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{"title"=>"Three-dimensional neurophenotyping of adult zebrafish behavior", "type"=>"journal", "authors"=>[{"first_name"=>"Jonathan", "last_name"=>"Cachat", "scopus_author_id"=>"6508267570"}, {"first_name"=>"Adam", "last_name"=>"Stewart", "scopus_author_id"=>"36098252500"}, {"first_name"=>"Eli", "last_name"=>"Utterback", "scopus_author_id"=>"36128079000"}, {"first_name"=>"Peter", "last_name"=>"Hart", "scopus_author_id"=>"26631939100"}, {"first_name"=>"Siddharth", "last_name"=>"Gaikwad", "scopus_author_id"=>"36097837300"}, {"first_name"=>"Keith", "last_name"=>"Wong", "scopus_author_id"=>"36098486100"}, {"first_name"=>"Evan", "last_name"=>"Kyzar", "scopus_author_id"=>"36608240500"}, {"first_name"=>"Nadine", "last_name"=>"Wu", "scopus_author_id"=>"36098508300"}, {"first_name"=>"Allan V.", "last_name"=>"Kalueff", "scopus_author_id"=>"6603827285"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-79952341317", "sgr"=>"79952341317", "pui"=>"361390418", "isbn"=>"1932-6203 (Electronic)\r1932-6203 (Linking)", "pmid"=>"21408171", "doi"=>"10.1371/journal.pone.0017597"}, "id"=>"a4ea9714-71b1-303e-8b5f-e747c4e64112", "abstract"=>"Sickle-cell anemia is a common disease, affecting more than 50,000 blacks in the United States. Since 1970 the morbidity and mortality have improved, with patients surviving well into their fourth decade. This article discusses the spectrum of serious complications of sickle-cell anemia. Crises and complications that result from the sickling process are presented with recommendations for emergency department evaluation and management. The painful bone crisis and pain control are also discussed.", "link"=>"http://www.mendeley.com/research/threedimensional-neurophenotyping-adult-zebrafish-behavior", "reader_count"=>179, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>4, "Researcher"=>40, "Student > Doctoral Student"=>9, "Student > Ph. D. Student"=>52, "Student > Postgraduate"=>6, "Student > Master"=>29, "Other"=>4, "Student > Bachelor"=>20, "Lecturer"=>2, "Professor"=>11}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>4, "Researcher"=>40, "Student > Doctoral Student"=>9, "Student > Ph. D. Student"=>52, "Student > Postgraduate"=>6, "Student > Master"=>29, "Other"=>4, "Student > Bachelor"=>20, "Lecturer"=>2, "Professor"=>11}, "reader_count_by_subject_area"=>{"Unspecified"=>6, "Agricultural and Biological Sciences"=>83, "Philosophy"=>1, "Business, Management and Accounting"=>1, "Chemistry"=>7, "Computer Science"=>6, "Earth and Planetary Sciences"=>1, "Engineering"=>15, "Environmental Science"=>12, "Biochemistry, Genetics and Molecular Biology"=>9, "Materials Science"=>1, "Medicine and Dentistry"=>8, "Neuroscience"=>13, "Pharmacology, Toxicology and Pharmaceutical Science"=>4, "Physics and Astronomy"=>2, "Psychology"=>9, "Sports and Recreations"=>1}, "reader_count_by_subdiscipline"=>{"Materials Science"=>{"Materials Science"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>8}, "Physics and Astronomy"=>{"Physics and Astronomy"=>2}, "Psychology"=>{"Psychology"=>9}, "Sports and Recreations"=>{"Sports and Recreations"=>1}, "Unspecified"=>{"Unspecified"=>6}, "Environmental Science"=>{"Environmental Science"=>12}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>4}, "Engineering"=>{"Engineering"=>15}, "Chemistry"=>{"Chemistry"=>7}, "Neuroscience"=>{"Neuroscience"=>13}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>83}, "Computer Science"=>{"Computer Science"=>6}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>9}, "Philosophy"=>{"Philosophy"=>1}}, "reader_count_by_country"=>{"United States"=>6, "United Kingdom"=>3, "Malaysia"=>2, "Switzerland"=>2, "Portugal"=>6, "India"=>2, "Austria"=>1, "Netherlands"=>1, "Norway"=>1, "Brazil"=>1, "Italy"=>1, "Chile"=>1, "Australia"=>1, "Germany"=>3}, "group_count"=>7}

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• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/e8e067f9-b01e-4e7b-9beb-c617f516bc46", "title"=>"Value of 3D swim paths", "body"=>"Highlight the sentence explaining the value of recreating swim paths. ", "highlightedText"=>"''The application of 3D swim path reconstructions consolidates behavioral data (while increasing data density) and provides a novel way to examine and represent zebrafish behavior.''\nhttp://plosone.org/article/info:doi/10.1371/journal.pone.0017597#article1.front1.article-meta1.abstract1.p1", "isRemoved"=>false, "created"=>"2011-04-04T22:10:43Z", "lastModified"=>"2011-04-04T22:10:43Z", "creator"=>{"userId"=>"140999"}, "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>true, "body"=>"I am the primary author, testing annotation features of PLoS one"}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0017597", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2011-04-04T22:10:43Z", "replies"=>[]}
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• {"id"=>"375610726775144448", "text"=>"@phylogenomics @plosone looking @ data sharing policy possible to associate a recent @figshare upload with 2011 pub? http://t.co/5Pww7I64r6", "created_at"=>"2013-09-05T13:25:50Z", "user"=>"jcachat", "user_name"=>"Jonathan Cachat", "user_profile_image"=>"http://a0.twimg.com/profile_images/74586671/signature_normal.jpg"}
• {"id"=>"375653265133678593", "text"=>"Hi @jcachat, you can post a link to the @figshare data related to your @PLOSONE paper in a comment at http://t.co/0OARjzBe5N @phylogenomics", "created_at"=>"2013-09-05T16:14:52Z", "user"=>"mattjhodgkinson", "user_name"=>"Matt Hodgkinson", "user_profile_image"=>"http://a0.twimg.com/profile_images/2595571976/bc2za9tnyui0wxobreb0_normal.jpeg"}
• {"id"=>"609175977202061312", "text"=>"Yo @Gramatik I'm a scientist and I jam to your flows - check out what happens when you mix good beats with science @ http://t.co/rtol7tfadM", "created_at"=>"2015-06-12T01:50:45Z", "user"=>"jcachat", "user_name"=>"Jonathan Cachat", "user_profile_image"=>"http://pbs.twimg.com/profile_images/561112701531742208/EowWI6Lq_normal.png"}

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Figshare

• {"files"=>["https://ndownloader.figshare.com/files/793802"], "description"=>"<p>After indicated experimental manipulations (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017597#pone-0017597-g003\" target=\"_blank\">Fig. 3</a>), zebrafish novel tank behavior was manually observed and video-tracked using EthoVision XT7 program. Raw track and behavioral endpoints were processed, formatted, and visualized in a 3D scatter plot using RapidMiner 5.0 software; traditional computer-generated two-dimensional (2D) swim path traces were placed at t = 0.0 s (top left part of each panel) for reference. Representative 3D reconstructions were selected by comparing swim paths of all subjects within a cohort, ranking them from 1 to n based on similarity to each other (low/no to high activity) and choosing the middle for the illustrations. For better visuality and consistency, fish used for spatial 3D imaging were the same as those used for the respective temporal 3D reconstructions. For a more detailed analysis of 3D reconstructions, the average velocity (m/s) of each fish was reflected by changes in color from blue to green, yellow and red, as the velocity increases. Note that any other computer-generated behavioral indices (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017597#pone.0017597.s003\" target=\"_blank\">Table S1</a> of Supporting Information) may be expressed in color on 3D reconstructions of zebrafish locomotion paths. Overall, these 3D traces reveal striking differences between zebrafish high- and low-anxiety behaviors, thereby enabling a rapid visualization and interpretation of the observed phenotypes.</p>", "links"=>[], "tags"=>["temporal", "spatial", "reconstructions", "zebrafish", "paths", "affective"], "article_id"=>464161, "categories"=>["Neuroscience", "Mental Health", "Pharmacology", "Evolutionary Biology"], "users"=>["Jonathan Cachat", "Adam Stewart", "Eli Utterback", "Peter Hart", "Siddharth Gaikwad", "Keith Wong", "Evan Kyzar", "Nadine Wu", "Allan V. Kalueff"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0017597.g006", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Three_dimensional_3D_temporal_and_spatial_reconstructions_of_adult_zebrafish_swim_paths_rapidly_expose_overall_affective_phenotype_/464161", "title"=>"Three-dimensional (3D) temporal and spatial reconstructions of adult zebrafish swim paths rapidly expose overall affective phenotype.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-03-07 01:09:21"}
• {"files"=>["https://ndownloader.figshare.com/files/793675"], "description"=>"<p>The reconstructed swim path presented here as an example was obtained from a naïve, wild-type control zebrafish tested in a standard novel tank test for 6 min (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017597#pone-0017597-g006\" target=\"_blank\">Fig. 6</a> for more examples). Wild-type fish can be considered “mild anxiety”, compared to both anxiolytic (low anxiety) and anxiogenic (high anxiety) cohorts listed in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017597#pone-0017597-g003\" target=\"_blank\">Fig. 3</a>. Although this fish spent a majority of the trial within the bottom half of the tank, the animal also made large sweeping transitions into the upper half. A detailed spatial dissection of 3D locomotion here revealed that (like temporal 3D reconstructions in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017597#pone-0017597-g004\" target=\"_blank\">Fig. 4</a>) manually scored erratic movement events generally overlap with periods of elevated velocity, rapid movement, high angular velocity, high mobility and sharp turn angles, identified by the computer analysis. For better visuality, the observed endpoints were color-coded, with the legend color scales representing proportional spectrum across min/max ranges of observed experimental values. Overall, this approach strongly supports the utility of 3D-based computer-aided analyses of zebrafish behavior, and for the first time creates 3D reconstructions of zebrafish <i>natural</i> exploratory locomotion, mapping anxiety-related behaviors to these traces. The striking overlap between observer- and computer-generated indices in “real” 3D traces open opportunities for further refinement of video-tracking, eventually leading to fully automated 3D-based neurophenotyping tools to quantify zebrafish anxiety. This method of multidimensional phenotyping of zebrafish locomotion can complement temporal 3D reconstructions (as shown in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017597#pone-0017597-g004\" target=\"_blank\">Fig. 4</a> and 5).</p>", "links"=>[], "tags"=>["micro-level", "three-dimensional", "spatial", "reconstruction"], "article_id"=>464036, "categories"=>["Neuroscience", "Mental Health", "Pharmacology", "Evolutionary Biology"], "users"=>["Jonathan Cachat", "Adam Stewart", "Eli Utterback", "Peter Hart", "Siddharth Gaikwad", "Keith Wong", "Evan Kyzar", "Nadine Wu", "Allan V. Kalueff"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0017597.g005", "stats"=>{"downloads"=>2, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Macro_and_micro_level_behavioral_analysis_with_three_dimensional_3D_spatial_reconstruction_of_swim_path_/464036", "title"=>"Macro- and micro-level behavioral analysis with three-dimensional (3D) spatial reconstruction of swim path.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-03-07 01:07:16"}
• {"files"=>["https://ndownloader.figshare.com/files/793548"], "description"=>"<p>The reconstructed swim path was obtained from a zebrafish tested in a standard novel tank test (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017597#pone-0017597-g001\" target=\"_blank\">Fig. 1</a>) for 6 min following repeated morphine withdrawal, an anxiogenic manipulation (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017597#pone-0017597-g003\" target=\"_blank\">Fig. 3</a>). Manual, event-based behaviors were scored by a human observer during automated video acquisition in EthoVision XT7 program. Subsequently, spatiotemporal (X,Y,time) coordinates, computer-generated movement parameters and manually-scored behaviors were integrated into a single track file for each subject using RapidMiner 5.0 software. After X,Y-coordinates were plotted over experimental time, behavioral endpoints were actively cycled across the swim path as the color attribute and examined for overlaps and patterns. The experimental manipulation used here caused long, prominent freezing bouts separated by short bursts of bottom swimming – a profile typically observed in zebrafish high-anxiety states (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017597#pone-0017597-g003\" target=\"_blank\">Fig. 3</a>). A detailed dissection reveals that manually scored erratic movements on a 3D reconstruction map within episodes of elevated velocity, rapid movement, high angular velocity, high mobility and sharp turn angles (generated by the computer). Conversely, manually scored periods of freezing correlate with lower velocity, slow movement and immobility bouts. For better visuality, the observed endpoints were color-coded, with the legend color scales representing proportional spectrum across min/max ranges of observed experimental values. This experiment shows that 3D temporal reconstructions permit rapid and objective macro- and micro-level behavioral analysis, thereby improving high-throughput phenotyping of zebrafish behavior. This method of multidimensional phenotyping of zebrafish locomotion can complement spatial 3D reconstructions (as shown in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017597#pone-0017597-g005\" target=\"_blank\">Fig. 5</a> and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017597#pone-0017597-g006\" target=\"_blank\">6</a>).</p>", "links"=>[], "tags"=>["zebrafish", "three-dimensional", "temporal", "reconstruction"], "article_id"=>463909, "categories"=>["Neuroscience", "Mental Health", "Pharmacology", "Evolutionary Biology"], "users"=>["Jonathan Cachat", "Adam Stewart", "Eli Utterback", "Peter Hart", "Siddharth Gaikwad", "Keith Wong", "Evan Kyzar", "Nadine Wu", "Allan V. Kalueff"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0017597.g004", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Dissection_of_zebrafish_behavior_using_three_dimensional_3D_temporal_reconstruction_of_swim_path_/463909", "title"=>"Dissection of zebrafish behavior using three-dimensional (3D) temporal reconstruction of swim path.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-03-07 01:05:09"}
• {"files"=>["https://ndownloader.figshare.com/files/793933"], "description"=>"<p>Experimental manipulations were hierarchically clustered to link compounds to behaviors (based on behavioral endpoints listed in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017597#pone.0017597.s003\" target=\"_blank\">Table S1</a> of Supporting Information, generated using the side-view video-tracking by EthoVision XT7). In the clustergram, each cell represents the average relative value in standard deviations (green – higher, red - lower than controls) for each behavioral endpoint. Clustering of all 8 treatments (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017597#pone-0017597-g003\" target=\"_blank\">Fig. 3</a>) resulted in two main clusters (I and II) strikingly corresponding to known anxiogenic and anxiolytic manipulations (Rpt WD - repeated withdrawal, Chr - chronic treatment). For behavioral clustering, dark bars (labeled 1–9) represent specific sub-clusters analyzed in detail for manual and automated endpoints organized in two main clusters (A and B). Note that anxiogenic manipulations (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017597#pone-0017597-g003\" target=\"_blank\">Fig. 3</a>; cluster I) generally reduce the cluster A endpoints and increase the cluster B indices. Anxiolytic treatments (cluster II) demonstrate the opposite phenotype, increasing the cluster A behaviors and reducing cluster B endpoints. Overall, this analysis not only reconfirms the validity of traditional novel tank endpoints and manipulations, but also identifies some novel computer-generated endpoints that reflect zebrafish high- and low-anxiety states. Notably, some of these novel indices already demonstrated sensitivity to anxiety-like states, as illustrated by three-dimensional (3D) reconstructions in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017597#pone-0017597-g004\" target=\"_blank\">Fig. 4</a>–<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017597#pone-0017597-g006\" target=\"_blank\">6</a>.</p>", "links"=>[], "tags"=>["6-min", "groups", "anxiogenic", "anxiolytic", "manipulations", "correlates", "computer-generated"], "article_id"=>464293, "categories"=>["Neuroscience", "Mental Health", "Pharmacology", "Evolutionary Biology"], "users"=>["Jonathan Cachat", "Adam Stewart", "Eli Utterback", "Peter Hart", "Siddharth Gaikwad", "Keith Wong", "Evan Kyzar", "Nadine Wu", "Allan V. Kalueff"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0017597.g007", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Hierarchical_cluster_analysis_performed_for_the_entire_6_min_test_duration_groups_anxiogenic_and_anxiolytic_manipulations_and_correlates_manual_and_computer_generated_behavioral_endpoints_/464293", "title"=>"Hierarchical cluster analysis (performed for the entire 6-min test duration) groups anxiogenic and anxiolytic manipulations and correlates manual and computer-generated behavioral endpoints.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-03-07 01:11:33"}
• {"files"=>["https://ndownloader.figshare.com/files/793292"], "description"=>"<p>Temporal three-dimensional (3D) reconstructions plotted X,Y-coordinates (exported from EthoVision XT7 video-tracking software) on respective X,Y-axes, with experimental time plotted across the Z-axis (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017597#pone-0017597-g004\" target=\"_blank\">Fig. 4</a> for an example). Spatial 3D reconstructions were generated in a similar fashion, with spatial coordinates from a top-view recording plotted on the Z-axis (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017597#pone-0017597-g005\" target=\"_blank\">Fig. 5</a> for an example). Arrows indicate swimming activity patterns of interest; note the overall similarity of behavioral dynamics across two different novel tanks. Track color reflects changes in velocity (m/s), moving from dark to light (i.e., from blue to green, yellow and red) as velocity increases. Zebrafish placed in standard (small) or large novel tank displayed similar exploratory behavior dynamics (also see transitions to top as an example). Two-way ANOVA (factors: tank type; test time) revealed no tank type effect across all manual endpoints, but a significant time effect with transitions to and time spent in the upper half, increasing and freezing bouts and duration decreasing over time (F_(1,5) = 2.1-9.3, p<0.05; ***p<0.01, post-hoc test vs. the respective min 1). This figure serves two purposes. First, it illustrates that the approach presented here can be applied to novel tanks of various shapes and sizes. Additionally, it validates the small novel tank test as a paradigm suitable for standardized phenotyping of zebrafish anxiety-like behavior.</p>", "links"=>[], "tags"=>["zebrafish"], "article_id"=>463661, "categories"=>["Neuroscience", "Mental Health", "Pharmacology", "Evolutionary Biology"], "users"=>["Jonathan Cachat", "Adam Stewart", "Eli Utterback", "Peter Hart", "Siddharth Gaikwad", "Keith Wong", "Evan Kyzar", "Nadine Wu", "Allan V. Kalueff"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0017597.g002", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Exploratory_behavior_of_adult_zebrafish_in_two_different_novel_tank_apparatuses_/463661", "title"=>"Exploratory behavior of adult zebrafish in two different novel tank apparatuses.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-03-07 01:01:01"}
• {"files"=>["https://ndownloader.figshare.com/files/793442"], "description"=>"<p>This analysis illustrates the strong predictive validity of traditional, manually quantified behavioral endpoints in the novel tank test. Well-established ‘reference’ anxiogenic manipulations include acute alarm pheromone (7 mL for 5 min), repeated morphine withdrawal (exposure for 1.5 mg/L for 2 weeks; withdrawal for 3 h twice daily for 1 week), acute caffeine (250 mg/L for 20 min) and the use of high-anxiety leopard zebrafish strain. Reference anxiolytic treatments include chronic fluoxetine (100 µg/L for 2 weeks), chronic ethanol (0.3% vol/vol for 1 week), chronic morphine (1.5 mg/L for 2 weeks) and acute nicotine (10 mg/L for 5 min). Statistically significant differences from matched controls (p<0.05, U-test) are represented by solid arrows (empty arrows denote trends; p = 0.05–0.085, U-test): up – increase, down – decrease; empty fields indicate no significant effects, n/a – data not available. In addition to behavioral endpoints, the table also includes whole-body cortisol data, presented here to parallel zebrafish behavioral and physiological anxiety-like responses.</p>", "links"=>[], "tags"=>["anxiogenic", "anxiolytic", "modulation", "zebrafish", "6-min", "supplementary", "materials"], "article_id"=>463799, "categories"=>["Neuroscience", "Mental Health", "Pharmacology", "Evolutionary Biology"], "users"=>["Jonathan Cachat", "Adam Stewart", "Eli Utterback", "Peter Hart", "Siddharth Gaikwad", "Keith Wong", "Evan Kyzar", "Nadine Wu", "Allan V. Kalueff"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0017597.g003", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_anxiogenic_and_anxiolytic_modulation_of_adult_zebrafish_behavior_in_standard_6_min_novel_tank_test_see_Fig_S1_in_Supplementary_Materials_for_raw_data_from_these_experiments_/463799", "title"=>"Summary of anxiogenic and anxiolytic modulation of adult zebrafish behavior in standard 6-min novel tank test (see Fig. S1 in Supplementary Materials for raw data from these experiments).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-03-07 01:03:19"}
• {"files"=>["https://ndownloader.figshare.com/files/396872", "https://ndownloader.figshare.com/files/396989", "https://ndownloader.figshare.com/files/397061", "https://ndownloader.figshare.com/files/397092", "https://ndownloader.figshare.com/files/397156", "https://ndownloader.figshare.com/files/397212"], "description"=>"<div><p>The use of adult zebrafish (Danio rerio) in neurobehavioral research is rapidly expanding. The present large-scale study applied the newest video-tracking and data-mining technologies to further examine zebrafish anxiety-like phenotypes. Here, we generated temporal and spatial three-dimensional (3D) reconstructions of zebrafish locomotion, globally assessed behavioral profiles evoked by several anxiogenic and anxiolytic manipulations, mapped individual endpoints to 3D reconstructions, and performed cluster analysis to reconfirm behavioral correlates of high- and low-anxiety states. The application of 3D swim path reconstructions consolidates behavioral data (while increasing data density) and provides a novel way to examine and represent zebrafish behavior. It also enables rapid optimization of video tracking settings to improve quantification of automated parameters, and suggests that spatiotemporal organization of zebrafish swimming activity can be affected by various experimental manipulations in a manner predicted by their anxiolytic or anxiogenic nature. Our approach markedly enhances the power of zebrafish behavioral analyses, providing innovative framework for high-throughput 3D phenotyping of adult zebrafish behavior.</p> </div>", "links"=>[], "tags"=>["three-dimensional", "neurophenotyping", "zebrafish"], "article_id"=>138399, "categories"=>["Neuroscience", "Mental Health", "Pharmacology", "Evolutionary Biology"], "users"=>["Jonathan Cachat", "Adam Stewart", "Eli Utterback", "Peter Hart", "Siddharth Gaikwad", "Keith Wong", "Evan Kyzar", "Nadine Wu", "Allan V. Kalueff"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0017597.s001", "https://dx.doi.org/10.1371/journal.pone.0017597.s002", "https://dx.doi.org/10.1371/journal.pone.0017597.s003", "https://dx.doi.org/10.1371/journal.pone.0017597.s004", "https://dx.doi.org/10.1371/journal.pone.0017597.s005", "https://dx.doi.org/10.1371/journal.pone.0017597.s006"], "stats"=>{"downloads"=>34, "page_views"=>121, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Three_Dimensional_Neurophenotyping_of_Adult_Zebrafish_Behavior/138399", "title"=>"Three-Dimensional Neurophenotyping of Adult Zebrafish Behavior", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-03-07 02:19:59"}
• {"files"=>["https://ndownloader.figshare.com/files/793190"], "description"=>"<p>The rationale (A) includes examining traditional, manually recorded novel tank test behavioral endpoints across several treatments and trials (Step 1). Video-tracking analysis was then performed to generate additional automated behavioral endpoints and raw spatiotemporal data for three-dimensional (3D) swim path reconstructions (Steps 2–3), followed by hierarchical clustering (Step 4) across all behavioral endpoints and experimental treatments in order to discover potential overlaps between manual and automated endpoints. These overlaps were reconfirmed using the 3D swim path reconstructions (Step 5). Finally, our interpretation of the observed affective states was verified with measured endocrine responses (Step 6). The experimental process (B) was standardized for all novel tank trials. Naïve, wild-type zebrafish were placed in an unfamiliar, novel tank for 6 min. Animal behavior was manually observed and two cameras recorded videos for automated analysis in EthoVision XT7 (during which manual, event-based scoring was also performed). Track data for each subject was exported, processed and visualized in a 3D scatter plot with RapidMiner 5.0.</p>", "links"=>[], "tags"=>["illustrating"], "article_id"=>463557, "categories"=>["Neuroscience", "Mental Health", "Pharmacology", "Evolutionary Biology"], "users"=>["Jonathan Cachat", "Adam Stewart", "Eli Utterback", "Peter Hart", "Siddharth Gaikwad", "Keith Wong", "Evan Kyzar", "Nadine Wu", "Allan V. Kalueff"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0017597.g001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Flowchart_illustrating_the_experimental_strategy_of_this_study_/463557", "title"=>"Flowchart illustrating the experimental strategy of this study.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-03-07 00:59:17"}

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Relative Metric

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F1000Prime