Changes in Postural Syntax Characterize Sensory Modulation and Natural Variation of C. elegans Locomotion
Publication Date
August 21, 2015
Journal
PLOS Computational Biology
Authors
Roland F. Schwarz, Robyn Branicky, Laura J. Grundy, William R. Schafer, et al
Volume
11
Issue
8
Pages
e1004322
DOI
http://doi.org/10.1371/journal.pcbi.1004322
Publisher URL
http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1004322
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/26295152
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4546679
Europe PMC
http://europepmc.org/abstract/MED/26295152
Web of Science
000360824500007
Scopus
84940759595
Mendeley
http://www.mendeley.com/research/changes-postural-syntax-characterize-sensory-modulation-natural-variation-c-elegans-locomotion
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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2220217"], "description"=>"<p><b>(A)</b><i>n</i>-gram accumulation curves for bigrams (sequences of two postures) to 5-grams (sequences of 5 postures). Over time, as more postures are observed (Total Postures), the number of unique <i>n</i>-grams that is observed (analogous to vocabulary size) grows sub-linearly. The grey dashed line has slope 1. Each blue line is calculated from data from 100 randomly chosen worms from the entire data set of 1262 individuals. Orange lines are averages calculated from the same data but with the sequences randomly shuffled. Black lines are averages calculated for data generated from a trigram model of the posture sequences. <b>(B)</b> Zipf plot of <i>n</i>-grams. The frequency distribution of <i>n</i>-grams ranked from most to least frequent. Each blue line is calculated from 400 randomly chosen worms. Black lines are averages calculated for data generated from a trigram model of the posture sequences. The red dashed line indicates the rank that divides the top 1% most frequent trigrams from the remaining 99%.</p>", "links"=>[], "tags"=>["shape changes", "postural syntax", "locomotor behaviour", "shape transitions", "language processing", "90 postures", "worms show", "frequency distribution", "nematode C", "Postural Syntax Characterize Sensory Modulation", "Natural variation", "postural sequences", "elegans Locomotion Locomotion"], "article_id"=>1516460, "categories"=>["Biological Sciences", "Science Policy"], "users"=>["Roland F. Schwarz", "Robyn Branicky", "Laura J. Grundy", "William R. Schafer", "André E. X. Brown"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004322.g002", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Worm_locomotion_sequences_are_complex_but_can_be_fit_by_a_trigram_model_/1516460", "title"=>"Worm locomotion sequences are complex but can be fit by a trigram model.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-21 03:27:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/2220257", "https://ndownloader.figshare.com/files/2220258", "https://ndownloader.figshare.com/files/2220259", "https://ndownloader.figshare.com/files/2220260"], "description"=>"<div><p>Locomotion is driven by shape changes coordinated by the nervous system through time; thus, enumerating an animal's complete repertoire of shape transitions would provide a basis for a comprehensive understanding of locomotor behaviour. Here we introduce a discrete representation of behaviour in the nematode <i>C</i>. <i>elegans</i>. At each point in time, the worm’s posture is approximated by its closest matching template from a set of 90 postures and locomotion is represented as sequences of postures. The frequency distribution of postural sequences is heavy-tailed with a core of frequent behaviours and a much larger set of rarely used behaviours. Responses to optogenetic and environmental stimuli can be quantified as changes in postural syntax: worms show different preferences for different sequences of postures drawn from the same set of templates. A discrete representation of behaviour will enable the use of methods developed for other kinds of discrete data in bioinformatics and language processing to be harnessed for the study of behaviour.</p></div>", "links"=>[], "tags"=>["shape changes", "postural syntax", "locomotor behaviour", "shape transitions", "language processing", "90 postures", "worms show", "frequency distribution", "nematode C", "Postural Syntax Characterize Sensory Modulation", "Natural variation", "postural sequences", "elegans Locomotion Locomotion"], "article_id"=>1516487, "categories"=>["Biological Sciences", "Science Policy"], "users"=>["Roland F. Schwarz", "Robyn Branicky", "Laura J. Grundy", "William R. Schafer", "André E. X. Brown"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1004322.s001", "https://dx.doi.org/10.1371/journal.pcbi.1004322.s002", "https://dx.doi.org/10.1371/journal.pcbi.1004322.s003", "https://dx.doi.org/10.1371/journal.pcbi.1004322.s004"], "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Changes_in_Postural_Syntax_Characterize_Sensory_Modulation_and_Natural_Variation_of_C_elegans_Locomotion/1516487", "title"=>"Changes in Postural Syntax Characterize Sensory Modulation and Natural Variation of <i>C</i>. <i>elegans</i> Locomotion", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-08-21 03:27:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/2220235"], "description"=>"<p><b>(A)</b> Zipf plots for 17 wild isolates of <i>C</i>. <i>elegans</i> all show a heavy tailed distribution similar to N2 worms. The red dashed line shows the rank dividing the top 1% of trigrams in the repertoire from the remaining 99%. The inset shows the distribution of R<sup>2</sup> values for fits between 90 N2-derived templates and the original postures for the 17 wild isolates as well as for N2 itself for comparison. The overall mean of the distributions is 0.86 with standard deviation 0.08. <b>(B)</b> Histogram of hit counts (not hit density) versus frequency on a log scale. Hits are trigrams with significantly different frequencies in at least one pairwise rank sum test comparing strains. Note that the bin widths increase to be constant on a log-scale. Blue line is the original data and the red line is for trigrams derived from the same data after random shuffling of the sequences. <b>(C)</b> Box plots of trigram frequencies for 4 trigrams showing hits in several strains. The trigram number indicates its column in the heatmap in D. The <i>p</i>-value threshold was set at 1.1 x 10<sup>−4</sup> to control the false discovery rate at 5% across comparisons. (D) A heatmap showing the relative frequency of all of the trigrams with significantly different frequencies in at least one strain comparison. Strains and trigrams have been hierarchically clustered. Sample trigrams are plotted above the heatmap with their columns indicated by the gray numbers.</p>", "links"=>[], "tags"=>["shape changes", "postural syntax", "locomotor behaviour", "shape transitions", "language processing", "90 postures", "worms show", "frequency distribution", "nematode C", "Postural Syntax Characterize Sensory Modulation", "Natural variation", "postural sequences", "elegans Locomotion Locomotion"], "article_id"=>1516468, "categories"=>["Biological Sciences", "Science Policy"], "users"=>["Roland F. Schwarz", "Robyn Branicky", "Laura J. Grundy", "William R. Schafer", "André E. X. Brown"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004322.g005", "stats"=>{"downloads"=>0, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Form_of_trigram_frequency_distribution_is_conserved_across_wild_isolates_despite_differences_in_preference_for_particular_sequences_/1516468", "title"=>"Form of trigram frequency distribution is conserved across wild isolates despite differences in preference for particular sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-21 03:27:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/2220230"], "description"=>"<p><b>(A)</b> Worm tracks in different conditions: on food (<i>n</i> = 34), off food (<i>n</i> = 23), and off food with an attractant (benzaldehyde) (<i>n</i> = 25). Tracks for different worms start at the red dot and are aligned with their long-axis arranged vertically. Worms on food explore the region of the food but rarely leave, while off food they explore a larger area. In the presence of an attractant, worms explore a large area, but in a more directed way. <b>(B)</b> A plot shows the distribution of R<sup>2</sup> values for worms in the different conditions. The fit quality is no worse for worms off food or performing chemotaxis even though the postures are derived only for worms on food. For comparison, the distribution of fits is also shown for an uncoordinated mutant <i>unc-79(e1068)</i> that is poorly fit using the wild type on food postures. Numbers in the legend are mean ± standard deviation of the R<sup>2</sup> distributions. <b>(C)</b> Comparisons between the frequencies of four selected trigrams in the three conditions. The rank of each sequence in the repertoire of worms in each condition is shown in red. * indicates <i>p</i> < 4.1 x 10<sup>−4</sup>, chosen to control the false discovery rate at 5% across multiple comparisons.</p>", "links"=>[], "tags"=>["shape changes", "postural syntax", "locomotor behaviour", "shape transitions", "language processing", "90 postures", "worms show", "frequency distribution", "nematode C", "Postural Syntax Characterize Sensory Modulation", "Natural variation", "postural sequences", "elegans Locomotion Locomotion"], "article_id"=>1516463, "categories"=>["Biological Sciences", "Science Policy"], "users"=>["Roland F. Schwarz", "Robyn Branicky", "Laura J. Grundy", "William R. Schafer", "André E. X. Brown"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004322.g004", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Worm_behaviour_is_compositional_across_different_conditions_/1516463", "title"=>"Worm behaviour is compositional across different conditions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-21 03:27:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/2220229"], "description"=>"<p>The left half of the figure (A-C) shows data from ZX46 worms expressing channelrhodopsin in the cholinergic motor neurons and the right half (D-F) from AQ2026 worms expressing channelrhodopsin in ASH, a neuron that detects aversive stimuli, as well as PVQ and ASI. <b>(A, D)</b> R<sup>2</sup> between original body angles and nearest-neighbour template over time. The blue line is the mean and the gray shading indicates the standard deviation (<i>n</i> = 23 in A; <i>n</i> = 34 in D). Yellow box indicates light stimulation period. <b>(B, E)</b> The relative probability of observing each posture over time. Colour indicates whether a posture is over-represented (red) or underrepresented (blue) at each time. Postures with similar temporal profiles are clustered independently in B and E for visualization. <b>(C, F)</b> The top 2 <i>n</i>-grams that are most significantly overrepresented (red) or underrepresented (blue) during the indicated time periods for <i>n</i> = 1–3 for each strain. Grey numbers show the row number for each posture in the corresponding heatmap. Dots indicate worm head, dorsal and ventral sides are as indicated by the arrows. The gray dashed lines approximately connect body bends from one posture to the next and can be used to distinguish forward from reverse locomotion. Lines with a negative slope indicate body bends propagating backwards and therefore forward locomotion. Lines with a positive slope show reversals.</p>", "links"=>[], "tags"=>["shape changes", "postural syntax", "locomotor behaviour", "shape transitions", "language processing", "90 postures", "worms show", "frequency distribution", "nematode C", "Postural Syntax Characterize Sensory Modulation", "Natural variation", "postural sequences", "elegans Locomotion Locomotion"], "article_id"=>1516462, "categories"=>["Biological Sciences", "Science Policy"], "users"=>["Roland F. Schwarz", "Robyn Branicky", "Laura J. Grundy", "William R. Schafer", "André E. X. Brown"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004322.g003", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Optogenetic_activation_of_subsets_of_neurons_drives_behavioural_transitions_/1516462", "title"=>"Optogenetic activation of subsets of neurons drives behavioural transitions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-21 03:27:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/2220216"], "description"=>"<p><b>(A)</b> As the number of template postures increases, the R<sup>2</sup> of the fit between original body angles and nearest neighbour matches increases (points show mean ± standard deviation for 50 worms, 15 000 frames each). The inset shows the rate of increase in R<sup>2</sup> for increasing <i>k</i>. The red dashed line is the average increase in R<sup>2</sup> per posture for <i>k</i> = 100–500 (2.4 x 10<sup>−4</sup> per posture). <b>(B)</b> Probability of observing each of the 90 template postures. Selected postures are shown as skeletons with the head indicated by the blue dot. The grey label indicates their rank by frequency with 1 being the most common posture. (<b>C)</b> Locomotion is represented by a series of discrete template postures. In each frame, the original skeleton (black) is represented by its nearest neighbour (coloured overlay) in the set of 90 template postures. The duration spent in each posture is also recorded and shown as the alternating coloured bands. Each segment of repeated postures is collapsed to a single label and it is this sequence of states that represents locomotion (i.e. {3, 3, 89, 5, 5, 5, 5, 87, 87, 87, …} becomes {3, 89, 5, 87}).</p>", "links"=>[], "tags"=>["shape changes", "postural syntax", "locomotor behaviour", "shape transitions", "language processing", "90 postures", "worms show", "frequency distribution", "nematode C", "Postural Syntax Characterize Sensory Modulation", "Natural variation", "postural sequences", "elegans Locomotion Locomotion"], "article_id"=>1516459, "categories"=>["Biological Sciences", "Science Policy"], "users"=>["Roland F. Schwarz", "Robyn Branicky", "Laura J. Grundy", "William R. Schafer", "André E. X. Brown"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004322.g001", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Discrete_representation_of_worm_locomotion_by_clustering_/1516459", "title"=>"Discrete representation of worm locomotion by clustering.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-21 03:27:17"}

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Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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