cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.h77n8
title: Data from: Phylogenetic variation in hind-limb bone scaling of flightless theropods

description: The robusticity of the weight-bearing limbs of large terrestrial animals
 is expected to increase at a more rapid rate than in their smaller
 relatives. This scaling has been hypothesized to allow large species to
 maintain stresses in the limb bones that are similar to those seen in
 smaller ones. Curvilinear scaling has previously been found in mammals and
 nonavian theropods but has not been demonstrated in birds. In this study,
 polynomial regressions of leg-bone length and circumference in terrestrial
 flightless birds were carried out to test for a relationship similar to
 that seen in nonavian theropods. Flightless birds exhibit curvilinear
 scaling, with the femora of large taxa becoming thicker relative to length
 at a greater rate than in smaller taxa. Evidence was found for nonlinear
 scaling in the leg bones of nonavian theropods. However, unlike in avians,
 there is also phylogenetic variation between taxonomic groups, with
 tyrannosaur leg bones in particular scaling differently than other groups.
 Phylogenetically corrected quadratic regressions and separate analyses of
 taxonomic groupings found little phylogenetic variation in flightless
 birds. It is suggested here that the nonlinear scaling seen in avian
 femora is due to the need to maintain the position of the knee under a
 more anterior center of mass, thereby restricting femoral length. The
 femur of nonavian theropods is not so constrained, with greater
 variability of the linear scaling relationships between clades.
 Phylogenetic variation in limb-bone scaling may broaden the errors for
 mass-predictive scaling equations based on limb-bone measurements of
 nonavian theropods.
description: Appendix
 S1Femur and tibia lengths
 and circumferences from flightless birds and non-avian theropods,
 including references for non-avian theropod data.Supplementary
 FiguresPhotographs of avian leg
 bones with key features labelled (Fig. S1A and S1B), and time scaled
 strict consenus trees of flightless birds (Fig. S2) and non-avian
 theropods (Fig. S3) included in regression analyses.Appendix
 S2Matrix representation
 parsimony codings for flightless avians and non-avian theropods with list
 of source phylogenies and first and last appearance dates of taxa with
 data sources listed.
DOI: 10.5061/dryad.9sj250q
title: Data from: Functional limb muscle innervation prior to cholinergic transmitter specification during early metamorphosis in Xenopus

description: In vertebrates, functional motoneurons are defined as differentiated
 neurons that are connected to a central premotor network and activate
 peripheral muscle using acetylcholine. Generally, motoneurons and muscles
 develop simultaneously during embryogenesis. However, during Xenopus
 metamorphosis, developing limb motoneurons must reach their target muscles
 through the already established larval cholinergic axial neuromuscular
 system. Here, we demonstrate that at metamorphosis onset, spinal neurons
 retrogradely labeled from the emerging hindlimbs initially express neither
 choline acetyltransferase nor vesicular acetylcholine transporter.
 Nevertheless, they are positive for the motoneuronal transcription factor
 Islet1/2 and exhibit intrinsic and axial locomotor-driven
 electrophysiological activity. Moreover, the early appendicular
 motoneurons activate developing limb muscles via nicotinic
 antagonist-resistant, glutamate antagonist-sensitive, neuromuscular
 synapses. Coincidently, the hindlimb muscles transiently express
 glutamate, but not nicotinic receptors. Subsequently, both pre- and
 postsynaptic neuromuscular partners switch definitively to typical
 cholinergic transmitter signaling. Thus, our results demonstrate a novel
 context-dependent respecification of neurotransmitter phenotype during
 neuromuscular system development.
description: Lambert et al 2018 Elife
 Raw data Figure 2Measures of fluorescence
 signals from immuno-labeled spinal slicesLambert et al 2018 Elife
 Raw data Figure 4 sup1Analysis of calcium
 signals during fictive locomotion in non-cholinergic hindlimb
 motoneuronsLambert et al 2018 Elife
 Raw data Figure 6Measures of EMG
 responses evoked by motor nerve in isolated nerve-limb preparations -
 effects of cholinergic and glutamatergic antagonist perfusion. Measure of
 EMG response delay.raw pix Fig1
 B1raw pix Fig1
 B2raw pix Fig1
 Craw pix Fig2
 AFig2b-e raw
 imagesraw pix Fig3
 AFig4sup1 imaging
 controlFig4sup1 imaging
 d-tuboraw pix Fig4
 sup1Fig5 raw
 imagesFig5sup1 raw
 images
DOI: 10.5061/dryad.pd256
title: Data from: Contests with deadly weapons: telson sparring in mantis shrimp (Stomatopoda)

description: Mantis shrimp strike with extreme impact forces that are deadly to prey.
 They also strike conspecifics during territorial contests, yet theoretical
 and empirical findings in aggressive behaviour research suggest
 competitors should resolve conflicts using signals before escalating to
 dangerous combat. We tested how Neogonodactylus bredini uses two
 ritualized behaviours to resolve size-matched contests: meral spread
 visual displays and telson (tailplate) strikes. We predicted that (i) most
 contests would be resolved by meral spreads, (ii) meral spreads would
 reliably signal strike force and (iii) strike force would predict contest
 success. The results were unexpected for each prediction. Contests were
 not resolved by meral spreads, instead escalating to striking in 33 of 34
 experiments. The size of meral spread components did not strongly
 correlate with strike force. Strike force did not predict contest success;
 instead, winners delivered more strikes. Size-matched N. bredini avoid
 deadly combat not by visual displays, but by ritualistically and
 repeatedly striking each other's telsons until the loser retreats. We
 term this behaviour ‘telson sparring', analogous to sparring in other
 weapon systems. We present an alternative framework for mantis shrimp
 contests in which the fight itself is the signal, serving as a non-lethal
 indicator of aggressive persistence or endurance.
description: Contest behaviours and
 striking datasetData on which contests
 escalated to striking, how many strikes each contest included, how many
 strikes were not on the telson, and the first behaviour of each
 contest.Green&Patek_SuppData_ContestBehavioursStriking.csvContests datasetData on each contestant, including: sex, residency status (resident/intruder), winner status (winner/loser), body length, body mass, maximum strike force, and number of strikes delivered during the contest.Green&Patek_SuppData_Contests.csvMorphology & force datasetData for each individual used in morphology and force correlations, including: sex, body length, body mass, carapace length, merus length, saddle length, dactyl heel width, and maximum strike force.Green&Patek_SuppData_MorphForce.csvSupplementary video 1Video showing contest behavioursGreen&Patek_SuppVideo1_HQ.mp4Supplementary video 2Video showing contest behavioursGreen&Patek_SuppVideo2_HQ.mp4
DOI: 10.5061/dryad.2s8422f
title: Data from: Distinct activity-gated pathways mediate attraction and aversion to CO2 in Drosophila

description: Carbon dioxide is produced by many organic processes, and is a convenient
 volatile cue for insects searching for blood hosts, flowers, communal
 nests, fruit, and wildfires. Curiously, although Drosophila melanogaster
 feed on yeast that produce CO2 and ethanol during fermentation, laboratory
 experiments suggest that walking flies avoid CO2. Here, we resolve this
 paradox by showing that both flying and walking Drosophila find CO2
 attractive, but only when in an active state associated with foraging.
 Aversion at low activity levels may be an adaptation to avoid
 CO2-seeking-parasites, or succumbing to respiratory acidosis in the
 presence of high concentrations of CO2 that exist in nature. In contrast
 to CO2, flies are attracted to ethanol in all behavioral states, and
 invest twice the time searching near ethanol compared to CO2. These
 behavioral differences reflect the fact that whereas CO2 is generated by
 many natural processes, ethanol is a unique signature of yeast
 fermentation. Using genetic tools, we determined that the evolutionarily
 ancient ionotropic co-receptor IR25a is required for CO2 attraction, and
 that the receptors necessary for CO2 avoidance are not involved. Our study
 lays the foundation for future research to determine the neural circuits
 underlying both state- and odorant- dependent decision making in
 Drosophila.
description: Processed data for all
 figures in markdown / CSV formatThis zip file contains a
 markdown (.md) file for each figure of our manuscript with all of the data
 necessary to regenerate that figure. The files are CSV (comma separated
 value) files with markdown formatting for the headings.co2_data_markdown.zipProcessed data for all figures in python pickle formatThis zip file contains a python pickle file that contains all of the data and matplotlib plotting instructions for each figure in our manuscript. For details on how to access the data, see: https://github.com/florisvb/drosophila_co2_attraction/tree/master/dataco2_data_python_dill_pickle.zipSVG figure templates for all of the figuresThis zip file contains individual SVG figure template files for all of the figures in our manuscript. For usage instructions, see: https://github.com/florisvb/drosophila_co2_attraction/tree/master/dataco2_data_figure_svgs.zip
DOI: 10.5061/dryad.b52p5
title: Data from: Nucleotide polymorphism and copy number variant detection using exome capture and next generation sequencing in the polyploid grass Panicum virgatum

description: Switchgrass (Panicum virgatum) is a polyploid, outcrossing grass species
 native to North America and has recently been recognized as a potential
 biofuel feedstock crop. Significant phenotypic variation including ploidy
 is present across the two primary ecotypes of switchgrass, referred to as
 upland and lowland switchgrass. The tetraploid switchgrass genome is
 approximately 1400 Mbp, split between two subgenomes, with significant
 repetitive sequence content limiting the efficiency of re-sequencing
 approaches for determining genome diversity. To characterize genetic
 diversity in upland and lowland switchgrass as a first step in linking
 genotype to phenotype, we designed an exome capture probe set based on
 transcript assemblies that represent ~50 Mb of annotated switchgrass exome
 sequences. We then evaluated and optimized the probe set using solid phase
 comparative genome hybridization and liquid phase exome capture followed
 by next generation sequencing. Using the optimized probe set, we assessed
 variation in the exomes of eight switchgrass genotypes representing
 tetraploid lowland and octoploid upland cultivars to benchmark our exome
 capture probe set design. We identified ample variation in the switchgrass
 genome including 1,395,501 single nucleotide polymorphisms (SNPs), 8,173
 putative copy number variants and 3,336 presence/absence variants. While
 the majority of the SNPs (84%) detected were biallelic, a substantial
 number were tri-allelic with limited occurrence of tetra-allelic
 polymorphisms consistent with the heterozygous and polyploid nature of the
 switchgrass genome. Collectively, these data demonstrate the efficacy of
 exome capture for discovery of genome variation in a polyploid species
 with a large, repetitive and heterozygous genome.
description: switchgrass_exome_capture_snp_matrix.tarSNP Matrix and allele count data for Panicum virgatum exome capture experiment.
DOI: 10.5061/dryad.qr81p
title: Data from: Gene similarity networks provide new tools for understanding eukaryote origins and evolution

description: The complexity and depth of the relationships between the three domains of
 life challenge the reliability of phylogenetic methods, encouraging the
 use of alternative analytical tools. We reconstructed a gene similarity
 network comprising the proteomes of 14 eukaryotes, 104 prokaryotes, 2,389
 viruses and 1,044 plasmids. This network contains multiple signatures of
 the chimerical origin of Eukaryotes as a fusion of an archaebacterium and
 a eubacterium that could not have been observed using phylogenetic trees.
 A number of connected components (gene sets with stronger similarities
 than expected by chance) contain pairs of eukaryotic sequences exhibiting
 no direct detectable similarity. Instead, many eukaryotic sequences were
 indirectly connected through a
 “eukaryote–archaebacterium–eubacterium–eukaryote” similarity path.
 Furthermore, eukaryotic genes highly connected to prokaryotic genes from
 one domain tend not to be connected to genes from the other prokaryotic
 domain. Genes of archaebacterial and eubacterial ancestry tend to perform
 different functions and to act at different subcellular compartments, but
 in such an intertwined way that suggests an early rather than late
 integration of both gene repertoires. The archaebacterial repertoire has a
 similar size in all eukaryotic genomes whereas the number of
 eubacterium-derived genes is much more variable, suggesting a higher
 plasticity of this gene repertoire. Consequently, highly reduced
 eukaryotic genomes contain more genes of archaebacterial than eubacterial
 affinity. Connected components with prokaryotic and eukaryotic genes tend
 to include viral and plasmid genes, compatible with a role of gene
 mobility in the origin of Eukaryotes. Our analyses highlight the power of
 network approaches to study deep evolutionary events.
description: Gene similarity
 networkThe folder
 "ConnectedComponents" contains one file for each connected
 component. In each file, each line represents a network edge. The file
 GeneAnnotations.txt contains basic information for each
 gene.Alvarez-PonceEtAlPNAS2013.rar
DOI: 10.5061/dryad.325ts
title: Data from: Why do markets crash? Bitcoin data offers unprecedented insights

description: Crashes have fascinated and baffled many canny observers of financial
 markets. In the strict orthodoxy of the efficient market theory, crashes
 must be due to sudden changes of the fundamental valuation of assets.
 However, detailed empirical studies suggest that large price jumps cannot
 be explained by news and are the result of endogenous feedback loops.
 Although plausible, a clear-cut empirical evidence for such a scenario is
 still lacking. Here we show how crashes are conditioned by the market
 liquidity, for which we propose a new measure inspired by recent theories
 of market impact and based on readily available, public information. Our
 results open the possibility of a dynamical evaluation of liquidity risk
 and early warning signs of market instabilities, and could lead to a
 quantitative description of the mechanisms leading to market crashes.
description: data
DOI: 10.5061/dryad.97bt8
title: Data from: Investigating the impact of feedback update interval on the efficacy of restorative brain–computer interfaces

description: Restorative brain–computer interfaces (BCIs) have been proposed to enhance
 stroke rehabilitation. Restorative BCIs are able to close the sensorimotor
 loop by rewarding motor imagery (MI) with sensory feedback. Despite the
 promising results from early studies, reaching clinically significant
 outcomes in a timely fashion is yet to be achieved. This lack of efficacy
 may be due to suboptimal feedback provision. To the best of our knowledge,
 the optimal feedback update interval (FUI) during MI remains unexplored.
 There is evidence that sensory feedback disinhibits the motor cortex.
 Thus, in this study, we explore how shorter than usual FUIs affect
 behavioural and neurophysiological measures following BCI training for
 stroke patients using a single-case proof-of-principle study design. The
 action research arm test was used as the primary behavioural measure and
 showed a clinically significant increase (36%) over the course of
 training. The neurophysiological measures including motor evoked
 potentials and maximum voluntary contraction showed distinctive changes in
 early and late phases of BCI training. Thus, this preliminary study may
 pave the way for running larger studies to further investigate the effect
 of FUI magnitude on the efficacy of restorative BCIs. It may also
 elucidate the role of early and late phases of motor learning along the
 course of BCI training.
description: Stroke_PoP_Data
DOI: 10.5061/dryad.36rs0
title: Data from: Development of a gridded meteorological data set over the Java island, Indonesia 1985-2014

description: We describe a gridded daily meteorology dataset consisting of
 precipitation, minimum and maximum temperature over Java Island, Indonesia
 at 0.125°×0.125° (~14 km) resolution spanning 30 years from 1985–2014.
 Importantly, this data set represents a marked improvement from existing
 gridded data sets over Java with higher spatial resolution, derived
 exclusively from ground-based observations unlike existing satellite or
 reanalysis-based products. Gap-infilling and gridding were performed via
 the Inverse Distance Weighting (IDW) interpolation method (radius, r, of
 25 km and power of influence, α, of 3 as optimal parameters) restricted to
 only those stations including at least 3,650 days (~10 years) of valid
 data. We employed MSWEP and CHIRPS rainfall products in the
 cross-validation. It shows that the gridded rainfall presented here
 produces the most reasonable performance. Visual inspection reveals an
 increasing performance of gridded precipitation from grid, watershed to
 island scale. The data set, stored in a network common data form (NetCDF),
 is intended to support watershed-scale and island-scale studies of
 short-term and long-term climate, hydrology and ecology.
description: Meteorology of Java
 IndonesiaThis data contains daily
 precipitation, minimum temperature, maximum temperature and wind speed
 over Java, Indonesia from 1985 - 2014. It has 707 grids/files over the
 island.met_java.tar.gzInterpolation codeThis a code for interpolating the rainfall data associated in this publicationgrid_idw.R
DOI: 10.5061/dryad.q2t18
title: Data from: Identification of immunity-related genes in Dialeurodes citri against entomopathogenic fungus Lecanicillium attenuatum by RNA-seq analysis

description: Dialeurodes citri is a major pest in citrus producing areas, and
 large-scale outbreaks have occurred increasingly often in recent years.
 Lecanicillium attenuatum is an important entomopathogenic fungus that can
 parasitize and kill D. citri. We separated the fungus from corpses of D.
 citri larvae. However, the sound immune defense system of pests makes
 infection by an entomopathogenic fungus difficult. Here we used RNA
 sequencing technology (RNA-Seq) to build a transcriptome database for D.
 citri and performed digital gene expression profiling to screen genes that
 act in the immune defense of D. citri larvae infected with a pathogenic
 fungus. De novo assembly generated 84,733 unigenes with mean length of 772
 nt. All unigenes were searched against GO, Nr, Swiss-Prot, COG, and KEGG
 databases and a total of 28,190 (33.3%) unigenes were annotated. We
 identified 129 immunity-related unigenes in transcriptome database that
 were related to pattern recognition receptors, information transduction
 factors and response factors. From the digital gene expression profile, we
 identified 441 unigenes that were differentially expressed in D. citri
 infected with L. attenuatum. Through calculated Log2Ratio values, we
 identified genes for which fold changes in expression were obvious,
 including cuticle protein, vitellogenin, cathepsin, prophenoloxidase,
 clip-domain serine protease, lysozyme, and others. Subsequent quantitative
 real-time polymerase chain reaction analysis verified the results. The
 identified genes genes may serve as target genes for microbial control of
 D. citri.
description: The cDNA library of
 D.citriFinal DNA sequence
 assemblyWhitefly.Unigene.faSSR informationSSR upload.xlsCDS of unigenesWhitefly.Unigene.cds.faRPKM values of control group and treatment groupRPKM of CG and TG.zipDifferential_analysis_resultsE01_vs_E02.annotation.xlsThe results of qRT-PCR for validated genes
DOI: 10.5061/dryad.63k6q
title: Data from: Hedging your bets: intermediate movements as optimal behavior in the context of an incomplete decision

description: Existing theories of movement planning suggest that it takes time to
 select and prepare the actions required to achieve a given goal. These
 theories often appeal to circumstances where planning apparently goes
 awry. For instance, if reaction times are forced to be very low, movement
 trajectories are often directed between two potential targets. These
 intermediate movements are generally interpreted as errors of movement
 planning, arising either from planning being incomplete or from parallel
 movement plans interfering with one another. Here we present an
 alternative view: that intermediate movements reflect uncertainty about
 movement goals. We show how intermediate movements are predicted by an
 optimal feedback control model that incorporates an ongoing decision about
 movement goals. According to this view, intermediate movements reflect an
 exploitation of compatibility between goals. Consequently, reducing the
 compatibility between goals should reduce the incidence of intermediate
 movements. In human subjects, we varied the compatibility between
 potential movement goals in two distinct ways: by varying the spatial
 separation between targets and by introducing a virtual barrier
 constraining trajectories to the target and penalizing intermediate
 movements. In both cases we found that decreasing goal compatibility led
 to a decreasing incidence of intermediate movements. Our results and
 theory suggest a more integrated view of decision-making and movement
 planning in which the primary bottleneck to generating a movement is
 deciding upon task goals. Determining how to move to achieve a given goal
 is rapid and automatic.
description: Expt1_DataMatlab .mat file containing data from Experiment 1.Expt2_DataMatlab .mat file containing data from Experiment 2.Expt3_DataMatlab .mat file containing data from Experiment 3.
DOI: 10.5061/dryad.r2342
title: Data from: Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures

description: Understanding plant gene promoter architecture has long been a challenge
 due to the lack of relevant large-scale data sets and analysis methods.
 Here, we present a publicly available, large-scale transcription start
 site (TSS) data set in plants using a high-resolution method for analysis
 of 5′ ends of mRNA transcripts. Our data set is produced using the
 paired-end analysis of transcription start sites (PEAT) protocol,
 providing millions of TSS locations from wild-type Columbia-0 Arabidopsis
 thaliana whole root samples. Using this data set, we grouped TSS reads
 into “TSS tag clusters” and categorized clusters into three spatial
 initiation patterns: narrow peak, broad with peak, and weak peak. We then
 designed a machine learning model that predicts the presence of TSS tag
 clusters with outstanding sensitivity and specificity for all three
 initiation patterns. We used this model to analyze the transcription
 factor binding site content of promoters exhibiting these initiation
 patterns. In contrast to the canonical notions of TATA-containing and more
 broad “TATA-less” promoters, the model shows that, in plants, the vast
 majority of transcription start sites are TATA free and are defined by a
 large compendium of known DNA sequence binding elements. We present
 results on the usage of these elements and provide our Plant PEAT Peaks
 (3PEAT) model that predicts the presence of TSSs directly from sequence.
description: Supplemental Data Sets
 1-7Supplemental Data Sets
 1-7tpc125617_SupplementalDatasets.zip