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Point process latent variable models of larval zebrafish behavior

Anuj Sharma, Robert Johnson, Florian Engert, Scott W. Linderman
2018 Neural Information Processing Systems  
We incorporate these variables as latent marks of a point process and explore various models for their dynamics.  ...  Larval zebrafish locomote via sequences of punctate swim bouts-brief flicks of the tail-which are naturally modeled as a marked point process.  ...  FE received funding from the National Institutes of Health's Brain Initiative U19NS104653, R24NS086601 and R43OD024879, as well as Simons Foundation grants (SCGB-542973 and 325207).  ... 
dblp:conf/nips/SharmaJEL18 fatcat:wjkyzukogze6fg5h6l36ztdyoa

Stressing zebrafish for behavioral genetics

Karl J. Clark, Nicole J. Boczek, Stephen C. Ekker
2011 Reviews in the Neurosciences  
More recently, the stress response of larval and adult zebrafish has been documented. High-throughput automated tracking systems make possible behavioral readouts of the stress response in zebrafish.  ...  The zebrafish (Danio rerio) is a major model organism with a strong record for use in developmental biology, genetic screening, and genomic studies.  ...  zebrafish behavioral assays Listed are data end points, experimental variables, and references of behavioral assays that could be adapted to look at stress responses in larval zebrafish. • Path of Travel  ... 
doi:10.1515/rns.2011.007 pmid:21615261 pmcid:PMC3470424 fatcat:lcvquh7ukzh2lpgrnb67fy6e5u

Dimensionality reduction of calcium-imaged neuronal population activity [article]

Tze Hui Koh, William E. Bishop, Takashi Kawashima, Brian B. Jeon, Ranjani Srinivasan, Sandra J. Kuhlman, Misha B. Ahrens, Steven M. Chase, Byron M. Yu
2022 bioRxiv   pre-print
CILDS also outperformed the other methods on calcium imaging recordings from larval zebrafish and mice.  ...  We thus carried out a systematic study of design choices based on standard dimensionality reduction methods.  ...  For the larval zebrafish recordings, there is no moment by moment behavior that can be decoded from the neural activity.  ... 
doi:10.1101/2022.03.11.480682 fatcat:icd4swqcd5fc3h7e6oxprc6roy

Collective behavior emerges from genetically controlled simple behavioral motifs in zebrafish [article]

Ariel Cacayuran Aspiras, Roy Harpaz, Sydney Chambule, Sierra Tseng, Florian Engert, Mark C Fishman, Armin Bahl
2021 bioRxiv   pre-print
We analyze how mutations in genes known to affect social behavior of humans perturb these simple reflexes in larval zebrafish and thereby affect their collective behaviors.  ...  Here we find that even at the early larval stage, zebrafish regulate their proximity and alignment with each other.  ...  permits modeling of latent, or hidden, 298 variables in wild-type and mutant fish.  ... 
doi:10.1101/2021.03.03.433803 fatcat:i6sisqr2rzajvc2vzlejoyntpm

Position- and quantity-dependent responses in zebrafish turning behavior

Keiko Umeda, Toru Ishizuka, Hiromu Yawo, Wataru Shoji
2016 Scientific Reports  
We report herein that zebrafish larval C-shaped turning is modulated by the stimulated position of Rohon-Beard (RB) neurons.  ...  Our results suggest that RB neurons transmit the position and quantity of sensory information, which are then processed separately to modulate behavioral strength and to select turning laterality.  ...  Anterograde labeling of RB central axons.  ... 
doi:10.1038/srep27888 pmid:27292818 pmcid:PMC4904276 fatcat:red5bp5nr5a65pntw7iyihvlze

Collective behavior emerges from genetically controlled simple behavioral motifs in zebrafish

Roy Harpaz, Ariel C Aspiras, Sydney Chambule, Sierra Tseng, Marie-Abèle Bind, Florian Engert, Mark C Fishman, Armin Bahl
2021 Science Advances  
RESULTS Visually driven aggregation and alignment in larval and juvenile zebrafish We examined the behavior of wild-type larval zebrafish in groups of five, swimming together in a circular arena, where  ...  DDM parameters extracted from motion integration assay Knowing that our multiobjective fitting algorithm can reveal the latent variables in our DDM, we next applied this strategy to real experimental behavioral  ... 
doi:10.1126/sciadv.abi7460 pmid:34613782 pmcid:PMC8494438 fatcat:gt2htwyefrh5norlzxlrabymmi

Probabilistic Models of Larval Zebrafish Behavior: Structure on Many Scales [article]

Robert Evan Johnson, Scott Linderman, Thomas Panier, Caroline Lei Wee, Erin Song, Kristian Joseph Herrera, Andrew Miller, Florian Engert
2019 bioRxiv   pre-print
Our simulations capture multiple timescales of structure in larval zebrafish behavior and expose many ways in which hunger state influences their action selection to promote food seeking during hunger  ...  Here, we collect high spatial resolution video of single zebrafish larvae swimming in a naturalistic environment and develop models of their action selection across exploration and hunting.  ...  We thank Ed Soucy, Joel Greenwood, and Adam Bercu of the Harvard Center for Brain Science Neuroengineering Core for technical support.  ... 
doi:10.1101/672246 fatcat:bykexdsk5vhe3hnnj56pttxmqi

Not so spontaneous: Multi-dimensional representations of behaviors and context in sensory areas

Lilach Avitan, Carsen Stringer
2022 Neuron  
Studies using these recordings have discovered high-dimensional spontaneous activity patterns, correlation between spontaneous activity and behavior, and dissimilarity between spontaneous and sensory-driven  ...  These newly revealed characteristics call for the formulation of a new role for spontaneous activity in neural sensory computation.  ...  The dimensionality of the neural activity d is often set as the number of latent variables required to explain a desired faction of neural variance.  ... 
doi:10.1016/j.neuron.2022.06.019 pmid:35863344 fatcat:gqh7gcfjdfaubcl53ovcdcxt74

A metabolomic study of fipronil for the anxiety-like behavior in zebrafish larvae at environmentally relevant levels

Cui Wang, Yi Qian, Xiaofeng Zhang, Fang Chen, Quan Zhang, Zhuoyu Li, Meirong Zhao
2016 Environmental Pollution  
Manipulating by video track, we observed an anxiety-like behavior including high speed and abnormal photoperiod accommodation after exposure to fipronil at environmental typical dose in zebrafish larvae  ...  Additionally, the body burden of neurotransmitter such as glycine and L-glutamate may concurrently stimulate the swimming behavior.  ...  component of OPLS model.  ... 
doi:10.1016/j.envpol.2016.01.016 pmid:26774772 fatcat:27iytsbljneibduti3k2auw4v4

A lexical approach for identifying behavioral action sequences [article]

Gautam Reddy, Laura Desban, Hidenori Tanaka, Julian Roussel, Claire Wyart
2020 bioRxiv   pre-print
When applied to navigating larval zebrafish, BASS extracts a dictionary of remarkably long, non-Markovian sequences consisting of repeats and mixtures of slow forward and turn bouts.  ...  To fill this gap, we develop a lexical, hierarchical model of behavior.  ...  that were not modeled previously: elevating motif templates to latent variables and introducing a data-generating process for elementary locomotor episodes.  ... 
doi:10.1101/2020.08.27.270694 fatcat:czptgqa77regtj2vdp5xjrug3m

Tracking Multiple Indistinguishable and Deformable Objects Based on Multi-Anchor Flow with Annular Sector Model

Biao Guo, Yuesheng Zhu
2019 IEEE Access  
The multi-anchor flow is built on anchor points which are extracted from the union contours of deformable objects.  ...  In this paper, a novel method based on multi-anchor flow with annular sector model (ASM) is proposed to handle occlusions and complex motions for tracking multiple of these kinds of objects.  ...  But the complexity of this approach explodes with the number of objects and frames because of the latent variables are combined with the intensity flows of pixels. Michels et al.  ... 
doi:10.1109/access.2019.2952598 fatcat:7gc4rdfnwre5rf7htdkarfaqsi

Developmental exposure to a POPs mixture or PFOS increased body weight and reduced swimming ability but had no effect on reproduction or behavior in zebrafish adults

Maria Christou, Erik Ropstad, Stephen Brown, Jorke H. Kamstra, Thomas W.K. Fraser
2021 Aquatic Toxicology  
are known to affect larval behavior.  ...  In addition, we assessed anxiety behavior of the adults and their offspring, as well as performing a transcriptomic analysis on the adult zebrafish brain, as the POP mixture and PFOS concentrations used  ...  Acknowledgments The authors thank Arturas Kavaliauskis, Carina Berentsen and the weekend staff for the husbandry and maintenance of fish populations.  ... 
doi:10.1016/j.aquatox.2021.105882 pmid:34139397 fatcat:w37gzg5ml5a3zp7i3aak7t6xfu

Zebrafish in Toxicology and Environmental Health [chapter]

Kathryn Bambino, Jaime Chu
2017 Current Topics in Developmental Biology  
As manufacturing processes and development of new synthetic compounds increase to keep pace with the expanding global demand, environmental health, and the effects of toxicant exposure are emerging as  ...  The benefits of zebrafish for studying vertebrate development are equally useful for studying teratogens.  ...  Sadler and Anjana Ramdas for critical reading of this chapter.  ... 
doi:10.1016/bs.ctdb.2016.10.007 pmid:28335863 pmcid:PMC5836480 fatcat:hkjzzczlyvei3aatgl2rvu3fpy

Thermal modulation of Zebrafish exploratory statistics reveals constraints on individual behavioral variability

Guillaume Le Goc, Julie Lafaye, Sophia Karpenko, Volker Bormuth, Raphaël Candelier, Georges Debrégeas
2021 BMC Biology  
By combining these various observations into a minimal stochastic model of navigation, we show that this thermal modulation of locomotor kinematics results in a thermophobic behavior, complementing direct  ...  Background Variability is a hallmark of animal behavior. It contributes to survival by endowing individuals and populations with the capacity to adapt to ever-changing environmental conditions.  ...  We are grateful to Carounagarane Dore for his contribution to the design of the experimental setup, Geoffrey Migault for engineering expertise, and Raphaël Voituriez for fruitful discussion on the modeling  ... 
doi:10.1186/s12915-021-01126-w pmid:34548084 pmcid:PMC8456632 fatcat:vudt3fok7nenpjflh4hbixxlrq

Embryonic Arsenic Exposure Triggers Long-Term Behavioral Impairment with Metabolite Alterations in Zebrafish

Noraini Abu Bakar, Wan Norhamidah Wan Ibrahim, Che Azurahanim Che Abdullah, Nurul Farhana Ramlan, Khozirah Shaari, Shamarina Shohaimi, Ahmed Mediani, Nurrul Shaqinah Nasruddin, Cheol-Hee Kim, Siti Munirah Mohd Faudzi
2022 Toxics  
Surviving larvae after 30 µM As2O3 exposure showed deficits in motor behavior without impairment of anxiety-like responses at 6 dpf and a slight impairment in color preference behavior at 11 dpf, which  ...  zebrafish.  ...  One hundred random permutations of the y variables confirmed the minimal validity of the current model of y-axis intercepts below zero, as indicated in SIMCA (Figure S11 ).  ... 
doi:10.3390/toxics10090493 pmid:36136458 pmcid:PMC9502072 fatcat:43eznpxhgjfurfhyevhymsunue
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