a limb in z-configuration will be explained and its advantage with respect to other potential solutions from modeling will be discussed. Finally, we describe how the emerging concept of self-stability can be explained for a tri-segmented leg template and how it affects the design of the musculoskeletal system and the operation of legs during locomotion. While locomotion has been considered as mainly a control problem in various disciplines, we stress the necessity to reduce control as much as possible. Central control can be cheap if the limbs are “intelligent” by means of their design. Gravity-induced movements and self-stability seem to be energy-saving mechanisms.},
}

@article{Fletcher1970,
    author = {Fletcher, R.},
    year = {1970},
    title = {{A new approach to variable metric algorithms}},
    doi = {10.1093/comjnl/13.3.317},
    journal = {The Computer Journal},
    volume = {13},
    number = {3},
    pages = {317-322},
    month = {01},
    abstract = {{An approach to variable metric algorithms has been investigated in which the linear search sub-problem no longer becomes necessary. The property of quadratic termination has been replaced by one of monotonic convergence of the eigenvalues of the approximating matrix to the inverse hessian. A convex class of updating formulae which possess this property has been established, and a strategy has been indicated for choosing a member of the class so as to keep the approximation away from both singularity and unboundedness. A FORTRAN program has been tested extensively with encouraging results.}},
    issn = {0010-4620},
}

@book{Fourier1822,
    author = {Fourier, Joseph},
    year = {1822},
    title = {{Theorie analytique de la chaleur, par M. Fourier}},
    publisher = {{Chez Firmin Didot, p{\`e}re et fils}},
}

% #### G ####
@book{Gallistel1982,
    title = {{The organization of action: A new synthesis}},
    author = {Gallistel, Charles R.},
    year = {1982},
    publisher = {Psychology Press}
}

@article{Goldfrab1970,
    author = {Goldfrab, D.},
    year = {1970},
    title = {{A Family of Variable Metric Methods Derived by Variations Means}},
    doi = {10.1090/S0025-5718-1970-0258249-6},
    journal = {Mathematics of Computation},
    volume = {24},
    pages = {23--26},
}

@article{Granatosky2022,
    author = {Granatosky, Michael C. and McElroy, Eric J.},
    year = {2022},
    title = {{Stride frequency or length? A phylogenetic approach to understand how animals regulate locomotor speed}},
    doi = {10.1242/jeb.243231},
    journal = {Journal of Experimental Biology},
    volume = {225},
    number = {Suppl1},
    pages = {jeb243231},
    month = {03},
    abstract = {Speed regulation in animals involves stride frequency and stride length. While the relationship between these variables has been well documented, it remains unresolved whether animals primarily modify stride frequency or stride length to increase speed. In this study, we explored the interrelationships between these three variables across a sample of 103 tetrapods and assessed whether speed regulation strategy is influenced by mechanical, allometric, phylogenetic or ecological factors. We observed that crouched terrestrial species tend to regulate speed through stride frequency. Such a strategy is energetically costly, but results in greater locomotor maneuverability and greater stability. In contrast, regulating speed through stride length is closely tied to larger arboreal animals with relatively extended limbs. Such movements reduce substrate oscillations on thin arboreal supports and/or helps to reduce swing phase costs. The slope of speed on frequency is lower in small crouched animals than in large-bodied erect species. As a result, substantially more rapid limb movements are matched with only small speed increases in crouched, small-bodied animals. Furthermore, the slope of speed on stride length was inversely proportional to body mass. As such, small changes in stride length can result in relatively rapid speed increases for small-bodied species. These results are somewhat counterintuitive, in that larger species, which have longer limbs and take longer strides, do not appear to gain as much speed increase out of lengthening their stride. Conversely, smaller species that cycle their limbs rapidly do not gain as much speed out of increasing stride frequency as do larger species.},
    issn = {0022-0949},
}

@article{Grasso2000,
    author = {Grasso, R. and Zago, M. and Lacquaniti, F.},
    year = {2000},
    title = {{Interactions Between Posture and Locomotion: Motor Patterns in Humans Walking With Bent Posture Versus Erect Posture}},
    doi = {10.1152/jn.2000.83.1.288},
    journal = {Journal of Neurophysiology},
    number = {1},
    pages = {288--300},
    volume = {83},
    abstract = {Human erect locomotion is unique among living primates. Evolution selected specific biomechanical features that make human locomotion mechanically efficient. These features are matched by the motor patterns generated in the CNS. What happens when humans walk with bent postures? Are normal motor patterns of erect locomotion maintained or completely reorganized? Five healthy volunteers walked straight and forward at different speeds in three different postures (regular, knee-flexed, and knee- and trunk-flexed) while their motion, ground reaction forces, and electromyographic (EMG) activity were recorded. The three postures imply large differences in the position of the center of body mass relative to the body segments. The elevation angles of the trunk, pelvis, and lower limb segments relative to the vertical in the sagittal plane, the ground reaction forces and the rectified EMGs were analyzed over the gait cycle. The waveforms of the elevation angles along the gait cycle remained essentially unchanged irrespective of the adopted postures. The first two harmonics of these kinematic waveforms explain >95\% of their variance. The phase shift but not the amplitude ratio between the first harmonic of the elevation angle waveforms of adjacent pairs was affected systematically by changes in posture. Thigh, shank, and foot angles covaried close to a plane in all conditions, but the plane orientation was systematically different in bent versus erect locomotion. This was explained by the changes in the temporal coupling among the three segments. For walking speeds >1 m s−1, the plane orientation of bent locomotion indicates a much lower mechanical efficiency relative to erect locomotion. Ground reaction forces differed prominently in bent versus erect posture displaying characteristics intermediate between those typical of walking and those of running. Mean EMG activity was greater in bent postures for all recorded muscles independent of the functional role. The waveforms of the muscle activities and muscle synergies also were affected by the adopted posture. We conclude that maintaining bent postures does not interfere either with the generation of segmental kinematic waveforms or with the planar constraint of intersegmental covariation. These characteristics are maintained at the expense of adjustments in kinetic parameters, muscle synergies and the temporal coupling among the oscillating body segments. We argue that an integrated control of gait and posture is made possible because these two motor functions share some common principles of spatial organization.},
}

@book{Gray1995,
    author = {Gray, Robert M. and Goodman, Joseph W.},
    year = {1995},
    title = {{Fourier Transforms: An Introduction for Engineers}},
    publisher = {Springer US},
    series = {The Springer International Series in Engineering and Computer Science 322},
    edition = {1},
    isbn = {978-1-4613-6001-8,978-1-4615-2359-8},
}


% #### H ####
@article{Hedrick2008,
    author = {Hedrick, Tyson L.},
    year = {2008},
    title = {{Software techniques for two- and three-dimensional kinematic measurements of biological and biomimetic systems}},
    doi = {10.1088/1748-3182/3/3/034001},
    journal = {Bioinspiration {\&} Biomimetics},
    month = {jul},
    publisher = {{IOP} Publishing},
    volume = {3},
    number = {3},
    pages = {034001},
    abstract = {{Researchers studying aspects of locomotion or movement in biological and biomimetic systems commonly use video or stereo video recordings to quantify the behaviour of the system in question, often with an emphasis on measures of position, velocity and acceleration. However, despite the apparent simplicity of video analysis, it can require substantial investment of time and effort, even when performed with adequate software tools. This paper reviews the underlying principles of video and stereo video analysis as well as its automation and is accompanied by fully functional and freely available software implementation.}},
}

@article{Heideman1984,
    author = {Heideman, M. and Johnson, D. and Burrus, C.},
    year = {1984},
    title = {{Gauss and the history of the fast fourier transform}},
    doi = {10.1109/MASSP.1984.1162257},
    journal = {{IEEE ASSP Magazine}},
    volume = {1},
    number = {4},
    pages = {14-21},
    issn = {1558-1284},
    month = {October},
}
{Herzog1989,
  author = {Herzog, Walter and Nigg, Benno M and Read, Lynda J and Olsson, Ewa},
  year = {1989}
  title = {{Asymmetries in ground reaction force patterns in normal human gait}},
  doi  =  {10.1249/00005768-198902000-00020}
  journal = {Medicine and Science in Sports and Exercise},
  volume = {21},
  number = {1},
  pages = {110--114},
  abstract = {{The purpose of this study was to propose a measure of symmetry/asymmetry for normal human gait and to quantify symmetries/asymmetries of normal human gait for selected gait variables using a force platform. Sixty-two subjects performed ten gait trials each, stepping on the force platform five times with each leg. From these gait trials a symmetry index was calculated for 34 gait variables. The upper and lower limits of normal gait were calculated such that 95\% of all symmetry indices obtained from this subject population fell within these limits. Upper and lower limits were found to vary from +/- 4\% to over +/- 13,000\%. Extremely high percentages were found for variables which had absolute magnitudes close to zero and/or variables which occurred at distinctly different instants during the gait cycle. The results of these variables need to be interpreted with caution.}}
}

@article{Huang1998,
  author   = {Huang, Norden E. and Shen, Zheng and Long, Steven R. and Wu, Manli C. and Shih, Hsing H. and Zheng, Quanan and Yen, Nai-Chyuan and Tung, Chi Chao and Liu, Henry H.},
  journal  = {Proceedings of the Royal Society of London. Series A: Mathematical, Physical and Engineering Sciences},
  title    = {{The empirical mode decomposition and the Hilbert spectrum for nonlinear and non-stationary time series analysis}},
  year     = {1998},
  number   = {1971},
  pages    = {903-995},
  volume   = {454},
  abstract = {{ A new method for analysing nonlinear and non-stationary data has been developed. The key part of the method is the ‘empirical mode decomposition’ method with which any complicated data set can be decomposed into a finite and often small number of ‘intrinsic mode functions’ that admit well-behaved Hilbert transforms. This decomposition method is adaptive, and, therefore, highly efficient. Since the decomposition is based on the local characteristic time scale of the data, it is applicable to nonlinear and non-stationary processes. With the Hilbert transform, the ‘instrinic mode functions’ yield instantaneous frequencies as functions of time that give sharp identifications of imbedded structures. The final presentation of the results is an energy-frequency-time distribution, designated as the Hilbert spectrum. In this method, the main conceptual innovations are the introduction of ‘intrinsic mode functions’ based on local properties of the signal, which make the instantaneous frequency meaningful; and the introduction of the instantaneous frequencies for complicated data sets, which eliminate the need for spurious harmonics to represent nonlinear and non-stationary signals. Examples from the numerical results of the classical nonlinear equation systems and data representing natural phenomena are given to demonstrate the power of this new method. Classical nonlinear system data are especially interesting, for they serve to illustrate the roles played by the nonlinear and non-stationary effects in the energy-frequency-time distribution. }},
  doi      = {10.1098/rspa.1998.0193},
  url      = {https://royalsocietypublishing.org/doi/abs/10.1098/rspa.1998.0193},
}

% #### I ####
% #### J ####
@article{Jackson1979,
    author = {Jackson, K. M.},
    year = {1979},
    title = {{Fitting of Mathematical Functions to Biomechanical Data}},
    doi = {10.1109/TBME.1979.326551},
    journal = {IEEE Transactions on Biomedical Engineering},
    volume = {BME-26},
    number = {2},
    pages = {122-124},
    issn = {1558-2531},
    abstract = {A method is presented to decide the order a polynomial or Fourier series best represents a set of biomechanical data points, with regard to the calculation of the first and second derivatives of the data.},
    }

@article{Jones2023,
    title = {{Terrestrial locomotor behaviors of the big brown bat (Vespertilionidae: \textit{Eptesicus fuscus})}},
    year = {2023},
    author = {Jones, Matthew F and Hasiotis, Stephen T},
    doi = {10.1007/s13364-022-00669-9},
    journal = {Mammal Research},
    volume = {68},
    number = {2},
    pages = {253--262},
    publisher = {Springer},
}


% #### K ####
@incollection{Kenwright2015,
    author = {Kenwright, Ben},
    year = {2015},
    title = {{Quaternion Fourier Transform for Character Motions}},
    doi = {10.2312/vriphys.20151328},
    booktitle = {Workshop on Virtual Reality Interaction and Physical Simulation},
    editor = {Jaillet, Fabrice and Zara, Florence and Zachmann, Gabriel},
    publisher = {The Eurographics Association},
    isbn = {978-3-905674-98-9},
}

@article{Knoerlein2016,
    author = {Kn\"orlein, Benjamin J. and Baier, David B. and Gatesy, Stephen M. and Laurence-Chasen, J. D. and Brainerd, Elizabeth L.},
    year = {2016},
    title = {{Validation of XMALab software for marker-based XROMM}},
    doi = {10.1242/jeb.145383},
    journal = {Journal of Experimental Biology},
    volume = {219},
    number = {23},
    pages = {3701-3711},
    month = {12},
    issn = {0022-0949},
    abstract = {{Marker-based XROMM requires software tools for: (1) correcting fluoroscope distortion; (2) calibrating X-ray cameras; (3) tracking radio-opaque markers; and (4) calculating rigid body motion. In this paper we describe and validate XMALab, a new open-source software package for marker-based XROMM (C++ source and compiled versions on Bitbucket). Most marker-based XROMM studies to date have used XrayProject in MATLAB. XrayProject can produce results with excellent accuracy and precision, but it is somewhat cumbersome to use and requires a MATLAB license. We have designed XMALab to accelerate the XROMM process and to make it more accessible to new users. Features include the four XROMM steps (listed above) in one cohesive user interface, real-time plot windows for detecting errors, and integration with an online data management system, XMAPortal. Accuracy and precision of XMALab when tracking markers in a machined object are ±0.010 and ±0.043 mm, respectively. Mean precision for nine users tracking markers in a tutorial dataset of minipig feeding was ±0.062 mm in XMALab and ±0.14 mm in XrayProject. Reproducibility of 3D point locations across nine users was 10-fold greater in XMALab than in XrayProject, and six degree-of-freedom bone motions calculated with a joint coordinate system were 3- to 6-fold more reproducible in XMALab. XMALab is also suitable for tracking white or black markers in standard light videos with optional checkerboard calibration. We expect XMALab to increase both the quality and quantity of animal motion data available for comparative biomechanics research.}},
}

@article{Kurz2011,
  author    = {Kurz, Max J. and Stuberg, Wayne and DeJong, Stacey L.},
  journal   = {Developmental Neurorehabilitation},
  title     = {{Body weight supported treadmill training improves the regularity of the stepping kinematics in children with Cerebral Palsy}},
  year      = {2011},
  number    = {2},
  pages     = {87-93},
  volume    = {14},
  abstract  = {Objective: To examine if body weight supported treadmill training (BWSTT) improves the regularity of stepping kinematics in children with cerebral palsy (CP).Methods: Twelve children with CP who had Gross Motor Function Classification Scores that ranged from II–IV participated in 12 weeks of body weight supported treadmill training that was performed 2 days a week. The primary outcome measure was the regularity of the stepping kinematics, which was assessed with Fourier analysis methods. The secondary measures were the preferred walking speed, step length, lower extremity strength and section E of the GMFM.Results: BWSTT improved the rhythmical control of the stepping kinematics, preferred walking speed, step length and GMFM score. The improvements in the regularity of the stepping kinematics were strongly correlated with changes in the preferred walking speed, step length and GMFM score.Conclusion: BWSTT can improve the motor control of the walk performance of children with CP.},
  doi       = {10.3109/17518423.2011.552459},
  publisher = {Taylor \& Francis},
}




% #### L ####
% #### M ####
@incollection{Marteniuk1983,
    author = {Ronald G. Marteniuk and Sandra K.E. Romanow},
    year = {1983},
    title = {{Human Movement Organization and Learning As Revealed by Variability of Movement, use of Kinematic Information, and Fourier Analysis}},
    doi = {10.1016/S0166-4115(08)61991-3},
    publisher = {North-Holland},
    editor = {Richard A. Magill},
    series = {Advances in Psychology},
    volume = {12},
    pages = {167-197},
    booktitle = {Memory and Control of Action},
    issn = {0166-4115},
    url = {https://www.sciencedirect.com/science/article/pii/S0166411508619913},
    abstract = {A case is made that motor performance and learning can be understood through hierarchical organization where an action plan is responsible for organizing relatively autonomous, lower order, units of activity. The action plan for movement is seen as consisting of information that systematically changes over learning as a function of the type of information the learner is attuned to. It is postulated that feedback about movement execution, specifically kinematic information, is the crucial source of information that supports the learning process. Data from two subjects, who practiced a sequential movement for 800 trials, did not support the idea that relatively autonomous units of activity serve as the basic building blocks for hierarchical motor control. Support was found for the idea that the subjects used displacement or spatial information early in acquisition, and then progressed to the use of velocity and perhaps acceleration information for the organization and control of their movements. Finally, a Fourier analysis of the data, as a function of practice, indicated subjects gradually modified their movements by progressively adding higher order harmonics to the fundamental harmonic of the movement which was established early in practice. Discussion of the results centered around the implications these results had for the hierarchical model of movement organization and the utility of adopting a Fourier synthesis/analysis approach to the study of motor learning.},
}

@article{Martin2016a,
    author = {Martin, Anne E. and Villarreal, Dario J. and Gregg, Robert D.},
    year = {2016},
    title = {{Characterizing and modeling the joint-level variability in human walking}},
    doi = {10.1016/j.jbiomech.2016.08.015},
    journal = {Journal of Biomechanics},
    volume = {49},
    number = {14},
    pages = {3298-3305},
    issn = {0021-9290},
    url = {https://www.sciencedirect.com/science/article/pii/S0021929016308983},
    keywords = {Variability, Human gait, Modeling},
    abstract = {Although human gait is often assumed to be periodic, significant variability exists. This variability appears to provide different information than the underlying periodic signal, particularly about fall risk. Most studies on variability have either used step-to-step metrics such as stride duration or point-wise standard deviations, neither of which explicitly capture the joint-level variability as a function of time. This work demonstrates that a second-order Fourier series for stance joints and a first-order Fourier series for swing joints can accurately capture the variability in joint angles as a function of time on a per-step basis for overground walking at the self-selected speed. It further demonstrates that a total of seven normal distributions, four linear relationships, and twelve continuity constraints can be used to describe how the Fourier series vary between steps. The ability of the proposed method to create curves that match human joint-level variability was evaluated both qualitatively and quantitatively using randomly generated curves.},
}

@article{Martin2016b,
    author = {Martin, Anne E. and Gregg, Robert D.},
    year = {2016},
    title = {{Incorporating Human-Like Walking Variability in an HZD-Based Bipedal Model}},
    doi = {10.1109/TRO.2016.2572687},
    journal = {{IEEE Transactions on Robotics}},
    volume = {32},
    number = {4},
    pages = {943-948},
    abstract = {Predictive simulations of human walking could be used to investigate a wide range of questions. Promising moderately complex models have been developed using the robotics control technique called hybrid zero dynamics (HZD). Existing simulations of human walking only consider the mean motion; therefore, they cannot be used to investigate fall risk, which is correlated with variability. This study determines how to incorporate human-like variability into an HZD-based healthy human model to generate a more realistic gait. The key challenge is determining how to combine the existing mathematical description of variability with the dynamic model so that the biped is still able to walk without falling. To do so, the commanded motion is augmented with a sinusoidal variability function and a polynomial correction function. The variability function captures the variation in joint angles, while the correction function prevents the variability function from growing uncontrollably. The necessity of the correction function and the improvements with a reduction of stance ankle variability are demonstrated via simulations. The variability in temporal measures is shown to be similar to experimental values.},
    keywords = {},
    ISSN = {1941-0468},
    month = {Aug},
    }

@article{Mathis2018,
    author = {Mathis, Alexander and Mamidanna, Pranav and Cury, Kevin M and Abe, Taiga and Murthy, Venkatesh N and Mathis, Mackenzie Weygandt and Bethge, Matthias},
    year = {2018},
    title = {{DeepLabCut: markerless pose estimation of user-defined body parts with deep learning}},
    doi = {10.1038/s41593-018-0209-y},
    journal = {Nature Neuroscience},
    volume = {21},
    number = {9},
    pages = {1281--1289},
    publisher = {Nature Publishing Group},
}


@article{MMielke2020,
    author = {Mielke, Maja and Aerts, Peter and Van Ginneken, Chris and Van Wassenbergh, Sam and Mielke, Falk},
    year = {2020},
    title = {{Progressive tracking: a novel procedure to facilitate manual digitization of videos}},
    doi = {10.1242/bio.055962},
    journal = {Biology Open},
    volume = {9},
    number = {11},
    month = {11},
    issn = {2046-6390},
    comment = {bio055962},
    abstract = {Digitization of video recordings often requires the laborious procedure of manually clicking points of interest on individual video frames. Here, we present progressive tracking, a procedure that facilitates manual digitization of markerless videos. In contrast to existing software, it allows the user to follow points of interest with a cursor in the progressing video, without the need to click. To compare the performance of progressive tracking with the conventional frame-wise tracking, we quantified speed and accuracy of both methods, testing two different input devices (mouse and stylus pen). We show that progressive tracking can be twice as fast as frame-wise tracking while maintaining accuracy, given that playback speed is controlled. Using a stylus pen can increase frame-wise tracking speed. The complementary application of the progressive and frame-wise mode is exemplified on a realistic video recording. This study reveals that progressive tracking can vastly facilitate video analysis in experimental research.},
}

@inproceedings{Mostayed2008,
    author = {Mostayed, A. and Mynuddin, M. and Mazumder, G. and Sikyung Kim and Se Jin Park},
    year = {2008},
    title = {{Abnormal Gait Detection Using Discrete Fourier Transform}},
    doi = {10.1109/MUE.2008.59},
    booktitle = {2008 International Conference on Multimedia and Ubiquitous Engineering (mue 2008)},
    pages = {36-40},
    abstract = {Detection of gait characteristics has found considerable interest in fields of biomechanics and rehabilitation sciences. In this paper an approach for abnormal gait detection employing discrete Fourier transform (DFT) analysis has been presented. The joint angle characteristics in frequency domain have been analyzed and using the harmonic coefficients, recognition for abnormal gait has been performed. The experimental results and analysis represent that the proposed algorithm based on DFT can not only reduce the gait data dimensionality effectively, but also lightens the computation cost, with a satisfactory distinction. In order to make the algorithm more generic, a mean square error (MSE) analysis is also presented. Future work will be the expansion of the detection introduced in this system to include abnormality detection instead of just an abnormal or normal detection that would prove to be a valuable addition for use in a variety of applications, including unobtrusive clinical gait analysis, automated surveillance etc.},
}


% #### N ####
@article{Nelder1965,
    author = {Nelder, J. A. and Mead, R.},
    year = {1965},
    title = {{A Simplex Method for Function Minimization}},
    doi = {10.1093/comjnl/7.4.308},
    journal = {The Computer Journal},
    volume = {7},
    number = {4},
    pages = {308-313},
    month = {01},
    abstract = {{A method is described for the minimization of a function of n variables, which depends on the comparison of function values at the (n + 1) vertices of a general simplex, followed by the replacement of the vertex with the highest value by another point. The simplex adapts itself to the local landscape, and contracts on to the final minimum. The method is shown to be effective and computationally compact. A procedure is given for the estimation of the Hessian matrix in the neighbourhood of the minimum, needed in statistical estimation problems.}},
    issn = {0010-4620},
}




% #### O ####
@misc{Osgood2007,
    author = {Osgood, Brad G.},
    year = {2007},
    title = {{Lecture Notes for EE261: The Fourier Transform and its Applications}},
    publisher = {{Electrical Engineering Department, Stanford University}},
    month = {fall},
    url = {https://see.stanford.edu/course/ee261},
}

@book{Osgood2019,
    author = {Osgood, Brad G},
    year = {2019},
    title = {{Lectures on the Fourier transform and its applications}},
    series = {Pure and Applied Undergraduate Texts},
    publisher = {{American Mathematical Soc.}},
    volume = {33},
}


% #### P ####
@article{Peham1996,
    author = {Peham, C. and Scheidl, M. and Licka, T.},
    year = {1996},
    title = {{A method of signal processing in motion analysis of the trotting horse}},
    doi = {10.1016/0021-9290(95)00179-4},
    journal = {Journal of Biomechanics},
    volume = {29},
    number = {8},
    pages = {1111-1114},
    issn = {0021-9290},
    url = {https://www.sciencedirect.com/science/article/pii/0021929095001794},
    keywords = {Horse, Motion analysis, Spectral analysis, Filter, Lameness},
    abstract = {The aim of this paper is to present a method of signal processing necessary for motion analysis in the trotting horse. Motion analysis is widely used to assess lameness in horses. By definition, lameness in trot is present if the movements during the stance phases of both fore or hind limbs differ. The motion of the horse is recorded using a system for motion analysis (Selcom, 1983, SELSPOT II User Manual, Pad Nr. 6710) and the vertical motion of the head during both stance phases is compared. The symmetry is analyzed comparing the values of the Fourier coefficients. Additional had movements are ‘single events’ and present a problem. In this article we propose a mode of data processing using a system matched filter that neglects the nonperiodic additional movements and allows calculation of the representative Fourier coefficients. In comparison with a filtering method previously used in motion analysis this method is proved to be advantageous, as the precision of symmetry comparison increases.},
}

@article{Porges1980,
    author = {Porges, Stephen W and Bohrer, Robert E and Cheung, Michael N and Drasgow, Fritz and McCabe, Philip M and Keren, Gideon},
    year = {1980},
    title = {{New time-series statistic for detecting rhythmic co-occurrence in the frequency domain: the weighted coherence and its application to psychophysiological research.}},
    doi = {10.1037/0033-2909.88.3.580},
    journal = {Psychological bulletin},
    volume = {88},
    number = {3},
    pages = {580},
    publisher = {American Psychological Association},
}

% #### Q ####
% #### R ####
@article{Ren2007,
    author = {Ren, Lei and Jones, Richard K. and Howard, David},
    year = {2007},
    title = {{Predictive modelling of human walking over a complete gait cycle}},
    doi = {10.1016/j.jbiomech.2006.07.017},
    journal = {Journal of Biomechanics},
    volume = {40},
    number = {7},
    pages = {1567-1574},
    issn = {0021-9290},
    url = {https://www.sciencedirect.com/science/article/pii/S0021929006002752},
    keywords = {Gait prediction, Inverse dynamics, Optimisation, Optimal motor task},
    abstract = {An inverse dynamics multi-segment model of the body was combined with optimisation techniques to simulate normal walking in the sagittal plane on level ground. Walking is formulated as an optimal motor task subject to multiple constraints with minimisation of mechanical energy expenditure over a complete gait cycle being the performance criterion. All segmental motions and ground reactions were predicted from only three simple gait descriptors (inputs): walking velocity, cycle period and double stance duration. Quantitative comparisons of the model predictions with gait measurements show that the model reproduced the significant characteristics of normal gait in the sagittal plane. The simulation results suggest that minimising energy expenditure is a primary control objective in normal walking. However, there is also some evidence for the existence of multiple concurrent performance objectives.},
}

@article{Rohlf1990,
    author = {Rohlf, F. James and Slice, Dennis},
    year = {1990},
    title = {{Extensions of the Procrustes Method for the Optimal Superimposition of Landmarks}},
    doi = {10.2307/2992207},
    journal = {Systematic Biology},
    volume = {39},
    number = {1},
    pages = {40-59},
    month = {03},
    issn = {1063-5157},
    abstract = {{Superimposition methods for comparing configurations of landmarks in two or more specimens are reviewed. These methods show differences in shape among specimens as residuals after rotation, translation, and scaling them so that they align as well as possible. A new method is presented that generalizes Siegel and Benson's (1982) resistant-fit theta-rho analysis so that more than two objects can be compared at the same time. Both least-squares and resistant-fit approaches are generalized to allow for affine transformations (uniform shape change). The methods are compared, using artificial data and data on 18 landmarks on the wings of 127 species of North American mosquitoes. Graphical techniques are also presented to help summarize the patterns of differences in shape among the objects being compared.}},
}



% #### S ####
@article {Schendel1995,
    author = {Schendel, MJ and Dekutoski, MB and Ogilvie, JW and Olsewski, JM and Wallace, LJ},
    year = {1995},
    title = {{Kinematics of the canine lumbar intervertebral joint: An in vivo study before and after adjacent instrumentation}},
    journal = {Spine},
    number = {23},
    volume = {20},
    iSSN = {0362-2436},
    pages = {2555—2564},
    uRL = {http://europepmc.org/abstract/MED/8610250},
}

@article{Schneider1983,
    author = {Schneider, E. and Chao, E.Y.},
    year = {1983},
    title = {{Fourier analysis of ground reaction forces in normals and patients with knee joint disease}},
    doi = {10.1016/0021-9290(83)90109-4},
    journal = {Journal of Biomechanics},
    volume = {16},
    number = {8},
    pages = {591-601},
    issn = {0021-9290},
    url = {https://www.sciencedirect.com/science/article/pii/0021929083901094},
    abstract = {{Fourier analysis was performed on the ground reaction force patterns during gait in 26 normals and 10 patients with knee joint disease prior to total knee replacement. A method was developed to determine the essential number of harmonics for each force component, based on data sampling rate and the level of accuracy required in reconstructing the original patterns. The criteria used to select the level of accuracy depend upon the type of analysis to be performed. Only the first two to four harmonics, plus the constant term, were found to be the dominating coefficients in describing each of the reaction force patterns, and they are subsequently used as the key parameters in differentiating normals and patients with knee joint disease. The advantages of this method and its implication to objective gait analysis in biomechanics are discussed.}},
}


@article{Shanno1970,
    author = {Shanno, D. F.},
    year = {1970},
    title = {{A family of variable-metric methods derived by variational means}},
    doi = {10.1090/S0025-5718-1970-0274029-X},
    journal = {Mathematics of Computation},
    volume = {24},
    pages = {647--656},
}

@article{Shannon1949,
    author = {Shannon, C.E.},
    year = {1949},
    title = {{Communication in the Presence of Noise}},
    doi = {10.1109/JRPROC.1949.232969},
    journal = {{Proceedings of the IRE}},
    volume = {37},
    number = {1},
    pages = {10-21},
    abstract = {{A method is developed for representing any communication system geometrically. Messages and the corresponding signals are points in two "function spaces," and the modulation process is a mapping of one space into the other. Using this representation, a number of results in communication theory are deduced concerning expansion and compression of bandwidth and the threshold effect. Formulas are found for the maxmum rate of transmission of binary digits over a system when the signal is perturbed by various types of noise. Some of the properties of "ideal" systems which transmit at this maxmum rate are discussed. The equivalent number of binary digits per second for certain information sources is calculated.}},
    issn = {2162-6634},
    month = {Jan},
}

@article{Skejo2021,
    author = {Skej{\o}, Sebastian Deisting and Lund, Morten Enemark and Stensvig, Martinx and Kaae, Nickolaj Mads and Rasmussen, John},
    year = {2021},
    title = {{Running in circles: Describing running kinematics using Fourier series}},
    doi = {10.1016/j.jbiomech.2020.110187},
    journal = {Journal of Biomechanics},
    volume = {115},
    pages = {110187},
    issn = {0021-9290},
    url = {https://www.sciencedirect.com/science/article/pii/S0021929020306114},
    keywords = {Motion analysis, Simulation, Gait},
    abstract = {We explore the use of Fourier series to describe the kinematics of human running. From a database of 285 trials of treadmill running, we drive a musculoskeletal model with 104 anatomical joint angles to obtain kinematics. Using FFT analysis, we determine a fundamental frequency for all independent joint angles and compute average step kinematics. Finally, we represent the average step kinematics using Fourier series with numbers of coefficient pairs ranging from one through ten. We find that five or fewer Fourier coefficient pairs provide an accurate (Pearson’s correlation > 0.99 and root mean square difference < 0.5 degrees) representation for most joint angles. In conclusion, Fourier series appear to provide a compact and valid representation of running kinematics, thus enabling researchers to confidently use Fourier series in research of human running.},
}

@incollection{Soudan1982,
    author = {Soudan, K.},
    year = {1982},
    title = {{Standardization of Gait Kinematic Data Using a Gait Symmetry Index and Fourier Analysis}},
    doi = {10.1007/978-94-009-7678-8\_10},
    editor = {Huiskes, Rik and van Campen, Dick H. and de Wijn, Joost R.},
    booktitle = {Biomechanics: Principles and Applications: Selected Proceedings of the 3rd General Meeting of the European Society of Biomechanics Nijmegen, The Netherlands, 21--23 January 1982},
    publisher = {Springer Netherlands},
    pages = {135--140},
    abstract = {In this study two concepts are introduced for standardization of gait data. A `gait symmetry index', based on the foot-to floor contacts during the walking cycle, is used as a control parameter to select a reference set of `normal' data (section 2).},
    isbn = {978-94-009-7678-8},
}

@article{Stockwell1996,
    author = {Stockwell, R.G. and Mansinha, L. and Lowe, R.P.},
    year = {1996},
    title = {{Localization of the complex spectrum: the S transform}},
    doi = {10.1109/78.492555},
    journal = {{IEEE Transactions on Signal Processing}},
    volume = {44},
    number = {4},
    pages = {998-1001},
    abstract = {{The S transform, which is introduced in the present correspondence, is an extension of the ideas of the continuous wavelet transform (CWT) and is based on a moving and scalable localizing Gaussian window. It is shown to have some desirable characteristics that are absent in the continuous wavelet transform. The S transform is unique in that it provides frequency-dependent resolution while maintaining a direct relationship with the Fourier spectrum. These advantages of the S transform are due to the fact that the modulating sinusoids are fixed with respect to the time axis, whereas the localizing scalable Gaussian window dilates and translates.}},
    ISSN = {1941-0476},
    month = {April},
    }


% #### T ####
@article{Tsang2019,
    author = {Tsang, Dorothea J. and Lukac, Meghan and Martin, Anne E.},
    year = {2019},
    title = {{Characterization of statistical persistence in joint angle variation during walking}},
    doi = {10.1016/j.humov.2019.102528},
    journal = {Human Movement Science},
    volume = {68},
    pages = {102528},
    issn = {0167-9457},
    url = {https://www.sciencedirect.com/science/article/pii/S0167945719302374},
    keywords = {Hurst exponent, DFA, Joint angle, Noise, Gait},
    abstract = {The objective of this study was to characterize joint angle variation across strides. Specifically, the statistical persistence of variations were quantified using the Hurst exponent. If a time series exhibits statistical persistence, then a parameter which is smaller (or larger) than average will tend to be followed by additional values that are also smaller (or larger) than average. Human walking has statistical persistence between stride durations. Variation in stride duration must arise from variation in the motion of the leg segments during walking. It is unclear, however, if the joint angle variation also exhibits statistical persistence. This study examined kinematic data collected from nine healthy adults walking for 10 min at a self-selected comfortable speed on a treadmill. The joint angle variation in the lower limbs was parameterized using first-order Fourier series which in turn were described by frequency and magnitude coefficients for each stride. To determine if the joint angle variation exhibited statistical persistence, the Hurst exponent was found for each coefficient at each joint. The mean Hurst exponents were 0.54 for the frequency coefficients and 0.61 for the magnitude coefficients. Neither the frequency or magnitude coefficients exhibited statistically significant persistence, although some of the magnitude coefficients were close to reaching statistical significance. This suggests that joint angle variability in healthy adults does not directly produce the statistical persistence observed in stride duration fluctuations.},
}

% #### U ####
% #### V ####
@article{vanWeeren1992,
    author = {van Weeren, P. R. and van den Bogert, A. J. and Barneveld, A.},
    year = {1992},
    title = {{Correction models for skin displacement in equine kinematics gait analysis}},
    doi = {10.1016/S0737-0806(06)81478-4},
    journal = {Journal of Equine Veterinary Science},
    volume = {12},
    number = {3},
    pages = {178--192},
    issn = {0737-0806},
    abstract = {General mathematical models are presented to be used in equine kinematic gait analysis for the correction of the biological error that is caused by sliding of the skin over the underlying bony landmarks. Ten sites in the front limb and 8 in the hind limb were investigated. In the distal parts of the limbs a linear relationship with the angle of the adjacent joint was found. The more complex pattern in the proximal parts of the limbs could be satisfactorily represented by truncated Fourier series. Analyses were principally done in the Dutch Warmblood horse, but investigations in other breeds were carried out to verify the general applicability of the models. Skin displacement appeared to be negligible in the lower parts of the limbs, but reached large values in proximally located sites such as the caudal part of the greater trochanter of the femur. It is concluded that skin displacement in equine gait analysis may account for major errors in applied biomechanical research and therefore should be corrected, although it may be of less importance for clinical applications.},
    url = {http://www.sciencedirect.com/science/article/pii/S0737080606814784},
}

@misc{Weber1836,
    author = {Weber, Wilhelm and Weber, Eduard},
    year = {1836},
    title = {{Die Mechanik Der Menschlichen Gerverzeuge}},
    publisher = {Dietrich, G\"ottingen}
}

@article{Welch1967,
    author = {Welch, P.},
    year = {1967},
    title = {{The use of fast Fourier transform for the estimation of power spectra: A method based on time averaging over short, modified periodograms}},
    journal = {IEEE Transactions on Audio and Electroacoustics},
    doi = {10.1109/TAU.1967.1161901},
    volume = {15},
    number = {2},
    pages = {70-73},
}


% #### X ####
% #### Y ####
@article{Young2023,
    author = {Young, Melody W. and McKamy, Andrew J. and Dickinson, Edwin and Yarbro, Johnathan and Ragupathi, Ashwin and Guru, Navjot and Avey-Arroyo, Judy A. and Butcher, Michael T. and Granatosky, Michael C.},
    year = {2023},
    title = {{Three toes and three modes: Dynamics of terrestrial, suspensory, and vertical locomotion in brown-throated three-toed sloths (Bradypodidae, Xenarthra)}},
    doi = {10.1002/jez.2684},
    journal = {{Journal of Experimental Zoology Part A: Ecological and Integrative Physiology}},
    volume = {339},
    number = {4},
    pages = {383-397},
    keywords = {arboreal, biomechanics, gait, inverted quadrupedalism, Pilosa},
    url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/jez.2684},
    abstract = {Abstract Living sloths exhibit numerous anatomical specializations towards inverted quadrupedalism, however, previous studies have noted a more varied locomotor repertoire than previously anticipated. In this study, we present spatiotemporal gait characteristics and triaxial kinetic data from the brown-throated three-toed sloth (Bradypus variegatus) across three locomotor modes: terrestrial quadrupedal “crawling”, suspensory walking, and vertical climbing. Compared to quadrupedal crawling and suspensory walking, B. variegatus adopted longer contact times and stride durations, larger duty factors, and greater speed during vertical climbing. Net fore-aft impulses were significantly greater during vertical climbing in both limb pairs than in quadrupedal crawling and suspensory walking. Functionally, during quadrupedal crawling and vertical climbing, both limb pairs served propulsive roles, while differentiation between a propulsive forelimb and braking hindlimb was observed during suspension. Net tangential forces differentiated vertical climbing kinetics from the other modes of locomotion, with the introduction of bidirectional pulling and pushing forces in the forelimb and hindlimb, respectively. The net mediolateral impulses were similar in vertical climbing and quadrupedal crawling as both limb pairs directed forces in one direction, whereas during suspensory walking, the laterally dominant forelimb was opposed by the medially dominant hindlimb. In total, this study provides novel data on the diverse locomotor dynamics in a slow-moving arboreal tetrapod and posits new testable hypotheses about the neuroplasticity and ease of transitioning between locomotor behaviors. The strikingly similar kinetic profiles of quadrupedal crawling and suspensory walking compared to vertical climbing suggest shared neuromuscular and mechanical demands between these mirrored locomotor modes.},
}


% #### Z ####
@article{Zhu1997,
    author = {Zhu, Ciyou and Byrd, Richard H and Lu, Peihuang and Nocedal, Jorge},
    year = {1997},
    title = {{Algorithm 778: L-BFGS-B: Fortran subroutines for large-scale bound-constrained optimization}},
    journal = {ACM Transactions on mathematical software (TOMS)},
    volume = {23},
    number = {4},
    pages = {550--560},
    publisher = {ACM New York, NY, USA},
}

@article{ParisiDutra2017,
  author    = {Parisi Dutra, Rodrigo and Casali, Daniel de Melo and Missagia, Rafaela Velloso and Gasparini, Germán Mariano and Perini, Fernando Araujo and Cozzuol, Mario Alberto},
  journal   = {Journal of Mammalian Evolution},
  title     = {Phylogenetic Systematics of Peccaries ({Tayassuidae: Artiodactyla}) and a Classification of {South American} Tayassuids},
  year      = {2017},
  issn      = {1573-7055},
  month     = sep,
  number    = {3},
  pages     = {345--358},
  volume    = {24},
  abstract  = {Tayassuidae is a family of pig-like Artiodactyla restricted to the New World. Despite its rich fossil history, they have received less attention from a taxonomic and phylogenetic perspective when compared to the Old World pigs, Suidae. In this study, we performed a computer assisted phylogenetic analysis using morphological and molecular data including fossil and extant Tayassuidae, using parsimony and Bayesian approaches. We recovered the monophyly of the family Tayassuidae, confirming previous proposals, as well as the monophyly of the subfamilies Hesperhyinae and Tayassuinae, and the genus Platygonus, which we placed in a new taxon of tribe level. The three living peccaries and a number of fossil species belong to a new, tribe level, monophyletic group. The genus Catagonus comes out as paraphyletic, leading us to propose to restrict the generic name to the type species, C. metropolitanus, and a new taxonomic arrangement for the remaining species previously included in it, revalidating the genera Brasiliochoerus and Parachoerus, and describing a new genus, Protherohyus, gen. nov.},
  doi       = {10.1007/s10914-016-9347-8},
  keywords  = {Tayassuidae, Phylogeny, Catagonus, Protherohyus gen. nov., Brasiliochoerus, Parachoerus},
}

@article{Frantz2015,
  author    = {Frantz, Laurent and Meijaard, Erik and Gongora, Jaime and Haile, James and Groenen, Martien A. M. and Larson, Greger},
  title     = {The Evolution of {Suidae}},
  journal   = {Annual Review of Animal Biosciences},
  year      = {2015},
  volume    = {4},
  number    = {1},
  pages     = {61--85},
  month     = mar,
  issn      = {2165-8102},
  abstract  = {The Suidae are a family of Cetartiodactyla composed of 17 species classified in a minimum of five extant genera that originated at least 20 million years ago. Their success is evident in the multitude of habitats in which they are found as both natural and feral populations in tropical Island Southeast Asia, the high plateau of the Himalayas, Siberia, North Africa, the Pacific Islands, Australia, and the Americas. Morphological and molecular analyses of these species have revealed numerous aspects of their biology, including the ease with which many lineages have and continue to hybridize. This trait has made them an ideal model for evolutionary biologists. Suid species have also shared a deep history with humans, from their association with early hominids in Africa to their domestication. Here we review the current knowledge of this fascinating group and provide a comprehensive evolutionary history from the Oligocene to the present day.},
  doi       = {10.1146/annurev-animal-021815-111155},
  keywords  = {pigs, hybridization, domestication, phylogeography},
  publisher = {Annual Reviews},
}

@article{Ryder2011,
  author    = {Ryder, Oliver A. and Steiner, Cynthia C.},
  title     = {Molecular phylogeny and evolution of the {Perissodactyla}},
  journal   = {Zoological Journal of the Linnean Society},
  year      = {2011},
  volume    = {163},
  number    = {4},
  pages     = {1289--1303},
  month     = may,
  issn      = {0024-4082},
  abstract  = {The evolution of perissodactyls (rhinoceroses, tapirs, and horses) has been well studied primarily because of their extensive fossil record. Nevertheless, controversy persists regarding relationships of some of the extant taxa, reflecting inconsistencies between molecular and morphological studies. Here we examine the phylogenetic relationships of 16 living perissodactyl species by concatenating two mitochondrial and nine nuclear genes, and we estimate their divergence times using a relaxed Bayesian molecular clock approach. Our analyses recovered the monophyly of the suborders Ceratomorpha and Hippomorpha, and the families Rhinoceratidae, Tapiridae, and Equidae. We supported the early divergence of the Indian rhinoceros in the late Oligocene (26 Mya) relative to the Sumatran and African rhinoceroses, and the split of caballine (domestic horse and Przewalski's wild horse) and noncaballine equids (zebras and African and Asiatic asses) in the Pliocene (4 Mya). An important implication of this study is that Equus asinus, the African wild ass was found to be the sister taxon of Asiatic asses and zebras, diverging from the common ancestor with caballine horses 2 Mya. Rates of chromosome rearrangements were also evaluated in perissodactyls, placing a notably high rate of variation amongst equids, particularly within the zebra clade. The robust phylogenetic results presented here are relevant in terms of understanding the evolutionary history of this highly threatened group of mammals.},
  doi       = {10.1111/j.1096-3642.2011.00752.x},
  keywords  = {chromosome evolution, horses, mitochondrial genes, nuclear genes, rhinoceroses, species tree, tapirs},
}

@article{Price2009,
  author    = {Price, Samantha A. and Bininda-Emonds, Olaf R. P.},
  title     = {A comprehensive phylogeny of extant horses, rhinos and tapirs ({Perissodactyla}) through data combination},
  journal   = {Zoosystematics and Evolution},
  year      = {2009},
  volume    = {85},
  number    = {2},
  pages     = {277--292},
  month     = mar,
  issn      = {1435-1935},
  abstract  = {Abstract We present the first phylogenies to include all extant species of Perissodactyla (odd-toed hoofed mammals) and the recently extinct quagga (Equus quagga). Two independent data sets were examined; one based on multiple genes and analyzed using both supertree and supermatrix approaches, and a second being a supertree constructed from trees collected from the scientific literature. All methods broadly confirmed the traditional view of perissodactyl interfamily relationships, with Equidae (= Hippomorpha) forming the sister-group to the clade Rhinocerotidae + Tapiridae (= Ceratomorpha). The contentious affinity of the Sumatran rhino (Dicerorhinus sumatrensis) is resolved in favour of it forming a clade with the two Asian rhinos (genus Rhinoceros). However, no data set or tree-building method managed to satisfactorily resolve the historically contentious relationships among extant equids; little agreement appears among the different trees for this group. In general, both the supertree and supermatrix approaches performed equally well, but both were hindered by the current paucity of data (e.g. no single gene has been sequenced to date for all 17 species) and its patchy distribution within Equidae. More data, both molecular and morphological, are required for all species to resolve the poorly supported nodes. (? 2009 WILEY-VCH Verlag GmbH \& Co. KGaA, Weinheim)},
  doi       = {10.1002/zoos.200900005},
  keywords  = {Supertree, Supermatrix, Systematics, Global congruence},
  publisher = {John Wiley \& Sons, Ltd},
}

@article{Gongora2011,
  author    = {Gongora, Jaime and Cuddahee, Rebecca E. and Nascimento, Fabrícia Ferreira do and Palgrave, Christopher J. and Lowden, Stewart and Ho, Simon Y. W. and Simond, Denbigh and Damayanti, Chandramaya Siska and White, Daniel James and Tay, Wee Tek and Randi, Ettore and Klingel, Hans and Rodrigues-Zarate, Clara J. and Allen, Kari and Moran, Chris and Larson, Greger},
  title     = {Rethinking the evolution of extant sub-{Saharan} {African} suids {(Suidae, Artiodactyla)}},
  journal   = {Zoologica Scripta},
  year      = {2011},
  volume    = {40},
  number    = {4},
  pages     = {327--335},
  month     = mar,
  issn      = {0300-3256},
  abstract  = {Rethinking the evolution of extant sub-Saharan African suids (Suidae, Artiodactyla). ?Zoologica Scripta, 40, 327?335. Although African suids have been of scientific interest for over two centuries, their origin, evolution, phylogeography and phylogenetic relationships remain contentious. There has been a long-running debate concerning the evolution of pigs and hogs (Suidae), particularly regarding the phylogenetic relationships among extant Eurasian and African species of the subfamily Suinae. To investigate these issues, we analysed the mitochondrial and nuclear DNA sequences of extant genera of Suidae from Eurasia and Africa. Molecular phylogenetic analyses revealed that all extant sub-Saharan African genera form a monophyletic clade separate from Eurasian suid genera, contradicting previous attempts to resolve the Suidae phylogeny. Two major sub-Saharan African clades were identified, with Hylochoerus and Phacochoerus grouping together as a sister clade to Potamochoerus. In addition, we find that the ancestors of extant African suids may have evolved separately from the ancestors of modern day Sus and Porcula in Eurasia before they colonised Africa. Our results provide a revision of the intergeneric relationships within the family Suidae.},
  doi       = {10.1111/j.1463-6409.2011.00480.x},
  publisher = {John Wiley \& Sons, Ltd (10.1111)},
}

@article{Funk2007,
  author    = {Funk, Stephan M. and Verma, Sunil Kumar and Larson, Greger and Prasad, Kasturi and Singh, Lalji and Narayan, Goutam and Fa, John E.},
  title     = {The pygmy hog is a unique genus: 19th century taxonomists got it right first time round},
  journal   = {Molecular Phylogenetics and Evolution},
  year      = {2007},
  volume    = {45},
  number    = {2},
  pages     = {427--436},
  month     = nov,
  issn      = {1055-7903},
  abstract  = {The pygmy hog, Sus salvanius, the smallest and rarest extant suid was first described as the only member of the genus Porcula. It is currently regarded as member of the genus Sus and a sister taxon of the domestic pig/Eurasian wild boar (Sus scrofa). Phylogenetic analyses of 2316bp from three mtDNA loci (control-region, cytochrome b, 16S) by Bayesian inference and statistical testing of alternative phylogenetic hypotheses all support the original classification of the pygmy hog as a unique genus. Thus, we propose that the species name Porcula salvania should be resurrected. The reclassification will heighten awareness of the need for the future protection and survival of this unique species.},
  doi       = {10.1016/j.ympev.2007.08.007},
  keywords  = {Pygmy hog, Porcula salvania, Sus, alternative phylogenetic hypotheses, Cytochrome b, Control region, 16S},
  url       = {http://www.sciencedirect.com/science/article/pii/S1055790307002928},
}

@article{Zurano2019,
  author    = {Zurano, Juan P. and Magalh\~{a}es, Felipe M. and Asato, Ana E. and Silva, Gabriel and Bidau, Claudio J. and Mesquita, Daniel O. and Costa, Gabriel C.},
  title     = {Cetartiodactyla: updating a time-calibrated molecular phylogeny},
  journal   = {Molecular Phylogenetics and Evolution},
  year      = {2019},
  volume    = {133},
  pages     = {256--262},
  month     = apr,
  issn      = {1055-7903},
  abstract  = {Cetartiodactyla comprises one of the most diverse mammal radiations. Currently, 23 families, 131 genera and more than 330 species are recognized. Several studies have been trying to resolve its phylogenetic relationships. The most comprehensive dated phylogenetic hypothesis available includes only 55% of the extant species, precluding a clear understanding of ecological and evolutionary patterns in Cetartiodactyla. Here, we gathered all mitochondrial genetic data available in GenBank to build a robust Cetartiodactyla calibrated phylogenetic tree using 21 fossil calibration points. We found mitogenomic data for 225 species and included other 93 species from which there was at least one mitochondrial gene available. Using a Bayesian approach, we generated a dated tree comprising 90% of the extant Cetartiodactyla species (n = 318). The major lineages showed robust support and families divergence times are congruent with the available fossil evidence and with previously published phylogenetic hypotheses. By making available a dated phylogeny with extensively sampled clades, we expect to foster future studies on the origin, tempo and mode of Cetartiodactyla diversification.},
  doi       = {10.1016/j.ympev.2018.12.015},
  keywords  = {Mammals, Cetacea, Artiodactyla, Mitogenomics, Phylogenetic relationships},
  url       = {http://www.sciencedirect.com/science/article/pii/S1055790318302720},
}

@article{Hassanin2012,
  author    = {Hassanin, Alexandre and Delsuc, Frédéric and Ropiquet, Anne and Hammer, Catrin and Jansen van Vuuren, Bettine and Matthee, Conrad and Ruiz-Garcia, Manuel and Catzeflis, François and Areskoug, Veronika and Nguyen, Trung Thanh and Couloux, Arnaud},
  title     = {Pattern and timing of diversification of {Cetartiodactyla (Mammalia, Laurasiatheria)}, as revealed by a comprehensive analysis of mitochondrial genomes},
  journal   = {Comptes Rendus Biologies},
  year      = {2012},
  volume    = {335},
  number    = {1},
  pages     = {32--50},
  month     = jan,
  issn      = {1631-0691},
  abstract  = {The order Cetartiodactyla includes cetaceans (whales, dolphins and porpoises) that are found in all oceans and seas, as well as in some rivers, and artiodactyls (ruminants, pigs, peccaries, hippos, camels and llamas) that are present on all continents, except Antarctica and until recent invasions, Australia. There are currently 332 recognized cetartiodactyl species, which are classified into 132 genera and 22 families. Most phylogenetic studies have focused on deep relationships, and no comprehensive time-calibrated tree for the group has been published yet. In this study, 128 new complete mitochondrial genomes of Cetartiodactyla were sequenced and aligned with those extracted from nucleotide databases. Our alignment includes 14,902 unambiguously aligned nucleotide characters for 210 taxa, representing 183 species, 107 genera, and all cetartiodactyl families. Our mtDNA data produced a statistically robust tree, which is largely consistent with previous classifications. However, a few taxa were found to be para- or polyphyletic, including the family Balaenopteridae, as well as several genera and species. Accordingly, we propose several taxonomic changes in order to render the classification compatible with our molecular phylogeny. In some cases, the results can be interpreted as possible taxonomic misidentification or evidence for mtDNA introgression. The existence of three new cryptic species of Ruminantia should therefore be confirmed by further analyses using nuclear data. We estimate divergence times using Bayesian relaxed molecular clock models. The deepest nodes appeared very sensitive to prior assumptions leading to unreliable estimates, primarily because of the misleading effects of rate heterogeneity, saturation and divergent outgroups. In addition, we detected that Whippomorpha contains slow-evolving taxa, such as large whales and hippos, as well as fast-evolving taxa, such as river dolphins. Our results nevertheless indicate that the evolutionary history of cetartiodactyls was punctuated by four main phases of rapid radiation during the Cenozoic era: the sudden occurrence of the three extant lineages within Cetartiodactyla (Cetruminantia, Suina and Tylopoda); the basal diversification of Cetacea during the Early Oligocene; and two radiations that involve Cetacea and Pecora, one at the Oligocene/Miocene boundary and the other in the Middle Miocene. In addition, we show that the high species diversity now observed in the families Bovidae and Cervidae accumulated mainly during the Late Miocene and Plio-Pleistocene.},
  doi       = {10.1016/j.crvi.2011.11.002},
  keywords  = {Cetartiodactyla, Ruminantia, MtDNA genome, Molecular systematics, Radiation, Taxonomy, Hybridization, Cryptic species},
  url       = {http://www.sciencedirect.com/science/article/pii/S1631069111002800},
}

@article{Kaashoek2019,
  author    = {Kaashoek, Mari\"{e}lle and Hobbs, Sarah Jane and Clayton, Hilary Mary and Aerts, Peter and Nauwelaerts, Sandra},
  title     = {Orientation and location of the finite helical axis of the equine forelimb joints},
  journal   = {Journal of Morphology},
  year      = {2019},
  volume    = {0},
  number    = {0},
  month     = mar,
  issn      = {0362-2525},
  abstract  = {Abstract To reduce anatomically unrealistic limb postures in a virtual musculoskeletal model of a horse's forelimb, accurate knowledge on forelimb joint constraints is essential. The aim of this cadaver study is to report all orientation and position changes of the finite helical axes (FHA) as a function of joint angle for different equine forelimb joints. Five horse cadaver forelimbs with standardized cuts at the midlevel of each segment were used. Bone pins with reflective marker triads were drilled into the forelimb bones. Unless joint angles were anatomically coupled, each joint was manually moved independently in all three rotational degrees of freedom (flexion?extension, abduction?adduction, internal?external rotation). The 3D coordinates of the marker triads were recorded using a six infra-red camera system. The FHA and its orientational and positional properties were calculated and expressed against joint angle over the entire range of motion using a finite helical axis method. When coupled, joint angles and FHA were expressed in function of flexion?extension angle. Flexion?extension movement was substantial in all forelimb joints, the shoulder allowed additional considerable motion in all three rotational degrees of freedoms. The position of the FHA was constant in the fetlock and elbow and a constant orientation of the FHA was found in the shoulder. Orientation and position changes of the FHA over the entire range of motion were observed in the carpus and the interphalangeal joints. We report FHA position and orientation changes as a function of flexion?extension angle to allow for inclusion in a musculoskeletal model of a horse to minimize calculation errors caused by incorrect location of the FHA.},
  doi       = {10.1002/jmor.20978},
  keywords  = {3D, joint axes, musculoskeletal model, range of motion, rotational degrees of freedom},
  publisher = {John Wiley \& Sons, Ltd},
}

@article{Jenkins1971,
  author    = {Jenkins, Farish A.},
  title     = {Limb posture and locomotion in the {Virginia} opossum (\textit{{Didelphis} marsupialis}) and in other non-cursorial mammals},
  journal   = {Journal of Zoology},
  year      = {1971},
  volume    = {165},
  number    = {3},
  pages     = {303--315},
  month     = mar,
  issn      = {0952-8369},
  abstract  = {Past studies of mammalian posture and locomotion have been made principally on cursorial species and current concepts are stereotyped accordingly. Mammalian limbs are usually characterized in terms of vertical orientation and parasagittal excursion; the assumption prevails that this type of stance and limb movement is typical of the class. In the present study, walking movements in eight mammalian species (Tachyglossus aculeatus, Didelphis marsupialis, Tupaia glis. Mesocricetus auratus, Rattus norvegicus, Mustela putorius, Heterohyrax brucei, and Felis domestica) were studied cineradiographically with particular attention given to limb posture and excursion relative to the parasagittal and horizontal planes. Only the cat and, to a lesser degree, the hyrax conform to the postural and locomotory pattern that has been regarded as characteristic of most terrestrial, quadrupedal mammals. In the other six species, the humeri and femora usually function in positions more horizontal than vertical and at angles oblique to the parasagittal plane. Furthermore, the excursion pattern of these species have interspecific differences; some patterns are more variable than others. The classical conception of ?mammalian posture? and ?mammalian locomotion? is inaccurate both as a description of the features possessed in common by living terrestrial mammals and as a hypothetical approximation of the condition in ancestral mammals. At present, non-cursorial mammals such as the opossum and tree shrew are more realistic models on which to base deductions concerning posture and locomotion in eatly mammals.},
  doi       = {10.1111/j.1469-7998.1971.tb02189.x},
  publisher = {John Wiley \& Sons, Ltd (10.1111)},
}

@article{Alexander1977,
  author    = {Alexander, R. McN. and Langman, V. A. and Jayes, A. S.},
  title     = {Fast locomotion of some {African} ungulates},
  journal   = {Journal of Zoology},
  year      = {1977},
  volume    = {183},
  number    = {3},
  pages     = {291--300},
  month     = mar,
  issn      = {0952-8369},
  abstract  = {Ten species of ungulate were filmed, galloping in their natural habitat. They ranged in size from Thomson's gazelle (about 20 kg) to giraffe (about 1000 kg). They were pursued to make them run as fast as possible. The films have been analysed to determine speed, stride frequency, stride and step lengths, and duty factors. The dependence of these quantities on body size is discussed. Summary: Fast locomotion of zebra, giraffe, warthog and seven species of Bovidae has been studied. The animals were filmed from a pursuing vehicle while galloping in their natural habitat. Stride frequency was more closely correlated with limb length (represented by hip height) than with body mass. Mean stride frequency was proportional to (hip height)-0·51 and maximum stride frequency to (hip height) -0·63. Maximum speed was between 10 and 14 m s -1 for all species except buffalo (7 m s -1). It was not significantly correlated with body mass. Since the small species ran at least as fast as the large ones they attained higher Froude numbers. Relative stride length was approximately 1·8 (Froude number)0·39 for all species, irrespective of size. Relative step length was approximately 0·65 (Froude number)0·2, both for the fore feet and for the hind ones. The vertical forces exerted by the feet are proportional to (body weight)?(Froude number)0·2 so the forces at maximum speed are larger multiples of body weight for small species than for large ones.},
  doi       = {10.1111/j.1469-7998.1977.tb04188.x},
  publisher = {John Wiley \& Sons, Ltd (10.1111)},
}

@article{Alexander1983,
  author    = {Alexander, R. McN. and Jayes, A. S.},
  title     = {A dynamic similarity hypothesis for the gaits of quadrupedal mammals},
  journal   = {Journal of Zoology},
  year      = {1983},
  volume    = {201},
  number    = {1},
  pages     = {135--152},
  month     = mar,
  issn      = {0952-8369},
  abstract  = {The dynamic similarity hypothesis postulates that different mammals move in a dynamically similar fashion whenever they travel at speeds that give them equal values of a dimensionless parameter, the Froude number. Thus, given information about one species, it could be possible to predict for others relationships between size, speed and features of gait such as stride length, duty factor, the phase relationships of the feet and the patterns of force exerted on the ground. Data for a diverse sample of mammals have been used to test the hypothesis. It is found to be tenable in many cases when comparisons are confined to quadrupedal mammals of the type described by Jenkins (1971) as ?cursorial?. Most mammals of mass greater than 5 kg are of this type. Although the hypothesis applies less successfully to comparisons between cursorial and non-cursorial mammals it is shown to be a reasonable approximation even for such comparisons and for comparisons between quadrupedal mammals and bipedal mammals and birds.},
  doi       = {10.1111/j.1469-7998.1983.tb04266.x},
  publisher = {John Wiley \& Sons, Ltd (10.1111)},
}

@article{McMahon1975,
  author    = {McMahon, Thomas A.},
  title     = {Allometry and Biomechanics: Limb Bones in Adult Ungulates},
  journal   = {The American Naturalist},
  year      = {1975},
  volume    = {109},
  number    = {969},
  pages     = {547--563},
  month     = mar,
  issn      = {0003-0147},
  doi       = {10.1086/283026},
  publisher = {The University of Chicago Press},
}

@article{Stein1997,
  author    = {Stein, B. R. and Casinos, A.},
  title     = {What is a cursorial mammal?},
  journal   = {Journal of Zoology},
  year      = {1997},
  volume    = {242},
  number    = {1},
  pages     = {185--192},
  month     = mar,
  issn      = {0952-8369},
  abstract  = {This paper focuses on the concept of cursoriality in mammals and aims to point out the confusion that can arise when a classical term is not explicitly redefined or expanded to incorporate the results of biomechanical techniques. Historically, the definition of ?cursorial? was based qualitatively on an animal's morphology and behaviour, generally referring to large, terrestrial mammals that ran fast or far across open spaces. However, in recent years, as biomechanicists have learned how to quantify aspects of limb movement and bone orientation, a more specific meaning of this term has come into use. Results from these new techniques have highlighted the lack of specificity in the historical definition and have led us to propose a clarified, quantitative definition of ?cursorial?. The exceptional nature of bovids and primates with respect to this new definition is also addressed in our analysis. We recognize that the definition we propose is, itself, not sufficient because it cannot be applied to fossil taxa and because kinematic data are still lacking for many taxa. Hence, we look forward to the eventual adoption of an even more expanded definition or suite of terms that will further distinguish between all attributes of cursorial mammals and that will reflect an increased understanding of their evolutionary origins.},
  doi       = {10.1111/j.1469-7998.1997.tb02939.x},
  publisher = {John Wiley \& Sons, Ltd (10.1111)},
}

@article{Pfau2011,
  author    = {Pfau, T. and Hinton, E. and Whitehead, C. and Wiktorowicz-Conroy, A. and Hutchinson, J. R.},
  title     = {Temporal gait parameters in the alpaca and the evolution of pacing and trotting locomotion in the {Camelidae}},
  journal   = {Journal of Zoology},
  year      = {2011},
  volume    = {283},
  number    = {3},
  pages     = {193--202},
  month     = mar,
  issn      = {0952-8369},
  abstract  = {Abstract Alpacas are increasingly popular as domesticated companion and commercial animals. Their footfall patterns, however, are not well documented. It would be fascinating to know if artificial selection has changed alpacas' locomotor patterns from the ancestral condition in the vicuña. Some members of the Camelidae pace rather than trot, but the gaits of most species have not been studied quantitatively. Thus, investigating alpacas' gaits might contribute to understanding the factors influencing gait choice and evolution. We aimed to quantify the temporal footfall patterns of alpacas to determine observed gaits and to describe gait parameters as a function of speed. Kinematic data (3D motion capture) of locomotor patterns over a range of speeds were collected from four alpacas. We quantified the influence of speed on stance time, swing time, stride time (and frequency), duty factor and stride length, and created gait diagrams for symmetrical and asymmetrical gaits. Alpacas moved using lateral sequence walks, mainly lateral couplets walks and runs with some lateral sequence, singlefoot footfall patterns. Remarkably, the alpacas never truly paced or trotted. At faster speeds, they switched to asymmetrical gaits, predominantly transverse gallops. With increasing speed, stance and stride times decreased, and stride frequencies and stride length increased. Swing times decreased slightly with speed for symmetrical gaits, and a tendency towards an increasing swing time was evident in asymmetrical gaits. It is still uncertain why quadrupeds choose particular gaits and intriguingly, extant camelids (alpacas, dromedary camels) do not trot. The apparent absence of pacing in alpacas deserves further investigation in an experimental and comparative framework. Yet, this absence seems inherited from their vicuña ancestors, indicating that pacing gaits may not be ancestral or common for Camelidae. Future studies should include kinetic and anatomical data to provide insight into whole-body mechanics, and include other unstudied species such as guanacos and vicuñas.},
  doi       = {10.1111/j.1469-7998.2010.00763.x},
  keywords  = {alpaca, Camelidae, gait, pace, walking, running, kinematics, locomotion},
  publisher = {John Wiley \& Sons, Ltd (10.1111)},
}

@article{Vaughan2005,
  author    = {Vaughan, Christopher L. and O'Malley, Mark J.},
  title     = {Froude and the contribution of naval architecture to our understanding of bipedal locomotion},
  journal   = {Gait \& Posture},
  year      = {2005},
  volume    = {21},
  number    = {3},
  pages     = {350--362},
  month     = apr,
  issn      = {0966-6362},
  abstract  = {It is fascinating to think that the ideas of two 19th century naval architects could offer useful insights for 21st century scientists contemplating the exploration of our planetary system or monitoring the long-term effects of a neurosurgical procedure on gait. The Froude number, defined as Fr=v2/gL, where v is velocity, g is gravitational acceleration and L is a characteristic linear dimension (such as leg length), has found widespread application in the biomechanics of bipedal locomotion. This review of two parameters, Fr and dimensionless velocity β=(Fr)1/2, that have served as the criterion for dynamic similarity, has been arranged in two parts: (I) historical development, including the contributions by William Froude and his son Edmund, two ship designers who lived more than 130 years ago, the classic insights of D’Arcy Wentworth Thompson who, in his magnum opus On Growth and Form, espoused the connection between mathematics and biology, and the pioneering efforts of Robert McNeill Alexander, who popularised the application of Fr to animal locomotion; and (II) selected applications, including a comparison of walking for people of different heights, exploring the effects of different gravitational fields on human locomotion, establishing the impact of pathology and the benefits of treatment, and understanding the walking patterns of bipedal robots. Although not all applications of Fr to locomotion have been covered, the review offers an important historical context for all researchers of bipedal gait, and extends the idea of dimensionless scaling of gait parameters.},
  keywords  = {Froude number, Gait, Dynamic similarity, Walking, Size, Gravity, Children},
  url       = {http://www.sciencedirect.com/science/article/pii/S0966636204000268},
  doi = {10.1016/j.gaitpost.2004.01.011},
}

@article{SteudelNumbers2006,
  author    = {Steudel-Numbers, Karen and Weaver, Timothy D.},
  title     = {Froude number corrections in anthropological studies},
  journal   = {American Journal of Physical Anthropology},
  year      = {2006},
  volume    = {131},
  number    = {1},
  pages     = {27--32},
  month     = mar,
  issn      = {0002-9483},
  abstract  = {Abstract The Froude number has been widely used in anthropology to adjust for size differences when comparing gait parameters or other nonmorphological locomotor variables (such as optimal walking speed or speed at gait transitions) among humans, nonhuman primates, and fossil hominins. However, the dynamic similarity hypothesis, which is the theoretical basis for Froude number corrections, was originally developed and tested at much higher taxonomic levels, for which the ranges of variation are much greater than in the intraspecific or intrageneric comparisons typical of anthropological studies. Here we present new experimental data on optimal walking speed and the mass-specific cost of transport at that speed from 19 adult humans walking on a treadmill, and evaluate the predictive power of the dynamic similarity hypothesis in this sample. Contrary to the predictions of the dynamic similarity hypothesis, we found that the mass-specific cost of transport at experimentally measured optimal walking speed and Froude number were not equal across individuals, but retained a significant correlation with body mass. Overall, the effect of lower limb length on optimal walking speed was weak. These results suggest that the Froude number may not be an effective way for anthropologists to correct for size differences across individuals, but more studies are needed. We suggest that researchers first determine whether geometric similarity characterizes their data before making inferences based on the dynamic similarity hypothesis, and then check the consistency of their results with and without Froude number corrections before drawing any firm conclusions. Am J Phys Anthropol, 2006. ? 2006 Wiley-Liss, Inc.},
  doi       = {10.1002/ajpa.20404},
  keywords  = {energetics, limb length, walking speed},
  publisher = {John Wiley \& Sons, Ltd},
}

@article{Raichlen2013,
  author    = {Raichlen, David A. and Pontzer, Herman and Shapiro, Liza J.},
  title     = {A new look at the Dynamic Similarity Hypothesis: the importance of swing phase},
  journal   = {Biology Open},
  year      = {2013},
  volume    = {2},
  number    = {10},
  pages     = {1032},
  month     = oct,
  abstract  = {The Dynamic Similarity Hypothesis (DSH) suggests that when animals of different size walk at similar Froude numbers (equal ratios of inertial and gravitational forces) they will use similar size-corrected gaits. This application of similarity theory to animal biomechanics has contributed to fundamental insights in the mechanics and evolution of a diverse set of locomotor systems. However, despite its popularity, many mammals fail to walk with dynamically similar stride lengths, a key element of gait that determines spontaneous speed and energy costs. Here, we show that the applicability of the DSH is dependent on the inertial forces examined. In general, the inertial forces are thought to be the centripetal force of the inverted pendulum model of stance phase, determined by the length of the limb. If instead we model inertial forces as the centripetal force of the limb acting as a suspended pendulum during swing phase (determined by limb center of mass position), the DSH for stride length variation is fully supported. Thus, the DSH shows that inter-specific differences in spatial kinematics are tied to the evolution of limb mass distribution patterns. Selection may act on morphology to produce a given stride length, or alternatively, stride length may be a “spandrel” of selection acting on limb mass distribution.},
  url       = {http://bio.biologists.org/content/2/10/1032.abstract},
  doi = {10.1242/bio.20135165},
}

@article{Kramer2013,
  author    = {Kramer, Patricia Ann and Sylvester, Adam D.},
  title     = {Humans, geometric similarity and the {Froude} number: is ''reasonably close'' really close enough?},
  journal   = {Biology Open},
  year      = {2013},
  volume    = {2},
  number    = {2},
  pages     = {111},
  month     = feb,
  abstract  = {Understanding locomotor energetics is imperative, because energy expended during locomotion, a requisite feature of primate subsistence, is lost to reproduction. Although metabolic energy expenditure can only be measured in extant species, using the equations of motion to calculate mechanical energy expenditure offers unlimited opportunities to explore energy expenditure, particularly in extinct species on which empirical experimentation is impossible. Variability, either within or between groups, can manifest as changes in size and/or shape. Isometric scaling (or geometric similarity) requires that all dimensions change equally among all individuals, a condition that will not be met in naturally developing populations. The Froude number (Fr), with lower limb (or hindlimb) length as the characteristic length, has been used to compensate for differences in size, but does not account for differences in shape. To determine whether or not shape matters at the intraspecific level, we used a mechanical model that had properties that mimic human variation in shape. We varied crural index and limb segment circumferences (and consequently, mass and inertial parameters) among nine populations that included 19 individuals that were of different size. Our goal in the current work is to understand whether shape variation changes mechanical energy sufficiently enough to make shape a critical factor in mechanical and metabolic energy assessments. Our results reaffirm that size does not affect mass-specific mechanical cost of transport (Alexander and Jayes, 1983) among geometrically similar individuals walking at equal Fr. The known shape differences among modern humans, however, produce sufficiently large differences in internal and external work to account for much of the observed variation in metabolic energy expenditure, if mechanical energy is correlated with metabolic energy. Any species or other group that exhibits shape differences should be affected similarly to that which we establish for humans. Unfortunately, we currently do not have a simple method to control or adjust for size-shape differences in individuals that are not geometrically similar, although musculoskeletal modeling is a viable, and promising, alternative. In mouse-to-elephant comparisons, size differences could represent the largest source of morphological variation, and isometric scaling factors such as Fr can compensate for much of the variability. Within species, however, shape differences may dominate morphological variation and Fr is not designed to compensate for shape differences. In other words, those shape differences that are “reasonably close” at the mouse-to-elephant level may become grossly different for within-species energetic comparisons.},
  url       = {http://bio.biologists.org/content/2/2/111.abstract},
  doi = {10.1242/bio.20122691},
}

@article{Christiansen2002,
  author    = {Christiansen, Per},
  title     = {Locomotion in terrestrial mammals: the influence of body mass, limb length and bone proportions on speed},
  journal   = {Zoological Journal of the Linnean Society},
  year      = {2002},
  volume    = {136},
  number    = {4},
  pages     = {685--714},
  month     = {12},
  issn      = {0024-4082},
  abstract  = {Traditionally a few limb proportions or total limb lengths have been regarded as indicative of peak running velocity. This is due to physical principles (inferred in- and outvelocities around the joints, stride lengths) and also the observation that fast-moving animals tend to share a number of purported key features which are either absent or not developed to near the same extent in slower moving forms. Previous studies have shown hind limb length and metatarsus/femur ratio to be correlated significantly, albeit modestly with running speed. These studies have nearly all been bivariate analyses. Based on the physical principles, there is reason to suppose that more variables than just m/f ratio could be important as adaptations for fast locomotion, and also that bivariate analyses are too simple. In this study a sample of 76 running mammals was used, with running speeds taken from literature. A number of osteological parameters were discovered to covary significantly with peak running speed, albeit only modestly. Using the information from phylogeny reduced all correlations, often significantly so. Multivariate analyses resulted in markedly higher correlation coefficients. Animals probably do not optimize their anatomy for the purpose of running very fast, which occurs only on rare occasions, but for reducing costs of locomotion.},
  doi       = {10.1046/j.1096-3642.2002.00041.x},
}

@article{Biancardi2012,
  author    = {Biancardi, Carlo M. and Minetti, Alberto E.},
  journal   = {Journal of Experimental Biology},
  title     = {Biomechanical determinants of transverse and rotary gallop in cursorial mammals},
  year      = {2012},
  month     = dec,
  number    = {23},
  pages     = {4144},
  volume    = {215},
  abstract  = {Transverse and rotary gallop differ in the placement of the leading hindfeet and forefeet: ipsilateral in the former gait, contralateral in the latter. We analysed 351 filmed sequences to assess the gallop type of 89 investigated mammalian species belonging to Carnivora, Artiodactyla and Perissodactyla orders. Twenty-three biometrical, ecological and physiological parameters were collected for each species both from literature data and from animal specimens. Most of the species showed only one kind of gallop: transverse (42\%) or rotary (39\%), while some species performed rotary gallop only at high speed (19\%). In a factorial analysis, the first principal component (PC), which accounted for 40\% of the total variance, was positively correlated to the relative speed and negatively correlated to size and body mass. The second PC was correlated to the ratio between distal and proximal limb segments. Large size and longer proximal limb segments were associated with transverse gallop, while rotary and speed-dependent species showed higher metacarpus/humerus and metatarsus/femur length ratio and faster relative speeds. The resulting limb excursion angles were proportional to the square-root of the Froude number, and significantly higher in rotary gallopers. The gait pattern analysis indicated significant differences between transverse and rotary gallop in forelimb and hindlimb duty factor (t-test; P 0.001), and in duration of the forelimb contact (t-test; P=0.045). Our results show that an exclusive gallop gait is adopted by a large number of mammalian species, and indicate that the gallop pattern depends on diverse environmental, morphometrical and biomechanical characters.},
  doi       = {10.1242/jeb.073031},
  url       = {https://air.unimi.it/handle/2434/166976},
}

@article{Stoessel2012,
  author    = {Stoessel, Alexander and Fischer, Martin S.},
  title     = {Comparative intralimb coordination in avian bipedal locomotion},
  journal   = {Journal of Experimental Biology},
  year      = {2012},
  volume    = {215},
  number    = {23},
  pages     = {4055},
  month     = dec,
  abstract  = {Analyses of how intralimb coordination during locomotion varies within and across different taxa are necessary for understanding the morphological and neurological basis for locomotion in general. Previous findings suggest that intralimb proportions are the major source of kinematic variation that governs intralimb coordination across taxa. Also, independence of kinematics from habitat preference and phylogenetic position has been suggested for mammals. This leads to the hypothesis that among equally sized bird species exhibiting equal limb proportions, similar kinematics can be observed. To test this hypothesis, the bipedal locomotion of two distantly related ground-dwelling bird species (Eudromia elegans and Coturnix coturnix) and of a less terrestrial species (Corvus monedula) was investigated by means of a biplanar high-speed X-ray videographic analysis. Birds exhibited similar intralimb proportions and were filmed over a broad range of speed while moving on a treadmill. Joint and limb element angles, as well as pelvic rotations, were quantified. Regarding fore-aft motions of the limb joints and elements, a congruent pattern of intralimb coordination was observed among all experimental species. The sample of species suggests that this is largely independent of their habitat preference and systematic position and seems to be related to demands for coping with an irregular terrain with a minimum of necessary control. Hence, the initial hypothesis was confirmed. However, this congruence is not found when looking at medio-lateral limb motions and pelvic rotations, showing distinct differences between ground-dwellers (e.g. largely restricted to a parasagittal plane) and C. monedula (e.g. increased mobility of the hip joint).},
  url       = {http://jeb.biologists.org/content/215/23/4055.abstract},
  doi = {10.1242/jeb.070458},
}

@article{Gatesy2011,
    author = {Gatesy, Stephen M. and Pollard, Nancy S.},
    year = {2011},
    title = {Apples, oranges, and angles: Comparative kinematic analysis of disparate limbs},
    doi = {10.1016/j.jtbi.2011.05.009},
    journal = {Journal of Theoretical Biology},
    volume = {282},
    number = {1},
    pages = {7--13},
    month = aug,
    issn = {0022-5193},
    abstract = {Tetrapod limbs exhibit diverse postures and movements during terrestrial locomotion. As with morphological traits, the history of kinematic evolution should be accessible to reconstruction through analysis of limb motion patterns in a phylogenetic framework. However, the angular data comprising most kinematic descriptions appear to suffer from limitations that preclude meaningful comparison among disparate species. Using simple planar models, we discuss how geometric constraints render joint and elevation angles independent of neither morphology, degree of crouch, nor one another during the stance phase of locomotion. The implicit null hypothesis of potential similarity is invalidated because angular data are not viably transferable among limbs of dissimilar proportion and/or degree of crouch. Overlooking or dismissing the effect of constraints on angular parameterization hampers efforts to quantitatively elucidate the evolution of locomotion. We advocate a search for alternative methods of measuring limb movement that can decouple intersegmental coordination from morphology and posture.},
    keywords = {Locomotion, Motion analysis, Evolution, Angle, Comparative methods},
    url = {http://www.sciencedirect.com/science/article/pii/S0022519311002517},
}


@article{Fischer2002,
  author    = {Fischer, Martin S. and Schilling, Nadja and Schmidt, Manuela and Haarhaus, Dieter and Witte, Hartmut},
  title     = {Basic limb kinematics of small therian mammals},
  journal   = {Journal of Experimental Biology},
  year      = {2002},
  volume    = {205},
  number    = {9},
  pages     = {1315},
  month     = may,
  abstract  = {A comparative study of quantitative kinematic data of fore- and hindlimb movements of eight different mammalian species leads to the recognition of basic principles in the locomotion of small therians. The description of kinematics comprises fore- and hindlimb movements as well as sagittal spine movements including displacement patterns of limb segments, their contribution to step length, and joint movements. The comparison of the contributions of different segments to step length clearly shows the proximal parts (scapula, femur) to produce more than half of the propulsive movement of the whole limb at symmetrical gaits. Basically, a three-segmented limb with zigzag configuration of segments is mainly displaced at the scapular pivot or hip joint, both of which have the same vertical distance to the ground. Two segments operate in matched motion during retraction of the limb. While kinematic parameters of forelimbs are independent of speed and gait (with the scapula as the dominant element), fundamental changes occur in hindlimb kinematics with the change from symmetrical to in-phase gaits. Forward motion of the hindlimbs is now mainly due to sagittal lumbar spine movements contributing to half of the step length. Kinematics of small therian mammals are independent of their systematic position, their natural habitat, and also of specific anatomical dispositions (e.g. reduction of fingers, toes, or clavicle). In contrast, the possession of a tail influences pelvic movements.},
  url       = {http://jeb.biologists.org/content/205/9/1315.abstract},
  doi = {10.1242/jeb.205.9.1315},
}

@Article{HsiaoWecksler2010,
  author    = {Hsiao-Wecksler, Elizabeth T. and Polk, John D. and Rosengren, Karl S. and Sosnoff, Jacob J. and Hong, Sungjin},
  title     = {A Review of New Analytic Techniques for Quantifying Symmetry in Locomotion},
  journal   = {Symmetry},
  year      = {2010},
  volume    = {2},
  number    = {2},
  pages     = {1135--1155},
  issn      = {2073-8994},
  abstract  = {We present a review of novel techniques developed by our research group to improve quantitative assessment of human movement, especially assessments related to symmetric and asymmetric gait patterns. These new methods use motion capture data of the lower limb joints (e.g., joint and body segment angular position and/or velocity, or joint center locations) and include: (1) Regions of Deviation (ROD) analysis, (2) complexity and variability of phase portraits, and (3) multivariate shape-alignment and decomposition. We provide example demonstrations of these techniques using data from infants, typical and atypically developing children, simulated injuries of a knee or ankle, and wheelchair propulsion.},
  doi       = {10.3390/sym2021135},
  url       = {http://www.mdpi.com/2073-8994/2/2/1135},
}

@Article{Polk2008,
  author    = {Polk, John D. and Spencer-Smith, Jesse B. and DiBerardino {III.}, Louis A. and Ellis, Daniel and Downen, Matthew and Rosengren, Karl S.},
  title     = {Quantifying variability in phase portraits: Application to gait ontogeny},
  journal   = {Infant Behavior and Development},
  year      = {2008},
  volume    = {31},
  number    = {2},
  pages     = {302--306},
  issn      = {0163-6383},
  abstract  = {We describe new Fourier- and shape-based methods for quantifying variation in phase-portraits, and re-analyze previously-published ontogenetic and adult data [Clark, J. E., & Phillips, S. J. (1993). A longitudinal study of intralimb coordination in the first year of independent walking: A dynamical systems approach. Child Development, 64, 1143–1157]. Results show considerable variation between individuals and through development, but after 6 months of walking some gait patterns stabilize.},
  doi       = {10.1016/j.infbeh.2007.10.005},
  keywords  = {Phase portraits, Variability, Development, Elliptical Fourier analysis, Gait},
  url       = {http://www.sciencedirect.com/science/article/pii/S0163638307001233},
}

@article{Wu2004,
  author    = {Wu, Wenhua and Meijer, Onno G. and Lamoth, Claudine J. C. and Uegaki, Kimi and van Dieën, Jaap H. and Wuisman, Paul I. J. M. and de Vries, Johanna I. P. and Beek, Peter J.},
  title     = {Gait coordination in pregnancy: transverse pelvic and thoracic rotations and their relative phase},
  journal   = {Clinical Biomechanics},
  year      = {2004},
  volume    = {19},
  number    = {5},
  pages     = {480--488},
  issn      = {0268-0033},
  abstract  = {Objective. To examine the effects of pregnancy on the coordination of transverse pelvic and thoracic rotations during gait. Design. Gait of healthy pregnant women and nulligravidae was studied during treadmill walking at predetermined velocities ranging from 0.17 to 1.72 m/s. Background. Pelvis–thorax coordination during walking is altered in women with postpartum pregnancy-related pelvic girdle pain. This coordination has not been investigated in a healthy pregnant population. Methods. Comfortable walking velocity was established. Amplitudes of pelvic and thoracic rotations were calculated. Their coordination was characterized by relative Fourier phase and its standard deviation. Results. Comfortable walking velocity was significantly reduced. The amplitudes of pelvic and thoracic rotations were somewhat reduced, with significantly smaller intra-individual standard deviations. Also pelvis–thorax relative Fourier phase was somewhat smaller, its intra-individual standard deviation was negatively correlated with week of pregnancy, and significantly lower at velocities ⩾1.06 m/s. Conclusions. The general pattern of gait kinematics in pregnant women is very similar to that of nulligravidae. Still, it appears that pregnant women experience difficulties in realizing the more anti-phase pelvis–thorax coordination that is required at higher walking velocities. Relevance The present study shows that gait in healthy pregnancy is remarkably normal, but some differences in pelvis–thorax coordination were detected. In healthy pregnancy, anti-phase pelvis–thorax coordination appears difficult, but less so than in pregnancy-related pelvic girdle pain. Better understanding of gait in healthy pregnancy may provide insight into the gait problems of women with pregnancy-related pelvic girdle pain.},
  doi       = {10.1016/j.clinbiomech.2004.02.003},
  keywords  = {Pregnancy, Treadmill walking, Kinematics, Transverse rotations, Trunk coordination},
}


@book{Bookstein1991,
  title     = {Morphometric tools for landmark data: geometry and biology},
  publisher = {Cambridge University Press},
  year      = {1991},
  author    = {Bookstein, Fred L},
}


@article{Kuhl1982,
  author    = {Kuhl, Frank P. and Giardina, Charles R.},
  title     = {Elliptic {Fourier} features of a closed contour},
  journal   = {Computer Graphics and Image Processing},
  year      = {1982},
  volume    = {18},
  number    = {3},
  pages     = {236--258},
  issn      = {0146-664X},
  abstract  = {A direct procedure for obtaining the Fourier coefficients of a chain-encoded contour is presented. Advantages of the procedure are that it does not require integration or the use of fast Fourier transform techniques, and that bounds on the accuracy of the image contour reconstruction are easy to specify. Elliptic properties of the Fourier coefficients are shown and used for a convenient and intuitively pleasing procedure of normalizing a Fourier contour representation. Extension of the contour representation to arbitrary objects at arbitrary aspect angle is discussed. The procedures have direct application to a variety of pattern recognition problems that involve analysis of well-defined image contours.},
  doi       = {10.1016/0146-664X(82)90034-X},
  url       = {http://www.sciencedirect.com/science/article/pii/0146664X8290034X},
}

@article{Rosengren2009,
  author    = {Rosengren, Karl S. and Deconinck, Frederik J. A. and DiBerardino {III.}, Louis A. and Polk, John D. and Spencer-Smith, Jesse B. and De Clercq, Dirk and Lenoir, Matthieu},
  title     = {Differences in gait complexity and variability between children with and without Developmental Coordination Disorder},
  journal   = {Gait \& Posture},
  year      = {2009},
  volume    = {29},
  number    = {2},
  pages     = {225--229},
  issn      = {0966-6362},
  abstract  = {We used elliptical Fourier analysis (EFA) to examine potential differences in the complexity and variability of gait of children with (N=10) and without (N=10) Developmental Coordination Disorder (DCD). Children with DCD generated movement patters with larger variability and complexity than typically developing (TD) children. In addition, children with DCD exhibited greater asymmetry in their movement patterns compared to TD children. Our results suggest that children with DCD have significantly greater difficulty producing consistent movement patterns both across their left and right legs and over repeated strides. EFA techniques show promise for distinguishing between different groups of individuals.},
  doi       = {10.1016/j.gaitpost.2008.08.005},
  keywords  = {Developmental Coordination Disorder, Gait, Variability, Complexity},
  url       = {http://www.sciencedirect.com/science/article/pii/S0966636208002403},
}

@article{Isler2005,
  author    = {Isler, Karin},
  title     = {{3D}-{Kinematics} of vertical climbing in hominoids},
  journal   = {American Journal of Physical Anthropology},
  year      = {2005},
  volume    = {126},
  number    = {1},
  pages     = {66--81},
  month     = mar,
  issn      = {0002-9483},
  abstract  = {Abstract Vertical climbing has played an important role in theories about the evolution of habitual bipedalism in early hominids and of locomotor specialization in hominoids. However, empirical data on vertical climbing in nonhuman primates are scarce, especially regarding kinematics. In this paper, the kinematics of flexed-elbow vertical climbing of four hominoid species are reported: western lowland gorillas (Gorilla gorilla gorilla), bonobos (Pan paniscus), Sumatran orangutans (Pongo pygmaeus abelii), and yellow-cheeked crested gibbons (Hylobates concolor gabriellae). The climbing sequences were recorded simultaneously by four digital video cameras in European zoos. Analyzed parameters include intersegmental flexion/extension angles of the shoulder, elbow, hip, and knee joints, horizontal abduction/adduction angles of the upper arm and thigh, and distance of the body center of gravity from the substrate. Analyses reveal that differences in climbing kinematics between individuals of different age/sex classes of one species are mostly size-related, whereas interspecific differences reflect specific locomotor adaptations. The climbing kinematics of bonobos and gorillas are more similar to each other than to those of orangutans or gibbons. The range of motion of the major limb joints in adult orangutans is larger than in African apes, although the hip is not more extended. Gibbons horizontally abduct the arm more and the thigh less during climbing than any of the great apes. These results allow us to question some qualitative descriptions of vertical climbing kinematics reported in the literature, and to discuss implications for the evolution of locomotor adaptations in hominoids. Am J Phys Anthropol 2004. ? 2004 Wiley-Liss, Inc.},
  doi       = {10.1002/ajpa.10419},
  keywords  = {locomotion, joint angles, kinematic analysis, primates, Hominoidea, Gorilla gorilla gorilla, Hylobates concolor gabriellae, Pan paniscus, Pongo pygmaeus abelii},
  publisher = {John Wiley \& Sons, Ltd},
}

@InCollection{Wheat2006,
  author    = {Wheat, Jonathan S. and Glazier, Paul S.},
  title     = {Measuring Coordination and Variability in Coordination},
  booktitle = {Movement System Variability},
  publisher = {Human Kinetics},
  year      = {2006},
  editor    = {Davids, Keith and Bennett, Simon and Newell, Karl M.},
  chapter   = {9},
}

@book{Robertson2018,
  title     = {Research Methods in Biomechanics},
  publisher = {Human Kinetics},
  year      = {2018},
  editor    = {Robertson, G. E. and Caldwell, G. E. and Hamill, J. and Kamen, G. and Whittlesey, S.},
  edition   = {\(2^{nd}\)},
  isbn      = {0736093400,9780736093408},
}

@article{Lees2016,
  author    = {Lees, John and Gardiner, James and Usherwood, James and Nudds, Robert},
  title     = {Locomotor preferences in terrestrial vertebrates: An online crowdsourcing approach to data collection},
  journal   = {Scientific Reports},
  year      = {2016},
  volume    = {6},
  pages     = {28825},
  month     = jul,
  doi       = {10.1038/srep28825},
}

@article{MaynardSmith1956,
  author    = {Maynard Smith, J. and Savage, R. J. G.},
  title     = {Some locomotory adaptations in mammals},
  journal   = {Zoological Journal of the Linnean Society},
  year      = {1956},
  volume    = {42},
  number    = {288},
  pages     = {603--622},
  issn      = {0024-4082},
  abstract  = {The pectoral girdle and fore limb of Equus and Dasypus are compared. It is shown that the shoulder muscles of the horse have a small mechanical advantage (1/13 for the m. teres major) and are therefore adapted to produce rapid movements of the limb; these muscles in the armadillo have a larger mechanical advantage (1/4 for the m. teres) to produce slower movements, while exerting a greater force. The broad scapulae and short legs of fossorial mammals are adaptations producing powerful movements of the foot, usually with strong abductor action. Aquatic mammals show similar modifications, though without the emphasis on abductor movements. The high, narrow senpulac and long legs of crvsorial inanimals are esplained as adaptations to speed, though the detailed arrangements by which this is achieved differ in cursorial ungulates and carnivores. The sharp angles at the ends of the vertebral border of the scapula in cursorial ungulates provide pints of insertion for two parts of the m. serratus, which act as antagonists in the fore-and-aft movement of the shoulder. Similarly in the dog, and probably all cursorial carnivores and lagomorphs, the sharp vertebro-axillary angle affords a point of insertion for the posterior digitations of the m. serratus. The mechanical adaptations of the olecranon process and the m. triceps are described. The structure of the vertebral column and axial musculature is shown to depend upon gait. Two types of gallop, the horse gallop and leaping gallop (e.g. dog) are analysed and the association between gait and structure described. The mechanics of gaits are discussed in an appendix. The extensor muscles from the pelvis to the femur fall into two groups, an iliac group adapted to rapid extension of the thigh, and an ischio-pubic group adapted to slower but more powerful thigh extension. The relative proportions of the two regions of the pelvis vary according to the gaits adopted. In cursorial ungulates the ilium is long and the ischio-pubic region short, whereas in aquatic mammals the latter region predominates. The lengths and cross-sectional areas of the bones of the hind limb are shown to be correlated with gait in aquatic, cursorial (leaping gallop and horse gallop), saltatorial and graviportal mammals.},
  doi       = {10.1111/j.1096-3642.1956.tb02220.x},
}

@article{Alexander1984,
  author    = {Alexander, R. McN.},
  title     = {Elastic Energy Stores in Running Vertebrates},
  doi = {10.1093/icb/24.1.85},
  journal   = {Integrative and Comparative Biology},
  year      = {1984},
  volume    = {24},
  number    = {1},
  pages     = {85--94},
  issn      = {0003-1569},
  abstract  = {Large mammals save much of the energy they would otherwise need for running by means of elastic structures in their legs. Kinetic and potential energy, lost at one stage of a stride, is stored temporarily as elastic strain energy and returned later in an elastic recoil. At high speeds, men and kangaroos seem to save in this way more than half the metabolic energy they would otherwise need for locomotion.It is shown by means of a generalized model that muscles and tendons could both be important as elastic energy stores. Analysis of films and force records of kangaroos hopping shows that strain energy stored while the feet are on the ground must be stored mainly distal to the knee. The principal muscles there have short fibres, and most of the storage must be in tendons. Investigation of camels shows that tendons in the feet, distal to the ankle and wrist, are especially important. The scope for elastic storage while the feet are off the groundis also considered.Though the evidence presented in this paper comes mainly from a few species, the conclusions presumably apply to large mammals in general.},
}

@article{Currie2013,
  author    = {Currie, Adrian},
  title     = {Convergence as Evidence},
  journal   = {The British Journal for the Philosophy of Science},
  year      = {2013},
  volume    = {64},
  number    = {4},
  pages     = {763},
  doi       = {10.1093/bjps/axs027},
}

@article{Harmon2007,
  author    = {Harmon, Luke J. and Kolbe, Jason J. and Cheverud, James M. and Losos, Jonathan B.},
  title     = {Convergence and the multidimensional niche},
  journal   = {Evolution},
  year      = {2007},
  volume    = {59},
  number    = {2},
  pages     = {409--421},
  month     = mar,
  issn      = {0014-3820},
  abstract  = {Abstract Convergent evolution has played an important role in the development of the ecological niche concept. We investigated patterns of convergent and divergent evolution of Caribbean Anolis lizards. These lizards diversified independently on each of the islands of the Greater Antilles, producing the same set of habitat specialists on each island. Using a phylogenetic comparative framework, we examined patterns of morphological convergence in five functionally distinct sets of morphological characters: body size, body shape, head shape, lamella number, and sexual size dimorphism. We find evidence for convergence among members of the habitat specialist types for each of these five datasets. Furthermore, the patterns of convergence differ among at least four of the five datasets; habitat specialists that are similar for one set of characters are often greatly different for another. This suggests that the habitat specialist niches into which these anoles have evolved are multidimensional, involving several distinct and independent aspects of morphology.},
  doi       = {10.1111/j.0014-3820.2005.tb00999.x},
  keywords  = {Anolis, Convergent evolution, Ecomorphology, Geomitric Morphomitrics, Mantel test},
  publisher = {John Wiley \& Sons, Ltd (10.1111)},
}

@article{Adams2014,
  author    = {Adams, Dean C.},
  title     = {A Generalized {K} Statistic for Estimating Phylogenetic Signal from Shape and Other High-Dimensional Multivariate Data},
  journal   = {Systematic Biology},
  year      = {2014},
  volume    = {63},
  number    = {5},
  pages     = {685-697},
  month     = {April},
  abstract  = {Phylogenetic signal is the tendency for closely related species to display similar trait values due to their common ancestry. Several methods have been developed for quantifying phylogenetic signal in univariate traits and for sets of traits treated simultaneously, and the statistical properties of these approaches have been extensively studied. However, methods for assessing phylogenetic signal in high-dimensional multivariate traits like shape are less well developed, and their statistical performance is not well characterized. In this article, I describe a generalization of the K statistic of Blomberg et al. that is useful for quantifying and evaluating phylogenetic signal in highly dimensional multivariate data. The method (Kmult) is found from the equivalency between statistical methods based on covariance matrices and those based on distance matrices. Using computer simulations based on Brownian motion, I demonstrate that the expected value of Kmult remains at 1.0 as trait variation among species is increased or decreased, and as the number of trait dimensions is increased. By contrast, estimates of phylogenetic signal found with a squared-change parsimony procedure for multivariate data change with increasing trait variation among species and with increasing numbers of trait dimensions, confounding biological interpretations. I also evaluate the statistical performance of hypothesis testing procedures based on Kmult and find that the method displays appropriate Type I error and high statistical power for detecting phylogenetic signal in high-dimensional data. Statistical properties of Kmult were consistent for simulations using bifurcating and random phylogenies, for simulations using different numbers of species, for simulations that varied the number of trait dimensions, and for different underlying models of trait covariance structure. Overall these findings demonstrate that Kmult provides a useful means of evaluating phylogenetic signal in high-dimensional multivariate traits. Finally, I illustrate the utility of the new approach by evaluating the strength of phylogenetic signal for head shape in a lineage of Plethodon salamanders.},
  doi       = {10.1093/sysbio/syu030},
  keywords  = {Geometric morphometrics; macroevolution; morphological evolution; phylogenetic comparative method},
  url       = {http://sysbio.oxfordjournals.org/content/63/5/685.abstract},
}

@article{Polly2013,
  author    = {Polly, P. David and Lawing, A. Michelle and Fabre, Anne-Claire and Goswami, Anjali},
  title     = {Phylogenetic Principal Components Analysis and Geometric Morphometrics},
  journal   = {Hystrix, the Italian Journal of Mammalogy},
  year      = {2013},
  volume    = {24},
  number    = {1},
  pages     = {33--41},
  issn      = {0394-1914},
  abstract  = {Phylogenetic Principal Components Analysis (pPCA) is a recently proposed method for ordinating multivariate data in a way that takes into account the phylogenetic non-independence among species means. We review this method in terms of geometric morphometric shape analysis and compare its properties to ordinary principal components analysis (PCA). We find that pPCA produces a shape space that preserves the Procrustes distances between objects, that allows shape models to be constructed, and that produces scores that can be used as shape variables for most purposes. Unlike ordinary PCA scores, however, the scores on pPC axes are correlated with one another and their variances do not correspond to the eigenvalues of the phylogenetically corrected axes. The pPC axes are oriented by the non-phylogenetic component of shape variation, but the positioning of the scores in the space retains phylogenetic covariance making the visual information presented in plots a hybrid of non-phylogenetic and phylogenetic. Presuming that all pPCA scores are used as shape variables, there is no difference between them and PCA scores for the construction of distance-based trees (such as UPGMA), for morphological disparity, or for ordinary multivariate statistical analyses (so long as the algorithms are suitable for correlated variables). pPCA scores yield different trait-based trees (such as maximum likelihood trees for continuous traits) because the scores are correlated and because the pPC axes differ from PC axes. pPCA eigenvalues represent the residual shape variance once the phylogenetic covariance has been removed (though there are scaling issues), and as such they provide information on covariance that is independent of phylogeny. Tests for modularity on pPCA eigenvalues will therefore yield different results than ordinary PCA eigenvalues. pPCA can be considered another tool in the kit of geometric morphometrics, but one whose properties are more difficult to interpret than ordinary PCA.},
  keywords  = {phylogenetic principal component analysis; geometric morphometrics; comparative phylogenetic methods; shape analysis},
  doi       = {10.4404/hystrix-24.1-6383},
}

@article{Revell2009,
  author    = {Revell, Liam J.},
  title     = {Size‐correction and principal components for interspecific comparative studies},
  journal   = {Evolution},
  year      = {2009},
  volume    = {63},
  number    = {12},
  pages     = {3258--3268},
  month     = mar,
  issn      = {0014-3820},
  abstract  = {Phylogenetic methods for the analysis of species data are widely used in evolutionary studies. However, preliminary data transformations and data reduction procedures (such as a size-correction and principal components analysis, PCA) are often performed without first correcting for nonindependence among the observations for species. In the present short comment and attached R and MATLAB code, I provide an overview of statistically correct procedures for phylogenetic size-correction and PCA. I also show that ignoring phylogeny in preliminary transformations can result in significantly elevated variance and type I error in our statistical estimators, even if subsequent analysis of the transformed data is performed using phylogenetic methods. This means that ignoring phylogeny during preliminary data transformations can possibly lead to spurious results in phylogenetic statistical analyses of species data.},
  doi       = {10.1111/j.1558-5646.2009.00804.x},
  keywords  = {Data transformation, evolutionary regression, least squares, linear regression, PCA, phylogenetic comparative methods, principal components analysis},
  publisher = {John Wiley \& Sons, Ltd (10.1111)},
}

@article{Day2007,
  author    = {Day, Lisa M. and Jayne, Bruce C.},
  title     = {Interspecific scaling of the morphology and posture of the limbs during the locomotion of cats ({Felidae})},
  journal   = {Journal of Experimental Biology},
  doi = {10.1242/jeb.02703},
  year      = {2007},
  volume    = {210},
  number    = {4},
  pages     = {642},
  month     = feb,
  abstract  = {For phylogenetically diverse mammals, ranging from small rodents to large ungulates, the generalization that limb erectness increases with increased size is supported by some size-dependent scaling relationships of appendicular skeletal anatomy as well as a limited number of direct observations of limb posture during locomotion. If size alone is the causal basis for different limb posture, then the erectness of limbs should increase significantly with increased size within a phylogenetically narrow lineage, but such data are sparse. Thus, to better establish the correlation between size and posture of mammalian limbs, we quantified the scaling relationships between mass and limb dimensions and kinematics during walking of nine species within the felid (cat) clade, which has qualitatively similar limb design. We studied the domestic cat, serval, ocelot, lynx, leopard, cheetah, cougar, lion and tiger, which had masses ranging from 4 kg to nearly 200 kg. Apart from variation associated with overall size, the lengths of the appendicular skeletal structures of most of the felid species were morphologically very similar in multivariate space. The kinematics of the limbs were also relatively uniform, and size had little predictive value for limb posture among felid species. Only three out of a total of 24 angular variables at footfall and midstance changed significantly (0.02 P 0.05) with increased mass. Thus, in contrast to previous broadly comparative studies of mammals, larger species of felids did not have more upright limbs than smaller species.},
  url       = {http://jeb.biologists.org/content/210/4/642.abstract},
}

@article{Schmidt2008,
  author    = {Schmidt, Manuela},
  title     = {Forelimb proportions and kinematics: how are small primates different from other small mammals?},
  journal   = {Journal of Experimental Biology},
  year      = {2008},
  volume    = {211},
  number    = {24},
  pages     = {3775},
  month     = dec,
  abstract  = {The crouched limb posture of small mammals enables them to react to unexpected irregularities in the support. Small arboreal primates would benefit from these kinematics in their arboreal habitat but it has been demonstrated that primates display certain differences in forelimb kinematics to other mammals. The objective of this paper is to find out whether these changes in forelimb kinematics are related to changes in body size and limb proportions. As primates descended from small ancestors, a comparison between living small primates and other small mammals makes it possible to determine the polarity of character transformations for kinematic and morphometric features proposed to be unique to primates. Walking kinematics of mouse lemurs, brown lemurs, cotton-top tamarins and squirrel monkeys was investigated using cineradiography. Morphometry was conducted on a sample of 110 mammals comprising of primates, marsupials, rodents and carnivores. It has been shown that forelimb kinematics change with increasing body size in such a way that limb protraction increases but retraction decreases. Total forelimb excursion, therefore, is almost independent of body size. Kinematic changes are linked to changes in forelimb proportions towards greater asymmetry between scapula and radius. Due to the spatial restriction inherent in the diagonal footfall sequence of primates, forelimb excursion is influenced by the excursion of the elongated hind limb. Hindlimb geometry, however, is highly conserved, as has been previously shown. The initial changes in forelimb kinematics might, therefore, be explained as solutions to a constraint rather than as adaptations to the particular demands of arboreal locomotion.},
  url       = {http://jeb.biologists.org/content/211/24/3775.abstract},
  doi = {10.1242/jeb.019802},
}

@article{DAout2002,
  author    = {D'Ao\^{u}t, Kristiaan and Aerts, Peter and De Clercq, Dirk and De Meester, Koen and Van Elsacker, Linda},
  title     = {Segment and joint angles of hind limb during bipedal and quadrupedal walking of the bonobo (\textit{Pan paniscus})},
  journal   = {American Journal of Physical Anthropology},
  year      = {2002},
  volume    = {119},
  number    = {1},
  pages     = {37--51},
  month     = mar,
  issn      = {0002-9483},
  abstract  = {Abstract We describe segment angles (trunk, thigh, shank, and foot) and joint angles (hip, knee, and ankle) for the hind limbs of bonobos walking bipedally (?bent-hip bent-knee walking,? 17 sequences) and quadrupedally (33 sequences). Data were based on video recordings (50 Hz) of nine subjects in a lateral view, walking at voluntary speed. The major differences between bipedal and quadrupedal walking are found in the trunk, thigh, and hip angles. During bipedal walking, the trunk is approximately 33?41° more erect than during quadrupedal locomotion, although it is considerably more bent forward than in normal human locomotion. Moreover, during bipedal walking, the hip has a smaller range of motion (by 12°) and is more extended (by 20?35°) than during quadrupedal walking. In general, angle profiles in bonobos are much more variable than in humans. Intralimb phase relationships of subsequent joint angles show that hip-knee coordination is similar for bipedal and quadrupedal walking, and resembles the human pattern. The coordination between knee and ankle differs much more from the human pattern. Based on joint angles observed throughout stance phase and on the estimation of functional leg length, an efficient inverted pendulum mechanism is not expected in bonobos.},
  doi       = {10.1002/ajpa.10112},
  keywords  = {bonobo, kinematics, segment angles, joint angles, bipedalism, quadrupedalism, gait analysis},
  publisher = {John Wiley \& Sons, Ltd},
}

@article{Goswami1998,
  author    = {Goswami, Ambarish},
  title     = {A new gait parameterization technique by means of cyclogram moments: Application to human slope walking},
  journal   = {Gait \& Posture},
  year      = {1998},
  volume    = {8},
  number    = {1},
  pages     = {15--36},
  issn      = {0966-6362},
  abstract  = {A new parameterization technique for the systematic characterization of human walking gait in diverse external conditions is proposed in this work. By parameterization we mean a quantitative expression of certain gait descriptors as the function of an external parameter, such as the ground slope. The mathematical quantities derived from the geometric features of the hip-knee cyclograms are the main gait descriptors considered in this study. We demonstrate that these descriptors, expressed in a general setting as the geometric moments of the cyclogram contours, can meaningfully reflect the evolution of the gait kinematics on different slopes. We provide a new interpretation of the cyclogram perimeter and discover two potential invariants of slope-walking gait. Experimental slope-walking data obtained at 1° interval within the range of −13 to +13° (±23.1%) on a variable-inclination treadmill was used in this study. The parameterization procedure presented here is general in nature and may be employed without restriction to any closed curve such as the phase diagram, the moment-angle diagram, and the velocity–velocity curves of human gait. The technique may be utilized for the quantitative characterization of normal gait, global comparison of two different gaits, clinical identification of pathological conditions and for the tracking of progress of patients under rehabilitation program.},
  doi       = {10.1016/S0966-6362(98)00014-9},
  keywords  = {Gait parameterization, Slope walking, Cyclogram, Geometric moments, Gait kinematics, Invariants},
  url       = {http://www.sciencedirect.com/science/article/pii/S0966636298000149},
}

@article{Hallemans2009,
  author    = {Hallemans, Ann and Aerts, Peter},
  title     = {Effects of visual deprivation on intra-limb coordination during walking in children and adults},
  journal   = {Experimental Brain Research},
  year      = {2009},
  volume    = {198},
  number    = {1},
  pages     = {95},
  month     = {Jul},
  issn      = {1432-1106},
  abstract  = {Following the laws of planar covariation, intersegmental coordination is defined with respect to the vertical and heading direction. This vertical reference can be estimated using multisensory information, amongst others visual cues play a role. In the past it was already shown that visual deprivation and/or perturbation of visual information largely affect gait kinematics. The goal of this study is to investigate the impact of visual deprivation on intra-limb movement coordination. Children aged between 3 and 11 years and young adults are included in this study to investigate age-related differences in the visual control of locomotion. Intersegmental coordination was tested under two different conditions: full vision (FV) and no vision (NV). Heading direction and walking speed were taken into account. A significant interaction effect was observed between visual condition and age for walking speed. Between age groups, no differences are observed in the FV condition but in the NV condition children walk significantly slower than adults. This shows that the relative importance of visual information is age dependent. Between age groups significant differences were found in heading direction. Coordination was characterized using the planar covariation technique, by constructing thigh versus shank and shank versus foot angle--angle plots and by cross-correlation function analysis. Regardless of the presence or absence of visual information, the planarity index remains high, indicating that the laws of planar covariation hold in the absence of visual afferent information. On the other hand, the shape of the gait loop does show significant differences between FV and NV conditions. Changes in the shape of the gait loop are primarily determined by changes in the coupling between the thigh and shank elevation angles. The coupling between the shank and foot elevation angles is dependent upon walking speed and does not differ between FV and NV conditions. Between age groups significant differences are observed in covariation plane orientation.},
  day       = {18},
  doi       = {10.1007/s00221-009-1937-8},
}

@article{Polk2002,
  author    = {Polk, J. D.},
  title     = {Adaptive and phylogenetic influences on musculoskeletal design in cercopithecine primates},
  journal   = {Journal of Experimental Biology},
  year      = {2002},
  volume    = {205},
  number    = {21},
  pages     = {3399},
  month     = nov,
  abstract  = {Broad allometric studies of the musculoskeletal system have frequently sought to explain how locomotor variables have been influenced by body mass. To examine animals that vary widely in body mass, these studies have included taxa that differ in their locomotor adaptations and phylogenetic relatedness. Because these sources of diversity could obscure the effects of body mass, this study was designed to test the effects of adaptive differences in limb proportions and phylogeny, as well as body mass, on locomotor kinematics and extensor muscle mechanical advantage. More specifically, two hypotheses were tested in a sample of closely related animals: (i) that, among animals with similar body mass, those with longer limb segments should adopt more extended limb postures to moderate the joint and midshaft bending moments that they experience, and (ii) that body mass will have similar influences on joint posture and joint moments in closely related and diverse mammalian samples. Three-dimensional kinematic and synchronous force-platform data were collected for six individual cercopithecine monkeys ranging in mass from 4kg to 24kg and at a range of walking speeds. Comparisons among three monkeys with similar body mass but different limb segment lengths reveal a significant effect of limb proportion on posture. That is, animals with longer limbs frequently use more extended limb postures and can have correspondingly lower joint moments. The scaling of locomotor variables across the entire sample of closely related monkeys was generally similar to published results for a diverse sample of mammals, with larger monkeys having more extended limb postures, lower joint moments and greater effective mechanical advantage (EMA) for their limb extensor musculature. Ankle EMA, however, did not increase with body mass in the primate sample, suggesting that clade-specific adaptive differences (e.g. the use of arboreal supports by primates) may constrain the effects of body mass.},
  url       = {http://jeb.biologists.org/content/205/21/3399.abstract},
  doi = {10.1242/jeb.205.21.3399},
}

@InCollection{Bernstein1934,
  author    = {Bernstein, Nikolai A.},
  title     = {The Techniques of the Study of Movements},
  booktitle = {Human Motor Actions: Bernstein Reassessed (1984)},
  publisher = {North-Holland},
  year      = {1934},
  editor    = {Whiting, H. T. A.},
  volume    = {17},
  series    = {Advances in Psychology},
  chapter   = {1},
  pages     = {1--26},
  abstract  = {This chapter discusses the techniques used for the study of movements. The cinematography study of movements is discussed in detail. The value of cinematography as a technique for the study of movements provides an opportunity to record and to fix the rapidly interchanging phases of live movements to subsequently analyze them with any required degree of accuracy. A series of successive phases of fast running by a human being is presented. The chapter discusses cyclography—the planar projection movements. Separate, independent cinematographic exposures illustrate every phase of a movement excellently but they do not give a direct representation of the interrelations between successive phases. Exact measurement of the frequencies given by the rotating shutter is essential for the quantitative study of movements.},
  doi       = {10.1016/S0166-4115(08)61367-9},
  issn      = {0166-4115},
  url       = {http://www.sciencedirect.com/science/article/pii/S0166411508613679},
}

@article{Nyakatura2010,
  author    = {Nyakatura, John A. and Petrovitch, Alexander and Fischer, Martin S.},
  title     = {Limb kinematics during locomotion in the two-toed sloth (\textit{Choloepus didactylus}, {Xenarthra}) and its implications for the evolution of the sloth locomotor apparatus},
  journal   = {Zoology},
  year      = {2010},
  volume    = {113},
  number    = {4},
  pages     = {221--234},
  month     = aug,
  issn      = {0944-2006},
  abstract  = {In order to gain insight into the function of the extant sloth locomotion and its evolution, we conducted a detailed videoradiographic analysis of two-toed sloth locomotion (Xenarthra: Choloepus didactylus). Both unrestrained as well as steady-state locomotion was analyzed. Spatio-temporal gait parameters, data on interlimb coordination, and limb kinematics are reported. Two-toed sloths displayed great variability in spatio-temporal gait parameters over the observed range of speeds. They increase speed by decreasing the durations of contact and swing phases, as well as by increasing step length. Gait utilization also varies with no strict gait sequence or interlimb timing evident in slow movements, but a tendency to employ diagonal sequence, diagonal couplet gaits in fast movements. In contrast, limb kinematics were highly conserved with respect to ‘normal’ pronograde locomotion. Limb element and joint angles at touch down and lift off, element and joint excursions, and contribution to body progression of individual elements are similar to those reported for non-cursorial mammals of small to medium size. Hands and feet are specialized to maintain firm connection to supports, and do not contribute to step length or progression. In so doing, the tarsometatarsus lost its role as an individual propulsive element during the evolution of suspensory locomotion. Conservative kinematic behavior of the remaining limb elements does not preclude that muscle recruitment and neuromuscular control for limb pro- and retraction are also conserved. The observed kinematic patterns of two-toed sloths improve our understanding of the convergent evolution of quadrupedal suspensory posture and locomotion in the two extant sloth lineages.},
  keywords  = {Arboreal locomotion, Convergent evolution, Gait parameters, Musculoskeletal apparatus, Sloth locomotor performance},
  url       = {http://www.sciencedirect.com/science/article/pii/S0944200610000462},
  doi = {10.1016/j.zool.2009.11.003},
}

@article{Ogihara2014,
  author    = {Ogihara, Naomichi and Oku, Takaaki and Andrada, Emanuel and Blickhan, Reinhard and Nyakatura, John A. and Fischer, Martin S.},
  title     = {Planar covariation of limb elevation angles during bipedal locomotion in common quails (\textit{Coturnix coturnix})},
  journal   = {Journal of Experimental Biology},
  year      = {2014},
  volume    = {217},
  number    = {22},
  pages     = {3968},
  month     = nov,
  abstract  = {In human bipedal walking, temporal changes in the elevation angle of the thigh, shank and foot segments covary to form a regular loop within a single plane in three-dimensional space. In this study, we quantified the planar covariation of limb elevation angles during bipedal locomotion in common quails to test whether the degree of planarity and the orientation of the covariance plane differ between birds, humans and Japanese macaques as reported in published accounts. Five quails locomoted on a treadmill and were recorded by a lateral X-ray fluoroscopy. The elevation angle of the thigh, shank and foot segments relative to the vertical axis was calculated and compared with published data on human and macaque bipedal locomotion. The results showed that the planar covariation applied to quail bipedal locomotion and planarity was stronger in quails than in humans. The orientation of the covariation plane in quails differed from that in humans, and was more similar to the orientation of the covariation plane in macaques. Although human walking is characterized by vaulting mechanics of the body center of mass, quails and macaques utilize spring-like running mechanics even though the duty factor is 0.5. Therefore, differences in the stance leg mechanics between quails and humans may underlie the difference in the orientation of the covariation plane. The planar covariation of inter-segmental coordination has evolved independently in both avian and human locomotion, despite the different mechanical constraints.},
  url       = {http://jeb.biologists.org/content/217/22/3968.abstract},
  doi = {10.1242/jeb.109355},
}

@article{Arbter1990,
  author      = {Arbter, K. and Snyder, W. E. and Burkhardt, H. and Hirzinger, G.},
  title       = {Application of affine-invariant {Fourier} descriptors to recognition of {3-D} objects},
  journal     = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  year        = {1990},
  volume      = {12},
  number      = {7},
  pages       = {640--647},
  month       = jul,
  issn        = {0162-8828},
  abstract    = {The method of Fourier descriptors is extended to produce a set of normalized coefficients which are invariant under any affine transformation (translation, rotation, scaling, and shearing). The method is based on a parameterized boundary description which is transformed to the Fourier domain and normalized there to eliminate dependencies on the affine transformation and on the starting point. Invariance to affine transforms allows considerable robustness when applied to images of objects which rotate in all three dimensions, as is demonstrated by processing silhouettes of aircraft maneuvering in three-space.},
  call-number = {12},
  doi         = {10.1109/34.56206},
  keywords    = {Fourier analysis, pattern recognition, picture processing, 3D object recognition, invariance, affine-invariant Fourier descriptors, boundary description, affine transformation, silhouettes, Shearing, Robustness, Aircraft},
}

@article{Hicheur2006,
  author    = {Hicheur, Halim and Terekhov, Alexander V. and Berthoz, Alain},
  journal   = {Journal of Neurophysiology},
  title     = {Intersegmental Coordination During Human Locomotion: Does Planar Covariation of Elevation Angles Reflect Central Constraints?},
  year      = {2006},
  number    = {3},
  pages     = {1406--1419},
  volume    = {96},
  abstract  = {To study intersegmental coordination in humans performing different locomotor tasks (backward, normal, fast walking, and running), we analyzed the spatiotemporal patterns of both elevation and joint angles bilaterally in the sagittal plane. In particular, we determined the origins of the planar covariation of foot, shank, and thigh elevation angles. This planar constraint is observable in the three-dimensional space defined by these three angles and corresponds to the plane described by the three time-varying elevation angle variables over each step cycle. Previous studies showed that this relation between elevation angles constrains lower limb coordination in various experimental situations. We demonstrate here that this planar covariation mainly arises from the strong correlation between foot and shank elevation angles, with thigh angle independently contributing to the pattern of intersegmental covariation. We conclude that the planar covariation of elevation angles does not reflect central constraints, as previously suggested. An alternative approach for analyzing the patterns of coordination of both elevation and joint (hip, knee, and ankle) angles is used, based on temporal cross-correlation and phase relationships between pairs of kinematic variables. We describe the changes in the pattern of intersegmental coordination that are associated with the changes of locomotor modes and locomotor speeds. We provide some evidence for a distinct control of thigh motion and discuss the respective contributions of passive mechanical factors and of active (arising from neural control) factors to the formation and the regulation of the locomotor pattern throughout the gait cycle.},
  doi       = {10.1152/jn.00289.2006},
}

@article{Austin1999,
  author    = {Austin, Gary P. and Garrett, Gladys E. and Bohannon, Richard W.},
  title     = {Kinematic analysis of obstacle clearance during locomotion},
  journal   = {Gait \& Posture},
  year      = {1999},
  volume    = {10},
  number    = {2},
  pages     = {109--120},
  month     = oct,
  issn      = {0966-6362},
  abstract  = {This study investigated the effect of obstacles of different heights on the locomotion of 15 healthy subjects. The following parameters were studied: (1) the distance of the toe and heel markers from the obstacle during toe-off and heel contact, respectively, (2) the minimum clearance distance of the toe and heel markers, and (3) the angular displacements and velocities of the hip, knee, and ankle. Results show significant differences in joint angular kinematics and clearance distances as obstacle height increased. The kinematic and distance differences exhibited both strong linear and non-linear trends. Toe-off distance and heel contact distance did not change significantly with changes in obstacle height.},
  doi       = {10.1016/S0966-6362(99)00022-3},
  keywords  = {Stepping over, Angular kinematics, Toe clearance, Heel clearance},
  url       = {http://www.sciencedirect.com/science/article/pii/S0966636299000223},
}

@article{MacLellan2010,
  author    = {MacLellan, Michael J. and McFadyen, Bradford J.},
  title     = {Segmental control for adaptive locomotor adjustments during obstacle clearance in healthy young adults},
  journal   = {Experimental Brain Research},
  year      = {2010},
  volume    = {202},
  number    = {2},
  pages     = {307--318},
  month     = apr,
  issn      = {1432-1106},
  abstract  = {Anticipatory locomotor adjustments (ALAs) are used during locomotion to perform tasks, such as obstacle clearance, although not much is known as to how these ALAs are implemented by the central nervous system (CNS). The current study applied the planar law of intersegmental coordination to both leading and trailing limbs in a paradigm in which obstacle height and depth were manipulated to propose how ALAs are controlled. Ten healthy young adults stepped over nine obstacle conditions. Full-body 3D kinematic data were collected and elevation angles of the foot, shank, and thigh in the sagittal plane were calculated. For each limb within each trial, a principal component analysis was applied to limb segment trajectories. As well, a Fourier harmonic series was used to represent segment elevation angle trajectories, and phase differences between adjacent segments were determined. Planarity was consistently high in both limbs for all obstacle conditions, although significant differences between obstacle heights were observed. Increases in covariance loop width and rotation of the covariance plane accompanied changes in planarity. As observed in previous studies, fundamental harmonic phase differences between adjacent segments were highly correlated to plane characteristics and these phase differences changed systematically with increases in obstacle height. From the results, it is proposed that if a given environment requires a change in locomotion, the CNS adjusts a basic locomotor pattern if needed through the manipulation of the phase differences in the fundamental harmonics of the elevation angles between adjacent segments and elevation angle amplitude (with a constraint being intersegmenal elevation angle planarity).},
  doi       = {10.1007/s00221-009-2133-6},
}

@article{Perrot2011,
  author    = {Perrot, Olivier and Laroche, Davy and Pozzo, Thierry and Marie, Christine},
  title     = {Kinematics of obstacle clearance in the rat},
  journal   = {Behavioural Brain Research},
  year      = {2011},
  volume    = {224},
  number    = {2},
  pages     = {241--249},
  month     = oct,
  issn      = {0166-4328},
  abstract  = {Although the rat has become the favourite animal model in preclinical research on locomotion, studies designed to assess the strategy used by rats to avoid obstacle are lacking. Using an optoelectronic 3D motion analysis system, we therefore, compared the step pattern, timing and length variables of locomotor cycles, trajectories and joint angles of limbs when rats step between and over obstacles (3cm-high) fixed on a treadmill belt (25cm/s). Motion in all four limbs of adult animals with an initial age of 11 weeks was serially recorded for a period of 10 weeks. The results showed that obstacle clearance is associated with the reorganization of the basic step pattern resulting in increased stride length of all limbs, increased duration of the swing phase of the hindlimbs only, and the appearance of two quadrupedal stance phases. They also revealed that the elevation of limbs above the obstacle not only involves flexion but also displacement of the corresponding girdles. Remarkably, the trajectory of the trailing forelimb to get over the obstacle is almost a mirror image of the trajectory of the leading forelimb. Lastly, all of the parameters measured remained stable over the observation period during which body weight gain reached 100g (one third of the initial body weight). In conclusion, our study may provide a basis for future studies aimed at understanding the neural pathways involved in pathologies associated with deficit/recovery of challenged locomotion in rats.},
  keywords  = {3D motion analysis, Kinematics, Challenged locomotion, Obstacle avoidance, Treadmill, Rats},
  url       = {http://www.sciencedirect.com/science/article/pii/S0166432811004323},
  doi = {10.1016/j.bbr.2011.05.027},
}

@article{Fuller2011,
  author    = {Fuller, Patrick O. and Higham, Timothy E. and Clark, Andrew J.},
  title     = {Posture, speed, and habitat structure: three-dimensional hindlimb kinematics of two species of padless geckos},
  journal   = {Zoology},
  doi = {10.1016/j.zool.2010.11.003},
  year      = {2011},
  volume    = {114},
  number    = {2},
  pages     = {104--112},
  month     = apr,
  issn      = {0944-2006},
  abstract  = {Differences in habitat use are often correlated with differences in morphology and behavior, while animals in similar habitats often exhibit similarities in form and function. However, this has not been tested extensively among lizards, especially geckos. Most studies of gecko locomotion have focused on the ability to adhere to surfaces. However, there are several species of geckos that have either secondarily lost adhesive capabilities or simply lack the capability. We quantified the three-dimensional locomotor kinematics for two desert-dwelling padless geckos, Teratoscincus scincus and Eublepharis macularius, on a level trackway over a range of speeds. Our results indicate that T. scincus landed with a high relative hip height of 48.7±2.4% of total limb length at footfall, while E. macularius exhibited hip heights averaging only 36.0±1.8% of total limb length for footfall. The three-dimensional knee angle of T. scincus averaged 120.6±3.9° at footfall, while E. macularius averaged only 101.6±1.8° at footfall. In addition, the femur of E. macularius was elevated to a much greater extent (i.e., was closer to being perpendicular to the long axis of the body) than that of T. scincus and every other lizard that has been studied, suggesting they move with a “hyper-sprawled” posture. Both of these gecko species live in deserts, but T. scincus is psammophilic while E. macularius inhabits a rocky, more densely vegetated environment. Benefits of the more upright posture of T. scincus on open sandy habitat may include a greater field of view and more efficient locomotion. The more sprawled posture of E. macularius may lower its center of gravity and aid in balance while climbing on rocks or shrubs.},
  keywords  = {Eublepharis macularius, Teratoscincus scincus, Locomotion, Semi-erect posture, Sprawled posture},
  url       = {http://www.sciencedirect.com/science/article/pii/S0944200611000183},
}

@article{Arnold1983,
  author    = {Arnold, Stevan J.},
  title     = {Morphology, Performance and Fitness},
  journal   = {Integrative and Comparative Biology},
  year      = {1983},
  volume    = {23},
  number    = {2},
  pages     = {347--361},
  issn      = {0003-1569},
  abstract  = {Selection can be measured in natural populations by the changes it causes in the means, variances and covariances of phenotypic characters. Furthermore the force of selection can be measured in conventional statistical terms that also play a key role in theoretical equations for evolutionary change. The problem of measuring selection on morphological traits is simplified by breaking the task into two parts: measurement of the effects of morphological variation on performance and measurement of the effects of performance on fitness. The first part can be pursued in the laboratory but the second part is best accomplished in the field. The approach is illustrated with a hypothetical analysis of selection acting on the complex trophic morphology of snakes.},
  doi       = {10.1093/icb/23.2.347},
}

@article{Schulte2004,
  author    = {Schulte, J. A. and Losos, J. B. and Cruz, F. B. and N\'{u}\~{n}ez, H.},
  title     = {The relationship between morphology, escape behaviour and microhabitat occupation in the lizard clade \textit{Liolaemus} ({Iguanidae: Tropidurinae*: Liolaemini})},
  journal   = {Journal of Evolutionary Biology},
  year      = {2004},
  volume    = {17},
  number    = {2},
  pages     = {408--420},
  month     = mar,
  issn      = {1010-061X},
  abstract  = {Abstract Phenotypic differences among species are known to have functional consequences that in turn allow species to use different habitats. However, the role of behaviour in this ecomorphological paradigm is not well defined. We investigated the relationship between morphology, ecology and escape behaviour among 25 species of the lizard clade Liolaemus in a phylogenetic framework. We demonstrate that the relationship between morphology and characteristics of habitat structure shows little or no association, consistent with a previous study on this group. However, a significant relationship was found between morphology and escape behaviour with the distance a lizard moved from a potential predator correlated with body width, axilla-groin length, and pelvis width. A significant relationship between escape behaviour and habitat structure occupation was found; lizards that occupied tree trunks and open ground ran longer distances from predators and were found greater distances from shelter. Behavioural strategies used by these lizards in open habitats appear to have made unnecessary the evolution of limb morphology that has occurred in other lizards from other clades that are found in open settings. Understanding differences in patterns of ecomorphological relationships among clades is an important component for studying adaptive diversification.},
  doi       = {10.1046/j.1420-9101.2003.00659.x},
  keywords  = {Argentina, behaviour, Chile, ecomorphology, Iguanidae, independent contrasts, Liolaemus, lizard, Squamata},
  publisher = {John Wiley \& Sons, Ltd (10.1111)},
}

@article{Reilly2007,
  author    = {Reilly, Stephen M. and McElroy, Eric J. and Biknevicius, Audrone R.},
  title     = {Posture, gait and the ecological relevance of locomotor costs and energy-saving mechanisms in tetrapods},
  journal   = {Zoology},
  year      = {2007},
  volume    = {110},
  number    = {4},
  pages     = {271--289},
  month     = sep,
  issn      = {0944-2006},
  abstract  = {A reanalysis of locomotor data from functional, energetic, mechanical and ecological perspectives reveals that limb posture has major effects on limb biomechanics, energy-saving mechanisms and the costs of locomotion. Regressions of data coded by posture (crouched vs. erect) reveal nonlinear patterns in metabolic cost, limb muscle mass, effective mechanical advantage, and stride characteristics. In small crouched animals energy savings from spring and pendular mechanisms are inconsequential and thus the metabolic cost of locomotion is driven by muscle activation costs. Stride frequency appears to be the principal functional parameter related to the decreasing cost of locomotion in crouched animals. By contrast, the shift to erect limb postures invoked a series of correlated effects on the metabolic cost of locomotion: effective mechanical advantage increases, relative muscle masses decrease, metapodial limb segments elongate dramatically (as limbs shift from digitigrade to unguligrade designs) and biological springs increase in size and effectiveness. Each of these factors leads to decreases in the metabolic cost of locomotion in erect forms resulting from real and increasing contributions of pendular savings and spring savings. Comparisons of the relative costs and ecological relevance of different gaits reveal that running is cheaper than walking in smaller animals up to the size of dogs but running is more expensive than walking in horses. Animals do not necessarily use their cheapest gaits for their predominant locomotor activity. Therefore, locomotor costs are driven more by ecological relevance than by the need to optimize locomotor economy.},
  keywords  = {Locomotor energetics, Limb posture, Mammal locomotion, Biomechanics, Behavioral repertoire},
  url       = {http://www.sciencedirect.com/science/article/pii/S094420060700013X},
  doi = {10.1016/j.zool.2007.01.003},
}

@article{Hoyt1981,
  author    = {Hoyt, Donald F. and Taylor, C. Richard},
  title     = {Gait and the energetics of locomotion in horses},
  journal   = {Nature},
  year      = {1981},
  volume    = {292},
  number    = {5820},
  pages     = {239--240},
  month     = jul,
  issn      = {1476-4687},
  abstract  = {It seems reasonable that quadrupeds should change gait from a walk to a trot to a gallop in such a way as to minimize their energy consumption, as human beings are known1 to change from a walk to a run at a particular speed (2.4 m s−1) below which walking requires less energy than running and above which the opposite is true. Thus by changing gait, human beings keep the energy cost of locomotion to a minimum as their speed increases. One reason this relation holds is that in humans, metabolic rate increases curvilinearly with walking speed1. If metabolism were a curvilinear function of speed within each of the gaits used by quadrupeds, it would support the hypothesis that they also change gait to minimize energetic cost. There is an old controversy about whether metabolic rate increases linearly or curvilinearly in running humans1,2 but all previous reports have suggested that metabolic rate increases linearly with speed in quadrupeds. Extended gaits were an important experimental tool in the study of human gait changes; thus we have trained three small horses (110-170 kg) to walk, trot and gallop on a motorized treadmill, and to extend their gaits on command. We report here that, using measurements of rates of oxygen consumption as an indicator of rates of energy consumption, we have confirmed that the natural gait at any speed indeed entails the smallest possible energy expenditure.},
  doi       = {10.1038/292239a0},
}

@article{Rezende2009,
  author    = {Rezende, Enrico L. and Gomes, Fernando R. and Chappell, Mark A. and Garland Jr., Theodore},
  title     = {Running Behavior and Its Energy Cost in Mice Selectively Bred for High Voluntary Locomotor Activity},
  journal   = {Physiological and Biochemical Zoology},
  year      = {2009},
  volume    = {82},
  number    = {6},
  pages     = {662--679},
  month     = mar,
  issn      = {1522-2152},
  abstract  = {Abstract Locomotion is central to behavior and intrinsic to many fitness?critical activities (e.g., migration, foraging), and it competes with other life?history components for energy. However, detailed analyses of how changes in locomotor activity and running behavior affect energy budgets are scarce. We quantified these effects in four replicate lines of house mice that have been selectively bred for high voluntary wheel running (S lines) and in their four nonselected control lines (C lines). We monitored wheel speeds and oxygen consumption for 24?48 h to determine daily energy expenditure (DEE), resting metabolic rate (RMR), locomotor costs, and running behavior (bout characteristics). Daily running distances increased roughly 50\%?90\% in S lines in response to selection. After we controlled for body mass effects, selection resulted in a 23\% increase in DEE in males and a 6\% increase in females. Total activity costs (DEE ? RMR) accounted for 50\%?60\% of DEE in both S and C lines and were 29\% higher in S males and 5\% higher in S females compared with their C counterparts. Energetic costs of increased daily running distances differed between sexes because S females evolved higher running distances by running faster with little change in time spent running, while S males also spent 40\% more time running than C males. This increase in time spent running impinged on high energy costs because the majority of running costs stemmed from ?postural costs? (the difference between RMR and the zero?speed intercept of the speed vs. metabolic rate relationship). No statistical differences in these traits were detected between S and C females, suggesting that large changes in locomotor behavior do not necessarily effect overall energy budgets. Running behavior also differed between sexes: within S lines, males ran with more but shorter bouts than females. Our results indicate that selection effects on energy budgets can differ dramatically between sexes and that energetic constraints in S males might partly explain the apparent selection limit for wheel running observed for over 15 generations.},
  doi       = {10.1086/605917},
  publisher = {The University of Chicago Press},
}

@article{Girard2001,
  author    = {Girard, Isabelle},
  title     = {Field Cost of Activity in the Kit Fox, \textit{Vulpes macrotis}},
  journal   = {Physiological and Biochemical Zoology},
  year      = {2001},
  volume    = {74},
  number    = {2},
  pages     = {191--202},
  month     = mar,
  issn      = {1522-2152},
  doi       = {10.1086/319668},
  publisher = {The University of Chicago Press},
}

@article{Johnson2002,
  author    = {Johnson, Chris J. and Parker, Katherine L. and Heard, Douglas C. and Gillingham, Michael P.},
  title     = {Movement parameters of ungulates and scale-specific responses to the environment},
  journal   = {Journal of Animal Ecology},
  year      = {2002},
  volume    = {71},
  number    = {2},
  pages     = {225--235},
  month     = mar,
  issn      = {0021-8790},
  abstract  = {Summary 1 Most studies of animal movements and habitat selection do not recognize empirically that different components of the environment are important to animals at different scales. Often, availability of habitats is defined at one or more arbitrary spatio-temporal scales, but use of those habitats is constrained to one scale. Identification of scalar movement is the first step in developing models to explain why animals select or move to certain parts of their range. We used a non-linear curve-fitting model of movement rates to identify discontinuities in the scales of movement by woodland caribou Rangifer tarandus caribou collared with global positioning system (GPS) collars. 2 We differentiated intrapatch from interpatch movements, but were unable to distinguish interpatch from migratory-type movements for most combinations of individual caribou by season. Model fit was stronger for winter than summer movements. We suggest that increased patch heterogeneity during the winter resulted in interseason variation in movements and corresponding model fit. 3 Responses by caribou to the environment were scale-dependent. When we applied logistic regressions, land-cover type, energetic costs of movement, and predation risk differentiated the two scales of movement. Intrapatch movements had a lower cost of movement, were associated with cover types where foraging behaviours probably occurred, and were closer to areas of higher predator risk than interpatch movements. 4 Application of the non-linear model will aid in developing mechanism-based approaches to studying resource selection and animal behaviour.},
  doi       = {10.1046/j.1365-2656.2002.00595.x},
  keywords  = {caribou, GPS, habitat patch, heterogeneity, predation risk},
  publisher = {John Wiley \& Sons, Ltd (10.1111)},
}

@article{Lejeune1998,
    author    = {Lejeune, T. M. and Willems, P. A. and Heglund, N. C.},
    title     = {Mechanics and energetics of human locomotion on sand},
    doi = {10.1242/jeb.201.13.2071},
    journal   = {Journal of Experimental Biology},
    year      = {1998},
    volume    = {201},
    number    = {13},
    pages     = {2071},
    month     = jul,
    abstract  = {Moving about in nature often involves walking or running on a soft yielding substratum such as sand, which has a profound effect on the mechanics and energetics of locomotion. Force platform and cinematographic analyses were used to determine the mechanical work performed by human subjects during walking and running on sand and on a hard surface. Oxygen consumption was used to determine the energetic cost of walking and running under the same conditions. Walking on sand requires 1.6-2.5 times more mechanical work than does walking on a hard surface at the same speed. In contrast, running on sand requires only 1.15 times more mechanical work than does running on a hard surface at the same speed. Walking on sand requires 2.1-2.7 times more energy expenditure than does walking on a hard surface at the same speed; while running on sand requires 1.6 times more energy expenditure than does running on a hard surface. The increase in energy cost is due primarily to two effects: the mechanical work done on the sand, and a decrease in the efficiency of positive work done by the muscles and tendons.},
    url       = {http://jeb.biologists.org/content/201/13/2071.abstract},
}

@article{Druelle2019,
  author    = {Druelle, François and Goyens, Jana and Vasilopoulou-Kampitsi, Menelia and Aerts, Peter},
  title     = {Compliant legs enable lizards to maintain high running speeds on complex terrains},
  journal   = {Journal of Experimental Biology},
  doi = {10.1242/jeb.195511},
  year      = {2019},
  volume    = {222},
  number    = {6},
  pages     = {jeb195511},
  month     = mar,
  abstract  = {Substrate variations are likely to constrain animal performance in natural environments, as running over complex terrains challenges the dynamic stability of the body differently in each step. Yet, being able to negotiate complex terrains at top speed is a strong advantage for animals that have to deal with predators and evasive prey. Little is known on how animals negotiate such terrain variability at high speed. We investigated this in fast-running Acanthodactylus boskianus lizards, by measuring their 3D kinematics using four synchronised high-speed video cameras (325 Hz) on an adaptable racetrack. This racetrack was covered with four different substrates, representing increasing levels of terrain complexity. We found that the lizards deal with this complexity gradient by gradually adopting more erect parasagittal leg postures. Legs in a more-erect position are more compliant and are therefore highly adjustable on complex terrains. Additionally, the lizards stabilise their head, which facilitates vestibular and visual perception. Together, compliant legs and head stabilisation enable the lizards to minimise movements of the body centre of mass, even when running on highly irregular terrains. This suggests that the head and the centre of mass are the priority targets for running on uneven terrains. As a result, running performance (mean forward speed) decreases only slightly, and only on the most challenging substrate under investigation.},
  url       = {http://jeb.biologists.org/content/222/6/jeb195511.abstract},
}

@article{Shepard2013,
  author    = {Shepard, Emily L. C. and Wilson, Rory P. and Rees, W. Gareth and Grundy, Edward and Lambertucci, Sergio A. and Vosper, Simon B.},
  title     = {Energy Landscapes Shape Animal Movement Ecology},
  journal   = {The American Naturalist},
  year      = {2013},
  volume    = {182},
  number    = {3},
  pages     = {298--312},
  month     = mar,
  issn      = {0003-0147},
  abstract  = {AbstractThe metabolic costs of animal movement have been studied extensively under laboratory conditions, although frequently these are a poor approximation of the costs of operating in the natural, heterogeneous environment. Construction of ?energy landscapes,? which relate animal locality to the cost of transport, can clarify whether, to what extent, and how movement properties are attributable to environmental heterogeneity. Although behavioral responses to aspects of the energy landscape are well documented in some fields (notably, the selection of tailwinds by aerial migrants) and scales (typically large), the principles of the energy landscape extend across habitat types and spatial scales. We provide a brief synthesis of the mechanisms by which environmentally driven changes in the cost of transport can modulate the behavioral ecology of animal movement in different media, develop example cost functions for movement in heterogeneous environments, present methods for visualizing these energy landscapes, and derive specific predictions of expected outcomes from individual- to population- and species-level processes. Animals modulate a suite of movement parameters (e.g., route, speed, timing of movement, and tortuosity) in relation to the energy landscape, with the nature of their response being related to the energy savings available. Overall, variation in movement costs influences the quality of habitat patches and causes nonrandom movement of individuals between them. This can provide spatial and/or temporal structure to a range of population- and species-level processes, ultimately including gene flow. Advances in animal-attached technology and geographic information systems are opening up new avenues for measuring and mapping energy landscapes that are likely to provide new insight into their influence in animal ecology.},
  doi       = {10.1086/671257},
  publisher = {The University of Chicago Press},
}

@article{Caro2004,
  author    = {Caro, T. M. and Graham, C. M. and Stoner, C. J. and Vargas, J. K.},
  title     = {Adaptive significance of antipredator behaviour in artiodactyls},
  journal   = {Animal Behaviour},
  year      = {2004},
  volume    = {67},
  number    = {2},
  pages     = {205--228},
  month     = feb,
  issn      = {0003-3472},
  abstract  = {We used comparative data to test functional hypotheses for 17 antipredator behaviour patterns in artiodactyls. We examined the literature for hypotheses about auditory and visual signals, defensive behaviour and group-related antipredator behaviour in this taxon and derived a series of predictions for each hypothesis. Next, we documented occurrences of these behaviour patterns and morphological, ecological and behavioural variables for 200 species and coded them in binary format. We then pitted presence of an antipredator behaviour against presence of an independent variable for cervids, bovids and all artiodactyls together using nonparametric tests. Finally, we reanalysed the data using Maddison's (1990, Evolution, 44, 539-557) concentrated-changes tests and a consensus molecular and taxonomic phylogeny. We found evidence that snorting is both a warning signal to conspecifics and a pursuit-deterrent signal, lack of evidence that whistling alerts conspecifics and indications that foot stamping is a visual signal to warn group members. Evidence suggested that tail flagging was a signal to both conspecifics and predators, that bounding, leaping and stotting were used both as a signal and to clear obstacles and that prancing functioned similarly to foot stamping. Analyses of tail flicking, zigzagging and tacking were equivocal. We confirmed that inspection occurs in large groups, freezing enhances crypticity, and species seeking refuge in cliffs tend to be small. Entering water and attacks on predators had few correlates. Finally, group living, a putative antipredator adaptation, was associated with large body size and species living in open habitats, confirming Jarman's (1974, Behaviour, 48, 215-267) classic hypothesis. Bunching and group attack apparently deter predators. Despite limitations, comparative and systematic analyses can bolster adaptive hypotheses and raise new functional explanations for antipredator behaviour patterns in general.},
  url       = {http://www.sciencedirect.com/science/article/pii/S0003347203003531},
  doi = {10.1016/j.anbehav.2002.12.007},
}

@article{Stankowich2009,
  author    = {Stankowich, Theodore and Caro, Tim},
  title     = {Evolution of weaponry in female bovids},
  journal   = {Proceedings of the Royal Society B: Biological Sciences},
  year      = {2009},
  volume    = {276},
  number    = {1677},
  pages     = {4329--4334},
  month     = apr,
  abstract  = {Weaponry is ubiquitous in male ungulates and is driven by intrasexual selection, but the mystery surrounding its sporadic presence in females remains unsolved. Female horns are often smaller and shaped differently to male horns, suggesting a different function; indeed, hypotheses explaining the presence of female horns include competition for food, male mollification and defence against predators. Here we use comparative phylogenetic analyses to show that females are significantly more likely to bear horns in bovids that are conspicuous due to large body size and living in open habitats than inconspicuous species living in closed habitats or that are small. An inability to rely on crypsis or take refuge in deep vegetation has apparently driven the evolution of horns for defence against predators in female bovids, a finding supported by many field observations. Typically, exceptions are small species where females are territorial (e.g. duikers) and use horns in intrasexual contests. Furthermore, we suggest that conspicuousness and territoriality hypotheses may explain other instances of female cranial weaponry (i.e. antlers and ossicones) in other horned ruminants. Our phylogenetic reconstruction indicates that the primary function of horns in females is linked to antipredator defence in most clades, but occasionally to intrasexual competition in others.},
  doi       = {10.1098/rspb.2009.1256},
  publisher = {Royal Society},
}

@Conference{Brugman2004,
  author       = {Brugman, H. and Russel, A.},
  title        = {Annotating Multimedia/Multi-modal resources with {ELAN}},
  booktitle    = {Proceedings of LREC 2004, Fourth International Conference on Language Resources and Evaluation},
  year         = {2004},
  organization = {Max Planck Institute for Psycholinguistics, The Language Archive, Nijmegen, The Netherlands},
  note         = {\nolinkurl{https://tla.mpi.nl/tools/tla-tools/elan}},
}

@article{Gower1975,
  author    = {Gower, J. C.},
  title     = {{Generalized Procrustes analysis}},
  journal   = {Psychometrika},
  year      = {1975},
  volume    = {40},
  number    = {1},
  pages     = {33--51},
  month     = mar,
  issn      = {1860-0980},
  abstract  = {SupposePi(i)(i = 1, 2, ...,m, j = 1, 2, ...,n) give the locations ofmn points inp-dimensional space. Collectively these may be regarded asm configurations, or scalings, each ofn points inp-dimensions. The problem is investigated of translating, rotating, reflecting and scaling them configurations to minimize the goodness-of-fit criterion Σi=1mΣi=1nΔ2(Pj(i)Gi), whereGiis the centroid of them pointsPi(i)(i = 1, 2, ...,m). The rotated positions of each configuration may be regarded as individual analyses with the centroid configuration representing a consensus, and this relationship with individual scaling analysis is discussed. A computational technique is given, the results of which can be summarized in analysis of variance form. The special casem = 2 corresponds to Classical Procrustes analysis but the choice of criterion that fits each configuration to the common centroid configuration avoids difficulties that arise when one set is fitted to the other, regarded as fixed.},
  doi       = {10.1007/BF02291478},
}

@article{Kendall1989,
  author    = {Kendall, David G.},
  title     = {A Survey of the Statistical Theory of Shape},
  doi = {10.1214/ss/1177012582},
  journal   = {Statistical Science},
  year      = {1989},
  volume    = {4},
  number    = {2},
  pages     = {87--99},
  issn      = {08834237},
  abstract  = {[This is a review of the current state of the "theory of shape" introduced by the author in 1977. It starts with a definition of "shape" for a set of k points in m dimensions. The first task is to identify the shape spaces in which such objects naturally live, and then to examine the probability structures induced on such a shape space by corresponding structures in R<sup>m</sup>. Against this theoretical background one formulates and solves statistical problems concerned with shape characteristics of empirical sets of points. Some applications (briefly sketched here) are to archeology, astronomy, geography and physical chemistry. We also outline more recent work on "size-and-shape," on shapes of sets of points in riemannian spaces, and on shape-theoretic aspects of random Delaunay tessellations.]},
  database  = {JSTOR},
  publisher = {Institute of Mathematical Statistics},
  url       = {http://www.jstor.org/stable/2245331},
}

@InCollection{Dryden2016,
  author    = {Dryden, Ian L. and Mardia, Kanti V.},
  title     = {Statistical Shape Analysis with applications in {R}},
  booktitle = {Wiley Series In Probability And Statistics},
  publisher = {John Wiley and Sons Ltd},
  year      = {2016},
  edition   = {2nd},
  isbn      = {9780470699621},
  abstract  = {Balding, David J. and Cressie, Noel A. C. and Fitzmaurice, Garrett M. and Givens, Geof H. and Goldstein, Harvey and Molenberghs, Geert and Scott, David W. and Smith, Adrian F. M. and Tsay, Ruey S. and Weisberg, Sanford},
  keyword   = {Shape theory (Topology), Statistical methods, Statistics, multivariate analysis.},
}

@article{Nyquist1928,
  author    = {Nyquist, H.},
  title     = {Certain Topics in Telegraph Transmission Theory},
  journal   = {Transactions of the American Institute of Electrical Engineers},
  year      = {1928},
  volume    = {47},
  number    = {2},
  pages     = {617--644},
  month     = {April},
  issn      = {0096-3860},
  abstract  = {The most obvious method for determining the distortion of telegraph signals is to calculate the transients of the telegraph system. This method has been treated by various writers, and solutions are available for telegraph lines with simple terminal conditions. It is well known that the extension of the same methods to more complicated terminal conditions, which represent the usual terminal apparatus, leads to great difficulties. The present paper attacks the same problem from the alternative standpoint of the steady-state characteristics of the system. This method has the advantage over the method of transients that the complication of the circuit which results from the use of terminal apparatus does not complicate the calculations materially. This method of treatment necessitates expressing the criteria of distortionless transmission in terms of the steady-state characteristics. Accordingly, a considerable portion of the paper describes and illustrates a method for making this translation. A discussion is given of the minimum frequency range required for transmission at a given speed of signaling. In the case of carrier telegraphy, this discussion includes a comparison of single-sideband and double-sideband transmission. A number of incidental topics is also discussed.},
  doi       = {10.1109/T-AIEE.1928.5055024},
  keywords  = {Telegraphy;Steady-state;Frequency conversion;Circuits;Costs;Distortion;Shape;Interference;Equalizers;Telephony},
}

@article{Hubel2015,
  author    = {Hubel, Tatjana Y. and Usherwood, James R.},
  title     = {Children and adults minimise activated muscle volume by selecting gait parameters that balance gross mechanical power and work demands},
  journal   = {Journal of Experimental Biology},
  doi = {10.1242/jeb.122135},
  year      = {2015},
  volume    = {218},
  number    = {18},
  pages     = {2830},
  month     = sep,
  abstract  = {Terrestrial locomotion on legs is energetically expensive. Compared with cycling, or with locomotion in swimming or flying animals, walking and running are highly uneconomical. Legged gaits that minimise mechanical work have previously been identified and broadly match walking and running at appropriate speeds. Furthermore, the ‘cost of muscle force’ approaches are effective in relating locomotion kinetics to metabolic cost. However, few accounts have been made for why animals deviate from either work-minimising or muscle-force-minimising strategies. Also, there is no current mechanistic account for the scaling of locomotion kinetics with animal size and speed. Here, we report measurements of ground reaction forces in walking children and adult humans, and their stance durations during running. We find that many aspects of gait kinetics and kinematics scale with speed and size in a manner that is consistent with minimising muscle activation required for the more demanding between mechanical work and power: spreading the duration of muscle action reduces activation requirements for power, at the cost of greater work demands. Mechanical work is relatively more demanding for larger bipeds - adult humans - accounting for their symmetrical M-shaped vertical force traces in walking, and relatively brief stance durations in running compared with smaller bipeds - children. The gaits of small children, and the greater deviation of their mechanics from work-minimising strategies, may be understood as appropriate for their scale, not merely as immature, incompletely developed and energetically sub-optimal versions of adult gaits.},
  url       = {http://jeb.biologists.org/content/218/18/2830.abstract},
}

@article{Basu2019,
  author    = {Basu, Christopher and Wilson, Alan M. and Hutchinson, John R.},
  title     = {The locomotor kinematics and ground reaction forces of walking giraffes},
  doi       = {10.1242/jeb.159277},
  journal   = {Journal of Experimental Biology},
  year      = {2019},
  volume    = {222},
  number    = {2},
  pages     = {jeb159277},
  month     = jan,
  abstract  = {Giraffes (Giraffa camelopardalis) possess specialised anatomy. Their disproportionately elongate limbs and neck confer recognised feeding advantages, but little is known about how their morphology affects locomotor function. In this study, we examined the stride parameters and ground reaction forces from three adult giraffes in a zoological park, across a range of walking speeds. The patterns of GRFs during walking indicate that giraffes, similar to other mammalian quadrupeds, maintain a forelimb-biased weight distribution. The angular excursion of the neck has functional links with locomotor dynamics in giraffes, and was exaggerated at faster speeds. The horizontal accelerations of the neck and trunk were out of phase compared with the vertical accelerations, which were intermediate between in and out of phase. Despite possessing specialised morphology, giraffes; stride parameters were broadly predicted from dynamic similarity, facilitating the use of other quadrupedal locomotion models to generate testable hypotheses in giraffes.},
  url       = {http://jeb.biologists.org/content/222/2/jeb159277.abstract},
}

@online{MacLeod2007,
    author       = {MacLeod, Norm},
    year         = {2007},
    title        = {{PalaeoMath101: Part 5 - PCA, Eigenanalysis \& Regression V}},
    organization = {Palaeontology Newsletter Nr. 64},
    url          = {https://www.palass.org/publications/newsletter/palaeomath-101/palaeomath-part-5-pca-eigenanalysis-regression-v},
    note         = {accessed 2019-04-05},
}

@Misc{UltimateUngulate,
  author       = {Huffman, Brent},
  title        = {Ultimate Ungulate Guide to the World's Hoofed Mammals},
  howpublished = {\nolinkurl{www.ultimateungulate.com}},
  year         = {2019},
  note         = {Accessed 2019-04-05},
}

@Misc{AnimalDiversityWeb,
  author       = {{Animal Diversity Web}},
  title        = {{[diverse animal profiles]}},
  howpublished = {The University of Michigan, Museum of Zoology, \nolinkurl{http://animaldiversity.org}},
  year         = {2019},
  note         = {Accessed 2019-04-05},
}

@article{VandenHole2018,
  author    = {Vanden Hole, Charlotte and Aerts, Peter and Prims, Sara and Ayuso, Miriam and Van Cruchten, Steven and Van Ginneken, Chris},
  year      = {2018},
  title     = {Does intrauterine crowding affect locomotor development? {A} comparative study of motor performance, neuromotor maturation and gait variability among piglets that differ in birth weight and vitality},
  doi       = {10.1371/journal.pone.0195961},
  journal   = {{PLOS ONE}},
  volume    = {13},
  number    = {4},
  pages     = {1--21},
  month     = {04},
  abstract  = {In polytocous species, such as pigs, the growth of an individual fetus is affected by competition from its littermates and the sow. This intrauterine competition greatly influences postnatal traits such as birth weight and vitality (physical strength). A lowered vitality is most often observed among low birth weight piglets. Since it has been argued that locomotion might be key to unraveling vitality-related differences, we compared gait development in piglets with a low birth weight and low vitality (L piglets) with piglets with a normal birth weight and normal vitality (N piglets) by means of spatio-temporal gait analysis during locomotion at self-selected speed. Video recordings of L and N piglets walking along a corridor at ten time points (between birth and 96 h after birth) were made and the footfalls were digitized. Hence, self-selected speed, spatio-temporal characteristics and gait symmetry were analyzed to compare motor performance, neuromotor maturation (motor task, interlimb and intralimb coordination) and gait variability for L and N piglets. The analysis included both absolute and normalized data (according to the dynamic similarity concept), to distinguish neuromotor maturation from effects caused by growth. Results indicate that intrauterine crowding affects locomotion, mainly by impairing growth in utero, with a lowered motor performance during the first 96 h of age as a consequence. A difference in neuromotor skills was also visible, though only for swing and stance duration, implying a difference in neuromotor development in utero. However, further maturation during the first days after birth does not seem to be affected by intrauterine crowding. We can therefore conclude that L piglets might be considered a smaller and fictitious younger version of N piglets.},
  publisher = {Public Library of Science},
}

@article{Holmes2006,
  author    = {Holmes, P. and Full, R. and Koditschek, D. and Guckenheimer, J.},
  title     = {The Dynamics of Legged Locomotion: Models, Analyses, and Challenges},
  journal   = {{SIAM Review}},
  year      = {2006},
  volume    = {48},
  number    = {2},
  pages     = {207--304},
  month     = apr,
  issn      = {0036-1445},
  doi       = {10.1137/s0036144504445133},
  publisher = {Society for Industrial and Applied Mathematics},
}

@article{Mitteroecker2011,
  author    = {Mitteroecker, Philipp and Bookstein, Fred},
  title     = {Linear Discrimination, Ordination, and the Visualization of Selection Gradients in Modern Morphometrics},
  journal   = {Evolutionary Biology},
  year      = {2011},
  volume    = {38},
  number    = {1},
  pages     = {100--114},
  month     = {feb},
  issn      = {1934-2845},
  doi       = {10.1007/s11692-011-9109-8},
  keyword   = {Canonical Variate Analysis, Linear discriminant function, Ordination, Principal component analysis, Procrustes, Selection gradient},
  url      = {http://link.springer.com/article/10.1007/s11692-011-9109-8},
}

@article{Hermanson1992,
  author    = {Hermanson, John W. and MacFadden, Bruce J.},
  title     = {Evolutionary and functional morphology of the shoulder region and stay-apparatus in fossil and extant horses ({Equidae})},
  journal   = {Journal of Vertebrate Paleontology},
  year      = {1992},
  volume    = {12},
  number    = {3},
  pages     = {377--386},
  month     = sep,
  issn      = {0272-4634},
  abstract  = {In advanced members of the Equidae, the shoulder joint evolved a unique morphology about 5 Ma ago. Anatomically this diarthrosis is notable for its lack or weak development of ligaments. In fact, the normal role of ligamentous structures in bracing the joint has been taken over by muscles. One of these, the biceps brachii, exhibits morphological specializations consistent with preventing collapse of the shoulder joint during long periods of quiet standing characteristic of extant horses, thus reducing the muscular effort required to stand for prolonged periods. Osteologically, the specialization of the biceps brachii in horses is reflected by the presence of a well-developed intermediate tubercle (INT) on the proximal aspect of the humerus and by a prominent muscle origin on the supraglenoid tubercle of the scapula. Primitive horses and both fossil and extant outgroups of diverse sizes (e.g., tapirs and titanotheres) lack the intermediate tubercle and have an intertubercular sulcus that spirals medially (passing proximal to distal) with respect to the humeral head. In the derived equid state the intermediate tubercle is well-developed, bordered by distinct greater and lesser tubercles, and it is aligned parallel to the long axis of the humerus. The derived state of this character complex is incipient in Dinohippus (ca. 5 Ma) and is first well-developed in Pliocene (ca. 3.5 Ma) extinct species of Equus; it is thus a synapomorphy to unite this monophyletic clade. The function of this musculoskeletal complex is discussed in terms of body size trends and the distribution of various character states in other clades.},
  doi       = {10.1080/02724634.1992.10011466},
  publisher = {Taylor \& Francis},
}

@book{Marey1878,
  title     = {La m{\'e}thode graphique dans les sciences exp{\'e}rimentales et particuli{\`e}rement en physiologie et en m{\'e}decine},
  publisher = {G. Masson},
  year      = {1878},
  author    = {Marey, Etienne-Jules},
}

@book{Muybridge1893,
  title     = {Descriptive zoopraxography, or, the science of animal locomotion made popular},
  publisher = {University of Pennsylvania},
  year      = {1893},
  author    = {Eadweard Muybridge},
  doi       = {10.5962/bhl.title.6478},
}

@book{Braune1904,
  title     = {Der Gang des Menschen},
  publisher = {B.G. Teubner},
  year      = {1895-1904},
  author    = {Braune, Wilhelm and Fischer, Otto},
  address   = {Leipzig},
}

@article{Lamb2014,
  author    = {Lamb, Peter F. and St\"{o}ckl, Michael},
  title     = {On the use of continuous relative phase: Review of current approaches and outline for a new standard},
  journal   = {Clinical Biomechanics},
  year      = {2014},
  volume    = {29},
  number    = {5},
  pages     = {484--493},
  month     = may,
  issn      = {0268-0033},
  abstract  = {Background In this paper we review applications of continuous relative phase and commonly reported methods for calculating the phase angle. Signals with known properties as well as empirical data were used to compare methods for calculating the phase angle. Findings Our results suggest that the most valid, robust and intuitive results are obtained from the following steps: 1) centering the amplitude of the original signals around zero, 2) creating analytic signals from the original signals using the Hilbert transform, 3) calculating the phase angle using the analytic signal and 4) calculating the continuous relative phase. Interpretations The resulting continuous relative phase values are free of frequency artifacts, a problem associated with most normalization techniques, and the interpretation remains intuitive. We propose these methods for future research using continuous relative phase in studies and analyses of human movement coordination.},
  keywords  = {Phase angle, Continuous relative phase, Normalization, Gait data, Coordination, Movement variability},
  url       = {http://www.sciencedirect.com/science/article/pii/S0268003314000618},
  doi = {10.1016/j.clinbiomech.2014.03.008},
}

@article{MacLaren2016,
  author    = {MacLaren, Jamie A. and Nauwelaerts, Sandra},
  title     = {A three-dimensional morphometric analysis of upper forelimb morphology in the enigmatic tapir ({Perissodactyla: Tapirus}) hints at subtle variations in locomotor ecology},
  journal   = {Journal of Morphology},
  year      = {2016},
  volume    = {277},
  number    = {11},
  pages     = {1469--1485},
  month     = may,
  issn      = {0362-2525},
  abstract  = {ABSTRACT Forelimb morphology is an indicator for terrestrial locomotor ecology. The limb morphology of the enigmatic tapir (Perissodactyla: Tapirus) has often been compared to that of basal perissodactyls, despite the lack of quantitative studies comparing forelimb variation in modern tapirs. Here, we present a quantitative assessment of tapir upper forelimb osteology using three-dimensional geometric morphometrics to test whether the four modern tapir species are monomorphic in their forelimb skeleton. The shape of the upper forelimb bones across four species (T. indicus; T. bairdii; T. terrestris; T. pinchaque) was investigated. Bones were laser scanned to capture surface morphology and 3D landmark analysis was used to quantify shape. Discriminant function analyses were performed to reveal features which could be used for interspecific discrimination. Overall our results show that the appendicular skeleton contains notable interspecific differences. We demonstrate that upper forelimb bones can be used to discriminate between species (>91% accuracy), with the scapula proving the most diagnostic bone (100% accuracy). Features that most successfully discriminate between the four species include the placement of the cranial angle of the scapula, depth of the humeral condyle, and the caudal deflection of the olecranon. Previous studies comparing the limbs of T. indicus and T. terrestris are corroborated by our quantitative findings. Moreover, the mountain tapir T. pinchaque consistently exhibited the greatest divergence in morphology from the other three species. Despite previous studies describing tapirs as functionally mediportal in their locomotor style, we find osteological evidence suggesting a spectrum of locomotor adaptations in the tapirs. We conclude that modern tapir forelimbs are neither monomorphic nor are tapirs as conserved in their locomotor habits as previously described. J. Morphol. 277:1469?1485, 2016. ? 2016 Wiley Periodicals, Inc.},
  doi       = {10.1002/jmor.20588},
  keywords  = {discriminant analysis, geometric morphometrics, osteology, scapular fossa ratio, Tapirus pinchaque},
  publisher = {John Wiley \& Sons, Ltd},
}

@article{Ruina2005,
  author    = {Ruina, Andy and Bertram, John E. A. and Srinivasan, Manoj},
  title     = {A collisional model of the energetic cost of support work qualitatively explains leg sequencing in walking and galloping, pseudo-elastic leg behavior in running and the walk-to-run transition},
  journal   = {Journal of Theoretical Biology},
  year      = {2005},
  volume    = {237},
  number    = {2},
  pages     = {170--192},
  month     = nov,
  issn      = {0022-5193},
  abstract  = {Terrestrial legged locomotion requires repeated support forces to redirect the body's vertical velocity component from down to up. We assume that the redirection is accomplished by impulsive leg forces that cause small-angle glancing collisions of a point-mass model of the animal. We estimate the energetic costs of these collisions by assuming a metabolic cost proportional to positive muscle work involved in generating the impulses. The cost of bipedal running estimated from this collisional model becomes less than that of walking at a Froude number (v2/gℓ) of about 0.7. Two strategies to reduce locomotion costs associated with the motion redirection are: (1) having legs simulate purely elastic springs, as is observed in human running; and (2) sequencing the leg forces during the redirection phase; examples of this sequencing are the ba-da-dump pattern of a horse gallop and having push-off followed by heel-strike in human walking.},
  keywords  = {Locomotion, Collision, Energy, Walk, Gallop},
  url       = {http://www.sciencedirect.com/science/article/pii/S0022519305001591},
  doi = {10.1016/j.jtbi.2005.04.004},
}

@article{Barrett2008,
  author    = {Barrett, Rod and Vonk Noordegraaf, Maarten and Morrison, Steven},
  journal   = {Journal of Motor Behavior},
  title     = {Gender Differences in the Variability of Lower Extremity Kinematics During Treadmill Locomotion},
  year      = {2008},
  number    = {1},
  pages     = {62--70},
  volume    = {40},
  abstract  = {The authors examined whether there were gender differences in the variability of basic gait parameters (stride length, stride time) and 3-dimensional (3D) rotations of the hip, knee, and ankle joints during treadmill locomotion of 18 men and 15 women at 4 different gait speeds (walking at 5 km/hr, running at 8, 10, and 12 km/hr). The authors used 2-way analyses of variance to assess the data. No gender differences in the mean values or variability of basic gait parameters were detected. However, the women exhibited lower variability than did the men for 6 individual joint rotations: (a) transverse plane rotations of the ankle joint at 8, 10, and 12 km/hr, (b) transverse plane rotations of the hip and knee joints at 12 km/hr, and (c) sagittal plane rotations of the ankle joint at 12 km/hr. When collapsed across all 3D lower extremity rotations, the data showed that the women had lower variability than did the men at 12 km/hr. Reduced variability may result in more localized mechanical stress on anatomical structures and could therefore be a risk factor for injury in women at high gait speeds. The results also suggested that gender differences in variability may not be consistent across different levels of the motor system.},
  doi       = {10.3200/JMBR.40.1.62-70},
  publisher = {Routledge},
}

@article{McGibbon2003,
  author    = {McGibbon, Chris A.},
  title     = {Toward a Better Understanding of Gait Changes With Age and Disablement: Neuromuscular Adaptation},
  journal   = {Exercise and Sport Sciences Reviews},
  year      = {2003},
  volume    = {31},
  number    = {2},
  issn      = {0091-6331},
  abstract  = {MCGIBBON, C. A. Toward a better understanding of gait changes with age and disablement: Neuromuscular adaptation. Exerc. Sport Sci. Rev., Vol. 31, No. 2, pp. 102-108, 2003. Gait changes in the elderly, such as reduced step length and walking speed, are well documented but not well understood. This review explores the hypothesis that neuromuscular adaptations are a response to age-related impairments and play a key role in causing gait changes in the elderly, and that different neuromuscular adaptations may exist depending on the impairment and presence of comorbidities, such as knee arthritis.},
  keywords  = {hip, knee, ankle, power and energy, compensation, neuromuscular, strength impairment, arthritis},
  url       = {https://journals.lww.com/acsm-essr/Fulltext/2003/04000/Toward_a_Better_Understanding_of_Gait_Changes_With.9.aspx},
}

@article{Mohling2014,
  author    = {Mohling, C. M. and Johnson, A. K. and Coetzee, J. F. and Karriker, L. A. and Abell, C. E. and Millman, S. T. and Stalder, K. J.},
  title     = {Kinematics as objective tools to evaluate lameness phases in multiparous sows},
  journal   = {Livestock Science},
  year      = {2014},
  volume    = {165},
  pages     = {120--128},
  month     = jul,
  issn      = {1871-1413},
  abstract  = {Lameness has been ranked as the third most common reason for culling sows, comprising 15% of the culls marketed in the U.S. Producers assess sow lameness using subjective evaluation, which have been shown to be variable in their application. Objective empirical tools to measure sow lameness on farm are required. Therefore, the purpose of this study were to evaluate the embedded force plate and the GAITFour gait analysis walkway system as objective assessment tools to discriminate between sound and lame phases in multiparous sows. Twenty-four mixed parity crossbred sows were anesthetized and injected with Amphotericin B in the distal interphalangeal joint of both claws of one hind hoof to induce transient lameness. Kinematic data was collected on D−1, D+1 and D+6 relative to induction (D0). For the embedded force plate, weight distributions on each hoof were collected. Gait analysis measures collected were stride time (defined as the time (s) between 2 successive footfalls by the same hoof), stride length (defined as the distance (cm) between 2 sequential footfalls from the same hoof), maximum pressure (defined as the greatest amount of weight (kg/cm2) placed on a single hoof) and stance time (defined as the duration of time (s) the sensors were activated by a hoof in a single stride). For the embedded microcomputer-based force plate system weight placed on the induced hoof decreased on D+1 when compared to D−1 (P<0.0001). For the GAITFour® pressure mat gait analysis walkway system, stride time increased on D+1 for all hooves, stride length decreased on D+1 compared to D−1 and maximum pressure placed on the induced hoof decreased on D+1 compared to baseline levels (P<0.05). Stance time increased for all sound hooves on D+1 compared to D−1 (P<0.05). In conclusion, the embedded force plate and GAITFour walkway system all demonstrated differences for mature sows during sound and most lame phases indicating promise as objective tools for use on farm.},
  keywords  = {Force plate, Gait analysis, Lameness, Pain, Sow},
  url       = {http://www.sciencedirect.com/science/article/pii/S1871141314002327},
  doi = {10.1016/j.livsci.2014.04.031},
}

@article{Vanhooydonck2014,
  author    = {Vanhooydonck, B. and James, R. S. and Tallis, J. and Aerts, P. and Tadic, Z. and Tolley, K. A. and Measey, G. J. and Herrel, A.},
  title     = {Is the whole more than the sum of its parts? {Evolutionary} trade-offs between burst and sustained locomotion in lacertid lizards},
  journal   = {Proceedings of the Royal Society of London B: Biological Sciences},
  year      = {2014},
  volume    = {281},
  pages     = {2132677},
  issn      = {0962-8452},
  abstract  = {Trade-offs arise when two functional traits impose conflicting demands on the same design trait. Consequently, excellence in one comes at the cost of performance in the other. One of the most widely studied performance trade-offs is the one between sprint speed and endurance. Although biochemical, physiological and (bio)mechanical correlates of either locomotor trait conflict with each other, results at the whole-organism level are mixed. Here, we test whether burst (speed, acceleration) and sustained locomotion (stamina) trade off at both the isolated muscle and whole-organism level among 17 species of lacertid lizards. In addition, we test for a mechanical link between the organismal and muscular (power output, fatigue resistance) performance traits. We find weak evidence for a trade-off between burst and sustained locomotion at the whole-organism level; however, there is a significant trade-off between muscle power output and fatigue resistance in the isolated muscle level. Variation in whole-animal sprint speed can be convincingly explained by variation in muscular power output. The variation in locomotor stamina at the whole-organism level does not relate to the variation in muscle fatigue resistance, suggesting that whole-organism stamina depends not only on muscle contractile performance but probably also on the performance of the circulatory and respiratory systems.},
  doi       = {10.1098/rspb.2013.2677},
  publisher = {The Royal Society},
  url       = {http://rspb.royalsocietypublishing.org/content/281/1777/20132677},
}

@article{Nyakatura2012,
  author    = {Nyakatura, J. A. and Andrada, E. and Grimm, N. and Weise, H. and Fischer, M. S.},
  title     = {Kinematics and Center of Mass Mechanics During Terrestrial Locomotion in Northern Lapwings {(\textit{Vanellus vanellus}, Charadriiformes)}},
  journal   = {Journal of Experimental Zoology Part A: Ecological Genetics and Physiology},
  year      = {2012},
  volume    = {317},
  number    = {9},
  pages     = {580--594},
  abstract  = {Abstract Avian bipedalism is best studied in derived walking/running specialists. Here, we use kinematics and center of mass (CoM) mechanical energy patterns to investigate gait transitions of lapwings—migratory birds that forage on the ground, and therefore may need a trade-off between the functional demands of terrestrial locomotion and long distance flights. The animals ran on a treadmill while high-speed X-ray videos were recorded within the sustainable speed range. Instantaneous CoM mechanics were computed from integrating kinematics and body segment properties. Lapwings exhibit similar locomotor characteristics to specialized walking/running birds, but have less distinct gaits. At slow speeds no clear separation between vaulting (i.e., walking) and bouncing (i.e., running) energy patterns exists. Mechanical energy recovery of non-bouncing gaits correlates poorly with speed and suggests inefficient use of the inverted pendulum mechanism. Speed ranges of gaits overlap considerably, especially those of grounded running, a gait with CoM mechanics indicative of running but without an aerial phase, and aerial phase running, with no preferential gait at most speeds. Compliant limb morphology and grounded running in birds can be regarded as an evolutionary constraint, but lapwings effectively make use of advantages offered by this gait for a great fraction of their speed range. Thus, effective usage of grounded running during terrestrial locomotion is suggested generally to be a part of striding avian bipedalism—even in species not specialized in walking/running locomotion. J. Exp. Zool. 317A:580–594, 2012. © 2012 Wiley Periodicals, Inc.},
  doi       = {10.1002/jez.1750},
  url       = {https://onlinelibrary.wiley.com/doi/abs/10.1002/jez.1750},
}

@article{Mielke2018b,
  author    = {Mielke, Falk and Amson, Eli and Nyakatura, John A.},
  title     = {Morpho-Functional Analysis Using {Procrustes} Superimposition by Static Reference},
  journal   = {Evolutionary Biology},
  year      = {2018},
  volume    = {45},
  number    = {4},
  pages     = {449--461},
  month     = dec,
  issn      = {1934-2845},
  abstract  = {In conventional geometric morphometric analyses of limb long bones, differences in the evolutionary capacity of articular surfaces and non-articular structures often remain unrecognised. It can be shown that areas of high spatial variance dominate shape data, which is problematic for the functional interpretation of limb long bone shape. We herein introduce Procrustes superimposition by static reference (PSSR), a novel analysis strategy that aims to facilitate morpho-functional inference. This procedure exploits the spatial constraint of some reference structures (in our case, articular surfaces) for the superimposition of other subareas (e.g. muscle attachment sites) in relation to that static reference. PSSR allows for the transformation of raw scan data, enabling researchers to extract geometric models of two- and three-dimensional substructures that cannot effectively be integrated with landmarks. As we demonstrate by a simple model analysis for one muscle attachment site, this procedure can yield measures of direct functional relevance. Multivariate analysis of an extensive set of subareas indicates how this type of data relates to conventional shape coordinates. The shape evolution of xenarthran humeri, which has previously been subject to a detailed study (Milne et al., J Zool 278(1):48-56, 2009), serves as a test case. The concept of a variance-based separation of landmark subsets expands mathematical methods by incorporating knowledge about evolutionary constraints. PSSR could therefore find application far beyond the intuitive case study of long bone shape.},
  doi       = {10.1007/s11692-018-9456-9},
  url       = {https://link.springer.com/article/10.1007\%2Fs11692-018-9456-9},
}

@article{Geyer2006,
  author    = {Geyer, Hartmut and Seyfarth, Andre and Blickhan, Reinhard},
  title     = {Compliant leg behaviour explains basic dynamics of walking and running},
  journal   = {{Proceedings of the Royal Society B: Biological Sciences}},
  year      = {2006},
  volume    = {273},
  number    = {1603},
  pages     = {2861--2867},
  month     = jun,
  abstract  = {The basic mechanics of human locomotion are associated with vaulting over stiff legs in walking and rebounding on compliant legs in running. However, while rebounding legs well explain the stance dynamics of running, stiff legs cannot reproduce that of walking. With a simple bipedal spring–mass model, we show that not stiff but compliant legs are essential to obtain the basic walking mechanics; incorporating the double support as an essential part of the walking motion, the model reproduces the characteristic stance dynamics that result in the observed small vertical oscillation of the body and the observed out-of-phase changes in forward kinetic and gravitational potential energies. Exploring the parameter space of this model, we further show that it not only combines the basic dynamics of walking and running in one mechanical system, but also reveals these gaits to be just two out of the many solutions to legged locomotion offered by compliant leg behaviour and accessed by energy or speed.},
  doi       = {10.1098/rspb.2006.3637},
  publisher = {Royal Society},
}


% #### CHAPTER 4 ####


@book{Gelman2013,
    title={Bayesian Data Analysis},
    author={Gelman, Andrew and Carlin, John and Stern, Hal and Dunson, David and Vehtari, Aki and Rubin, Donald},
    year={2020},
    edition={3rd},
    publisher={freely available online},
    url={http://www.stat.columbia.edu/~gelman/book/},
    note={\nolinkurl{http://www.stat.columbia.edu/~gelman/book}}
}


@article{LKJ2009,
    title = {Generating random correlation matrices based on vines and extended onion method},
    journal = {Journal of Multivariate Analysis},
    volume = {100},
    number = {9},
    pages = {1989-2001},
    year = {2009},
    issn = {0047-259X},
    doi = {10.1016/j.jmva.2009.04.008},
    url = {https://www.sciencedirect.com/science/article/pii/S0047259X09000876},
    author = {Lewandowski, Daniel and Kurowicka, Dorota and Joe, Harry},
    keywords = {Dependence vines, Correlation matrix, Partial correlation, Onion method},
    abstract = {We extend and improve two existing methods of generating random correlation matrices, the onion method of Ghosh and Henderson [S. Ghosh, S.G. Henderson, Behavior of the norta method for correlated random vector generation as the dimension increases, ACM Transactions on Modeling and Computer Simulation (TOMACS) 13 (3) (2003) 276–294] and the recently proposed method of Joe [H. Joe, Generating random correlation matrices based on partial correlations, Journal of Multivariate Analysis 97 (2006) 2177–2189] based on partial correlations. The latter is based on the so-called D-vine. We extend the methodology to any regular vine and study the relationship between the multiple correlation and partial correlations on a regular vine. We explain the onion method in terms of elliptical distributions and extend it to allow generating random correlation matrices from the same joint distribution as the vine method. The methods are compared in terms of time necessary to generate 5000 random correlation matrices of given dimensions.}
}


@article{Shikano2019,
    author = {Shikano, Susumu},
    title = {Hypothesis Testing in the Bayesian Framework},
    journal = {Swiss Political Science Review},
    volume = {25},
    number = {3},
    pages = {288-299},
    keywords = {Bayesian Inference, Credible Intervals, Bayes Factor, Model Selection},
    doi = {10.1111/spsr.12375},
    url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/spsr.12375},
    abstract = {Abstract While the Bayesian parameter estimation has gained a wider acknowledgement among political scientists, they seem to have less discussed the Bayesian version of hypothesis testing. This paper introduces two Bayesian approaches to hypothesis testing: one based on estimated posterior distributions and the other based on Bayes factors. By using an example based on a linear regression model, I demonstrate similarities and differences not only between the null-hypothesis significance tests and Bayesian hypothesis tests, but also those among two different Bayesian approaches, which are also critically discussed.},
    year = {2019}
}


% #### CHAPTER 5 ####

% ### A ###
@article{Abell2014,
    author = {Abell, Caitlyn E and Johnson, Anna K and Karriker, Locke A and Rothschild, Max F and Hoff, Steven J and Sun, G and Fitzgerald, RF and Stalder, Kenneth J},
    year = {2014},
    title = {{Using classification trees to detect induced sow lameness with a transient model}},
    doi = {10.1017/S1751731114000871},
    journal = {Animal},
    volume = {8},
    number = {6},
    pages = {1000--1009},
    publisher = {Cambridge University Press},
}

@article{Aerts2000,
    author = {Aerts, Peter and Van Damme, Raoul and Van Elsacker, Linda and Duchêne, Vicky},
    year = {2000},
    title = {{Spatio-temporal gait characteristics of the hind-limb cycles during voluntary bipedal and quadrupedal walking in bonobos (Pan paniscus)}},
    doi = {10.1002/(SICI)1096-8644(200004)111:4<503::AID-AJPA6>3.0.CO;2-J},
    journal = {American Journal of Physical Anthropology},
    volume = {111},
    number = {4},
    pages = {503-517},
    keywords = {primate locomotion, gait variables, bipedal/quadrupedal walking},
    url = {https://onlinelibrary.wiley.com/doi/10.1002/(SICI)1096-8644(200004)111:4\%3C503::AID-AJPA6\%3E3.0.CO;2-J},
    abstract = {{Abstract Spatio-temporal gait characteristics (step and stride length, stride frequency, duty factor) were determined for the hind-limb cycles of nine bonobos (Pan paniscus) walking quadrupedally and bipedally at a range of speeds. The data were recalculated to dimensionless quantities according to the principle of dynamic similarity. Lower leg length was used as the reference length. Interindividual variability in speed modulation strategy of bonobos appears to be low. Compared to quadrupedal walking, bipedal bonobos use smaller steps to attain a given speed (differences increase with speed), resulting in shorter strides at a higher frequency. In the context of the (“hybrid”) dynamic pattern approach to locomotion (Latach, 1998) we argue that, despite these absolute differences, intended walking speed is the basic control variable which elicits both quadrupedal and bipedal walking kinematics in a similar way. Differences in the initial status of the dynamic system may be responsible for the differences in step length between both gaits. Comparison with data deduced from the literature shows that the effects of walking speed on stride length and frequency are similar in bonobos, common chimpanzees, and humans. This suggests that (at least) within extant homininae, spatio-temporal gait characteristics are highly comparable, and this in spite of obvious differences in mass distribution and bipedal posture. Am J Phys Anthropol 111:503–517, 2000. © 2000 Wiley-Liss, Inc.}},
}


@article{Amdi2013,
    author = {Amdi, C. and Krogh, U. and Flummer, C. and Oksbjerg, N. and Hansen, C. F. and Theil, P. K.},
    year = {2013},
    title = {{Intrauterine growth restricted piglets defined by their head shape ingest insufficient amounts of colostrum}},
    doi = {10.2527/jas.2013-6824},
    journal = {Journal of Animal Science},
    volume = {91},
    number = {12},
    pages = {5605-5613},
    month = {12},
    issn = {0021-8812},
    abstract = {The increasing litter sizes of modern pig breeds have led to a significant number of piglets that are born undersized (“small” piglets) and some have been exposed to different degrees of intrauterine growth restriction (IUGR). The aim of this study was to investigate the physiology and capability to ingest colostrum of these small piglets, suffering from various degrees of IUGR, to see if their IUGR score could be a useful tool for easy identification of piglets in need of intervention in the colostrum period. Piglets were classified at birth based on head morphology. Piglets were classified either “normal,” “mildly IUGR” (m-IUGR), or “severe IUGR” (s-IUGR), based on head morphology. Blood samples were collected at birth and at 24 h, and colostrum intake during two 12-h periods and blood metabolites at 0 and 24 h were measured. At 24 h, piglets weighing 900 g at birth and the median piglet in birth order were sacrificed, and organ weights and hepatic glycogen were measured. Overall, there was an influence of the piglets' classification on most characteristics, with normal piglets having a greater colostrum intake between 0 and 12 h (P  0.001) and between 12 and 24 h (P  0.05), and higher birth weight, crown rump length, body mass index, and ponderal index (P 0.001), and a tendency toward a higher vitality score (P 0.069) than s-IUGR piglets. There was a time × IUGR interaction, with plasma glucose levels being lowered (P 0.001) and lactate levels elevated (P 0.001) in s-IUGR piglets at 24 h compared with normal and m-IUGR piglets. Some differences were found in electrolytes; sodium plasma concentrations were greatest for normal piglets (P 0.05) and highest at 0 h (P 0.05). At 24 h of age, s-IUGR piglets had a higher heart (P 0.001) and brain percentage (P 0.001), and a lower liver percentage (P 0.001) relative to body weight, compared with normal piglets. In addition, s-IUGR piglets had less hepatic glycogen than m-IUGR piglets and normal piglets. The present study showed that the physiology of piglets in the colostrum period was affected by IUGR status at birth and their intermediary metabolism was altered due to different colostrum intakes. Furthermore, it was demonstrated that the head shape of newborn piglets is a good selection criteria for identifying piglets that need oral supplementation during the neonatal stage.},
}


@article{Andersen2016,
    author = {Andersen, Anders D. and Sangild, Per T. and Munch, Sara L. and van der Beek, Eline M. and Renes, Ingrid B. and Ginneken, Chris van and Greisen, Gorm O. and Thymann, Thomas},
    year = {2016},
    title = {{Delayed growth, motor function and learning in preterm pigs during early postnatal life}},
    doi = {10.1152/ajpregu.00349.2015},
    journal = {American Journal of Physiology-Regulatory, Integrative and Comparative Physiology},
    volume = {310},
    number = {6},
    pages = {R481-R492},
    abstract = {Preterm birth interrupts normal fetal growth with consequences for postnatal growth and organ development. In preterm infants, many physiological deficits adapt and disappear with advancing postnatal age, but some may persist into childhood. We hypothesized that preterm birth would induce impaired organ growth and function during the first postnatal week in pigs, while motor abilities and behavioral characteristics would show more persistent developmental delay. Cesarean-delivered preterm (n = 112, 90\% gestation) or term (n = 56, 100\% gestation) piglets were reared under identical conditions and euthanized for blood and organ collection on postnatal days 0, 5, or 26. Body weight gain remained lower in preterm vs. term pigs up to day 26 (25.5 ± 1.5 vs. 31.0 ± 0.5 g·kg−1·day−1, P < 0.01) when relative weights were higher for brain and kidneys and reduced for liver and spleen. Neonatal preterm pigs had reduced values for blood pH, Po2, glucose, lactate, hematocrit, and cortisol, but at day 26, most values were normalized, although plasma serotonin and IGF 1 levels remained reduced. Preterm pigs showed delayed neonatal arousal and impaired physical activity, coordination, exploration, and learning, relative to term pigs (all P < 0.05). Supplementation of parenteral nutrition during the first 5 days with an enteral milk diet did not affect later outcomes. In preterm pigs, many physiological characteristics of immaturity disappeared by 4 wk, while some neurodevelopmental deficits remained. The preterm pig is a relevant animal model to study early dietary and pharmacological interventions that support postnatal maturation and neurodevelopment in preterm infants.},
}

@article{Austin2015,
    author = {Austin, Peter C. and Steyerberg, Ewout W.},
    year = {2015},
    title = {{The number of subjects per variable required in linear regression analyses}},
    doi = {10.1016/j.jclinepi.2014.12.014},
    journal = {Journal of Clinical Epidemiology},
    volume = {68},
    number = {6},
    pages = {627-636},
    issn = {0895-4356},
    url = {https://www.sciencedirect.com/science/article/pii/S0895435615000141},
    keywords = {Regression, Linear regression, Bias, Monte Carlo simulations, Explained variation, Statistical methods},
    abstract = {Objectives: To determine the number of independent variables that can be included in a linear regression model.; Study Design and Setting: We used a series of Monte Carlo simulations to examine the impact of the number of subjects per variable (SPV) on the accuracy of estimated regression coefficients and standard errors, on the empirical coverage of estimated confidence intervals, and on the accuracy of the estimated R2 of the fitted model.; Results: A minimum of approximately two SPV tended to result in estimation of regression coefficients with relative bias of less than 10\%. Furthermore, with this minimum number of SPV, the standard errors of the regression coefficients were accurately estimated and estimated confidence intervals had approximately the advertised coverage rates. A much higher number of SPV were necessary to minimize bias in estimating the model R2, although adjusted R2 estimates behaved well. The bias in estimating the model R2 statistic was inversely proportional to the magnitude of the proportion of variation explained by the population regression model.; Conclusion: Linear regression models require only two SPV for adequate estimation of regression coefficients, standard errors, and confidence intervals.},
}

@article{Ayuso2021,
    author = {Ayuso, Miriam and Irwin, Rachelle and Walsh, Colum and Van Cruchten, Steven and Van Ginneken, Chris},
    year = {2021},
    title = {{Low birth weight female piglets show altered intestinal development, gene expression, and epigenetic changes at key developmental loci}},
    doi = {10.1096/fj.202002587R},
    journal = {The FASEB Journal},
    volume = {35},
    number = {4},
    pages = {e21522},
    keywords = {gene expression, gene methylation, intestinal development, LBW, piglet},
    url = {https://faseb.onlinelibrary.wiley.com/doi/abs/10.1096/fj.202002587R},
    abstract = {Abstract Intestinal development is compromised in low birth weight (LBW) pigs, negatively impacting their growth, health, and resilience. We investigated the molecular mechanisms of the altered intestinal maturation observed in neonatal and juvenile LBW female piglets by comparing the changes in intestinal morphology, gene expression, and methylation in LBW versus normal birth weight (NBW) female piglets. A total of 16 LBW/NBW sibling pairs were sacrificed at 0 hours, 8 hours, 10 days, and 8 weeks of age. The gastrointestinal tract was weighed, measured, and the small intestine was sampled for histomorphology, gene expression, and methylation analyses. Impaired intestinal development, with shorter villi and shallower crypts, was observed in LBW female piglets. The expression of intestinal development markers (ALPI and OLFM) rapidly peaked after birth in NBW but not in LBW female piglets. The lower expression of genes involved in nutrient digestion (ANPEP and SI) and barrier function (OCLN and CLDN4) in LBW, together with their delayed development of intestinal villi and crypts could help to explain the compromised health and growth potential of LBW female piglets. The changes in methylation observed in LBW in key regulators of intestinal development (OLFM4 and FZD5) suggest long-term effects of BW on intestinal gene expression, development, and function. Accordingly, experimental demethylation induced in IPEC-J2 cells led to increased expression of intestinal genes (MGA, DPP4, and GLUT2). Overall, we have identified the alterations in transcription or epigenetic marking at a number of genes critical to intestinal development, which may contribute to both the short- and long-term failure of LBW female piglets to thrive.},
}

@article{Azarpajouh2020,
    author = {Azarpajouh, Samaneh and D\'iaz, Julia A. Calder\'on and Taheri, Hossein},
    year = {2020},
    title = {{Precision livestock farming: automatic lameness detection in intensive livestock systems}},
    journal = {{CABI Reviews}},
    issue_date = {February 2020},
    publisher = {CABI International},
    volume = {2020},
    doi = {10.1079/PAVSNNR202015031},
    abstract = {{Lameness is a major production disease affecting animal welfare and profitability. Although lameness is a prevalent condition in livestock production systems, its identification can be unreliable due to lack of individual animal observation for gait and posture abnormalities and standard evaluation criteria. To prevent financial losses and welfare problems, early and accurate lameness detection and treatment are essential. Visual scoring is the most common method to evaluate lameness, which is time and labor involved and is prone to observer error. Therefore, automated lameness detection methods that do not rely on the human eyes and are not subjective may offer a more accurate lameness identification method. Application of engineering techniques in livestock farming to monitor, model, and manage animal production is called precision livestock farming (PLF). Using PLF, a large amount of data can be collected in short period of time, which can improve lameness prediction accuracy. This review paper will (a) explain engineering advances in PLF; (b) describe lameness and visual and automatic lameness detection; and (c) discuss sensors applied in PLF research.}},
    numpages = {12},
}


% ### B ###
@article{Baxter2008,
    author = {Baxter, E.M. and Jarvis, S. and D’Eath, R.B. and Ross, D.W. and Robson, S.K. and Farish, M. and Nevison, I.M. and Lawrence, A.B. and Edwards, S.A.},
    year = {2008},
    title = {{Investigating the behavioural and physiological indicators of neonatal survival in pigs}},
    doi = {10.1016/j.theriogenology.2007.12.007},
    journal = {Theriogenology},
    volume = {69},
    number = {6},
    pages = {773-783},
    issn = {0093-691X},
    url = {https://www.sciencedirect.com/science/article/pii/S0093691X07007248},
    keywords = {Survival, Piglet, Placenta, Ponderal index, Body mass index},
    abstract = {Survival is reduced in low birth weight piglets, which display poor thermoregulatory abilities and are slow to acquire colostrum. Our aim was to identify additional behavioural and physiological indicators of piglet survival incorporating traits reflective of both the intrauterine and extrauterine environment. Data were collected from 135 piglets from 10 Large White×Landrace sows to investigate which physiological measurements (e.g. individual placental traits), and which behavioural measurements (e.g. the quantification of piglet vigour), were the best indicators of piglet survival. Generalised linear models confirmed piglet birth weight as a critical survival factor. However, with respect to stillborn mortality, piglet shape and size, as measured by ponderal index (birth weight/(crown–rump length)3), body mass index (birth weight/(crown–rump length)2), respectively, and farrowing birth order were better indicators. With respect to live-born mortality, postnatal survival factors identified as crucial were birth weight, vigour independent of birth weight, and the latency to first suckle. These results highlight the importance of the intrauterine environment for postnatal physiological and behavioural adaptation and identify additional factors influencing piglet neonatal survival.},
}


@article{Baxter2012,
    author = {Baxter, Emma M. and Jarvis, Susan and Palarea-Albaladejo, Javier and Edwards, Sandra A.},
    year = {2012},
    title = {{The Weaker Sex? The Propensity for Male-Biased Piglet Mortality}},
    doi = {10.1371/journal.pone.0030318},
    journal = {PLOS ONE},
    publisher = {Public Library of Science},
    month = {01},
    volume = {7},
    pages = {1-9},
    number = {1},
    abstract = {For the most part solutions to farm animal welfare issues, such as piglet mortality, are likely to lie within the scientific disciplines of environmental design and genetic selection, however understanding the ecological basis of some of the complex dynamics observed between parent and offspring could make a valuable contribution. One interesting, and often discussed, aspect of mortality is the propensity for it to be sex-biased. This study investigated whether known physiological and behavioural indicators of piglet survival differed between the sexes and whether life history strategies (often reported in wild or feral populations) relating to parental investment were being displayed in a domestic population of pigs. Sex ratio (proportion of males (males/males+females)) at birth was 0.54 and sex allocation (maternal investment measured as piglet birth weight/litter weight) was statistically significantly male-biased at 0.55 (t35 = 2.51 P = 0.017), suggesting that sows invested more in sons than daughters during gestation. Despite this investment in birth weight, a known survival indicator, total pre-weaning male mortality was statistically significantly higher than female mortality (12\% vs. 7\% respectively z = 2.06 P = 0.040). Males tended to suffer from crushing by the sow more than females and statistically significantly more males died from disease-related causes. Although males were born on average heavier, with higher body mass index and ponderal index, these differences were not sustained. In addition male piglets showed impaired thermoregulation compared to females. These results suggest male-biased mortality exists despite greater initial maternal investment, and therefore reflects the greater susceptibility of this sex to causal mortality factors. Life history strategies are being displayed by a domestic population of pigs with sows in this study displaying a form of parental optimism by allocating greater resources at birth to males and providing an over-supply of this more vulnerable sex in expectation of sex-biased mortality.},
}


@inproceedings{Benasson2020,
    author = {Benasson, I. and Wagnac, E. and Diotalevi, L. and Moore, D. and Mac-Thiong, J-M. and Petit, Y.},
    year = {2020},
    title = {{Gait analysis of a post induced traumatic spinal cord injury porcine model}},
    doi = {10.1109/EMBC44109.2020.9175280},
    volume = {},
    number = {},
    pages = {3803-3806},
    booktitle = {{2020 42nd Annual International Conference of the IEEE Engineering in Medicine Biology Society (EMBC)}},
    keywords = {},
    ISSN = {2694-0604},
    month = {July},
    abstract = {Porcine model constitutes a potential translational model to study traumatic spinal cord injuries (TSCI) considering its recent use in numerous studies. Recovery of the animal is currently monitored through a qualitative evaluation of the gait. Adding a quantitative evaluation might help to better assess the functional recovery of the animal. In this study, a new controlled method involving the use of an electro-magnetic actuator was used on a pig to induce a TSCI. Chronic monitoring was done using a quantitative analysis of the gait. Results show both, the injury of the pig and its functional recovery. This large animal model will help to provide a better understanding of injury and recovery mechanisms and thus could constitute a strong preclinical model for future therapeutic studies.},
}


@book{Bracewell2000,
    author    = {Bracewell, Ronald N.},
    year      = {2000},
    title     = {{The Fourier Transform And Its Applications}},
    publisher = {McGraw Hill},
    series    = {McGraw-Hill series in electrical and computer engineering. Circuits and systems},
    edition   = {3},
    isbn      = {9780071160438, 0-07-116043-4, 0-07-303938-1},
}


@article{Bruton2013,
    author = {Bruton, Michaela R. and O’Dwyer, Nicholas and Adams, Roger},
    year = {2013},
    title = {{Sex differences in the kinematics and neuromuscular control of landing: Biological, environmental and sociocultural factors}},
    doi = {10.1016/j.jelekin.2013.04.012},
    journal = {Journal of Electromyography and Kinesiology},
    volume = {23},
    number = {4},
    pages = {747-758},
    issn = {1050-6411},
    url = {https://www.sciencedirect.com/science/article/pii/S1050641113001090},
    keywords = {Gender, Biomechanics, Electromyography, Self-objectification, Body comportment},
    abstract = {Potential sex differences in patterns of movement of recreational and competitive athletes were investigated in a systematic review of lower limb kinematics, muscle activation and stiffness during landing and hopping tasks. Little support for sex-specific lower limb kinematic patterns was found in 17 studies retrieved on landing and hopping. Ten studies retrieved on muscle activation during landing provided no support for sex-specific patterns. Four articles retrieved on leg stiffness established that absolute stiffness was lower in females, but differences in stiffness normalized to body mass were less clear. The wider literature indicates that a combination of biological, environmental and sociocultural constraints may shape movement patterns differently in females and males. Sociocultural factors differentially affect accumulated motor experience, practice opportunities and focus of attention in females, leading to differences in motor skill that confound the comparison of female and male movements. The findings of the review support the hypothesis that such sex differences in athletic performance are likely to diminish or disappear with increasing skill. In everyday movement tasks, however, where level of skill is a less meaningful dimension than in sport, differences in movement patterns observed between females and males point instead to the influence of subtle societal expectations on movement patterns.},
}


% ### C ###
@article{Cheu2022,
    author = {Cheu, Amy Y and Reed, Samantha A and Mann, Sara D and Bergmann, Philip J},
    doi = {10.1093/icb/icac031},
    year = {2022},
    title = {{Performance and Kinematic Differences Between Terrestrial and Aquatic Running in Anolis Sagrei}},
    journal = {Integrative and Comparative Biology},
    volume = {62},
    number = {4},
    pages = {840-851},
    month = {05},
    abstract = {Many animals frequently transition between different media while navigating their heterogeneous environments. These media vary in compliance, moisture content, and other characteristics that affect their physical properties. As a result, animals may need to alter their kinematics to adapt to potential changes in media while maintaining performance during predator escape and foraging. Due to its fluid nature, water is highly compliant, and although usually associated with swimming, water running has evolved in a variety of animals ranging from insects to mammals. While the best studied large water runners are the bipedal basilisk lizards (Basiliscus spp.), other lizards have also been observed to run across the surface of water, namely, Hemidactylus platyurus, a house gecko, and in this study, Anolis sagrei, the brown anole. Unlike the basilisk lizard, the primarily arboreal Anolis sagrei is not adapted for water running. Moreover, water running in A. sagrei, similar to that of the house gecko, was primarily quadrupedal. Here, we tested for performance and kinematic differences between aquatic and terrestrial running and if the variance in performance and kinematic variables differed between the two media. We found no difference in average and maximum velocity between running on land and water. We also found that Anolis sagrei had higher hindlimb stride frequencies, decreased duty factor, and shorter stride lengths on water, as well as more erect postures. Finally, we found that most kinematics did not differ in variance between the two media, but of those that were different, almost all were more variable during terrestrial running. Our findings show that animals may be capable of specialized modes of locomotion, even if they are not obviously adapted for them, and that they may do this by modulating their kinematics to facilitate locomotion through novel environments.},
    issn = {1540-7063},
}

@article {Corcoran2021,
    author = {Corcoran, Aaron J. and Schirmacher, Michael R. and Black, Eric and Hedrick, Tyson L.},
    year = {2021},
    title = {{ThruTracker: Open-Source Software for 2-D and 3-D Animal Video Tracking}},
    doi = {10.1101/2021.05.12.443854},
    journal = {bioRxiv},
    elocation-id = {2021.05.12.443854},
    publisher = {Cold Spring Harbor Laboratory},
    URL = {https://www.biorxiv.org/content/early/2021/05/13/2021.05.12.443854},
    abstract = {Tracking animal movement patterns using videography is an important tool in many biological disciplines ranging from biomechanics to conservation. Reduced costs of technology such as thermal videography and unmanned aerial vehicles has made video-based animal tracking more accessible, however existing software for processing acquired video limits the application of these methods.Here, we present a novel software program for high-throughput 2-D and 3-D animal tracking. ThruTracker provides tools to allow video tracking under a variety of conditions with minimal technical expertise or coding background and without the need for paid licenses. Notable capabilities include calibrating the intrinsic properties of thermal cameras; tracking and counting hundreds of animals at a time; and the ability to make 3-D calibrations without dedicated calibration objects. Automated 2-D and 3-D workflows are integrated to allow for analysis of largescale datasets.We tested ThruTracker with two case studies. The 2-D workflow is demonstrated by counting bats emerging from bridges and caves using thermal Videography. Tests show that ThruTracker has a similar accuracy compared to humans under a variety of conditions. The 3-D workflow is shown for making accurate calibrations for tracking bats and birds at wind turbines using only the wind turbine itself as a calibration object.ThruTracker is a robust software program for tracking moving animals in 2-D and 3-D. Major applications include counting animals such as bats, birds, and fish that form large aggregations, and documenting movement trajectories over medium spatial scales (\~{}100,000 m3). When combined with emerging technologies, we expect videographic techniques to continue to see widespread adoption for an increasing range of biological applications.Competing Interest StatementThe authors have declared no competing interest.},
}



% ### D ###
@article{DEath2012,
    author = {D'Eath, RB},
    year = {2012},
    title = {{Repeated locomotion scoring of a sow herd to measure lameness: consistency over time, the effect of sow characteristics and inter-observer reliability}},
    doi = {10.7120/09627286.21.2.219},
    journal = {Animal Welfare},
    parent_itemid = {infobike://ufaw/aw},
    publishercode = {ufaw},
    volume = {21},
    number = {2},
    publication_date ={2012-05-01T00:00:00},
    pages = {219-231},
    issn = {0962-7286},
    url = {https://www.ingentaconnect.com/content/ufaw/aw/2012/00000021/00000002/art00008},
    keyword = {locomotion scoring, lameness, inter-observer agreement, sows, pigs, animal welfare},
    abstract = {Investigating variability of scores between different observers, between animals and over time aids the design of valid sampling methodologies for measuring animal welfare. Locomotion scores (0 to 5 scale) were collected: i) from 154 sows in one herd, using three to five observers each time, and scoring sows on up to ten occasions over a 19-month period; and ii) for 123 of these sows, locomotion scoring also took place prior to farrowing and at weaning. The distribution of scores was highly skewed towards low scores (0: 84.8\%, 1: 9.5\%, 2: 4.0\%, 3+: 1.7\%). Sows showed moderate consistency in their scores over time and later parity sows had higher scores, but there was no effect of stage in the reproductive cycle (days pregnant, pre-farrowing, post-weaning). This suggests that infrequent visits to a farm (eg annual) might provide an accurate estimate of the extent of lameness if a representative range of parities was sampled, although a larger study of more farms would be required to investigate this. The three different types of agreement between observers (absolute differences, matching and association) were assessed as follows: i) analysis of absolute differences between observers showed that the farm manager scored lower than researchers/technicians; ii) exact matching approaches suggested fair or good agreement agreement was poorest for mild gait abnormalities (score 1 'stiff'), and agreement improved if scores were combined into 'sound' (01) and 'lame' (25) categories; and iii) measures of association suggested moderate agreement. Inter-observer reliability improved over time until the 5th scoring event. To improve inter-observer agreement, observer training/practice and the use of fewer categories are recommended, and inter-observer agreement should be checked regularly.},
}

@article{Devillers2019,
    author = {Devillers, Nicolas and Janvier, Emmanuel and Delijani, Farhoud and Méthot, Steve and Dick, Kristopher J. and Zhang, Qiang and Connor, Laurie},
    year = {2019},
    title = {{Effect of Slat and Gap Width of Slatted Concrete Flooring on Sow Gait Using Kinematics Analysis}},
    doi = {10.3390/ani9050206},
    journal = {Animals},
    volume = {9},
    number = {5},
    article-number = {206},
    url = {https://www.mdpi.com/2076-2615/9/5/206},
    pubmedid = {31052233},
    issn = {2076-2615},
    abstract = {The housing of gestating sows in groups requires sound information about the adapted design of the pen floor. Slatted concrete floors are commonly used for effective drainage of manure but can cause feet injuries and lameness. In the present study, kinematics were used to characterize the gait of 12 gilts and 12 lame sows walking in a corridor on slatted concrete floors with different combinations of slat (85, 105 or 125 mm) and gap (19, 22 or 25 mm) widths. The nine experimental floors were tested with slats in the perpendicular and parallel orientation to the direction of animal walk, according to a duplicated lattice design. Gait parameters were quantified using spatial, temporal and angular kinematics for front and rear limbs. Some parameters were significantly affected by the treatments (p 0.05), but the effects differed between gilts and lame sows and between slat orientations. Gap width had a significant effect on parameters such as back angle, stride length, foot height, and carpal and tarsal joint angle amplitudes. Slat width significantly affected parameters such as foot height, and carpal and tarsal joint angle amplitudes. Comparisons of the different combinations of slat and gap widths revealed that slats with a width of 105–125 mm and gap width of 19–22 mm had the least effect on the gait characteristics of the gilts and sows.},
}

@article{DInca2011,
    author = {D’Inca, Romain and Gras-Le Guen, Christele and Che, Lianqiang and Sangild, Per T and Le Hu{\"e}rou-Luron, Isabelle},
    year = {2011},
    title = {{Intrauterine growth restriction delays feeding-induced gut adaptation in term newborn pigs}},
    doi = {10.1159/000314919},
    journal = {Neonatology},
    volume = {99},
    number = {3},
    pages = {208--216},
    publisher = {Karger Publishers},
}


@article{Douglas2014,
    author = {Douglas, S. L. and Edwards, S. A. and Kyriazakis, I.},
    year = {2014},
    title = {{Management strategies to improve the performance of low birth weight pigs to weaning and their long-term consequences1,2}},
    doi = {10.2527/jas.2013-7388},
    journal = {Journal of Animal Science},
    volume = {92},
    number = {5},
    pages = {2280-2288},
    month = {05},
    abstract = {Performance of pigs from birth to slaughter is a result of a complex interaction of factors, with the early stages of a pig's life likely to affect lifetime performance. During the preweaning stage, piglets are reliant on the sow for nutrition, and sibling competition is likely to affect growth, in particular for low birth weight (LBiW) piglets. The objective of the experiment was to determine the effect of litter composition (littermate weight) and milk supplementation during lactation on the performance of LBiW pigs to weaning and the long-term consequences of treatment to slaughter. The experiment was a 2 × 2 factorial with littermate weight (normal or LBiW) and provision of supplementary milk from d 1 to 28 (yes or no) as factors. A total of 265 piglets were selected within 24 h of birth and cross-fostered to create 2 litter types (LOW = LBiW pigs [≤1.25 kg] only and MX = both LBiW and normal birth weight pigs [1.6 to 2.0 kg]); half of the litters within a type were supplemented with milk and the other half were not. The behavior of litters given milk was recorded to identify milk consumption patterns. Piglets were weaned at d 28 and kept in their litters until d 70 and then subsequently housed in mixed groups until slaughter. No difference was observed at any stage in the ADG of pigs given access to supplementary milk or not (P 0.05) nor was there any significant interaction between milk provision and litter composition (P 0.05). However, LOW litters drank significantly more supplementary milk than MX litters (P 0.001). There was a significant effect of litter type on ADG from d 14 to 28, with LBiW pigs in LOW litters performing better than those in MX litters (0.252 versus 0.217 kg/d; P 0.05). At weaning, LBiW piglets in LOW litters weighed over 500 g more than those in MX litters (P 0.05). In MX litters there was a significant interaction between birth weight and supplementary milk on the CV of BW from d 14 to slaughter (P 0.05). In conclusion, grouping LBiW piglets with similar sized littermates preweaning can improve preweaning performance by reducing competition from heavier littermates; however, this advantage does not persist after weaning. Although supplementary milk does not improve LBiW pig performance before or after weaning, it affects their drinking behavior and can reduce the variation in the BW of LBiW piglets in mixed litters to slaughter.},
    issn = {0021-8812},
}


% ### E ###

@InProceedings{Edwards2015,
  author    = {Edwards, S.A. and Baxter, E.M.},
  booktitle = {The gestating and lactating sow},
  title     = {{Chapter 11. Piglet mortality: causes and prevention}},
  year      = {2015},
  pages     = {253-278},
  abstract  = {The evolutionary biology of the pig means that it is predisposed to produce more offspring than it is likely to rear, and this tendency has been exacerbated under farm conditions by genetic selection pressure for increased prolificacy. Piglet mortality from birth to weaning typically amounts to 16-20\%, with the major causes attributed to stillbirth, crushing and starvation. However, these ultimate causes mask the true predisposing factors, with interactive risk factors arising from the biology of the sow and piglets and the challenges of the neonatal environment. Intra-uterine competition for nutrients can result in a stillborn piglet or a live-born piglet with reduced viability, low birth weight and compromised chances for postnatal survival. Prenatal insults can impact on vigour and thermoregulatory abilities, resulting in a piglet unable to survive the challenges of asphyxia during birth, hypothermia following delivery and intense competition for colostrum. Reduction in piglet mortality requires co-ordinated genetic, nutritional, management and stockperson interventions. The incorporation of survival traits in genetic selection goals, the optimisation of maternal nutrition during breeding and gestation, and the avoidance of prenatal maternal stress through appropriate environmental conditions will promote delivery of more vital piglets and stimulate good maternal behaviour. Supervision and assistance during farrowing, with stockperson intervention to facilitate early and adequate ingestion of colostrum by all piglets, provision of appropriate thermal microclimates to reduce hypothermia, and skilful cross-fostering to ensure early establishment of litters of appropriate size and uniformity, are all key components of success. With an increasing societal focus on the ethical and welfare issues in pig production, but no alleviation of the financial pressures on pig farmers to remain competitive, the requirement to achieve a high number of piglets weaned per sow per year in an environment allowing adequate expression of sow behavioural needs will continue to pose challenges.},
  chapter   = {11},
  doi       = {10.3920/978-90-8686-803-2_11},
  url       = {https://www.wageningenacademic.com/doi/abs/10.3920/978-90-8686-803-2_11},
}


% ### F ###
@article{Farmer2021,
    author = {Farmer, C. and Edwards, S.A.},
    year = {2021},
    title = {{Review: Improving the performance of neonatal piglets}},
    doi = {10.1016/j.animal.2021.100350},
    journal = {Animal},
    pages = {100350},
    issn = {1751-7311},
    url = {https://www.sciencedirect.com/science/article/pii/S1751731121001932},
    keywords = {Gestation, Lactation, Management, Mortality, Sow},
    abstract = {Newborn piglets have a high incidence of preweaning mortality that is not only associated with low birth weights but also with the presence of intra-uterine growth-restricted (IUGR) piglets. Such IUGR piglets are commonly seen in litters from hyperprolific sows as a result of insufficient placental transfer of nutrients. Nutritional strategies can be used prior to and during gestation to enhance foetal development and can also be implemented in the transition period to reduce the duration of farrowing and increase colostrum yield. Recent findings showed that the energy status of sows at the onset of farrowing is crucial to diminish stillbirth rate. Newborn piglets often fail to consume enough colostrum to promote thermostability and subsequent growth, and this is particularly problematic in very large litters when there are fewer available teats than the number of suckling piglets. One injection of 75 IU of oxytocin approximately 14 h after farrowing can prolong the colostral phase, hence increasing the supply of immunoglobulins to piglets. Nevertheless, assistance must be provided to piglets after birth in order to increase their chance of survival. Various approaches can be used, such as: (1) optimising the farrowing environment, (2) supervising farrowing and assisting newborn piglets, (3) using cross-fostering techniques, (4) providing nurse sows, and 5) providing artificial milk. Although research advances have been made in developing feeding and management strategies for sows that increase performance of their newborn piglets, much work still remains to be done to ensure that maximal outcomes are achieved.}
}


@article{Feldpausch2019,
    author = {Feldpausch, Julie A and Jourquin, Jan and Bergstrom, Jon R and Bargen, Jason L and Bokenkroger, Courtney D and Davis, Duane L and Gonzalez, John M and Nelssen, Jim L and Puls, Christopher L and Trout, William E and Ritter, Matthew J},
    year = {2019},
    title = {{Birth weight threshold for identifying piglets at risk for preweaning mortality}},
    doi = {10.1093/tas/txz076},
    journal = {Translational Animal Science},
    volume = {3},
    number = {2},
    pages = {633-640},
    month = {06},
    issn = {2573-2102},
    abstract = {Several studies have suggested there is a critical relationship between piglet birth weight and preweaning mortality. Thus, the objective of the current work was to identify a birth weight threshold value for preweaning mortality. Birth weight and survival data from two studies involving a combined total of 4,068 piglets from 394 litters on four commercial farms (three European, one U.S.) were compiled for a pooled, multistudy analysis. Overall preweaning mortality across the two studies was 12.2\%. Key variables used in the analysis were piglet birth weight (measured within 24 h of birth) and corresponding survival outcome (dead or live) by weaning at 3–4 wk of age. A mixed effects logistic regression model was fit to estimate the relationship between preweaning mortality and birth weight. A random effect of study was included to account for overall differences in mortality between the two studies. A piecewise linear predictor was selected to best represent the drastic decrease in preweaning mortality found as birth weight increased in the range of 0.5–1.0 kg and the less extreme change in weight above 1.0 kg. The change point of the birth weight and preweaning mortality model was determined by comparing model fit based on maximizing the likelihood over the interval ranging from 0.5 to 2.3 kg birth weight. Results from the analysis showed a curvilinear relationship between birth weight and preweaning mortality where the birth weight change point value or threshold value was 1.11 kg. In the combined data set, 15.2\% of pigs had birth weights ≤1.11 kg. This subpopulation of pigs had a 34.4\% preweaning mortality rate and represented 43\% of total preweaning mortalities. These findings imply interventions targeted at reducing the incidence of piglets with birth weights ≤1.11 kg have potential to improve piglet survivability. Additional research is needed to validate 1.11 kg as the birth weight threshold for increased risk of preweaning mortality.},
}

@article{FernandezCarrion2017,
    author = {Fern\'andez-Carri\'on, Eduardo and Mart\'inez-Avil\'es, Marta and Ivorra, Benjamin and Mart\'inez-L\'opez, Beatriz and Ramos, \'Angel Manuel and S\'anchez-Vizca\'ino, Jos\'e Manuel},
    year = {2017},
    title = {{Motion-based video monitoring for early detection of livestock diseases: The case of African swine fever}},
    doi = {10.1371/journal.pone.0183793},
    journal = {{PLOS ONE}},
    publisher = {Public Library of Science},
    month = {09},
    volume = {12},
    pages = {1-13},
    abstract = {Early detection of infectious diseases can substantially reduce the health and economic impacts on livestock production. Here we describe a system for monitoring animal activity based on video and data processing techniques, in order to detect slowdown and weakening due to infection with African swine fever (ASF), one of the most significant threats to the pig industry. The system classifies and quantifies motion-based animal behaviour and daily activity in video sequences, allowing automated and non-intrusive surveillance in real-time. The aim of this system is to evaluate significant changes in animals’ motion after being experimentally infected with ASF virus. Indeed, pig mobility declined progressively and fell significantly below pre-infection levels starting at four days after infection at a confidence level of 95%. Furthermore, daily motion decreased in infected animals by approximately 10% before the detection of the disease by clinical signs. These results show the promise of video processing techniques for real-time early detection of livestock infectious diseases.},
    number = {9},
}

@article{Figueiredo2018,
    author = {Figueiredo, Joana and Santos, Cristina P. and Moreno, Juan C.},
    year = {2018},
    title = {{Automatic recognition of gait patterns in human motor disorders using machine learning: A review}},
    doi = {10.1016/j.medengphy.2017.12.006},
    journal = {Medical Engineering \& Physics},
    volume = {53},
    pages = {1-12},
    issn = {1350-4533},
    url = {https://www.sciencedirect.com/science/article/pii/S1350453318300043},
    keywords = {Lower limb motor disorders, Human gait pattern recognition, Machine learning approaches, Dimensional data reduction},
    abstract = {automatic recognition of human movement is an effective strategy to assess abnormal gait patterns. Machine learning approaches are mainly applied due to their ability to work with multidimensional nonlinear features. to compare several machine learning algorithms employed for gait pattern recognition in motor disorders using discriminant features extracted from gait dynamics. Additionally, this work highlights procedures that improve gait recognition performance. we conducted an electronic literature search on Web of Science, IEEE, and Scopus, using “human recognition”, “gait patterns’’, and “feature selection methods” as relevant keywords. analysis of the literature showed that kernel principal component analysis and genetic algorithms are efficient at reducing dimensional features due to their ability to process nonlinear data and converge to global optimum. Comparative analysis of machine learning performance showed that support vector machines (SVMs) exhibited higher accuracy and proper generalization for new instances. automatic recognition by combining dimensional data reduction, cross-validation and normalization techniques with SVMs may offer an objective and rapid tool for investigating the subject's clinical status. Future directions comprise the real-time application of these tools to drive powered assistive devices in free-living conditions.},
}

@article{Frick1996,
    author = {Frick, Robert W.},
    year = {1996},
    title = {{The appropriate use of null hypothesis testing.}},
    doi = {10.1037/1082-989X.1.4.379},
    journal = {Psychological Methods},
    volume = {1},
    number = {4},
    pages = {379},
    publisher = {American Psychological Association},
}


% ### G ###
@article{Ganley2005,
    author = {Ganley, Kathleen J. and Powers, Christopher M.},
    year = {2005},
    title = {{Gait kinematics and kinetics of 7-year-old children: a comparison to adults using age-specific anthropometric data}},
    doi = {10.1016/j.gaitpost.2004.01.007},
    journal = {Gait \& Posture},
    volume = {21},
    number = {2},
    pages = {141-145},
    issn = {0966-6362},
    url = {https://www.sciencedirect.com/science/article/pii/S0966636204000220},
    keywords = {Gait, Pediatrics, Anthropometry, Kinetics, Kinematics},
    abstract = {The purpose of this study was to determine if sagittal plane gait kinematics and kinetics of 7-year-old children differed from those of adults when age-specific anthropometrics were used in the calculations. Joint angles, moments, and power obtained during level walking in 7-year-old children (n=15) were compared to data from adults (n=15). Calculations were performed using age-specific anthropometric data obtained from dual energy X-ray absorptiometry. For most of the variables examined, 7-year-olds were similar to adults, however children demonstrated a diminished peak plantarflexor moment and less peak power absorption and generation at the ankle during late stance. These results provide support for the hypothesis that children lack the neuromuscular maturity, especially at the ankle, to produce an adult-like gait pattern.},
}

@article{Gomez2021,
    author = {Gómez, Yaneth and Stygar, Anna H. and Boumans, Iris J. M. M. and Bokkers, Eddie A. M. and Pedersen, Lene J. and Niemi, Jarkko K. and Pastell, Matti and Manteca, Xavier and Llonch, Pol},
    year = {2021},
    doi = {10.3389/fvets.2021.660565},
    title = {A Systematic Review on Validated Precision Livestock Farming Technologies for Pig Production and Its Potential to Assess Animal Welfare},
    journal = {Frontiers in Veterinary Science},
    volume = {8},
    url = {https://www.frontiersin.org/articles/10.3389/fvets.2021.660565},
    issn = {2297-1769},
    abstract = {Several precision livestock farming (PLF) technologies, conceived for optimizing farming processes, are developed to detect the physical and behavioral changes of animals continuously and in real-time. The aim of this review was to explore the capacity of existing PLF technologies to contribute to the assessment of pig welfare. In a web search for commercially available PLF for pigs, 83 technologies were identified. A literature search was conducted, following systematic review guidelines (PRISMA), to identify studies on the validation of sensor technologies for assessing animal-based welfare indicators. Two validation levels were defined: internal (evaluation during system building within the same population that were used for system building) and external (evaluation on a different population than during system building). From 2,463 articles found, 111 were selected, which validated some PLF that could be applied to the assessment of animal-based welfare indicators of pigs (7\% classified as external, and 93\% as internal validation). From our list of commercially available PLF technologies, only 5\% had been externally validated. The more often validated technologies were vision-based solutions (n = 45), followed by load-cells (n = 28; feeders and drinkers, force plates and scales), accelerometers (n = 14) and microphones (n = 14), thermal cameras (n = 10), photoelectric sensors (n = 5), radio-frequency identification (RFID) for tracking (n = 2), infrared thermometers (n = 1), and pyrometer (n = 1). Externally validated technologies were photoelectric sensors (n = 2), thermal cameras (n = 2), microphone (n = 1), load-cells (n = 1), RFID (n = 1), and pyrometer (n = 1). Measured traits included activity and posture-related behavior, feeding and drinking, other behavior, physical condition, and health. In conclusion, existing PLF technologies are potential tools for on-farm animal welfare assessment in pig production. However, validation studies are lacking for an important percentage of market available tools, and in particular research and development need to focus on identifying the feature candidates of the measures (e.g., deviations from diurnal pattern, threshold levels) that are valid signals of either negative or positive animal welfare. An important gap identified are the lack of technologies to assess affective states (both positive and negative states).},
}


@article{Guesgen2017,
    author = {Guesgen, M.J. and Bench, C.J.},
    year = {2017},
    title = "{{What can kinematics tell us about the affective states of animals?}}",
    doi = {10.7120/09627286.26.4.383},
    journal = {Animal Welfare},
    volume = {26},
    pages = {383--397},
}

% ### H ###
@article{Hales2013,
    author = {Hales, J. and Moustsen, V. A. and Nielsen, M. B. F. and Hansen, C. F.},
    year = {2013},
    title = {{Individual physical characteristics of neonatal piglets affect preweaning survival of piglets born in a noncrated system}},
    doi = {10.2527/jas.2012-5740},
    journal = {Journal of Animal Science},
    volume = {91},
    number = {10},
    pages = {4991-5003},
    month = {10},
    issn = {0021-8812},
    abstract = {The aim of this study was to investigate the effects of individual physical characteristics on preweaning survival and growth of piglets born in a noncrate system. Data were collected from 3,402 neonatal piglets from 203 Landrace × Yorkshire sows housed in noncrate pens in a commercial Danish sow herd. Piglets were categorized into groups according to their survivability: surviving to weaning (SURV), stillborn (STILL), or dead between birth and weaning (DBW), which was subdivided into dead d 0 to 1 after farrowing (DEAD1) or dead d 2 to 26 after farrowing (DEAD26). Linear models were used to determine which physical characteristics affected survivability and growth of piglets. Results showed that characteristics related to the individual piglets had a greater degree of explanatory power in relation to survival than variables related to the sow. Survival of piglets increased if piglets were females (P 0.001), had a greater body mass index (P 0.001), and were born to sows of parity 3 or more (P = 0.017). Piglets with a greater birth weight were more likely to survive (P 0.001), but birth weight was inferior to body mass index in explaining differences between SURV and DBW. Piglets that died 2 to 26 d after birth had a lower birth weight (P 0.001), were born to sows of parity 1 or 2 (P = 0.014), and were born after a shorter gestation (P = 0.011) compared with SURV. Piglets that died on d 0 to 1 after birth had a lower body mass index (P 0.001), displayed a greater degree of growth restriction (P = 0.004), and were born in large litters (P = 0.005). The gender of the piglets affected survivability at both d 0 to 1 (P 0.001) and d 2 to 26 (P 0.001). Piglets in DEAD1 differed from STILL by having a shorter crown to rump length (P 0.001), a birth weight that deviated more from the mean weight of the litter (P = 0.001), and being more likely to be born before d 116 of gestation (P = 0.008). The only physical characteristic that was important for growth performance in the suckling period was birth weight (P 0.001), yet using only birth weight as an indicator for survivability was too simplistic. The results of this study emphasize that individual characteristics of neonatal piglets could serve as indicators of survivability of piglets born in noncrate systems; however, the results suggest that the importance of characteristics differed in different periods of the preweaning period.},
}

@article{Hof1996,
    author = {Hof, At L.},
    year = {1996},
    title = {{Scaling gait data to body size}},
    doi = {10.1016/0966-6362(95)01057-2},
    journal = {Gait \& Posture},
    volume = {4},
    number = {3},
    pages = {222-223},
    issn = {0966-6362},
    url = {https://www.sciencedirect.com/science/article/pii/0966636295010572},
}

@article{Howson2017,
    author = {Howson, E.L.A. and Soldan, A. and Webster, K. and Beer, M. and Zientara, S. and Belak, S. and Sanchez-Vizcaino, J.M. and Van Borm, S. and King, D.P. and Fowler, V.L.},
    year = {2017},
    title = {Technological advances in veterinary diagnostics: Opportunities to deploy rapid decentralised tests to detect pathogens affecting livestock},
    doi = {10.20506/rst.36.2.2668},
    journal = {Rev Sci Tech Off Int Epiz},
    volume = {36},
    number = {2},
    pages = {479--498},
}

@article{Hutchinson2006,
    author = {Hutchinson, John R. and Schwerda, Delf and Famini, Daniel J. and Dale, Robert H. I. and Fischer, Martin S. and Kram, Rodger},
    year = {2006},
    title = {{The locomotor kinematics of Asian and African elephants: changes with speed and size}},
    doi = {10.1242/jeb.02443},
    journal = {Journal of Experimental Biology},
    volume = {209},
    number = {19},
    pages = {3812-3827},
    month = {10},
    abstract = {For centuries, elephant locomotion has been a contentious and confusing challenge for locomotion scientists to understand, not only because of technical difficulties but also because elephant locomotion is in some ways atypical of more familiar quadrupedal gaits. We analyzed the locomotor kinematics of over 2400 strides from 14 African and 48 Asian elephant individuals (body mass 116-4632 kg) freely moving over ground at a 17-fold range of speeds, from slow walking at 0.40 m s-1 to the fastest reliably recorded speed for elephants, 6.8 m s-1. These data reveal that African and Asian elephants have some subtle differences in how size-independent kinematic parameters change with speed. Although elephants use a lateral sequence footfall pattern, like many other quadrupeds, they maintain this footfall pattern at all speeds, shifting toward a 25\% phase offset between limbs (singlefoot) as they increase speed. The duty factors of elephants are greater for the forelimbs than for the hindlimbs, so an aerial phase for the hindquarters is reached at slower speeds than for the forequarters. This aerial phase occurs at a Froude number of around 1,matching theoretical predictions. At faster speeds, stance and swing phase durations approach asymptotes, with the duty factor beginning to level off,concurrent with an increase in limb compliance that likely keeps peak forces relatively low. This increase of limb compliance is reflected by increased compression of the hindlimbs. Like other tetrapods, smaller elephants are relatively more athletic than larger ones, but still move very similarly to adults even at \\&lt;500 kg. At any particular speed they adopt greater relative stride frequencies and relative stride lengths compared to larger elephants. This extends to near-maximal locomotor performance as well - smaller elephants reach greater Froude numbers and smaller duty factors, hence likely reach relatively greater peak loads on their limbs and produce this force more rapidly. A variety of lines of kinematic evidence support the inference that elephants change their mechanics near a Froude number of 1 (if not at slower speeds), at least to using more compliant limbs, if not spring-like whole-body kinetics. In some ways, elephants move similarly to many other quadrupeds,such as increasing speed mainly by increasing stride frequency (except at fast speeds), and they match scaling predictions for many stride parameters. The main difference from most other animals is that elephants never change their footfall pattern to a gait that uses a whole-body aerial phase. Our large dataset establishes what the normal kinematics of elephant locomotion are, and can also be applied to identify gait abnormalities that may signal musculoskeletal pathologies, a matter of great importance to keepers of captive elephants.},
    issn = {0022-0949},
}


% ### I ###
@article{Irschick1999,
    author = {Irschick, D.J. and Jayne, B.C.},
    year = {1999},
    title = {{Comparative three-dimensional kinematics of the hindlimb for high-speed bipedal and quadrupedal locomotion of lizards}},
    doi = {10.1242/jeb.202.9.1047},
    journal = {Journal of Experimental Biology},
    volume = {202},
    number = {9},
    pages = {1047-1065},
    month = {05},
    abstract = {{Although lizards have been model organisms for testing locomotor performance and in ecomorphological studies, the limb movements of lizards during high-speed locomotion are poorly understood. Thus, we quantified the three-dimensional kinematics of the hindlimb, body and tail for five morphologically distinct species of lizard during steady-speed locomotion near maximum sprinting speed (2–5 m s-1). The kinematics of different species had little multivariate overlap. More than half of the strides of all species had digitigrade foot posture, but the frequency of using digitigrade foot posture varied among species. The combination of digitigrade foot posture and large foot size of the lizards contributed substantially to the high values of hip height. For each species, different suites of kinematic variables distinguished bipedal from quadrupedal strides. Interspecific morphological variation did not correspond globally to variation in kinematics, although lizard species with elongated hindlimbs took longer strides than species with shorter hindlimbs. The Froude numbers and relative stride lengths of all lizards running near maximal speeds were large compared with those reported previously for other vertebrates.}},
    issn = {0022-0949},
}



% ### J ###
@article{Jackson2016,
    author = {Jackson, Brandon E. and Evangelista, Dennis J. and Ray, Dylan D. and Hedrick, Tyson L.},
    year = {2016},
    title = {{3D for the people: multi-camera motion capture in the field with consumer-grade cameras and open source software}},
    journal = {Biology Open},
    volume = {5},
    number = {9},
    pages = {1334-1342},
    month = {07},
    issn = {2046-6390},
    doi = {10.1242/bio.018713},
    abstract = {Ecological, behavioral and biomechanical studies often need to quantify animal movement and behavior in three dimensions. In laboratory studies, a common tool to accomplish these measurements is the use of multiple, calibrated high-speed cameras. Until very recently, the complexity, weight and cost of such cameras have made their deployment in field situations risky; furthermore, such cameras are not affordable to many researchers. Here, we show how inexpensive, consumer-grade cameras can adequately accomplish these measurements both within the laboratory and in the field. Combined with our methods and open source software, the availability of inexpensive, portable and rugged cameras will open up new areas of biological study by providing precise 3D tracking and quantification of animal and human movement to researchers in a wide variety of field and laboratory contexts.},
}



% ### K ###
@article{Karashchuk2021,
    author = {Karashchuk, Pierre and Rupp, Katie L. and Dickinson, Evyn S. and Walling-Bell, Sarah and Sanders, Elischa and Azim, Eiman and Brunton, Bingni W. and Tuthill, John C.},
    year = {2021},
    title = {{Anipose: A toolkit for robust markerless 3D pose estimation}},
    journal = {Cell Reports},
    volume = {36},
    number = {13},
    pages = {109730},
    issn = {2211-1247},
    doi = {10.1016/j.celrep.2021.109730},
    url = {https://www.sciencedirect.com/science/article/pii/S2211124721011797},
    keywords = {pose estimation, robust tracking, markerless tracking, behavior, 3D, deep learning, camera calibration, visualization, Drosophila joint rotation, neuroscience},
    abstract = {Quantifying movement is critical for understanding animal behavior. Advances in computer vision now enable markerless tracking from 2D video, but most animals move in 3D. Here, we introduce Anipose, an open-source toolkit for robust markerless 3D pose estimation. Anipose is built on the 2D tracking method DeepLabCut, so users can expand their existing experimental setups to obtain accurate 3D tracking. It consists of four components: (1) a 3D calibration module, (2) filters to resolve 2D tracking errors, (3) a triangulation module that integrates temporal and spatial regularization, and (4) a pipeline to structure processing of large numbers of videos. We evaluate Anipose on a calibration board as well as mice, flies, and humans. By analyzing 3D leg kinematics tracked with Anipose, we identify a key role for joint rotation in motor control of fly walking. To help users get started with 3D tracking, we provide tutorials and documentation at \nolinkurl{http://anipose.org}.},
}


% ### L ###
@article{Lamy2012,
    author = {Lamy, Elsa and Mau, Marcus},
    year = {2012},
    title = {{Saliva proteomics as an emerging, non-invasive tool to study livestock physiology, nutrition and diseases}},
    doi = {10.1016/j.jprot.2012.05.007},
    journal = {Journal of Proteomics},
    volume = {75},
    number = {14},
    pages = {4251-4258},
    note = {Special Issue: Farm Animal Proteomics},
    issn = {1874-3919},
    url = {https://www.sciencedirect.com/science/article/pii/S1874391912002953},
    keywords = {Farm animals, Nutrition, Proteomics, Ruminants, Saliva},
    abstract = {Saliva is an extraordinary fluid in terms of research and diagnostic possibilities. Its composition in electrolytes, hormones and especially its proteome contains information about feeding status, nutritional requirements and adaptations to diet and environment, and also about health status of animals. It is easy to collect on a non-invasive and routine basis without any need for special training. Therefore, the analysis of salivary proteomes is going to emerge into a field of high interest with the future goal to maintain and improve livestock productivity and welfare. Moreover, the comprehensive analysis and identification of salivary proteins and peptides in whole and glandular saliva is a necessary pre-requisite to identify animal disease biomarkers and a powerful tool to better understand animal physiology. This review focuses on the different approaches used to study the salivary proteomes of farm animals, in respect to the physiology of nutrition and food perception in relation to food choices. The potential of animal saliva as a source of disease biomarkers will also be pointed out. Special emphasis is laid on the ‘ruminating triad’ – cattle, goat and sheep – as well as swine as major species of animal production in Western and Southern Europe. This article is part of a Special Issue entitled: Farm animal proteomics.}
}

@article{LaVallee2020,
    author = {LaVallee, Katherine T. and Maus, Timothy P. and Stock, Joseph D. and Stalder, Kenneth J. and Karriker, Locke A. and Murthy, Naveen S. and Kanwar, Rahul and Beutler, Andrea S. and Unger, Mark D.},
    year = {2020},
    title = {{Quantitation of Gait and Stance Alterations Due to Monosodium Iodoacetate--induced Knee Osteoarthritis in Yucatan Swine}},
    doi = {10.30802/AALAS-CM-19-000075},
    journal = {Comparative medicine},
    volume = {70},
    number = {3},
    pages = {248--257},
    publisher = {American Association for Laboratory Animal Science},
}

@article{LeDividich2017,
    author = {Le Dividich, Jean and Charneca, Rui and Thomas, Francoise},
    year = {2017},
    title = {{Relationship between birth order, birth weight, colostrum intake, acquisition of passive immunity and pre-weaning mortality of piglets}},
    doi = {10.5424/sjar/2017152-9921},
    journal = {Spanish Journal of Agricultural Research},
    volume = {15},
    number = {2},
    pages = {e0603},
    url = {https://hal.archives-ouvertes.fr/hal-01592224},
    keywords = {birth weight ; immunoglobulin g ; survival ; mortality ; Neonatal pig ; Colostrum consumption ; sucking pig ; porcelet ; p{\'e}riode neonatale ; immunoglobuline g ; survie ; colostrum ; mortalit{\'e} ; poids {\`a} la naissance},
    hal_id = {hal-01592224},
    hal_version = {v1},
}

@article{Litten2003,
    author = {Litten, JC and Drury, PC and Corson, AM and Lean, IJ and Clarke, L},
    year = {2003},
    title = {{The influence of piglet birth weight on physical and behavioural development in early life}},
    doi = {10.1159/000073640},
    journal = {Neonatology},
    volume = {84},
    number = {4},
    pages = {311--318},
    publisher = {Karger Publishers},
}


% ### M ###
@article{Marchant2000,
    author = {Marchant, J. N. and Rudd, A. R. and Mendl, M. T. and Broom, D. M. and Meredith, M. J. and Corning, S. and Simmins, P. H.},
    year = {2000},
    title = {Timing and causes of piglet mortality in alternative and conventional farrowing systems},
    doi = {10.1136/vr.147.8.209},
    journal = {Veterinary Record},
    volume = {147},
    number = {8},
    pages = {209-214},
    url = {https://bvajournals.onlinelibrary.wiley.com/doi/abs/10.1136/vr.147.8.209},
    abstract = {The causes and timing of piglet mortality were studied in different farrowing systems. In the first experiment 198 litters were recorded in three systems, two of which allowed the sows to move freely, and the third restricted them in conventional crates. More piglets were weaned from the conventional crates than from the open systems and they grew more quickly. More than half the liveborn mortality occurred during the first four days after parturition. In the open systems, 17 per cent and 14 per cent of the piglets born alive were crushed, compared with only 8 per cent in the crates. In the second experiment, 29 sows and litters were studied in detail in a communal pen system during the first seven days of lactation. Three-quarters of the liveborn mortality was due to crushing. The total number of piglets dying per litter, including stillbirths, was significantly associated with the total litter size and the sow's parity. The percentage livebom mortality was significantly associated with the parity and body length of the sows and with the within-litter variation in the birth weight of the piglets. Individual birth weight was closely associated with percentage survival. Only 28 per cent of piglets weighing less than 1.1 kg at birth survived to seven days.},
}

@article{Mathis2020,
    author = {Mathis, Alexander and Schneider, Steffen and Lauer, Jessy and Mathis, Mackenzie Weygandt},
    year = {2020},
    title = {{A Primer on Motion Capture with Deep Learning: Principles, Pitfalls, and Perspectives}},
    journal = {Neuron},
    volume = {108},
    number = {1},
    pages = {44-65},
    issn = {0896-6273},
    doi = {10.1016/j.neuron.2020.09.017},
    url = {https://www.sciencedirect.com/science/article/pii/S0896627320307170},
    abstract = {Extracting behavioral measurements non-invasively from video is stymied by the fact that it is a hard computational problem. Recent advances in deep learning have tremendously advanced our ability to predict posture directly from videos, which has quickly impacted neuroscience and biology more broadly. In this primer, we review the budding field of motion capture with deep learning. In particular, we will discuss the principles of those novel algorithms, highlight their potential as well as pitfalls for experimentalists, and provide a glimpse into the future.},
}

@book{Maxwell2017,
    author={Maxwell, Scott E and Delaney, Harold D and Kelley, Ken},
    year={2017},
    title={{Designing Experiments and Analyzing Data: a Model Comparison Perspective}},
    doi={10.4324/9781315642956},
    publisher={{Routledge, New York}},
    keywords={Behavioral Sciences, Education, Health and Social Care, Mathematics \& Statistics, Social Sciences},
    isbn={9781315642956},
}

@article{McHenry2023,
    author = {McHenry, Matthew J. and Hedrick, Tyson L.},
    year = {2023},
    title = {{The science and technology of kinematic measurements in a century of Journal of Experimental Biology}},
    doi = {10.1242/jeb.245147},
    journal = {Journal of Experimental Biology},
    volume = {226},
    number = {Suppl1},
    pages = {jeb245147},
    month = {01},
    abstract = {{Kinematic measurements have been essential to the study of comparative biomechanics and offer insight into relationships between technological development and scientific progress. Here, we review the 100 year history of kinematic measurements in Journal of Experimental Biology (JEB) through eras that used film, analog video and digital video, and approaches that have circumvented the use of image capture. This history originated with the career of Sir James Gray and has since evolved over the generations of investigators that have followed. Although some JEB studies have featured technological developments that were ahead of their time, the vast majority of research adopted equipment that was broadly available through the consumer or industrial markets. We found that across eras, an emphasis on high-speed phenomena outpaced the growth of the number of articles published by JEB and the size of datasets increased significantly. Despite these advances, the number of species studied within individual reports has not differed significantly over time. Therefore, we find that advances in technology have helped to enable a growth in the number of JEB studies that have included kinematic measurements, contributed to an emphasis on high-speed phenomena, and yielded biomechanical studies that are more data rich, but are no more comparative now than in previous decades.}},
    issn = {0022-0949},
}

@article{Meijer2014,
    author = {Meijer, Ellen and Bertholle, Christian P and Oosterlinck, Maarten and van der Staay, Franz Josef and Back, Willem and van Nes, Arie},
    year = {2014},
    title = {{Pressure mat analysis of the longitudinal development of pig locomotion in growing pigs after weaning}},
    doi = {10.1186/1746-6148-10-37},
    journal = {BMC veterinary research},
    volume = {10},
    number = {1},
    pages = {1--11},
    publisher = {Springer},
}

@article{Michelini2020,
    author = {Michelini, Alexandria and Eshraghi, Arezoo and Andrysek, Jan},
    year = {2020},
    title = {{Two-dimensional video gait analysis: A systematic review of reliability, validity, and best practice considerations}},
    doi = {10.1177/030936462092129},
    journal = {Prosthetics and Orthotics International},
    volume = {44},
    number = {4},
    pages = {245--262},
    publisher = {SAGE Publications Sage UK: London, England}
}

@article{Mielke2018,
    author = {Mielke, Falk and Schunke, Vivian and Wölfer, Jan and Nyakatura, John A.},
    year = {2018},
    title = "{{Motion analysis of non-model organisms using a hierarchical model: Influence of setup enclosure dimensions on gait parameters of Swinhoe’s striped squirrels as a test case}}",
    doi = {10.1016/j.zool.2018.05.009},
    journal = {Zoology},
    volume = {129},
    pages = {35-44},
    issn = {0944-2006},
    url = {https://www.sciencedirect.com/science/article/pii/S0944200617302520},
    keywords = {Motion analysis, , Generalized linear model, Bayesian statistics, PyMC3},
    abstract = {In in-vivo motion analyses, data from a limited number of subjects and trials is used as proxy for locomotion properties of entire populations, yet the inherent hierarchy of the individual and population level is usually not accounted for. Despite the increasing availability of hierarchical model frameworks for statistical analyses, they have not been applied extensively to comparative motion analysis. As a case study for the use of hierarchical models, we analyzed locomotor parameters of four Swinhoe’s striped squirrels. The small-bodied arboreal mammals exhibit brief bouts of rapid asymmetric gaits. Spatio-temporal parameters on runways with experimentally varied dimensions of the setup enclosure were compared to test for their potentially confounding effects. We applied principal component analysis to evaluate changes to the overall locomotor pattern. A common, non-hierarchical, pooled statistical analysis of the data revealed significant differences in some of the parameters depending on enclosure dimensions. In contrast, we used a hierarchical Bayesian generalized linear model (GLM) that considers subject specific differences and population effects to compare the effect of enclosure dimensions on the measured parameters and the principal components. None of the population effects were confirmed by the hierarchical GLM. The confounding effect of a single subject that deviates in its locomotor behavior is potentially bigger than the influence of the experimental variation in enclosure dimensions. Our findings justify the common practice of researchers to intuitively select an enclosure with dimensions assumed as “non-constraining”. Hierarchical models can easily be designed to cope with limited sample size and bias introduced by deviating behavior of individuals. When limited data is available—a typical restriction of in-vivo motion analyses of non-model organisms—density distributions of the Bayesian GLM used here remain reliable and the hierarchical structure of the model optimally exploits all available information. We provide code to be adjusted to other research questions.},
}



@article{Mirkiani2021,
    author = {Mirkiani, Soroush and Roszko, David A. and O'Sullivan, Carly L. and Faridi, Pouria and Hu, David S. and Fang, Daniel and Everaert, Dirk G. and Toossi, Amirali and Robinson, Kevin and Mushahwar, Vivian K.},
    year = {2021},
    title = {{Overground Gait Kinematics and Muscle Activation Patterns in the Yucatan Mini Pig}},
    doi = {10.1101/2021.10.19.465020},
    journal = {bioRxiv},
    elocation-id = {2021.10.19.465020},
    publisher = {Cold Spring Harbor Laboratory},
    URL = {https://www.biorxiv.org/content/early/2021/10/20/2021.10.19.465020},
    abstract = {A growing number of spinal cord injury, neuromodulation, and cell therapy studies on porcine models, especially the Yucatan minipigs (YMPs), have been recently reported. This is due to the large similarities between human and porcine neuroanatomy and biomechanics. To assess treatment modalities and locomotor recovery in this model, there is an obvious need for detailed characterization of normative overground gait in neurologically intact YMPs. The objective of this study was to assess gait biomechanics and the effect of overground walking speed on gait parameters, kinematics, and electromyographic (EMG) activity in the hindlimb muscles of YMPs. Nine neurologically-intact adult YMPs were trained to walk overground in a straight line. Whole-body kinematics and EMG activity of hindlimb muscles were recorded and analyzed at 6 different speed ranges (0.4-0.59, 0.6-0.79, 0.8-0.99, 1.0-1.19, 1.2-1.39, and 1.4-1.6 m/s). A MATLAB program was developed to detect strides and gait events automatically from motion-captured data. Significant decreases in stride duration, stance and swing times and an increase in stride length were observed with increasing speed. A transition in gait pattern occurred at the 1.0m/s walking speed. Significant increases in the range of motion of the knee and ankle joints were observed at higher speeds. Also, the points of minimum and maximum knee and ankle joint angles occurred earlier in the gait cycle at higher speeds. The onset of EMG activity in the biceps femoris muscle occurred significantly earlier in the gait cycle with increasing speed. A comprehensive characterization of overground walking in neurologically-intact YMPs is provided. These normative measures set the basis against which the effects of future interventions on locomotor capacity in YMPs can be compared.Competing Interest StatementThe authors have declared no competing interest.},
}

@article{Muns2013,
    author = {Muns, R. and Manzanilla, E. G. and Sol, C. and Manteca, X. and Gasa, J.},
    year = {2013},
    title = {{Piglet behavior as a measure of vitality and its influence on piglet survival and growth during lactation}},
    doi = {10.2527/jas.2012-5501},
    journal = {Journal of Animal Science},
    volume = {91},
    number = {4},
    pages = {1838-1843},
    month = {04},
    issn = {0021-8812},
    abstract = {The aim of the study was to develop a vitality scoring method, based on piglet behavior and relate it to piglet growth and survival. From 21 sows (Sus scrofa), 287 piglets were used. After farrowing (d 0), piglets were weighed and tested for 4 behavioral parameters in a circular enclosure (55 cm diam.): movement capacity (M), udder stimulation (U), number of completed circles around the enclosure (NCC), and screaming (Sc). Piglets were weighed again on d 1, 2, 3, and 17. Piglet rectal temperature (RT) was recorded on d 0, 1, 2, and 3. Farrowing information of the sow was also recorded. Multiple regression analyses for survival and BW gain at weaning as dependent variables were performed. Piglet BW gain at weaning was influenced by BW at birth (P 0.001), sow parity (P = 0.024), total number of piglets born alive per sow (P 0.001), and sum of U and NCC parameters (UN; P = 0.023). Piglet survival during lactation was influenced by BW at birth (P = 0.015), UNCC parameter (P = 0.026), and RT on d 3 (P = 0.085). The sum of U and NCC parameters, in combination with BW at birth and information of the sow, might be useful to predict piglet growth survival during lactation, thus becoming a useful tool to improve piglet management during the first days of lactation. In conclusion, UNCC parameter seems to be an easy and useful way to assess piglet vitality for both scientific and commercial purposes.},
}


% ### N ###
@article{Needham2021,
    author = {Needham, Laurie and Evans, Murray and Cosker, Darren P and Wade, Logan and McGuigan, Polly M and Bilzon, James L and Colyer, Steffi L},
    year = {2021},
    title = {{The accuracy of several pose estimation methods for 3D joint centre localisation}},
    doi = {10.1038/s41598-021-00212-x},
    journal = {Scientific reports},
    volume = {11},
    number = {1},
    pages = {1--11},
    publisher = {Nature Publishing Group}
}

@article{Neethirajan2020,
    author = {Neethirajan, Suresh},
    year = {2020},
    title = {{The role of sensors, big data and machine learning in modern animal farming}},
    doi = {10.1016/j.sbsr.2020.100367},
    journal = {Sensing and Bio-Sensing Research},
    volume = {29},
    pages = {100367},
    issn = {2214-1804},
    url = {https://www.sciencedirect.com/science/article/pii/S2214180420301343},
    keywords = {Smart farming, Animal health, Well-being, Sensor systems, Precision livestock farming},
    abstract = {Ever since man began domesticating animals several thousand years ago, we have always relied on our intuition, collective knowledge, and sensory signals to make effective animal production decisions. So far, this has helped us make significant gains in animal husbandry and farming. Together the growing demand for food and the advancement in sensing technology have the potential to make animal farming more centralized, large scale and efficient. It has the potential to change animal farming as we know it. At a broader level, this paper explores the challenges and opportunities that sensor technologies present in terms of helping animal farmers produce more meat and animal products. More specifically, this paper explores the role of sensors, big data, artificial intelligence and machine learning in helping animal farmers to lower production costs, increase efficiencies, enhance animal welfare and grow more animals per hectare. It also explores the challenges and limitations of technology. The paper reviews various animal farming technology applications to understand its value in helping farmers improve animal health, increase profits and lower environmental footprint.}
}

@article{Netukova2021,
    author   = {Netukova, Slavka and Duspivova, Tereza and Tesar, Jan and Bejtic, Martin and Baxa, Monika and Ellederova, Zdenka and Szabo, Zoltan and Krupicka, Radim},
    journal  = {Journal of Veterinary Behavior},
    title    = {{Instrumented pig gait analysis: State-of-the-art}},
    year     = {2021},
    issn     = {1558-7878},
    pages    = {51-59},
    volume   = {45},
    abstract = {There are 2 main reasons why pig gait is analysed. First, assessment of a pig's health and welfare is major reason for gait analysis. Also, the pig, as a large animal model, has become important in biomedical research, especially in preclinical testing of therapeutics. Gait is an essential part of pig movement and its analysis is of great interest, especially when following the phenotype and the effectivity of treatment in pig models for movement and neurological disorders. The aim of this state-of-the-art review is 3-fold: (1) to present and summarize the current instrument base used in pig gait assessment, (2) to point out promising technologies for pig gait analysis, and (3) to outline the suitability of technology for pig gait analysis. The review encompasses 27 studies in total. We included papers published since 2010 and classified them according to which type of measurement instrument was used: 2D camera systems, 3D camera systems, force plates and pressure sensitive mats. In each category we reviewed the data acquisition systems, utilized signals and gait parameters used. An analysis of the literature showed that video-based systems and pressure sensitive mats were the most frequently used. The utilization of 3D camera systems was less common. Force plates were only used occasionally. In conclusion, despite growing interest in using inertial sensor units in movement analysis, they were missing in pig gait analysis. Along with the progress in instrumentation and its ability to produce a huge amount of information, simpler and more user-friendly tools should be developed to provide easy interpretation of the data captured by pig practitioners in the pig industry, or by scientists.},
    doi      = {10.1016/j.jveb.2021.06.006},
    keywords = {Camera system, Force plate, Pressure sensitive mat, Swine, Walking},
    url      = {https://www.sciencedirect.com/science/article/pii/S155878782100071X},
}

@article{Newell2021,
    author    = {Newell, Karl M. and Liu, Yeou-Teh},
    journal   = {Journal of Motor Behavior},
    title     = {{Collective Variables and Task Constraints in Movement Coordination, Control and Skill}},
    year      = {2021},
    number    = {6},
    pages     = {770-796},
    volume    = {53},
    abstract  = {In this paper we review studies that have identified collective variables (order parameters) in movement coordination, control and skill with emphasis on whole-body multiple joint degree of freedom (DF) tasks. Collective variables of a dynamical system have been proposed formally and informally from a diverse set of perceptual-motor tasks, from which we emphasize: bimanual coordination, locomotion (pedalo, walking, running, bicycle riding), roller ball task, static (quiet standing) and dynamic (moving on a ski-simulator) balance, grasping, and juggling. Several types of candidate collective variables have been identified, including: relative phase, frequency ratio, number of hands active in grasping, synchrony, learning rate and relative timing. There is a strong influence of the task goal in determining the collective variable that can be body or environment relative. The emergence of the task relevant collective variable is typically in the early stage of skill learning where subjects through practice adapt movement organization to realize a never previously produced movement coordination pattern. Throughout, the paper elaborates on open theoretical, experimental and analysis issues for collective variables in the context of task constraints and Bernstein’s (1967) view of skill acquisition as learning to master redundant DF.},
    doi       = {10.1080/00222895.2020.1835799},
    pmid      = {33103621},
    publisher = {Routledge},
}


@article{Nishikawa2007,
    author = {Nishikawa, Kiisa and Biewener, Andrew A. and Aerts, Peter and Ahn, Anna N. and Chiel, Hillel J. and Daley, Monica A. and Daniel, Thomas L. and Full, Robert J. and Hale, Melina E. and Hedrick, Tyson L. and Lappin, A. Kristopher and Nichols, T. Richard and Quinn, Roger D. and Satterlie, Richard A. and Szymik, Brett},
    year = {2007},
    title = {{Neuromechanics: an integrative approach for understanding motor control}},
    doi = {10.1093/icb/icm024},
    journal = {Integrative and Comparative Biology},
    volume = {47},
    number = {1},
    pages = {16-54},
    month = {05},
    issn = {1540-7063},
    abstract = {Neuromechanics seeks to understand how muscles, sense organs, motor pattern generators, and brain interact to produce coordinated movement, not only in complex terrain but also when confronted with unexpected perturbations. Applications of neuromechanics include ameliorating human health problems (including prosthesis design and restoration of movement following brain or spinal cord injury), as well as the design, actuation and control of mobile robots. In animals, coordinated movement emerges from the interplay among descending output from the central nervous system, sensory input from body and environment, muscle dynamics, and the emergent dynamics of the whole animal. The inevitable coupling between neural information processing and the emergent mechanical behavior of animals is a central theme of neuromechanics. Fundamentally, motor control involves a series of transformations of information, from brain and spinal cord to muscles to body, and back to brain. The control problem revolves around the specific transfer functions that describe each transformation. The transfer functions depend on the rules of organization and operation that determine the dynamic behavior of each subsystem (i.e., central processing, force generation, emergent dynamics, and sensory processing). In this review, we (1) consider the contributions of muscles, (2) sensory processing, and (3) central networks to motor control, (4) provide examples to illustrate the interplay among brain, muscles, sense organs and the environment in the control of movement, and (5) describe advances in both robotics and neuromechanics that have emerged from application of biological principles in robotic design. Taken together, these studies demonstrate that (1) intrinsic properties of muscle contribute to dynamic stability and control of movement, particularly immediately after perturbations; (2) proprioceptive feedback reinforces these intrinsic self-stabilizing properties of muscle; (3) control systems must contend with inevitable time delays that can simplify or complicate control; and (4) like most animals under a variety of circumstances, some robots use a trial and error process to tune central feedforward control to emergent body dynamics.},
}



% ### O ###
% ### P ###
@InProceedings{Patua2021,
    author = {Patua, Rupali and Muchhal, Tripti and Basu, Saikat},
    year = {2021},
    title = {{Gait-Based Person Identification, Gender Classification, and Age Estimation: A Review}},
    doi = {10.1007/978-981-15-6584-7\_7},
    editor = {Panigrahi, Chhabi Rani and Pati, Bibudhendu and Mohapatra, Prasant and Buyya, Rajkumar and Li, Kuan-Ching},
    booktitle = {{Progress in Advanced Computing and Intelligent Engineering}},
    publisher = {Springer Singapore},
    address = {Singapore},
    pages = {62--74},
    isbn = {978-981-15-6584-7},
    abstract = {In this era where both techniques and technology are going digital, there is a need of designing and developing such a system that automatically identifies the person and also the person's attributes with the help of the biometric system. The biometric of every person is unique. Therefore, in this context, the use of the biometric system to identify the identity of an individual is a popular approach. Gait is a biometric approach that helps to verify the identity of a person by their walking patterns. Owing to the advantages of gait as a biometric, its popularity among the researchers is amplified in recent years. In this paper, a review is represented, where several papers with different methods, have been mentioned which recognize the person and its attributes such as gender and age based on the gait of the person.},
}

@article{Pineiro2019,
    author = {Pi\~neiro, Carlos and Morales, Joaqu\'in and Rodr\'iguez, Mar\'ia and Aparicio, Mar\'ia and Manzanilla, Edgar Garc\'ia and Koketsu, Yuzo},
    year = {2019},
    title = {{Big (pig) data and the internet of the swine things: a new paradigm in the industry}},
    doi = {10.1093/af/vfz002},
    journal = {Animal Frontiers},
    volume = {9},
    number = {2},
    pages = {6-15},
    month = {04},
    issn = {2160-6056},
}


% ### Q ###
@article{Qiao2021,
    author = {Qiao, Yongliang and Kong, He and Clark, Cameron and Lomax, Sabrina and Su, Daobilige and Eiffert, Stuart and Sukkarieh, Salah},
    year = {2021},
    title = {{Intelligent Perception-Based Cattle Lameness Detection and Behaviour Recognition: A Review}},
    doi = {10.3390/ani11113033},
    journal = {Animals},
    volume = {11},
    number = {11},
    article-number = {3033},
    url = {https://www.mdpi.com/2076-2615/11/11/3033},
    issn = {2076-2615},
    abstract = {The growing world population has increased the demand for animal-sourced protein. However, animal farming productivity is faced with challenges from traditional farming practices, socioeconomic status, and climate change. In recent years, smart sensors, big data, and deep learning have been applied to animal welfare measurement and livestock farming applications, including behaviour recognition and health monitoring. In order to facilitate research in this area, this review summarises and analyses some main techniques used in smart livestock farming, focusing on those related to cattle lameness detection and behaviour recognition. In this study, more than 100 relevant papers on cattle lameness detection and behaviour recognition have been evaluated and discussed. Based on a review and a comparison of recent technologies and methods, we anticipate that intelligent perception for cattle behaviour and welfare monitoring will develop towards standardisation, a larger scale, and intelligence, combined with Internet of things (IoT) and deep learning technologies. In addition, the key challenges and opportunities of future research are also highlighted and discussed.},
}

% ### R ###
@article{Riley2020,
    author = {Riley, Richard D and Ensor, Joie and Snell, Kym I E and Harrell, Frank E and Martin, Glen P and Reitsma, Johannes B and Moons, Karel G M and Collins, Gary and van Smeden, Maarten},
    year = {2020},
    title = {{Calculating the sample size required for developing a clinical prediction model}},
    doi = {10.1136/bmj.m441},
    journal = {BMJ},
    volume = {368},
    publisher = {BMJ Publishing Group Ltd},
    URL = {https://www.bmj.com/content/368/bmj.m441},
}

@article{Roehe2000,
    author = {Roehe, R. and Kalm, E.},
    year = {2000},
    title = {{Estimation of genetic and environmental risk factors associated with pre-weaning mortality in piglets using generalized linear mixed models}},
    doi = {10.1017/S1357729800054692},
    journal = {Animal Science},
    volume = {70},
    number = {2},
    pages = {227–240},
    publisher = {Cambridge University Press},
}


@article{Roelofs2019,
    author = {Roelofs, Sanne and Meijer, Ellen and Baas, Valesca and Dobrovolski, Mark and van der Staay, Franz Josef and Nordquist, Rebecca E.},
    year = {2019},
    title = {{Neurological functioning and fear responses in low and normal birth weight piglets}},
    doi = {10.1016/j.applanim.2019.104853},
    journal = {Applied Animal Behaviour Science},
    volume = {220},
    pages = {104853},
    issn = {0168-1591},
    url = {https://www.sciencedirect.com/science/article/pii/S0168159118305045},
    keywords = {Pigs, Birth weight, Neurological development, Neurological examination, Human approach test, Emotion},
    abstract = {Low birth weight (LBW) piglets are an increasingly common occurrence on commercial pig farms, due to selection for sow fecundity. In humans, LBW is a known risk factor for impaired brain development, resulting in impaired neurological functioning and increased vulnerability to stressors. In pigs, the pre-weaning effects of LBW on neurological and emotional functioning are less well known. To assess neurological development, 60 LBW and 60 normal birth weight (NBW) piglets were subjected to a neurological examination at day one after birth. To assess fear responses, another 60 LBW-NBW pairs were compared in a human approach test (HAT) at three weeks of age. In the neurological exam, neonatal LBW piglets were found to be less likely to display a withdrawal reflex in response to a painful stimulus (P = 0.022) and showed impaired coordination during locomotion on a balance beam (P  =  0.030). These findings suggest LBW piglets’ increased neonatal mortality, often due to an impaired ability to compete over food or avoid crushing by the sow, could be influenced by a delayed neuromotor development. No effects of birth weight were found on behavioral responses in the HAT, such as latency to approach an unfamiliar human and rate of vocalizations. This suggests LBW and NBW piglets have similar levels of fear in this test. However, we also found indications that the fearfulness displayed by nursing piglets in the HAT is likely due to the temporary removal from the farrowing pen, instead of the presence of an unfamiliar human. Therefore, we can only conclude that LBW does not influence the behavioral response to this combination of stressors (i.e., social isolation from the sow and the piglets’ litter mates, whilst being in a novel environment), as measured by the HAT. Future studies are required to assess whether fear responses to less salient on-farm stressors are affected by birth weight.},
}


% ### S ###
@article{Salvatier2016,
    author = {Salvatier, John and Wiecki, Thomas V and Fonnesbeck, Christopher},
    year = {2016},
    title = {{Probabilistic programming in Python using PyMC3}},
    doi = {10.7717/peerj-cs.55},
    journal = {PeerJ Computer Science},
    volume = {2},
    pages = {e55},
    publisher = {PeerJ Inc.},
}

@article{SchlageterTello2014,
    author   = {Schlageter-Tello, Andr\'es and Bokkers, Eddie A.M. and Groot Koerkamp, Peter W.G. and {Van Hertem}, Tom and Viazzi, Stefano and Romanini, Carlos E.B. and Halachmi, Ilan and Bahr, Claudia and Berckmans, Dani\"el and Lokhorst, Kees},
    journal  = {Preventive Veterinary Medicine},
    title    = {{Manual and automatic locomotion scoring systems in dairy cows: A review}},
    year     = {2014},
    issn     = {0167-5877},
    number   = {1},
    pages    = {12-25},
    volume   = {116},
    abstract = {The objective of this review was to describe, compare and evaluate agreement, reliability, and validity of manual and automatic locomotion scoring systems (MLSSs and ALSSs, respectively) used in dairy cattle lameness research. There are many different types of MLSSs and ALSSs. Twenty-five MLSSs were found in 244 articles. MLSSs use different types of scale (ordinal or continuous) and different gait and posture traits need to be observed. The most used MLSS (used in 28\% of the references) is based on asymmetric gait, reluctance to bear weight, and arched back, and is scored on a five-level scale. Fifteen ALSSs were found that could be categorized according to three approaches: (a) the kinetic approach measures forces involved in locomotion, (b) the kinematic approach measures time and distance of variables associated to limb movement and some specific posture variables, and (c) the indirect approach uses behavioural variables or production variables as indicators for impaired locomotion. Agreement and reliability estimates were scarcely reported in articles related to MLSSs. When reported, inappropriate statistical methods such as PABAK and Pearson and Spearman correlation coefficients were commonly used. Some of the most frequently used MLSSs were poorly evaluated for agreement and reliability. Agreement and reliability estimates for the original four-, five- or nine-level MLSS, expressed in percentage of agreement, kappa and weighted kappa, showed large ranges among and sometimes also within articles. After the transformation into a two-level scale, agreement and reliability estimates showed acceptable estimates (percentage of agreement ≥75\%; kappa and weighted kappa ≥0.6), but still estimates showed a large variation between articles. Agreement and reliability estimates for ALSSs were not reported in any article. Several ALSSs use MLSSs as a reference for model calibration and validation. However, varying agreement and reliability estimates of MLSSs make a clear definition of a lameness case difficult, and thus affect the validity of ALSSs. MLSSs and ALSSs showed limited validity for hoof lesion detection and pain assessment. The utilization of MLSSs and ALSSs should aim to the prevention and efficient management of conditions that induce impaired locomotion. Long-term studies comparing MLSSs and ALSSs while applying various strategies to detect and control unfavourable conditions leading to impaired locomotion are required to determine the usefulness of MLSSs and ALSSs for securing optimal production and animal welfare in practice.},
    doi      = {10.1016/j.prevetmed.2014.06.006},
    keywords = {Agreement, Animal welfare, Locomotion score, Reliability, Sensors, Validity},
    url      = {https://www.sciencedirect.com/science/article/pii/S0167587714002049},
}

@article{Scott2022,
    author = {Scott, Bradley and Seyres, Martin and Philp, Fraser and Chadwick, Edward K. and Blana, Dimitra},
    year = {2022},
    title = {{Healthcare applications of single camera markerless motion capture: a scoping review}},
    doi = {10.7717/peerj.13517},
    journal = {PeerJ},
    keywords = {Markerless motion capture, Markerless, Single camera markerless motion capture, Scoping review, Single camera human motion analysis, Single camera movement analysis of humans, Clinical motion capture, Neurological injuries, Telerehabilitation, Musculoskeletal},
    abstract = {{Background: Single camera markerless motion capture has the potential to facilitate at home movement assessment due to the ease of setup, portability, and affordable cost of the technology. However, it is not clear what the current healthcare applications of single camera markerless motion capture are and what information is being collected that may be used to inform clinical decision making. This review aims to map the available literature to highlight potential use cases and identify the limitations of the technology for clinicians and researchers interested in the collection of movement data. Survey Methodology: Studies were collected up to 14 January 2022 using Pubmed, CINAHL and SPORTDiscus using a systematic search. Data recorded included the description of the markerless system, clinical outcome measures, and biomechanical data mapped to the International Classification of Functioning, Disability and Health Framework (ICF). Studies were grouped by patient population. Results: A total of 50 studies were included for data collection. Use cases for single camera markerless motion capture technology were identified for Neurological Injury in Children and Adults; Hereditary/Genetic Neuromuscular Disorders; Frailty; and Orthopaedic or Musculoskeletal groups. Single camera markerless systems were found to perform well in studies involving single plane measurements, such as in the analysis of infant general movements or spatiotemporal parameters of gait, when evaluated against 3D marker-based systems and a variety of clinical outcome measures. However, they were less capable than marker-based systems in studies requiring the tracking of detailed 3D kinematics or fine movements such as finger tracking. Conclusions: Single camera markerless motion capture offers great potential for extending the scope of movement analysis outside of laboratory settings in a practical way, but currently suffers from a lack of accuracy where detailed 3D kinematics are required for clinical decision making. Future work should therefore focus on improving tracking accuracy of movements that are out of plane relative to the camera orientation or affected by occlusion, such as supination and pronation of the forearm.}},
    month = {may},
    volume = {10},
    pages = {e13517},
    issn = {2167-8359},
}

@article{Seethapathi2019,
    author = {Seethapathi, Nidhi and Wang, Shaofei and Saluja, Rachit and Blohm, Gunnar and Kording, Konrad P.},
    year = {2019},
    title = {{Movement science needs different pose tracking algorithms}},
    doi = {10.48550/arXiv.1907.10226},
    volume = {1907.10226},
    journal = {arXiv},
}

@article{SerraBraganca2018,
    author = {{Serra Bragança}, F.M. and Rhodin, M. and {van Weeren}, P.R.},
    year = {2018},
    title = {{On the brink of daily clinical application of objective gait analysis: What evidence do we have so far from studies using an induced lameness model?}},
    doi = {10.1016/j.tvjl.2018.01.006},
    journal = {The Veterinary Journal},
    volume = {234},
    pages = {11-23},
    issn = {1090-0233},
    url = {https://www.sciencedirect.com/science/article/pii/S1090023318300066},
    keywords = {Asymmetry, Gait analysis, Horse, Lameness, Motion capture},
    abstract = {{Quantitative gait analysis has the potential to offer objective and unbiased gait information that can assist clinical decision-making. In recent years, a growing number of gait analysis systems have come onto the market, highlighting the demand for such technology in equine orthopaedics. However, it is imperative that the measured variables which are used as outcome parameters are supported by scientific evidence and that the interpretation of such measurements is backed by a proper understanding of the biomechanical principles of equine locomotion. This review, which is based on studies on experimentally induced lameness, summarises the currently most widely used methods for gait analysis and the available evidence concerning gait parameters that can be used to quantify gait changes due to lameness. These are discussed regarding their current and future potential for routine clinical application.}},
}
{Shikano2019,
    author = {Shikano, Susumu},
    year = {2019}
    title = {{Hypothesis Testing in the Bayesian Framework}},
    doi = {10.1111/spsr.12375},
    journal = {Swiss Political Science Review},
    volume = {25},
    number = {3},
    pages = {288-299},
    keywords = {Bayesian Inference, Credible Intervals, Bayes Factor, Model Selection},
    url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/spsr.12375},
    abstract = {Abstract While the Bayesian parameter estimation has gained a wider acknowledgement among political scientists, they seem to have less discussed the Bayesian version of hypothesis testing. This paper introduces two Bayesian approaches to hypothesis testing: one based on estimated posterior distributions and the other based on Bayes factors. By using an example based on a linear regression model, I demonstrate similarities and differences not only between the null-hypothesis significance tests and Bayesian hypothesis tests, but also those among two different Bayesian approaches, which are also critically discussed.},
}

@article{Stavrakakis2014,
    author = {Stavrakakis, S. and Guy, J.H. and Warlow, O.M.E. and Johnson, G.R. and Edwards, S.A.},
    year = {2014},
    title = {{Walking kinematics of growing pigs associated with differences in musculoskeletal conformation, subjective gait score and osteochondrosis}},
    doi = {10.1016/j.livsci.2014.04.008},
    journal = {Livestock Science},
    volume = {165},
    pages = {104-113},
    issn = {1871-1413},
    url = {https://www.sciencedirect.com/science/article/pii/S1871141314001887},
    keywords = {Pig, Gait analysis, Musculoskeletal conformation, Visual assessment, Osteochondrosis},
    abstract = {{Despite orthopaedic problems being a major concern for the pig industry, there is a lack of biomechanical, hence quantitative, investigation of locomotor pathology in pigs. The objective of this study was to determine whether there are detectable changes in joint and stride kinematics of clinically sound and unsound pigs, with or without post mortem joint lesions of osteochondrosis. A cohort of 24 pigs underwent five camera-based motion captures, 7–10d apart and between 63kg and 90kg average liveweight, during which 3D coordinate data of reflective skin markers attached to leg anatomical landmarks were collected. Pigs walked on the same solid concrete walkway during captures. Statistical analysis was performed within captures across pigs which were categorised based on a series of deficiency characteristics. Results showed that pigs with clinical deficiencies and degenerative joint lesions had altered kinematics, although there were capture-related fluctuations in the findings. For pigs with conformational and perceived gait abnormalities there were significant differences in joint flexion values and left and right flexion symmetry, mainly reflected in the swing ranges of motion, compared to sound animals. Buck-kneed front legs were found to cause flexion deficiencies during the stance phase of stride cycles (P≤0.05; −9 degrees). Pigs with osteochondral joint lesions had mainly stance-related angular changes (P≤0.05) and asymmetry. Irregularity in the step-to-stride length relationship was elevated in both clinically and subclinically deficient pigs (respectively P=0.06, 1.5 times greater; P≤0.05; 1.5 times greater), but not the healthy pigs. These data provide basic kinematic values for clinically sound and affected pigs which could be used for further research into early and automated detection of leg disorders as well as for improved selection of breeding animals for longevity characteristics.}},
}


@article{StifflerJoachim2020,
    author = {Stiffler-Joachim, Mikel R and Wille, Christa and Kliethermes, Stephanie and Heiderscheit, Bryan},
    year = {2020},
    title = {{Factors Influencing Base of Gait During Running: Consideration of Sex, Speed, Kinematics, and Anthropometrics}},
    doi = {10.4085/1062-6050-565-19},
    journal = {Journal of Athletic Training},
    volume = {55},
    number = {12},
    pages = {1300-1306},
    month = {10},
    abstract = {{A narrow base of gait (BOG), the mediolateral distance between the foot and the body's line of gravity at midstance, during running is a suggested cause of injuries such as iliotibial band syndrome and tibial stress injury. However, an understanding of modifiable and nonmodifiable factors that influence BOG is lacking, which limits the development of corrective strategies.To determine if BOG varies by sex and running speed and the influence of running kinematics and anthropometrics on BOG.Cross-sectional study.Record review of routinely collected performance data from a National Collegiate Athletic Association Division I intercollegiate athletic program.A total of 166 Division I collegiate athletes (basketball, cross-country, football, soccer).Running biomechanics (N = 166) and dual-energy x-ray absorptiometry-derived anthropometric data (n = 68) were extracted. Running variables were BOG, step rate, stride length, foot-inclination angle, center-of-mass vertical displacement, heel-to-center of mass anteroposterior distance, and peak stance-phase angles: hip flexion, hip adduction, pelvic drop, knee flexion, and ankle dorsiflexion. Extracted anthropometric variables were height; leg, femur, and tibia length; and anterior-superior iliac spine, hip-joint, and greater trochanter width. We calculated linear mixed-effects models to assess the influence of sex and running speed on BOG and identify the kinematic and anthropometric variables most associated with BOG.A significant interaction between sex and running speed on BOG was observed, with males demonstrating a smaller BOG than females at faster speeds and BOG decreasing overall with speed. The kinematic measures most associated with BOG at preferred running speed were foot-inclination angle at initial contact and peak stance-phase hip adduction and ankle dorsiflexion. Anterior-superior iliac spine width was the anthropometric variable most associated with BOG at preferred running speed.Sex and running speed must be considered when determining the appropriateness of an individual's BOG. Additionally, BOG was associated with several potentially modifiable kinematic parameters.}},
    issn = {1062-6050},
}

@article{VandenHole2018b,
    author = {Vanden Hole, Charlotte and Cleuren, Silke and Van Ginneken, Chris and Prims, Sara and Ayuso, Miriam and Van Cruchten, Steven and Aerts, Peter},
    year = {2018},
    title = {{How does intrauterine crowding affect locomotor performance in newborn pigs? A study of force generating capacity and muscle composition of the hind limb}},
    doi = {10.1371/journal.pone.0209233},
    journal = {PLOS ONE},
    publisher = {Public Library of Science},
    month = {12},
    volume = {13},
    number = {12},
    pages = {1-18},
    abstract = {Intrauterine crowding (IUC) considerably influences postnatal traits in a polytocous species such as the pig. Previously, our group described how IUC affects locomotion during the piglet’s first days of life (until 96 h after birth). We noted a reduced motor performance in piglets with a low birth weight and low vitality (L piglets), compared to piglets with a normal birth weight and normal vitality (N piglets), indicating L piglets are unable to produce enough force. Our current study investigates whether this observed force deficit in L piglets is caused by a reduced force generating capacity in the muscles and/or a lower percentage of type II (fast-contracting) fibers. Volume and fiber length of the main extensor muscles of the hind limb were used to estimate the physiological cross-sectional area (PSCA) and hence calculate the maximal isometric force generating capacity (Fiso-max) of the hind limb. To check for developmental differences between the muscles of L and N piglets, Fiso-max was normalized to body weight (BW), thus yielding a dimensionless variable F’iso-max. To check for differences in muscle composition, m. vastus lateralis was stained immunohistochemically in order to determine the percentage of type II fibers through image analysis. Our results indicate that L piglets have a reduced absolute force generating capacity due to a lesser muscle mass, compared to N piglets. However, when normalized to BW L piglets actually show a larger force generating capacity, suggesting their muscles are more voluminous, given their body mass, than those of N piglets. However, no differences between L and N piglets were detected with regard to muscle composition of the m. vastus lateralis. Based on our data, we can say that neither normalized force generating capacity, nor muscle composition (of the m. vastus lateralis) can explain the observed force deficit in L piglets and as such the effect of IUC on locomotor performance.},
}


@article{VandenHole2019,
    author={Vanden Hole, Charlotte and Ayuso, Miriam and Aerts, Peter and Prims, Sara and Van Cruchten, Steven and Van Ginneken, Chris},
    year = {2019},
    title = {{Glucose and glycogen levels in piglets that differ in birth weight and vitality}},
    doi = {10.1016/j.heliyon.2019.e02510},
    journal = {Heliyon},
    volume = {5},
    number = {9},
    pages = {e02510},
    issn = {2405-8440},
    url = {https://www.sciencedirect.com/science/article/pii/S2405844019361705},
    keywords = {Animal nutrition, Animal product, Livestock management, Veterinary medicine, Sus scrofa, Energy, Skeletal muscle, Liver, Intrauterine crowding},
    abstract = {In the pig, intrauterine crowding can greatly affect postnatal characteristics, among which birth weight and locomotion. In a previous study, we discovered that piglets with a low birth weight/low vitality (L piglets) have a reduced motor performance compared to piglets with a normal birth weight/normal vitality (N piglets). A possible explanation is that L piglets lack the energy to increase their motor performance to the level of that of N piglets. Blood glucose levels (GLU) and glycogen concentrations in skeletal muscle of the front (GLYFRONT) and hind leg (GLYHIND) and the liver (GLYLIVER) at birth and during the first 96 h postpartum were compared between L and N piglets. GLU at birth was the same for both groups. After birth, GLU immediately increased in N piglets, whereas it only increased after 8 h in L piglets. L piglets showed a lower GLYHIND at birth and did not use this glycogen during the first 8 h postpartum, while N piglets showed a gradual depletion. GLYLIVER at birth was 50\% lower for L piglets and was unused during the studied period while N piglets consumed half of their GLYLIVER during the first 8 h. Based on these results, it is possible that lower glycogen concentrations at birth, the delayed increase in GLU and the lower use of glycogen during the first 8 h after birth negatively affect motor performance in L piglets. However, based on this study, it is unclear whether the low mobilization of glycogen by L piglets is a consequence, rather than a cause of their lower motor performance.},
}

@article{VandenHole2021,
    author = {Vanden Hole, Charlotte and Ayuso, Miriam and Aerts, Peter and Van Cruchten, Steven and Thymann, Thomas and Sangild, Per Torp and Van Ginneken, Chris},
    year = {2021},
    title = {{Preterm Birth Affects Early Motor Development in Pigs}},
    doi = {10.3389/fped.2021.731877},
    journal = {Frontiers in Pediatrics},
    volume = {9},
    pages = {1003},
    url = {https://www.frontiersin.org/article/10.3389/fped.2021.731877},
    issn = {2296-2360},
    abstract = {Background: Preterm infants frequently show neuromotor dysfunctions, but it is not clear how reduced gestational age at birth may induce developmental coordination disorders. Advancing postnatal age, not only post-conceptional age, may determine neuromuscular development, and early interventions in preterm newborns may improve their later motor skills. An animal model of preterm birth that allows early postnatal detection of movement patterns may help to investigate this hypothesis.Methods: Using pigs as a model for moderately preterm infants, preterm (106-day gestation, equivalent to 90\% of normal gestation time; n = 38) and term (115-day gestation, equivalent to 99\% of normal gestation time; n = 20) individuals were delivered by cesarean section and artificially reared until postnatal day 19 (preweaning period). The neuromotor skills of piglets were documented using spatiotemporal gait analyses on video recordings of locomotion at self-selected speed at postnatal age 3, 4, 5, 8, and 18 days. Results were controlled for effects of body weight and sex.Results: Both preterm and term piglets reached mature neuromotor skills and performance between postnatal days 3–5. However, preterm pigs took shorter steps at a higher frequency, than term piglets, irrespective of their body size. Within preterm pigs, males and low birth weight individuals took the shortest steps, and with the highest frequency.Conclusion: Postnatal development of motor skills and gait characteristics in pigs delivered in late gestation may show similarity to the compromised development of gait pattern in preterm infants. Relative to term pigs, the postnatal delay in gait development in preterm pigs was only few days, that is, much shorter than the 10-day reduction in gestation length. This indicates rapid postnatal adaptation of gait pattern after reduced gestational age at birth. Early-life physical training and medical interventions may support both short- and long-term gait development after preterm birth in both pigs and infants.},
}

@article{vandeSchoot2021,
    author = {van de Schoot, Rens and Depaoli, Sarah and King, Ruth and Kramer, Bianca and M{\"a}rtens, Kaspar and Tadesse, Mahlet G and Vannucci, Marina and Gelman, Andrew and Veen, Duco and Willemsen, Joukje and others},
    year = {2021},
    title = {{Bayesian Statistics and Modelling}},
    doi = {10.1038/s43586-020-00001-2},
    journal = {Nature Reviews Methods Primers},
    volume = {1},
    number = {1},
    pages = {1--26},
    publisher = {Nature Publishing Group},
}

@article{VanGinneken2022,
    author = {Van Ginneken, Chris and Ayuso, Miriam and Van Bockstal, Lieselotte and Van Cruchten, Steven},
    year = {2022},
    title = {{Preweaning performance in intrauterine growth-restricted piglets: Characteristics and interventions}},
    doi = {10.1002/mrd.23614},
    journal = {Molecular Reproduction and Development},
    keywords = {birth weight, development, growth restriction, piglet, sex},
    url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/mrd.23614},
    abstract = {{Abstract Intrauterine growth restriction (IUGR) is frequently observed in pig production, especially when using highly prolific sows. IUGR piglets are born with low body weight and shape indicative of differences in organ growth. Insufficient uteroplacental nutrient transfer to the fetuses is the leading cause of growth restriction in the pig. Supplementing the sow's gestation diet with arginine and/or glutamine improves placenta growth and functionality and consequently is able to reduce IUGR incidence. IUGR piglets are at higher risk of dying preweaning and face higher morbidity than their normal-weight littermates. A high level of surveillance during farrowing and individual nutrient supplementation can reduce the mortality rates. Still, these do not reverse the long-term consequences of IUGR, which are induced by persistent structural deficits in different organs. Dietary interventions peri-weaning can optimize performance but these are less effective in combating the metabolic changes that occurred in IUGR, which affect reproductive performance later in life. IUGR piglets share many similarities with IUGR infants, such as a poorer outcome of males. Using the IUGR piglet as an animal model to further explore the structural and molecular basis of the long-term consequences of IUGR and the potential sex bias could aid in fully understanding the impact of prenatal undernutrition and finding solutions for both species and sexes.}},
}

@article{VanKerschaver2021,
    author = {Van Kerschaver, C. and Vandaele, M. and Degroote, J. and Van Tichelen, K. and Fremaut, D. and Van Ginneken, C. and Michiels, J.},
    year = {2021},
    title = {{Effect of starting time of co-mingling non-littermates during lactation on performance and skin lesions of sows and piglets}},
    doi = {10.1016/j.livsci.2021.104563},
    journal = {Livestock Science},
    volume = {250},
    pages = {104563},
    issn = {1871-1413},
    url = {https://www.sciencedirect.com/science/article/pii/S1871141321001712},
    keywords = {Co-mingling, Piglet, Performance, Weaning, Stress},
    abstract = {The natural weaning process of piglets is a gradual event, whereas in current commercial pig production weaning is a sudden, stressful phase in the pigs’ life. Management strategies such as co-mingling of non-littermates before weaning aim to mimic (semi)natural conditions and to stimulate social skills in piglets in order to minimize the adverse effects of stress around weaning. The present study investigated in which way timing of co-mingling non-littermate piglets during lactation in conventional farrowing units had implications for the sow and affected the performance and behaviour of piglets before and after weaning. In the experimental treatments, 3 litters were co-mingled either at day 16 before weaning (n  =  27 sows and their litters), day 11 before weaning (n  =  27) or day 6 before weaning (n  =  27). In the control treatment, piglets were not grouped before weaning (n  =  27). In total, 1294 piglets were weaned at 21 days of age. At weaning, piglets from 3 litters within each treatment were mixed. Piglets from the co-mingling system were housed with those they were co-mingled with during lactation, whereas control piglets were mixed with unfamiliar piglets. Co-mingling of non-littermate piglets did not affect sow body condition and lesion scores of udder and teats during lactation. Piglets co-mingled 6 days before weaning tended to gain less weight during d-6 – d-1 before weaning (P  =  0.082), but piglet growth was not affected during d-16 – d-1. After weaning, the feed to gain ratio in piglets which were co-mingled 6 days before weaning tended to be lowest during the first week after weaning (P  =  0.086), but no other treatment effects were observed in the post-weaning phase. Skin lesion score of the shoulders and flanks tended to be higher at day 11 before weaning in piglets co-mingled 16 days before weaning (P  =  0.051) and was highest at day 6 before weaning in piglets co-mingled 11 days before weaning (P < 0.001). However, 1 day before weaning no differences in skin lesions were observed. After weaning, the socialized piglets had less skin lesions at the shoulders and flanks compared to control piglets (P < 0.001). In conclusion, pre-weaning co-mingling of non-littermates resulted in less aggression (i.e. lesions) at weaning, suggesting better social skills and a reduction of stress, consistent with a tendency for improved feed to gain ratio in the first week after weaning. Time of co-mingling seemed not crucial.},
}


@article{VanTichelen2021,
    author = {Van Tichelen, Kevin and Prims, Sara and Ayuso, Miriam and Van Kerschaver, Céline and Vandaele, Mario and Degroote, Jeroen and Van Cruchten, Steven and Michiels, Joris and Van Ginneken, Chris},
    year = {2021},
    title = {{Handling Associated with Drenching Does Not Impact Survival and General Health of Low Birth Weight Piglets}},
    doi = {10.3390/ani11020404},
    journal = {Animals},
    volume = {11},
    number = {2},
    article-number = {404},
    url = {https://www.mdpi.com/2076-2615/11/2/404},
    pubmedid = {33562568},
    issn = {2076-2615},
    abstract = {The increase in litter sizes in recent years has resulted in more low birth weight (LBW) piglets, accompanied by a higher mortality. A potential intervention to overcome this is drenching bioactive substances. However, if the act of drenching provokes additional stress in LBW piglets, it might counteract the supplement’s effect and be detrimental for the piglet’s survival. To study the effect of the drenching act, piglets from 67 sows were weighed within 4 h after birth. The mean litter birth weight (MLBW) and standard deviation (SD) were calculated. LBW piglets (n = 76) were defined as weighing between (MLBW-1*SD) and (MLBW-2.5*SD). They were randomly allocated to two treatments: “sham” (conducting the act of drenching by inserting an empty 2.5 mL syringe in the mouth during 20 s, once a day, d1 till d7; n = 37) or “no treatment” (no handling; n = 39). On day 1, 3, 9, 24 and 38, piglets were weighed and scored for skin lesions. Blood samples were collected on day 9 and 38 and analyzed to determine glucose, non-esterified fatty acids (NEFA), urea, immunoglobulin G (IgG), insulin-like growth factor 1 (IGF-1) and a standard blood panel test. There was no difference between sham drenched and untreated piglets regarding any of the parameters. In conclusion, this study showed that drenching does not impose a significant risk to LBW piglets and can be applied safely during the first 7 days after birth.},
}


@article{VanWachenfelt2008,
    author = {von Wachenfelt, Hans and Pinzke, Stefan and Nilsson, Christer and Olsson, Ove and Ehlorsson, Carl-Johan},
    year = {2008},
    title = {{Gait analysis of unprovoked pig gait on clean and fouled concrete surfaces}},
    doi = {10.1016/j.biosystemseng.2008.09.002},
    journal = {Biosystems Engineering},
    volume = {101},
    number = {3},
    pages = {376-382},
    issn = {1537-5110},
    url = {https://www.sciencedirect.com/science/article/pii/S1537511008002717},
    abstract = {Inadequate floor properties are considered the primary cause of the majority of claw disorders in pigs but to date no clear relationship has been found between claw disorders and floor properties such as friction and surface abrasiveness. To determine this relationship, the factors controlling pig gait must be characterised. This study examined unprovoked pig gait on a concrete floor in clean conditions and compared it with gait in fouled floor conditions. Kinematics were used to record gait parameters such as walking speed, stride length, swing and stance time, stride elevation together with limb support phases, gait symmetry, diagonality and duty factor. On clean floors, pigs had an unprovoked symmetrical gait with alternating two- and three-beat support phases and a high rate of diagonality. Stride length, swing and stance time and stride elevation showed little variation. Pigs altered their gait in accordance with floor conditions to maintain gait control by reducing walking speed, lowering diagonality and employing more three-limb support phases. Pigs also shortened their stride length and prolonged their stance time.},
}

@article{Vranken2017,
    author = {Vranken, Erik and Berckmans, Dries},
    year = {2017},
    title = {{Precision livestock farming for pigs}},
    doi = {10.2527/af.2017.0106},
    journal = {Animal Frontiers},
    volume = {7},
    number = {1},
    pages = {32-37},
    month = {01},
    abstract = {{It was demonstrated that laboratory-developed precision livestock farming (PLF) tools can be fully operational on farms and can bring value to the farmers and other stakeholders in the production chains. In the PLF concept, the animal is used as a sensor, and algorithms translate the measured animal responses into key indicators for optimal performance, improved animal welfare, and farm sustainability. In a further development phase, PLF applications assist farmers in taking their daily management decisions and generate early warnings when something is going wrong in the production process. Attention must be paid to adequate training of farmers and the further integration of PLF system in operational management systems.}},
    issn = {2160-6056},
}


% ### W ###
@article{Wang2016,
    author = {Wang, Jun and Yang, Mei and Cao, Meng and Lin, Yan and Che, Lianqiang and Duraipandiyan, Veeramuthu and Al-Dhabi, Naif Abdullah and Fang, Zhengfeng and Xu, Shengyu and Feng, Bin and Liu, Gang and Wu, De},
    year = {2016},
    title = {{Moderately increased energy intake during gestation improves body condition of primiparous sows, piglet growth performance, and milk fat and protein output}},
    doi = {10.1016/j.livsci.2016.09.012},
    journal = {Livestock Science},
    volume = {194},
    pages = {23-30},
    issn = {1871-1413},
    url = {https://www.sciencedirect.com/science/article/pii/S1871141316302177},
    keywords = {Dietary energy allowance, Gestation, Reproductive performance, Milk composition, Primiparous sows},
    abstract = {This study determined the effect of dietary energy allowance during gestation on reproductive performance, blood metabolites, and milk composition in primiparous sows. Forty-four Landrace×Yorkshire gilts were randomly assigned to receive one of four dietary energy allowances (n = 11): low (L), medium (M), high (H), and extremely high (EH). The gilts in L, M, H, and EH treatments were provided 75, 100, 125, and 150\% of the energy requirement for maintenance from 0 to 30 d of gestation, respectively. Compared to d 0–30 of gestation, dietary energy allowances in each group increased by 20\% from d 30–90 of gestation and increased by 50\% from d 90 of gestation to parturition. After parturition, all primiparous sows received the same diet and fed ad libitum during lactation. The results showed that dietary energy linearly and quadratically increased (P<0.01) sow body weight and backfat thickness at d 0 and 28 of lactation. Dietary energy linearly and quadratically increased (P<0.01) sow body weight gain and backfat gain from d 0 of gestation to d 0 of lactation. With increasing dietary energy allowance, there were linear and quadratic increases (P<0.01) in sow body weight loss and backfat loss during lactation, and linear and quadratic decreases (P<0.01) in average daily feed intake during lactation. However, with increasing dietary energy allowance, individual birth and weaning weight linearly and quadratically increased (P<0.05), and litter weight quadratically increased at birth (P<0.05) and tended to increase at weaning (quadratic, P = 0.06). The greatest litter weight at birth and weaning was observed when sows were provided the H energy allowance. The number of total born and born alive was not influenced by dietary energy. With increasing dietary energy allowance, the fat and protein content linearly and quadratically increased (P<0.01) in colostrum, and the fat and protein content quadratically increased (P = 0.01) in mature milk. The greatest fat and protein content in mature milk was observed when sows were provided the H energy allowance. The results indicated that providing 125, 150, and 187.5\% of the energy requirement for maintenance during early, mid, and late gestation was beneficial in maintaining optimal body condition of primiparous sows, as well as improving piglet growth performance and milk fat and protein output.},
}


@article{Wathes2008,
    author = {Wathes, C.M. and Kristensen, H.H. and Aerts, J.-M. and Berckmans, D.},
    year = {2008},
    title = {{Is precision livestock farming an engineer's daydream or nightmare, an animal's friend or foe, and a farmer's panacea or pitfall?}},
    doi = {10.1016/j.compag.2008.05.005},
    journal = {{Computers and Electronics in Agriculture}},
    volume = {64},
    number = {1},
    pages = {2-10},
    note = {Smart Sensors in precision livestock farming},
    issn = {0168-1699},
    url = {https://www.sciencedirect.com/science/article/pii/S0168169908001476},
    keywords = {Precision livestock farming, Welfare, Bioethics, Health, Production, Environment},
    abstract = {This paper reviews the development of precision livestock farming (PLF), from the view point of the engineer, the farm animal and the farmer; PLF is the principal means by which ‘smart’ sensors will be used in livestock farming. It considers the technological principles upon which PLF is based, gives several examples of PLF, considers which livestock processes are suitable for the PLF approach, addresses whether PLF constitutes technology push or market pull, and stresses the need for a prospective bioethical analysis of PLF. We conclude that PLF is an embryonic technology with great promise but one that requires considerable research and development before uptake.}
}

@article{Wurtz2019,
    author = {Wurtz, Kaitlin and Camerlink, Irene and D’Eath, Richard B. and Fern\'andez, Alberto Peña and Norton, Tomas and Steibel, Juan and Siegford, Janice},
    year = {2019},
    title = {{Recording behaviour of indoor-housed farm animals automatically using machine vision technology: A systematic review}},
    doi = {10.1371/journal.pone.0226669},
    journal = {{PLOS ONE}},
    publisher = {Public Library of Science},
    month = {12},
    volume = {14},
    pages = {1-35},
    abstract = {Large-scale phenotyping of animal behaviour traits is time consuming and has led to increased demand for technologies that can automate these procedures. Automated tracking of animals has been successful in controlled laboratory settings, but recording from animals in large groups in highly variable farm settings presents challenges. The aim of this review is to provide a systematic overview of the advances that have occurred in automated, high throughput image detection of farm animal behavioural traits with welfare and production implications. Peer-reviewed publications written in English were reviewed systematically following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. After identification, screening, and assessment for eligibility, 108 publications met these specifications and were included for qualitative synthesis. Data collected from the papers included camera specifications, housing conditions, group size, algorithm details, procedures, and results. Most studies utilized standard digital colour video cameras for data collection, with increasing use of 3D cameras in papers published after 2013. Papers including pigs (across production stages) were the most common (n = 63). The most common behaviours recorded included activity level, area occupancy, aggression, gait scores, resource use, and posture. Our review revealed many overlaps in methods applied to analysing behaviour, and most studies started from scratch instead of building upon previous work. Training and validation sample sizes were generally small (mean±s.d. groups = 3.8±5.8) and in data collection and testing took place in relatively controlled environments. To advance our ability to automatically phenotype behaviour, future research should build upon existing knowledge and validate technology under commercial settings and publications should explicitly describe recording conditions in detail to allow studies to be reproduced.},
    number = {12},
}


% ### X ###
% ### Y ###
@article{Yitbarek2022,
    author = {Yitbarek, Dagmawi and Dagnaw, Gashaw Getaneh},
    year = {2022},
    title = {{Application of Advanced Imaging Modalities in Veterinary Medicine: A Review}},
    doi = {10.2147/VMRR.S367040},
    journal = {Veterinary Medicine: Research and Reports},
    volume = {13},
    pages = {117},
    publisher = {Dove Press}
}

@article{Young2018,
    author = {Young, Jesse W. and Shapiro, Liza J.},
    year = {2018},
    title = {{Developments in development: What have we learned from primate locomotor ontogeny?}},
    doi = {10.1002/ajpa.23388},
    journal = {American Journal of Physical Anthropology},
    volume = {165},
    number = {S65},
    pages = {37-71},
    keywords = {allometry, gait mechanics, life history, locomotor independence, ontogeny},
    url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ajpa.23388},
    abstract = {Abstract The importance of locomotion to evolutionary fitness has led to extensive study of primate locomotor behavior, morphology and ecology. Most previous research has focused on adult primates, but in the last few decades, increased attention to locomotor development has provided new insights toward our broader understanding of primate adaptation and evolution. Here, we review the contributions of this body of work from three basic perspectives. First, we assess possible determinants on the timing of locomotor independence, an important life history event. Significant influences on timing of locomotor independence include adult female body mass, age at weaning, and especially relative brain size, a significant predictor of other primate life history variables. Additionally, we found significant phylogenetic differences in the timing of locomotor independence, even accounting for these influences. Second, we discuss how structural aspects of primate growth may enhance the locomotor performance and safety of young primates, despite their inherent neuromotor and musculoskeletal limitations. For example, compared to adults, growing primates have greater muscle mechanical advantage, greater bone robusticity, and larger extremities with relatively long digits. Third, focusing on primate quadrupedalism, we provide examples that illustrate how ontogenetic transitions in morphology and locomotion can serve as a model system for testing broader principles underlying primate locomotor biomechanics. This approach has led to a better understanding of the key features that contribute to primates’ stride characteristics, gait patterns, limb force distribution, and limb postures. We have learned a great deal from the study of locomotor ontogeny, but there is much left to explore. We conclude by offering guidelines for future research, both in the laboratory and the field.},
}


% ### Z ###

@article{Zupan2016,
    author = {Zupan, M. and Rehn, T. and de Oliveira, D. and Keeling, L. J.},
    year = {2016},
    title = {{Promoting positive states: the effect of early human handling on play and exploratory behaviour in pigs}},
    doi = {10.1017/S1751731115001743},
    journal = {animal},
    volume = {10},
    number = {1},
    publisher = {Cambridge University Press},
    pages = {135–141}
}

@book{McElreath2018,
    author    = {McElreath, Richard},
    publisher = {Chapman and Hall/CRC},
    title     = {Statistical rethinking: A Bayesian course with examples in R and Stan},
    year      = {2018},
    doi       = {10.1201/9780429029608},
}


% #### CHAPTER 6 ####

@article{DuPlessis2013,
    author = {Du Plessis, A and Meincken, M and Seifert, T},
    year = {2013},
    title = {Quantitative determination of density and mass of polymeric materials using microfocus computed tomography},
    doi = {10.1007/s10921-013-0195-7},
    journal = {Journal of Nondestructive Evaluation},
    volume = {32},
    pages = {413--417},
    publisher = {Springer}
}


@article{Schmitt2019,
    author = {Schmitt, Oc\'eane and Baxter, Emma M. and Lawlor, Peadar G. and Boyle, Laura A. and O'Driscoll, Keelin},
    year = {2019},
    title = {{A Single Dose of Fat-Based Energy Supplement to Light Birth Weight Pigs Shortly After Birth Does Not Increase Their Survival and Growth}},
    doi = {10.3390/ani9050227},
    journal = {Animals},
    volume = {9},
    number = {5},
    article-number = {227},
    url = {https://www.mdpi.com/2076-2615/9/5/227},
    pubmedid = {31075904},
    issn = {2076-2615},
    abstract = {{Low birth weight piglets are at high risk of mortality, because of the rapid depletion of their energy reserves after birth. At 3 h postpartum, 405 piglets weighing 1.1 kg were either dosed orally with 2 mL of (1) coconut oil (CO, 74 kJ/2 mL, n = 107 piglets), (2) commercial product (CP, 71 kJ/2 mL, n = 101 piglets), (3) water (W, 0 kJ/2 mL, n = 100 piglets) or (4) were sham-dosed (S, n = 97 piglets). Treatments were applied within litter (97 sows). Before treatment piglets were weighed, scored for vitality and blood glucose concentration (subset: CO = 45 piglets, CP = 38 piglets, W = 49 piglets and S = 44 piglets) and rectal temperature were measured. Rectal temperature was remeasured 1 h post-treatment (4 h postpartum). At 24 h post-treatment (27 h postpartum), vitality, weight and blood glucose were remeasured. Piglets were weighed on D5, D7, D10, D14, D21 and at weaning (27 ± 0.1 day old). Mortality rate and cause were recorded until 24h period post-treatment and until weaning. Data were analysed using Generalised Linear Mixed Models in SAS. There was no overall effect of treatment on any of the parameters measured. In conclusion, a single oral of fat-based energy supplement dose at birth did not improve growth, survival, rectal temperature or vitality of low birth weight piglets.}},
}

@article{Muk2023,
    author = {Muk, Tik and Leto, Azra and Brunse, Anders and Stensballe, Allan and Thymann, Thomas and Sangild, Per and Nguyen, Duc Ninh},
    year = {2023},
    title = {{Neonatal prophylactic antibiotics after preterm birth affect plasma proteome and immune development in pigs}},
    journal = {Pediatric Research},
    doi = {10.1038/s41390-023-02492-7},
    month = {02},
}

@book{Laczko2016,
    author = {Laczko, Jozsef and Latash, Mark L},
    year = {2016},
    title = {{Progress in Motor Control: Theories and Translations}},
    volume = {957},
    publisher = {Springer},
}

@article{Latash2010,
      author = {Latash, Mark L.},
      year = {2010},
      title = {Motor Synergies and the Equilibrium-Point Hypothesis},
      doi = {10.1123/mcj.14.3.294},
      journal = {Motor Control},
      publisher = {Human Kinetics, Inc.},
      address = {Champaign IL, USA},
      volume = {14},
      number = {3},
      pages= {294 - 322},
      url = {https://journals.humankinetics.com/view/journals/mcj/14/3/article-p294.xml},
}

@book{Latash2008,
    author = {Latash, Mark L.},
    year = {2008},
    title = {Synergy},
    publisher = {Oxford University Press},
}

@book{Latash1998,
    author = {Latash, Mark L},
    year = {1998},
    title = {{Progress in motor control: Bernstein's traditions in movement studies}},
    volume = {1},
    publisher = {Human kinetics},
}



@online{Baker1999,
        author = {Baker, Martin John},
        year = {1999},
        title = {{Euclidean Space: Maths/Quaternions}},
        organization = {EuclideanSpace.com},
        url = {https://www.euclideanspace.com/maths/algebra/realNormedAlgebra/quaternions},
        note = {accessed 2023-06-15, \nolinkurl{https://www.euclideanspace.com/physics/kinematics/angularvelocity/QuaternionDifferentiation2.pdf}},
}

@article{Ball1876,
    author = {Ball, Robert Stawell},
    year = {1876},
    title = {{The theory of screws: A study in the dynamics of a rigid body}},
    doi = {10.1007/BF01442479},
    journal = {Mathematische Annalen},
    volume = {9},
    number = {4},
    pages = {541--553},
    publisher = {Springer},
}

@article{Bol2013,
  author = {B{\"o}l, Markus and Leichsenring, Kay and Weichert, Christine and Sturmat, Maike and Schenk, Philipp and Blickhan, Reinhard and Siebert, Tobias},
  year = {2013},
  title = {Three-dimensional surface geometries of the rabbit soleus muscle during contraction: input for biomechanical modelling and its validation},
  doi = {10.1007/s10237-013-0476-1},
  journal = {Biomechanics and modeling in mechanobiology},
  volume = {12},
  pages = {1205--1220},
  publisher = {Springer},
}

@article{Buytaert2014,
    author = {Buytaert, Jan and Goyens, Jana and De Greef, Daniel and Aerts, Peter and Dirckx, Joris},
    year = {2014},
    title = {{Volume Shrinkage of Bone, Brain and Muscle Tissue in Sample Preparation for Micro-CT and Light Sheet Fluorescence Microscopy (LSFM)}},
    doi = {10.1017/S1431927614001329},
    journal = {Microscopy and Microanalysis},
    volume = {20},
    number = {4},
    pages = {1208-1217},
    month = {06},
    abstract = {{Two methods are especially suited for tomographic imaging with histological detail of macroscopic samples that consist of multiple tissue types (bone, muscle, nerve or fat): Light sheet (based) fluorescence microscopy (LSFM) and micro-computed tomography (micro-CT). Micro-CT requires staining with heavy chemical elements (and thus fixation and sometimes dehydration) in order to make soft tissue imageable when measured alongside denser structures. LSMF requires fixation, decalcification, dehydration, clearing and staining with a fluorescent dye. The specimen preparation of both imaging methods is prone to shrinkage, which is often not mentioned, let alone quantified. In this paper the presence and degree of shrinkage are quantitatively identified for the selected preparation methods/stains. LSFM delivers a volume shrinkage of 17\% for bone, 56\% for muscle and 62\% for brain tissue. The three most popular micro-CT stains (phosphotungstic acid, iodine with potassium iodide, and iodine in absolute ethanol) deliver a volume shrinkage ranging from 10 to 56\% for muscle and 27–66\% for brain, while bone does not shrink in micro-CT preparation.}},
    issn = {1431-9276},
}


@article{Dumas2004,
    author = {Dumas, R. and Aissaoui, R. and de Guise, J.A. },
    title = {A 3D Generic Inverse Dynamic Method using Wrench Notation and Quaternion Algebra},
    journal = {Computer Methods in Biomechanics and Biomedical Engineering},
    volume = {7},
    number = {3},
    pages = {159-166},
    year  = {2004},
    publisher = {Taylor \& Francis},
    doi = {10.1080/10255840410001727805},
}

@article{Dumas2007,
    author = {Dumas, R. and Nicol, E. and Chèze, L.},
    year = {2007},
    title = {{Influence of the 3D Inverse Dynamic Method on the Joint Forces and Moments During Gait}},
    doi = {10.1115/1.2768114},
    journal = {Journal of Biomechanical Engineering},
    volume = {129},
    number = {5},
    pages = {786-790},
    month = {04},
    issn = {0148-0731},
    abstract = {{The joint forces and moments are commonly used in gait analysis. They can be computed by four different 3D inverse dynamic methods proposed in the literature, either based on vectors and Euler angles, wrenches and quaternions, homogeneous matrices, or generalized coordinates and forces. In order to analyze the influence of the inverse dynamic method, the joint forces and moments were computed during gait on nine healthy subjects. A ratio was computed between the relative dispersions (due to the method) and the absolute amplitudes of the gait curves. The influence of the inverse dynamic method was negligible at the ankle (2\%) but major at the knee and the hip joints (40\%). This influence seems to be due to the dynamic computation rather than the kinematic computation. Compared to the influence of the joint center location, the body segment inertial parameter estimation, and more, the influence of the inverse dynamic method is at least of equivalent importance. This point should be confirmed with other subjects, possibly pathologic, and other movements.}},
}

@online{DumasMatlab,
    author = {Dumas, Raphael},
    year = {1999},
    title = {3D Kinematics and Inverse Dynamics},
    organization = {MATLAB Central File Exchange},
    url = {https://www.mathworks.com/matlabcentral/fileexchange/58021-3d-kinematics-and-inverse-dynamics},
    note = {accessed 2023-06-15},
}

@article{Kabsch1976,
    author = {Kabsch, W.},
    year = {1976},
    title = {{A solution for the best rotation to relate two sets of vectors}},
    doi = {10.1107/S0567739476001873},
    journal = {Acta Crystallographica Section A},
    volume = {32},
    number = {5},
    pages = {922--923},
    abstract = {{A simple procedure is derived which determines a best rotation of a given vector set into a second vector set by minimizing the weighted sum of squared deviations. The method is generalized for any given metric constraint on the transformation.}},
}

@article{Kneller1991,
    author = {Kneller, Gerald R. },
    year  = {1991},
    title = {Superposition of Molecular Structures using Quaternions},
    doi = {10.1080/08927029108022453},
    journal = {Molecular Simulation},
    volume = {7},
    number = {1-2},
    pages = {113-119},
    publisher = {Taylor \& Francis},
}

@techreport{Korr1962,
  author = {Korr, A. L. and Hyer, Paul},
  year = {1962},
  title = {A trifilar pendulum for the determination moments of inertia},
  institution = {Frankford Arsenal Philadelphia PA Pitman-Dunn Research Labs},
  url = {https://apps.dtic.mil/sti/citations/AD0287534},
}

@article{Lawrence2019,
    title = {A purely algebraic justification of the Kabsch-Umeyama algorithm},
    author = {Lawrence, Jim and Bernal, Javier and Witzgall, Christoph},
    journal = {Journal of research of the National Institute of Standards and Technology},
    volume = {124},
    pages = {1},
    year = {2019},
    publisher = {National Institute of Standards and Technology},
    doi = {10.6028/jres.124.028},
}

@online{Lewin801L20,
    author = {Lewin, Walter},
    year = {1999},
    title = {8.01x - Lect 20 - Angular Momentum, Torques, Conservation of Angular Momentum},
    organization = {MIT / via youtube.com},
    url = {https://www.youtube.com/watch?v=sNaaL19opxw},
    note = {accessed 2023-06-15},
    }

@online{Lewin801L24,
    author = {Lewin, Walter},
    year = {1999},
    title = {{8.01x - Lect 24 - Rolling Motion, Gyroscopes, VERY NON-INTUITIVE}},
    organization = {MIT / via youtube.com},
    url = {https://youtu.be/XPUuF_dECVI},
    note = {accessed 2023-11-02},
    }

%Lynch, K. M., \& Park, F. C. (2017). Modern Robotics. Cambridge University Press. ISBN 9781107156302. http://www.modernrobotics.org
@book{Lynch2017,
    author = {Lynch, Kevin M and Park, Frank C},
    year = {2017},
    title = {{Modern Robotics}},
    publisher = {Cambridge University Press},
    isbn = {9781107156302},
    url = {http://www.modernrobotics.org},
}

@online{Mielke2020wrenches,
    author = {Mielke, Falk},
    year = {2020},
    title = {Notebook Series on Inverse Dynamics},
    organization = {"PhD Notes" blog by the author},
    url = {http://mielke-bio.info/falk/posts/10.id_lmx0a_wrenches},
    note = {accessed 2023-06-22},
}

@online{Mielke2021id,
    author = {Mielke, Falk},
    year = {2021},
    title = {Inverse Dynamics Procedure in Python and Blender},
    organization = {Git repository by the author},
    url = {https://git.sr.ht/~falk/flying_femur},
    note = {accessed 2023-06-22},
}

@online{Mielke2024lm,
    author = {Mielke, Falk},
    year = {2024},
    title = {Linear Models: Can out-of-sample prediction yield novel results?},
    organization = {"PhD Notes" blog by the author},
    url = {http://mielke-bio.info/falk/posts/33.linearmodels},
    note = {accessed 2024-01-31},
}

@article{Mueller2018,
    author = {M{\"u}ller, Andreas},
    year = {2018},
    title = {{Screw and Lie group theory in multibody dynamics: recursive algorithms and equations of motion of tree-topology systems}},
    doi = {10.1007/s11044-017-9583-6},
    journal = {Multibody System Dynamics},
    volume = {42},
    number = {2},
    pages = {219--248},
    publisher = {Springer},
}


@book{Newton1687,
    title = {\textit{Philosophiae naturalis principia mathematica}},
    author = {Newton, Isaac},
    year = {1687},
    publisher = {Trin. Coll. Cantab. Soc.},
}

@article{Pech1987,
    author = {P. Pech and K. Bergström and W. Rauschning and Victor M. Haughton},
    year  = {1987},
    title = {Attenuation Values, Volume Changes and Artifacts in Tissue Due to Freezing},
    doi = {10.3109/02841858709177444},
    journal = {Acta Radiologica},
    volume = {28},
    number = {6},
    pages = {779-782},
    publisher = {Taylor \& Francis},
}


@book{Robertson2013,
    author = {Robertson, D Gordon E and Caldwell, Graham E and Hamill, Joseph and Kamen, Gary and Whittlesey, Saunders},
    year = {2013},
    title = {Research methods in biomechanics},
    publisher = {Human kinetics},
    note = {p. 115},
}

@article{Schedlinski2001,
    author = {Schedlinski, Carsten and Link, Michael },
    year = {2001},
    title = {A Survey Of Current Inertia Parameter Identification Methods},
    doi = {10.1006/mssp.2000.1345},
    journal = {Mechanical Systems and Signal Processing},
    volume = {15},
    number = {1},
    pages = {189-211},
    issn = {0888-3270},
    url = {https://www.sciencedirect.com/science/article/pii/S0888327000913451},
    abstract = {The knowledge of the 10 inertia parameters mass, centre of gravity and inertia tensor (moments and products of inertia) of mechanical systems is of great interest whenever the dynamic behaviour is significantly governed by these parameters. In this paper, a survey of currently available inertia parameter identification methods shall be given. At first, the governing equations of motion will be summarised. Then a classification of the identification methods will be presented that is based on the general equations of motion of a rigid body and their simplifications with respect to several linearisation steps. In addition, the individual methods will be highlighted in detail while the requirements will be discussed and attainable accuracy limits are given where possible.},
}

@book{Tipler2007,
  title = {Physics for scientists and engineers},
  author = {Tipler, Paul A and Mosca, Gene},
  year = {2007},
  publisher = {Macmillan},
  edition = {\(6^{th}\)}
}


% https://ocw.mit.edu/courses/16-07-dynamics-fall-2009/pages/lecture-notes/
@book{Widnall2009,
    author = {Widnall, Sheila and Deyst, John and Greitzer, Edward},
    year = {2009},
    title = {{Lecture Notes: 16.07 Dynamics (undergraduate course)/Lecture L26 The Inertia Tensor}},
    publisher = {MIT Open Courseware},
    url = {https://ocw.mit.edu/courses/16-07-dynamics-fall-2009/dd277ec654440f4c2b5b07d6c286c3fd_MIT16_07F09_Lec26.pdf},
    note = {accessed 2023-06-02}
}

@article{Andersen1984,
    author = {Andersen, A. H. and Kak, A. C.},
    year = {1984},
    title = {{Simultaneous Algebraic Reconstruction Technique (SART): A Superior Implementation of the Art Algorithm}},
    doi = {10.1177/016173468400600107},
    journal = {Ultrasonic Imaging},
    volume = {6},
    number = {1},
    pages = {81-94},
    abstract = { In this paper we have discussed what appears to be a superior implementation of the Algebraic Reconstruction Technique (ART). The method is based on 1) simultaneous application of the error correction terms as computed by ART for all rays in a given projection; 2) longitudinal weighting of the correction terms back-distributed along the rays; and 3) using bilinear elements for discrete approximation to the ray integrals of a continuous image. Since this implementation generates a good reconstruction in only one iteration, it also appears to have a computational advantage over the more traditional implementation of ART. Potential applications of this implementation include image reconstruction in conjunction with ray tracing for ultrasound and microwave tomography in which the curved nature of the rays leads to a non-uniform ray density across the image. },
}

@article{Andrada2017,
    author = {Andrada, Emanuel and Reinhardt, Lars and Lucas, Karin and Fischer, Martin S.},
    year = {2017},
    title = {Three-dimensional inverse dynamics of the forelimb of {Beagles} at a walk and trot},
    doi = {10.2460/ajvr.78.7.804},
    journal = {American Journal of Veterinary Research},
    volume = {78},
    number = {7},
    pages = {804--817},
    month = jul,
    issn = {0002-9645},
    publisher = {American Veterinary Medical Association},
}

@article{Batenburg2011,
    author = {Batenburg, Kees Joost and Sijbers, Jan},
    year = {2011},
    title = {{DART: A Practical Reconstruction Algorithm for Discrete Tomography}},
    doi = {10.1109/TIP.2011.2131661},
    journal = {{IEEE Transactions on Image Processing}},
    volume = {20},
    number = {9},
    pages = {2542-2553},
}

@article{Beckmann2006,
    author = {Beckmann, E. C.},
    title = {{CT scanning the early days}},
    journal = {The British Journal of Radiology},
    volume = {79},
    number = {937},
    pages = {5-8},
    year = {2006},
    doi = {10.1259/bjr/29444122},
    abstract = { CT scanning has become an established diagnostic tool within the radiology department. This article covers some of the history of the development and early days of CT scanning. It is based upon the lecture given on the Memorial Day for Sir Godfrey Hounsfield during the British Institute of Radiology President's Conference 2005. },
}

@article{Berger2018fig8,
    author = {Berger, M and Yang, Q and Maier, A},
    year = {2018},
    title = {{X-ray Imaging. Figure 7.8 ``X-ray spectrum of a tungsten tube''.}},
    journal = {{Medical Imaging Systems: An Introductory Guide [Internet]}},
    editors = {Maier A, Steidl S, Christlein V, et al.},
    publisher = {Springer},
    abstract = {X-ray spectrum of a tungsten tube. The peaks correspond to the characteristic radiation; the continuous part of the spectrum represents the Bremsstrahlung.},
    note = {Available from: \nolinkurl{https://www.ncbi.nlm.nih.gov/books/NBK546155/figure/ch7.fig8}},
    doi = {10.1007/978-3-319-96520-8\_7},
}

@incollection{Berger2018,
    author = {Berger, Martin and Yang, Qiao and Maier, Andreas},
    year = {2018},
    title = {{X-ray Imaging}},
    doi = {10.1007/978-3-319-96520-8\_7},
    booktitle = {Medical Imaging Systems: An Introductory Guide [Internet]},
    publisher = {Springer},
    editors = {Maier A, Steidl S, Christlein V, et al.},
}


@article{Brainerd2010,
    author = {Brainerd, Elizabeth L. and Baier, David B. and Gatesy, Stephen M. and Hedrick, Tyson L. and Metzger, Keith A. and Gilbert, Susannah L. and Crisco, Joseph J.},
    year = {2010},
    title = {{X-ray reconstruction of moving morphology (XROMM): precision, accuracy and applications in comparative biomechanics research}},
    doi = {10.1002/jez.589},
    journal = {Journal of Experimental Zoology Part A: Ecological Genetics and Physiology},
    volume = {313A},
    number = {5},
    pages = {262-279},
    url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/jez.589},
    abstract = {Abstract X-Ray Reconstruction of Moving Morphology (XROMM) comprises a set of 3D X-ray motion analysis techniques that merge motion data from in vivo X-ray videos with skeletal morphology data from bone scans into precise and accurate animations of 3D bones moving in 3D space. XROMM methods include: (1) manual alignment (registration) of bone models to video sequences, i.e., Scientific Rotoscoping; (2) computer vision-based autoregistration of bone models to biplanar X-ray videos; and (3) marker-based registration of bone models to biplanar X-ray videos. Here, we describe a novel set of X-ray hardware, software, and workflows for marker-based XROMM. Refurbished C-arm fluoroscopes retrofitted with high-speed video cameras offer a relatively inexpensive X-ray hardware solution for comparative biomechanics research. Precision for our biplanar C-arm hardware and analysis software, measured as the standard deviation of pairwise distances between 1 mm tantalum markers embedded in rigid objects, was found to be ±0.046 mm under optimal conditions and ±0.084 mm under actual in vivo recording conditions. Mean error in measurement of a known distance between two beads was within the 0.01 mm fabrication tolerance of the test object, and mean absolute error was 0.037 mm. Animating 3D bone models from sets of marker positions (XROMM animation) makes it possible to study skeletal kinematics in the context of detailed bone morphology. The biplanar fluoroscopy hardware and computational methods described here should make XROMM an accessible and useful addition to the available technologies for studying the form, function, and evolution of vertebrate animals. J. Exp. Zool. 313A:262–279, 2010. © 2010 Wiley-Liss, Inc.},
}


@book{Buzug2008,
    author = {Buzug, Thorsten M.},
    year = {2008},
    title = {Computed tomography: From photon statistics to modern cone-beam CT},
    publisher = {Springer},
    isbn = {9783540394075},
}

@incollection{Buzug2011,
    title = {Computed Tomography},
    author = {Buzug, Thorsten M},
    doi = {10.1007/978-3-540-74658-4_16},
    booktitle = {Springer handbook of medical technology},
    pages = {311--342},
    year = {2011},
    publisher = {Springer}
}


@article{Durston2022,
    author = {Durston, Nicholas E. and Mahadik, Yusuf and Windsor, Shane P.},
    year = {2022},
    title = {{Quantifying avian inertial properties using calibrated computed tomography}},
    doi = {10.1242/jeb.242280},
    journal = {Journal of Experimental Biology},
    volume = {225},
    number = {1},
    month = {01},
    abstract = {{Estimating centre of mass and mass moments of inertia is an important aspect of many studies in biomechanics. Characterising these parameters accurately in three dimensions is challenging with traditional methods requiring dissection or suspension of cadavers. Here, we present a method to quantify the three-dimensional centre of mass and inertia tensor of birds of prey using calibrated computed tomography (CT) scans. The technique was validated using several independent methods, providing body segment mass estimates within approximately 1\% of physical dissection measurements and moment of inertia measurements with a 0.993 R2 correlation with conventional trifilar pendulum measurements. Calibrated CT offers a relatively straightforward, non-destructive approach that yields highly detailed mass distribution data that can be used for three-dimensional dynamics modelling in biomechanics. Although demonstrated here with birds, this approach should work equally well with any animal or appendage capable of being CT scanned.}},
    issn = {0022-0949},
}

@article{Fath2023,
    author = {Fath, M A and Nguyen, S V and Donahue, J and McMenamin, S K and Tytell, E D},
    year = {2023},
    title = {{Static Stability and Swim Bladder Volume in the Bluegill Sunfish (\textit{Lepomis macrochirus})}},
    doi = {10.1093/iob/obad005},
    journal = {Integrative Organismal Biology},
    volume = {5},
    number = {1},
    pages = {obad005},
    month = {02},
    abstract = {{Static stability is a property inherent to every organism. More stable bodies benefit from a lower energy cost associated with maintaining a desired orientation, while less stable bodies can be more maneuverable. The static stability of a fish is determined by the relative locations of its center of mass (COM) and center of buoyancy (COB), which may change with changes in swim bladder volume. We hypothesized, however, that fish would benefit from consistent static stability, and predicted that changes in swim bladder volume would not alter the overall pattern of COM and COB locations. We used micro-computed tomography to estimate the locations of the COM and COB in bluegill sunfish (Lepomis macrochirus). Using this technique, we were able to find a small but significant difference between the location of the COM and COB for a given orientation. We found that the swim bladder can change shape within the body cavity, changing relative locations of the COM and COB. At one extreme, the COB is located 0.441 ± 0.007 BL from the snout and 0.190 ± 0.010 BL from the ventral surface of the pelvic girdle, and that the COM is 0.0030 ± 0.0020 BL posterior and 0.0006 ± 0.0005 BL ventral to the COB, a pattern that causes a nose-up pitching torque. At the other extreme, the COM is anterior and dorsal to the COB, a pattern that causes the opposite torque. These changes in location seems to be caused by changes in the shape and centroid location of the swim bladder within the body: The centroid of the swim bladder is located significantly more posteriorly in fish oriented head-down. The air in the bladder “rises” while heavier tissues “sink,” driving a change in tissue distribution and changing the location of the COM relative to the COB. Supporting our hypothesis, we found no correlation between swim bladder volume and the distance between the COM and COB. We conclude that bluegill are statically unstable, requiring them to expend energy constantly to maintain their normal orientation, but that the pitch angle of the body could alter the relative locations of COM and COB, changing their static stability.}},
    issn = {2517-4843},
}

@article{Frenkel2022,
    title = {{Tabu-DART: a dynamic update strategy for efficient discrete algebraic reconstruction}},
    year = {2022},
    author = {Frenkel, Daniel and Six, Nathana{\"e}l and De Beenhouwer, Jan and Sijbers, Jan},
    doi = {10.1007/s00371-022-02616-w},
    journal = {The Visual Computer},
    pages = {1--13},
    publisher = {Springer},
}

@article{Gao2012,
    author = {Gao, Fuchang and Han, Lixing},
    year = {2012},
    title = {{Implementing the Nelder-Mead simplex algorithm with adaptive parameters}},
    doi = {10.1007/s10589-010-9329-3},
    journal = {Computational Optimization and Applications},
    volume = {51},
    number = {1},
    pages = {259--277},
    publisher = {Springer},
}

@article{Geyer2015,
    author = {Geyer, Lucas L. and Schoepf, U. Joseph and Meinel, Felix G. and Nance, John W. and Bastarrika, Gorka and Leipsic, Jonathon A. and Paul, Narinder S. and Rengo, Marco and Laghi, Andrea and De Cecco, Carlo N.},
    year = {2015},
    title = {State of the Art: Iterative CT Reconstruction Techniques},
    doi = {10.1148/radiol.2015132766},
    journal = {Radiology},
    volume = {276},
    number = {2},
    pages = {339-357},
    abstract = {Owing to recent advances in computing power, iterative reconstruction (IR) algorithms have become a clinically viable option in computed tomographic (CT) imaging. Substantial evidence is accumulating about the advantages of IR algorithms over established analytical methods, such as filtered back projection. IR improves image quality through cyclic image processing. Although all available solutions share the common mechanism of artifact reduction and/or potential for radiation dose savings, chiefly due to image noise suppression, the magnitude of these effects depends on the specific IR algorithm. In the first section of this contribution, the technical bases of IR are briefly reviewed and the currently available algorithms released by the major CT manufacturers are described. In the second part, the current status of their clinical implementation is surveyed. Regardless of the applied IR algorithm, the available evidence attests to the substantial potential of IR algorithms for overcoming traditional limitations in CT imaging. },
}

@article{Gilbert1972,
    author = {Gilbert, Peter},
    year = {1972},
    title = {{Iterative methods for the three-dimensional reconstruction of an object from projections}},
    doi = {10.1016/0022-5193(72)90180-4},
    journal = {Journal of Theoretical Biology},
    volume = {36},
    number = {1},
    pages = {105-117},
    issn = {0022-5193},
    url = {https://www.sciencedirect.com/science/article/pii/0022519372901804},
    abstract = {A method of reconstruction (ART) has recently been proposed (Gordon, Bender \& Herman, 1970) which consists in iteratively changing a trial structure until its projections are consistent with the original projections of the unknown structure. It is shown that in general ART produces erroneous reconstructions. An alternative iterative method is proposed which will give correct reconstructions under certain conditions. One of the potential applications of this method is in determining the three-dimensional structure of objects from electron micrographs.},
}

@book{Hughes2010,
    title = {Measurements and their uncertainties: a practical guide to modern error analysis},
    author = {Hughes, Ifan and Hase, Thomas},
    year = {2010},
    publisher = {OUP Oxford},
    isbn = {9780191576560},
}

@article{Feldkamp1984,
    author = {Feldkamp, L. A. and Davis, L. C. and Kress, J. W.},
    year = {1984},
    title = {Practical cone-beam algorithm},
    doi = {10.1364/JOSAA.1.000612},
    journal = {Journal of the Optical Society of America A},
    keywords = {Detector arrays; Image intensifiers; Reconstruction algorithms; Scanners; Three dimensional reconstruction; X ray imaging},
    number = {6},
    pages = {612--619},
    publisher = {Optica Publishing Group},
    volume = {1},
    month = {Jun},
    url = {https://opg.optica.org/josaa/abstract.cfm?URI=josaa-1-6-612},
    abstract = {A convolution-backprojection formula is deduced for direct reconstruction of a three-dimensional density function from a set of two-dimensional projections. The formula is approximate but has useful properties, including errors that are relatively small in many practical instances and a form that leads to convenient computation. It reduces to the standard fan-beam formula in the plane that is perpendicular to the axis of rotation and contains the point source. The algorithm is applied to a mathematical phantom as an example of its performance.},
}

@book{Hansen2021,
    author = {Hansen, Per Christian and J{\o}rgensen, Jakob and Lionheart, William RB},
    year = {2021},
    title = {{Computed tomography: algorithms, insight, and just enough theory}},
    doi = {10.1137/1.9781611976670},
    publisher = {SIAM},
}


@article{Hounsfield1973,
    author = {Hounsfield, G. N.},
    year = {1973},
    title = {Computerized transverse axial scanning (tomography): Part 1. Description of system},
    doi = {10.1259/0007-1285-46-552-1016},
    journal = {The British Journal of Radiology},
    volume = {46},
    number = {552},
    pages = {1016-1022},
    abstract = { Abstract This article describes a technique in which X-ray transmission readings are taken through the head at a multitude of angles: from these data, absorption values of the material contained within the head are calculated on a computer and presented as a series of pictures of slices of the cranium. The system is approximately 100 times more sensitive than conventional X-ray systems to such an extent that variations in soft tissues of nearly similar density can be displayed. },
}


@article{Lennie2021,
    author = {Lennie, Eve and Tsoumpas, Charalampos and Sourbron, Steven},
    year = {2021},
    title = {{Multimodal phantoms for clinical PET/MRI}},
    doi = {10.1186/s40658-021-00408-0},
    journal = {{EJNMMI physics}},
    volume = {8},
    number = {1},
    pages = {1--24},
    publisher = {SpringerOpen},
}

@online{Lewin801L19,
    author = {Lewin, Walter},
    year = {1999},
    title = {{8.01x - Lect 19 - Rotating Objects, Moment of Inertia, Rotational KE, Neutron Stars}},
    organization = {MIT / via youtube.com},
    url = {https://www.youtube.com/watch?v=fDJeVR0o__w},
    note = {accessed 2023-07-11},
    }

@online{LewinMOI,
    author = {Sagar Dalvi},
    year = {2017},
    title = {{Moment of inertia by Walter Lewin}},
    organization = {via youtube.com},
    url = {https://www.youtube.com/watch?v=lvfzdibrUFA},
    note = {accessed 2023-07-11},
    }


@article{Liu2023,
    author = {Liu, Leening P and Hwang, Matthew and Hung, Matthew and Soulen, Michael C and Schaer, Thomas P and Shapira, Nadav and No{\"e}l, Peter B},
    year = {2023},
    title = {Non-invasive mass and temperature quantifications with spectral CT},
    doi = {10.1038/s41598-023-33264-2},
    journal = {Scientific Reports},
    volume = {13},
    number = {1},
    pages = {6109},
    publisher = {Nature Publishing Group UK London},
}


@article{Macaulay2017,
    author = {Macaulay, Sophie and Hutchinson, John R. and Bates, Karl T.},
    year = {2017},
    title = {A quantitative evaluation of physical and digital approaches to centre of mass estimation},
    doi = {10.1111/joa.12667},
    journal = {Journal of Anatomy},
    volume = {231},
    number = {5},
    pages = {758-775},
    keywords = {biomechanics, centre of gravity, inertial properties, mass properties, validation, volumetric modelling},
    url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/joa.12667},
    abstract = {Abstract Centre of mass is a fundamental anatomical and biomechanical parameter. Knowledge of centre of mass is essential to inform studies investigating locomotion and other behaviours, through its implications for segment movements, and on whole body factors such as posture. Previous studies have estimated centre of mass position for a range of organisms, using various methodologies. However, few studies assess the accuracy of the methods that they employ, and often provide only brief details on their methodologies. As such, no rigorous, detailed comparisons of accuracy and repeatability within and between methods currently exist. This paper therefore seeks to apply three methods common in the literature (suspension, scales and digital modelling) to three ‘calibration objects’ in the form of bricks, as well as three birds to determine centre of mass position. Application to bricks enables conclusions to be drawn on the absolute accuracy of each method, in addition to comparing these results to assess the relative value of these methodologies. Application to birds provided insights into the logistical challenges of applying these methods to biological specimens. For bricks, we found that, provided appropriate repeats were conducted, the scales method yielded the most accurate predictions of centre of mass (within 1.49 mm), closely followed by digital modelling (within 2.39 mm), with results from suspension being the most distant (within 38.5 mm). Scales and digital methods both also displayed low variability between centre of mass estimates, suggesting they can accurately and consistently predict centre of mass position. Our suspension method resulted not only in high margins of error, but also substantial variability, highlighting problems with this method.},
}


@article{Mull1984,
    author = {Mull, RT},
    year = {1984},
    title = {{Mass estimates by computed tomography: physical density from CT numbers}},
    doi = {10.2214/ajr.143.5.1101},
    journal = {American Journal of Roentgenology},
    volume = {143},
    number = {5},
    pages = {1101-1104},
    abstract = { The premise is suggested that attenuation in CT scanning should be expressed in terms of physical density rather than CT numbers. A simple experiment was performed to establish a calibration curve of physical density vs. CT number which, within the constraints of beam hardening and other sources of CT number variation and drift, is unique to the specific scanner being calibrated. By expressing attenuation values in terms of physical density, the mass in grams of any organ or tumor can be calculated in vivo, from its volume determined also by CT. As an example, density of bone becomes additional information with any CT scan done for another purpose that includes plane(s) across a skeletal structure. },
}


@article{Nguyen2021,
    author = {Nguyen, Van and Sanctorum, Joaquim G. and Van Wassenbergh, Sam and Dirckx, Joris J. J. and Sijbers, Jan and De Beenhouwer, Jan},
    year = {2021},
    title = {Geometry Calibration of a Modular Stereo Cone-Beam X-ray CT System},
    doi = {10.3390/jimaging7030054},
    journal = {Journal of Imaging},
    volume = {7},
    number = {3},
    article-number = {54},
    url = {https://www.mdpi.com/2313-433X/7/3/54},
    pubmedid = {34460710},
    issn = {2313-433X},
    abstract = {Compared to single source systems, stereo X-ray CT systems allow acquiring projection data within a reduced amount of time, for an extended field-of-view, or for dual X-ray energies. To exploit the benefit of a dual X-ray system, its acquisition geometry needs to be calibrated. Unfortunately, in modular stereo X-ray CT setups, geometry misalignment occurs each time the setup is changed, which calls for an efficient calibration procedure. Although many studies have been dealing with geometry calibration of an X-ray CT system, little research targets the calibration of a dual cone-beam X-ray CT system. In this work, we present a phantom-based calibration procedure to accurately estimate the geometry of a stereo cone-beam X-ray CT system. With simulated as well as real experiments, it is shown that the calibration procedure can be used to accurately estimate the geometry of a modular stereo X-ray CT system thereby reducing the misalignment artifacts in the reconstruction volumes.},
}

@online{Normann2016,
    author = {Normann, Ben David},
    year = {2016},
    title = {{Gauss' Law of Error Propagation `'Explained''}},
    organization = {{Norwegian University of Science and Technology (NTNU), Department of Physics}},
    url = {https://penofben.files.wordpress.com/2016/02/gausserrorpropagation2.pdf},
    note = {accessed 2023-07-11},
}


@article{Phillips1997,
    author = {Phillips, D.H. and Lannutti, J.J.},
    year = {1997},
    title = {{Measuring physical density with X-ray computed tomography}},
    doi = {10.1016/S0963-8695(97)00020-0},
    journal = {{NDT \& E International}},
    volume = {30},
    number = {6},
    pages = {339-350},
    issn = {0963-8695},
    url = {https://www.sciencedirect.com/science/article/pii/S0963869597000200},
    keywords = {CT, computed tomography, ceramics, powders, compaction, density},
    abstract = {X-ray computed tomography (CT) can quantify variations in material density. However, little practical information concerning accurate translation of CT numbers (an approximation of the material's linear attenuation coefficient) into mass density exists. We describe our development of this methodology. Issues addressed include the physics of mapping CT density to mass density; development and scanning of density standards; post-reconstruction filtering to reduce the effects of quantum noise; and segmentation of the object data from the surrounding medium. Examples of our use of this procedure in studying density gradients during powder pressing and firing are given.},
}

@article{Phelps1975,
    author = {Phelps, Michael E. and Gado, Mokhtar H. and Hoffman, Edward J.},
    year = {1975},
    title = {Correlation of Effective Atomic Number and Electron Density with Attenuation Coefficients Measured with Polychromatic X Rays},
    doi = {10.1148/117.3.585},
    journal = {Radiology},
    volume = {117},
    number = {3},
    pages = {585-588},
    abstract = { Attenuation coefficients of nine different plastics and water were measured with EMI computed transaxial tomography (CT) and radioisotopic sources with photons of 14 to 136 keV. The EMI values were correlated with physical density, electron density and atomic number cubed (Z3) The best correlation was obtained with electron density, the exception being the value for water. This discrepancy was explained on the basis of Z-dependent photoelectric absorption with verification from monoenergetic measurements. },
}

@article{Sanctorum2020,
    author = {Sanctorum, Joaquim G and Van Wassenbergh, Sam and Nguyen, Van and De Beenhouwer, Jan and Sijbers, Jan and Dirckx, Joris JJ},
    year = {2020},
    title = {Projection-angle-dependent distortion correction in high-speed image-intensifier-based x-ray computed tomography},
    doi = {10.1088/1361-6501/abb33e},
    journal = {Measurement Science and Technology},
    publisher = {IOP Publishing},
    volume = {32},
    number = {3},
    pages = {035404},
}


@article{Sijbers2004,
    author = {Sijbers, Jan and Postnov, Andrei },
    year = {2004},
    title = {Reduction of ring artefacts in high resolution micro-CT reconstructions},
    doi = {10.1088/0031-9155/49/14/N06},
    journal = {Physics in Medicine \& Biology},
    month = {jul},
    volume = {49},
    number = {14},
    pages = {N247},
    abstract = {High resolution micro-CT images are often corrupted by ring artefacts, prohibiting quantitative analysis and hampering post processing. Removing or at least significantly reducing such artefacts is indispensable. However, since micro-CT systems are pushed to the extremes in the quest for the ultimate spatial resolution, ring artefacts can hardly be avoided. Moreover, as opposed to clinical CT systems, conventional correction schemes such as flat-field correction do not lead to satisfactory results. Therefore, in this note a simple but efficient and fast post processing method is proposed that effectively reduces ring artefacts in reconstructed μ-CT images.},
}

@article{Six2019,
    author = {Six, Nathana\"{e}l and De Beenhouwer, Jan and Sijbers, Jan},
    year = {2019},
    title = {{poly-DART: A discrete algebraic reconstruction technique for polychromatic X-ray CT}},
    doi = {10.1364/OE.27.033670},
    journal = {Opt. Express},
    keywords = {Image quality; Image reconstruction; Inverse problems; Magnetic resonance imaging; X ray computed tomography; X ray imaging},
    number = {23},
    pages = {33670--33682},
    publisher = {Optica Publishing Group},
    volume = {27},
    month = {Nov},
    url = {https://opg.optica.org/oe/abstract.cfm?URI=oe-27-23-33670},
    abstract = {The discrete algebraic reconstruction technique (DART) is a tomographic method to reconstruct images from X-ray projections in which prior knowledge on the number of object materials is exploited. In monochromatic X-ray CT (e.g., synchrotron), DART has been shown to lead to high-quality reconstructions, even with a low number of projections or a limited scanning view. However, most X-ray sources are polychromatic, leading to beam hardening effects, which significantly degrade the performance of DART. In this work, we propose a new discrete tomography algorithm, poly-DART, that exploits sparsity in the attenuation values using DART and simultaneously accounts for the polychromatic nature of the X-ray source. The results show that poly-DART leads to a vastly improved segmentation on polychromatic data obtained from Monte Carlo simulations as well as on experimental data, compared to DART.},
}

@inproceedings{Tanabe2005,
    author = {Tanabe, Setsuhisa and Fujita, Shunsuke and Yoshihara, Satoru and Sakamoto, Akihiko and Yamamoto, Shigeru},
    year = {2005},
    title = {{YAG glass-ceramic phosphor for white LED (II): luminescence characteristics}},
    doi = {10.1117/12.614681},
    organization = {International Society for Optics and Photonics},
    volume = {5941},
    booktitle = {Fifth International Conference on Solid State Lighting},
    editor = {Ian T. Ferguson and John C. Carrano and Tsunemasa Taguchi and Ian E. Ashdown},
    publisher = {SPIE},
    pages = {594112},
    keywords = {white LED, phosphors, YAG, glass-ceramic, Solid state lighting, Cerium, Gadolinium},
}


@article{VandeCasteele2004,
    title = {{A model-based correction method for beam hardening artefacts in X-ray microtomography}},
    year = {2004},
    author = {Van de Casteele, Elke and Van Dyck, Dirk and Sijbers, Jan and Raman, Erik},
    journal = {{Journal of X-ray Science and Technology}},
    volume = {12},
    number = {1},
    pages = {43--57},
    publisher = {IOS Press},
}

@article{VanGompel2011,
    author = {Van Gompel, G. and Van Slambrouck, K. and Defrise, M. and Batenburg, K. J. and de Mey, J. and Sijbers, J. and Nuyts, J.},
    year = {2011},
    title = {Iterative correction of beam hardening artifacts in CT},
    doi = {10.1118/1.3577758},
    journal = {Medical Physics},
    volume = {38},
    number = {S1},
    pages = {S36-S49},
    keywords = {Computed tomography, Artifacts and distortion, Reconstruction, computerised tomography, image reconstruction, iterative methods, medical image processing, X-ray absorption, computed tomography, beam hardening, Computed tomography, Image reconstruction, Medical imaging, Medical image reconstruction, Materials properties, Medical image segmentation, Medical image artifacts, Iteration theory, Photons, Optimization},
    url = {https://aapm.onlinelibrary.wiley.com/doi/abs/10.1118/1.3577758},
    abstract = {Purpose: To reduce beam hardening artifacts in CT in case of an unknown x-ray spectrum and unknown material properties. Methods: The authors assume that the object can be segmented into a few materials with different attenuation coefficients, and parameterize the spectrum using a small number of energy bins. The corresponding unknown spectrum parameters and material attenuation values are estimated by minimizing the difference between the measured sinogram data and a simulated polychromatic sinogram. Three iterative algorithms are derived from this approach: two reconstruction algorithms IGR and IFR, and one sinogram precorrection method ISP. Results: The methods are applied on real x-ray data of a high and a low-contrast phantom. All three methods successfully reduce the cupping artifacts caused by the beam polychromaticity in such a way that the reconstruction of each homogeneous region is to good accuracy homogeneous, even in case the segmentation of the preliminary reconstruction image is poor. In addition, the results show that the three methods tolerate relatively large variations in uniformity within the segments. Conclusions: We show that even without prior knowledge about materials or spectrum, effective beam hardening correction can be obtained.},
}


@online{WikipediaMOI,
    author = {{Wikipedia/Moment of Inertia}},
    year = {2023},
    title = {Moment of Inertia Tensor},
    organization = {Wikimedia Foundation},
    url = {https://en.wikipedia.org/wiki/Moment_of_inertia#Inertia_tensor},
    note = {accessed 2023-07-09},
}

@inproceedings{Yang2021,
    author = {Yang, Qiheng and Chakraborty, Nirjhor and Lakshtanov, Dmitry and Sheppard, Adrian and Kingston, Andrew},
    year = {2021},
    title = {{Density estimation in x-ray computed tomography using the Alvarez-Macovski model}},
    doi = {10.1117/12.2595473},
    booktitle = {{Developments in X-Ray Tomography XIII}},
    volume = {11840},
    pages = {64--77},
    organization = {SPIE Digital Library},
}

@article{Zscheile1934,
    author = {Zscheile, F. Paul},
    year = {1934},
    title = {{An Improved Method for the Purification of Chlorophylls A and B; Quantitative Measurement of Their Absorption Spectra; Evidence for the Existence of a Third Component of Chlorophyll}},
    doi = {10.1086/334429},
    journal = {Botanical Gazette},
    volume = {95},
    number = {4},
    pages = {529-562},
    abstract = { 1. An improved method for the isolation of chlorophyll components a and b has been developed. The methods of WILLSTATTER and STOLL and of TSWETT were combined and modified. The final purification processes involve differential adsorption on talc and fractional precipitation from petroleum ether, for components a and b respectively. The steps of the procedure are presented in detail. 2. The absorption spectra of chlorophylls a and b were measured accurately from λ 3950-7800 Å. by a photoelectric method. Absorption coefficients at the maxima and minima were determined with an accuracy of 1.0\%. The visible spectrum of each component consists of seven bands. 3. Spectral data indicate that the components prepared by WILLSTATTER and STOLL and by TSWETT were not separated completely from one another. The spectral method for detection of impurities is discussed. 4. A comparative study was made of the colors of a and b in various solvents and of certain chlorophyll derivatives. 5. Different tests of purity are discussed and it is concluded that a critical examination of the absorption spectrum is the most reliable and sensitive test. 6. Sources of leaf material and component yields are presented. 7. The improved preparation procedure is critically compared with previous methods. 8. It is suggested that there is at least one component other than chlorophylls a and b in the chlorophyll complex. Possible sources of error in the purification procedure are discussed. 9. Attempts to isolate the third "component c" were unsuccessful. Its properties are intermediate between those of components a and b. 10. Quantitative analytical data affirm the existence of a third component c. },
}

@online{2022Probability,
    author = {LibreTexts},
    year = {2022},
    title = {{29. Introduction to Quantum Physics: Probability and The Heisenberg Uncertainty Principle}},
    organization = {LibreTexts College Physics 1e},
    url = {https://phys.libretexts.org/@go/page/2763},
    note = {accessed 2023-07-17},
}

@article{Busemeyer2015,
    author = { Busemeyer, Jerome R. and Wang, Zheng },
    year = {2015},
    title = {{What Is Quantum Cognition, and How Is It Applied to Psychology?}},
    doi = {10.1177/0963721414568663},
    journal = {Current Directions in Psychological Science},
    volume = {24},
    number = {3},
    pages = {163-169},
    abstract = { Quantum cognition is a new research program that uses mathematical principles from quantum theory as a framework to explain human cognition, including judgment and decision making, concepts, reasoning, memory, and perception. This research is not concerned with whether the brain is a quantum computer. Instead, it uses quantum theory as a fresh conceptual framework and a coherent set of formal tools for explaining puzzling empirical findings in psychology. In this introduction, we focus on two quantum principles as examples to show why quantum cognition is an appealing new theoretical direction for psychology: complementarity, which suggests that some psychological measures have to be made sequentially and that the context generated by the first measure can influence responses to the next one, producing measurement order effects, and superposition, which suggests that some psychological states cannot be defined with respect to definite values but, instead, that all possible values within the superposition have some potential for being expressed. We present evidence showing how these two principles work together to provide a coherent explanation for many divergent and puzzling phenomena in psychology. },
}

@article{Aerts1995,
    title={{Applications of quantum statistics in psychological studies of decision processes}},
    year={1995},
    author={Aerts, Diedrik and Aerts, Sven},
    doi={10.1007/BF00208726},
    journal={Foundations of Science},
    volume={1},
    pages={85--97},
    publisher={Springer},
}

@article{Shmueli2010,
    author = {Shmueli, Galit },
    year = {2010},
    title = {{To Explain or to Predict?}},
    doi = {10.1214/10-STS330},
    journal = {Statistical Science},
    volume = {25},
    number = {3},
    publisher = {Institute of Mathematical Statistics},
    pages = {289 -- 310},
    keywords = {causality, data mining, Explanatory modeling, predictive modeling, predictive power, scientific research, statistical strategy},
}

@article{Shmueli2011,
    author = {Shmueli, Galit and Koppius, Otto R.},
    year = {2011},
    title = {{Predictive Analytics in Information Systems Research}},
    doi = {10.2307/23042796},
    journal = {{MIS Quarterly}},
    ISSN = {02767783},
    URL = {http://www.jstor.org/stable/23042796},
    abstract = {This research essay highlights the need to integrate predictive analytics into information systems research and shows several concrete ways in which this goal can be accomplished. Predictive analytics include empirical methods (statistical and other) that generate data predictions as well as methods for assessing predictive power. Predictive analytics not only assist in creating practically useful models, they also play an important role alongside explanatory modeling in theory building and theory testing. We describe six roles for predictive analytics: new theory generation, measurement development, comparison of competing theories, improvement of existing models, relevance assessment, and assessment of the predictability of empirical phenomena. Despite the importance of predictive analytics, we find that they are rare in the empirical IS literature. Extant IS literature relies nearly exclusively on explanatory statistical modeling, where statistical inference is used to test and evaluate the explanatory power of underlying causal models, and predictive power is assumed to follow automatically from the explanatory model. However, explanatory power does not imply predictive power and thus predictive analytics are necessary for assessing predictive power and for building empirical models that predict well. To show that predictive analytics and explanatory statistical modeling are fundamentally disparate, we show that they are different in each step of the modeling process. These differences translate into different final models, so that a pure explanatory statistical model is best tuned for testing causal hypotheses and a pure predictive model is best in terms of predictive power. We convert a well-known explanatory paper on TAM to a predictive context to illustrate these differences and show how predictive analytics can add theoretical and practical value to IS research.},
    number = {3},
    pages = {553--572},
    publisher = {Management Information Systems Research Center, University of Minnesota},
    urldate = {2023-07-17},
    volume = {35},
}

@article{Alexander1989,
    author = {Alexander, R. M.},
    year = {1989},
    title = {Optimization and gaits in the locomotion of vertebrates},
    doi = {10.1152/physrev.1989.69.4.1199},
    journal = {Physiological Reviews},
    volume = {69},
    number = {4},
    pages = {1199-1227},
}

@article{Polk2004,
    author = {Polk, J.D. },
    year = {2004},
    title = {{Influences of limb proportions and body size on locomotor kinematics in terrestrial primates and fossil hominins}},
    doi = {10.1016/j.jhevol.2004.07.003},
    journal = {Journal of Human Evolution},
    volume = {47},
    number = {4},
    pages = {237-252},
    issn = {0047-2484},
    url = {https://www.sciencedirect.com/science/article/pii/S0047248404001022},
    keywords = {Kinematics, Hominin, Posture, Biomechanics, Locomotion, Mechanical advantage, Cercopithecine monkey},
    abstract = {During locomotion, mammalian limb postures are influenced by many factors including the animal's limb length and body mass. Polk (2002) compared the gait of similar-sized cercopithecine monkeys that differed limb proportions and found that longer-limbed monkeys usually adopt more extended joint postures than shorter-limbed monkeys in order to moderate their joint moments. Studies of primates as well as non-primate mammals that vary in body mass have demonstrated that larger animals use more extended limb postures than smaller animals. Such extended postures in larger animals increase the extensor muscle mechanical advantage and allow postures to be maintained with relatively less muscular effort (Polk, 2002; Biewener 1989). The results of these previous studies are used here to address two anthropological questions. The first concerns the postural effects of body mass and limb proportion differences between australopithecines and members of the genus Homo. That is, H. erectus and later hominins all have larger body mass and longer legs than australopithecines, and these anatomical differences suggest that Homo probably used more extended postures and probably required relatively less muscular force to resist gravity than the smaller and shorter-limbed australopithecines. The second question investigates how animals with similar size but different limb proportions differ in locomotor performance. The effects of limb proportions on gait are relevant to inferring postural and locomotor differences between Neanderthals and modern Homo sapiens which differ in their crural indices and relative limb length. This study demonstrates that primates with relatively long limbs achieve higher walking speeds while using lower stride frequencies and lower angular excursions than shorter-limbed monkeys, and these kinematic differences may allow longer-limbed taxa to locomote more efficiently than shorter-limbed species of similar mass. Such differences may also have characterized the gait of Homo sapiens in comparison to Neanderthals, but more experimental data on humans that vary in limb proportions are necessary in order to evaluate this question more thoroughly.},
}

@article{Stamos2023,
    author = {Stamos, Peter A. and Alemseged, Zeresenay},
    year = {2023},
    title = {{Hominin locomotion and evolution in the Late Miocene to Late Pliocene}},
    doi = {10.1016/j.jhevol.2023.103332},
    journal = {Journal of Human Evolution},
    volume = {178},
    pages = {103332},
    issn = {0047-2484},
    url = {https://www.sciencedirect.com/science/article/pii/S004724842300009X},
    keywords = {Early hominins, Locomotion, Bipedal, Arboreal, Paleobiology, Stabilizing selection},
    abstract = {In this review, we present on the evolution of the locomotor adaptation of hominins in the Late Miocene to Late Pliocene, with emphasis on some of the prominent advances and debates that have occurred over the past fifty years. We start with the challenging issue of defining hominin locomotor grades that are currently used liberally and offer our own working definitions of facultative, habitual, and obligate bipedalism. We then discuss the nature of the Pan-Homo last common ancestor and characterize the locomotor adaptation of Sahelanthropus, Orrorin, and Ardipithecus—often referred to as facultative bipeds—and examine the debates on the extent of bipedality and arboreality in these taxa. Moreover, the question of Middle Pliocene hominin locomotor diversity is addressed based on information derived from the ‘Little Foot’ specimen from Sterkfontein, footprints from Laetoli, and the Burtele Foot in Ethiopia. Our review suggests that the most convincing evidence for locomotor diversity comes from Burtele, whereas the evidence from Sterkfontein and Laetoli is unconvincing and equivocal, respectively. Finally, we address the decades old issue of the significance of arboreality in the otherwise habitual biped, Australopithecus, with emphasis on Australopithecus afarensis and its implications for the paleobiology of these creatures. We conclude that many of the apelike features encountered, mostly in the upper part of the Australopithecus skeleton, were retained for their significance in climbing. Approaches that have investigated character plasticity and those exploring internal bone structure have shown that the shoulder and limbs in Au. afarensis and Australopithecus africanus were involved in arboreal activities that are thought to be key for feeding, nesting, and predator avoidance. We conclude that many of the so-called retained ape-like features persisted due to stabilizing selection, that early hominins engaged in a considerable amount of arboreality even after Australopithecus had become a habitual biped, and arboreality only ceased to be an important component of hominin locomotor behavior after the emergence of Homo erectus.},
}

@article{Cazenave2023,
    author = {Cazenave, Marine and Kivell, Tracy L.},
    year = {2023},
    title = {{Challenges and perspectives on functional interpretations of australopith postcrania and the reconstruction of hominin locomotion}},
    doi = {10.1016/j.jhevol.2022.103304},
    journal = {Journal of Human Evolution},
    volume = {175},
    pages = {103304},
    issn = {0047-2484},
    url = {https://www.sciencedirect.com/science/article/pii/S0047248422001646},
    keywords = { Bone functional adaptation, Trabecular bone, Cortical bone, African apes},
    abstract = {In 1994, Hunt published the ‘postural feeding hypothesis’—a seminal paper on the origins of hominin bipedalism—founded on the detailed study of chimpanzee positional behavior and the functional inferences derived from the upper and lower limb morphology of the Australopithecus afarensis A.L. 288-1 partial skeleton. Hunt proposed a model for understanding the potential selective pressures on hominins, made robust, testable predictions based on Au. afarensis functional morphology, and presented a hypothesis that aimed to explain the dual functional signals of the Au. afarensis and, more generally, early hominin postcranium. Here we synthesize what we have learned about Au. afarensis functional morphology and the dual functional signals of two new australopith discoveries with relatively complete skeletons (Australopithecus sediba and StW 573 ‘Australopithecus prometheus’). We follow this with a discussion of three research approaches that have been developed for the purpose of drawing behavioral inferences in early hominins: (1) developments in the study of extant apes as models for understanding hominin origins; (2) novel and continued developments to quantify bipedal gait and locomotor economy in extant primates to infer the locomotor costs from the anatomy of fossil taxa; and (3) novel developments in the study of internal bone structure to extract functional signals from fossil remains. In conclusion of this review, we discuss some of the inherent challenges of the approaches and methodologies adopted to reconstruct the locomotor modes and behavioral repertoires in extinct primate taxa, and notably the assessment of habitual terrestrial bipedalism in early hominins.},
}

@article{Arroyave2022,
    title = {Kinematic modeling at the ant scale: propagation of model parameter uncertainties},
    author = {Arroyave-Tobon, Santiago and Drapin, Jordan and Kaniewski, Anton and Linares, Jean-Marc and Moretto, Pierre},
    doi = {10.3389/fbioe.2022.767914},
    journal = {Frontiers in Bioengineering and Biotechnology},
    volume = {10},
    pages = {767914},
    year = {2022},
    publisher = {Frontiers},
}

@article{Myers2015,
    title = {A probabilistic approach to quantify the impact of uncertainty propagation in musculoskeletal simulations},
    author = {Myers, Casey A and Laz, Peter J and Shelburne, Kevin B and Davidson, Bradley S},
    doi = {10.1007/s10439-014-1181-7},
    journal = {Annals of biomedical engineering},
    volume = {43},
    pages = {1098--1111},
    year = {2015},
    publisher = {Springer},
}

@online{NASA2021,
    author = {NASA},
    year = {2021},
    title = {Conservation of Momentum},
    organization = {NASA, ed. Nancy Hall },
    url = {https://www.grc.nasa.gov/www/k-12/airplane/conmo.html},
    note = {accessed 2023-07-18}},
}


@article{Nyakatura2019,
    author = {Nyakatura, John A. and Melo, Kamilo and Horvat, Tomislav and Karakasiliotis, Kostas and Allen, Vivian R. and Andikfar, Amir and Andrada, Emanuel and Arnold, Patrick and Laustr{\"o}er, Jonas and Hutchinson, John R. and Fischer, Martin S. and Ijspeer, Auke J.},
    year = {2019},
    title = {Reverse-engineering the locomotion of a stem amniote},
    doi = {10.1038/s41586-018-0851-2},
    journal = {Nature},
    volume = {565},
    number = {7739},
    pages = {351--355},
    publisher = {Nature Publishing Group},
}

@article{Spengler2019,
    author = {Spengler, Dietmar and Rintz, Nele and Krause, Martin F.},
    year = {2019},
    title = {{An Unsettled Promise: The Newborn Piglet Model of Neonatal Acute Respiratory Distress Syndrome (NARDS). Physiologic Data and Systematic Review}},
    doi = {10.3389/fphys.2019.01345},
    journal = {Frontiers in Physiology},
    volume = {10},
    url = {https://www.frontiersin.org/articles/10.3389/fphys.2019.01345},
    issn = {1664-042X},
    abstract = {Despite great advances in mechanical ventilation and surfactant administration for the newborn infant with life-threatening respiratory failure no specific therapies are currently established to tackle major pro-inflammatory pathways. The susceptibility of the newborn infant with neonatal acute respiratory distress syndrome (NARDS) to exogenous surfactant is linked with a suppression of most of the immunologic responses by the innate immune system, however, additional corticosteroids applied in any severe pediatric lung disease with inflammatory background do not reduce morbidity or mortality and may even cause harm. Thus, the neonatal piglet model of acute lung injury serves as an excellent model to study respiratory failure and is the preferred animal model for reasons of availability, body size, similarities of porcine and human lung, robustness, and costs. In addition, similarities to the human toll-like receptor 4, the existence of intraalveolar macrophages, the sensitivity to lipopolysaccharide, and the production of nitric oxide make the piglet indispensable in anti-inflammatory research. Here we present the physiologic and immunologic data of newborn piglets from three trials involving acute lung injury secondary to repeated airway lavage (and others), mechanical ventilation, and a specific anti-inflammatory intervention via the intratracheal route using surfactant as a carrier substance. The physiologic data from many organ systems of the newborn piglet—but with preference on the lung—are presented here differentiating between baseline data from the uninjured piglet, the impact of acute lung injury on various parameters (24 h), and the follow up data after 72 h of mechanical ventilation. Data from the control group and the intervention groups are listed separately or combined. A systematic review of the newborn piglet meconium aspiration model and the repeated airway lavage model is finally presented. While many studies assessed lung injury scores, leukocyte infiltration, and protein/cytokine concentrations in bronchoalveolar fluid, a systematic approach to tackle major upstream pro-inflammatory pathways of the innate immune system is still in the fledgling stages. For the sake of newborn infants with life-threatening NARDS the newborn piglet model still is an unsettled promise offering many options to conquer neonatal physiology/immunology and to establish potent treatment modalities.},
}

@article{Cooper1975,
    author = { Cooper, J. E.},
    year = {1975},
    title = {The use of the pig as an animal model to study problems associated with low birthweight},
    doi = {10.1258/002367775780957188},
    journal = {Laboratory Animals},
    volume = {9},
    number = {4},
    pages = {329-336},
    abstract = { Attention is drawn to some of the consequences associated with the postnatal development of low birthweight human infants and the use of the piglet as a model to study such problems. A description is given of the production and methods of rearing of these animals along with an outline of studies currently in progress. },
}

@article{Widdowson1971,
    author = {Widdowson, E.M.},
    year = {1971},
    title = {{Intra-Uterine Growth Retardation in the Pig. I. Organ Size and Cellular Development at Birth and after Growth to Maturity: I. Organ Size and Cellular Development at Birth and after Growth to Maturity}},
    doi = {10.1159/000240427},
    journal = {Biologia Neonatorum},
    volume = {19},
    number = {4-6},
    pages = {329-340},
    month = {09},
    issn = {0523-6525},
}
@article{MotaRojas2011,
    author = {Mota-Rojas, D and Orozco-Gregorio, H and Villanueva-Garcia, D and Bonilla-Jaime, H and Suarez-Bonilla, X and Hernandez-Gonzalez, R and Roldan-Santiago, P and Trujillo-Ortega, ME and others},
    year = {2011},
    title = {Foetal and neonatal energy metabolism in pigs and humans: a review},
    doi = {10.17221/1565-VETMED},
    journal = {Veterinarni Medicina},
    volume = {56},
    number = {5},
    pages = {215--225},
    url = {https://www.agriculturejournals.cz/pdfs/vet/2011/05/01.pdf},
}

@article{Book1974,
    author = {Book, Steven A. and Bustad, Leo K.},
    year = {1974},
    title = {{The Fetal and Neonatal Pig in Biomedical Research}},
    doi = {10.2527/jas1974.385997x},
    journal = {Journal of Animal Science},
    volume = {38},
    number = {5},
    pages = {997-1002},
    month = {05},
    abstract = {{The application of fetal and neonatal pigs to research has led to a number of advances in perinatal biology and medicine. Baby pigs have been utilized in diversified areas of biomedical research, including embryology, teratology, nutrition, metabolism and immunology. They have also found use in the study of several pathologic conditions, both spontaneous and iatrogenic, that occur in the human infant.}},
    issn = {0021-8812},
}

@article{Mellor1986,
    author = {Mellor, D. J. and Cockburn, F.},
    year = {1986},
    title = {A comparison of energy metabolism in the new-born infant, piglet and lamb},
    doi = {10.1113/expphysiol.1986.sp002995},
    journal = {Quarterly Journal of Experimental Physiology},
    volume = {71},
    number = {3},
    pages = {361-379},
    url = {https://physoc.onlinelibrary.wiley.com/doi/abs/10.1113/expphysiol.1986.sp002995},
    abstract = {Characteristics of energy metabolism in the new-born infant, piglet and lamb have been compared quantitatively in order to assess how the constraints imposed by the availabilities of energy substrates in body reserves and colostrum differ between species and affect the new-born's well being during the first day after birth. Three air temperature ranges, described as thermoneutral (32-38 °C), moderate (18-26 °C) and cold (0-10 °C) and representing the usual birth environments of infants, piglets and lambs, respectively, have been considered. The analysis revealed the following noteworthy points. Carbohydrate and lipid are the major energy substrates for heat production because protein catabolism is minimal during the first day after birth in all three species. The availability of carbohydrate determines how long the new-born can avoid hypoglycaemia, which threatens well being because it leads to hypothermia or compromised cerebral function, but lipid availability can affect the periods for which the carbohydrate can last. Thus, in unfed piglets and lambs the available reserves of liver and skeletal muscle glycogen (g/kg body weight) are similar in normal (n.) and growth retarded (g.r.) individuals, but glycogen exhaustion occurs earlier in g.r. new-borns because a reduced lipid availability in them increases their dependence on carbohydrate. In contrast, lipid energy is plentiful in g.r., preterm (p.) and n. infants, so that the faster depletion of glycogen in g.r./p. than in n. individuals is primarily due to a restricted prenatal glycogen deposition in the former. The usual colostrum intakes of n. infants are very low during the first day, but their body reserves can supply the required energy, the major source of carbohydrate being liver glycogen. However, g.r./p. infants require supplementary feeding, the choice of feed being determined by factors such as the intakes the infants can achieve, the carbohydrate content of the feed and the need to ensure a balanced supply of minerals, electrolytes and other substances. In their usual birth environments piglets and lambs, whether growth retarded or not, require colostrum to avoid hypothermia during the first day. The colostrum of both species is rich in lipid, which corrects any deficit in the new-born and thus extends the availability of glycogen, but at the usual colostrum intakes the amounts of lactose can provide sufficient carbohydrate energy for only about half a day. Piglets and lambs, even when fed fully, are therefore obliged to call on their body glycogen reserves in order to make up the difference. After the first day in all three species milk must rapidly become the only source of carbohydrate, lipid and protein. It is suggested that despite differences between them, the piglet or lamb could prove to be useful animal models of the infant's metabolism, but only if the experimental conditions are chosen carefully.},
}

@article{Williams1974,
    author = {Williams, Margaret L. and Galvis, Antonio G.},
    year = {1974},
    title = {Pulmonary Complications in Infants. Symposium on Pulmonary Problems in Surgery},
    doi = {10.1016/S0039-6109(16)40443-3},
    journal = {Surgical Clinics of North America},
    volume = {54},
    number = {5},
    pages = {1137-1154},
    issn = {0039-6109},
    url = {https://www.sciencedirect.com/science/article/pii/S0039610916404433},
    abstract = {The advent of neonatal intensive care units has led to familiarity with problems of alveolar instability, ventilation-perfusion inequality, airway obstruction, and interstitial disease, all of which may be seen in infants who must have surgery in the newborn period. The basis of these advances has been an increased understanding of infant pulmonary physiology.},
}

@article{Mudd2017,
    author = {Mudd, Austin T and Dilger, Ryan N},
    year = {2017},
    title = {Early-Life Nutrition and Neurodevelopment: Use of the Piglet as a Translational Model},
    doi = {10.3945/an.116.013243},
    journal = {Advances in Nutrition},
    volume = {8},
    number = {1},
    pages = {92-104},
    issn = {2161-8313},
    url = {https://www.sciencedirect.com/science/article/pii/S2161831323002259},
    keywords = {piglet, pediatric nutrition, neurodevelopment, magnetic resonance imaging, animal model, early-life nutrition},
    abstract = {Optimal nutrition early in life is critical to ensure proper structural and functional development of infant organ systems. Although pediatric nutrition historically has emphasized research on the relation between nutrition, growth rates, and gastrointestinal maturation, efforts increasingly have focused on how nutrition influences neurodevelopment. The provision of human milk is considered the gold standard in pediatric nutrition; thus, there is interest in understanding how functional nutrients and bioactive components in milk may modulate developmental processes. The piglet has emerged as an important translational model for studying neurodevelopmental outcomes influenced by pediatric nutrition. Given the comparable nutritional requirements and strikingly similar brain developmental patterns between young pigs and humans, the piglet is being used increasingly in developmental nutritional neuroscience studies. The piglet primarily has been used to assess the effects of dietary fatty acids and their accretion in the brain throughout neurodevelopment. However, recent research indicates that other dietary components, including choline, iron, cholesterol, gangliosides, and sialic acid, among other compounds, also affect neurodevelopment in the pig model. Moreover, novel analytical techniques, including but not limited to MRI, behavioral assessments, and molecular quantification, allow for a more holistic understanding of how nutrition affects neurodevelopmental patterns. By combining early-life nutritional interventions with innovative analytical approaches, opportunities abound to quantify factors affecting neurodevelopmental trajectories in the neonate. This review discusses research using the translational pig model with primary emphasis on early-life nutrition interventions assessing neurodevelopment outcomes, while also discussing nutritionally-sensitive methods to characterize brain maturation.},
}

@article{Lind2007,
    author = {Lind, Nanna Marie and Moustgaard, Anette and Jelsing, Jacob and Vajta, Gabor and Cumming, Paul and Hansen, Axel K.},
    year = {2007},
    title = {The use of pigs in neuroscience: Modeling brain disorders},
    doi = {10.1016/j.neubiorev.2007.02.003},
    journal = {Neuroscience \& Biobehavioral Reviews},
    volume = {31},
    number = {5},
    pages = {728-751},
    issn = {0149-7634},
    url = {https://www.sciencedirect.com/science/article/pii/S014976340700019X},
    keywords = {Pig, Swine, Brain, Behavior, Learning, Memory, Cognition, Anatomy, Receptor, Animal model, Ethics},
    abstract = {The use of pigs in neuroscience research has increased in the past decade, which has seen broader recognition of the potential of pigs as an animal for experimental modeling of human brain disorders. The volume of available background data concerning pig brain anatomy and neurochemistry has increased considerably in recent years. The pig brain, which is gyrencephalic, resembles the human brain more in anatomy, growth and development than do the brains of commonly used small laboratory animals. The size of the pig brain permits the identification of cortical and subcortical structures by imaging techniques. Furthermore, the pig is an increasingly popular laboratory animal for transgenic manipulations of neural genes. The present paper focuses on evaluating the potential for modeling symptoms, phenomena or constructs of human brain diseases in pigs, the neuropsychiatric disorders in particular. Important practical and ethical aspects of the use of pigs as an experimental animal as pertaining to relevant in vivo experimental brain techniques are reviewed. Finally, current knowledge of aspects of behavioral processes including learning and memory are reviewed so as to complete the summary of the status of pigs as a species suitable for experimental models of diverse human brain disorders.},
}

@article{Radlowski2014,
    author = {Radlowski, Emily C. AND Conrad, Matthew S. AND Lezmi, Stephane AND Dilger, Ryan N. AND Sutton, Brad AND Larsen, Ryan AND Johnson, Rodney W.},
    year = {2014},
    title = {A Neonatal Piglet Model for Investigating Brain and Cognitive Development in Small for Gestational Age Human Infants},
    doi = {10.1371/journal.pone.0091951},
    journal = {PLOS ONE},
    publisher = {Public Library of Science},
    month = {03},
    volume = {9},
    pages = {1-12},
    abstract = {The piglet was investigated as a potential model for studying brain and cognitive deficits associated with being born small for gestational age (SGA). Naturally farrowed SGA (0.7–1.0 kg BW) and average for gestational age (AGA, 1.3–1.6 kg BW) piglets were obtained on postnatal day (PD) 2, placed in individual cages, and provided a nutritionally adequate milk replacer diet (285 ml/kg/d). Beginning at PD14, performance in a spatial T-maze task was assessed. At PD28, piglets were anesthetized for magnetic resonance (MR) imaging to assess brain structure (voxel-based morphometry), connectivity (diffusion-tensor imaging) and metabolites in the hippocampus and corpus callosum (proton MR spectroscopy). Piglets born SGA showed compensatory growth such that BW of SGA and AGA piglets was similar (P>0.05), by PD15. Birth weight affected maze performance, with SGA piglets taking longer to reach criterion than AGA piglets (p<0.01). Total brain volume of SGA and AGA piglets was similar (P<0.05), but overall, SGA piglets had less gray matter than AGA piglets (p<0.01) and tended to have a smaller internal capsule (p = 0.07). Group comparisons between SGA and AGA piglets defined 9 areas (≥ 20 clusters) where SGA piglets had less white matter (p<0.01); 2 areas where SGA piglets had more white matter (p<0.01); and 3 areas where SGA piglets had more gray matter (p<0.01). The impact of being born SGA on white matter was supported by a lower (p<0.04) fractional anisotropy value for SGA piglets, suggesting reduced white matter development and connectivity. None of the metabolites measured were different between groups. Collectively, the results show that SGA piglets have spatial learning deficits and abnormal development of white matter. As learning deficits and abnormalities in white matter are common in SGA human infants, the piglet is a tractable translational model that can be used to investigate SGA-associated cognitive deficits and potential interventions.},
    number = {3},
}

@article{Fanous2020,
    author = {Fanous, Michael AND Caputo, Megan P. AND Lee, Young Jae AND Rund, Laurie A. AND Best-Popescu, Catherine AND Kandel, Mikhail E. AND Johnson, Rodney W. AND Das, Tapas AND Kuchan, Matthew J. AND Popescu, Gabriel},
    year = {2020},
    title = {Quantifying myelin content in brain tissue using color Spatial Light Interference Microscopy (cSLIM)},
    doi = {10.1371/journal.pone.0241084},
    journal = {PLOS ONE},
    publisher = {Public Library of Science},
    month = {11},
    volume = {15},
    pages = {1-13},
    abstract = {Deficient myelination of the brain is associated with neurodevelopmental delays, particularly in high-risk infants, such as those born small in relation to their gestational age (SGA). New methods are needed to further study this condition. Here, we employ Color Spatial Light Interference Microscopy (cSLIM), which uses a brightfield objective and RGB camera to generate pathlength-maps with nanoscale sensitivity in conjunction with a regular brightfield image. Using tissue sections stained with Luxol Fast Blue, the myelin structures were segmented from a brightfield image. Using a binary mask, those portions were quantitatively analyzed in the corresponding phase maps. We first used the CLARITY method to remove tissue lipids and validate the sensitivity of cSLIM to lipid content. We then applied cSLIM to brain histology slices. These specimens are from a previous MRI study, which demonstrated that appropriate for gestational age (AGA) piglets have increased internal capsule myelination (ICM) compared to small for gestational age (SGA) piglets and that a hydrolyzed fat diet improved ICM in both. The identity of samples was blinded until after statistical analyses.},
    number = {11},
}

@article{Leyshon2016,
    author = {Leyshon, Brian J and Radlowski, Emily C and Mudd, Austin T and Steelman, Andrew J and Johnson, Rodney W},
    year = {2016},
    title = {{Postnatal Iron Deficiency Alters Brain Development in Piglets}},
    doi = {10.3945/jn.115.223636},
    journal = {The Journal of Nutrition},
    volume = {146},
    number = {7},
    pages = {1420-1427},
    month = {06},
    abstract = {{Background: Cognitive deficits associated with postnatal iron deficiency (ID) suggest abnormal brain development, but little is known about animals with gyrencephalic brains.Objective: The objective was to assess the impact of ID on brain development in piglets.Methods: Male and female Yorkshire piglets were reared from postnatal day (PD) 2 until PD 29 or 30 by using milk replacer adequate [control (CON)] or deficient (100 compared with 10 mg/kg) in iron and subjected to MRI to assess brain macrostructure, microstructure, and metabolites in the dorsal hippocampi and intervening space. After MRI, brains were collected for histology. Hematocrit, hemoglobin, and liver iron were measured to determine iron status.Results: Hematocrit and hemoglobin in ID piglets were less than CON after PD 14 (P \\&lt; 0.001), and at the study end liver iron in ID piglets was less than CON (P \\&lt; 0.001). Brain region volumes were not affected by ID, but changes in brain composition were evident. ID piglets had less white matter in 78,305 voxels, with large clusters in the hippocampus and cortex. ID piglets had less gray matter in 13,625 voxels primarily in cortical areas and more gray matter in 28,017 voxels, most notably in olfactory bulbs and hippocampus. The major effect of ID on white matter was supported by lower fractional anisotropy values in the corpus callosum (0.300 compared with 0.284, P = 0.006) and in whole brain white matter (0.313 compared with 0.307, P = 0.002) in ID piglets. In coronal brain sections, corpus callosum width was less (P = 0.043) in ID piglets. Inositol was lower (P = 0.01) and phosphocholine was higher (P = 0.03) in hippocampus of ID piglets.Conclusions: Postnatal ID in piglets affects brain development, especially white matter. If the effects of ID persist, it might explain the lasting detrimental effects on cognition.}},
    issn = {0022-3166},
}

@article{Wu2006,
    author = {Wu, G. and Bazer, F. W. and Wallace, J. M. and Spencer, T. E.},
    year = {2006},
    title = {Intrauterine growth retardation: Implications for the animal sciences},
    doi = {10.2527/jas.2006-156},
    journal = {Journal of Animal Science},
    volume = {84},
    number = {9},
    pages = {2316-2337},
    month = {09},
    abstract = {{Intrauterine growth retardation (IUGR), defined as impaired growth and development of the mammalian embryo/fetus or its organs during pregnancy, is a major concern in domestic animal production. Fetal growth restriction reduces neonatal survival, has a permanent stunting effect on postnatal growth and the efficiency of feed/forage utilization in offspring, negatively affects whole body composition and meat quality, and impairs long-term health and athletic performance. Knowledge of the underlying mechanisms has important implications for the prevention of IUGR and is crucial for enhancing the efficiency of livestock production and animal health. Fetal growth within the uterus is a complex biological event influenced by genetic, epigenetic, and environmental factors, as well as maternal maturity. These factors impact on the size and functional capacity of the placenta, uteroplacental blood flows, transfer of nutrients and oxygen from mother to fetus, conceptus nutrient availability, the endocrine milieu, and metabolic pathways. Alterations in fetal nutrition and endocrine status may result in developmental adaptations that permanently change the structure, physiology, metabolism, and postnatal growth of the offspring. Impaired placental syntheses of nitric oxide (a major vasodilator and angiogenic factor) and polyamines (key regulators of DNA and protein synthesis) may provide a unified explanation for the etiology of IUGR in response to maternal undernutrition and overnutrition. There is growing evidence that maternal nutritional status can alter the epigenetic state (stable alterations of gene expression through DNA methylation and histone modifications) of the fetal genome. This may provide a molecular mechanism for the role of maternal nutrition on fetal programming and genomic imprinting. Innovative interdisciplinary research in the areas of nutrition, reproductive physiology, and vascular biology will play an important role in designing the next generation of nutrient-balanced gestation diets and developing new tools for livestock management that will enhance the efficiency of animal production and improve animal well being.}},
    issn = {0021-8812},
}

@article{Conrad2012,
    author = {Conrad, Matthew S. and Dilger, Ryan N. and Johnson, Rodney W.},
    year = {2012},
    title = {{Brain Growth of the Domestic Pig (Sus scrofa) from 2 to 24 Weeks of Age: A Longitudinal MRI Study}},
    doi = {10.1159/000339311},
    journal = {Developmental Neuroscience},
    volume = {34},
    number = {4},
    pages = {291-298},
    month = {07},
    abstract = {{An animal model with brain growth similar to humans, that can be used in MRI studies to investigate brain development, would be valuable. Our laboratory has developed and validated MRI methods for regional brain volume quantification in the neonatal piglet. The aim of this study was to utilize the MRI-based volume quantification technique in a longitudinal study to determine brain growth in domestic pigs from 2 to 24 weeks of age. MRI data were acquired from pigs 2–24 weeks of age using a 3-dimensional magnetization-prepared gradient echo sequence on a Magnetom Trio 3-tesla imager. Manual segmentation was performed for volume estimates of total brain, cortical, diencephalon, brainstem, cerebellar and hippocampal regions. Logistic modeling procedures were used to characterize brain growth. Total brain volume increased 130\% (±12\%) and 121\% (±7\%) from 2 to 24 weeks in males and females, respectively. The maximum increase in total brain volume occurred about the age of 4 weeks and 95\% of whole brain growth occurred by the age of 21–23 weeks. Logistical modeling suggests there are sexually dimorphic effects on brain growth. For example, in females, the cortex was smaller (p = 0.04). Furthermore, the maximum growth of the hippocampus occurred about 5 weeks earlier in females than males, and the window for hippocampal growth was significantly shorter in females than males (p = 0.02, p = 0.002 respectively). These sexual dimorphisms are similar to what is seen in humans. In addition to providing important data on brain growth for pigs, this study shows pigs can be used to obtain longitudinal MRI data. The large increase in brain volume in the postnatal period is similar to that of human neonates and suggests pigs can be used to investigate brain development.}},
    issn = {0378-5866},
}

@article{Dickerson1971,
    author={Dickerson, JWT and Merat, A and Widdowson, EM and others},
    year={1971},
    title={{Intra-uterine growth retardation in the pig. 3. The chemical structure of the brain.}},
    doi={10.1159/000240429},
    journal={Biology of the Neonate},
    volume={19},
    number={4/6},
    pages={354--362},
}

@article{Wootton1983,
    author = {R. Wootton and P. A. Flecknell and J. P. Royston and M. John},
    year = {1983},
    title = {Intrauterine growth retardation detected in several species by non-normal birthweight distributions},
    doi = {10.1530/jrf.0.0690659},
    journal = {Reproduction},
    publisher = {Bioscientifica Ltd},
    address = {Bristol, UK},
    volume = {69},
    number = {2},
    pages = {659 - 663},
    url = {https://rep.bioscientifica.com/view/journals/rep/69/2/jrf_69_2_032.xml},
}

@article{Timetree2017,
    author = {Kumar, Sudhir and Stecher, Glen and Suleski, Michael and Hedges, S. Blair},
    year = {2017},
    title = {{TimeTree: A Resource for Timelines, Timetrees, and Divergence Times}},
    doi = {10.1093/molbev/msx116},
    journal = {Molecular Biology and Evolution},
    volume = {34},
    number = {7},
    pages = {1812-1819},
    month = {04},
    abstract = {{Evolutionary information on species divergence times is fundamental to studies of biodiversity, development, and disease. Molecular dating has enhanced our understanding of the temporal patterns of species divergences over the last five decades, and the number of studies is increasing quickly due to an exponential growth in the available collection of molecular sequences from diverse species and large number of genes. Our TimeTree resource is a public knowledge-base with the primary focus to make available all species divergence times derived using molecular sequence data to scientists, educators, and the general public in a consistent and accessible format. Here, we report a major expansion of the TimeTree resource, which more than triples the number of species (\\&gt;97,000) and more than triples the number of studies assembled (\\&gt;3,000). Furthermore, scientists can access not only the divergence time between two species or higher taxa, but also a timetree of a group of species and a timeline that traces a species’ evolution through time. The new timetree and timeline visualizations are integrated with display of events on earth and environmental history over geological time, which will lead to broader and better understanding of the interplay of the change in the biosphere with the diversity of species on Earth. The next generation TimeTree resource is publicly available online at http://www.timetree.org.}},
    issn = {0737-4038},
}

@article{Liang2023,
    author={Liang, Fengyan and Yu, Shanshan and Pang, Siqi and Wang, Xiao and Jie, Jing and Gao, Fei and Song, Zhenhua and Li, Binbin and Liao, Wei-Hsin and Yin, Ming},
    year={2023},
    title={Non-human primate models and systems for gait and neurophysiological analysis},
    doi={10.3389/fnins.2023.1141567},
    journal={Frontiers in Neuroscience},
    volume={17},
    url={https://www.frontiersin.org/articles/10.3389/fnins.2023.1141567},
    issn={1662-453X},
    abstract={Brain–computer interfaces (BCIs) have garnered extensive interest and become a groundbreaking technology to restore movement, tactile sense, and communication in patients. Prior to their use in human subjects, clinical BCIs require rigorous validation and verification (V&V). Non-human primates (NHPs) are often considered the ultimate and widely used animal model for neuroscience studies, including BCIs V&V, due to their proximity to humans. This literature review summarizes 94 NHP gait analysis studies until 1 June, 2022, including seven BCI-oriented studies. Due to technological limitations, most of these studies used wired neural recordings to access electrophysiological data. However, wireless neural recording systems for NHPs enabled neuroscience research in humans, and many on NHP locomotion, while posing numerous technical challenges, such as signal quality, data throughout, working distance, size, and power constraint, that have yet to be overcome. Besides neurological data, motion capture (MoCap) systems are usually required in BCI and gait studies to capture locomotion kinematics. However, current studies have exclusively relied on image processing-based MoCap systems, which have insufficient accuracy (error: ≥4° and 9 mm). While the role of the motor cortex during locomotion is still unclear and worth further exploration, future BCI and gait studies require simultaneous, high-speed, accurate neurophysiological, and movement measures. Therefore, the infrared MoCap system which has high accuracy and speed, together with a high spatiotemporal resolution neural recording system, may expand the scope and improve the quality of the motor and neurophysiological analysis in NHPs.},
}

@article{Nardone2017,
    author = {Nardone, Raffaele  and Florea, Cristina and Höller, Yvonne and Brigo, Francesco and Versace, Viviana and Lochner, Piergiorgio and Golaszewski, Stefan and Trinka, Eugen},
    year = {2017},
    title = {Rodent, large animal and non-human primate models of spinal cord injury},
    doi = {10.1016/j.zool.2017.06.004},
    journal = {Zoology},
    volume = {123},
    pages = {101-114},
    issn = {0944-2006},
    url = {https://www.sciencedirect.com/science/article/pii/S0944200617300107},
    keywords = {Spinal cord injury, Animal models, Rodent models, Large animal models, Primate models},
    abstract = {In this narrative review we aimed to assess the usefulness of the different animal models in identifying injury mechanisms and developing therapies for humans suffering from spinal cord injury (SCI). Results obtained from rodent studies are useful but, due to the anatomical, molecular and functional differences, confirmation of these findings in large animals or non-human primates may lead to basic discoveries that cannot be made in rodent models and that are more useful for developing treatment strategies in humans. SCI in dogs can be considered as intermediate between rodent models and human clinical trials, but the primate models could help to develop appropriate methods that might be more relevant to humans. Ideally, an animal model should meet the requirements of availability and repeatability as well as reproduce the anatomical features and the clinical pathological changing process of SCI. An animal model that completely simulates SCI in humans does not exist. The different experimental models of SCI have advantages and disadvantages for investigating the different aspects of lesion development, recovery mechanisms and potential therapeutic interventions. The potential advantages of non-human primate models include genetic similarities, similar caliber/length of the spinal cord as well as biological and physiological responses to injury which are more similar to humans. Among the potential disadvantages, high operating costs, infrastructural requirements and ethical concerns should be considered. The translation from experimental repair strategies to clinical applications needs to be investigated in future carefully designed studies.},
}


@article{BoulinguezAmbroise2021,
    author = {Boulinguez-Ambroise, Grégoire and Herrel, Anthony and Berillon, Gilles and Young, Jesse W. and Cornette, Raphaël and Meguerditchian, Adrien and Cazeau, Cyrille and Bellaiche, Laurence and Pouydebat, Emmanuelle},
    year = {2021},
    title = {Increased performance in juvenile baboons is consistent with ontogenetic changes in morphology},
    doi = {10.1002/ajpa.24235},
    journal = {American Journal of Physical Anthropology},
    volume = {175},
    number = {3},
    pages = {546-558},
    keywords = {allometry, development, grasping performance, limb morphology, primate evolution},
    url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ajpa.24235},
    abstract = {Abstract Objectives In many primates, the greater proportion of climbing and suspensory behaviors in the juvenile repertoire likely necessitates good grasping capacities. Here, we tested whether very young individuals show near-maximal levels of grasping strength, and whether such an early onset of grasping performance could be explained by ontogenetic variability in the morphology of the limbs in baboons. Material and methods We quantified a performance trait, hand pull strength, at the juvenile and adult stages in a cross-sectional sample of 15 olive baboons (Papio anubis). We also quantified bone dimensions (i.e., lengths, widths, and heights) of the fore- (n = 25) and hind limb (n = 21) elements based on osteological collections covering the whole development of olive baboons. Results One-year old individuals demonstrated very high pull strengths (i.e., 200\% of the adult performance, relative to body mass), that are consistent with relatively wider phalanges and digit joints in juveniles. The mature proportions and shape of the forelimb elements appeared only at full adulthood (i.e., ≥4.5 years), whereas the mature hind limb proportions and shape were observed much earlier during development. Discussion These changes in limb performance and morphology across ontogeny may be explained with regard to behavioral transitions that olive baboons experience during their development. Our findings highlight the effect of infant clinging to mother, an often-neglected feature when discussing the origins of grasping in primates. The differences in growth patterns, we found between the forelimb and the hind limb further illustrate their different functional roles, having likely evolved under different ecological pressures (manipulation and locomotion, respectively).},
}

@article{Druelle2017,
    author = {Druelle, François and Aerts, Peter and D'Août, Kristiaan and Moulin, Valérie and Berillon, Gilles},
    year = {2017},
    title = {Segmental morphometrics of the olive baboon (Papio anubis): a longitudinal study from birth to adulthood},
    doi = {10.1111/joa.12602},
    journal = {Journal of Anatomy},
    volume = {230},
    number = {6},
    pages = {805-819},
    keywords = {development, inertial properties, locomotion, Papio anubis, primate model},
    url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/joa.12602},
    abstract = {Abstract The linear dimensions and inertial characteristics of the body are important in locomotion and they change considerably during the ontogeny of animals, including humans. This longitudinal and ontogenetic study has produced the largest dataset to date of segmental morphometrics in a Catarrhini species, the olive baboon. The objectives of the study were to quantify the changes in body linear and inertial dimensions and to explore their (theoretical) mechanical significance for locomotion. We took full-body measurements of captive individuals at regular intervals. Altogether, 14 females and 16 males were followed over a 7-year period, i.e. from infancy to adulthood. Our results show that individual patterns of growth are very consistent and follow the general growth pattern previously described in olive baboons. Furthermore, we obtained similar growth curve structures for segment lengths and masses, although the respective time scales were slightly different. The most significant changes in body morphometrics occurred during the first 2 years of life and concerned the distal parts of the body. Females and males were similar in size and shape at birth. The rate and duration of growth produced substantial size-related differences throughout ontogeny, while body shapes remained very similar between the sexes. We also observed significant age-related variations in limb composition, with a proximal shift of the centre of mass within the limbs, mainly due to changes in mass distribution and in the length of distal segments. Finally, we observed what we hypothesize to be ‘early biomechanical optimization’ of the limbs for quadrupedal walking. This is due to a high degree of convergence between the limbs’ natural pendular periods in infants, which may facilitate the onset of quadrupedal walking. Furthermore, the mechanical significance of the morphological changes observed in growing baboons may be related to changing functional demands with the onset of autonomous (quadrupedal) locomotion. From a wider perspective, these data provide unique insights into questions surrounding both the processes of locomotor development in primates and how these processes might evolve.},
}

@online{WikipediaNewtonEuler,
    author = {{Wikipedia/Newton-Euler equations}},
    year = {2012},
    title = {Moment of Inertia Tensor},
    organization = {Wikimedia Foundation},
    url = {https://en.wikipedia.org/wiki/Newton-Euler_equations},
    note = {accessed 2023-07-21},
}

@online{WikipediaTorque,
    author = {{Wikipedia/Torque}},
    year = {2012},
    title = {Moment of Inertia, Resultant Torque},
    organization = {Wikimedia Foundation},
    url = {https://en.wikipedia.org/wiki/Moment_of_inertia#Resultant_torque},
    note = {accessed 2023-07-21},
}

@article{Hansraj2022,
    author={Hansraj, Kenneth K and Hansraj, Jonathan A and Hansraj, Marcia D Griffin and Ro{\v{z}}i{\v{c}}, Uro{\v{s}} and Choudhary, Deepak},
    year={2022},
    title={{Belly Fat Forces on the Spine: Finite Element Analysis of Belly Fat Forces by Waist Circumference}},
    journal={Surgical technology international},
    volume={40},
    pages={405--410},
}

@article{Roraas2019,
    author = {Røraas, Thomas and Sandberg, Sverre and Aarsand, Aasne K and Støve, Bård},
    year = {2019},
    title = {{A Bayesian Approach to Biological Variation Analysis}},
    doi = {10.1373/clinchem.2018.300145},
    journal = {Clinical Chemistry},
    volume = {65},
    number = {8},
    pages = {995-1005},
    month = {08},
    abstract = {Biological variation (BV) data have many applications for diagnosing and monitoring disease. The standard statistical approaches for estimating BV are sensitive to “noisy data” and assume homogeneity of within-participant CV. Prior knowledge about BV is mostly ignored. The aims of this study were to develop Bayesian models to calculate BV that (a) are robust to “noisy data,” (b) allow heterogeneity in the within-participant CVs, and (c) take advantage of prior knowledge.We explored Bayesian models with different degrees of robustness using adaptive Student t distributions instead of the normal distributions and when the possibility of heterogeneity of the within-participant CV was allowed. Results were compared to more standard approaches using chloride and triglyceride data from the European Biological Variation Study.Using the most robust Bayesian approach on a raw data set gave results comparable to a standard approach with outlier assessments and removal. The posterior distribution of the fitted model gives access to credible intervals for all parameters that can be used to assess reliability. Reliable and relevant priors proved valuable for prediction.The recommended Bayesian approach gives a clear picture of the degree of heterogeneity, and the ability to crudely estimate personal within-participant CVs can be used to explore relevant subgroups. Because BV experiments are expensive and time-consuming, prior knowledge and estimates should be considered of high value and applied accordingly. By including reliable prior knowledge, precise estimates are possible even with small data sets.},
    issn = {0009-9147},
}

@article{Noether1918,
    author = {Noether, E.},
    year = {1918},
    journal = {{Nachrichten von der Gesellschaft der Wissenschaften zu G\"ottingen, Mathematisch-Physikalische Klasse}},
    language = {ger},
    pages = {235-257},
    title = {{Invariante Variationsprobleme}},
    url = {http://eudml.org/doc/59024},
    volume = {1918},
}

@online{2022Pendulums,
    author = {LibreTexts},
    year = {2022},
    title = {{15.5: Pendulums}},
    organization = {LibreTexts: University Physics I - Mechanics, Sound, Oscillations, and Waves},
    url = {https://phys.libretexts.org/@go/page/4065},
    note = {accessed 2023-07-17},
}

@article{Zehr2016,
    author = {Zehr, E Paul and Barss, Trevor S and Dragert, Katie and Frigon, Alain and Vasudevan, Erin V and Haridas, Carlos and Hundza, Sandra and Kaupp, Chelsea and Klarner, Taryn and Klimstra, Marc and others},
    year = {2016},
    title = {Neuromechanical interactions between the limbs during human locomotion: an evolutionary perspective with translation to rehabilitation},
    doi = {10.1007/s00221-016-4715-4},
    journal = {Experimental brain research},
    volume = {234},
    pages = {3059--3081},
    publisher = {Springer},
}

@article{Daley2018,
    author = {Daley, Monica A},
    year = {2018},
    title = {{Understanding the Agility of Running Birds: Sensorimotor and Mechanical Factors in Avian Bipedal Locomotion}},
    doi = {10.1093/icb/icy058},
    journal = {Integrative and Comparative Biology},
    volume = {58},
    number = {5},
    pages = {884-893},
    month = {06},
    abstract = {Birds are a diverse and agile lineage of vertebrates that all use bipedal locomotion for at least part of their life. Thus birds provide a valuable opportunity to investigate how biomechanics and sensorimotor control are integrated for agile bipedal locomotion. This review summarizes recent work using terrain perturbations to reveal neuromechanical control strategies used by ground birds to achieve robust, stable, and agile running. Early experiments in running guinea fowl aimed to reveal the immediate intrinsic mechanical response to an unexpected drop (“pothole”) in terrain. When navigating the pothole, guinea fowl experience large changes in leg posture in the perturbed step, which correlates strongly with leg loading and perturbation recovery. Analysis of simple theoretical models of running has further confirmed the crucial role of swing-leg trajectory control for regulating foot contact timing and leg loading in uneven terrain. Coupling between body and leg dynamics results in an inherent trade-off in swing leg retraction rate for fall avoidance versus injury avoidance. Fast leg retraction minimizes injury risk, but slow leg retraction minimizes fall risk. Subsequent experiments have investigated how birds optimize their control strategies depending on the type of perturbation (pothole, step, obstacle), visibility of terrain, and with ample practice negotiating terrain features. Birds use several control strategies consistently across terrain contexts: (1) independent control of leg angular cycling and leg length actuation, which facilitates dynamic stability through simple control mechanisms, (2) feedforward regulation of leg cycling rate, which tunes foot-contact timing to maintain consistent leg loading in uneven terrain (minimizing fall and injury risks), (3) load-dependent muscle actuation, which rapidly adjusts stance push-off and stabilizes body mechanical energy, and (4) multi-step recovery strategies that allow body dynamics to transiently vary while tightly regulating leg loading to minimize risks of fall and injury. In future work, it will be interesting to investigate the learning and adaptation processes that allow animals to adjust neuromechanical control mechanisms over short and long timescales.},
    issn = {1540-7063},
}

@article{Ting2015,
    author = { Ting, Lena H. and Chiel, Hillel J. and Trumbower, Randy D. and Allen, Jessica L. and McKay, J. Lucas and Hackney, Madeleine E. and Kesar, Trisha M.},
    year = {2015},
    title = {Neuromechanical Principles Underlying Movement Modularity and Their Implications for Rehabilitation},
    doi = {10.1016/j.neuron.2015.02.042},
    journal = {Neuron},
    volume = {86},
    number = {1},
    pages = {38-54},
    issn = {0896-6273},
    url = {https://www.sciencedirect.com/science/article/pii/S0896627315001579},
    abstract = {Neuromechanical principles define the properties and problems that shape neural solutions for movement. Although the theoretical and experimental evidence is debated, we present arguments for consistent structures in motor patterns, i.e., motor modules, that are neuromechanical solutions for movement particular to an individual and shaped by evolutionary, developmental, and learning processes. As a consequence, motor modules may be useful in assessing sensorimotor deficits specific to an individual and define targets for the rational development of novel rehabilitation therapies that enhance neural plasticity and sculpt motor recovery. We propose that motor module organization is disrupted and may be improved by therapy in spinal cord injury, stroke, and Parkinson’s disease. Recent studies provide insights into the yet-unknown underlying neural mechanisms of motor modules, motor impairment, and motor learning and may lead to better understanding of the causal nature of modularity and its underlying neural substrates.},
}

@article{DeGroote2021,
    author = {De Groote, Friedl and Falisse, Antoine },
    year = {2021},
    title = {Perspective on musculoskeletal modelling and predictive simulations of human movement to assess the neuromechanics of gait},
    doi = {10.1098/rspb.2020.2432},
    journal = {Proceedings of the Royal Society B: Biological Sciences},
    volume = {288},
    number = {1946},
    pages = {20202432},
    url = {https://royalsocietypublishing.org/doi/abs/10.1098/rspb.2020.2432},
    abstract = { Locomotion results from complex interactions between the central nervous system and the musculoskeletal system with its many degrees of freedom and muscles. Gaining insight into how the properties of each subsystem shape human gait is challenging as experimental methods to manipulate and assess isolated subsystems are limited. Simulations that predict movement patterns based on a mathematical model of the neuro-musculoskeletal system without relying on experimental data can reveal principles of locomotion by elucidating cause–effect relationships. New computational approaches have enabled the use of such predictive simulations with complex neuro-musculoskeletal models. Here, we review recent advances in predictive simulations of human movement and how those simulations have been used to deepen our knowledge about the neuromechanics of gait. In addition, we give a perspective on challenges towards using predictive simulations to gain new fundamental insight into motor control of gait, and to help design personalized treatments in patients with neurological disorders and assistive devices that improve gait performance. Such applications will require more detailed neuro-musculoskeletal models and simulation approaches that take uncertainty into account, tools to efficiently personalize those models, and validation studies to demonstrate the ability of simulations to predict gait in novel circumstances. },
}

@article{Full1999,
    author = {Full, R. J. and Koditschek,  D. E.},
    year = {1999},
    title = {Templates and anchors: neuromechanical hypotheses of legged locomotion on land},
    doi = {10.1242/jeb.202.23.3325},
    journal = {Journal of Experimental Biology},
    volume = {202},
    number = {23},
    pages = {3325-3332},
    month = {12},
    abstract = {{Locomotion results from complex, high-dimensional, non-linear, dynamically coupled interactions between an organism and its environment. Fortunately, simple models we call templates have been and can be made to resolve the redundancy of multiple legs, joints and muscles by seeking synergies and symmetries. A template is the simplest model (least number of variables and parameters) that exhibits a targeted behavior. For example, diverse species that differ in skeletal type, leg number and posture run in a stable manner like sagittal- and horizontal-plane spring-mass systems. Templates suggest control strategies that can be tested against empirical data. Templates must be grounded in more detailed morphological and physiological models to ask specific questions about multiple legs, the joint torques that actuate them, the recruitment of muscles that produce those torques and the neural networks that activate the ensemble. We term these more elaborate models anchors. They introduce representations of specific biological details whose mechanism of coordination is of interest. Since mechanisms require controls, anchors incorporate specific hypotheses concerning the manner in which unnecessary motion or energy from legs, joints and muscles is removed, leaving behind the behavior of the body in the low-degree-of-freedom template. Locating the origin of control is a challenge because neural and mechanical systems are dynamically coupled and both play a role. The control of slow, variable-frequency locomotion appears to be dominated by the nervous system, whereas during rapid, rhythmic locomotion, the control may reside more within the mechanical system. Anchored templates of many-legged, sprawled-postured animals suggest that passive, dynamic self-stabilization from a feedforward, tuned mechanical system can reject rapid perturbations and simplify control. Future progress would benefit from the creation of a field embracing comparative neuromechanics.}},
    issn = {0022-0949},
}

@article{Sponberg2023,
    author = {Sponberg, Simon and Abbott, Emily and Sawicki, Gregory S.},
    title = {Perturbing the muscle work loop paradigm to unravel the neuromechanics of unsteady locomotion},
    journal = {Journal of Experimental Biology},
    volume = {226},
    number = {7},
    pages = {jeb243561},
    year = {2023},
    month = {04},
    abstract = {Muscle function during movement is more than a simple, linear transformation of neural activity into force. The classic work loop technique has pioneered our understanding of muscle, but typically only characterizes function during unperturbed movement cycles, such as those experienced during steady walking, running, swimming and flying. Yet perturbations away from steady movement often place greater demands on muscle structure and function and offer a unique window into muscle's broader capacity. Recently, studies in diverse organisms from cockroaches to humans have started to grapple with muscle function in unsteady (perturbed, transient and fluctuating) conditions, but the vast range of possible parameters and the challenge of connecting in vitro to in vivo experiments are daunting. Here, we review and organize these studies into two broad approaches that extend the classic work loop paradigm. First, in the top-down approach, researchers record length and activation patterns of natural locomotion under perturbed conditions, replay these conditions in isolated muscle work loop experiments to reveal the mechanism by which muscle mediates a change in body dynamics and, finally, generalize across conditions and scale. Second, in the bottom-up approach, researchers start with an isolated muscle work loop and then add structural complexity, simulated loads and neural feedback to ultimately emulate the muscle's neuromechanical context during perturbed movement. In isolation, each of these approaches has several limitations, but new models and experimental methods coupled with the formal language of control theory give several avenues for synthesizing an understanding of muscle function under unsteady conditions.},
    issn = {0022-0949},
    doi = {10.1242/jeb.243561},
}

@online{2021Chaos,
    author = {Harrison, David},
    year = {2021},
    title = {{Chaos}},
    organization = {LibreTexts: Modern Physics, Supplemental Modules },
    url = {https://phys.libretexts.org/@go/page/4113},
    note = {accessed 2023-07-17},
}

@article{Pennestri2010,
    author = {Pennestri, E. and Valentini, P. P.},
    year = {2010},
    title = {Dual quaternions as a tool for rigid body motion analysis: a tutorial with an application to biomechanics},
    journal = {Archive of Mechanical Engineering},
    volume = {LVII},
    ISSN = {0004-0738},
    number = {2},
    pages = {187–205},
    url = {http://yadda.icm.edu.pl/baztech/element/bwmeta1.element.baztech-article-BOS3-0023-0016},
}

@article{Challis2020,
    author={Challis, John H.},
    year={2020},
    title={Quaternions as a solution to determining the angular kinematics of human movement},
    doi={10.1186/s42490-020-00039-z},
    journal={{BMC Biomedical Engineering}},
    volume={2},
    number={1},
    pages={5},
    publisher={Springer},
}

@incollection{Flashner2019,
    author = {Flashner, Henryk and McNitt-Gray, Jill L.},
    editor = {Pallis, Jani Macari and McNitt-Gray, Jill L. and Hung, George K.},
    title = {{3D Kinematics: Using Quaternions for Modeling Orientation and Rotations in Biomechanics}},
    bookTitle = {Biomechanical Principles and Applications in Sports},
    year = {2019},
    publisher = {Springer International Publishing},
    address = {Cham},
    pages = {155--233},
    abstract = {Analysis of human movement requires mathematical formulation of rotations in three-dimensional space. The need for appropriate description of rotations occurs both in the analysis of experimental data and in the modeling of human movement. To capture the characteristics human body motion using experimental data, one often needs to initially assume joints with three rotational degrees of freedom (spherical joints). Then, using measured data, one can determine the number of rotational degrees of freedom of a joint under consideration. In complex whole-body movements, such as in various athletic disciplines, the athlete may undergo a rotation in three-dimensional rotation that requires also adequate mathematical formulation. In this chapter we introduce a mathematical representation of orientation and rotation that is based on the notion of quaternions. The quaternion-based representation of rotations has a physical interpretation that is meaningful in biomechanical context. It is computationally efficient since it has small number of parameters with the least number of constraints without mathematical singularities that lead to false results and numerical instability. Another important feature of the quaternion formulation is that successive rotations that often occur in human movements are easily composed within the representation. Finally, efficient identification and interpolation procedures of data obtained experimentally based on the quaternion representation are presented.},
    isbn = {978-3-030-13467-9},
    doi = {10.1007/978-3-030-13467-9\_7},
}

@article{Triche2019,
    author = {Triche, Benjamin L. and Nelson, John T. and McGill, Noah S. and Porter, Kristin K. and Sanyal, Rupan and Tessler, Franklin N. and McConathy, Jonathan E. and Gauntt, David M. and Yester, Michael V. and Singh, Satinder P.},
    year = {2019},
    title = {{Recognizing and Minimizing Artifacts at CT, MRI, US, and Molecular Imaging}},
    doi = {10.1148/rg.2019180022},
    journal = {{RadioGraphics}},
    volume = {39},
    number = {4},
    pages = {1017-1018},
}

@article{Kilbourne2016,
    author = {Kilbourne, Brandon M. and Andrada, Emanuel and Fischer, Martin S. and Nyakatura, John A.},
    year = {2016},
    title = {{Morphology and motion: hindlimb proportions and swing phase kinematics in terrestrially locomoting charadriiform birds}},
    doi = {10.1242/jeb.124081},
    journal = {Journal of Experimental Biology},
    volume = {219},
    number = {9},
    pages = {1405-1416},
    month = {05},
    abstract = {{Differing limb proportions in terms of length and mass, as well as differences in mass being concentrated proximally or distally, influence the limb's moment of inertia (MOI), which represents its resistance to being swung. Limb morphology – including limb segment proportions – thus probably has direct relevance for the metabolic cost of swinging the limb during locomotion. However, it remains largely unexplored how differences in limb proportions influence limb kinematics during swing phase. To test whether differences in limb proportions are associated with differences in swing phase kinematics, we collected hindlimb kinematic data from three species of charadriiform birds differing widely in their hindlimb proportions: lapwings, oystercatchers and avocets. Using these three species, we tested for differences in maximum joint flexion, maximum joint extension and range of motion (RoM), in addition to differences in maximum segment angular velocity and excursion. We found that the taxa with greater limb MOI – oystercatchers and avocets – flex their limbs more than lapwings. However, we found no consistent differences in joint extension and RoM among species. Likewise, we found no consistent differences in limb segment angular velocity and excursion, indicating that differences in limb inertia in these three avian species do not necessarily underlie the rate or extent of limb segment movements. The observed increased limb flexion among these taxa with distally heavy limbs resulted in reduced MOI of the limb when compared with a neutral pose. A trade-off between exerting force to actively flex the limb and potential savings by a reduction of MOI is skewed towards reducing the limb's MOI as a result of MOI being in part a function of the radius of gyration squared. Increased limb flexion is a likely means to lower the cost of swinging the limbs.}},
    issn = {0022-0949},
}

@article{Wells1987,
    author = {Wells, James P. and DeMenthon, Daniel F.},
    year = {1987},
    title = {Measurement of body segment mass, center of gravity, and determination of moments of inertia by double pendulum in Lemur fulvus},
    doi = {10.1002/ajp.1350120307},
    journal = {American Journal of Primatology},
    volume = {12},
    number = {3},
    pages = {299-308},
    keywords = {Lemur fulvus, segment mass moment of inertia, biomechanics, positional behavior, segment mass},
    url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ajp.1350120307},
    abstract = {Abstract The collection of data on physical parameters of body segments is a preliminary critical step in studying the biomechanics of locomotion. Little data on nonhuman body segment parameters has been published. The lack of standardization of techniques for data collection and presentation has made the comparative use of these data difficult and at times impossible. This study offers an approach for collecting data on center of gravity and moments of inertia for standardized body segments. The double swing pendulum approach is proposed as a solution for difficulties previously encountered in calculating moments of inertia for body segments. A format for prompting a computer to perform these calculations is offered, and the resulting segment mass data for Lemur fulvus is presented.},
}

@article{Allen2009,
    author = {Allen, Vivian and Paxton, Heather and Hutchinson, John R.},
    year = {2009},
    title = {Variation in Center of Mass Estimates for Extant Sauropsids and its Importance for Reconstructing Inertial Properties of Extinct Archosaurs},
    doi = {10.1002/ar.20973},
    journal = {The Anatomical Record},
    volume = {292},
    number = {9},
    pages = {1442-1461},
    keywords = {center of mass, biomechanics, sensitivity analysis, computer modeling, archosaur, dinosaur, bird, locomotion},
    url = {https://anatomypubs.onlinelibrary.wiley.com/doi/abs/10.1002/ar.20973},
    abstract = {Abstract Inertial properties of animal bodies and segments are critical input parameters for biomechanical analysis of standing and moving, and thus are important for paleobiological inquiries into the broader behaviors, ecology and evolution of extinct taxa such as dinosaurs. But how accurately can these be estimated? Computational modeling was used to estimate the inertial properties including mass, density, and center of mass (COM) for extant crocodiles (adult and juvenile Crocodylus johnstoni) and birds (Gallus gallus; junglefowl and broiler chickens), to identify the chief sources of variation and methodological errors, and their significance. High-resolution computed tomography scans were segmented into 3D objects and imported into inertial property estimation software that allowed for the examination of variable body segment densities (e.g., air spaces such as lungs, and deformable body outlines). Considerable biological variation of inertial properties was found within groups due to ontogenetic changes as well as evolutionary changes between chicken groups. COM positions shift in variable directions during ontogeny in different groups. Our method was repeatable and the resolution was sufficient for accurate estimations of mass and density in particular. However, we also found considerable potential methodological errors for COM related to (1) assumed body segment orientation, (2) what frames of reference are used to normalize COM for size-independent comparisons among animals, and (3) assumptions about tail shape. Methods and assumptions are suggested to minimize these errors in the future and thereby improve estimation of inertial properties for extant and extinct animals. In the best cases, 10\%–15\% errors in these estimates are unavoidable, but particularly for extinct taxa errors closer to 50\% should be expected, and therefore, cautiously investigated. Nonetheless in the best cases these methods allow rigorous estimation of inertial properties.},
}

@article{Hutchinson2007,
    author = {Hutchinson, John R. and Ng-Thow-Hing, Victor and Anderson, Frank C. },
    year = {2007},
    title = {{A 3D interactive method for estimating body segmental parameters in animals: Application to the turning and running performance of \textit{Tyrannosaurus rex}}},
    doi = {10.1016/j.jtbi.2007.01.023},
    journal = {Journal of Theoretical Biology},
    volume = {246},
    number = {4},
    pages = {660-680},
    issn = {0022-5193},
    url = {https://www.sciencedirect.com/science/article/pii/S0022519307000550},
    keywords = {B-spline, Mass, Inertia, Tyrannosaurus, Model},
    abstract = {We developed a method based on interactive B-spline solids for estimating and visualizing biomechanically important parameters for animal body segments. Although the method is most useful for assessing the importance of unknowns in extinct animals, such as body contours, muscle bulk, or inertial parameters, it is also useful for non-invasive measurement of segmental dimensions in extant animals. Points measured directly from bodies or skeletons are digitized and visualized on a computer, and then a B-spline solid is fitted to enclose these points, allowing quantification of segment dimensions. The method is computationally fast enough so that software implementations can interactively deform the shape of body segments (by warping the solid) or adjust the shape quantitatively (e.g., expanding the solid boundary by some percentage or a specific distance beyond measured skeletal coordinates). As the shape changes, the resulting changes in segment mass, center of mass (CM), and moments of inertia can be recomputed immediately. Volumes of reduced or increased density can be embedded to represent lungs, bones, or other structures within the body. The method was validated by reconstructing an ostrich body from a fleshed and defleshed carcass and comparing the estimated dimensions to empirically measured values from the original carcass. We then used the method to calculate the segmental masses, centers of mass, and moments of inertia for an adult Tyrannosaurus rex, with measurements taken directly from a complete skeleton. We compare these results to other estimates, using the model to compute the sensitivities of unknown parameter values based upon 30 different combinations of trunk, lung and air sac, and hindlimb dimensions. The conclusion that T. rex was not an exceptionally fast runner remains strongly supported by our models—the main area of ambiguity for estimating running ability seems to be estimating fascicle lengths, not body dimensions. Additionally, the craniad position of the CM in all of our models reinforces the notion that T. rex did not stand or move with extremely columnar, elephantine limbs. It required some flexion in the limbs to stand still, but how much flexion depends directly on where its CM is assumed to lie. Finally we used our model to test an unsolved problem in dinosaur biomechanics: how fast a huge biped like T. rex could turn. Depending on the assumptions, our whole body model integrated with a musculoskeletal model estimates that turning 45° on one leg could be achieved slowly, in about 1–2s.},
}

@article{Cronin2021,
    author = { Cronin, Neil J.},
    year = {2021},
    title = {{Using deep neural networks for kinematic analysis: Challenges and opportunities}},
    doi = {10.1016/j.jbiomech.2021.110460},
    journal = {Journal of Biomechanics},
    volume = {123},
    pages = {110460},
    issn = {0021-9290},
    url = {https://www.sciencedirect.com/science/article/pii/S0021929021002402},
    keywords = {Motion analysis, Kinematics, Deep neural network, Markerless tracking, AI},
    abstract = {Kinematic analysis is often performed in a lab using optical cameras combined with reflective markers. With the advent of artificial intelligence techniques such as deep neural networks, it is now possible to perform such analyses without markers, making outdoor applications feasible. In this paper I summarise 2D markerless approaches for estimating joint angles, highlighting their strengths and limitations. In computer science, so-called “pose estimation” algorithms have existed for many years. These methods involve training a neural network to detect features (e.g. anatomical landmarks) using a process called supervised learning, which requires “training” images to be manually annotated. Manual labelling has several limitations, including labeller subjectivity, the requirement for anatomical knowledge, and issues related to training data quality and quantity. Neural networks typically require thousands of training examples before they can make accurate predictions, so training datasets are usually labelled by multiple people, each of whom has their own biases, which ultimately affects neural network performance. A recent approach, called transfer learning, involves modifying a model trained to perform a certain task so that it retains some learned features and is then re-trained to perform a new task. This can drastically reduce the required number of training images. Although development is ongoing, existing markerless systems may already be accurate enough for some applications, e.g. coaching or rehabilitation. Accuracy may be further improved by leveraging novel approaches and incorporating realistic physiological constraints, ultimately resulting in low-cost markerless systems that could be deployed both in and outside of the lab.},
}

@online{Dallal2003,
    author       = { Dallal, Gerard E.},
    year         = {2003},
    title        = {{Why P=0.05?}},
    organization = {Tufts University},
    url          = {https://www.webpages.uidaho.edu/~brian/why_significance_is_five_percent.pdf},
    note         = {accessed 2023-07-25},
}

@online{Downey2013,
    author       = {Downey, Allen },
    year         = {2013},
    title        = {{Are your data normal? Hint: no.}},
    organization = {Probably Overthinking It (blog)},
    url          = {https://allendowney.blogspot.com/2013/08/are-my-data-normal.html},
    note         = {accessed 2023-07-25},
}

@online{Wiecki2013,
    author       = {Wiecki, Thomas },
    year         = {2013},
    title        = {{This world is far from Normal(ly distributed): Bayesian Robust Regression in PyMC3}},
    organization = {While My MCMC Gently Samples (blog)},
    url          = {https://twiecki.io/blog/2013/08/27/bayesian-glms-2},
    note         = {accessed 2023-07-25},
}

@article{Loscher2016,
    author = {Loscher, David M.  and Meyer, Fiete  and Kracht, Kerstin  and Nyakatura, John A. },
    year = {2016},
    title = {Timing of head movements is consistent with energy minimization in walking ungulates},
    doi = {10.1098/rspb.2016.1908},
    journal = {Proceedings of the Royal Society B: Biological Sciences},
    volume = {283},
    number = {1843},
    pages = {20161908},
    url = {https://royalsocietypublishing.org/doi/abs/10.1098/rspb.2016.1908},
    abstract = { Many ungulates show a conspicuous nodding motion of the head when walking. Until now, the functional significance of this behaviour remained unclear. Combining in vivo kinematics of quadrupedal mammals with a computer model, we show that the timing of vertical displacements of the head and neck is consistent with minimizing energy expenditure for carrying these body parts in an inverted pendulum walking gait. Varying the timing of head movements in the model resulted in increased metabolic cost estimate for carrying the head and neck of up to 63\%. Oscillations of the head–neck unit result in weight force oscillations transmitted to the forelimbs. Advantageous timing increases the load in single support phases, in which redirecting the trajectory of the centre of mass (COM) is thought to be energetically inexpensive. During double support, in which—according to collision mechanics—directional changes of the impulse of the COM are expensive, the observed timing decreases the load. Because the head and neck comprise approximately 10\% of body mass, the effect shown here should also affect the animals' overall energy expenditure. This mechanism, working analogously in high-tech backpacks for energy-saving load carriage, is widespread in ungulates, and provides insight into how animals economize locomotion. },
}

@article{JYoung2023,
    author = {Young, Jesse W and Mayerl, Christopher J and Mannava, Alekhya and Lewis, Claire and Fan, Tianhui and Nair, Manas and Mamone, Christopher and Schapker, Nicole M and Mossor, Angela M and German, Rebecca Z},
    year = {2023},
    title = {{Evaluating The Precocial-altricial Axis of Motor Skill at Birth in A Preterm Pig Model}},
    doi = {10.1093/icb/icad013},
    journal = {Integrative and Comparative Biology},
    pages = {icad013},
    month = {04},
    abstract = {{The pace of locomotor development is a critical component of lifetime evolutionary fitness. Developmental researchers often divide species into two broad categories based on functional competence at birth: precocial infants who can independently stand and locomote soon after birth versus altricial infants who are either incapable of independent movement or can only do so in a rudimentary manner. However, investigating the lower level neuromotor and biomechanical traits that account for perinatal variation in motor development is complicated by the lack of experimental control inherent to all comparative analyses. Precocial and altricial animals often differ along a host of dimensions that can obfuscate the specific factors controlling motor development per se. Here, we propose an alternative approach of examining locomotor development in a nominally precocial species—the domestic pig (Sus scrofa)—in which gestation length has been experimentally manipulated, thereby creating “functionally altricial” cohorts for comparison. We have used standard biomechanical testing to evaluate balance and locomotor performance in preterm pigs born at 94\% full-term gestation (N = 29 individuals) and compared these data to a similar dataset on age-matched full-term piglets (N = 15 individuals). Static balance tests showed that preterm pigs were characterized by increased postural sway, particularly in the fore-aft (anteroposterior) direction. Locomotor analyses showed that preterm piglets tended to take shorter, more frequent strides, use higher duty factors, and preferentially choose gait patterns that ensured they were supported by at least three limbs during most of the stride cycle, though differences between preterm and full-term animals were often modulated by variation in locomotor speed. Morphometric analysis showed no differences in relative extensor muscle mass between preterm and full-term animals, suggesting that neurological immaturity might be more determinant of preterm piglet motor dysfunctions than musculoskeletal immaturity per se (though much work remains to be done to fully document the neuromotor phenotype of the preterm infant pig model). In many ways, the postural and locomotor deficits shown by the preterm piglets paralleled the locomotor phenotype of altricial mammals. Overall, our study demonstrates the utility of a “within-species” design for studying the biomechanical correlates and neuromotor basis of evolutionary variation in motor skill at birth.}},
    issn = {1540-7063},
}

@article{Mayerl2023,
    author = {Mayerl, Christopher J and Dial, Terry R and Mainwaring, Mark C and Heers, Ashley M and German, Rebecca Z},
    title = {{Birth and the pathway to adulthood: integration across development, environment, and evolution}},
    doi = {10.1093/icb/icad101},
    journal = {Integrative and Comparative Biology},
    pages = {icad101},
    year = {2023},
    month = {07},
    issn = {1540-7063},
}

@article{Magrini2023,
    author = {Magrini, Samantha H. and Mossor, Angela M. and German, Rebecca Z. and Young, Jesse W.},
    year = {2023},
    title = {Developmental factors influencing bone strength in precocial mammals: An infant pig model},
    doi = {10.1111/joa.13848},
    journal = {Journal of Anatomy},
    volume = {243},
    number = {1},
    pages = {174-181},
    keywords = {altricial, biomechanics, development, ontogeny, precocial, skeleton},
    url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/joa.13848},
    abstract = {Abstract Most vertebrates are precocial in locomotion, able to walk and run soon after birth. Precociality requires a bony skeleton of sufficient strength to resist mechanical loading during early locomotor efforts. The aim of this study was to use an animal model—the preterm infant pig—to investigate some of the proximate factors that might determine variation in bone strength in precocial animals. Based on the prior literature, we tested the null predictions that skeletal integrity would be significantly compromised by truncated gestation (i.e., preterm birth) and reduced body mass at birth. We generated a suite of both morphometric measures (tissue mineral density and cross-sectional geometry) and performance-related metrics (ability to resist loading, deformation, and fracture during three-point bending tests) of the appendicular skeleton of preterm and full-term infant pigs. Results showed that very few measures in our ontogenetic infant pig sample significantly varied with either gestation length or birth mass. Overall, our results contribute to a growing body of literature demonstrating the early functional capacity of the precocial infant musculoskeletal system and suggest that bone strength in perinatal precocial mammals may be robust to the factors shown to compromise skeletal integrity in more altricial taxa.},
}

@article{Mayerl2023b,
    author = {Mayerl, CJ and Gould, FDH and Adjerid, K and Edmonds, C and German, RZ},
    year = {2023},
    title = {{The Pathway from Anatomy and Physiology to Diagnosis: A Developmental Perspective on Swallowing and Dysphagia}},
    doi = {10.1007/s00455-022-10449-x},
    journal = {Dysphagia},
    volume = {38},
    number = {1},
    pages = {33--41},
    publisher = {Springer},
}

@article{Aerts1998,
    author = {Aerts, P. },
    year = {1998},
    title = {{Vertical jumping in \textit{Galago senegalensis}: the quest for an obligate mechanical power amplifier}},
    doi = {10.1098/rstb.1998.0313},
    journal = {Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences},
    volume = {353},
    number = {1375},
    pages = {1607-1620},
    url = {https://royalsocietypublishing.org/doi/abs/10.1098/rstb.1998.0313},
    abstract = { Bushbabies (Galago senegalensis) are renowned for their phenomenal jumping capacity. It was postulated that mechanical power amplification must be involved. Dynamic analysis of the vertical jumps performed by two bushbabies confirms the need for a power amplifier. Inverse dynamics coupled to a geometric musculo–skeletal model were used to elucidate the precise nature of the mechanism powering maximal vertical jumps. Most of the power required for jumping is delivered by the vastus muscle–tendon systems (knee extensor). Comparison with the external joint–powers revealed, however, an important power transport from this extensor (about 65\%) to the ankle and the midfoot via the bi–articular calf muscles. Peak power output likely implies elastic recoil of the complex aponeurotic system of the vastus muscle. Patterns of changes in length and tension of the muscle–tendon complex during different phases of the jump were found which provide strong evidence for substantial power amplification (times 15). It is argued here that the multiple internal connective tissue sheets and attachment structures of the well–developed bundles of the vastus muscle become increasingly stretched during preparatory crouching and throughout the extension phase, except for the last 13 ms of the push–off (i.e. when power requirements peak). Then, tension in the knee extensors abruptly falls from its maximum, allowing the necessary fast recoil of the tensed tendon structures to occur. },
}

@article{Druelle2020,
    author = {Druelle, Fran{\c{c}}ois and Aerts, Peter and Ngawolo, Jean Christophe Bokika and Narat, Victor},
    year = {2020},
    title = {{Impressive arboreal gap-crossing behaviors in wild bonobos, \textit{Pan paniscus}}},
    doi = {10.1007/s10764-020-00140-z},
    journal = {International Journal of Primatology},
    volume = {41},
    pages = {129--140},
    publisher = {Springer},
}

@article{Scheidt2022,
    author = {Scheidt, Adrian and Ditzel, Paulo C. and Geiger, Sandra M. and Wagner, Franziska C. and Mülling, Christoph K. W. and Nyakatura, John A.},
    year = {2022},
    title = {{A therian mammal with sprawling kinematics? Gait and 3D forelimb X-ray motion analysis in tamanduas}},
    doi = {10.1242/jeb.243625},
    journal = {Journal of Experimental Biology},
    volume = {225},
    number = {12},
    pages = {jeb243625},
    month = {06},
    abstract = {Therian mammals are known to move their forelimbs in a parasagittal plane, retracting the mobilised scapula during stance phase. Non-cursorial therian mammals often abduct the elbow out of the shoulder–hip parasagittal plane. This is especially prominent in Tamandua (Xenarthra), which suggests they employ aspects of sprawling (e.g. lizard-like) locomotion. Here, we tested whether tamanduas use sprawling forelimb kinematics, i.e. a largely immobile scapula with pronounced lateral spine bending and long-axis rotation of the humerus. We analysed high-speed videos and used X-ray motion analysis of tamanduas walking and balancing on branches of varying inclinations and provide a quantitative characterization of gaits and forelimb kinematics. Tamanduas displayed lateral sequence/lateral couplets on flat ground and horizontal branches, but increased diagonality on steeper inclines and declines, resulting in lateral sequence/diagonal couplets gaits. This result provides further evidence for high diagonality in arboreal species, probably maximising stability in arboreal environments. Further, the results reveal a mosaic of sprawling and parasagittal kinematic characteristics. The abducted elbow results from a constantly internally rotated scapula about its long axis and a retracted humerus. Scapula retraction contributes considerably to stride length. However, lateral rotation in the pectoral region of the spine (range: 21 deg) is higher than reported for other therian mammals. Instead, it is similar to that of skinks and alligators, indicating an aspect generally associated with sprawling locomotion is characteristic for forelimb kinematics of tamanduas. Our study contributes to a growing body of evidence of highly variable non-cursorial therian mammal locomotor kinematics.},
    issn = {0022-0949},
}

@article{Astley2012,
    author = {Astley, Henry C.  and Roberts, Thomas J. },
    year = {2012},
    title = {Evidence for a vertebrate catapult: elastic energy storage in the plantaris tendon during frog jumping},
    doi = {10.1098/rsbl.2011.0982},
    journal = {Biology Letters},
    volume = {8},
    number = {3},
    pages = {386-389},
    url = {https://royalsocietypublishing.org/doi/abs/10.1098/rsbl.2011.0982},
    abstract = { Anuran jumping is one of the most powerful accelerations in vertebrate locomotion. Several species are hypothesized to use a catapult-like mechanism to store and rapidly release elastic energy, producing power outputs far beyond the capability of muscle. Most evidence for this mechanism comes from measurements of whole-body power output; the decoupling of joint motion and muscle shortening expected in a catapult-like mechanism has not been demonstrated. We used high-speed marker-based biplanar X-ray cinefluoroscopy to quantify plantaris muscle fascicle strain and ankle joint motion in frogs in order to test for two hallmarks of a catapult mechanism: (i) shortening of fascicles prior to joint movement (during tendon stretch), and (ii) rapid joint movement during the jump without rapid muscle-shortening (during tendon recoil). During all jumps, muscle fascicles shortened by an average of 7.8 per cent (54\% of total strain) prior to joint movement, stretching the tendon. The subsequent period of initial joint movement and high joint angular acceleration occurred with minimal muscle fascicle length change, consistent with the recoil of the elastic tendon. These data support the plantaris longus tendon as a site of elastic energy storage during frog jumping, and demonstrate that catapult mechanisms may be employed even in sub-maximal jumps. },
}

@article{Dawson2011,
    author = {Dawson, Megan M. and Metzger, Keith A. and Baier, David B. and Brainerd, Elizabeth L.},
    year = {2011},
    title = {{Kinematics of the quadrate bone during feeding in mallard ducks}},
    doi = {10.1242/jeb.047159},
    journal = {Journal of Experimental Biology},
    volume = {214},
    number = {12},
    pages = {2036-2046},
    month = {06},
    abstract = {Avian cranial kinesis, in which mobility of the quadrate, pterygoid and palatine bones contribute to upper bill elevation, is believed to occur in all extant birds. The most widely accepted model for upper bill elevation is that the quadrate rotates rostrally and medially towards the pterygoid, transferring force to the mobile pterygoid–palatine complex, which pushes on the upper bill. Until now, however, it has not been possible to test this hypothesis in vivo because quadrate motions are rapid, three-dimensionally complex and not visible externally. Here we use a new in vivo X-ray motion analysis technique, X-ray reconstruction of moving morphology (XROMM), to create precise (±0.06 mm) 3-D animations of the quadrate, braincase, upper bill and mandible of three mallard ducks, Anas platyrhynchos. We defined a joint coordinate system (JCS) for the quadrato-squamosal joint with the axes aligned to the anatomical planes of the skull. In this coordinate system, the quadrate's 3-D rotations produce an elliptical path of pterygoid process motion, with medial and rostrodorsal then lateral and rostrodorsal motion as the upper bill elevates. As the upper bill depresses, the pterygoid process continues along the ellipsoidal path, with lateral and caudoventral then medial and caudoventral motion. We also found that the mandibular rami bow outwards (streptognathy) during mandibular depression, which may cause the lateral component of quadrate rotation that we observed. Relative to the JCS aligned with the anatomical planes of the skull, a second JCS aligned with quadrato-squamosal joint anatomy did not produce a simpler description of quadrate kinematics.},
    issn = {0022-0949},
}

@article{Schwarz2020,
    author = {Schwarz, Daniel and Konow, Nicolai and Roba, Yonas Tolosa and Heiss, Egon},
    year = {2020},
    title = {{A salamander that chews using complex, three-dimensional mandible movements}},
    doi = {10.1242/jeb.220749},
    journal = {Journal of Experimental Biology},
    volume = {223},
    number = {5},
    pages = {jeb220749},
    month = {03},
    abstract = {Most non-mammal tetrapods have a hinge-like jaw operation restricted to vertical opening and closing movements. Many mammal jaw joints, by contrast, operate in more complex, three-dimensional (3D) ways, involving not only vertical but also propalinal (rostro-caudal) and transverse (lateral) movements. Data on intraoral food processing in lissamphibians and sauropsids has prompted a generally accepted view that these groups mostly swallow food unreduced, and that in those cases where lissamphibians and sauropsids chew, they mostly use simple vertical jaw movements for food processing. The exception to this generally accepted view is the occurrence of some propalinal chewing in sauropsids. We combined 3D kinematics and morphological analyses from biplanar high-speed video fluoroscopy and micro-computed tomography to determine how the paedomorphic salamander Siren intermedia treats captured food. We discovered not only that S. intermedia uses intraoral food processing but also that the elaborated morphology of its jaw joint facilitates mandibular motions in all three planes, resulting in complex 3D chewing. Thus, our data challenge the commonly held view that complex 3D chewing movements are exclusive to mammals, by suggesting that such mechanisms might have evolved early in the tetrapod evolution.},
    issn = {0022-0949},
}

@article{Montuelle2015,
    author = {Montuelle, Stéphane J. and Williams, Susan H.},
    year = {2015},
    title = {{In Vivo Measurement of Mesokinesis in Gekko gecko: The Role of Cranial Kinesis during Gape Display, Feeding and Biting}},
    doi = {10.1371/journal.pone.0134710},
    journal = {PLOS ONE},
    publisher = {Public Library of Science},
    month = {07},
    volume = {10},
    pages = {1-23},
    abstract = {Cranial kinesis refers to movements of skeletal sub-units relative to one another at mobile sutures within the skull. The presence and functional significance of cranial kinesis has been investigated in various vertebrates, with much of our understanding coming from comparative studies and manipulation of ligamentous specimens. Drawing on these studies, cranial kinesis in lizards has been modeled as a four-bar linkage system involving streptostyly (rotation of the quadrate), hypokinesis (dorsoventral flexion and extension of the palato-maxillary sub-unit), mesokinesis (dorsoventral flexion and extension of the snout at the fronto-parietal suture) and metakinesis (sliding movements between parietal and supraocciptal bones). In vivo studies, although limited, suggest that cranial kinesis serves an important role during routine behaviors such as feeding. Here, we use X-ray Reconstruction Of Moving Morphology to further quantify mesokinesis in vivo in Gekko gecko during three routine behaviors: gape display, biting and post-ingestion feeding. During gape display, the snout rotates dorsally above rest position, with mesokinesis accounting for a 10\% increase in maximum gape over that achieved solely by the depression of the lower jaw. During defensive biting, the snout rotates ventrally below rest position to participate in gape closure. Finally, ventroflexion of the snout also occurs during post-ingestion feeding, accounting for 42\% of gape closure during intra-oral transport, 86\% during puncture-crushing, and 61\% during pharyngeal packing. Mesokinesis thus appears to facilitate prey puncturing by allowing the snout to rotate ventrally so that the upper teeth pierce the prey item, thus limiting the need for large movements of the lower jaw. This is suggested to maintain a firm grip on the prey and reduce the possibility of prey escape. More generally, this study demonstrates that mesokinesis is a key component of defensive biting and gape display behaviors, as well as post-ingestion feeding, all of which are linked to organismal fitness.},
    number = {7},
}

@online{Falkingham2023,
    author = {Falkingham, Peter},
    year = {2023},
    title = {{XROMM Blender Tools}},
    organization = {github repository},
    url = {https://github.com/pfalkingham/XROMM_BlenderTools},
    note = {accessed 2023-08-11},
}

@article{Rohlf2000,
    author = {Rohlf, F. James and Corti, Marco},
    year = {2000},
    title = {{Use of Two-Block Partial Least-Squares to Study Covariation in Shape}},
    doi = {10.1080/106351500750049806},
    journal = {Systematic Biology},
    volume = {49},
    number = {4},
    pages = {740-753},
    month = {12},
    abstract = {{The relatively new two-block partial least-squares method for analyzing the covariance between two sets of variables is described and contrasted with the well-known method of canonical correlation analysis. Their statistical properties, types of answers, and visualization techniques are discussed. Examples are given to show its usefulness in comparing two sets of variables—especially when one or both of the sets of variables are shape variables from a geometric morphometric study.}},
    issn = {1063-5157},
}

@article{Gupta2016,
    author = {Gupta, Daya S. and Chen, Lihan},
    year = {2016},
    title = {{Brain oscillations in perception, timing and action}},
    doi = {10.1016/j.cobeha.2016.02.021},
    journal = {Current Opinion in Behavioral Sciences},
    volume = {8},
    pages = {161-166},
    series = {Time in perception and action},
    issn = {2352-1546},
    url = {https://www.sciencedirect.com/science/article/pii/S2352154616300444},
    abstract = {Catching a thrown ball requires a tight coupling between perception and motor control. In this review, we examine multidimensional information processing across various perceptual and motor tasks. We summarize how perception, timing and action can be understood in terms of the coupling of gamma band oscillations, which represent the local activities of brain circuits, to a specific phase of long-range low-frequency oscillations. We propose a temporal window of integration that emerges from cross-frequency coupling that serves to produce optimized action.},
}

%### SPM
@online{Friston2008,
    author       = {Flandin, Guillaume and Friston, Karl J.},
    year         = {2008},
    title        = {\chng{Statistical parametric mapping (SPM)}},
    organization = {Scholarpedia},
    url          = {http://www.scholarpedia.org/article/Statistical\_parametric\_mapping},
    pages        = {6232},
    volume       = {3},
    number       = {4},
}

@inbook{Friston2003,
    author = {Friston, Karl J.},
    year = {2003},
    title = {\chng{Statistical Parametric Mapping}},
    doi = {10.1007/978-1-4615-1079-6_16},
    booktitle = {Neuroscience Databases: A Practical Guide},
    editor = {K{\"o}tter, Rolf},
    publisher = {Springer US},
    address = {Boston, MA},
    pages = {237--250},
    abstract = {This chapter deals with the experimental design and analysis of functional brain imaging studies. It considers the neurobiological motivations for different designs and describes some standard approaches, developed to analyse the ensuing data. Functional neuroimaging (positron emission tomography - PET and functional magnetic resonance imaging fMRI) are generally used to make inferences about functional anatomy on the basis of evoked patterns of cortical activity. Functional anatomy refers to the anatomical organisation of the brain, as it relates to function. It involves an understanding of what each part of the brain does, and how different brain systems interact to support various sensori-motor and cognitive functions. This chapter discusses how this understanding is attained from the perspective of design and analysis of neuroimaging data.},
    isbn = {978-1-4615-1079-6},
}

@article{Friston1994,
    author = {Friston, K. J. and Holmes, A. P. and Worsley, K. J. and Poline, J.-P. and Frith, C. D. and Frackowiak, R. S. J.},
    year = {1994},
    title = {\chng{Statistical parametric maps in functional imaging: A general linear approach}},
    doi = {10.1002/hbm.460020402},
    journal = {Human Brain Mapping},
    volume = {2},
    number = {4},
    pages = {189-210},
    keywords = {statistical parametric maps, analysis of variance, general linear model, statistics, functional imaging, Gaussian fields, functional anatomy},
    url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/hbm.460020402},
    abstract = {Abstract Statistical parametric maps are spatially extended statistical processes that are used to test hypotheses about regionally specific effects in neuroimaging data. The most established sorts of statistical parametric maps (e.g., Friston et al. [1991]: J Cereb Blood Flow Metab 11:690–699; Worsley et al. [1992]: J Cereb Blood Flow Metab 12:900–918) are based on linear models, for example ANCOVA, correlation coefficients and t tests. In the sense that these examples are all special cases of the general linear model it should be possible to implement them (and many others) within a unified framework. We present here a general approach that accomodates most forms of experimental layout and ensuing analysis (designed experiments with fixed effects for factors, covariates and interaction of factors). This approach brings together two well established bodies of theory (the general linear model and the theory of Gaussian fields) to provide a complete and simple framework for the analysis of imaging data. The importance of this framework is twofold: (i) Conceptual and mathematical simplicity, in that the same small number of operational equations is used irrespective of the complexity of the experiment or nature of the statistical model and (ii) the generality of the framework provides for great latitude in experimental design and analysis. © 1995 Wiley-Liss, Inc.},
}

@article{Worsley2004,
    author = { Worsley, Keith J. and Taylor, Jonathan E. and Tomaiuolo, Francesco and Lerch, Jason},
    year = {2004},
    title = {\chng{Unified univariate and multivariate random field theory}},
    doi = {10.1016/j.neuroimage.2004.07.026},
    journal = {NeuroImage},
    volume = {23},
    pages = {S189-S195},
    note = {Mathematics in Brain Imaging},
    issn = {1053-8119},
    url = {https://www.sciencedirect.com/science/article/pii/S1053811904003982},
    keywords = {SPMs, Deformation-based morphometry, Random field theory},
    abstract = {We report new random field theory P values for peaks of canonical correlation SPMs for detecting multiple contrasts in a linear model for multivariate image data. This completes results for all types of univariate and multivariate image data analysis. All other known univariate and multivariate random field theory results are now special cases, so these new results present a true unification of all currently known results. As an illustration, we use these results in a deformation-based morphometry (DBM) analysis to look for regions of the brain where vector deformations of nonmissile trauma patients are related to several verbal memory scores, to detect regions of changes in anatomical effective connectivity between the trauma patients and a group of age- and sex-matched controls, and to look for anatomical connectivity in cortical thickness.},
}

@article{Pataky2008,
    author = { Pataky, Todd C. and Caravaggi, Paolo and Savage, Russell and Parker, Daniel and Goulermas, John Y. and Sellers, William I. and Crompton, Robin H.},
    year = {2008},
    title = {\chng{New insights into the plantar pressure correlates of walking speed using pedobarographic statistical parametric mapping (pSPM)}},
    doi = {10.1016/j.jbiomech.2008.03.034},
    journal = {Journal of Biomechanics},
    volume = {41},
    number = {9},
    pages = {1987-1994},
    issn = {0021-9290},
    url = {https://www.sciencedirect.com/science/article/pii/S0021929008001516},
    keywords = {Plantar pressure, Gait biomechanics, Stance phase, Biomedical image processing, Plantar aponeurosis, Longitudinal arch, Midfoot, Locomotor efficiency},
    abstract = {This study investigates the relation between walking speed and the distribution of peak plantar pressure and compares a traditional ten-region subsampling (10RS) technique with a new technique: pedobarographic statistical parametric mapping (pSPM). Adapted from cerebral fMRI methodology, pSPM is a digital image processing technique that registers foot pressure images such that homologous structures optimally overlap, thereby enabling statistical tests to be conducted at the pixel level. Following previous experimental protocols, we collected pedobarographic records from 10 subjects walking at three different speeds: slow, normal, and fast. Walking speed was recorded and correlated with the peak pressures extracted from the 10 regions, and subsequently with the peak pixel data extracted after pSPM preprocessing. Both methods revealed significant positive correlation between peak plantar pressure and walking speed over the rearfoot and distal forefoot after Bonferroni correction for multiple comparisons. The 10RS analysis found positive correlation in the midfoot and medial proximal forefoot, but the pixel data exhibited significant negative correlation throughout these regions (p<5×10−5). Comparing the statistical maps from the two approaches shows that subsampling may conflate pressure differences evident in pixel-level data, obscuring or even reversing statistical trends. The negative correlation observed in the midfoot implies reduced longitudinal arch collapse with higher walking speeds. We infer that this results from pre- or early-stance phase muscle activity and speculate that preferred walking speed reflects, in part, a balance between the energy required to tighten the longitudinal arch and the apparent propulsive benefits of the stiffened arch.},
}

@article{Pataky2010,
    author = { Pataky, Todd C.},
    year = {2010},
    title = {\chng{Generalized n-dimensional biomechanical field analysis using statistical parametric mapping}},
    doi = {10.1016/j.jbiomech.2010.03.008},
    journal = {Journal of Biomechanics},
    volume = {43},
    number = {10},
    pages = {1976-1982},
    issn = {0021-9290},
    url = {https://www.sciencedirect.com/science/article/pii/S0021929010001533},
    keywords = {Random field theory, Probabilistic finite element analysis, Mechanical deformation fields, Multivariate statistics, Pedobarography},
    abstract = {A variety of biomechanical data are sampled from smooth n-dimensional spatiotemporal fields. These data are usually analyzed discretely, by extracting summary metrics from particular points or regions in the continuum. It has been shown that, in certain situations, such schemes can compromise the spatiotemporal integrity of the original fields. An alternative methodology called statistical parametric mapping (SPM), designed specifically for continuous field analysis, constructs statistical images that lie in the original, biomechanically meaningful sampling space. The current paper demonstrates how SPM can be used to analyze both experimental and simulated biomechanical field data of arbitrary spatiotemporal dimensionality. Firstly, 0-, 1-, 2-, and 3-dimensional spatiotemporal datasets derived from a pedobarographic experiment were analyzed using a common linear model to emphasize that SPM procedures are (practically) identical irrespective of the data's physical dimensionality. Secondly two probabilistic finite element simulation studies were conducted, examining heel pad stress and femoral strain fields, respectively, to demonstrate how SPM can be used to probe the significance of field-wide simulation results in the presence of uncontrollable or induced modeling uncertainty. Results were biomechanically intuitive and suggest that SPM may be suitable for a wide variety of mechanical field applications. SPM's main theoretical advantage is that it avoids problems associated with a priori assumptions regarding the spatiotemporal foci of field signals. SPM's main practical advantage is that a unified framework, encapsulated by a single linear equation, affords comprehensive statistical analyses of smooth scalar fields in arbitrarily bounded n-dimensional spaces.},
}

@article{Pataky2013,
    author = { Pataky, Todd C. and Robinson, Mark A. and Vanrenterghem, Jos},
    year = {2013},
    title = {\chng{Vector field statistical analysis of kinematic and force trajectories}},
    doi = {10.1016/j.jbiomech.2013.07.031},
    journal = {Journal of Biomechanics},
    volume = {46},
    number = {14},
    pages = {2394-2401},
    issn = {0021-9290},
    url = {https://www.sciencedirect.com/science/article/pii/S0021929013003564},
    keywords = {Biomechanics, Random field theory, Statistical parametric mapping, Multivariate statistics},
    abstract = {When investigating the dynamics of three-dimensional multi-body biomechanical systems it is often difficult to derive spatiotemporally directed predictions regarding experimentally induced effects. A paradigm of ‘non-directed’ hypothesis testing has emerged in the literature as a result. Non-directed analyses typically consist of ad hoc scalar extraction, an approach which substantially simplifies the original, highly multivariate datasets (many time points, many vector components). This paper describes a commensurately multivariate method as an alternative to scalar extraction. The method, called ‘statistical parametric mapping’ (SPM), uses random field theory to objectively identify field regions which co-vary significantly with the experimental design. We compared SPM to scalar extraction by re-analyzing three publicly available datasets: 3D knee kinematics, a ten-muscle force system, and 3D ground reaction forces. Scalar extraction was found to bias the analyses of all three datasets by failing to consider sufficient portions of the dataset, and/or by failing to consider covariance amongst vector components. SPM overcame both problems by conducting hypothesis testing at the (massively multivariate) vector trajectory level, with random field corrections simultaneously accounting for temporal correlation and vector covariance. While SPM has been widely demonstrated to be effective for analyzing 3D scalar fields, the current results are the first to demonstrate its effectiveness for 1D vector field analysis. It was concluded that SPM offers a generalized, statistically comprehensive solution to scalar extraction's over-simplification of vector trajectories, thereby making it useful for objectively guiding analyses of complex biomechanical systems.},
}

@online{Pataky2020,
    author       = {Pataky, Todd C.},
    year         = {2020},
    title        = {\chng{Online lecture: Discrete vs Continuous Biomechanical Data Analysis}},
    organization = {{Sports Biomechanics Lecture Series (host: Stuart McErlain-Naylor)}},
    url          = {https://www.youtube.com/live/isLDO0iE6kQ},
    note         = {accessed 31/10/2023},
}

@article{Brett2003,
    author = {Brett, Matthew and Penny, Will and Kiebel, Stefan},
    year = {2003},
    title = {\chng{Introduction to random field theory}},
    journal = {Human brain function},
    volume = {2},
    pages = {867--879},
    publisher = {Academic Press London},
    note = {\url{https://www.fil.ion.ucl.ac.uk/spm/doc/books/hbf2/pdfs/Ch14.pdf}},
}

@article{Kemeny1976,
    author = {Kemeny, John G and Snell, J Laurie and Knapp, Anthony W and Griffeath, David},
    year = {1976},
    title = {\chng{Introduction to random fields}},
    journal = {Denumerable Markov Chains: with a chapter of Markov Random Fields by David Griffeath},
    pages = {425--458},
    publisher = {Springer}
}

% ### walking speed
@article{Kirtley1985,
    author = {Kirtley, C. and Whittle, M.W. and Jefferson, R.J.},
    year = {1985},
    title = {\chng{Influence of walking speed on gait parameters}},
    doi = {10.1016/0141-5425(85)90055-X},
    journal = {Journal of Biomedical Engineering},
    volume = {7},
    number = {4},
    pages = {282-288},
    issn = {0141-5425},
    url = {https://www.sciencedirect.com/science/article/pii/014154258590055X},
    keywords = {Musculoskeletal system, gait analysis, walking speed},
    abstract = {Modern three-dimensional gait analysis systems give information on joint angles and moments in the sagittal and coronal planes, for which normal ranges may not be readily available in the literature. Since patients with joint disease tend to walk slowly and with a short stride, it is essential that normal ranges for gait parameters should be defined with reference to speed of walking. This we have done using a population of 10 normal male subjects agea from 18 to 63 years, walking at speeds which range from very slow to very fast. The ranges of knee angle and moment are given, together with the changes in these parameters with walking speed. Peak knee flexion moment is strongly related to walking speed, whereas coronal plane knee angle is virtually independent of it. The stride length is probably the best basis for deciding the normal range for a particular measurement.},
}

@article{Fukuchi2019,
    author = {Fukuchi, Claudiane Arakaki and Fukuchi, Reginaldo Kisho and Duarte, Marcos},
    year = {2019},
    title = {\chng{Effects of walking speed on gait biomechanics in healthy participants: a systematic review and meta-analysis}},
    doi = {10.1186/s13643-019-1063-z},
    journal = {Systematic reviews},
    volume = {8},
    number = {1},
    pages = {1--11},
    publisher = {BioMed Central},
}

@article{Schwartz2008,
    author = {Schwartz, Michael H. and Rozumalski, Adam and Trost, Joyce P.},
    year = {2008},
    title = {\chng{The effect of walking speed on the gait of typically developing children}},
    doi = {10.1016/j.jbiomech.2008.03.015},
    journal = {Journal of Biomechanics},
    volume = {41},
    number = {8},
    pages = {1639-1650},
    issn = {0021-9290},
    url = {https://www.sciencedirect.com/science/article/pii/S0021929008001450},
    keywords = {Gait, Walking, Speed, Children, Kinematics, Kinetics, Electromyography, Spatio-temporal parameters},
    abstract = {Many gait studies include subjects walking well below or above typical self-selected comfortable (free) speed. For this reason, a descriptive study examining the effect of walking speed on gait was conducted. The purpose of the study was to create a single-source, readily accessible repository of comprehensive gait data for a large group of children walking at a wide variety of speeds. Three-dimensional lower extremity joint kinematics, joint kinetics, surface electromyographic (EMG), and spatio-temporal data were collected on 83 typically developing children (ages 4–17) walking at speeds ranging from very slow (>3 standard deviations below mean free speed) to very fast (>3 standard deviations above mean free speed). The resulting data show that speed has a significant influence on many measures of interest, such as kinematic parameters in the sagittal, coronal, and transverse planes. The same was true for kinetic data (ground reaction force, moment, and power), normalized EMG signals, and spatio-temporal parameters. Examples of parameters with linear and various nonlinear speed dependencies are provided. The data from this study, including an extensive electronic addendum, can be used as a reference for both basic biomechanical and clinical gait studies.},
}


% #### extinct bracketing
@article{Pronost2006,
    author = {Pronost, Nicolas and Dumont, Georges and Berillon, Gilles and Nicolas, Guillaume},
    year = {2006},
    title = {\chng{Morphological and stance interpolations in database for simulating bipedalism of virtual humans}},
    doi = {10.1007/s00371-005-0350-y},
    journal = {The Visual Computer},
    volume = {22},
    pages = {4--13},
    publisher = {Springer},
}

@InProceedings{Nicolas2006,
    author = {Nicolas, Guillaume and Multon, Franck and Berillon, Gilles and Marchal, Francois},
    year = {2006},
    title = {\chng{Plausible Locomotion for Bipedal Creatures Using Motion Warping and Inverse Kinematics}},
    doi = {10.1007/11784203_55},
    publisher = {Springer Berlin Heidelberg},
    editor = {Nishita, Tomoyuki and Peng, Qunsheng and Seidel, Hans-Peter},
    booktitle = {Advances in Computer Graphics},
    address = {Berlin, Heidelberg},
    pages = {586--593},
    abstract = {One of the main question addressed by paleoanthropologists is the recovery of plausible motions for extinct species whose knowledge is generally limited to incomplete bones and skeletons. Calculating locomotion for extinct species is mainly based on the direct application of captured trajectories to numerically reconstructed skeletons. The gait is judged realistic compared to another if it minimizes energy and preserves balance. In computer animation, adapting a motion to a skeleton is addressed by so-called motion retargeting techniques. The goal is then to ensure that the resulting motion is close to the initial one while dealing with new bones' dimensions. In this paper, we adapt methods used in computer animation in order to solve such a problem. This approach is based on a two-steps framework: first, a reference motion of the feet is warped in order to optimize a set of biomechanical general laws, such as energy and Jerk minimization. Second, the remaining degrees of freedom (denoted DOF) are calculated thanks to inverse kinematics (denoted IK). This method is applied on a small woman, a tall man, a chimpanzee and Lucy (Australopithecus afarensis).},
    isbn = {978-3-540-35639-4},
}

@article{Nicolas2007,
    author = {Nicolas, Guillaume and Multon, Franck and Berillon, Gilles and Marchal, François},
    year = {2007},
    title = {\chng{From bone to plausible bipedal locomotion using inverse kinematics}},
    doi = {10.1016/j.jbiomech.2006.04.010},
    journal = {Journal of Biomechanics},
    volume = {40},
    number = {5},
    pages = {1048-1057},
    issn = {0021-9290},
    url = {https://www.sciencedirect.com/science/article/pii/S0021929006001424},
    keywords = {Inverse kinematics, 3D locomotion, Paleoanthropology, Optimization},
    abstract = {The purpose of this study is to validate a method based on anatomical data and biomechanical locomotor hypotheses that could be applied in palaeontology to simulate locomotion in fossil hominids. The main problem is to ensure that purely mathematical simulation, based on anatomical descriptions, is enough to test hypotheses on human motion control. A 3D geometric model of the lower limb was therefore processed from anatomical descriptions. From this 3D model, we developed a method to retrieve natural lower-limb motion depending on chosen constraints. We assumed that the role of lower-limb motion is to make the feet move from one footprint to the next by following a trajectory that resembles that of living humans (primary task). This method based on inverse kinematics also allows biomechanical laws of bipedal locomotion to be taken into account (secondary tasks). The laws tested in this study relate to preserving joint limits, minimizing energy and minimizing the distance to a rest posture proposed by anthropologists and viewed as input to our system. A weighted sum of the resulting derivable cost functions enabled us to select a specific solution in the null space of the primary task. In order to validate this approach, we compared simulated and captured motion from ten subjects for whom anthropometrical data were recorded. We concluded that this “anatomically based bipedalism simulation” seems promising as a means of investigating natural locomotion behaviour and might also be used to retrieve natural locomotion in fossil hominids where only little knowledge is available.},
}

@article{Hatala2016,
    author = {Hatala, Kevin G.  and Demes, Brigitte  and Richmond, Brian G. },
    year = {2016},
    title = {\chng{Laetoli footprints reveal bipedal gait biomechanics different from those of modern humans and chimpanzees}},
    doi = {10.1098/rspb.2016.0235},
    journal = {{Proceedings of the Royal Society B: Biological Sciences}},
    volume = {283},
    number = {1836},
    pages = {20160235},
    abstract = { Bipedalism is a key adaptation that shaped human evolution, yet the timing and nature of its evolution remain unclear. Here we use new experimentally based approaches to investigate the locomotor mechanics preserved by the famous Pliocene hominin footprints from Laetoli, Tanzania. We conducted footprint formation experiments with habitually barefoot humans and with chimpanzees to quantitatively compare their footprints to those preserved at Laetoli. Our results show that the Laetoli footprints are morphologically distinct from those of both chimpanzees and habitually barefoot modern humans. By analysing biomechanical data that were collected during the human experiments we, for the first time, directly link differences between the Laetoli and modern human footprints to specific biomechanical variables. We find that the Laetoli hominin probably used a more flexed limb posture at foot strike than modern humans when walking bipedally. The Laetoli footprints provide a clear snapshot of an early hominin bipedal gait that probably involved a limb posture that was slightly but significantly different from our own, and these data support the hypothesis that important evolutionary changes to hominin bipedalism occurred within the past 3.66 Myr. },
}

% ### piglet neonate locomotion
@article{Sullivan2013,
    author = {Sullivan, Sarah and Friess, Stuart H. and Ralston, Jill and Smith, Colin and Propert, Kathleen J. and Rapp, Paul E. and Margulies, Susan S.},
    year = {2013},
    title = {\chng{Improved Behavior, Motor, and Cognition Assessments in Neonatal Piglets}},
    doi = {10.1089/neu.2013.2913},
    journal = {Journal of Neurotrauma},
    volume = {30},
    number = {20},
    pages = {1770-1779},
    abstract = { Abstract The alterations of animal behavior after traumatic brain injury (TBI) can be subtle, and their quantitative characterization can present significant methodological challenges. Meeting these challenges is a critical need, because quantitative measures are required in studies that compare the efficacy of different clinical interventions. We developed a battery of assessments to quantify behavioral, motor, and cognitive changes in neonatal piglets with good sensitivity and specificity to the detection of persistent deficits that correlate with axonal injury severity after a rapid non-impact head rotation with a diffuse pattern of axonal injury. The battery of measures developed included open field behaviors of sniffing and moving a toy, locomotion measures of Lempel-Ziv complexity and the probability of remaining in the current location, and a novel metric for evaluating motor performance. Our composite porcine disability score was able to detect brain injury with a sensitivity of 100\% and specificity of 85.7\% at day +4 post-injury for n=8 injured and n=7 sham piglets and significantly correlated with the percent axonal injury in these animals (day +4: ρ=0.76, p=0.0011). A significant improvement over our previous assessments, this new porcine disability score has potential use in a wide variety of porcine disease and injury models. },
}
@article{Kashiha2014,
    author = {Kashiha, Mohammad Amin and Bahr, Claudia and Ott, Sanne and Moons, Christel P.H. and Niewold, Theo A. and Tuyttens, Frank and Berckmans, Daniel},
    title = {\chng{Automatic monitoring of pig locomotion using image analysis}},
    journal = {Livestock Science},
    volume = {159},
    pages = {141-148},
    year = {2014},
    issn = {1871-1413},
    doi = {10.1016/j.livsci.2013.11.007},
    url = {https://www.sciencedirect.com/science/article/pii/S1871141313005003},
    keywords = {Ellipse fitting, eYeNamic, Image analysis, Locomotion, Pig},
    abstract = {The purpose of this study was to investigate the feasibility and validity of an automated image processing method to detect the locomotion of pigs in a group housed environment and under experimental conditions. Topview video images were captured for forty piglets, housed ten per pen. On average, piglets had a weight of 27kg (SD=4.4kg) at the start of experiments and 40kg (SD=6.5) at the end. Each pen was monitored by a topview CCD camera. The image analysis protocol to automatically quantify locomotion involved localising pigs through background subtraction and tracking them over a set period of time. To validate the accuracy of detecting pigs “In Locomotion” or “Not In Locomotion”, they were compared to offline manually labelled behavioural data (“In Locomotion” versus “Not In Locomotion”). This is the first study to show that the locomotion of pigs in a group can be determined using image analysis with an accuracy of 89.8\%. Since locomotion is known to be associated with issues such as lameness, careful monitoring can give an accurate indication of the health and welfare of pigs.},
}

@article{Beattie2000,
    author = {Beattie, V. E. and O’Connell, N. E. and Kilpatrick, D. J. and Moss, B. W.},
    year = {2000},
    title = {\chng{Influence of environmental enrichment on welfare-related behavioural and physiological parameters in growing pigs}},
    doi = {10.1017/S1357729800051791},
    journal = {Animal Science},
    number = {3},
    volume = {70},
    publisher = {Cambridge University Press},
    pages = {443–450},
}

@article{Trivers1974,
    author = {Trivers, Robert L.},
    year = {1974},
    title = {\chng{Parent-Offspring Conflict}},
    doi = {10.1093/icb/14.1.249},
    journal = {American Zoologist},
    volume = {14},
    number = {1},
    pages = {249-264},
    month = {08},
    abstract = {{When parent-offspring relations in sexually reproducing species are viewed from the standpoint of the offspring as well as the parent, conflict is seen to be an expected feature of such relations. In particular, parent and offspring are expected to disagree over how long the period of parental investment should last, over the amount of parental investment that should be given, and over the altruistic and egoistic tendencies of the offspring as these tendencies affect other relatives. In addition, under certain conditions parents and offspring are expected to disagree over the preferred sex of the potential offspring. In general, parent-offspring conflict is expected to increase during the period of parental care, and offspring are expected to employ psychological weapons in order to compete with their parents. Detailed data on mother-offspring relations in mammals are consistent with the arguments presented. Conflict in some species, including the human species, is expected to extend to the adult reproductive role of the offspring: under certain conditions parents are expected to attempt to mold an offspring, against its better interests, into a permanent nonreproductive.}},
    issn = {0003-1569},
}

@article{Smith1974,
    author = {Smith, Christopher C. and Fretwell, Stephen D.},
    year = {1974},
    title = {\chng{The Optimal Balance between Size and Number of Offspring}},
    doi = {10.1086/282929},
    journal = {The American Naturalist},
    volume = {108},
    number = {962},
    pages = {499-506},
    abstract = { The relationship between the energy expended per offspring, fitness of offspring, and parental fitness is presented in a two-dimensional graphical model. The validity of the model in determining an optimal parental strategy is demonstrated analytically. The model applies under various conditions of parental care and sibling care for the offspring but is most useful for species that produce numerous small offspring which are given no parental care. },
}

@article{Andersen2011,
    author = {Andersen, Inger Lise and N{\ae}vdal, Eric and B{\o}e, Knut Egil},
    year = {2011},
    title = {\chng{Maternal investment, sibling competition, and offspring survival with increasing litter size and parity in pigs (\textit{Sus scrofa})}},
    doi = {10.1007/s00265-010-1128-4},
    journal = {Behavioral ecology and sociobiology},
    volume = {65},
    pages = {1159--1167},
    publisher = {Springer},
}


@article{Denayer2014,
    author = {Denayer, Tinneke and Stöhr, Thomas and {Van Roy}, Maarten},
    year = {2014},
    title = {\chng{Animal models in translational medicine: Validation and prediction}},
    doi = {10.1016/j.nhtm.2014.08.001},
    journal = {{New Horizons in Translational Medicine}},
    volume = {2},
    number = {1},
    pages = {5-11},
    issn = {2307-5023},
    url = {https://www.sciencedirect.com/science/article/pii/S2307502314000022},
    keywords = {Animal model, Drug development, Translational value, Fit-for-purpose validation},
    abstract = {{Despite large investments in drug development, the overall success rate of drugs during clinical development remains low. One prominent explanation is flawed preclinical research, in which the use and outcome of animal models is pivotal to bridge the translational gap to the clinic. Therefore, the selection of a validated and predictive animal model is essential to address the clinical question. In this review, the current challenges and limitations of animal models are discussed, with a focus on the fit-for-purpose validation. Moreover, guidance is provided on the selection, design and conduct of an animal model, including the recommendation of assessing both efficacy and safety endpoints. In order to improve the clinical translation, the use of humanized mouse models and preclinical applications of clinical features are discussed. On top, the translational value of animal models could be further enhanced when combined with emerging alternative translational approaches. Focal points: •BedsideAnimal models are essential for translation of drug findings from bench to bedside. Hence, critical evaluation of the face and predictive validity of these models is important. Reversely, clinical bedside findings that were not predicted by animal testing should be back translated and used to refine the animal models.•BenchsideProper design, execution and reporting of animal model results help to make preclinical data more reproducible and translatable to the clinic.•IndustryDesign of an animal model strategy is part of the translational plan rather than (a) single experiment(s). Data from animal models are essential in predicting the clinical outcome for a specific drug in development.•CommunityReview, standardization and refinement of animal models by disease expert groups helps to improve rigor of animal model testing. It is important that the applied animal models are validated fit-for-purpose according to stringent criteria and reproducible.•GovernmentsAs during drug development fit-for-purpose animal models are key for success in clinical translation, financial investments and support from the government to develop, optimize, validate and run such translation tools are important. Over time, this will be of benefit for patients and healthcare institutions.•Regulatory agenciesPreclinical testing of a drug in an animal model is not a prerequisite for regulatory agencies before entering clinical trials, but does unquestionably provide valuable data on the expected clinical performance of the drug. Hence, testing in animal models is largely recommended from both a business and patient perspective. In addition, inclusion of safety parameters in animal models will help to build the required safety data package of drugs in development.}},
}