@article{zheng-trajectory-2015,
	title = {Trajectory {Data} {Mining}: {An} {Overview}},
	url = {https://www.microsoft.com/en-us/research/publication/trajectory-data-mining-an-overview/},
	journal = {ACM Transaction on Intelligent Systems and Technology},
	author = {Zheng, Yu},
	year = {2015},
	note = {Type: Journal Article},
}

@ARTICLE{10.3389/fnsys.2019.00020,
	AUTHOR={Arac, Ahmet and Zhao, Pingping and Dobkin, Bruce H. and Carmichael, S. Thomas and Golshani, Peyman},
	TITLE={DeepBehavior: A Deep Learning Toolbox for Automated Analysis of Animal and Human Behavior Imaging Data},
	JOURNAL={Frontiers in Systems Neuroscience},
	VOLUME={13},
	PAGES={20},
	YEAR={2019},
	URL={https://www.frontiersin.org/article/10.3389/fnsys.2019.00020},
	DOI={10.3389/fnsys.2019.00020},
	ISSN={1662-5137},
	ABSTRACT={Detailed behavioral analysis is key to understanding the brain-behavior relationship. Here, we present deep learning-based methods for analysis of behavior imaging data in mice and humans. Specifically, we use three different convolutional neural network architectures and five different behavior tasks in mice and humans and provide detailed instructions for rapid implementation of these methods for the neuroscience community. We provide examples of three dimensional (3D) kinematic analysis in the food pellet reaching task in mice, three-chamber test in mice, social interaction test in freely moving mice with simultaneous miniscope calcium imaging, and 3D kinematic analysis of two upper extremity movements in humans (reaching and alternating pronation/supination). We demonstrate that the transfer learning approach accelerates the training of the network when using images from these types of behavior video recordings. We also provide code for post-processing of the data after initial analysis with deep learning. Our methods expand the repertoire of available tools using deep learning for behavior analysis by providing detailed instructions on implementation, applications in several behavior tests, and post-processing methods and annotated code for detailed behavior analysis. Moreover, our methods in human motor behavior can be used in the clinic to assess motor function during recovery after an injury such as stroke.}
}


@inproceedings{pandas,
  title={Data structures for statistical computing in python},
  author={McKinney, Wes and others},
  booktitle={Proceedings of the 9th Python in Science Conference},
  volume={445},
  pages={51--56},
  year={2010},
  doi ={10.25080/majora-92bf1922-00a},
  organization={Austin, TX}
}

  @Article{adehabitat,
    title = {The package adehabitat for the R software: tool for the
      analysis of space and habitat use by animals},
    journal = {Ecological Modelling},
    volume = {197},
    pages = {1035},
    year = {2006},
    author = {C. Calenge},
  }

  @Misc{shapely,
  author =    {Sean Gillies and others},
  organization = {toblerity.org},
  title =     {Shapely: manipulation and analysis of geometric objects},
  year =      {2007--},
  url = "https://github.com/Toblerity/Shapely"
}

@article{kilkenny_improving_2010,
	title = {Improving bioscience research reporting: {The} {ARRIVE} guidelines for reporting animal research},
	volume = {1},
	issn = {0976-500X},
	shorttitle = {Improving bioscience research reporting},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3043335/},
	doi = {10.4103/0976-500X.72351},
	number = {2},
	urldate = {2020-01-13},
	journal = {Journal of Pharmacology \& Pharmacotherapeutics},
	author = {Kilkenny, Carol and Browne, William J. and Cuthill, Innes C. and Emerson, Michael and Altman, Douglas G.},
	year = {2010},
	pmid = {21350617},
	pmcid = {PMC3043335},
	pages = {94--99}
}

@article{stroke_therapy_academic_industry_roundtable_stair_recommendations_1999,
	title = {Recommendations for standards regarding preclinical neuroprotective and restorative drug development},
	volume = {30},
	issn = {0039-2499},
	doi = {10.1161/01.str.30.12.2752},
	abstract = {The plethora of failed clinical trials with neuroprotective drugs for acute ischemic stroke have raised justifiable concerns about how best to proceed for the future development of such interventions. Preclinical testing of neuroprotective drugs is an important aspect of assessing their therapeutic potential, but guidelines concerning how to perform preclinical development of purported neuroprotective drugs for acute ischemic stroke are lacking. This conference of academicians and industry representatives was convened to suggest such guidelines for the preclinical evaluation of neuroprotective drugs and to recommend to potential clinical investigators the data they should review to reassure themselves that a particular neuroprotective drug has a reasonable chance to succeed in an appropriately designed clinical trial. Without rigorous, robust, and detailed preclinical evaluation, it is unlikely that novel neuroprotective drugs will prove to be effective when tested in large, time-consuming, and expensive clinical trials. Additionally, similar recommendations are provided for drugs with the potential to enhance recovery after acute ischemic stroke, a burgeoning new field with great potential but little currently available data. The suggestions contained in this document are meant to serve as overall guidelines that must be adapted to the individual characteristics related to particular drugs and their preclinical and clinical development needs.},
	language = {eng},
	number = {12},
	journal = {Stroke},
	author = {{Stroke Therapy Academic Industry Roundtable (STAIR)}},
	month = dec,
	year = {1999},
	pmid = {10583007},
	keywords = {Animals, Disease Models, Animal, Drug Combinations, Drug Evaluation, Preclinical, Enzymes, Guidelines as Topic, Neuroprotective Agents, Outcome Assessment, Health Care, Primates, Rats, Remission, Spontaneous, Sex Factors, Stroke},
	pages = {2752--2758}
}

@misc{noauthor_1_nodate,
	title = {(1) {Stroke} {Therapy} {Academic} {Industry} {Roundtable} ({STAIR}) {Recommendations} {For} {Extended} {Window} {Acute} {Stroke} {Therapy} {Trials} {\textbar} {Request} {PDF}},
	url = {https://www.researchgate.net/publication/26249404_Stroke_Therapy_Academic_Industry_Roundtable_STAIR_Recommendations_For_Extended_Window_Acute_Stroke_Therapy_Trials},
	abstract = {ResearchGate is a network dedicated to science and research. Connect, collaborate and discover scientific publications, jobs and conferences. All for free.},
	language = {en},
	urldate = {2020-01-13},
	journal = {ResearchGate}
}

@article{fisher_update_2009,
	title = {Update of the {Stroke} {Therapy} {Academic} {Industry} {Roundtable} {Preclinical} {Recommendations}},
	volume = {40},
	issn = {0039-2499},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2888275/},
	doi = {10.1161/STROKEAHA.108.541128},
	abstract = {The initial Stroke Therapy Academic Industry Roundtable (STAIR) recommendations published in 1999 were intended to improve the quality of preclinical studies of purported acute stroke therapies. Although recognized as reasonable, they have not been closely followed nor rigorously validated. Substantial advances have occurred regarding the appropriate quality and breadth of preclinical testing for candidate acute stroke therapies for better clinical translation. The updated STAIR preclinical recommendations reinforce the previous suggestions that reproducibly defining dose response and time windows with both histological and functional outcomes in multiple animal species with appropriate physiological monitoring is appropriate. The updated STAIR recommendations include: the fundamentals of good scientific inquiry should be followed by eliminating randomization and assessment bias, a priori defining inclusion/exclusion criteria, performing appropriate power and sample size calculations, and disclosing potential conflicts of interest. After initial evaluations in young, healthy male animals, further studies should be performed in females, aged animals, and animals with comorbid conditions such as hypertension, diabetes, and hypercholesterolemia. Another consideration is the use of clinically relevant biomarkers in animal studies. Although the recommendations cannot be validated until effective therapies based on them emerge from clinical trials, it is hoped that adherence to them might enhance the chances for success.},
	number = {6},
	urldate = {2020-01-13},
	journal = {Stroke; a journal of cerebral circulation},
	author = {Fisher, Marc and Feuerstein, Giora and Howells, David W. and Hurn, Patricia D. and Kent, Thomas A. and Savitz, Sean I. and Lo, Eng H.},
	month = jun,
	year = {2009},
	pmid = {19246690},
	pmcid = {PMC2888275},
	pages = {2244--2250}
}

@article{savitzky_smoothing_1964,
	title = {Smoothing and {Differentiation} of {Data} by {Simplified} {Least} {Squares} {Procedures}.},
	volume = {36},
	issn = {0003-2700},
	url = {https://doi.org/10.1021/ac60214a047},
	doi = {10.1021/ac60214a047},
	number = {8},
	urldate = {2021-02-13},
	journal = {Analytical Chemistry},
	author = {Savitzky, Abraham. and Golay, M. J. E.},
	month = jul,
	year = {1964},
	note = {Publisher: American Chemical Society},
	pages = {1627--1639},
}

@misc{noauthor_hydroxytyrosol_nodate,
	title = {Hydroxytyrosol, the {Major} {Phenolic} {Compound} of {Olive} {Oil}, as an {Acute} {Therapeutic} {Strategy} after {Ischemic} {Stroke}. - {PubMed} - {NCBI}},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/31614692},
	urldate = {2020-01-13}
}

@inproceedings{kim_trajectory_2017,
	title = {Trajectory {Flow} {Map}: {Graph}-based {Approach} to {Analysing} {Temporal} {Evolution} of {Aggregated} {Traffic} {Flows} in {Large}-scale {Urban} {Networks}},
	shorttitle = {Trajectory {Flow} {Map}},
	urldate = {2019-12-02},
	author = {Kim, Jiwon and Zheng, Kai and Corcoran, Jonathan and Ahn, Sanghyung and Papamanolis, Marty},
	year = {2017}
}

@article{abbas_computer_2019,
	title = {Computer {Methods} for {Automatic} {Locomotion} and {Gesture} {Tracking} in {Mice} and {Small} {Animals} for {Neuroscience} {Applications}: {A} {Survey}},
	volume = {19},
	shorttitle = {Computer {Methods} for {Automatic} {Locomotion} and {Gesture} {Tracking} in {Mice} and {Small} {Animals} for {Neuroscience} {Applications}},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6696321/},
	doi = {10.3390/s19153274},
	abstract = {Neuroscience has traditionally relied on manually observing laboratory animals in controlled environments. Researchers usually record animals behaving freely or in a restrained manner and then annotate the data manually. The manual annotation is not desirable ...},
	language = {en},
	number = {15},
	urldate = {2020-01-13},
	journal = {Sensors (Basel, Switzerland)},
	author = {Abbas, Waseem and Rodo, David Masip},
	month = aug,
	year = {2019},
	pmid = {31349617}
}

@article{zinnhardt_multimodal_2015,
	title = {Multimodal imaging reveals temporal and spatial microglia and matrix metalloproteinase activity after experimental stroke},
	volume = {35},
	issn = {0271-678X},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4635244/},
	doi = {10.1038/jcbfm.2015.149},
	abstract = {Stroke is the most common cause of death and disability from neurologic disease in humans. Activation of microglia and matrix metalloproteinases (MMPs) is involved in positively and negatively affecting stroke outcome. Novel, noninvasive, multimodal imaging methods visualizing microglial and MMP alterations were employed. The spatio-temporal dynamics of these parameters were studied in relation to blood flow changes. Micro positron emission tomography (μPET) using [18F]BR-351 showed MMP activity within the first days after transient middle cerebral artery occlusion (tMCAo), followed by increased [18F]DPA-714 uptake as a marker for microglia activation with a maximum at 14 days after tMCAo. The inflammatory response was spatially located in the infarct core and in adjacent (penumbral) tissue. For the first time, multimodal imaging based on PET, single photon emission computed tomography, and magnetic resonance imaging revealed insight into the spatio-temporal distribution of critical parameters of poststroke inflammation. This allows further evaluation of novel treatment paradigms targeting the postischemic inflammation.},
	number = {11},
	urldate = {2020-01-13},
	journal = {Journal of Cerebral Blood Flow \& Metabolism},
	author = {Zinnhardt, Bastian and Viel, Thomas and Wachsmuth, Lydia and Vrachimis, Alexis and Wagner, Stefan and Breyholz, Hans-Jörg and Faust, Andreas and Hermann, Sven and Kopka, Klaus and Faber, Cornelius and Dollé, Frédéric and Pappata, Sabina and Planas, Anna M and Tavitian, Bertrand and Schäfers, Michael and Sorokin, Lydia M and Kuhlmann, Michael T and Jacobs, Andreas H},
	month = nov,
	year = {2015},
	pmid = {26126867},
	pmcid = {PMC4635244},
	pages = {1711--1721}
}

@article{fluri_animal_2015,
	title = {Animal models of ischemic stroke and their application in clinical research},
	volume = {9},
	issn = {1177-8881},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4494187/},
	doi = {10.2147/DDDT.S56071},
	abstract = {This review outlines the most frequently used rodent stroke models and discusses their strengths and shortcomings. Mimicking all aspects of human stroke in one animal model is not feasible because ischemic stroke in humans is a heterogeneous disorder with a complex pathophysiology. The transient or permanent middle cerebral artery occlusion (MCAo) model is one of the models that most closely simulate human ischemic stroke. Furthermore, this model is characterized by reliable and well-reproducible infarcts. Therefore, the MCAo model has been involved in the majority of studies that address pathophysiological processes or neuroprotective agents. Another model uses thromboembolic clots and thus is more convenient for investigating thrombolytic agents and pathophysiological processes after thrombolysis. However, for many reasons, preclinical stroke research has a low translational success rate. One factor might be the choice of stroke model. Whereas the therapeutic responsiveness of permanent focal stroke in humans declines significantly within 3 hours after stroke onset, the therapeutic window in animal models with prompt reperfusion is up to 12 hours, resulting in a much longer action time of the investigated agent. Another major problem of animal stroke models is that studies are mostly conducted in young animals without any comorbidity. These models differ from human stroke, which particularly affects elderly people who have various cerebrovascular risk factors. Choosing the most appropriate stroke model and optimizing the study design of preclinical trials might increase the translational potential of animal stroke models.},
	urldate = {2020-01-13},
	journal = {Drug Design, Development and Therapy},
	author = {Fluri, Felix and Schuhmann, Michael K and Kleinschnitz, Christoph},
	month = jul,
	year = {2015},
	pmid = {26170628},
	pmcid = {PMC4494187},
	pages = {3445--3454}
}

@article{williams_identification_2017,
	title = {Identification of animal movement patterns using tri-axial magnetometry},
	volume = {5},
	issn = {2051-3933},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5367006/},
	doi = {10.1186/s40462-017-0097-x},
	abstract = {Background
Accelerometers are powerful sensors in many bio-logging devices, and are increasingly allowing researchers to investigate the performance, behaviour, energy expenditure and even state, of free-living animals. Another sensor commonly used in animal-attached loggers is the magnetometer, which has been primarily used in dead-reckoning or inertial measurement tags, but little outside that. We examine the potential of magnetometers for helping elucidate the behaviour of animals in a manner analogous to, but very different from, accelerometers. The particular responses of magnetometers to movement means that there are instances when they can resolve behaviours that are not easily perceived using accelerometers.

Methods
We calibrated the tri-axial magnetometer to rotations in each axis of movement and constructed 3-dimensional plots to inspect these stylised movements. Using the tri-axial data of Daily Diary tags, attached to individuals of number of animal species as they perform different behaviours, we used these 3-d plots to develop a framework with which tri-axial magnetometry data can be examined and introduce metrics that should help quantify movement and behaviour.﻿﻿

Results
Tri-axial magnetometry data reveal patterns in movement at various scales of rotation that are not always evident in acceleration data. Some of these patterns may be obscure until visualised in 3D space as tri-axial spherical plots (m-spheres). A tag-fitted animal that rotates in heading while adopting a constant body attitude produces a ring of data around the pole of the m-sphere that we define as its Normal Operational Plane (NOP). Data that do not lie on this ring are created by postural rotations of the animal as it pitches and/or rolls. Consequently, stereotyped behaviours appear as specific trajectories on the sphere (m-prints), reflecting conserved sequences of postural changes (and/or angular velocities), which result from the precise relationship between body attitude and heading. This novel approach shows promise for helping researchers to identify and quantify behaviours in terms of animal body posture, including heading.

Conclusion
Magnetometer-based techniques and metrics can enhance our capacity to identify and examine animal behaviour, either as a technique used alone, or one that is complementary to tri-axial accelerometry.

Electronic supplementary material
The online version of this article (doi:10.1186/s40462-017-0097-x) contains supplementary material, which is available to authorized users.},
	urldate = {2020-01-13},
	journal = {Movement Ecology},
	author = {Williams, Hannah J. and Holton, Mark D. and Shepard, Emily L. C. and Largey, Nicola and Norman, Brad and Ryan, Peter G. and Duriez, Olivier and Scantlebury, Michael and Quintana, Flavio and Magowan, Elizabeth A. and Marks, Nikki J. and Alagaili, Abdulaziz N. and Bennett, Nigel C. and Wilson, Rory P.},
	month = mar,
	year = {2017},
	pmid = {28357113},
	pmcid = {PMC5367006}
}

@article{wiesmann_dietary_2016,
	title = {A {Dietary} {Treatment} {Improves} {Cerebral} {Blood} {Flow} and {Brain} {Connectivity} in {Aging} {apoE}4 {Mice}},
	volume = {2016},
	issn = {1687-5443},
	doi = {10.1155/2016/6846721},
	abstract = {APOE ε4 (apoE4) polymorphism is the main genetic determinant of sporadic Alzheimer's disease (AD). A dietary approach (Fortasyn) including docosahexaenoic acid, eicosapentaenoic acid, uridine, choline, phospholipids, folic acid, vitamins B12, B6, C, and E, and selenium has been proposed for dietary management of AD. We hypothesize that the diet could inhibit AD-like pathologies in apoE4 mice, specifically cerebrovascular and connectivity impairment. Moreover, we evaluated the diet effect on cerebral blood flow (CBF), functional connectivity (FC), gray/white matter integrity, and postsynaptic density in aging apoE4 mice. At 10-12 months, apoE4 mice did not display prominent pathological differences compared to wild-type (WT) mice. However, 16-18-month-old apoE4 mice revealed reduced CBF and accelerated synaptic loss. The diet increased cortical CBF and amount of synapses and improved white matter integrity and FC in both aging apoE4 and WT mice. We demonstrated that protective mechanisms on vascular and synapse health are enhanced by Fortasyn, independent of apoE genotype. We further showed the efficacy of a multimodal translational approach, including advanced MR neuroimaging, to study dietary intervention on brain structure and function in aging.},
	language = {eng},
	journal = {Neural Plasticity},
	author = {Wiesmann, Maximilian and Zerbi, Valerio and Jansen, Diane and Haast, Roy and Lütjohann, Dieter and Broersen, Laus M. and Heerschap, Arend and Kiliaan, Amanda J.},
	year = {2016},
	pmid = {27034849},
	pmcid = {PMC4806294},
	keywords = {Aging, Alzheimer Disease, Animals, Apolipoprotein E4, Apolipoproteins E, Brain, Brain Mapping, Diet, Disks Large Homolog 4 Protein, Fatty Acids, Female, Guanylate Kinases, Magnetic Resonance Imaging, Male, Membrane Proteins, Mice, Mice, Inbred C57BL, Mice, Transgenic, Neural Pathways, Sterols},
	pages = {6846721}
}

@article{balkaya_assessing_2013,
	title = {Assessing post-stroke behavior in mouse models of focal ischemia},
	volume = {33},
	issn = {1559-7016},
	doi = {10.1038/jcbfm.2012.185},
	abstract = {Experimental treatment strategies and neuroprotective drugs that showed therapeutic promise in animal models of stroke have failed to produce beneficial effects in human stroke patients. The difficulty in translating preclinical findings to humans represents a major challenge in cerebrovascular research. The reasons behind this translational road block might be explained by a number of factors, including poor quality control in various stages of the research process, the validity of experimental stroke models, and differences in drug administration and pharmacokinetics. Another major difference between animal studies and clinical trials is the choice of end point or outcome measures. Here, we discuss the necessity of poststroke behavioral testing to bridge the gap between clinical and experimental end points. We review established sensory-motor tests for outcome determination after focal ischemia based on the published literature as well as our own personal experience. Selected tests are described in more detail and good laboratory practice standards for behavioral testing are discussed. This review is intended for stroke researchers planning to use behavioral testing in mice.},
	language = {eng},
	number = {3},
	journal = {Journal of Cerebral Blood Flow and Metabolism: Official Journal of the International Society of Cerebral Blood Flow and Metabolism},
	author = {Balkaya, Mustafa and Kröber, Jan M. and Rex, Andre and Endres, Matthias},
	month = mar,
	year = {2013},
	pmid = {23232947},
	pmcid = {PMC3587814},
	keywords = {Animals, Behavior, Animal, Brain Ischemia, Disease Models, Animal, Humans, Mice, Stroke},
	pages = {330--338}
}

@misc{noauthor_assessing_nodate,
	title = {Assessing post-stroke behavior in mouse models of focal ischemia. - {PubMed} - {NCBI}},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/23232947},
	urldate = {2020-01-09}
}

@article{zerbi_multinutrient_2014,
	title = {Multinutrient diets improve cerebral perfusion and neuroprotection in a murine model of {Alzheimer}'s disease},
	volume = {35},
	issn = {0197-4580},
	url = {http://www.sciencedirect.com/science/article/pii/S0197458013004508},
	doi = {10.1016/j.neurobiolaging.2013.09.038},
	abstract = {Nutritional intervention may retard the development of Alzheimer's disease (AD). In this study we tested the effects of 2 multi-nutrient diets in an AD mouse model (APPswe/PS1dE9). One diet contained membrane precursors such as omega-3 fatty acids and uridine monophosphate (DEU), whereas another diet contained cofactors for membrane synthesis as well (Fortasyn); the diets were developed to enhance synaptic membranes synthesis, and contain components that may improve vascular health. We measured cerebral blood flow (CBF) and water diffusivity with ultra-high-field magnetic resonance imaging, as alterations in these parameters correlate with clinical symptoms of the disease. APPswe/PS1dE9 mice on control diet showed decreased CBF and changes in brain water diffusion, in accordance with findings of hypoperfusion, axonal disconnection and neuronal loss in patients with AD. Both multinutrient diets were able to increase cortical CBF in APPswe/PS1dE9 mice and Fortasyn reduced water diffusivity, particularly in the dentate gyrus and in cortical regions. We suggest that a specific diet intervention has the potential to slow AD progression, by simultaneously improving cerebrovascular health and enhancing neuroprotective mechanisms.},
	language = {en},
	number = {3},
	urldate = {2020-01-09},
	journal = {Neurobiology of Aging},
	author = {Zerbi, Valerio and Jansen, Diane and Wiesmann, Maximilian and Fang, Xiaotian and Broersen, Laus M. and Veltien, Andor and Heerschap, Arend and Kiliaan, Amanda J.},
	month = mar,
	year = {2014},
	keywords = {AD mouse model, APPswe/Ps1de9, Alzheimer's disease, Cerebral blood flow, Diffusion tensor imaging, MRI, Mice, Nutrition, Omega-3 fatty acids},
	pages = {600--613}
}

@article{huang_hidden_2018,
	title = {Hidden {Markov} models for monitoring circadian rhythmicity in telemetric activity data},
	volume = {15},
	url = {https://royalsocietypublishing.org/doi/full/10.1098/rsif.2017.0885},
	doi = {10.1098/rsif.2017.0885},
	abstract = {Wearable computing devices allow collection of densely sampled real-time information on movement enabling researchers and medical experts to obtain objective and non-obtrusive records of actual activity of a subject in the real world over many days. Our interest here is motivated by the use of activity data for evaluating and monitoring the circadian rhythmicity of subjects for research in chronobiology and chronotherapeutic healthcare. In order to translate the information from such high-volume data arising we propose the use of a Markov modelling approach which (i) naturally captures the notable square wave form observed in activity data along with heterogeneous ultradian variances over the circadian cycle of human activity, (ii) thresholds activity into different states in a probabilistic way while respecting time dependence and (iii) gives rise to circadian rhythm parameter estimates, based on probabilities of transitions between rest and activity, that are interpretable and of interest to circadian research.},
	number = {139},
	urldate = {2019-12-22},
	journal = {Journal of The Royal Society Interface},
	author = {Huang, Qi and Cohen, Dwayne and Komarzynski, Sandra and Li, Xiao-Mei and Innominato, Pasquale and Lévi, Francis and Finkenstädt, Bärbel},
	month = feb,
	year = {2018},
	pages = {20170885}
}

@article{patterson_migration_2018,
	title = {Migration dynamics of juvenile southern bluefin tuna},
	volume = {8},
	copyright = {2018 The Author(s)},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/s41598-018-32949-3},
	doi = {10.1038/s41598-018-32949-3},
	abstract = {Large scale migrations are a key component of the life history of many marine species. We quantified the annual migration cycle of juvenile southern bluefin tuna (Thunnus maccoyii; SBT) and spatiotemporal variability in this cycle, based on a multi-decadal electronic tagging dataset. Behaviour-switching models allowed for the identification of cohesive areas of residency and classified the temporal sequence of movements within a migration cycle from austral summer foraging grounds in the Great Australian Bight (GAB) to winter foraging grounds in the Indian Ocean and Tasman Sea and back to the GAB. Although specific regions within the Indian Ocean were frequented, individuals did not always return to the same area in consecutive years. Outward migrations from the GAB were typically longer than return migrations back to the GAB. The timing of individual arrivals to the GAB, which may be driven by seasonality in prey availability, was more cohesive than the timing of departures from the GAB, which may be subject to the physiological condition of SBT. A valuable fishery for SBT operates in the GAB, as do a number of scientific research programs designed to monitor SBT for management purposes; thus, understanding SBT migration to and from the area is of high importance to a number of stakeholders.},
	language = {en},
	number = {1},
	urldate = {2019-12-22},
	journal = {Scientific Reports},
	author = {Patterson, Toby A. and Eveson, J. Paige and Hartog, Jason R. and Evans, Karen and Cooper, Scott and Lansdell, Matt and Hobday, Alistair J. and Davies, Campbell R.},
	month = sep,
	year = {2018},
	pages = {1--10},
}

@article{patterson_statistical_2017,
	title = {Statistical modelling of individual animal movement: an overview of key methods and a discussion of practical challenges},
	volume = {101},
	issn = {1863-818X},
	shorttitle = {Statistical modelling of individual animal movement},
	url = {https://doi.org/10.1007/s10182-017-0302-7},
	doi = {10.1007/s10182-017-0302-7},
	abstract = {With the influx of complex and detailed tracking data gathered from electronic tracking devices, the analysis of animal movement data has recently emerged as a cottage industry among biostatisticians. New approaches of ever greater complexity are continue to be added to the literature. In this paper, we review what we believe to be some of the most popular and most useful classes of statistical models used to analyse individual animal movement data. Specifically, we consider discrete-time hidden Markov models, more general state-space models and diffusion processes. We argue that these models should be core components in the toolbox for quantitative researchers working on stochastic modelling of individual animal movement. The paper concludes by offering some general observations on the direction of statistical analysis of animal movement. There is a trend in movement ecology towards what are arguably overly complex modelling approaches which are inaccessible to ecologists, unwieldy with large data sets or not based on mainstream statistical practice. Additionally, some analysis methods developed within the ecological community ignore fundamental properties of movement data, potentially leading to misleading conclusions about animal movement. Corresponding approaches, e.g. based on Lévy walk-type models, continue to be popular despite having been largely discredited. We contend that there is a need for an appropriate balance between the extremes of either being overly complex or being overly simplistic, whereby the discipline relies on models of intermediate complexity that are usable by general ecologists, but grounded in well-developed statistical practice and efficient to fit to large data sets.},
	language = {en},
	number = {4},
	urldate = {2019-12-22},
	journal = {AStA Advances in Statistical Analysis},
	author = {Patterson, Toby A. and Parton, Alison and Langrock, Roland and Blackwell, Paul G. and Thomas, Len and King, Ruth},
	month = oct,
	year = {2017},
	pages = {399--438}
}

@misc{noauthor_19_nodate,
	title = {(19) ({PDF}) {Hidden} {Markov} models for circular and linear-circular time series},
	url = {https://www.researchgate.net/publication/226694240_Hidden_Markov_models_for_circular_and_linear-circular_time_series},
	abstract = {ResearchGate is a network dedicated to science and research. Connect, collaborate and discover scientific publications, jobs and conferences. All for free.},
	language = {en},
	urldate = {2019-12-22},
	journal = {ResearchGate}
}


@inproceedings{ibrahim_-line_2008,
	title = {On-line {Signature} {Verification} {Using} {Most} {Discriminating} {Features} and {Fisher} {Linear} {Discriminant} {Analysis} ({FLD})},
	doi = {10.1109/ISM.2008.115},
	abstract = {In this work, we employ a combination of strategies for partitioning and detecting abnormal fluctuations in the horizontal and vertical trajectories of an on-line generated signature profile. Alternative partitions of these spatial trajectories are generated by splitting each of the related angle, velocity and pressure profiles into two regions representing both high and low activity. The overall process can be thought of as one that exploits inter-feature dependencies by decomposing signature trajectories based upon angle, velocity and pressure - information quite characteristic to an individualpsilas signature. In the verification phase, distances of each partitioned trajectory of a test signature are calculated against a similarly partitioned template trajectory for a known signer. Finally, these distances become inputs to Fisherpsilas Linear Discriminant Analysis (FLD). Experimental results demonstrate the superiority of our approach in On-line signature verification in comparison with other techniques.},
	booktitle = {2008 {Tenth} {IEEE} {International} {Symposium} on {Multimedia}},
	author = {Ibrahim, Muhammad Talal and Kyan, Matthew and Guan, Ling},
	month = dec,
	year = {2008},
	note = {ISSN: null},
	keywords = {Acceleration, Cameras, Data acquisition, FLD, Fisher linear discriminant analysis, Fluctuations, Forgery, Handwriting recognition, Histograms, Linear discriminant analysis, Shape, Testing, data acquisition, feature extraction, handwriting recognition, most discriminating features, online generated signature profile, online signature verification},
	pages = {172--177}
}

@book{rasmussen_gaussian_2006,
	address = {Cambridge, MA, USA},
	series = {Adaptive {Computation} and {Machine} {Learning}},
	title = {Gaussian {Processes} for {Machine} {Learning}},
	publisher = {Biologische Kybernetik},
	author = {Rasmussen, CE. and Williams, CKI.},
	month = jan,
	year = {2006},
	note = {Backup Publisher: Max-Planck-Gesellschaft},
}

@inproceedings{jeong_linear_2016,
	title = {Linear discriminant analysis for symmetric lifting recognition of skilled logistic experts by center of pressure trajectory},
	doi = {10.1109/EMBC.2016.7591745},
	abstract = {Goal: The main purpose of the present study was to propose a recognizing method to analyze characteristics of symmetric lifting of skilled logistic experts by center of pressure (CoP) trajectories. Although it has been known that good posture helps reduce the intradiscal loads on lumbar discs, the most significant problem was that most of logistic workers did not know whether the current posture was proper or not. Methods : The experiment of lifting was performed three times under 18 kg loads with closed eyes. Six skilled logistic experts and six unskilled beginners were participated in. The linear discriminant analysis (LDA) was designed by seven indices which were derived from measured CoP trajectories with the Wii Balance Board. The strong point of experimental system was practical, reliable, and cheap. Results : As a result, it was found that the designed LDA discriminated difference of symmetric lifting between skilled experts and unskilled beginners with the error rate of 0.005. Discussion : It was discussed that not only most of unskilled beginners had mainly characteristics of poor lifting posture, but also the proposed method showed a high possibility to self-evaluate the symmetric lifting in order to check whether the current posture of logistic worker is proper or not.},
	booktitle = {2016 38th {Annual} {International} {Conference} of the {IEEE} {Engineering} in {Medicine} and {Biology} {Society} ({EMBC})},
	author = {Jeong, Hieyong and Kido, Michiko and Ohno, Yuko},
	month = aug,
	year = {2016},
	note = {ISSN: 1557-170X},
	keywords = {Biomechanical Phenomena, CoP trajectory, Discriminant Analysis, Employment, Error analysis, Hip, Humans, LDA, Lifting, Linear discriminant analysis, Logistics, Posture, Principal component analysis, Trajectory, Wii Balance Board, biomechanics, center of pressure trajectory, intradiscal loads, lifting posture, linear discriminant analysis, logistic worker, lumbar discs, mass 18 kg, mechanoception, skilled logistic experts, symmetric lifting recognition, unskilled beginners},
	pages = {4573--4576}
}

@misc{noauthor_8_nodate,
	title = {(8) ({PDF}) {Gaussian} {Process} {Regression} for {Trajectory} {Analysis} {\textbar} {George} {Kachergis} - {Academia}.edu},
	url = {https://www.academia.edu/2986743/Gaussian_Process_Regression_for_Trajectory_Analysis},
	urldate = {2019-12-01}
}

@inproceedings{cox_gaussian_2012,
	title = {Gaussian {Process} {Regression} for {Trajectory} {Analysis}},
	abstract = {Cognitive scientists have begun collecting the trajectories of hand movements as participants make decisions in experiments. These response trajectories offer a ﬁne-grained glimpse into ongoing cognitive processes. For example, difﬁcult decisions show more hesitation and deﬂection from the optimal path than easy decisions. However, many summary statistics used for trajectories throw away much information, or are correlated and thus partially redundant. To alleviate these issues, we introduce Gaussian process regression for the purpose of modeling trajectory data collected in psychology experiments. Gaussian processes are a well-developed statistical model that can ﬁnd parametric differences in trajectories and their derivatives (e.g., velocity and acceleration) rather than a summary statistic. We show how Gaussian process regression can be implemented hierarchically across conditions and subjects, and used to model the actual shape and covariance of the trajectories. Finally, we demonstrate how to construct a generative hierarchical Bayesian model of trajectories using Gaussian processes.},
	language = {en},
	author = {Cox, Gregory E and Kachergis, George and Shiffrin, Richard M},
	year = {2012},
	pages = {6},
}


@article{kareiva_analyzing_1983,
	title = {Analyzing insect movement as a correlated random walk},
	volume = {56},
	issn = {1432-1939},
	doi = {10.1007/BF00379695},
	abstract = {This paper develops a procedure for quantifying movement sequences in terms of move length and turning angle probability distributions. By assuming that movement is a correlated random walk, we derive a formula that relates expected square displacements to the number of consecutive moves. We show this displacement formula can be used to highlight the consequences of different searching behaviors (i.e. different probability distributions of turning angles or move lengths). Observations of Pieris rapae (cabbage white butterfly) flight and Battus philenor (pipe-vine swallowtail) crawling are analyzed as a correlated random walk. The formula that we derive aptly predicts that net displacements of ovipositing cabbage white butterflies. In other circumstances, however, net displacements are not well-described by our correlated random walk formula; in these examples movement must represent a more complicated process than a simple correlated random walk. We suggest that progress might be made by analyzing these more complicated cases in terms of higher order markov processes.},
	language = {eng},
	number = {2-3},
	journal = {Oecologia},
	author = {Kareiva, P. M. and Shigesada, N.},
	month = feb,
	year = {1983},
	pmid = {28310199},
	pages = {234--238}
}


@misc{noauthor_assessing_nodate-1,
	title = {Assessing post-stroke behavior in mouse models of focal ischemia. - {PubMed} - {NCBI}},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/23232947},
	urldate = {2019-11-25}
}

@misc{noauthor_functional_nodate,
	title = {Functional subdivisions of the rat somatic sensorimotor cortex - {Google} {Search}},
	url = {https://www.google.com/search?q=Functional+subdivisions+of+the+rat+somatic+sensorimotor+cortex&oq=Functional+subdivisions+of+the+rat+somatic+sensorimotor+cortex&aqs=chrome..69i57.281j0j7&sourceid=chrome&ie=UTF-8},
	urldate = {2019-11-25}
}

@misc{noauthor_17_nodate,
	title = {(17) ({PDF}) {Characterizing} {Visual} {Performance} in {Mice}: {An} {Objective} and {Automated} {System} {Based} on the {Optokinetic} {Reflex}},
	shorttitle = {(17) ({PDF}) {Characterizing} {Visual} {Performance} in {Mice}},
	url = {https://www.researchgate.net/publication/255984748_Characterizing_Visual_Performance_in_Mice_An_Objective_and_Automated_System_Based_on_the_Optokinetic_Reflex},
	abstract = {ResearchGate is a network dedicated to science and research. Connect, collaborate and discover scientific publications, jobs and conferences. All for free.},
	language = {en},
	urldate = {2019-11-25},
	journal = {ResearchGate}
}

@misc{noauthor_17_nodate-1,
	title = {(17) ({PDF}) {Behavioural} and endocrinological responses of mature male goldfish to the sex pheromone 17alpha,20beta-dihydroxy-4-pregnen-3-one in the water},
	url = {https://www.researchgate.net/publication/13904826_Behavioural_and_endocrinological_responses_of_mature_male_goldfish_to_the_sex_pheromone_17alpha20beta-dihydroxy-4-pregnen-3-one_in_the_water},
	abstract = {ResearchGate is a network dedicated to science and research. Connect, collaborate and discover scientific publications, jobs and conferences. All for free.},
	language = {en},
	urldate = {2019-11-25},
	journal = {ResearchGate}
}

@misc{noauthor_use_nodate,
	title = {Use of the {Open} {Field} {Maze} to measure locomotor and anxiety-like behavior in mice. - {PubMed} - {NCBI}},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25742564},
	urldate = {2019-11-25}
}

@article{wang_modeling_2017,
	title = {Modeling {Trajectory} as {Image}: {Convolutional} {Neural} {Networks} for {Multi}-scale {Taxi} {Trajectory} {Prediction}},
	shorttitle = {Modeling {Trajectory} as {Image}},
	url = {https://www.academia.edu/34767293/Modeling_Trajectory_as_Image_Convolutional_Neural_Networks_for_Multi-scale_Taxi_Trajectory_Prediction},
	abstract = {Precise destination prediction of Taxi trajectories can benefit both efficient schedule of taxies and accurate advertisement for customers.In this paper, we propose T-CONV, a novel trajectory prediction algorithm, which models trajectories as},
	language = {en},
	urldate = {2019-11-23},
	author = {Wang, Xintong},
	year = {2017},
}

@article{meng_overview_2019,
	title = {An overview on trajectory outlier detection},
	volume = {52},
	issn = {1573-7462},
	url = {https://doi.org/10.1007/s10462-018-9619-1},
	doi = {10.1007/s10462-018-9619-1},
	abstract = {The task of trajectory outlier detection is to discover trajectories or their segments which differ substantially from or are inconsistent with the remaining set. In this paper, we make an overview on trajectory outlier detection algorithms from three aspects. Firstly, algorithms considering multi-attribute. In this kind of algorithms, as many key attributes as possible, such as speed, direction, position, time, are explored to represent the original trajectory and to compare with the others. Secondly, suitable distance metric. Many researches try to find or develop suitable distance metric which can measure the divergence between trajectories effectively and reliably. Thirdly, other studies attempt to improve existing algorithms to find outliers with less time and space complexity, and even more reliable. In this paper, we survey and summarize some classic trajectory outlier detection algorithms. In order to provide an overview, we analyze their features from the three dimensions above and discuss their benefits and shortcomings. It is hope that this review will serve as the steppingstone for those interested in advancing moving object outlier detection.},
	language = {en},
	number = {4},
	urldate = {2019-11-22},
	journal = {Artificial Intelligence Review},
	author = {Meng, Fanrong and Yuan, Guan and Lv, Shaoqian and Wang, Zhixiao and Xia, Shixiong},
	month = dec,
	year = {2019},
	keywords = {Moving object data mining, Outlier detection, Spatial-temporal data, Trajectory},
	pages = {2437--2456}
}

@article{graser_movingpandas_2019,
	title = {{MovingPandas}: {Efficient} {Structures} for {Movement} {Data} in {Python}},
	volume = {Volume 7,},
	copyright = {Österreichische Akademie der Wissenschaften},
	issn = {2308-1708},
	shorttitle = {{MovingPandas}},
	url = {https://www.austriaca.at?arp=0x003aba2b},
	doi = {10.1553/giscience2019_01_s54},
	abstract = {Movement data analysis is a high-interest topic in many scientific domains. Even though Python is the scripting language of choice in the GIS world, currently there is no Python library that would enable researchers and practitioners to interact with and analyse movement data efficiently. To close this gap, we present MovingPandas, a new Python library for dealing with movement data. Its development is based on an analysis of state-of-the-art conceptual frameworks and existing implementations (in PostGIS, Hermes, and the R package trajectories). We describe how MovingPandas avoids limitations of Simple Feature-based movement data models commonly used to handle trajectories in the GIS world. Finally, we present the current state of the MovingPandas implementation and demonstrate its use in stand-alone Python scripts, as well as within the context of the desktop GIS application QGIS. This work represents the first step towards a general-purpose Python library that enables researchers and practitioners in the GIS field and beyond to handle and analyse movement data more efficiently},
	language = {de},
	urldate = {2021-02-02},
	journal = {GI\_Forum 2019,},
	author = {Graser, Anita},
	month = jun,
	year = {2019},
	note = {Publisher: Verlag der Österreichischen Akademie der Wissenschaften},
	pages = {54--68},
}

@misc{word2vec,
      title={Distributed Representations of Words and Phrases and their Compositionality},
      author={Tomas Mikolov and Ilya Sutskever and Kai Chen and Greg Corrado and Jeffrey Dean},
      year={2013},
      eprint={1310.4546},
      archivePrefix={arXiv},
      primaryClass={cs.CL}
}

@article{huber_robust_1964,
	title = {Robust {Estimation} of a {Location} {Parameter}},
	volume = {35},
	issn = {0003-4851, 2168-8990},
	url = {https://projecteuclid.org/euclid.aoms/1177703732},
	doi = {10.1214/aoms/1177703732},
	abstract = {This paper contains a new approach toward a theory of robust estimation; it treats in detail the asymptotic theory of estimating a location parameter for contaminated normal distributions, and exhibits estimators--intermediaries between sample mean and sample median--that are asymptotically most robust (in a sense to be specified) among all translation invariant estimators. For the general background, see Tukey (1960) (p. 448 ff.) Let x1,⋯,xnx1,⋯,xnx\_1, {\textbackslash}cdots, x\_n be independent random variables with common distribution function F(t−ξ)F(t−ξ)F(t - {\textbackslash}xi). The problem is to estimate the location parameter ξξ{\textbackslash}xi, but with the complication that the prototype distribution F(t)F(t)F(t) is only approximately known. I shall primarily be concerned with the model of indeterminacy F=(1−ϵ)Φ+ϵHF=(1−ϵ)Φ+ϵHF = (1 - {\textbackslash}epsilon){\textbackslash}Phi + {\textbackslash}epsilon H, where 0≦ϵ{\textless}10≦ϵ{\textless}10 {\textbackslash}leqq {\textbackslash}epsilon {\textless} 1 is a known number, Φ(t)=(2π)−12∫t−∞exp(−12s2)dsΦ(t)=(2π)−12∫−∞texp⁡(−12s2)ds{\textbackslash}Phi(t) = (2{\textbackslash}pi){\textasciicircum}\{-{\textbackslash}frac\{1\}\{2\}\} {\textbackslash}int{\textasciicircum}t\_\{-{\textbackslash}infty\} {\textbackslash}exp(-{\textbackslash}frac\{1\}\{2\}s{\textasciicircum}2) ds is the standard normal cumulative and HHH is an unknown contaminating distribution. This model arises for instance if the observations are assumed to be normal with variance 1, but a fraction ϵϵ{\textbackslash}epsilon of them is affected by gross errors. Later on, I shall also consider other models of indeterminacy, e.g., supt{\textbar}F(t)−Φ(t){\textbar}≦ϵsupt{\textbar}F(t)−Φ(t){\textbar}≦ϵ{\textbackslash}sup\_t {\textbar}F(t) - {\textbackslash}Phi(t){\textbar} {\textbackslash}leqq {\textbackslash}epsilon. Some inconvenience is caused by the fact that location and scale parameters are not uniquely determined: in general, for fixed ϵϵ{\textbackslash}epsilon, there will be several values of ξξ{\textbackslash}xi and σσ{\textbackslash}sigma such that supt{\textbar}F(t)−Φ((t−ξ)/σ){\textbar}≦ϵsupt{\textbar}F(t)−Φ((t−ξ)/σ){\textbar}≦ϵ{\textbackslash}sup\_t{\textbar}F(t) - {\textbackslash}Phi((t - {\textbackslash}xi)/{\textbackslash}sigma){\textbar} {\textbackslash}leqq {\textbackslash}epsilon, and similarly for the contaminated case. Although this inherent and unavoidable indeterminacy is small if ϵϵ{\textbackslash}epsilon is small and is rather irrelevant for practical purposes, it poses awkward problems for the theory, especially for optimality questions. To remove this difficulty, one may either (i) restrict attention to symmetric distributions, and estimate the location of the center of symmetry (this works for ξξ{\textbackslash}xi but not for σσ{\textbackslash}sigma); or (ii) one may define the parameter to be estimated in terms of the estimator itself, namely by its asymptotic value for sample size n→∞n→∞n {\textbackslash}rightarrow {\textbackslash}infty; or (iii) one may define the parameters by arbitrarily chosen functionals of the distribution (e.g., by the expectation, or the median of FFF). All three possibilities have unsatisfactory aspects, and I shall usually choose the variant which is mathematically most convenient. It is interesting to look back to the very origin of the theory of estimation, namely to Gauss and his theory of least squares. Gauss was fully aware that his main reason for assuming an underlying normal distribution and a quadratic loss function was mathematical, i.e., computational, convenience. In later times, this was often forgotten, partly because of the central limit theorem. However, if one wants to be honest, the central limit theorem can at most explain why many distributions occurring in practice are approximately normal. The stress is on the word "approximately." This raises a question which could have been asked already by Gauss, but which was, as far as I know, only raised a few years ago (notably by Tukey): What happens if the true distribution deviates slightly from the assumed normal one? As is now well known, the sample mean then may have a catastrophically bad performance: seemingly quite mild deviations may already explode its variance. Tukey and others proposed several more robust substitutes--trimmed means, Winsorized means, etc.--and explored their performance for a few typical violations of normality. A general theory of robust estimation is still lacking; it is hoped that the present paper will furnish the first few steps toward such a theory. At the core of the method of least squares lies the idea to minimize the sum of the squared "errors," that is, to adjust the unknown parameters such that the sum of the squares of the differences between observed and computed values is minimized. In the simplest case, with which we are concerned here, namely the estimation of a location parameter, one has to minimize the expression ∑i(xi−T)2∑i(xi−T)2{\textbackslash}sum\_i (x\_i - T){\textasciicircum}2; this is of course achieved by the sample mean T=∑ixi/nT=∑ixi/nT = {\textbackslash}sum\_i x\_i/n. I should like to emphasize that no loss function is involved here; I am only describing how the least squares estimator is defined, and neither the underlying family of distributions nor the true value of the parameter to be estimated enters so far. It is quite natural to ask whether one can obtain more robustness by minimizing another function of the errors than the sum of their squares. We shall therefore concentrate our attention to estimators that can be defined by a minimum principle of the form (for a location parameter): T=Tn(x1,⋯,xn)minimizes∑iρ(xi−T),T=Tn(x1,⋯,xn)minimizes∑iρ(xi−T),T = T\_n(x\_1, {\textbackslash}cdots, x\_n) minimizes {\textbackslash}sum\_i {\textbackslash}rho(x\_i - T), whereρisanon−constantfunction.(M)(M)whereρisanon−constantfunction.{\textbackslash}begin\{equation*\} {\textbackslash}tag\{M\} where {\textbackslash}rho is a non-constant function. {\textbackslash}end\{equation*\} Of course, this definition generalizes at once to more general least squares type problems, where several parameters have to be determined. This class of estimators contains in particular (i) the sample mean (ρ(t)=t2)(ρ(t)=t2)({\textbackslash}rho(t) = t{\textasciicircum}2), (ii) the sample median (ρ(t)={\textbar}t{\textbar})(ρ(t)={\textbar}t{\textbar})({\textbackslash}rho(t) = {\textbar}t{\textbar}), and more generally, (iii) all maximum likelihood estimators (ρ(t)=−logf(t)(ρ(t)=−log⁡f(t)({\textbackslash}rho(t) = -{\textbackslash}log f(t), where fff is the assumed density of the untranslated distribution). These (MMM)-estimators, as I shall call them for short, have rather pleasant asymptotic properties; sufficient conditions for asymptotic normality and an explicit expression for their asymptotic variance will be given. How should one judge the robustness of an estimator Tn(x)=Tn(x1,⋯,xn)Tn(x)=Tn(x1,⋯,xn)T\_n(x) = T\_n(x\_1, {\textbackslash}cdots, x\_n)? Since ill effects from contamination are mainly felt for large sample sizes, it seems that one should primarily optimize large sample robustness properties. Therefore, a convenient measure of robustness for asymptotically normal estimators seems to be the supremum of the asymptotic variance (n→∞)(n→∞)(n {\textbackslash}rightarrow {\textbackslash}infty) when FFF ranges over some suitable set of underlying distributions, in particular over the set of all F=(1−ϵ)Φ+ϵHF=(1−ϵ)Φ+ϵHF = (1 - {\textbackslash}epsilon){\textbackslash}Phi + {\textbackslash}epsilon H for fixed ϵϵ{\textbackslash}epsilon and symmetric HHH. On second thought, it turns out that the asymptotic variance is not only easier to handle, but that even for moderate values of nnn it is a better measure of performance than the actual variance, because (i) the actual variance of an estimator depends very much on the behavior of the tails of HHH, and the supremum of the actual variance is infinite for any estimator whose value is always contained in the convex hull of the observations. (ii) If an estimator is asymptotically normal, then the important central part of its distribution and confidence intervals for moderate confidence levels can better be approximated in terms of the asymptotic variance than in terms of the actual variance. If we adopt this measure of robustness, and if we restrict attention to (MMM)-estimators, then it will be shown that the most robust estimator is uniquely determined and corresponds to the following ρ:ρ(t)=12t2ρ:ρ(t)=12t2{\textbackslash}rho:{\textbackslash}rho(t) = {\textbackslash}frac\{1\}\{2\}t{\textasciicircum}2 for {\textbar}t{\textbar}{\textless}k,ρ(t)=k{\textbar}t{\textbar}−12k2{\textbar}t{\textbar}{\textless}k,ρ(t)=k{\textbar}t{\textbar}−12k2{\textbar}t{\textbar} {\textless} k, {\textbackslash}rho(t) = k{\textbar}t{\textbar} - {\textbackslash}frac\{1\}\{2\}k{\textasciicircum}2 for {\textbar}t{\textbar}≧k{\textbar}t{\textbar}≧k{\textbar}t{\textbar} {\textbackslash}geqq k, with kkk depending on ϵϵ{\textbackslash}epsilon. This estimator is most robust even among all translation invariant estimators. Sample mean (k=∞)(k=∞)(k = {\textbackslash}infty) and sample median (k=0)(k=0)(k = 0) are limiting cases corresponding to ϵ=0ϵ=0{\textbackslash}epsilon = 0 and ϵ=1ϵ=1{\textbackslash}epsilon = 1, respectively, and the estimator is closely related and asymptotically equivalent to Winsorizing. I recall the definition of Winsorizing: assume that the observations have been ordered, x1≦x2≦⋯≦xnx1≦x2≦⋯≦xnx\_1 {\textbackslash}leqq x\_2 {\textbackslash}leqq {\textbackslash}cdots {\textbackslash}leqq x\_n, then the statistic T=n−1(gxg+1+xg+1+xg+2+⋯+xn−h+hxn−h)T=n−1(gxg+1+xg+1+xg+2+⋯+xn−h+hxn−h)T = n{\textasciicircum}\{-1\}(gx\_\{g + 1\} + x\_\{g + 1\} + x\_\{g + 2\} + {\textbackslash}cdots + x\_\{n - h\} + hx\_\{n - h\}) is called the Winsorized mean, obtained by Winsorizing the ggg leftmost and the hhh rightmost observations. The above most robust (MMM)-estimators can be described by the same formula, except that in the first and in the last summand, the factors xg+1xg+1x\_\{g + 1\} and xn−hxn−hx\_\{n - h\} have to be replaced by some numbers u,vu,vu, v satisfying xg≦u≦xg+1xg≦u≦xg+1x\_g {\textbackslash}leqq u {\textbackslash}leqq x\_\{g + 1\} and xn−h≦v≦xn−h+1xn−h≦v≦xn−h+1x\_\{n - h\} {\textbackslash}leqq v {\textbackslash}leqq x\_\{n - h + 1\}, respectively; g,h,ug,h,ug, h, u and vvv depend on the sample. In fact, this (MMM)-estimator is the maximum likelihood estimator corresponding to a unique least favorable distribution F0F0F\_0 with density f0(t)=(1−ϵ)(2π)−12e−ρ(t)f0(t)=(1−ϵ)(2π)−12e−ρ(t)f\_0(t) = (1 - {\textbackslash}epsilon)(2{\textbackslash}pi){\textasciicircum}\{-{\textbackslash}frac\{1\}\{2\}\}e{\textasciicircum}\{-{\textbackslash}rho(t)\}. This f0f0f\_0 behaves like a normal density for small ttt, like an exponential density for large ttt. At least for me, this was rather surprising--I would have expected an f0f0f\_0 with much heavier tails. This result is a particular case of a more general one that can be stated roughly as follows: Assume that FFF belongs to some convex set CCC of distribution functions. Then the most robust (MMM)-estimator for the set CCC coincides with the maximum likelihood estimator for the unique F0εCF0εCF\_0 {\textbackslash}varepsilon C which has the smallest Fisher information number I(F)=∫(f′/f)2fdtI(F)=∫(f′/f)2fdtI(F) = {\textbackslash}int (f'/f){\textasciicircum}2f dt among all FεCFεCF {\textbackslash}varepsilon C. Miscellaneous related problems will also be treated: the case of non-symmetric contaminating distributions; the most robust estimator for the model of indeterminacy supt{\textbar}F(t)−Φ(t){\textbar}≦ϵsupt{\textbar}F(t)−Φ(t){\textbar}≦ϵ{\textbackslash}sup\_t{\textbar}F(t) - {\textbackslash}Phi(t){\textbar} {\textbackslash}leqq {\textbackslash}epsilon; robust estimation of a scale parameter; how to estimate location, if scale and ϵϵ{\textbackslash}epsilon are unknown; numerical computation of the estimators; more general estimators, e.g., minimizing ∑i{\textless}jρ(xi−T,xj−T)∑i{\textless}jρ(xi−T,xj−T){\textbackslash}sum\_\{i {\textless} j\} {\textbackslash}rho(x\_i - T, x\_j - T), where ρρ{\textbackslash}rho is a function of two arguments. Questions of small sample size theory will not be touched in this paper.},
	language = {EN},
	number = {1},
	urldate = {2021-02-03},
	journal = {Annals of Mathematical Statistics},
	author = {Huber, Peter J.},
	month = mar,
	year = {1964},
	mrnumber = {MR161415},
	zmnumber = {0136.39805},
	note = {Publisher: Institute of Mathematical Statistics},
	pages = {73--101},
}

@article{franke_analysis_2004,
	title = {Analysis of movements and behavior of caribou ({Rangifer} tarandus) using hidden {Markov} models},
	volume = {173},
	issn = {0304-3800},
	url = {http://www.sciencedirect.com/science/article/pii/S0304380003003983},
	doi = {10.1016/j.ecolmodel.2003.06.004},
	abstract = {We explore how doubly stochastic, multiple-observation hidden Markov models (HMMs) may infer meaningful descriptions of woodland caribou (Rangifer tarandus) movement and behavior. Parameterized models allowed us to predict behavioral states (bedding, feeding and relocating), relative bout length and transitions, as well as most likely behavioral state sequences. Identification of state transitions and bout lengths appear specific to individuals and may identify dissimilar strategies of resource selection, behavior-specific habitats that are more important than is simply suggested by time spent there (pattern) and transitions between the same or different states that may be evidence for decision-making (process). Using only estimated model parameters, multiple-observation HMMs permitted us to successfully simulate movement and behavior representative of individual caribou through space and time.},
	language = {en},
	number = {2},
	urldate = {2019-12-22},
	journal = {Ecological Modelling},
	author = {Franke, Alastair and Caelli, Terry and Hudson, Robert J},
	month = apr,
	year = {2004},
	keywords = {Activity, Animal behavior, Animal movement, Hidden Markov model, Resource selection},
	pages = {259--270},
}

@book{hastie01statisticallearning,
  added-at = {2008-05-16T16:17:42.000+0200},
  address = {New York, NY, USA},
  author = {Hastie, Trevor and Tibshirani, Robert and Friedman, Jerome},
  biburl = {https://www.bibsonomy.org/bibtex/2f58afc5c9793fcc8ad8389824e57984c/sb3000},
  interhash = {d585aea274f2b9b228fc1629bc273644},
  intrahash = {f58afc5c9793fcc8ad8389824e57984c},
  keywords = {ml statistics},
  publisher = {Springer New York Inc.},
  series = {Springer Series in Statistics},
  timestamp = {2008-05-16T16:17:43.000+0200},
  title = {The Elements of Statistical Learning},
  year = 2001
}

@article{holzmann_hidden_2006,
	title = {Hidden {Markov} models for circular and linear-circular time series},
	volume = {13},
	issn = {1352-8505, 1573-3009},
	url = {http://link.springer.com/10.1007/s10651-006-0015-7},
	doi = {10.1007/s10651-006-0015-7},
	number = {3},
	journal = {Environmental and Ecological Statistics},
	author = {Holzmann, Hajo and Munk, Axel and Suster, Max and Zucchini, Walter},
	year = {2006},
	note = {Type: Journal Article},
	pages = {325--347},
}


@article{richardson_power_2015,
	title = {The power of automated behavioural homecage technologies in characterizing disease progression in laboratory mice: {A} review},
	volume = {163},
	issn = {0168-1591},
	shorttitle = {The power of automated behavioural homecage technologies in characterizing disease progression in laboratory mice},
	url = {http://www.sciencedirect.com/science/article/pii/S0168159114003050},
	doi = {10.1016/j.applanim.2014.11.018},
	abstract = {Behavioural changes that occur as animals become sick have been characterized in a number of species and include the less frequent occurrence of ‘luxury behaviours’ such as playing, grooming and socialization. ‘Sickness behaviours’ or behavioural changes following exposure to infectious agents, have been particularly well described; animals are typically less active, sleep more, exhibit postural changes and consume less food/water. Disease is frequently induced in laboratory mice to model pathophysiological processes and investigate potential therapies but despite what is known about behavioural changes as animals become sick, behavioural phenotyping of mice involved in disease studies is relatively rare. A detailed understanding of how behaviour changes as mice get sick could be applied to improve welfare of laboratory mice and support the underlying biomedical research. Specifically, characterizing behavioural changes in ill health could help those working with laboratory mice to recognize when refinements should be introduced, when severity limits are being approached and when humane endpoints should be implemented. Understanding how behaviour changes with illness may also help to identify compounds that have a clinical effect as well as when these agents act. There are an increasing number of automated systems to monitor the behaviour of laboratory mice in their homecages incorporating technologies such as the quantification of cage movement, automated video analysis and radiofrequency identification transponders/readers. Mouse models of neurodegenerative diseases particularly Huntington's disease have been well characterized using these systems and behavioural biomarkers of pathology, including changes in the animals’ use of environmental enrichment, changes in food/water consumption and alterations in circadian rhythms, are now monitored by laboratories worldwide and used to refine studies and develop therapies. In contrast, automated behavioural technologies have not been used to characterize the behaviour of mice with systemic diseases such as cancer and liver disease. In this review, common behavioural changes that occur in animals with declining health will be discussed with an emphasis on progressive disease studies involving mice. Automated homecage behaviour recording technologies will then be summarized, studies in which these systems have been used to characterize the behaviour of mice with progressive diseases will be reviewed and the potential to apply automated technologies to refine disease studies involving mice will be discussed.},
	language = {en},
	urldate = {2019-11-21},
	journal = {Applied Animal Behaviour Science},
	author = {Richardson, Claire A.},
	month = feb,
	year = {2015},
	keywords = {Animal welfare, Automated behavioural analysis, Disease, Humane endpoints, Mice, Replacement, reduction, refinement (3Rs)},
	pages = {19--27}
}

@software{sgoldenlab_2021_4521178,
  author       = {sgoldenlab and
                  Jia Jie Choong and
                  Simon Nilsson and
                  Aasiya Islam and
                  sophihwang26},
  title        = {sgoldenlab/simba: SimBA: release v1.3},
  month        = feb,
  year         = 2021,
  publisher    = {Zenodo},
  version      = {v1.3},
  doi          = {10.5281/zenodo.4521178},
  url          = {https://doi.org/10.5281/zenodo.4521178}
}

@article {Hsu770271,
	author = {Hsu, Alexander I. and Yttri, Eric A.},
	title = {B-SOiD: An Open Source Unsupervised Algorithm for Discovery of Spontaneous Behaviors},
	elocation-id = {770271},
	year = {2020},
	doi = {10.1101/770271},
	publisher = {Cold Spring Harbor Laboratory},
	abstract = {Capturing the performance of naturalistic behaviors remains a prohibitively difficult objective. Recent machine learning applications have enabled localization of limb position; however, position alone does not yield behavior. To provide a bridge from positions to actions and their kinematics, we developed Behavioral Segmentation of Open-field in DeepLabCut (B-SOiD). This unsupervised learning algorithm discovers natural patterns in position and extracts their inherent statistics. The cluster statistics are then used to train a machine learning algorithm to classify behaviors with greater speed and accuracy due to improved ability to generalize from subject to subject. Through the application of a novel fram-eshift paradigm, B-SOiD provides the fast temporal resolution required for comparison with neural activity. B-SOiD also provides high-resolution behavioral measures such as stride and grooming kinematics, that are difficult but critical to obtain, particularly in the study of pain, compulsion, and other neurological disorders. This open-source platform surpasses the current state of the field in its improved analytical accessibility, objectivity, and ease of use.},
	URL = {https://www.biorxiv.org/content/early/2020/03/07/770271},
	eprint = {https://www.biorxiv.org/content/early/2020/03/07/770271.full.pdf},
	journal = {bioRxiv}
}

@software{vivek_hari_sridhar_2017_1134016,
  author       = {Vivek Hari Sridhar},
  title        = {vivekhsridhar/tracktor: Tracktor},
  month        = dec,
  year         = 2017,
  publisher    = {Zenodo},
  version      = {tracktor},
  doi          = {10.5281/zenodo.1134016},
  url          = {https://doi.org/10.5281/zenodo.1134016}
}


@article{wijeyakulasuriya_machine_2020,
	title = {Machine learning for modeling animal movement},
	volume = {15},
	url = {https://doi.org/10.1371/journal.pone.0235750},
	doi = {10.1371/journal.pone.0235750},
	abstract = {Animal movement drives important ecological processes such as migration and the spread of infectious disease. Current approaches to modeling animal tracking data focus on parametric models used to understand environmental effects on movement behavior and to fill in missing tracking data. Machine Learning and Deep learning algorithms are powerful and flexible predictive modeling tools but have rarely been applied to animal movement data. In this study we present a general framework for predicting animal movement that is a combination of two steps: first predicting movement behavioral states and second predicting the animal’s velocity. We specify this framework at the individual level as well as for collective movement. We use Random Forests, Neural and Recurrent Neural Networks to compare performance predicting one step ahead as well as long range simulations. We compare results against a custom constructed Stochastic Differential Equation (SDE) model. We apply this approach to high resolution ant movement data. We found that the individual level Machine Learning and Deep Learning methods outperformed the SDE model for one step ahead prediction. The SDE model did comparatively better at simulating long range movement behaviour. Of the Machine Learning and Deep Learning models the Long Short Term Memory (LSTM) individual level model did best at long range simulations. We also applied the Random Forest and LSTM individual level models to model gull migratory movement to demonstrate the generalizability of this framework. Machine Learning and deep learning models are easier to specify compared to traditional parametric movement models which can have restrictive assumptions. However, machine learning and deep learning models are less interpretable than parametric movement models. The type of model used should be determined by the goal of the study, if the goal is prediction, our study provides evidence that machine learning and deep learning models could be useful tools.},
	number = {7},
	journal = {PLOS ONE},
	author = {Wijeyakulasuriya, Dhanushi A. and Eisenhauer, Elizabeth W. and Shaby, Benjamin A. and Hanks, Ephraim M.},
	year = {2020},
	note = {Publisher: Public Library of Science},
	pages = {1--30},
}

@article{Mathisetal2018,
    title={DeepLabCut: markerless pose estimation of user-defined body parts with deep learning},
    author = {Alexander Mathis and Pranav Mamidanna and Kevin M. Cury and Taiga Abe  and Venkatesh N. Murthy and Mackenzie W. Mathis and Matthias Bethge},
    journal={Nature Neuroscience},
    year={2018},
	doi={10.1038/s41593-018-0209-y},
    url={https://www.nature.com/articles/s41593-018-0209-y}
}


@incollection{pytorch,
title = {PyTorch: An Imperative Style, High-Performance Deep Learning Library},
author = {Paszke, Adam and Gross, Sam and Massa, Francisco and Lerer, Adam and Bradbury, James and Chanan, Gregory and Killeen, Trevor and Lin, Zeming and Gimelshein, Natalia and Antiga, Luca and Desmaison, Alban and Kopf, Andreas and Yang, Edward and DeVito, Zachary and Raison, Martin and Tejani, Alykhan and Chilamkurthy, Sasank and Steiner, Benoit and Fang, Lu and Bai, Junjie and Chintala, Soumith},
booktitle = {Advances in Neural Information Processing Systems 32},
editor = {H. Wallach and H. Larochelle and A. Beygelzimer and F. d\textquotesingle Alch\'{e}-Buc and E. Fox and R. Garnett},
pages = {8024--8035},
year = {2019},
publisher = {Curran Associates, Inc.},
url = {http://papers.neurips.cc/paper/9015-pytorch-an-imperative-style-high-performance-deep-learning-library.pdf}
}

@inproceedings{zhou_micro_2018,
	title = {Micro {Behaviors}: {A} {New} {Perspective} in {E}-commerce {Recommender} {Systems}},
	shorttitle = {Micro {Behaviors}},
	doi = {10.1145/3159652.3159671},
	abstract = {The explosive popularity of e-commerce sites has reshaped users» shopping habits and an increasing number of users prefer to spend more time shopping online. This evolution allows e-commerce sites to observe rich data about users. The majority of traditional recommender systems have focused on the macro interactions between users and items, i.e., the purchase history of a customer. However, within each macro interaction between a user and an item, the user actually performs a sequence of micro behaviors, which indicate how the user locates the item, what activities the user conducts on the item (e.g., reading the comments, carting, and ordering) and how long the user stays with the item. Such micro behaviors offer fine-grained and deep understandings about users and provide tremendous opportunities to advance recommender systems in e-commerce. However, exploiting micro behaviors for recommendations is rather limited, which motivates us to investigate e-commerce recommendations from a micro-behavior perspective in this paper. Particularly, we uncover the effects of micro behaviors on recommendations and propose an interpretable Recommendation framework RIB, which models inherently the sequence of mIcro Behaviors and their effects. Experimental results on datasets from a real e-commence site demonstrate the effectiveness of the proposed framework and the importance of micro behaviors for recommendations.},
	booktitle = {{WSDM}},
	author = {Zhou, Meizi and Ding, Zhuoye and Tang, Jiliang and Yin, Dawei},
	year = {2018},
	keywords = {E-commerce, E-commerce payment system, IBM Notes, Interaction, Online shopping, Recommender system}
}

@article{pedregosa_scikit-learn:_2011,
	title = {Scikit-learn: {Machine} {Learning} in {Python}},
	volume = {12},
	issn = {ISSN 1533-7928},
	shorttitle = {Scikit-learn},
	url = {http://www.jmlr.org/papers/v12/pedregosa11a.html},
	number = {Oct},
	urldate = {2019-11-06},
	journal = {Journal of Machine Learning Research},
	author = {Pedregosa, Fabian and Varoquaux, Gaël and Gramfort, Alexandre and Michel, Vincent and Thirion, Bertrand and Grisel, Olivier and Blondel, Mathieu and Prettenhofer, Peter and Weiss, Ron and Dubourg, Vincent and Vanderplas, Jake and Passos, Alexandre and Cournapeau, David and Brucher, Matthieu and Perrot, Matthieu and Duchesnay, Édouard},
	year = {2011},
	pages = {2825--2830}
}

@article{singh_low-cost_2019,
	title = {Low-cost solution for rodent home-cage behaviour monitoring},
	volume = {14},
	issn = {1932-6203},
	url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0220751},
	doi = {10.1371/journal.pone.0220751},
	abstract = {In the current research on measuring complex behaviours/phenotyping in rodents, most of the experimental design requires the experimenter to remove the animal from its home-cage environment and place it in an unfamiliar apparatus (novel environment). This interaction may influence behaviour, general well-being, and the metabolism of the animal, affecting the phenotypic outcome even if the data collection method is automated. Most of the commercially available solutions for home-cage monitoring are expensive and usually lack the flexibility to be incorporated with existing home-cages. Here we present a low-cost solution for monitoring home-cage behaviour of rodents that can be easily incorporated to practically any available rodent home-cage. To demonstrate the use of our system, we reliably predict the sleep/wake state of mice in their home-cage using only video. We validate these results using hippocampal local field potential (LFP) and electromyography (EMG) data. Our approach provides a low-cost flexible methodology for high-throughput studies of sleep, circadian rhythm and rodent behaviour with minimal experimenter interference.},
	language = {en},
	number = {8},
	urldate = {2019-11-06},
	journal = {PLOS ONE},
	author = {Singh, Surjeet and Bermudez-Contreras, Edgar and Nazari, Mojtaba and Sutherland, Robert J. and Mohajerani, Majid H.},
	month = aug,
	year = {2019},
	keywords = {Algorithms, Animal behavior, Cameras, Electromyography, Mice, Rodents, Sleep, Web-based applications},
	pages = {e0220751}
}

@misc{noauthor_m-track:_nodate,
	title = {M-{Track}: {A} {New} {Software} for {Automated} {Detection} of {Grooming} {Trajectories} in {Mice}},
	url = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005115},
	urldate = {2019-11-06},
	doi = {10.1371/journal.pcbi.1005115},
}

@article{jiang_trajectorynet:_2017,
	title = {{TrajectoryNet}: {An} {Embedded} {GPS} {Trajectory} {Representation} for {Point}-based {Classification} {Using} {Recurrent} {Neural} {Networks}},
	shorttitle = {{TrajectoryNet}},
	url = {http://arxiv.org/abs/1705.02636},
	abstract = {Understanding and discovering knowledge from GPS (Global Positioning System) traces of human activities is an essential topic in mobility-based urban computing. We propose TrajectoryNet-a neural network architecture for point-based trajectory classification to infer real world human transportation modes from GPS traces. To overcome the challenge of capturing the underlying latent factors in the low-dimensional and heterogeneous feature space imposed by GPS data, we develop a novel representation that embeds the original feature space into another space that can be understood as a form of basis expansion. We also enrich the feature space via segment-based information and use Maxout activations to improve the predictive power of Recurrent Neural Networks (RNNs). We achieve over 98\% classification accuracy when detecting four types of transportation modes, outperforming existing models without additional sensory data or location-based prior knowledge.},
	urldate = {2019-11-06},
	journal = {arXiv:1705.02636 [cs]},
	author = {Jiang, Xiang and de Souza, Erico N. and Pesaranghader, Ahmad and Hu, Baifan and Silver, Daniel L. and Matwin, Stan},
	month = aug,
	year = {2017},
	note = {arXiv: 1705.02636},
	keywords = {Computer Science - Artificial Intelligence, Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning, H.2.8, I.2.1, I.2.6}
}
@article{zheng_trajectory_2015,
	title = {Trajectory {Data} {Mining}: {An} {Overview}},
	shorttitle = {Trajectory {Data} {Mining}},
	url = {https://www.microsoft.com/en-us/research/publication/trajectory-data-mining-an-overview/},
	abstract = {The advances in location-acquisition and mobile computing techniques have generated massive spatial trajectory data, which represent the mobility of a diversity of moving objects, such as people, vehicles and animals. Many techniques have been proposed for processing, managing and mining trajectory data in the past decade, fostering a broad range of applications. In this article, …},
	language = {en-US},
	urldate = {2019-11-06},
	journal = {ACM Transaction on Intelligent Systems and Technology},
	author = {Zheng, Yu},
	month = sep,
	year = {2015}
}

@article{zheng_trajectory_2015-1,
	title = {Trajectory {Data} {Mining}: {An} {Overview}},
	volume = {6},
	issn = {21576904},
	shorttitle = {Trajectory {Data} {Mining}},
	url = {http://dl.acm.org/citation.cfm?doid=2764959.2743025},
	doi = {10.1145/2743025},
	language = {en},
	number = {3},
	urldate = {2019-11-06},
	journal = {ACM Transactions on Intelligent Systems and Technology},
	author = {Zheng, Yu},
	month = may,
	year = {2015},
	pages = {1--41}
}

@article{calahorra_hydroxytyrosol_2019,
	title = {Hydroxytyrosol, the {Major} {Phenolic} {Compound} of {Olive} {Oil}, as an {Acute} {Therapeutic} {Strategy} after {Ischemic} {Stroke}},
	volume = {11},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	url = {https://www.mdpi.com/2072-6643/11/10/2430},
	doi = {10.3390/nu11102430},
	abstract = {Stroke is one of the leading causes of adult disability worldwide. After ischemic stroke, damaged tissue surrounding the irreversibly damaged core of the infarct, the penumbra, is still salvageable and is therefore a target for acute therapeutic strategies. The Mediterranean diet (MD) has been shown to lower stroke risk. MD is characterized by increased intake of extra-virgin olive oil, of which hydroxytyrosol (HT) is the foremost phenolic component. This study investigates the effect of an HT-enriched diet directly after stroke on regaining motor and cognitive functioning, MRI parameters, neuroinflammation, and neurogenesis. Stroke mice on an HT diet showed increased strength in the forepaws, as well as improved short-term recognition memory probably due to improvement in functional connectivity (FC). Moreover, mice on an HT diet showed increased cerebral blood flow (CBF) and also heightened expression of brain derived neurotrophic factor (Bdnf), indicating a novel neurogenic potential of HT. This result was additionally accompanied by an enhanced transcription of the postsynaptic marker postsynaptic density protein 95 (Psd-95) and by a decreased ionized calcium-binding adapter molecule 1 (IBA-1) level indicative of lower neuroinflammation. These results suggest that an HT-enriched diet could serve as a beneficial therapeutic approach to attenuate ischemic stroke-associated damage.},
	language = {en},
	number = {10},
	urldate = {2019-11-05},
	journal = {Nutrients},
	author = {Calahorra, Jesús and Shenk, Justin and Wielenga, Vera H. and Verweij, Vivienne and Geenen, Bram and Dederen, Pieter J. and Peinado, M. Ángeles and Siles, Eva and Wiesmann, Maximilian and Kiliaan, Amanda J.},
	month = oct,
	year = {2019},
	keywords = {MRI, animal model, cerebral blood flow, cerebral connectivity, dietary treatment, hydroxytyrosol, neuroinflammation, stroke},
	pages = {2430}
}

@article{iannello_non-intrusive_2019,
	title = {Non-intrusive high throughput automated data collection from the home cage},
	volume = {5},
	issn = {2405-8440},
	doi = {10.1016/j.heliyon.2019.e01454},
	abstract = {Automated home cage monitoring represents a key technology to collect animal activity information directly from the home cage. The availability of 24/7 cage data enables extensive and quantitative assessment of mouse behavior and activity over long periods of time than possible otherwise. When home cage monitoring is performed directly at the home cage rack, it is possible to leverage additional advantages, including, e.g., partial (or total) reduction of animal handling, no need for setting up external data collection system as well as not requiring dedicated labs and personnel to perform tests. In this work we introduce a home cage-home rack monitoring system that is capable of continuously detecting spontaneous animal activity occurring in the home cage directly from the home cage rack. The proposed system is based on an electrical capacitance sensing technology that enables non-intrusive and continuous home cage monitoring. We then present a few animal activity metrics that are validated via comparison against a video camera-based tracking system. The results show that the proposed home-cage monitoring system can provide animal activity metrics that are comparable to the ones derived via a conventional video tracking system, with the advantage of system scalability, limited amount of both data generated and computational capabilities required to derive metrics.},
	language = {eng},
	number = {4},
	journal = {Heliyon},
	author = {Iannello, Fabio},
	month = apr,
	year = {2019},
	pmid = {30997429},
	pmcid = {PMC6451168},
	keywords = {Bioengineering, Bioinformatics, Cancer research, Genetics, Neuroscience, Physiology, Toxicology},
	pages = {e01454}
}

@article{pernold_towards_2019,
	title = {Towards large scale automated cage monitoring – {Diurnal} rhythm and impact of interventions on in-cage activity of {C}57BL/6J mice recorded 24/7 with a non-disrupting capacitive-based technique},
	volume = {14},
	issn = {1932-6203},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6361443/},
	doi = {10.1371/journal.pone.0211063},
	abstract = {Background and aims
Automated recording of laboratory animal’s home cage behavior is receiving increasing attention since such non-intruding surveillance will aid in the unbiased understanding of animal cage behavior potentially improving animal experimental reproducibility.

Material and methods
Here we investigate activity of group held female C57BL/6J mice (mus musculus) housed in standard Individually Ventilated Cages across three test-sites: Consiglio Nazionale delle Ricerche (CNR, Rome, Italy), The Jackson Laboratory (JAX, Bar Harbor, USA) and Karolinska Insititutet (KI, Stockholm, Sweden). Additionally, comparison of female and male C57BL/6J mice was done at KI. Activity was recorded using a capacitive-based sensor placed non-intrusively on the cage rack under the home cage collecting activity data every 250 msec, 24/7. The data collection was analyzed using non-parametric analysis of variance for longitudinal data comparing sites, weekdays and sex.

Results
The system detected an increase in activity preceding and peaking around lights-on followed by a decrease to a rest pattern. At lights off, activity increased substantially displaying a distinct temporal variation across this period. We also documented impact on mouse activity that standard animal handling procedures have, e.g. cage-changes, and show that such procedures are stressors impacting in-cage activity., These key observations replicated across the three test-sites, however, it is also clear that, apparently minor local environmental differences generate significant behavioral variances between the sites and within sites across weeks. Comparison of gender revealed differences in activity in the response to cage-change lasting for days in male but not female mice; and apparently also impacting the response to other events such as lights-on in males. Females but not males showed a larger tendency for week-to-week variance in activity possibly reflecting estrous cycling.

Conclusions
These data demonstrate that home cage monitoring is scalable and run in real time, providing complementary information for animal welfare measures, experimental design and phenotype characterization.},
	number = {2},
	urldate = {2019-11-05},
	journal = {PLoS ONE},
	author = {Pernold, Karin and Iannello, F. and Low, B. E. and Rigamonti, M. and Rosati, G. and Scavizzi, F. and Wang, J. and Raspa, M. and Wiles, M. V. and Ulfhake, B.},
	month = feb,
	year = {2019},
	pmid = {30716111},
	pmcid = {PMC6361443}
}

@article{liang_peeking_2019,
	title = {Peeking into the {Future}: {Predicting} {Future} {Person} {Activities} and {Locations} in {Videos}},
	shorttitle = {Peeking into the {Future}},
	url = {http://arxiv.org/abs/1902.03748},
	abstract = {Deciphering human behaviors to predict their future paths/trajectories and what they would do from videos is important in many applications. Motivated by this idea, this paper studies predicting a pedestrian's future path jointly with future activities. We propose an end-to-end, multi-task learning system utilizing rich visual features about human behavioral information and interaction with their surroundings. To facilitate the training, the network is learned with an auxiliary task of predicting future location in which the activity will happen. Experimental results demonstrate our state-of-the-art performance over two public benchmarks on future trajectory prediction. Moreover, our method is able to produce meaningful future activity prediction in addition to the path. The result provides the first empirical evidence that joint modeling of paths and activities benefits future path prediction.},
	urldate = {2019-11-01},
	journal = {arXiv:1902.03748 [cs]},
	author = {Liang, Junwei and Jiang, Lu and Niebles, Juan Carlos and Hauptmann, Alexander and Fei-Fei, Li},
	month = may,
	year = {2019},
	note = {arXiv: 1902.03748},
	doi = {10.1109/cvprw.2019.00358},
	keywords = {Computer Science - Computer Vision and Pattern Recognition}
}

@article{amirian_social_2019,
	title = {Social {Ways}: {Learning} {Multi}-{Modal} {Distributions} of {Pedestrian} {Trajectories} with {GANs}},
	shorttitle = {Social {Ways}},
	url = {http://arxiv.org/abs/1904.09507},
	abstract = {This paper proposes a novel approach for predicting the motion of pedestrians interacting with others. It uses a Generative Adversarial Network (GAN) to sample plausible predictions for any agent in the scene. As GANs are very susceptible to mode collapsing and dropping, we show that the recently proposed Info-GAN allows dramatic improvements in multi-modal pedestrian trajectory prediction to avoid these issues. We also left out L2-loss in training the generator, unlike some previous works, because it causes serious mode collapsing though faster convergence. We show through experiments on real and synthetic data that the proposed method leads to generate more diverse samples and to preserve the modes of the predictive distribution. In particular, to prove this claim, we have designed a toy example dataset of trajectories that can be used to assess the performance of different methods in preserving the predictive distribution modes.},
	urldate = {2019-11-01},
	journal = {arXiv:1904.09507 [cs]},
	author = {Amirian, Javad and Hayet, Jean-Bernard and Pettre, Julien},
	month = apr,
	year = {2019},
	note = {arXiv: 1904.09507},
	doi = {10.1109/cvprw.2019.00359},
	keywords = {Computer Science - Computer Vision and Pattern Recognition}
}

@article{chesler_identification_2002,
	title = {Identification and ranking of genetic and laboratory environment factors influencing a behavioral trait, thermal nociception, via computational analysis of a large data archive},
	volume = {26},
	issn = {0149-7634},
	url = {http://www.sciencedirect.com/science/article/pii/S0149763402001033},
	doi = {10.1016/S0149-7634(02)00103-3},
	abstract = {Laboratory conditions in biobehavioral experiments are commonly assumed to be ‘controlled’, having little impact on the outcome. However, recent studies have illustrated that the laboratory environment has a robust effect on behavioral traits. Given that environmental factors can interact with trait-relevant genes, some have questioned the reliability and generalizability of behavior genetic research designed to identify those genes. This problem might be alleviated by the identification of the most relevant environmental factors, but the task is hindered by the large number of factors that typically vary between and within laboratories. We used a computational approach to retrospectively identify and rank sources of variability in nociceptive responses as they occurred in a typical research laboratory over several years. A machine-learning algorithm was applied to an archival data set of 8034 independent observations of baseline thermal nociceptive sensitivity. This analysis revealed that a factor even more important than mouse genotype was the experimenter performing the test, and that nociception can be affected by many additional laboratory factors including season/humidity, cage density, time of day, sex and within-cage order of testing. The results were confirmed by linear modeling in a subset of the data, and in confirmatory experiments, in which we were able to partition the variance of this complex trait among genetic (27\%), environmental (42\%) and genetic×environmental (18\%) sources.},
	language = {en},
	number = {8},
	urldate = {2019-11-01},
	journal = {Neuroscience \& Biobehavioral Reviews},
	author = {Chesler, Elissa J and Wilson, Sonya G and Lariviere, William R and Rodriguez-Zas, Sandra L and Mogil, Jeffrey S},
	month = dec,
	year = {2002},
	keywords = {CART, Data mining, Environment, Genetic, Mice, Nociception, Pain},
	pages = {907--923}
}

@article{valletta_applications_2017,
	title = {Applications of machine learning in animal behaviour studies},
	volume = {124},
	issn = {0003-3472},
	url = {http://www.sciencedirect.com/science/article/pii/S0003347216303360},
	doi = {10.1016/j.anbehav.2016.12.005},
	abstract = {In many areas of animal behaviour research, improvements in our ability to collect large and detailed data sets are outstripping our ability to analyse them. These diverse, complex and often high-dimensional data sets exhibit nonlinear dependencies and unknown interactions across multiple variables, and may fail to conform to the assumptions of many classical statistical methods. The field of machine learning provides methodologies that are ideally suited to the task of extracting knowledge from these data. In this review, we aim to introduce animal behaviourists unfamiliar with machine learning (ML) to the promise of these techniques for the analysis of complex behavioural data. We start by describing the rationale behind ML and review a number of animal behaviour studies where ML has been successfully deployed. The ML framework is then introduced by presenting several unsupervised and supervised learning methods. Following this overview, we illustrate key ML approaches by developing data analytical pipelines for three different case studies that exemplify the types of behavioural and ecological questions ML can address. The first uses a large number of spectral and morphological characteristics that describe the appearance of pheasant, Phasianus colchicus, eggs to assign them to putative clutches. The second takes a continuous data stream of feeder visits from PIT (passive integrated transponder)-tagged jackdaws, Corvus monedula, and extracts foraging events from it, which permits the construction of social networks. Our final example uses aerial images to train a classifier that detects the presence of wildebeest, Connochaetes taurinus, to count individuals in a population. With the advent of cheaper sensing and tracking technologies an unprecedented amount of data on animal behaviour is becoming available. We believe that ML will play a central role in translating these data into scientific knowledge and become a useful addition to the animal behaviourist's analytical toolkit.},
	language = {en},
	urldate = {2019-11-01},
	journal = {Animal Behaviour},
	author = {Valletta, John Joseph and Torney, Colin and Kings, Michael and Thornton, Alex and Madden, Joah},
	month = feb,
	year = {2017},
	keywords = {animal behaviour data, classification, clustering, dimensionality reduction, machine learning, predictive modelling, random forests, social networks, supervised learning, unsupervised learning},
	pages = {203--220}
}


@article{kerster_spatial_2016,
	title = {Spatial memory in foraging games},
	volume = {148},
	issn = {1873-7838},
	doi = {10.1016/j.cognition.2015.12.015},
	abstract = {Foraging and foraging-like processes are found in spatial navigation, memory, visual search, and many other search functions in human cognition and behavior. Foraging is commonly theorized using either random or correlated movements based on Lévy walks, or a series of decisions to remain or leave proximal areas known as "patches". Neither class of model makes use of spatial memory, but search performance may be enhanced when information about searched and unsearched locations is encoded. A video game was developed to test the role of human spatial memory in a canonical foraging task. Analyses of search trajectories from over 2000 human players yielded evidence that foraging movements were inherently clustered, and that clustering was facilitated by spatial memory cues and influenced by memory for spatial locations of targets found. A simple foraging model is presented in which spatial memory is used to integrate aspects of Lévy-based and patch-based foraging theories to perform a kind of area-restricted search, and thereby enhance performance as search unfolds. Using only two free parameters, the model accounts for a variety of findings that individually support competing theories, but together they argue for the integration of spatial memory into theories of foraging.},
	language = {eng},
	journal = {Cognition},
	author = {Kerster, Bryan E. and Rhodes, Theo and Kello, Christopher T.},
	month = mar,
	year = {2016},
	pmid = {26752603},
	keywords = {Area-restricted search, Cognition, Feeding Behavior, Foraging, Humans, Search model, Spatial Behavior, Spatial memory, Spatial Memory, Spatial Navigation, Video Games},
	pages = {85--96},
}


@article{ross_influence_2016,
	title = {Influence of musical groove on postural sway},
	volume = {42},
	issn = {1939-1277(Electronic),0096-1523(Print)},
	doi = {10.1037/xhp0000198},
	abstract = {Timescales of postural fluctuation reflect underlying neuromuscular processes in balance control that are influenced by sensory information and the performance of concurrent cognitive and motor tasks. An open question is how postural fluctuations entrain to complex environmental rhythms, such as in music, which also vary on multiple timescales. Musical groove describes the property of music that encourages auditory-motor synchronization and is used to study voluntary motor entrainment to rhythmic sounds. The influence of groove on balance control mechanisms remains unexplored. We recorded fluctuations in center of pressure (CoP) of standing participants (N = 40) listening to low and high groove music and during quiet stance. We found an effect of musical groove on radial sway variability, with the least amount of variability in the high groove condition. In addition, we observed that groove influenced postural sway entrainment at various temporal scales. For example, with increasing levels of groove, we observed more entrainment to shorter, local timescale rhythmic musical occurrences. In contrast, we observed more entrainment to longer, global timescale features of the music, such as periodicity, with decreasing levels of groove. Finally, musical experience influenced the amount of postural variability and entrainment at local and global timescales. We conclude that groove in music and musical experience can influence the neural mechanisms that govern balance control, and discuss implications of our findings in terms of multiscale sensorimotor coupling. (PsycINFO Database Record (c) 2016 APA, all rights reserved)},
	number = {3},
	journal = {Journal of Experimental Psychology: Human Perception and Performance},
	author = {Ross, Jessica M. and Warlaumont, Anne S. and Abney, Drew H. and Rigoli, Lillian M. and Balasubramaniam, Ramesh},
	year = {2016},
	note = {Place: US
Publisher: American Psychological Association},
	keywords = {Auditory Stimulation, Motor Processes, Music, Posture, Rhythm},
	pages = {308--319},
	file = {Snapshot:/Users/justinshenk/Zotero/storage/DNH9UD9R/2015-58954-001.html:text/html},
}

@article{ayers,
author = {Ayers, Carolyn and Armsworth, Paul and Brosi, Berry},
year = {2015},
month = {08},
pages = {},
title = {Determinism as a statistical metric for ecologically important recurrent behaviors with trapline foraging as a case study},
volume = {69},
journal = {Behavioral Ecology and Sociobiology},
doi = {10.1007/s00265-015-1948-3}
}

@article{morato_jaguar_2018,
	title = {Jaguar movement database: a {GPS}-based movement dataset of an apex predator in the {Neotropics}},
	volume = {99},
	copyright = {© 2018 The Authors. Ecology © 2018 The Ecological Society of America.},
	issn = {1939-9170},
	shorttitle = {Jaguar movement database},
	url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1002/ecy.2379},
	doi = {10.1002/ecy.2379},
	abstract = {The field of movement ecology has rapidly grown during the last decade, with important advancements in tracking devices and analytical tools that have provided unprecedented insights into where, when, and why species move across a landscape. Although there has been an increasing emphasis on making animal movement data publicly available, there has also been a conspicuous dearth in the availability of such data on large carnivores. Globally, large predators are of conservation concern. However, due to their secretive behavior and low densities, obtaining movement data on apex predators is expensive and logistically challenging. Consequently, the relatively small sample sizes typical of large carnivore movement studies may limit insights into the ecology and behavior of these elusive predators. The aim of this initiative is to make available to the conservation-scientific community a dataset of 134,690 locations of jaguars (Panthera onca) collected from 117 individuals (54 males and 63 females) tracked by GPS technology. Individual jaguars were monitored in five different range countries representing a large portion of the species’ distribution. This dataset may be used to answer a variety of ecological questions including but not limited to: improved models of connectivity from local to continental scales; the use of natural or human-modified landscapes by jaguars; movement behavior of jaguars in regions not represented in this dataset; intraspecific interactions; and predator-prey interactions. In making our dataset publicly available, we hope to motivate other research groups to do the same in the near future. Specifically, we aim to help inform a better understanding of jaguar movement ecology with applications towards effective decision making and maximizing long-term conservation efforts for this ecologically important species. There are no costs, copyright, or proprietary restrictions associated with this data set. When using this data set, please cite this article to recognize the effort involved in gathering and collating the data and the willingness of the authors to make it publicly available.},
	language = {en},
	number = {7},
	urldate = {2021-06-04},
	journal = {Ecology},
	author = {Morato, Ronaldo G. and Thompson, Jeffrey J. and Paviolo, Agustin and Torre, Jesus A. de La and Lima, Fernando and McBride, Roy T. and Paula, Rogerio C. and Cullen, Laury and Silveira, Leandro and Kantek, Daniel L. Z. and Ramalho, Emiliano E. and Maranhão, Louise and Haberfeld, Mario and Sana, Denis A. and Medellin, Rodrigo A. and Carrillo, Eduardo and Montalvo, Victor and Monroy-Vilchis, Octavio and Cruz, Paula and Jacomo, Anah T. and Torres, Natalia M. and Alves, Giselle B. and Cassaigne, Ivonne and Thompson, Ron and Saens-Bolanos, Carolina and Cruz, Juan Carlos and Alfaro, Luiz D. and Hagnauer, Isabel and Silva, Xavier Marina da and Vogliotti, Alexandre and Moraes, Marcela F. D. and Miyazaki, Selma S. and Pereira, Thadeu D. C. and Araujo, Gediendson R. and Silva, Leanes Cruz da and Leuzinger, Lucas and Carvalho, Marina M. and Rampin, Lilian and Sartorello, Leonardo and Quigley, Howard and Tortato, Fernando and Hoogesteijn, Rafael and Crawshaw, Peter G. and Devlin, Allison L. and May, Joares A. and Azevedo, Fernando C. C. de and Concone, Henrique V. B. and Quiroga, Veronica A. and Costa, Sebastian A. and Arrabal, Juan P. and Vanderhoeven, Ezequiel and Blanco, Yamil E. Di and Lopes, Alexandre M. C. and Widmer, Cynthia E. and Ribeiro, Milton Cezar},
	year = {2018},
	note = {\_eprint: https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1002/ecy.2379},
	keywords = {behavior, conservation, GPS radio-collars, habitat use, landscape, movement ecology, Panthera onca},
	pages = {1691--1691},
	file = {Full Text PDF:/Users/justinshenk/Zotero/storage/FG8IDDP7/Morato et al. - 2018 - Jaguar movement database a GPS-based movement dat.pdf:application/pdf;Snapshot:/Users/justinshenk/Zotero/storage/FJT5T8D9/ecy.html:text/html},
}

@article{neves_recurrence_2017,
	title = {Recurrence analysis of ant activity patterns},
	volume = {12},
	url = {https://doi.org/10.1371/journal.pone.0185968},
	doi = {10.1371/journal.pone.0185968},
	abstract = {In this study, we used recurrence quantification analysis (RQA) and recurrence plots (RPs) to compare the movement activity of individual workers of three ant species, as well as a gregarious beetle species. RQA and RPs quantify the number and duration of recurrences of a dynamical system, including a detailed quantification of signals that could be stochastic, deterministic, or both. First, we found substantial differences between the activity dynamics of beetles and ants, with the results suggesting that the beetles have quasi-periodic dynamics and the ants do not. Second, workers from different ant species varied with respect to their dynamics, presenting degrees of predictability as well as stochastic signals. Finally, differences were found among minor and major caste of the same (dimorphic) ant species. Our results underscore the potential of RQA and RPs in the analysis of complex behavioral patterns, as well as in general inferences on animal behavior and other biological phenomena.},
	number = {10},
	journal = {PLOS ONE},
	author = {Neves, Felipe Marcel and Viana, Ricardo Luiz and Pie, Marcio Roberto},
	year = {2017},
	note = {Publisher: Public Library of Science},
	pages = {1--15},
}

@article{shockley,
author = {Shockley, Kevin and Santana, Marie-Vee and Fowler, Carol},
year = {2003},
month = {05},
pages = {326-32},
title = {Mutual Interpersonal Postural Constraints are Involved in Cooperative Conversation},
volume = {29},
journal = {Journal of experimental psychology. Human perception and performance},
doi = {10.1037/0096-1523.29.2.326}
}

@article{huette_drawing_2013,
	title = {Drawing from {Memory}: {Hand}-{Eye} {Coordination} at {Multiple} {Scales}},
	volume = {8},
	shorttitle = {Drawing from {Memory}},
	doi = {10.1371/journal.pone.0058464},
	abstract = {Eyes move to gather visual information for the purpose of guiding behavior. This guidance takes the form of perceptual-motor interactions on short timescales for behaviors like locomotion and hand-eye coordination. More complex behaviors require perceptual-motor interactions on longer timescales mediated by memory, such as navigation, or designing and building artifacts. In the present study, the task of sketching images of natural scenes from memory was used to examine and compare perceptual-motor interactions on shorter and longer timescales. Eye and pen trajectories were found to be coordinated in time on shorter timescales during drawing, and also on longer timescales spanning study and drawing periods. The latter type of coordination was found by developing a purely spatial analysis that yielded measures of similarity between images, eye trajectories, and pen trajectories. These results challenge the notion that coordination only unfolds on short timescales. Rather, the task of drawing from memory evokes perceptual-motor encodings of visual images that preserve coarse-grained spatial information over relatively long timescales as well.},
	journal = {PloS one},
	author = {Huette, Stephanie and Kello, Christopher and Rhodes, Theo and Spivey, Michael},
	month = mar,
	year = {2013},
	pages = {e58464},
	file = {Full Text PDF:/Users/justinshenk/Zotero/storage/JZ4JJ7T7/Huette et al. - 2013 - Drawing from Memory Hand-Eye Coordination at Mult.pdf:application/pdf},
}


@article{clustering_mice,
author = {Bak, Peter and Mansmann, Florian and Janetzko, Halldor and Keim, Daniel},
year = {2009},
month = {11},
pages = {913-20},
title = {Spatiotemporal Analysis of Sensor Logs using Growth Ring Maps},
volume = {15},
journal = {IEEE transactions on visualization and computer graphics},
doi = {10.1109/TVCG.2009.182}
}

@article{huang_mapping_2020,
	title = {Mapping {Mouse} {Behavior} with an {Unsupervised} {Spatio}-temporal {Sequence} {Decomposition} {Framework}},
	url = {https://www.biorxiv.org/content/early/2020/09/14/2020.09.14.295808},
	doi = {10.1101/2020.09.14.295808},
	abstract = {Objective quantification of animal behavior is crucial to understanding the relationship between brain activity and behavior. For rodents, this has remained a challenge due to the high-dimensionality and large temporal variability of their behavioral features. Inspired by the natural structure of animal behavior, the present study uses a parallel, multi-stage approach to decompose motion features and generate an objective metric for mapping rodent behavior into the animal’s feature space. Incorporating a three-dimensional (3D) motion-capture system and unsupervised clustering into this approach, we developed a framework that can automatically identify animal behavioral phenotypes from experimental monitoring. We demonstrate the efficacy of our framework by generating an “autistic-like behavior space” that can robustly characterize a transgenic mouse disease model based on motor activity without human supervision. Our results suggest that our framework features a broad range of applications, including animal disease model phenotyping and the modeling of relationships between neural circuits and behavior.Competing Interest StatementThe authors have declared no competing interest.},
	journal = {bioRxiv},
	author = {Huang, Kang and Han, Yaning and Chen, Ke and Pan, Hongli and Yi, Wenling and Li, Xiaoxi and Liu, Siyuan and Wei, Pengfei and Wang, Liping},
	year = {2020},
	note = {Publisher: Cold Spring Harbor Laboratory
\_eprint: https://www.biorxiv.org/content/early/2020/09/14/2020.09.14.295808.full.pdf},
}


@article{mclean_trajr:_2018,
	title = {trajr: {An} {R} package for characterisation of animal trajectories},
	volume = {124},
	copyright = {© 2018 The Authors. Ethology Published by Blackwell Verlag GmbH},
	issn = {1439-0310},
	shorttitle = {trajr},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/eth.12739},
	doi = {10.1111/eth.12739},
	abstract = {Quantitative characterisation of the trajectories of moving animals is an important component of many behavioural and ecological studies, however methods are complicated and varied, and sometimes require well-developed programming skills to implement. Here, we introduce trajr, an R package that serves to analyse animal paths, from unicellular organisms, through insects to whales. It makes a variety of statistical characterisations of trajectories, such as tortuosity, speed and changes in direction, available to biologists who may not have a background in programming. We discuss a range of indices that have been used by researchers, describe the package in detail, then use movement observations of whales and clearwing moths to demonstrate some of the capabilities of trajr. As an open-source R package, trajr encourages open and reproducible research. It supports the implementation of additional methods by providing access to trajectory analysis “building blocks,” allows the full suite of R statistical analysis tools to be applied to trajectory analysis, and the source code can be independently validated.},
	language = {en},
	number = {6},
	urldate = {2019-07-30},
	journal = {Ethology},
	author = {McLean, Donald James and Volponi, Marta A. Skowron},
	year = {2018},
	keywords = {behaviour, locomotor mimicry, navigation, speed, tortuosity, whales},
	pages = {440--448}
}

@article{mullner_modern_2011,
	title = {Modern hierarchical, agglomerative clustering algorithms},
	url = {http://arxiv.org/abs/1109.2378},
	abstract = {This paper presents algorithms for hierarchical, agglomerative clustering which perform most efficiently in the general-purpose setup that is given in modern standard software. Requirements are: (1) the input data is given by pairwise dissimilarities between data points, but extensions to vector data are also discussed (2) the output is a "stepwise dendrogram", a data structure which is shared by all implementations in current standard software. We present algorithms (old and new) which perform clustering in this setting efficiently, both in an asymptotic worst-case analysis and from a practical point of view. The main contributions of this paper are: (1) We present a new algorithm which is suitable for any distance update scheme and performs significantly better than the existing algorithms. (2) We prove the correctness of two algorithms by Rohlf and Murtagh, which is necessary in each case for different reasons. (3) We give well-founded recommendations for the best current algorithms for the various agglomerative clustering schemes.},
	urldate = {2019-07-29},
	journal = {arXiv:1109.2378 [cs, stat]},
	author = {Müllner, Daniel},
	month = sep,
	year = {2011},
	note = {arXiv: 1109.2378},
	keywords = {62H30, Computer Science - Data Structures and Algorithms, I.5.3, Statistics - Machine Learning}
}

@article{chaumont_live_2018,
	title = {Live {Mouse} {Tracker}: real-time behavioral analysis of groups of mice},
	copyright = {© 2018, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/},
	shorttitle = {Live {Mouse} {Tracker}},
	url = {https://www.biorxiv.org/content/10.1101/345132v2},
	doi = {10.1101/345132},
	abstract = {{\textless}p{\textgreater}Preclinical studies of psychiatric disorders require the use of animal models to investigate the impact of environmental factors or genetic mutations on complex traits such as decision-making and social interactions. Here, we present a real-time method for behavior analysis of mice housed in groups that couples computer vision, machine learning and Triggered-RFID identification to track and monitor animals over several days in enriched environments. The system extracts a thorough list of individual and collective behavioral traits and provides a unique phenotypic profile for each animal. On mouse models, we study the impact of mutations of genes Shank2 and Shank3 involved in autism. Characterization and integration of data from behavioral profiles of mutated female mice reveals distinctive activity levels and involvement in complex social configuration.{\textless}/p{\textgreater}},
	language = {en},
	urldate = {2019-07-28},
	journal = {bioRxiv},
	author = {Chaumont, Fabrice de and Ey, Elodie and Torquet, Nicolas and Lagache, Thibault and Dallongeville, Stéphane and Imbert, Albane and Legou, Thierry and Sourd, Anne-Marie Le and Faure, Philippe and Bourgeron, Thomas and Olivo-Marin, Jean-Christophe},
	month = jun,
	year = {2018},
	pages = {345132}
}

@article{hetze_gait_2012,
	title = {Gait analysis as a method for assessing neurological outcome in a mouse model of stroke},
	volume = {206},
	issn = {1872-678X},
	doi = {10.1016/j.jneumeth.2012.02.001},
	abstract = {Ameliorating stroke induced neurological deficits is one of the most important goals of stroke therapy. In order to improve stroke outcome, novel treatment approaches as well as animal stroke models predictive for the clinical setting are of urgent need. One of the main obstacles in experimental stroke research is measuring long-term outcome, in particular in mouse models of stroke. On the other hand, assessing functional deficits in animal models of stroke is critical to improve the prediction of preclinical findings. Automated gait analysis provides a sensitive tool to examine locomotion and limb coordination in small rodents. Comparing mice before and 10 days after experimental stroke (60 min MCAo) we observed a significant decrease in maximum contact area, stride length and swing speed in the hind limbs, especially the contralateral one. Mice showed a disturbed interlimb coordination represented by changes in regularity index and phase dispersion. To assess whether gait analysis is applicable to assess improvements by neuroprotective compounds, we applied a model calculation and approached common statistical problems. In conclusion, gait analysis is a promising tool to assess mid- to long-term outcome in experimental stroke research.},
	language = {eng},
	number = {1},
	journal = {Journal of Neuroscience Methods},
	author = {Hetze, Susann and Römer, Christine and Teufelhart, Carena and Meisel, Andreas and Engel, Odilo},
	month = apr,
	year = {2012},
	pmid = {22343052},
	keywords = {Animals, Disease Models, Animal, Gait, Male, Mice, Mice, Inbred C57BL, Neurologic Examination, Predictive Value of Tests, Stroke, Treatment Outcome},
	pages = {7--14}
}

@article{encarnacion_long-term_2011,
	title = {Long-term behavioral assessment of function in an experimental model for ischemic stroke},
	volume = {196},
	issn = {01650270},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0165027011000367},
	doi = {10.1016/j.jneumeth.2011.01.010},
	abstract = {Middle cerebral artery occlusion (MCAO) in rats is a well-studied experimental model for ischemic stroke leading to brain infarction and functional deficits. Many preclinical studies have focused on a small time window after the ischemic episode to evaluate functional outcome for screening therapeutic candidates. Short evaluation periods following injury have led to significant setbacks due to lack of information on the delayed effects of treatments, as well as short-lived and reversible neuroprotection, so called false-positive results. In this report, we evaluated long-term functional deficit for 90 days after MCAO in two rat strains with two durations of ischemic insult, in order to identify the best experimental paradigm to assess injury and subsequent recovery. Behavioral outcomes were measured pre-MCAO followed by weekly assessment post-stroke. Behavioral tests included the 18-point composite neurological score, 28-point neuroscore, rearing test, vibrissae-evoked forelimb placing test, foot fault test and the CatWalk. Brain lesions were assessed to correlate injury to behavior outcomes at the end of study. Our results indicate that infarction volume in Sprague-Dawley rats was dependent on occlusion duration. In contrast, the infarction volume in Wistar rats did not correlate with the duration of ischemic episode. Functional outcomes were not dependent on occlusion time in either strain; however, measureable deficits were detectable long-term in limb asymmetry, 18- and 28-point neuroscores, forelimb placing, paw swing speed, and gait coordination. In conclusion, these behavioral assays, in combination with an extended long-term assessment period, can be used for evaluating therapeutic candidates in preclinical models of ischemic stroke.},
	language = {en},
	number = {2},
	urldate = {2019-07-28},
	journal = {Journal of Neuroscience Methods},
	author = {Encarnacion, Angelo and Horie, Nobutaka and Keren-Gill, Hadar and Bliss, Tonya M. and Steinberg, Gary K. and Shamloo, Mehrdad},
	month = mar,
	year = {2011},
	pages = {247--257}
}

@article{park_method_2014,
	title = {A {Method} for {Generate} a {Mouse} {Model} of {Stroke}: {Evaluation} of {Parameters} for {Blood} {Flow}, {Behavior}, and {Survival}},
	volume = {23},
	issn = {1226-2560},
	shorttitle = {A {Method} for {Generate} a {Mouse} {Model} of {Stroke}},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3984953/},
	doi = {10.5607/en.2014.23.1.104},
	abstract = {Stroke is one of the common causes of death and disability. Despite extensive efforts in stroke research, therapeutic options for improving the functional recovery remain limited in clinical practice. Experimental stroke models using genetically modified mice could aid in unraveling the complex pathophysiology triggered by ischemic brain injury. Here, we optimized the procedure for generating mouse stroke model using an intraluminal suture in the middle cerebral artery and verified the blockage of blood flow using indocyanine green coupled with near infra-red radiation. The first week after the ischemic injury was critical for survivability. The survival rate of 11\% in mice without any treatment but increased to 60\% on administering prophylactic antibiotics. During this period, mice showed severe functional impairment but recovered spontaneously starting from the second week onward. Among the various behavioral tests, the pole tests and neurological severity score tests remained reliable up to 4 weeks after ischemia, whereas the rotarod and corner tests became less sensitive for assessing the severity of ischemic injury with time. Further, loss of body weight was also observed for up 4 weeks after ischemia induction. In conclusion, we have developed an improved approach which allows us to investigate the role of the cell death-related genes in the disease progression using genetically modified mice and to evaluate the modes of action of candidate drugs.},
	number = {1},
	urldate = {2019-07-28},
	journal = {Experimental Neurobiology},
	author = {Park, Sin-Young and Marasini, Subash and Kim, Geu-Hee and Ku, Taeyun and Choi, Chulhee and Park, Min-Young and Kim, Eun-Hee and Lee, Young-Don and Suh-Kim, Haeyoung and Kim, Sung-Soo},
	month = mar,
	year = {2014},
	pmid = {24737945},
	pmcid = {PMC3984953},
	pages = {104--114}
}

@misc{noauthor_f1000workspace_nodate,
	title = {F1000Workspace},
	url = {https://f1000.com/work/#/items/553731},
	urldate = {2019-07-28}
}

@article{bailoo_precision_2010,
	title = {The precision of video and photocell tracking systems and the elimination of tracking errors with infrared backlighting},
	volume = {188},
	issn = {1872-678X},
	doi = {10.1016/j.jneumeth.2010.01.035},
	abstract = {Automated tracking offers a number of advantages over both manual and photocell tracking methodologies, including increased reliability, validity, and flexibility of application. Despite the advantages that video offers, our experience has been that video systems cannot track a mouse consistently when its coat color is in low contrast with the background. Furthermore, the local lab lighting can influence how well results are quantified. To test the effect of lighting, we built devices that provide a known path length for any given trial duration, at a velocity close to the average speed of a mouse in the open-field and the circular water maze. We found that the validity of results from two commercial video tracking systems (ANY-maze and EthoVision XT) depends greatly on the level of contrast and the quality of the lighting. A photocell detection system was immune to lighting problems but yielded a path length that deviated from the true length. Excellent precision was achieved consistently, however, with video tracking using infrared backlighting in both the open field and water maze. A high correlation (r=0.98) between the two software systems was observed when infrared backlighting was used with live mice.},
	language = {eng},
	number = {1},
	journal = {Journal of Neuroscience Methods},
	author = {Bailoo, Jeremy D. and Bohlen, Martin O. and Wahlsten, Douglas},
	month = apr,
	year = {2010},
	pmid = {20138914},
	pmcid = {PMC2847046},
	keywords = {Animals, Behavior, Animal, Electronic Data Processing, Exploratory Behavior, Image Enhancement, Image Processing, Computer-Assisted, Mice, Motor Activity, Movement, Pattern Recognition, Automated, Signal Processing, Computer-Assisted, Spatial Behavior, User-Computer Interface, Video Recording},
	pages = {45--52}
}

@article{spink_ethovision_2001,
	series = {Molecular {Behavior} {Genetics} of the {Mouse}},
	title = {The {EthoVision} video tracking system—{A} tool for behavioral phenotyping of transgenic mice},
	volume = {73},
	issn = {0031-9384},
	url = {http://www.sciencedirect.com/science/article/pii/S0031938401005303},
	doi = {10.1016/S0031-9384(01)00530-3},
	abstract = {Video tracking systems enable behavior to be studied in a reliable and consistent way, and over longer time periods than if they are manually recorded. The system takes an analog video signal, digitizes each frame, and analyses the resultant pixels to determine the location of the tracked animals (as well as other data). Calculations are performed on a series of frames to derive a set of quantitative descriptors of the animal's movement. EthoVision (from Noldus Information Technology) is a specific example of such a system, and its functionality that is particularly relevant to transgenic mice studies is described. Key practical aspects of using the EthoVision system are also outlined, including tips about lighting, marking animals, the arena size, and sample rate. Four case studies are presented, illustrating various aspects of the system: (1) The effects of disabling the Munc 18-1 gene were clearly shown using the straightforward measure of how long the mice took to enter a zone in an open field. (2) Differences in exploratory behavior between short and long attack latency mice strains were quantified by measuring the time spent in inner and outer zones of an open field. (3) Mice with hypomorphic CREB alleles were shown to perform less well in a water maze, but this was only clear when a range of different variables were calculated from their tracks. (4) Mice with the trkB receptor knocked out in the forebrain also performed poorly in a water maze, and it was immediately apparent from examining plots of the tracks that this was due to thigmotaxis. Some of the latest technological developments and possible future directions for video tracking systems are briefly discussed.},
	number = {5},
	urldate = {2019-07-28},
	journal = {Physiology \& Behavior},
	author = {Spink, A. J and Tegelenbosch, R. A. J and Buma, M. O. S and Noldus, L. P. J. J},
	month = aug,
	year = {2001},
	keywords = {Automated observation, Rodent, Video tracking, Water maze},
	pages = {731--744}
}

@article{dunne_development_2007,
	title = {Development of a home cage locomotor tracking system capable of detecting the stimulant and sedative properties of drugs in rats},
	volume = {31},
	issn = {0278-5846},
	url = {http://www.sciencedirect.com/science/article/pii/S0278584607002163},
	doi = {10.1016/j.pnpbp.2007.06.023},
	abstract = {The advent of automated locomotor activity methodologies has been extremely useful in removing the subjectivity and bias out of measuring this parameter in rodents. However, many of these behavioural studies are still conducted in novel environments, rather than in ones that the animals are familiar with, such as their home cage. The purpose of the present series of experiments was to develop an automated home cage tracking (HCT) profile using EthoVision® software and assessing the acute effects of stimulant (amphetamine and methamphetamine, 0–5 mg/kg, sc) and sedative (diazepam, 0–20 mg/kg, sc and chlordiazepoxide, 0–50 mg/kg sc) drugs in this apparatus. Young adult male Sprague–Dawley rats were used, and the home cage locomotor activity was recorded for 11–60 min following administration (n=4 per group). For amphetamine and methamphetamine, a dose-dependent increase in home cage activity was evident for both drugs, with a plateau, followed by reduction at higher doses. Methamphetamine was more potent, whereas amphetamine produced greater maximal responses. Both diazepam and chlordiazepoxide dose-dependently reduced locomotor activity, with diazepam exhibiting a greater potency and having stronger sedative effects than chlordiazepoxide. Three doses of each drug were selected at the 31–40 min time period following administration, and compared to open field responses. Diazepam, chlordiazepoxide and amphetamine did not produce significant changes in the open field, whilst methamphetamine produced a significant increase in the 2.5 mg/kg group. In conclusion, these studies have successfully developed a sensitive HCT methodology that has been validated using drugs with stimulant and sedative properties in the same test conditions, with relatively small numbers of animals required to produce statistically significant results. It has proven superior to the open field investigations in allowing dose-response effects to be observed over a relatively short observation period (i.e. 10 min) for both stimulants and sedatives. In addition, the HCT system can determine differences in potency and efficacy between drugs of a similar chemical class.},
	number = {7},
	urldate = {2019-07-28},
	journal = {Progress in Neuro-Psychopharmacology and Biological Psychiatry},
	author = {Dunne, Fergal and O'Halloran, Ambrose and Kelly, John P.},
	month = oct,
	year = {2007},
	keywords = {Home cage, Locomotor activity, Rats, Sedatives, Stimulants},
	pages = {1456--1463}
}

@article{young_combined_2000,
	title = {A combined system for measuring animal motion activities},
	volume = {95},
	issn = {0165-0270},
	url = {http://www.sciencedirect.com/science/article/pii/S0165027099001569},
	doi = {10.1016/S0165-0270(99)00156-9},
	abstract = {In this study, we have developed a combined animal motion activity measurement system that combines an infrared light matrix subsystem with an ultrasonic phase shift subsystem for animal activity measurement. Accordingly, in conjunction with an IBM PC/AT compatible personal computer, the combined system has the advantages of both infrared and ultrasonic subsystems. That is, it can at once measure and directly analyze detailed changes in animal activity ranging from locomotion to tremor. The main advantages of this combined system are that it features real time data acquisition with the option of animated real time or recorded display/playback of the animal’s motion. Additionally, under the multi-task operating condition of IBM PC, it can acquire and process behavior using both IR and ultrasound systems simultaneously. Traditional systems have had to make separate runs for gross and fine movement recording. This combined system can be profitably employed for normative behavioral activity studies and for neurological and pharmacological research.},
	number = {1},
	urldate = {2019-07-28},
	journal = {Journal of Neuroscience Methods},
	author = {Young, M. S. and Young, C. W. and Li, Y. C.},
	month = jan,
	year = {2000},
	keywords = {Animal activity, Infrared Light, Measurement, Real time, Single-chip microcomputer, Ultrasound},
	pages = {55--63}
}

@article{aragao_automatic_2011,
	title = {Automatic system for analysis of locomotor activity in rodents—{A} reproducibility study},
	volume = {195},
	issn = {0165-0270},
	url = {http://www.sciencedirect.com/science/article/pii/S0165027010007041},
	doi = {10.1016/j.jneumeth.2010.12.016},
	abstract = {Automatic analysis of locomotion in studies of behavior and development is of great importance because it eliminates the subjective influence of evaluators on the study. This study aimed to develop and test the reproducibility of a system for automated analysis of locomotor activity in rats. For this study, 15 male Wistar were evaluated at P8, P14, P17, P21, P30 and P60. A monitoring system was developed that consisted of an open field of 1m in diameter with a black surface, an infrared digital camera and a video capture card. The animals were filmed for 2min as they moved freely in the field. The images were sent to a computer connected to the camera. Afterwards, the videos were analyzed using software developed using MATLAB® (mathematical software). The software was able to recognize the pixels constituting the image and extract the following parameters: distance traveled, average speed, average potency, time immobile, number of stops, time spent in different areas of the field and time immobile/number of stops. All data were exported for further analysis. The system was able to effectively extract the desired parameters. Thus, it was possible to observe developmental changes in the patterns of movement of the animals. We also discuss similarities and differences between this system and previously described systems.},
	number = {2},
	urldate = {2019-07-28},
	journal = {Journal of Neuroscience Methods},
	author = {Aragão, Raquel da Silva and Rodrigues, Marco Aurélio Benedetti and de Barros, Karla Mônica Ferraz Teixeira and Silva, Sebastião Rogério Freitas and Toscano, Ana Elisa and de Souza, Ricardo Emmanuel and Manhães-de-Castro, Raul},
	month = feb,
	year = {2011},
	keywords = {Automated analysis, Behavioral analysis, Biomechanical analysis, Locomotor activity, Open field},
	pages = {216--221}
}

@article{benjamini_ten_2010,
	title = {Ten ways to improve the quality of descriptions of whole-animal movement},
	volume = {34},
	issn = {0149-7634},
	url = {http://www.sciencedirect.com/science/article/pii/S0149763410000886},
	doi = {10.1016/j.neubiorev.2010.04.004},
	abstract = {The demand for replicability of behavioral results across laboratories is viewed as a burden in behavior genetics. We demonstrate how it can become an asset offering a quantitative criterion that guides the design of better ways to describe behavior. Passing the high benchmark dictated by the replicability demand requires less stressful and less restraining experimental setups, less noisy data, individually customized cutoff points between the building blocks of movement, and less variable yet discriminative dynamic representations that would capture more faithfully the nature of the behavior, unmasking similarities and differences and revealing novel animal-centered measures. Here we review ten tools that enhance replicability without compromising discrimination. While we demonstrate the usefulness of these tools in the context of inbred mouse exploratory behavior they can readily be used in any study involving a high-resolution analysis of spatial behavior. Viewing replicability as a design concept and using the ten methodological improvements may prove useful in many fields not necessarily related to spatial behavior.},
	number = {8},
	urldate = {2019-07-28},
	journal = {Neuroscience \& Biobehavioral Reviews},
	author = {Benjamini, Yoav and Lipkind, Dina and Horev, Guy and Fonio, Ehud and Kafkafi, Neri and Golani, Ilan},
	month = jul,
	year = {2010},
	keywords = {Compression of kinematic data, Description of behavior, Discriminability between strains and preparations, Exploratory behavior, Genotype-laboratory interaction, Mixed-Model Anova, Open field behavior, Phenotyping mouse behavior, Replicability of results, Segmentation of behavior, Smoothing kinematic data},
	pages = {1351--1365}
}

@article{Arpteg2018SoftwareEC,
  title={Software Engineering Challenges of Deep Learning},
  author={A. Arpteg and B. Brinne and Luka Crnkovic-Friis and J. Bosch},
  journal={2018 44th Euromicro Conference on Software Engineering and Advanced Applications (SEAA)},
  year={2018},
  pages={50-59},
  doi={10.1109/seaa.2018.00018},
}

@InProceedings{ mckinney-proc-scipy-2010,
  author    = { {W}es {M}c{K}inney },
  title     = { {D}ata {S}tructures for {S}tatistical {C}omputing in {P}ython },
  booktitle = { {P}roceedings of the 9th {P}ython in {S}cience {C}onference },
  pages     = { 56 - 61 },
  year      = { 2010 },
  editor    = { {S}t\'efan van der {W}alt and {J}arrod {M}illman },
  doi       = { 10.25080/Majora-92bf1922-00a }
}

@article{van_galen_effects_1990,
	title = {Effects of motor programming on the power spectral density function of finger and wrist movements},
	volume = {16},
	issn = {1939-1277(Electronic),0096-1523(Print)},
	doi = {10.1037/0096-1523.16.4.755},
	abstract = {Power spectral density analysis was applied to the frequency content of the acceleration signal of pen movements in line drawing using 10 right-handed college students. The relative power in frequency bands between 1 and 32 Hz was measured as a function of motoric and anatomic task demands. Results showed a decrease of power at the lower frequencies (1–4 Hz) of the spectrum and an increase in the middle (9–22 Hz) with increasing motor demands. These findings evidence the inhibition of visual control and the disinhibition of physiological tremor under conditions of increased programming demands. Adductive movements displayed less power than abductive movements in the lower end of the spectrum, with a simultaneous increase at the higher frequencies. The relevance of the method for the measurement of neuromotor noise as a possible origin of delays in motor behavior is discussed. (PsycINFO Database Record (c) 2016 APA, all rights reserved)},
	number = {4},
	journal = {Journal of Experimental Psychology: Human Perception and Performance},
	author = {Van Galen, Gerard P. and Van Doorn, Robert R. and Schomaker, Lambert R.},
	year = {1990},
	note = {Place: US
Publisher: American Psychological Association},
	keywords = {Fingers (Anatomy), Motion Perception, Task Complexity, Wrist},
	pages = {755--765},
}

@software{reback2020pandas,
    author       = {The pandas development team},
    title        = {pandas-dev/pandas: Pandas},
    month        = feb,
    year         = 2020,
    publisher    = {Zenodo},
    version      = {latest},
    doi          = {10.5281/zenodo.3509134},
    url          = {https://doi.org/10.5281/zenodo.3509134}
}

@article{noonan_scale-insensitive_2019,
	title = {Scale-insensitive estimation of speed and distance traveled from animal tracking data},
	volume = {7},
	issn = {2051-3933},
	url = {https://doi.org/10.1186/s40462-019-0177-1},
	doi = {10.1186/s40462-019-0177-1},
	abstract = {Speed and distance traveled provide quantifiable links between behavior and energetics, and are among the metrics most routinely estimated from animal tracking data. Researchers typically sum over the straight-line displacements (SLDs) between sampled locations to quantify distance traveled, while speed is estimated by dividing these displacements by time. Problematically, this approach is highly sensitive to the measurement scale, with biases subject to the sampling frequency, the tortuosity of the animal’s movement, and the amount of measurement error. Compounding the issue of scale-sensitivity, SLD estimates do not come equipped with confidence intervals to quantify their uncertainty.},
	number = {1},
	urldate = {2021-02-13},
	journal = {Movement Ecology},
	author = {Noonan, Michael J. and Fleming, Christen H. and Akre, Thomas S. and Drescher-Lehman, Jonathan and Gurarie, Eliezer and Harrison, Autumn-Lynn and Kays, Roland and Calabrese, Justin M.},
	month = nov,
	year = {2019},
	keywords = {Continuous-time, GPS, correlated velocity, ctmm, movement models, step length, telemetry, travel distance},
	pages = {35},
}


@misc{noauthor_f1000workspace_nodate-1,
	title = {F1000Workspace},
	url = {https://f1000.com/work/#/items/6352976},
	urldate = {2019-07-28}
}

@article{kilkenny_improving_2010,
	title = {Improving {Bioscience} {Research} {Reporting}: {The} {ARRIVE} {Guidelines} for {Reporting} {Animal} {Research}},
	volume = {8},
	issn = {1545-7885},
	shorttitle = {Improving {Bioscience} {Research} {Reporting}},
	url = {https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1000412},
	doi = {10.1371/journal.pbio.1000412},
	language = {en},
	number = {6},
	urldate = {2019-07-28},
	journal = {PLOS Biology},
	author = {Kilkenny, Carol and Browne, William J. and Cuthill, Innes C. and Emerson, Michael and Altman, Douglas G.},
	month = jun,
	year = {2010},
	keywords = {Laboratory animals, Peer review, Research design, Research laboratories, Research reporting guidelines, Routes of administration, Statistical data, Statistical methods},
	pages = {e1000412}
}

@article{fisher_update_2009,
	title = {Update of the {Stroke} {Therapy} {Academic} {Industry} {Roundtable} {Preclinical} {Recommendations}},
	volume = {40},
	issn = {0039-2499},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2888275/},
	doi = {10.1161/STROKEAHA.108.541128},
	abstract = {The initial Stroke Therapy Academic Industry Roundtable (STAIR) recommendations published in 1999 were intended to improve the quality of preclinical studies of purported acute stroke therapies. Although recognized as reasonable, they have not been closely followed nor rigorously validated. Substantial advances have occurred regarding the appropriate quality and breadth of preclinical testing for candidate acute stroke therapies for better clinical translation. The updated STAIR preclinical recommendations reinforce the previous suggestions that reproducibly defining dose response and time windows with both histological and functional outcomes in multiple animal species with appropriate physiological monitoring is appropriate. The updated STAIR recommendations include: the fundamentals of good scientific inquiry should be followed by eliminating randomization and assessment bias, a priori defining inclusion/exclusion criteria, performing appropriate power and sample size calculations, and disclosing potential conflicts of interest. After initial evaluations in young, healthy male animals, further studies should be performed in females, aged animals, and animals with comorbid conditions such as hypertension, diabetes, and hypercholesterolemia. Another consideration is the use of clinically relevant biomarkers in animal studies. Although the recommendations cannot be validated until effective therapies based on them emerge from clinical trials, it is hoped that adherence to them might enhance the chances for success.},
	number = {6},
	urldate = {2019-07-28},
	journal = {Stroke; a journal of cerebral circulation},
	author = {Fisher, Marc and Feuerstein, Giora and Howells, David W. and Hurn, Patricia D. and Kent, Thomas A. and Savitz, Sean I. and Lo, Eng H.},
	month = jun,
	year = {2009},
	pmid = {19246690},
	pmcid = {PMC2888275},
	pages = {2244--2250}
}

@article{engel_modeling_2011,
	title = {Modeling stroke in mice - middle cerebral artery occlusion with the filament model},
	issn = {1940-087X},
	doi = {10.3791/2423},
	abstract = {Stroke is among the most frequent causes of death and adult disability, especially in highly developed countries. However, treatment options to date are very limited. To meet the need for novel therapeutic approaches, experimental stroke research frequently employs rodent models of focal cerebral ischaemia. Most researchers use permanent or transient occlusion of the middle cerebral artery (MCA) in mice or rats. Proximal occlusion of the middle cerebral artery (MCA) via the intraluminal suture technique (so called filament or suture model) is probably the most frequently used model in experimental stroke research. The intraluminal MCAO model offers the advantage of inducing reproducible transient or permanent ischaemia of the MCA territory in a relatively non-invasive manner. Intraluminal approaches interrupt the blood flow of the entire territory of this artery. Filament occlusion thus arrests flow proximal to the lenticulo-striate arteries, which supply the basal ganglia. Filament occlusion of the MCA results in reproducible lesions in the cortex and striatum and can be either permanent or transient. In contrast, models inducing distal (to the branching of the lenticulo-striate arteries) MCA occlusion typically spare the striatum and primarily involve the neocortex. In addition these models do require craniectomy. In the model demonstrated in this article, a silicon coated filament is introduced into the common carotid artery and advanced along the internal carotid artery into the Circle of Willis, where it blocks the origin of the middle cerebral artery. In patients, occlusions of the middle cerebral artery are among the most common causes of ischaemic stroke. Since varying ischemic intervals can be chosen freely in this model depending on the time point of reperfusion, ischaemic lesions with varying degrees of severity can be produced. Reperfusion by removal of the occluding filament at least partially models the restoration of blood flow after spontaneous or therapeutic (tPA) lysis of a thromboembolic clot in humans. In this video we will present the basic technique as well as the major pitfalls and confounders which may limit the predictive value of this model.},
	language = {eng},
	number = {47},
	journal = {Journal of Visualized Experiments: JoVE},
	author = {Engel, Odilo and Kolodziej, Sabine and Dirnagl, Ulrich and Prinz, Vincent},
	month = jan,
	year = {2011},
	pmid = {21248698},
	pmcid = {PMC3182649},
	keywords = {Animals, Brain Ischemia, Disease Models, Animal, Infarction, Middle Cerebral Artery, Mice, Middle Cerebral Artery, Silicon}
}

@article{endres_ischemia_2002,
	title = {Ischemia and stroke},
	volume = {513},
	issn = {0065-2598},
	doi = {10.1007/978-1-4615-0123-7_17},
	abstract = {Cell death following cerebral ischemia is mediated by a complex pathophysiologic interaction of different mechanisms. In this Chapter we will outline the basic principles as well as introduce in vitro and in vivo models of cerebral ischemia. Mechanistically, excitotoxicity, peri-infarct depolarization, inflammation and apoptosis seem to be the most relevant mediators of damage and are promising targets for neuroprotective strategies.},
	language = {eng},
	journal = {Advances in Experimental Medicine and Biology},
	author = {Endres, Matthias and Dirnagl, Ulrich},
	year = {2002},
	pmid = {12575832},
	keywords = {Acidosis, Animals, Apoptosis, Brain, Brain Ischemia, Caspase Inhibitors, Caspases, Disease Models, Animal, Humans, Inflammation, Necrosis, Receptors, Glutamate, Stroke, Temperature},
	pages = {455--473}
}

@article{crone_mice_2009,
	title = {In {Mice} {Lacking} {V}2a {Interneurons}, {Gait} {Depends} on {Speed} of {Locomotion}},
	volume = {29},
	copyright = {Copyright © 2009 Society for Neuroscience 0270-6474/09/297098-12\$15.00/0},
	issn = {0270-6474, 1529-2401},
	url = {https://www.jneurosci.org/content/29/21/7098},
	doi = {10.1523/JNEUROSCI.1206-09.2009},
	abstract = {Many animals are capable of changing gait with speed of locomotion. The neural basis of gait control and its dependence on speed are not fully understood. Mice normally use a single “trotting” gait while running at all speeds, either over ground or on a treadmill. Transgenic mouse mutants in which the trotting is replaced by hopping also lack a speed-dependent change in gait. Here we describe a transgenic mouse model in which the V2a interneurons have been ablated by targeted expression of diphtheria toxin A chain (DTA) under the control of the Chx10 gene promoter (Chx10::DTA mice). Chx10::DTA mice show normal trotting gait at slow speeds but transition to a galloping gait as speed increases. Although left–right limb coordination is altered in Chx10::DTA mice at fast speed, alternation of forelegs and hindlegs and the relative duration of swing and stance phases for individual limbs is unchanged compared with wild-type mice. The speed-dependent loss of left–right alternation is recapitulated during drug-induced fictive locomotion in spinal cords isolated from neonatal Chx10::DTA mice, and high-speed fictive locomotion evoked by caudal spinal cord stimulation also shows synchronous left–right bursting. These results show that spinal V2a interneurons are required for maintaining left–right alternation at high speeds. Whether animals that generate galloping or hopping gaits, characterized by synchronous movement of left and right forelegs and hindlegs, have lost or modified the function of V2a interneurons is an intriguing question.},
	language = {en},
	number = {21},
	urldate = {2019-07-28},
	journal = {Journal of Neuroscience},
	author = {Crone, Steven A. and Zhong, Guisheng and Harris-Warrick, Ronald and Sharma, Kamal},
	month = may,
	year = {2009},
	pmid = {19474336},
	pages = {7098--7109}
}

@article{solla_eliminating_1999,
	title = {Eliminating autocorrelation reduces biological relevance of home range estimates},
	volume = {68},
	issn = {1365-2656},
	url = {https://besjournals.onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-2656.1999.00279.x},
	doi = {10.1046/j.1365-2656.1999.00279.x},
	abstract = {1. Destructive subsampling or restrictive sampling are often standard procedures to obtain independence of spatial observations in home range analyses. We examined whether home range estimators based upon kernel densities require serial independence of observations, by using a Monte Carlo simulation, antler flies and snapping turtles as models. 2. Home range size, time partitioning and total straight line distances travelled were tested to determine if subsampling improved kernel performance and estimation of home range parameters. 3. The accuracy and precision of home range estimates from the simulated data set improved at shorter time intervals despite the increase in autocorrelation among the observations. 4. Subsampling did not reduce autocorrelation among locational observations of snapping turtles or antler flies, and home range size, time partitioning and total distance travelled were better represented by autocorrelated observations. 5. We found that kernel densities do not require serial independence of observations when estimating home range, and we recommend that researchers maximize the number of observations using constant time intervals to increase the accuracy and precision of their estimates.},
	language = {en},
	number = {2},
	urldate = {2021-02-13},
	journal = {Journal of Animal Ecology},
	author = {Solla, Shane R. DE and Bonduriansky, Russell and Brooks, Ronald J.},
	year = {1999},
	note = {\_eprint: https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-2656.1999.00279.x},
	keywords = {Chelydra serpentina, Monte Carlo, Protopiophila litigata, kernel density estimation, statistical independence},
	pages = {221--234},
}

@article{bothe_genetic_2004,
	title = {Genetic and behavioral differences among five inbred mouse strains commonly used in the production of transgenic and knockout mice},
	volume = {3},
	issn = {1601-183X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1601-183x.2004.00064.x},
	doi = {10.1111/j.1601-183x.2004.00064.x},
	abstract = {Five strains of mice commonly used in transgenic and knockout production were compared with regard to genetic background and behavior. These strains were: C57BL/6J, C57BL/6NTac, 129P3/J (formerly 129/J), 129S6/SvEvTac (formerly 129/SvEvTac) and FVB/NTac. Genotypes for 342 microsatellite markers and performance in three behavioral tests (rotorod, open field activity and habituation, and contextual and cued fear conditioning) were determined. C57BL/6J and C57BL/6NTac were found to be true substrains; there were only 12 microsatellite differences between them. Given the data on the genetic background, one might predict that the two C57BL/6 substrains should be very similar behaviorally. Indeed, there were no significant behavioral differences between C57BL/6J and C57BL/6NTac. Contrary to literature reports on other 129 strains, 129S6/SvEvTac often performed similarly to C57BL/6 strains, except that it was less active. FVB/NTac showed impaired rotorod learning and cued fear conditioning. Therefore, both 129S6/SvEvTac and C57BL/6 are recommended as background strains for targeted mutations when researchers want to evaluate their mice in any of these three behavior tests. However, any transgene on the FVB/NTac background should be transferred to B6. Habituation to the open field was analyzed using the parameters: total distance, center distance, velocity and vertical activity. Contrary to earlier studies, we found that all strains habituated to the open field in at least two of these parameters (center distance and velocity).},
	language = {en},
	number = {3},
	urldate = {2019-07-28},
	journal = {Genes, Brain and Behavior},
	author = {Bothe, G. W. M. and Bolivar, V. J. and Vedder, M. J. and Geistfeld, J. G.},
	year = {2004},
	keywords = {Behavior, center avoidance, contextual and cued fear conditioning, genetics, habituation, inbred strain, leaning, microsatellite, motor coordination, mouse, open-field activity, rearing, rotorod},
	pages = {149--157}
}

@article{masocha_assessment_2009,
	title = {Assessment of weight bearing changes and pharmacological antinociception in mice with {LPS}-induced monoarthritis using the {Catwalk} gait analysis system},
	volume = {85},
	issn = {1879-0631},
	doi = {10.1016/j.lfs.2009.07.015},
	abstract = {AIMS: We evaluated the possibility of using the video-based Catwalk gait analysis method to measure weight bearing changes and for testing pharmacological antinociception in freely moving mice with lipopolysaccharide (LPS)-induced monoarthritis.
MAIN METHODS: LPS or its solvent (PBS) was injected intra-articularly into the right hind (RH) limb ankle joint through the Achilles tendon of C57BL/6 mice. The Catwalk system was used to assess behavioral changes in freely moving mice. The effects of indomethacin on changes in LPS-inoculated mice were examined.
KEY FINDINGS: Mice inoculated with LPS into the RH limb showed reduced paw pressure (measured as light intensity) and print area on the RH limb, whereas they exerted more pressure with the left hind (LH) and front limbs, showing a transfer of weight bearing from RH to LH and front limbs, which was significant at 2 days post-LPS inoculation. There were no differences between the front limbs. No changes were observed in the PBS injected controls. There were no changes in interlimb coordination (regularity index) in both PBS- and LPS-injected mice. Treatment with indomethacin (10 and 100mg/kg) restored the weight bearing (measured as the ratio of the pressure exerted by the paws) and the print area ratios of LPS-inoculated mice similar to that observed in control mice.
SIGNIFICANCE: This study shows that the Catwalk gait analysis system can be used to objectively quantify LPS-induced monoarthritis weight bearing changes in all four limbs and evaluate pharmacological antinociception in freely moving mice.},
	language = {eng},
	number = {11-12},
	journal = {Life Sciences},
	author = {Masocha, Willias and Parvathy, Subramanian S. and Pavarthy, Subramanian S.},
	month = sep,
	year = {2009},
	pmid = {19683012},
	keywords = {Achilles Tendon, Analgesics, Animals, Anti-Inflammatory Agents, Non-Steroidal, Arthritis, Experimental, Foot, Functional Laterality, Gait, Hindlimb, Indomethacin, Injections, Intra-Articular, Joints, Lighting, Lipopolysaccharides, Mice, Mice, Inbred C57BL, Weight-Bearing},
	pages = {462--469}
}

@article{hampton_gait_2004,
	title = {Gait dynamics in trisomic mice: quantitative neurological traits of {Down} syndrome},
	volume = {82},
	issn = {0031-9384},
	shorttitle = {Gait dynamics in trisomic mice},
	doi = {10.1016/j.physbeh.2004.04.006},
	abstract = {The segmentally trisomic mouse Ts65Dn is a model of Down syndrome (DS). Gait abnormalities are almost universal in persons with DS. We applied a noninvasive imaging method to quantitatively compare the gait dynamics of Ts65Dn mice (n=10) to their euploid littermates (controls) (n=10). The braking duration of the hind limbs in Ts65Dn mice was prolonged compared to that in control mice (60+/-3 ms vs. 49+/-2 ms, P{\textless}.05) at a slow walking speed (18 cm/s). Stride length and stride frequency of forelimbs and hind limbs were comparable between Ts65Dn mice and control mice. Stride dynamics were significantly different in Ts65Dn mice at a faster walking speed (36 cm/s). Stride length was shorter in Ts65Dn mice (5.9+/-0.1 vs. 6.3+/-0.3 cm, P{\textless}.05), and stride frequency was higher in Ts65Dn compared to control mice (5.9+/-0.1 vs. 5.3+/-0.1 strides/s, P{\textless}.05). Hind limb swing duration was prolonged in Ts65Dn mice compared to control mice (93+/-3 vs. 76+/-3 ms, P{\textless}.05). Propulsion of the forelimbs contributed to a significantly larger percentage of stride duration in Ts65Dn mice than in control mice at the faster walking speed. Indices of gait dynamics in Ts65Dn mice correspond to previously reported findings in children with DS. The methods used in the present study provide quantitative markers for genotype and phenotype relationship studies in DS. This technique may provide opportunities for testing the efficacy of therapies for motor dysfunction in persons with DS.},
	language = {eng},
	number = {2-3},
	journal = {Physiology \& Behavior},
	author = {Hampton, Thomas G. and Stasko, Melissa R. and Kale, Ajit and Amende, Ivo and Costa, Alberto C. S.},
	month = sep,
	year = {2004},
	pmid = {15276802},
	keywords = {Animals, Disease Models, Animal, Down Syndrome, Gait, Male, Mice, Mice, Neurologic Mutants, Motor Activity, Phenotype, Reference Values},
	pages = {381--389}
}

@article{parker_gait_1980,
	title = {Gait of children with {Down} syndrome},
	volume = {61},
	issn = {0003-9993},
	language = {eng},
	number = {8},
	journal = {Archives of Physical Medicine and Rehabilitation},
	author = {Parker, A. W. and Bronks, R.},
	month = aug,
	year = {1980},
	pmid = {6447490},
	keywords = {Child, Child Development, Down Syndrome, Female, Gait, Humans, Joints, Male, Muscle Contraction},
	pages = {345--351}
}

@article{amende_gait_2005,
	title = {Gait dynamics in mouse models of {Parkinson}'s disease and {Huntington}'s disease},
	volume = {2},
	issn = {1743-0003},
	doi = {10.1186/1743-0003-2-20},
	abstract = {BACKGROUND: Gait is impaired in patients with Parkinson's disease (PD) and Huntington's disease (HD), but gait dynamics in mouse models of PD and HD have not been described. Here we quantified temporal and spatial indices of gait dynamics in a mouse model of PD and a mouse model of HD.
METHODS: Gait indices were obtained in C57BL/6J mice treated with the dopaminergic neurotoxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP, 30 mg/kg/day for 3 days) for PD, the mitochondrial toxin 3-nitropropionic acid (3NP, 75 mg/kg cumulative dose) for HD, or saline. We applied ventral plane videography to generate digital paw prints from which indices of gait and gait variability were determined. Mice walked on a transparent treadmill belt at a speed of 34 cm/s after treatments.
RESULTS: Stride length was significantly shorter in MPTP-treated mice (6.6 +/- 0.1 cm vs. 7.1 +/- 0.1 cm, P {\textless} 0.05) and stride frequency was significantly increased (5.4 +/- 0.1 Hz vs. 5.0 +/- 0.1 Hz, P {\textless} 0.05) after 3 administrations of MPTP, compared to saline-treated mice. The inability of some mice treated with 3NP to exhibit coordinated gait was due to hind limb failure while forelimb gait dynamics remained intact. Stride-to-stride variability was significantly increased in MPTP-treated and 3NP-treated mice compared to saline-treated mice. To determine if gait disturbances due to MPTP and 3NP, drugs affecting the basal ganglia, were comparable to gait disturbances associated with motor neuron diseases, we also studied gait dynamics in a mouse model of amyotrophic lateral sclerosis (ALS). Gait variability was not increased in the SOD1 G93A transgenic model of ALS compared to wild-type control mice.
CONCLUSION: The distinct characteristics of gait and gait variability in the MPTP model of Parkinson's disease and the 3NP model of Huntington's disease may reflect impairment of specific neural pathways involved.},
	language = {eng},
	journal = {Journal of Neuroengineering and Rehabilitation},
	author = {Amende, Ivo and Kale, Ajit and McCue, Scott and Glazier, Scott and Morgan, James P. and Hampton, Thomas G.},
	month = jul,
	year = {2005},
	pmid = {16042805},
	pmcid = {PMC1201165},
	pages = {20}
}

@incollection{jeung_mining_2007,
	address = {Berlin, Heidelberg},
	title = {Mining {Trajectory} {Patterns} {Using} {Hidden} {Markov} {Models}},
	volume = {4654},
	isbn = {978-3-540-74552-5 978-3-540-74553-2},
	url = {http://link.springer.com/10.1007/978-3-540-74553-2_44 https://espace.library.uq.edu.au/view/UQ:164937/MIC12UQ164937.pdf},
	booktitle = {Data {Warehousing} and {Knowledge} {Discovery}},
	publisher = {Springer Berlin Heidelberg},
	author = {Jeung, Hoyoung and Shen, Heng Tao and Zhou, Xiaofang},
	editor = {Song, Il Yeal and Eder, Johann and Nguyen, Tho Manh},
	year = {2007},
	note = {Type: Book Section},
	doi ={10.1007/978-3-540-74553-2_44},
	pages = {470--480},
}

@Article{         harris2020array,
 title         = {Array programming with {NumPy}},
 author        = {Charles R. Harris and K. Jarrod Millman and St{'{e}}fan J.
                 van der Walt and Ralf Gommers and Pauli Virtanen and David
                 Cournapeau and Eric Wieser and Julian Taylor and Sebastian
                 Berg and Nathaniel J. Smith and Robert Kern and Matti Picus
                 and Stephan Hoyer and Marten H. van Kerkwijk and Matthew
                 Brett and Allan Haldane and Jaime Fern{'{a}}ndez del
                 R{'{\i}}o and Mark Wiebe and Pearu Peterson and Pierre
                 G{'{e}}rard-Marchant and Kevin Sheppard and Tyler Reddy and
                 Warren Weckesser and Hameer Abbasi and Christoph Gohlke and
                 Travis E. Oliphant},
 year          = {2020},
 month         = sep,
 journal       = {Nature},
 volume        = {585},
 number        = {7825},
 pages         = {357--362},
 doi           = {10.1038/s41586-020-2649-2},
 publisher     = {Springer Science and Business Media {LLC}},
 url           = {https://doi.org/10.1038/s41586-020-2649-2}
}

@article{Waskom2021,
  doi = {10.21105/joss.03021},
  url = {https://doi.org/10.21105/joss.03021},
  year = {2021},
  publisher = {The Open Journal},
  volume = {6},
  number = {60},
  pages = {3021},
  author = {Michael L. Waskom},
  title = {seaborn: statistical data visualization},
  journal = {Journal of Open Source Software}
}

@Article{Hunter:2007,
  Author    = {Hunter, J. D.},
  Title     = {Matplotlib: A 2D graphics environment},
  Journal   = {Computing in Science \& Engineering},
  Volume    = {9},
  Number    = {3},
  Pages     = {90--95},
  abstract  = {Matplotlib is a 2D graphics package used for Python for
  application development, interactive scripting, and publication-quality
  image generation across user interfaces and operating systems.},
  publisher = {IEEE COMPUTER SOC},
  doi       = {10.1109/MCSE.2007.55},
  year      = 2007
}

@article{rowcliffe_bias_2012,
	title = {Bias in estimating animal travel distance: the effect of sampling frequency},
	volume = {3},
	copyright = {© 2012 The Authors. Methods in Ecology and Evolution © 2012 British Ecological Society},
	issn = {2041-210X},
	shorttitle = {Bias in estimating animal travel distance},
	url = {https://besjournals.onlinelibrary.wiley.com/doi/abs/10.1111/j.2041-210X.2012.00197.x},
	doi = {10.1111/j.2041-210X.2012.00197.x},
	abstract = {1. The distance travelled by animals is an important ecological variable that links behaviour, energetics and demography. It is usually measured by summing straight-line distances between intermittently sampled locations along continuous animal movement paths. The extent to which this approach underestimates travel distance remains a rarely addressed and unsolved problem, largely because true movement paths are rarely, if ever, available for comparison. Here, we use simulated movement paths parameterized with empirical movement data to study how estimates of distance travelled are affected by sampling frequency. 2. We used a novel method to obtain fine-scale characteristics of animal movement from camera trap videos for a set of tropical forest mammals and used these characteristics to generate detailed movement paths. We then sampled these paths at different frequencies, simulating telemetry studies, and quantified the accuracy of sampled travel distance estimation. 3. For our focal species, typical telemetry studies would underestimate distances travelled by 67–93\%, and extremely high sampling frequencies (several fixes per minute) would be required to get tolerably accurate estimates. The form of the relationship between tortuosity, sample frequency, and distance travelled was such that absolute distance cannot accurately be estimated by the infrequent samples used in typical tracking studies. 4. We conclude that the underestimation of distance travelled is a serious but underappreciated problem. Currently, there is no reliable, widely applicable method to obtain approximately unbiased estimates of distance travelled by animals. Further research on this problem is needed.},
	language = {en},
	number = {4},
	urldate = {2021-02-14},
	journal = {Methods in Ecology and Evolution},
	author = {Rowcliffe, J. Marcus and Carbone, Chris and Kays, Roland and Kranstauber, Bart and Jansen, Patrick A.},
	year = {2012},
	note = {\_eprint: https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/j.2041-210X.2012.00197.x},
	keywords = {Barro Colorado Island, camera traps, daily distance, day range, movement models, radiotracking, random walk, telemetry, travel distance, tropical forest},
	pages = {653--662},
}

@article{patterson_statistical_2017,
	title = {Statistical modelling of individual animal movement: an overview of key methods and a discussion of practical challenges},
	volume = {101},
	issn = {1863-818X},
	url = {https://doi.org/10.1007/s10182-017-0302-7},
	doi = {10.1007/s10182-017-0302-7},
	number = {4},
	journal = {AStA Advances in Statistical Analysis},
	author = {Patterson, Toby A. and Parton, Alison and Langrock, Roland and Blackwell, Paul G. and Thomas, Len and King, Ruth},
	year = {2017},
	note = {Type: Journal Article},
	pages = {399--438},
}

@article{morris_stride_1996,
	title = {Stride length regulation in {Parkinson}'s disease. {Normalization} strategies and underlying mechanisms},
	volume = {119 ( Pt 2)},
	issn = {0006-8950},
	doi = {10.1093/brain/119.2.551},
	abstract = {Results of our previous studies have shown that the slow, shuffling gait of Parkinson's disease patients is due to an inability to generate appropriate stride length and that cadence control is intact and is used as a compensatory mechanism. The reason for the reduced stride length is unclear, although deficient internal cue production or inadequate contribution to cortical motor set by the basal ganglia are two possible explanations. In this study we have examined the latter possibility by comparing the long-lasting effects of visual cues in improving stride length with that of attentional strategies. Computerized stride analysis was used to measure the spatial (distance) and temporal (timing) parameters of the walking pattern in a total of 54 subjects in three separate studies. In each study Parkinson's disease subjects were trained for 20 min by repeated 10 m walks set at control stride length (determined from control subjects matched for age, sex and height), using either visual floor markers or a mental picture of the appropriate stride size. Following training, the gait patterns were monitored (i) every 15 min for 2 h; (ii) whilst interspersing secondary tasks of increasing levels of complexity; (iii) covertly, when subjects were unaware that measurement was taking place. The results demonstrated that training with both visual cues and attentional strategies could maintain normal gait for the maximum recording time of 2 h. Secondary tasks reduced stride length towards baseline values as did covert monitoring. The findings confirm that the ability to generate a normal stepping pattern is not lost in Parkinson's disease and that gait hypokinesia reflects a difficulty in activating the motor control system. Normal stride length can be elicited in Parkinson's disease using attentional strategies and visual cues. Both strategies appear to share the same mechanism of focusing attention on the stride length. The effect of attention appears to require constant vigilance to prevent reverting to more automatic control mechanisms.},
	language = {eng},
	journal = {Brain: A Journal of Neurology},
	author = {Morris, M. E. and Iansek, R. and Matyas, T. A. and Summers, J. J.},
	month = apr,
	year = {1996},
	pmid = {8800948},
	keywords = {Aged, Aged, 80 and over, Attention, Cues, Female, Gait, Humans, Male, Middle Aged, Parkinson Disease, Time Factors},
	pages = {551--568}
}

@article{miller_locomotion_1975,
	title = {Locomotion in the cat: basic programmes of movement},
	volume = {91},
	issn = {0006-8993},
	shorttitle = {Locomotion in the cat},
	doi = {10.1016/0006-8993(75)90545-4},
	abstract = {Observations in cats of flexion and extension movements of the 4 limbs have led to the conclusion that the different forms of alternative locomotion (e.g. walking, trotting, swimming) and in-phase locomotion (galloping, jumping) result from the interaction of 'programmes' for the coordination of (1) the homologous limbs (pair of hindlimbs or pair of forelimbs) and (2) the homolateral limbs (hind- and forelimb of the same side of the body). The movements of the homologous pairs of limbs are coupled out of phase in alternate locomotion and approximately in phase in the phase form of locomotion. The movements of the homolateral pairs of limbs occur approximately out of phase in the trotting type of coupling and approximately in phase in the pacing type of coupling. Transitions between the different forms of coupling occur abruptly over 1 or 2 steps. Therefore, for each type of coupling (homologous or homolateral) there are two distinct forms or 'programmes' of movement. The hypothesis is advanced that (a) all the characteristic patterns of locomotion in the cat result from different combinations of these 'programmes' of homologous and homolateral limb coupling; (b) the 'programmes' are mutually self reinforcing in the gaits in which the coordination of the movements of the 4 limbs is bilaterally symmetrical; (c) the 'programmes' act in competition in certain gaits which are not bilaterally symmetrical giving rise at times to a changing gait pattern, and (d) the temporary dominance of one 'programme' or another can determine the gait of the particular step.},
	language = {eng},
	number = {2},
	journal = {Brain Research},
	author = {Miller, S. and Van Der Burg, J. and Van Der Meché, F.},
	month = jun,
	year = {1975},
	pmid = {1080684},
	keywords = {5-Hydroxytryptophan, Animals, Cats, Clonidine, Decerebrate State, Forelimb, Gait, Hindlimb, Levodopa, Movement, Spinal Cord, Swimming},
	pages = {239--253}
}

@article{morris_gait_2001,
	title = {Gait disorders and gait rehabilitation in {Parkinson}'s disease},
	volume = {87},
	issn = {0091-3952},
	language = {eng},
	journal = {Advances in Neurology},
	author = {Morris, M. E. and Huxham, F. E. and McGinley, J. and Iansek, R.},
	year = {2001},
	pmid = {11347239},
	keywords = {Biomechanical Phenomena, Gait, Gait Disorders, Neurologic, Humans, Parkinson Disease},
	pages = {347--361}
}

@article{barriere_prominent_2008,
	title = {Prominent role of the spinal central pattern generator in the recovery of locomotion after partial spinal cord injuries},
	volume = {28},
	issn = {1529-2401},
	doi = {10.1523/JNEUROSCI.5692-07.2008},
	abstract = {The re-expression of hindlimb locomotion after complete spinal cord injuries (SCIs) is caused by the presence of a spinal central pattern generator (CPG) for locomotion. After partial SCI, however, the role of this spinal CPG in the recovery of hindlimb locomotion in the cat remains mostly unknown. In the present work, we devised a dual-lesion paradigm to determine its possible contribution after partial SCI. After a partial section of the left thoracic segment T10 or T11, cats gradually recovered voluntary quadrupedal locomotion. Then, a complete transection was performed two to three segments more caudally (T13-L1) several weeks after the first partial lesion. Cats that received intensive treadmill training after the partial lesion expressed bilateral hindlimb locomotion within hours of the complete lesion. Untrained cats however showed asymmetrical hindlimb locomotion with the limb on the side of the partial lesion walking well before the other hindlimb. Thus, the complete spinalization revealed that the spinal CPG underwent plastic changes after the partial lesions, which were shaped by locomotor training. Over time, with further treadmill training, the asymmetry disappeared and a bilateral locomotion was reinstated. Therefore, although remnant intact descending pathways must contribute to voluntary goal-oriented locomotion after partial SCI, the recovery and re-expression of the hindlimb locomotor pattern mostly results from intrinsic changes below the lesion in the CPG and afferent inputs.},
	language = {eng},
	number = {15},
	journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience},
	author = {Barrière, Grégory and Leblond, Hugues and Provencher, Janyne and Rossignol, Serge},
	month = apr,
	year = {2008},
	pmid = {18400897},
	keywords = {Animals, Cats, Extremities, Female, Lumbar Vertebrae, Male, Motor Activity, Neuronal Plasticity, Physical Conditioning, Animal, Recovery of Function, Spinal Cord, Spinal Cord Injuries, Thoracic Vertebrae},
	pages = {3976--3987}
}

@article{cascallares_role_2018,
	title = {Role of the circadian clock in the statistics of locomotor activity in {Drosophila}.},
	volume = {13},
	url = {http://dx.doi.org/10.1371/journal.pone.0202505},
	doi = {10.1371/journal.pone.0202505},
	abstract = {In many animals the circadian rhythm of locomotor activity is controlled by an endogenous circadian clock. Using custom made housing and video tracking software in order to obtain high spatial and temporal resolution, we studied the statistical properties of the locomotor activity of wild type and two clock mutants of Drosophila melanogaster. We show here that the distributions of activity and quiescence bouts for the clock mutants in light-dark conditions (LD) are very different from the distributions obtained when there are no external cues from the environment (DD). In the wild type these distributions are very similar, showing that the clock controls this aspect of behavior in both regimes (LD and DD). Furthermore, the distributions are very similar to those reported for Wistar rats. For the timing of events we also observe important differences, quantified by how the event rate distributions scale for increasing time windows. We find that for the wild type these distributions can be rescaled by the same function in DD as in LD. Interestingly, the same function has been shown to rescale the rate distributions in Wistar rats. On the other hand, for the clock mutants it is not possible to rescale the rate distributions, which might indicate that the extent of circadian control depends on the statistical properties of activity and quiescence.},
	number = {8},
	urldate = {2019-07-12},
	journal = {Plos One},
	author = {Cascallares, Guadalupe and Riva, Sabrina and Franco, D Lorena and Risau-Gusman, Sebastian and Gleiser, Pablo M},
	month = aug,
	year = {2018},
	pmid = {30138403},
	pmcid = {PMC6107170},
	pages = {e0202505}
}

@book{batschelet_circular_1981,
	address = {London},
	title = {Circular {Statistics} {In} {Biology} (mathematics {In} {Biology})},
	isbn = {0-12-081050-6},
	urldate = {2019-07-12},
	publisher = {Academic Press},
	author = {Batschelet, Edward},
	year = {1981}
}

@article{wiesmann_specific_2017,
	title = {A specific dietary intervention to restore brain structure and function after ischemic stroke.},
	volume = {7},
	url = {http://dx.doi.org/10.7150/thno.17559},
	doi = {10.7150/thno.17559},
	abstract = {Occlusion of the middle cerebral artery (MCAo) is among the most common causes of ischemic stroke in humans. Cerebral ischemia leads to brain lesions existing of an irreversibly injured core and an ischemic boundary zone, the penumbra, containing damaged but potentially salvageable tissue. Using a transient occlusion (30 min) of the middle cerebral artery (tMCAo) mouse model in this cross-institutional study we investigated the neurorestorative efficacy of a dietary approach (Fortasyn) comprising docosahexaenoic acid, eicosapentaenoic acid, uridine, choline, phospholipids, folic acid, vitamins B12, B6, C, and E, and selenium as therapeutic approach to counteract neuroinflammation and impairments of cerebral (structural+functional) connectivity, cerebral blood flow (CBF), and motor function. Male adult C57BL/6j mice were subjected to right tMCAo using the intraluminal filament model. Following tMCAo, animals were either maintained on Control diet or switched to the multicomponent Fortasyn diet. At several time points after tMCAo, behavioral tests, and MRI and PET scanning were conducted to identify the impact of the multicomponent diet on the elicited neuroinflammatory response, loss of cerebral connectivity, and the resulting impairment of motor function after experimental stroke. Mice on the multicomponent diet showed decreased neuroinflammation, improved functional and structural connectivity, beneficial effect on CBF, and also improved motor function after tMCAo. Our present data show that this specific dietary intervention may have beneficial effects on structural and functional recovery and therefore therapeutic potential after ischemic stroke.},
	number = {2},
	urldate = {2019-03-14},
	journal = {Theranostics},
	author = {Wiesmann, Maximilian and Zinnhardt, Bastian and Reinhardt, Dirk and Eligehausen, Sarah and Wachsmuth, Lydia and Hermann, Sven and Dederen, Pieter J and Hellwich, Marloes and Kuhlmann, Michael T and Broersen, Laus M and Heerschap, Arend and Jacobs, Andreas H and Kiliaan, Amanda J},
	month = jan,
	year = {2017},
	pmid = {28255345},
	pmcid = {PMC5327363},
	pages = {493--512}
}

@article{benjamini_ten_2010,
	title = {Ten ways to improve the quality of descriptions of whole-animal movement.},
	volume = {34},
	url = {http://dx.doi.org/10.1016/j.neubiorev.2010.04.004},
	doi = {10.1016/j.neubiorev.2010.04.004},
	abstract = {The demand for replicability of behavioral results across laboratories is viewed as a burden in behavior genetics. We demonstrate how it can become an asset offering a quantitative criterion that guides the design of better ways to describe behavior. Passing the high benchmark dictated by the replicability demand requires less stressful and less restraining experimental setups, less noisy data, individually customized cutoff points between the building blocks of movement, and less variable yet discriminative dynamic representations that would capture more faithfully the nature of the behavior, unmasking similarities and differences and revealing novel animal-centered measures. Here we review ten tools that enhance replicability without compromising discrimination. While we demonstrate the usefulness of these tools in the context of inbred mouse exploratory behavior they can readily be used in any study involving a high-resolution analysis of spatial behavior. Viewing replicability as a design concept and using the ten methodological improvements may prove useful in many fields not necessarily related to spatial behavior.},
	number = {8},
	urldate = {2019-03-11},
	journal = {Neuroscience and Biobehavioral Reviews},
	author = {Benjamini, Yoav and Lipkind, Dina and Horev, Guy and Fonio, Ehud and Kafkafi, Neri and Golani, Ilan},
	month = jul,
	year = {2010},
	pmid = {20399806},
	pages = {1351--1365}
}

@article{maier_big_2017,
	title = {Big data in large-scale systemic mouse phenotyping},
	volume = {4},
	issn = {24523100},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S2452310017300525},
	doi = {10.1016/j.coisb.2017.07.012},
	abstract = {Systemic phenotyping of mutant mice has been established at large scale in the last decade as a new tool to uncover the relations between genotype, phenotype and environment. Recent advances in that field led to the generation of a valuable open access data resource that can be used to better understanding the underlying causes for human diseases. From an ethical perspective, systemic phenotyping significantly contributes to the reduction of experimental animals and the refinement of animal experiments by enforcing standardisation efforts. There are particular logistical, experimental and analytical challenges of systemic large-scale mouse phenotyping. On all levels, IT solutions are critical to implement and efficiently support breeding, phenotyping and data analysis processes that lead to the generation of high-quality systemic phenotyping data accessible for the scientific community.},
	urldate = {2019-01-13},
	journal = {Current Opinion in Systems Biology},
	author = {Maier, Holger and Leuchtenberger, Stefanie and Fuchs, Helmut and Gailus-Durner, Valerie and Hrabe de Angelis, Martin},
	month = aug,
	year = {2017},
	pages = {97--104}
}

@article{wiesmann_effect_2018,
	title = {Effect of a multinutrient intervention after ischemic stroke in female {C}57Bl/6 mice.},
	volume = {144},
	url = {http://dx.doi.org/10.1111/jnc.14213},
	doi = {10.1111/jnc.14213},
	abstract = {Stroke can affect females very differently from males, and therefore preclinical research on underlying mechanisms and the effects of interventions should not be restricted to male subjects, and treatment strategies for stroke should be tailored to benefit both sexes. Previously, we demonstrated that a multinutrient intervention (Fortasyn) improved impairments after ischemic stroke induction in male C57Bl/6 mice, but the therapeutic potential of this dietary treatment remained to be investigated in females. We now induced a transient middle cerebral artery occlusion (tMCAo) in C57Bl/6 female mice and immediately after surgery switched to either Fortasyn or an isocaloric Control diet. The stroke females performed several behavioral and motor tasks before and after tMCAo and were scanned in an 11.7 Tesla magnetic resonance imaging (MRI) scanner to assess brain perfusion, integrity, and functional connectivity. To assess brain plasticity, inflammation, and vascular integrity, immunohistochemistry was performed after killing of the mice. We found that the multinutrient intervention had diverse effects on the stroke-induced impairments in females. Similar to previous observations in male stroke mice, brain integrity, sensorimotor integration and neurogenesis benefitted from Fortasyn, but impairments in activity and motor skills were not improved in female stroke mice. Overall, Fortasyn effects in the female stroke mice seem more modest in comparison to previously investigated male stroke mice. We suggest that with further optimization of treatment protocols more information on the efficacy of specific interventions in stroked females can be gathered. This in turn will help with the development of (gender-specific) treatment regimens for cerebrovascular diseases such as stroke. This article is part of the Special Issue "Vascular Dementia". {\textbackslash}copyright 2017 International Society for Neurochemistry.},
	number = {5},
	urldate = {2019-01-13},
	journal = {Journal of Neurochemistry},
	author = {Wiesmann, Maximilian and Timmer, Nienke M and Zinnhardt, Bastian and Reinhard, Dirk and Eligehausen, Sarah and Königs, Anja and Ben Jeddi, Hasnae and Dederen, Pieter J and Jacobs, Andreas H and Kiliaan, Amanda J},
	month = mar,
	year = {2018},
	pmid = {28888042},
	pages = {549--564}
}

@article{zheng_trajectory_2015,
	title = {Trajectory {Data} {Mining}},
	volume = {6},
	issn = {21576904},
	url = {http://dl.acm.org/citation.cfm?doid=2764959.2743025},
	doi = {10.1145/2743025},
	abstract = {The advances in location-acquisition and mobile computing techniques have generated massive spatial trajectory data, which represent the mobility of a diversity of moving objects, such as people, vehicles, and animals. Many techniques have been proposed for processing, managing, and mining trajectory data in the past decade, fostering a broad range of applications. In this article, we conduct a systematic survey on the major research into trajectory data mining , providing a panorama of the field as well as the scope of its research topics. Following a road map from the derivation of trajectory data, to trajectory data preprocessing, to trajectory data management, and to a variety of mining tasks (such as trajectory pattern mining, outlier detection, and trajectory classification), the survey explores the connections, correlations, and differences among these existing techniques. This survey also introduces the methods that transform trajectories into other data formats, such as graphs, matrices, and tensors, to which more data mining and machine learning techniques can be applied. Finally, some public trajectory datasets are presented. This survey can help shape the field of trajectory data mining , providing a quick understanding of this field to the community.},
	number = {3},
	urldate = {2019-03-23},
	journal = {ACM transactions on intelligent systems and technology},
	author = {Zheng, Yu},
	month = may,
	year = {2015},
	pages = {1--41}
}

@article{valletta_applications_2017,
	title = {Applications of machine learning in animal behaviour studies},
	volume = {124},
	issn = {00033472},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0003347216303360},
	doi = {10.1016/j.anbehav.2016.12.005},
	abstract = {Highlights•Machine learning (ML) offers a hypothesis-free approach to modelling complex data.•We present a review of ML techniques pertinent to the study of animal behaviour.•Key ML approaches are illustrated using three different case studies.•ML offers a useful addition to the animal behaviourist's analytical toolbox. In many areas of animal behaviour research, improvements in our ability to collect large and detailed data sets are outstripping our ability to analyse them. These diverse, complex and often high-dimensional data sets exhibit nonlinear dependencies and unknown interactions across multiple variables, and may fail to conform to the assumptions of many classical statistical methods. The field of machine learning provides methodologies that are ideally suited to the task of extracting knowledge from these data. In this review, we aim to introduce animal behaviourists unfamiliar with machine learning (ML) to the promise of these techniques for the analysis of complex behavioural data. We start by describing the rationale behind ML and review a number of animal behaviour studies where ML has been successfully deployed. The ML framework is then introduced by presenting several unsupervised and supervised learning methods. Following this overview, we illustrate key ML approaches by developing data analytical pipelines for three different case studies that exemplify the types of behavioural and ecological questions ML can address. The first uses a large number of spectral and morphological characteristics that describe the appearance of pheasant, Phasianus colchicus, eggs to assign them to putative clutches. The second takes a continuous data stream of feeder visits from PIT (passive integrated transponder)-tagged jackdaws, Corvus monedula, and extracts foraging events from it, which permits the construction of social networks. Our final example uses aerial images to train a classifier that detects the presence of wildebeest, Connochaetes taurinus, to count individuals in a population. With the advent of cheaper sensing and tracking technologies an unprecedented amount of data on animal behaviour is becoming available. We believe that ML will play a central role in translating these data into scientific knowledge and become a useful addition to the animal behaviourist's analytical toolkit.},
	urldate = {2019-07-12},
	journal = {Animal Behaviour},
	author = {Valletta, John Joseph and Torney, Colin and Kings, Michael and Thornton, Alex and Madden, Joah},
	month = feb,
	year = {2017},
	pages = {203--220}
}

@article{brown_compass:_2016,
	title = {{COMPA}{\textbackslash}{SS}: continuous open mouse phenotyping of activity and sleep status.},
	volume = {1},
	url = {http://dx.doi.org/10.12688/wellcomeopenres.9892.2},
	doi = {10.12688/wellcomeopenres.9892.2},
	abstract = {Background Disruption of rhythms in activity and rest occur in many diseases, and provide an important indicator of healthy physiology and behaviour. However, outside the field of sleep and circadian rhythm research, these rhythmic processes are rarely measured due to the requirement for specialised resources and expertise. Until recently, the primary approach to measuring activity in laboratory rodents has been based on voluntary running wheel activity. By contrast, measuring sleep requires the use of electroencephalography (EEG), which involves invasive surgical procedures and time-consuming data analysis. Methods Here we describe a simple, non-invasive system to measure home cage activity in mice based upon passive infrared (PIR) motion sensors. Careful calibration of this system will allow users to simultaneously assess sleep status in mice. The use of open-source tools and simple sensors keeps the cost and the size of data-files down, in order to increase ease of use and uptake. Results In addition to providing accurate data on circadian activity parameters, here we show that extended immobility of {\textbackslash}textgreater40 seconds provides a reliable indicator of sleep, correlating well with EEG-defined sleep (Pearson's r {\textbackslash}textgreater0.95, 4 mice). Conclusions Whilst any detailed analysis of sleep patterns in mice will require EEG, behaviourally-defined sleep provides a valuable non-invasive means of simultaneously phenotyping both circadian rhythms and sleep. Whilst previous approaches have relied upon analysis of video data, here we show that simple motion sensors provide a cheap and effective alternative, enabling real-time analysis and longitudinal studies extending over weeks or even months. The data files produced are small, enabling easy deposition and sharing. We have named this system COMPA{\textbackslash}SS - Continuous Open Mouse Phenotyping of Activity and Sleep Status. This simple approach is of particular value in phenotyping screens as well as providing an ideal tool to assess activity and rest cycles for non-specialists.},
	urldate = {2019-03-14},
	journal = {Wellcome Open Research},
	author = {Brown, Laurence A and Hasan, Sibah and Foster, Russell G and Peirson, Stuart N},
	month = nov,
	year = {2016},
	pmid = {27976750},
	pmcid = {PMC5140024},
	pages = {2}
}

@article{dickinson_high-throughput_2016,
	title = {High-throughput discovery of novel developmental phenotypes.},
	volume = {537},
	url = {http://dx.doi.org/10.1038/nature19356},
	doi = {10.1038/nature19356},
	abstract = {Approximately one-third of all mammalian genes are essential for life. Phenotypes resulting from knockouts of these genes in mice have provided tremendous insight into gene function and congenital disorders. As part of the International Mouse Phenotyping Consortium effort to generate and phenotypically characterize 5,000 knockout mouse lines, here we identify 410 lethal genes during the production of the first 1,751 unique gene knockouts. Using a standardized phenotyping platform that incorporates high-resolution 3D imaging, we identify phenotypes at multiple time points for previously uncharacterized genes and additional phenotypes for genes with previously reported mutant phenotypes. Unexpectedly, our analysis reveals that incomplete penetrance and variable expressivity are common even on a defined genetic background. In addition, we show that human disease genes are enriched for essential genes, thus providing a dataset that facilitates the prioritization and validation of mutations identified in clinical sequencing efforts.},
	number = {7621},
	urldate = {2018-02-07},
	journal = {Nature},
	author = {Dickinson, Mary E and Flenniken, Ann M and Ji, Xiao and Teboul, Lydia and Wong, Michael D and White, Jacqueline K and Meehan, Terrence F and Weninger, Wolfgang J and Westerberg, Henrik and Adissu, Hibret and Baker, Candice N and Bower, Lynette and Brown, James M and Caddle, L Brianna and Chiani, Francesco and Clary, Dave and Cleak, James and Daly, Mark J and Denegre, James M and Doe, Brendan and Dolan, Mary E and Edie, Sarah M and Fuchs, Helmut and Gailus-Durner, Valerie and Galli, Antonella and Gambadoro, Alessia and Gallegos, Juan and Guo, Shiying and Horner, Neil R and Hsu, Chih-Wei and Johnson, Sara J and Kalaga, Sowmya and Keith, Lance C and Lanoue, Louise and Lawson, Thomas N and Lek, Monkol and Mark, Manuel and Marschall, Susan and Mason, Jeremy and McElwee, Melissa L and Newbigging, Susan and Nutter, Lauryl M J and Peterson, Kevin A and Ramirez-Solis, Ramiro and Rowland, Douglas J and Ryder, Edward and Samocha, Kaitlin E and Seavitt, John R and Selloum, Mohammed and Szoke-Kovacs, Zsombor and Tamura, Masaru and Trainor, Amanda G and Tudose, Ilinca and Wakana, Shigeharu and Warren, Jonathan and Wendling, Olivia and West, David B and Wong, Leeyean and Yoshiki, Atsushi and Consortium, International Mouse Phenotyping and Laboratory, Jackson and Infrastructure Nationale PHENOMIN, Institut Clinique de la Souris (ICS) and Laboratories, Charles River and Harwell, M. R. C. and Phenogenomics, Toronto Centre for and Institute, Wellcome Trust Sanger and Center, RIKEN BioResource and MacArthur, Daniel G and Tocchini-Valentini, Glauco P and Gao, Xiang and Flicek, Paul and Bradley, Allan and Skarnes, William C and Justice, Monica J and Parkinson, Helen E and Moore, Mark and Wells, Sara and Braun, Robert E and Svenson, Karen L and de Angelis, Martin Hrabe and Herault, Yann and Mohun, Tim and Mallon, Ann-Marie and Henkelman, R Mark and Brown, Steve D M and Adams, David J and Lloyd, K C Kent and McKerlie, Colin and Beaudet, Arthur L and Bućan, Maja and Murray, Stephen A},
	month = sep,
	year = {2016},
	pmid = {27626380},
	pmcid = {PMC5295821},
	pages = {508--514}
}

@article{pack_novel_2007,
	title = {Novel method for high-throughput phenotyping of sleep in mice.},
	volume = {28},
	url = {http://dx.doi.org/10.1152/physiolgenomics.00139.2006},
	doi = {10.1152/physiolgenomics.00139.2006},
	abstract = {Assessment of sleep in mice currently requires initial implantation of chronic electrodes for assessment of electroencephalogram (EEG) and electromyogram (EMG) followed by time to recover from surgery. Hence, it is not ideal for high-throughput screening. To address this deficiency, a method of assessment of sleep and wakefulness in mice has been developed based on assessment of activity/inactivity either by digital video analysis or by breaking infrared beams in the mouse cage. It is based on the algorithm that any episode of continuous inactivity of {\textbackslash}textgreater or =40 s is predicted to be sleep. The method gives excellent agreement in C57BL/6J male mice with simultaneous assessment of sleep by EEG/EMG recording. The average agreement over 8,640 10-s epochs in 24 h is 92\% (n = 7 mice) with agreement in individual mice being 88-94\%. Average EEG/EMG determined sleep per 2-h interval across the day was 59.4 min. The estimated mean difference (bias) per 2-h interval between inactivity-defined sleep and EEG/EMG-defined sleep was only 1.0 min (95\% confidence interval for mean bias -0.06 to +2.6 min). The standard deviation of differences (precision) was 7.5 min per 2-h interval with 95\% limits of agreement ranging from -13.7 to +15.7 min. Although bias significantly varied by time of day (P = 0.0007), the magnitude of time-of-day differences was not large (average bias during lights on and lights off was +5.0 and -3.0 min per 2-h interval, respectively). This method has applications in chemical mutagenesis and for studies of molecular changes in brain with sleep/wakefulness.},
	number = {2},
	urldate = {2019-03-14},
	journal = {Physiological Genomics},
	author = {Pack, Allan I and Galante, Raymond J and Maislin, Greg and Cater, Jacqueline and Metaxas, Dimitris and Lu, Shan and Zhang, Lin and Von Smith, Randy and Kay, Timothy and Lian, Jie and Svenson, Karen and Peters, Luanne L},
	month = jan,
	year = {2007},
	pmid = {16985007},
	pages = {232--238}
}

@article{eckel-mahan_phenotyping_2015,
	title = {Phenotyping circadian rhythms in mice.},
	volume = {5},
	url = {http://dx.doi.org/10.1002/9780470942390.mo140229},
	doi = {10.1002/9780470942390.mo140229},
	abstract = {Circadian rhythms take place with a periodicity of 24 hr, temporally following the rotation of the earth around its axis. Examples of circadian rhythms are the sleep/wake cycle, feeding, and hormone secretion. Light powerfully entrains the mammalian clock and assists in keeping animals synchronized to the 24-hour cycle of the earth by activating specific neurons in the "central pacemaker" of the brain, the suprachiasmatic nucleus. Absolute periodicity of an animal can deviate slightly from 24 hr as manifest when an animal is placed into constant dark or "free-running" conditions. Simple measurements of an organism's activity in free-running conditions reveal its intrinsic circadian period. Mice are a particularly useful model for studying circadian rhythmicity due to the ease of genetic manipulation, thus identifying molecular contributors to rhythmicity. Furthermore, their small size allows for monitoring locomotion or activity in their homecage environment with relative ease. Several tasks commonly used to analyze circadian periodicity and plasticity in mice are presented here including the process of entrainment, determination of tau (period length) in free-running conditions, determination of circadian periodicity in response to light disruption (e.g., jet lag studies), and evaluation of clock plasticity in non-24-hour conditions (T-cycles). Studying the properties of circadian periods such as their phase, amplitude, and length in response to photic perturbation, can be particularly useful in understanding how humans respond to jet lag, night shifts, rotating shifts, or other transient or chronic disruption of environmental surroundings. Copyright {\textbackslash}copyright 2015 John Wiley \& Sons, Inc.},
	number = {3},
	urldate = {2019-03-15},
	journal = {Current protocols in mouse biology},
	author = {Eckel-Mahan, Kristin and Sassone-Corsi, Paolo},
	month = sep,
	year = {2015},
	pmid = {26331760},
	pmcid = {PMC4732881},
	pages = {271--281}
}

@article{rosenthal_mouse_2007,
	title = {The mouse ascending: perspectives for human-disease models.},
	volume = {9},
	url = {http://dx.doi.org/10.1038/ncb437},
	doi = {10.1038/ncb437},
	abstract = {The laboratory mouse is widely considered the model organism of choice for studying the diseases of humans, with whom they share 99\% of their genes. A distinguished history of mouse genetic experimentation has been further advanced by the development of powerful new tools to manipulate the mouse genome. The recent launch of several international initiatives to analyse the function of all mouse genes through mutagenesis, molecular analysis and phenotyping underscores the utility of the mouse for translating the information stored in the human genome into increasingly accurate models of human disease.},
	number = {9},
	urldate = {2019-01-12},
	journal = {Nature Cell Biology},
	author = {Rosenthal, Nadia and Brown, Steve},
	month = sep,
	year = {2007},
	pmid = {17762889},
	pages = {993--999}
}

@article{noldus_ethovision:_2001,
	title = {{EthoVision}: a versatile video tracking system for automation of behavioral experiments.},
	volume = {33},
	url = {http://dx.doi.org/10.3758/BF03195394},
	doi = {10.3758/BF03195394},
	abstract = {The need for automating behavioral observations and the evolution of systems developed for that purpose is outlined. Video tracking systems enable researchers to study behavior in a reliable and consistent way and over longer time periods than if they were using manual recording. To overcome limitations of currently available systems, we have designed EthoVision, an integrated system for automatic recording of activity, movement, and interactions of animals. The EthoVision software is presented, highlighting some key features that separate EthoVision from other systems: easy file management, independent variable definition, flexible arena and zone design, several methods of data acquisition allowing identification and tracking of multiple animals in multiple arenas, and tools for visualization of the tracks and calculation of a range of analysis parameters. A review of studies using EthoVision is presented, demonstrating the system's use in a wide variety of applications. Possible future directions for development are discussed.},
	number = {3},
	urldate = {2019-07-12},
	journal = {Behavior research methods, instruments, \& computers : a journal of the Psychonomic Society, Inc},
	author = {Noldus, L P and Spink, A J and Tegelenbosch, R A},
	month = aug,
	year = {2001},
	pmid = {11591072},
	pages = {398--414}
}

@article{goulding_robust_2008,
	title = {A robust automated system elucidates mouse home cage behavioral structure.},
	volume = {105},
	issn = {1091-6490},
	url = {http://dx.doi.org/10.1073/pnas.0809053106},
	doi = {10.1073/pnas.0809053106},
	abstract = {Patterns of behavior exhibited by mice in their home cages reflect the function and interaction of numerous behavioral and physiological systems. Detailed assessment of these patterns thus has the potential to provide a powerful tool for understanding basic aspects of behavioral regulation and their perturbation by disease processes. However, the capacity to identify and examine these patterns in terms of their discrete levels of organization across diverse behaviors has been difficult to achieve and automate. Here, we describe an automated approach for the quantitative characterization of fundamental behavioral elements and their patterns in the freely behaving mouse. We demonstrate the utility of this approach by identifying unique features of home cage behavioral structure and changes in distinct levels of behavioral organization in mice with single gene mutations altering energy balance. The robust, automated, reproducible quantification of mouse home cage behavioral structure detailed here should have wide applicability for the study of mammalian physiology, behavior, and disease.},
	number = {52},
	urldate = {2019-03-11},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Goulding, Evan H and Schenk, A Katrin and Juneja, Punita and MacKay, Adrienne W and Wade, Jennifer M and Tecott, Laurence H},
	month = dec,
	year = {2008},
	pmid = {19106295},
	pmcid = {PMC2634928},
	pages = {20575--20582}
}

@article{jhuang_automated_2010,
	title = {Automated home-cage behavioural phenotyping of mice.},
	volume = {1},
	url = {http://dx.doi.org/10.1038/ncomms1064},
	doi = {10.1038/ncomms1064},
	abstract = {Neurobehavioural analysis of mouse phenotypes requires the monitoring of mouse behaviour over long periods of time. In this study, we describe a trainable computer vision system enabling the automated analysis of complex mouse behaviours. We provide software and an extensive manually annotated video database used for training and testing the system. Our system performs on par with human scoring, as measured from ground-truth manual annotations of thousands of clips of freely behaving mice. As a validation of the system, we characterized the home-cage behaviours of two standard inbred and two non-standard mouse strains. From these data, we were able to predict in a blind test the strain identity of individual animals with high accuracy. Our video-based software will complement existing sensor-based automated approaches and enable an adaptable, comprehensive, high-throughput, fine-grained, automated analysis of mouse behaviour.},
	urldate = {2019-03-11},
	journal = {Nature Communications},
	author = {Jhuang, Hueihan and Garrote, Estibaliz and Mutch, Jim and Yu, Xinlin and Khilnani, Vinita and Poggio, Tomaso and Steele, Andrew D and Serre, Thomas},
	month = sep,
	year = {2010},
	pmid = {20842193},
	pages = {68}
}

@article{casadesus_automated_2001,
	title = {Automated measurement of age-related changes in the locomotor response to environmental novelty and home-cage activity.},
	volume = {122},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/11557287},
	abstract = {The likelihood to explore in an open-field environment decreases with age. Older animals tend to be less active and explore less both in novel and home-cage environments. The locomotor performance (fine movements, ambulatory movements, and rearing) of male Fischer 344 (F344) rats that were 6 (n=6) or 22 (n=6) months of age was evaluated by continuous automated counting of photobeam interruptions, every 30 min, during 60 consecutive hours, in standard polycarbonate cages. Novel environment performance was determined by photobeam interruption counting during the first hour in the new cage. The remaining 59 h were evaluated as home-cage activity. A significant age-related decrease in ambulatory and fine motor activity was seen during the first hour of testing (novel environment). In addition, aged rats showed a decreased number of ambulatory and fine movements in home-cage activity, predominantly during the dark portion of the light cycle and during or around both light-switch periods (05:00 and 17:00). No differences were seen in rearing behavior. These findings provide a more detailed analysis and additional evidence of the activity decreases and rhythmic changes seen in aged F344 rats under uninterrupted testing conditions.},
	number = {15},
	urldate = {2019-07-12},
	journal = {Mechanisms of Ageing and Development},
	author = {Casadesus, G and Shukitt-Hale, B and Joseph, J A},
	month = oct,
	year = {2001},
	pmid = {11557287},
	pages = {1887--1897},
	doi ={10.1016/s0047-6374(01)00324-4 },
}

@article{crawley_behavioral_2008,
	title = {Behavioral phenotyping strategies for mutant mice.},
	volume = {57},
	url = {http://dx.doi.org/10.1016/j.neuron.2008.03.001},
	doi = {10.1016/j.neuron.2008.03.001},
	abstract = {Comprehensive behavioral analyses of transgenic and knockout mice have successfully identified the functional roles of many genes in the brain. Over the past 10 years, strategies for mouse behavioral phenotyping have evolved to maximize the scope and replicability of findings from a cohort of mutant mice, minimize the interpretation of procedural artifacts, and provide robust translational tools to test hypotheses and develop treatments. This Primer addresses experimental design issues and offers examples of high-throughput batteries, learning and memory tasks, and anxiety-related tests.},
	number = {6},
	urldate = {2019-03-14},
	journal = {Neuron},
	author = {Crawley, Jacqueline N},
	month = mar,
	year = {2008},
	pmid = {18367082},
	pages = {809--818}
}

@article{tester_arm_2012,
	title = {Arm and leg coordination during treadmill walking in individuals with motor incomplete spinal cord injury: a preliminary study.},
	volume = {36},
	url = {http://dx.doi.org/10.1016/j.gaitpost.2012.01.004},
	doi = {10.1016/j.gaitpost.2012.01.004},
	abstract = {Arm and leg coordination naturally emerges during walking, but can be affected by stroke or Parkinson's disease. The purpose of this preliminary study was to characterize arm and leg coordination during treadmill walking at self-selected comfortable walking speeds (CWSs) in individuals using arm swing with motor incomplete spinal cord injury (iSCI). Hip and shoulder angle cycle durations and amplitudes, strength of peak correlations between contralateral hip and shoulder joint angle time series, the time shifts at which these peak correlations occur, and associated variability were quantified. Outcomes in individuals with iSCI selecting fast CWSs (range, 1.0-1.3m/s) and speed-matched individuals without neurological injuries are similar. Differences, however, are detected in individuals with iSCI selecting slow CWSs (range, 0.25-0.65 m/s) and may represent compensatory strategies to improve walking balance or forward propulsion. These individuals elicit a 1:1, arm:leg frequency ratio versus the 2:1 ratio observed in non-injured individuals. Shoulder and hip movement patterns, however, are highly reproducible (coordinated) in participants with iSCI, regardless of CWS. This high degree of inter-extremity coordination could reflect an inability to modify a single movement pattern post-iSCI. Combined, these data suggest inter-extremity walking coordination may be altered, but is present after iSCI, and therefore may be regulated, in part, by neural control. Published by Elsevier B.V.},
	number = {1},
	urldate = {2019-07-26},
	journal = {Gait \& Posture},
	author = {Tester, Nicole J and Barbeau, Hugues and Howland, Dena R and Cantrell, Amy and Behrman, Andrea L},
	month = may,
	year = {2012},
	pmid = {22341058},
	pmcid = {PMC3362672},
	pages = {49--55}
}

@article{tester_device_2011,
	title = {Device use, locomotor training and the presence of arm swing during treadmill walking after spinal cord injury.},
	volume = {49},
	url = {http://dx.doi.org/10.1038/sc.2010.128},
	doi = {10.1038/sc.2010.128},
	abstract = {STUDY DESIGN: Observational, cross-sectional study from a convenience sample with pretest/posttest data from a sample subset. OBJECTIVES: Determine the presence of walking-related arm swing after spinal cord injury (SCI), its associated factors and whether arm swing may change after locomotor training (LT). SETTING: Malcom Randall VAMC and University of Florida, Gainesville, FL. METHODS: Arm movement was assessed during treadmill stepping, pre-LT, in 30 individuals with motor incomplete SCI (iSCI, American Spinal Injury Association Impairment Scale grade C/D, as defined by the International Standards for Neurological Classifications of SCI, with neurological level of impairment at or below C4). Partial body weight support and manual-trainer assistance were provided, as needed, to achieve stepping and allow arm swing. Arm swing presence was compared on the basis of cervical versus thoracic neurological levels of impairment and device type. Leg and arm strength and walking independence were compared between individuals with and without arm swing. Arm swing was reevaluated post-LT in the 21 out of 30 individuals who underwent LT. RESULTS: Of 30 individuals with iSCI, 12 demonstrated arm swing during treadmill stepping, pre-LT. Arm movement was associated with device type, lower extremity motor scores and walking independence. Among the 21 individuals who received LT, only 5 demonstrated arm swing pre-LT. Of the 16 individuals lacking arm swing pre-LT, 8 integrated arm swing post-LT. CONCLUSION: Devices routinely used for walking post-iSCI appeared associated with arm swing. Post-LT, arm swing presence increased. Therefore, arm swing may be experience dependent. Daily neuromuscular experiences provided to the arms may produce training effects, thereby altering arm swing expression.},
	number = {3},
	urldate = {2019-07-26},
	journal = {Spinal Cord},
	author = {Tester, N J and Howland, D R and Day, K V and Suter, S P and Cantrell, A and Behrman, A L},
	month = mar,
	year = {2011},
	pmid = {20938449},
	pmcid = {PMC3021654},
	pages = {451--456}
}

@article{masocha_assessment_2009,
	title = {Assessment of weight bearing changes and pharmacological antinociception in mice with {LPS}-induced monoarthritis using the {Catwalk} gait analysis system.},
	volume = {85},
	url = {http://dx.doi.org/10.1016/j.lfs.2009.07.015},
	doi = {10.1016/j.lfs.2009.07.015},
	abstract = {AIMS: We evaluated the possibility of using the video-based Catwalk gait analysis method to measure weight bearing changes and for testing pharmacological antinociception in freely moving mice with lipopolysaccharide (LPS)-induced monoarthritis. MAIN METHODS: LPS or its solvent (PBS) was injected intra-articularly into the right hind (RH) limb ankle joint through the Achilles tendon of C57BL/6 mice. The Catwalk system was used to assess behavioral changes in freely moving mice. The effects of indomethacin on changes in LPS-inoculated mice were examined. KEY FINDINGS: Mice inoculated with LPS into the RH limb showed reduced paw pressure (measured as light intensity) and print area on the RH limb, whereas they exerted more pressure with the left hind (LH) and front limbs, showing a transfer of weight bearing from RH to LH and front limbs, which was significant at 2 days post-LPS inoculation. There were no differences between the front limbs. No changes were observed in the PBS injected controls. There were no changes in interlimb coordination (regularity index) in both PBS- and LPS-injected mice. Treatment with indomethacin (10 and 100mg/kg) restored the weight bearing (measured as the ratio of the pressure exerted by the paws) and the print area ratios of LPS-inoculated mice similar to that observed in control mice. SIGNIFICANCE: This study shows that the Catwalk gait analysis system can be used to objectively quantify LPS-induced monoarthritis weight bearing changes in all four limbs and evaluate pharmacological antinociception in freely moving mice.},
	number = {11-12},
	urldate = {2019-07-26},
	journal = {Life Sciences},
	author = {Masocha, Willias and Parvathy, Subramanian S},
	month = sep,
	year = {2009},
	pmid = {19683012},
	pages = {462--469}
}

@article{lemieux_speed-dependent_2016,
	title = {Speed-{Dependent} {Modulation} of the {Locomotor} {Behavior} in {Adult} {Mice} {Reveals} {Attractor} and {Transitional} {Gaits}.},
	volume = {10},
	url = {http://dx.doi.org/10.3389/fnins.2016.00042},
	doi = {10.3389/fnins.2016.00042},
	abstract = {Locomotion results from an interplay between biomechanical constraints of the muscles attached to the skeleton and the neuronal circuits controlling and coordinating muscle activities. Quadrupeds exhibit a wide range of locomotor gaits. Given our advances in the genetic identification of spinal and supraspinal circuits important to locomotion in the mouse, it is now important to get a better understanding of the full repertoire of gaits in the freely walking mouse. To assess this range, young adult C57BL/6J mice were trained to walk and run on a treadmill at different locomotor speeds. Instead of using the classical paradigm defining gaits according to their footfall pattern, we combined the inter-limb coupling and the duty cycle of the stance phase, thus identifying several types of gaits: lateral walk, trot, out-of-phase walk, rotary gallop, transverse gallop, hop, half-bound, and full-bound. Out-of-phase walk, trot, and full-bound were robust and appeared to function as attractor gaits (i.e., a state to which the network flows and stabilizes) at low, intermediate, and high speeds respectively. In contrast, lateral walk, hop, transverse gallop, rotary gallop, and half-bound were more transient and therefore considered transitional gaits (i.e., a labile state of the network from which it flows to the attractor state). Surprisingly, lateral walk was less frequently observed. Using graph analysis, we demonstrated that transitions between gaits were predictable, not random. In summary, the wild-type mouse exhibits a wider repertoire of locomotor gaits than expected. Future locomotor studies should benefit from this paradigm in assessing transgenic mice or wild-type mice with neurotraumatic injury or neurodegenerative disease affecting gait.},
	urldate = {2019-07-26},
	journal = {Frontiers in Neuroscience},
	author = {Lemieux, Maxime and Josset, Nicolas and Roussel, Marie and Couraud, Sébastien and Bretzner, Frédéric},
	month = feb,
	year = {2016},
	pmid = {26941592},
	pmcid = {PMC4763020},
	pages = {42}
}

@article{aragao_automatic_2011,
	title = {Automatic system for analysis of locomotor activity in rodents–a reproducibility study.},
	volume = {195},
	url = {http://dx.doi.org/10.1016/j.jneumeth.2010.12.016},
	doi = {10.1016/j.jneumeth.2010.12.016},
	abstract = {Automatic analysis of locomotion in studies of behavior and development is of great importance because it eliminates the subjective influence of evaluators on the study. This study aimed to develop and test the reproducibility of a system for automated analysis of locomotor activity in rats. For this study, 15 male Wistar were evaluated at P8, P14, P17, P21, P30 and P60. A monitoring system was developed that consisted of an open field of 1m in diameter with a black surface, an infrared digital camera and a video capture card. The animals were filmed for 2 min as they moved freely in the field. The images were sent to a computer connected to the camera. Afterwards, the videos were analyzed using software developed using MATLAB® (mathematical software). The software was able to recognize the pixels constituting the image and extract the following parameters: distance traveled, average speed, average potency, time immobile, number of stops, time spent in different areas of the field and time immobile/number of stops. All data were exported for further analysis. The system was able to effectively extract the desired parameters. Thus, it was possible to observe developmental changes in the patterns of movement of the animals. We also discuss similarities and differences between this system and previously described systems. {\textbackslash}copyright 2010 Elsevier B.V. All rights reserved.},
	number = {2},
	urldate = {2019-07-26},
	journal = {Journal of Neuroscience Methods},
	author = {Aragão, Raquel da Silva and Rodrigues, Marco Aurélio Benedetti and de Barros, Karla Mônica Ferraz Teixeira and Silva, Sebastião Rogério Freitas and Toscano, Ana Elisa and de Souza, Ricardo Emmanuel and Manhães-de-Castro, Raul},
	month = feb,
	year = {2011},
	pmid = {21182870},
	pages = {216--221}
}

@article{park_method_2014,
	title = {A method for generating a mouse model of stroke: evaluation of parameters for blood flow, behavior, and survival [corrected].},
	volume = {23},
	url = {http://dx.doi.org/10.5607/en.2014.23.1.104},
	doi = {10.5607/en.2014.23.1.104},
	abstract = {Stroke is one of the common causes of death and disability. Despite extensive efforts in stroke research, therapeutic options for improving the functional recovery remain limited in clinical practice. Experimental stroke models using genetically modified mice could aid in unraveling the complex pathophysiology triggered by ischemic brain injury. Here, we optimized the procedure for generating mouse stroke model using an intraluminal suture in the middle cerebral artery and verified the blockage of blood flow using indocyanine green coupled with near infra-red radiation. The first week after the ischemic injury was critical for survivability. The survival rate of 11\% in mice without any treatment but increased to 60\% on administering prophylactic antibiotics. During this period, mice showed severe functional impairment but recovered spontaneously starting from the second week onward. Among the various behavioral tests, the pole tests and neurological severity score tests remained reliable up to 4 weeks after ischemia, whereas the rotarod and corner tests became less sensitive for assessing the severity of ischemic injury with time. Further, loss of body weight was also observed for up 4 weeks after ischemia induction. In conclusion, we have developed an improved approach which allows us to investigate the role of the cell death-related genes in the disease progression using genetically modified mice and to evaluate the modes of action of candidate drugs.},
	number = {1},
	urldate = {2019-07-26},
	journal = {Experimental neurobiology},
	author = {Park, Sin-Young and Marasini, Subash and Kim, Geu-Hee and Ku, Taeyun and Choi, Chulhee and Park, Min-Young and Kim, Eun-Hee and Lee, Young-Don and Suh-Kim, Haeyoung and Kim, Sung-Soo},
	month = mar,
	year = {2014},
	pmid = {24737945},
	pmcid = {PMC3984953},
	pages = {104--114}
}

@article{bailoo_precision_2010,
	title = {The precision of video and photocell tracking systems and the elimination of tracking errors with infrared backlighting.},
	volume = {188},
	url = {http://dx.doi.org/10.1016/j.jneumeth.2010.01.035},
	doi = {10.1016/j.jneumeth.2010.01.035},
	abstract = {Automated tracking offers a number of advantages over both manual and photocell tracking methodologies, including increased reliability, validity, and flexibility of application. Despite the advantages that video offers, our experience has been that video systems cannot track a mouse consistently when its coat color is in low contrast with the background. Furthermore, the local lab lighting can influence how well results are quantified. To test the effect of lighting, we built devices that provide a known path length for any given trial duration, at a velocity close to the average speed of a mouse in the open-field and the circular water maze. We found that the validity of results from two commercial video tracking systems (ANY-maze and EthoVision XT) depends greatly on the level of contrast and the quality of the lighting. A photocell detection system was immune to lighting problems but yielded a path length that deviated from the true length. Excellent precision was achieved consistently, however, with video tracking using infrared backlighting in both the open field and water maze. A high correlation (r=0.98) between the two software systems was observed when infrared backlighting was used with live mice. Copyright 2010 Elsevier B.V. All rights reserved.},
	number = {1},
	urldate = {2019-07-26},
	journal = {Journal of Neuroscience Methods},
	author = {Bailoo, Jeremy D and Bohlen, Martin O and Wahlsten, Douglas},
	month = apr,
	year = {2010},
	pmid = {20138914},
	pmcid = {PMC2847046},
	pages = {45--52}
}

@article{samson_mousemove:_2015,
	title = {{MouseMove}: an open source program for semi-automated analysis of movement and cognitive testing in rodents.},
	volume = {5},
	url = {http://dx.doi.org/10.1038/srep16171},
	doi = {10.1038/srep16171},
	abstract = {The Open Field (OF) test is one of the most commonly used assays for assessing exploratory behaviour and generalised locomotor activity in rodents. Nevertheless, the vast majority of researchers still rely upon costly commercial systems for recording and analysing OF test results. Consequently, our aim was to design a freely available program for analysing the OF test and to provide an accompanying protocol that was minimally invasive, rapid, unbiased, without the need for specialised equipment or training. Similar to commercial systems, we show that our software-called MouseMove-accurately quantifies numerous parameters of movement including travel distance, speed, turning and curvature. To assess its utility, we used MouseMove to quantify unilateral locomotor deficits in mice following the filament-induced middle cerebral artery occlusion model of acute ischemic stroke. MouseMove can also monitor movement within defined regions-of-interest and is therefore suitable for analysing the Novel Object Recognition test and other field-related cognitive tests. To the best of our knowledge, MouseMove is the first open source software capable of providing qualitative and quantitative information on mouse locomotion in a semi-automated and high-throughput fashion, and hence MouseMove represents a sound alternative to commercial movement analysis systems.},
	urldate = {2017-04-10},
	journal = {Scientific reports},
	author = {Samson, Andre L and Ju, Lining and Ah Kim, Hyun and Zhang, Shenpeng R and Lee, Jessica A A and Sturgeon, Sharelle A and Sobey, Christopher G and Jackson, Shaun P and Schoenwaelder, Simone M},
	month = nov,
	year = {2015},
	pmid = {26530459},
	pmcid = {PMC4632026},
	pages = {16171}
}

@book{bishop_pattern_2006,
	address = {New York},
	series = {Information {Science} and {Statistics}},
	title = {Pattern {Recognition} and {Machine} {Learning}},
	isbn = {978-0-387-31073-2},
	url = {https://www.springer.com/de/book/9780387310732},
	abstract = {The dramatic growth in practical applications for machine learning over the last ten years has been accompanied by many important developments in the underlying algorithms and techniques. For example, Bayesian methods have grown from a specialist niche to become mainstream, while graphical models have emerged as a general framework for describing and applying probabilistic techniques. The practical applicability of Bayesian methods has been greatly enhanced by the development of a range of approximate inference algorithms such as variational Bayes and expectation propagation, while new models based on kernels have had a significant impact on both algorithms and applications. This completely new textbook reflects these recent developments while providing a comprehensive introduction to the fields of pattern recognition and machine learning. It is aimed at advanced undergraduates or first-year PhD students, as well as researchers and practitioners. No previous knowledge of pattern recognition or machine learning concepts is assumed. Familiarity with multivariate calculus and basic linear algebra is required, and some experience in the use of probabilities would be helpful though not essential as the book includes a self-contained introduction to basic probability theory. The book is suitable for courses on machine learning, statistics, computer science, signal processing, computer vision, data mining, and bioinformatics. Extensive support is provided for course instructors, including more than 400 exercises, graded according to difficulty. Example solutions for a subset of the exercises are available from the book web site, while solutions for the remainder can be obtained by instructors from the publisher. The book is supported by a great deal of additional material, and the reader is encouraged to visit the book web site for the latest information. Christopher M. Bishop is Deputy Director of Microsoft Research Cambridge, and holds a Chair in Computer Science at the University of Edinburgh. He is a Fellow of Darwin College Cambridge, a Fellow of the Royal Academy of Engineering, and a Fellow of the Royal Society of Edinburgh. His previous textbook "Neural Networks for Pattern Recognition" has been widely adopted. Coming soon: *For students, worked solutions to a subset of exercises available on a public web site (for exercises marked "www" in the text) *For instructors, worked solutions to remaining exercises from the Springer web site *Lecture slides to accompany each chapter *Data sets available for download},
	language = {en},
	urldate = {2020-06-28},
	publisher = {Springer-Verlag},
	author = {Bishop, Christopher},
	year = {2006},
}

@misc{bosch_engineering_2021,
	type = {chapter},
	title = {Engineering {AI} {Systems}: {A} {Research} {Agenda}},
	copyright = {Access limited to members},
	shorttitle = {Engineering {AI} {Systems}},
	url = {www.igi-global.com/chapter/engineering-ai-systems/266130},
	abstract = {Artificial intelligence (AI) and machine learning (ML) are increasingly broadly adopted in industry. However, based on well over a dozen case studies, we have learned that deploying industry-strength, production quality ML models in systems proves to be challenging. Companies experience challenges r...},
	language = {en},
	urldate = {2021-02-02},
	journal = {Artificial Intelligence Paradigms for Smart Cyber-Physical Systems},
	author = {Bosch, Jan and Olsson, Helena Holmström and Crnkovic, Ivica},
	year = {2021},
	doi = {10.4018/978-1-7998-5101-1.ch001},
	note = {ISBN: 9781799851011
Pages: 1-19
Publisher: IGI Global},
}

@article{shenk_automated_2020,
	title = {Automated {Analysis} of {Stroke} {Mouse} {Trajectory} {Data} {With} {Traja}},
	volume = {14},
	issn = {1662-453X},
	url = {https://www.frontiersin.org/articles/10.3389/fnins.2020.00518/full},
	doi = {10.3389/fnins.2020.00518},
	abstract = {Quantitative characterization of mouse activity, locomotion and walking patterns requires the monitoring of position and activity over long periods of time. Manual behavioral phenotyping, however, is time and skill-intensive, vulnerable to researcher bias and often stressful for the animals. We present examples for using a platform-independent open source trajectory analysis software, Traja, for semi-automated analysis of high throughput mouse home-cage data for neurobehavioral research. Our software quantifies numerous parameters of movement including travelled distance, velocity, turnings, and laterality which are demonstrated for application to neurobehavioral analysis. In this study, the open source software for trajectory analysis Traja is applied to movement and walking pattern observations of transient stroke induced female C57BL/6 mice (30 min middle cerebral artery occlusion) on an acute multinutrient diet intervention (Fortasyn). Mice were housed individually in Digital Ventilated Cages (DVC, GM500, Tecniplast S.p.A., Buguggiate (VA), Italy) and activity was recorded 24/7, every 250 ms using a DVC board. Significant changes in activity, velocity, and distance walked are computed with Traja. Traja identified increased walked distance and velocity in Control and Fortasyn animals over time. No diet effect was found in preference of turning direction (laterality) and distance travelled. As open source software for trajectory analysis, Traja supports independent development and validation of numerical methods and provides a useful tool for computational analysis of 24/7 mouse locomotion in home-cage environment for application in behavioral research or movement disorders.},
	language = {English},
	urldate = {2020-12-21},
	journal = {Frontiers in Neuroscience},
	author = {Shenk, Justin and Lohkamp, Klara J. and Wiesmann, Maximilian and Kiliaan, Amanda J.},
	year = {2020},
	note = {Publisher: Frontiers},
	keywords = {animal tracking, Home-cage, machine learning, Mouse, neuropsychiatric disorders, Stroke},
	file = {Full Text PDF:C\:\\Users\\hpaye\\Zotero\\storage\\IBNLUH9P\\Shenk et al. - 2020 - Automated Analysis of Stroke Mouse Trajectory Data.pdf:application/pdf},
}

@misc{shenk_towards_2020,
	title = {Towards {Explainable} {AI} with {Feature} {Space} {Exploration}},
	url = {https://towardsdatascience.com/towards-explainable-ai-with-feature-space-exploration-628930baf8ef},
	abstract = {Neural networks trained on large amounts of data have led to incredible technological leaps affecting nearly every part of our lives.},
	language = {en},
	urldate = {2021-02-08},
	journal = {Medium},
	author = {Shenk, Justin},
	month = jun,
	year = {2020},
}

@book{grus_data_2015,
	address = {Beijing},
	title = {Data {Science} from {Scratch}: {First} {Principles} with {Python}},
	isbn = {978-1-4919-0142-7},
	url = {http://my.safaribooksonline.com/97814919-01427},
	abstract = {Data science libraries, frameworks, modules, and toolkits are great for doing data science, but they're also a good way to dive into the discipline without actually understanding data science. In this book, you'll learn how many of the most fundamental data science tools and algorithms work by implementing them from scratch. If you have an aptitude for mathematics and some programming skills, author Joel Grus will help you get comfortable with the math and statistics at the core of data science, and with hacking skills you need to get started as a data scientist.},
	publisher = {O'Reilly},
	author = {Grus, Joel},
	year = {2015},
	keywords = {01624 103 safari book ai software development data pattern recognition analysis python},
}

@article{chandra_traphic_2019,
	title = {{TraPHic}: {Trajectory} {Prediction} in {Dense} and {Heterogeneous} {Traffic} {Using} {Weighted} {Interactions}},
	url = {http://arxiv.org/abs/1812.04767 https://arxiv.org/abs/1812.04767},
	journal = {arXiv:1812.04767 [cs]},
	author = {Chandra, Rohan and Bhattacharya, Uttaran and Bera, Aniket and Manocha, Dinesh},
	year = {2019},
	doi = {10.1109/cvpr.2019.00868},
	note = {Type: Journal Article},
}
