cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ns135
title: Data from: De novo assembly and characterization of the skeletal muscle and electric organ transcriptomes of the African weakly-electric fish Campylomormyrus compressirostris (Mormyridae, Teleostei)

description: African weakly electric-fishes (Mormyridae) underwent an outstanding
 adaptive radiation (about 200 species), putatively owing to their ability
 to communicate through species-specific weak electric signals. The
 electric organ discharge (EOD) is produced by muscle-derived electrocytes
 organized in piles to form an electric organ. Despite the importance of
 this trait as a pre-zygotic isolation mechanism, genomic resources
 remained limited. We present here a first draft of the skeletal muscle and
 electric organ transcriptomes from the weakly-electric fish species
 Campylomormyrus compressirostris, obtained using the Illumina HiSeq2000
 sequencing technology. Approximately 6.8 Gbp of cDNA sequence data were
 produced from both tissues, resulting in 57,268,109 raw reads for the
 skeletal muscle and 46,934,923 for the electric organ, and assembled de
 novo into 46,143 and 89,270 contigs, respectively. About 50% of both
 transcriptomes were annotated after protein databases search. The two
 transcriptomes show similar profiles in terms of Gene Ontology categories
 composition. We identified several candidate genes which are likely to
 play a central role in the production and evolution of the electric
 signal. For most of these genes, and for many other housekeeping genes, we
 were able to obtain the complete or partial coding DNA sequences (CDS),
 which can be used for the development of primers to be utilized in qRT-PCR
 experiments. We present also the complete mitochondrial genome and compare
 it to those available from other weakly-electric species. Additionally we
 located 1671 SSR containing regions with their flanking sites and designed
 the relative primers. The present study establishes a first step in the
 development of genomic tools aimed at understanding the role of
 electric-communication during speciation.
description: C. compressirostris
 electric organ contigs (Velvet/Oases)Set of contigs assembled
 from the electric organ reads using Velvet/Oases.transcripts_EO.faC. compressirostris skeletal muscle contigs (Velvet/Oases)Set of contigs assembled from the skeletaal muscle reads using Velvet/Oases.transcripts_MU.faGene Ontology annotation (electric organ)List of electric organ contig names with the corresponding annotated GO code.EO_vs_uniprot_sprot_oases.annotGene Ontology annotation (skeletal muscle)List of skeletal muscle contig names with the corresponding annotated GO code.MU_vs_uniprot_sprot_oases.annotC. compressirostris reads mapping vs C.numenius mt genome.Result of C. compressirostris transcriptome reads mapping against the mitochondrial genome of C.numenius.AP011571_reads_mapping.bamMormyridae mt-genomes alignment.Alignment of the reconstructed C. compressirostris mt-genome against other mormyrids mt-genomes available from Genbank.mt_genomes_alignment.fastaFisher Exact TestR script used to perform the Fisher's Exact Test with FDR p-value correction.multi_fisher.r
DOI: 10.5061/dryad.bn960cq
title: Data from: Neural control of balance during walking

description: Neural control of standing balance has been extensively studied. However,
 most falls occur during walking rather than standing, and findings from
 standing balance research do not necessarily carry over to walking. This
 is primarily due to the constraints of the gait cycle: Body configuration
 changes dramatically over the gait cycle, necessitating different
 responses as this configuration changes. Notably, certain responses can
 only be initiated at specific points in the gait cycle, leading to onset
 times ranging from 350 to 600ms, much longer than what is observed during
 standing (50–200ms). Here, we investigated the neural control of upright
 balance during walking. Specifically, how the brain transforms sensory
 information related to upright balance into corrective motor responses. We
 used visual disturbances of 20 healthy young subjects walking in a virtual
 reality cave to induce the perception of a fall to the side and analyzed
 the muscular responses, changes in ground reaction forces and body
 kinematics. Our results showed changes in swing leg foot placement and
 stance leg ankle roll that accelerate the body in the direction opposite
 of the visually induced fall stimulus, consistent with previous results.
 Surprisingly, ankle musculature activity changed rapidly in response to
 the stimulus, suggesting the presence of a direct reflexive pathway from
 the visual system to the spinal cord, similar to the vestibulospinal
 pathway. We also observed systematic modulation of the ankle push-off,
 indicating the discovery of a previously unobserved balance mechanism.
 Such modulation has implications not only for balance but plays a role in
 modulation of step width and length as well as cadence. These results
 indicated a temporally-coordinated series of balance responses over the
 gait cycle that insures flexible control of upright balance during
 walking.
description: VisionDataThis archive contains the data from all relevant variables for the four steps following a visual perturbation trigger (stimulus), and two steps preceding it (control) in MATLAB format (file results.mat). The file results.csv contains a sub-set of the data for statistical analysis. The matlab R-script used for the statistical analysis (visionStats.R) and the MATLAB script used to generate the published figures (createFigures.m) are also provided. The folders anovaResults and confintResults contain text files with the results of the statistical analysis.
DOI: 10.5061/dryad.h02q0
title: Data from: Low fossilization potential of keratin protein revealed by experimental taphonomy

description: Recent studies have suggested the presence of keratin in fossils dating
 back to the Mesozoic. However, ultrastructural studies revealing exposed
 melanosomes in many fossil keratinous tissues suggest that keratin should
 rarely, if ever, be preserved. In this study, keratin's stability
 through diagenesis was tested using microbial decay and maturation
 experiments on various keratinous structures. The residues were analysed
 using pyrolysis-gas chromatography-mass spectrometry and compared to
 unpublished feather and hair fossils and published fresh and fossil
 melanin from squid ink. Results show that highly matured feathers
 (200–250°C/250 bars/24 h) become a volatile-rich, thick fluid with
 semi-distinct pyrolysis compounds from those observed in less degraded
 keratins (i.e. fresh, decayed, moderately matured, and decayed and
 moderately matured) suggesting hydrolysis of peptide bonds and potential
 degradation of free amino acids. Neither melanization nor keratin
 (secondary) structure (e.g. ⍺- vs β-keratin) produced different pyrograms;
 melanin pyrolysates are largely a subset of those from proteins, and
 proteins have characteristic pyrolysates. Analyses of fossil fur and
 feather found a lack of amides, succinimide and piperazines (present even
 in highly matured keratin) and showed pyrolysis compounds more similar to
 fossil and fresh melanin than to non-matured or matured keratin. Although
 the highly matured fluid was not water soluble at room temperature, it
 readily dissolved at elevated temperatures easily attained during
 diagenesis, meaning it could leach away from the fossil. Future
 interpretations of fossils must consider that calcium phosphate and
 pigments are the only components of keratinous structures known to survive
 fossilization in mature sediments.
description: Appendix
 S1Extended methods and
 discussionPy/GC/MS .RAW
 files.zipRAW.zipPy/GC/MS .CDF files.zipCDF.zip
DOI: 10.5061/dryad.1rf7d
title: Data from: Adélie penguin population diet monitoring by analysis of food DNA in scats

description: The Adélie penguin is the most important animal currently used for
 ecosystem monitoring in the Southern Ocean. The diet of this species is
 generally studied by visual analysis of stomach contents; or ratios of
 isotopes of carbon and nitrogen incorporated into the penguin from its
 food. There are significant limitations to the information that can be
 gained from these methods. We evaluated population diet assessment by
 analysis of food DNA in scats as an alternative method for ecosystem
 monitoring with Adélie penguins as an indicator species. Scats were
 collected at four locations, three phases of the breeding cycle, and in
 four different years. A novel molecular diet assay and bioinformatics
 pipeline based on nuclear small subunit ribosomal RNA gene (SSU rDNA)
 sequencing was used to identify prey DNA in 389 scats. Analysis of the
 twelve population sample sets identified spatial and temporal dietary
 change in Adélie penguin population diet. Prey diversity was found to be
 greater than previously thought. Krill, fish, copepods and amphipods were
 the most important food groups, in general agreement with other Adélie
 penguin dietary studies based on hard part or stable isotope analysis.
 However, our DNA analysis estimated that a substantial portion of the diet
 was gelatinous groups such as jellyfish and comb jellies. A range of other
 prey not previously identified in the diet of this species were also
 discovered. The diverse prey identified by this DNA-based scat analysis
 confirms that the generalist feeding of Adélie penguins makes them a
 useful indicator species for prey community composition in the coastal
 zone of the Southern Ocean. Scat collection is a simple and non-invasive
 field sampling method that allows DNA-based estimation of prey community
 differences at many temporal and spatial scales and provides significant
 advantages over alternative diet analysis approaches.
description: 1_AdelieDietPopulationResults2_FASTQfiles3_SampleKeyFiles4_SSUdietPipeline
DOI: 10.5061/dryad.ct3s3
title: Data from: Social learning in otters

description: The use of information provided by others to tackle life's challenges
 is widespread, but should not be employed indiscriminately if it is to be
 adaptive. Evidence is accumulating that animals are indeed selective and
 adopt ‘social learning strategies’. However, studies have generally
 focused on fish, bird and primate species. Here we extend research on
 social learning strategies to a taxonomic group that has been neglected
 until now: otters (subfamily Lutrinae). We collected social association
 data on captive groups of two gregarious species: smooth-coated otters
 (Lutrogale perspicillata), known to hunt fish cooperatively in the wild,
 and Asian short-clawed otters (Aonyx cinereus), which feed individually on
 prey requiring extractive foraging behaviours. We then presented otter
 groups with a series of novel foraging tasks, and inferred social
 transmission of task solutions with network-based diffusion analysis. We
 show that smooth-coated otters can socially learn how to exploit novel
 food sources and may adopt a ‘copy when young’ strategy. We found no
 evidence for social learning in the Asian short-clawed otters. Otters are
 thus a promising model system for comparative research into social
 learning strategies, while conservation reintroduction programmes may
 benefit from facilitating the social transmission of survival skills in
 these vulnerable species.
description: Otter social learning
 DataData of otter social
 networks, individual characteristics, and order / time of each individual
 solving the novel foraging tasks.AICsmoothInputData file used to run a Network-Based Diffusion Analysis on the smooth-coated otter dataNBDA code smooth-coated otterThis is the Network-Based Diffusion Analysis code to be used with the AICsmoothInput.csv file in R to run the NBDA.Otter social learning Supplementary Video1Video 1: Smooth-coated otters are presented with task 5 (see main text Fig. 1)Otter social learning Supplementary Video2Otter social learning Supplementary Video3Asian short-clawed otters are presented with task 4 (see main text Fig. 2)
DOI: 10.5061/dryad.5vd61
title: Data from: Simulation assisted analysis of the intrinsic stiffness for short DNA molecules imaged with scanning atomic force microscopy

description: Studying the mechanical properties of short segments of dsDNA can provide
 insight into various biophysical phenomena, from DNA looping to the
 organization of nucleosomes. Scanning atomic force microscopy (AFM) is
 able to acquire images of single DNA molecules with near-basepair
 resolution. From many images, one may use equilibrium statistical
 mechanics to quantify the intrinsic stiffness (or persistence length) of
 the DNA. However, this approach is highly dependent upon both the correct
 microscopic polymer model and a correct image analysis of DNA contours.
 These complications have led to significant debate over the flexibility of
 dsDNA at short length scales. We first show how to extract accurate
 measures of DNA contour lengths by calibrating to DNA traces of simulated
 AFM data. After this calibration, we show that DNA adsorbed on an
 aminopropyl-mica surface behaves as a worm-like chain (WLC) for contour
 lengths as small as ~20 nm. We also show that a DNA binding protein can
 modify the mechanics of the DNA from that of a WLC.
description: STM&MHNSdata
DOI: 10.5061/dryad.18kk6
title: Data from: Multivariate analysis of electrophysiological diversity of Xenopus visual neurons during development and plasticity

description: Biophysical properties of neurons become increasingly diverse over
 development, but mechanisms underlying and constraining this diversity are
 not fully understood. Here we investigate electrophysiological
 characteristics of Xenopus tadpole midbrain neurons across development and
 during homeostatic plasticity induced by patterned visual stimulation. We
 show that in development tectal neuron properties not only change on
 average, but also become increasingly diverse. After sensory stimulation,
 both electrophysiological diversity and functional differentiation of
 cells are reduced. At the same time, the amount of cross-correlations
 between cell properties increase after patterned stimulation as a result
 of homeostatic plasticity. We show that tectal neurons with similar
 spiking profiles often have strikingly different electrophysiological
 properties, and demonstrate that changes in intrinsic excitability during
 development and in response to sensory stimulation are mediated by
 different underlying mechanisms. Overall, this analysis and the
 accompanying dataset provide a unique framework for further studies of
 network maturation in Xenopus tadpoles.
description: Raw Electrophysiological
 Data, and extracted parameters from Optic Tectum Neurons of Xenopus
 tadpolesThis dataset contains
 the raw electrophysiological recording data that was used to quantify cell
 diversity in the Optic Tectum of premetamorphic Xenopus tadpoles. The
 recordings were performed in pClamp, and are stored here as Matlab
 MAT-files. The raw data is accompanied by a summary table of measurements
 presented in the paper, and a "master file" that matches raw
 data files to cell ids from the summary table. The ZIP archive contains
 several folders that separately store: (1) Voltage gated current traces in
 response to voltage steps that were used to build Na and K IV-curves
 (folder "01 IV curve"); (2) Active changes in membrane potential
 (spiking) in response to step current injections (folder "02 Current
 step injections"); (3) Spiking in response to cosine current
 injections (folder "03 Current cosine injections"); (4) Synaptic
 currents recorded in voltage clamp after synaptic stimulation of the optic
 nerve with equally spaced impulses and with different inter-stimulus
 intervals (folder "04 Synaptic bursts"); (5) Miniature
 spontaneous excitatory postsynaptic currents (folder "05
 Minis").eLife_Data-2015-10-27.zip
DOI: 10.5061/dryad.cf66jb7
title: Data from: Conservation of preparatory neural events in monkey motor cortex regardless of how movement is initiated

description: A time-consuming preparatory stage is hypothesized to precede voluntary
 movement. A putative neural substrate of motor preparation occurs when a
 delay separates instruction and execution cues. When readiness is
 sustained during the delay, sustained neural activity is observed in motor
 and premotor areas. Yet whether delay-period activity reflects an
 essential preparatory stage is controversial. In particular, it has
 remained ambiguous whether delay-period-like activity appears before
 non-delayed movements. To overcome that ambiguity, we leveraged a recently
 developed analysis method that parses population responses into putatively
 preparatory and movement-related components. We examined cortical
 responses when reaches were initiated after an imposed delay, at a
 self-chosen time, or reactively with low latency and no delay. Putatively
 preparatory events were conserved across all contexts. Our findings
 support the hypothesis that an appropriate preparatory state is
 consistently achieved before movement onset. However, our results reveal
 that this process can consume surprisingly little time.
description: Figure
 2AData for figure 2A,
 monkey BaFigure2_A_monkeyBa_RTs.matFigure2_BData for figure 2BFigure2_CDData for Figure 2CDFigure2_EFData for Figure 2EFFigure2_GData for Figure 2GFigure2_HData for Figure 2HFigure2_S1_monkeyAxData for Figure 2 - supplement 1, monkey AxFigure2_S1_monkeyBaData for Figure 2 - supplement 1, monkey BaFigure2_S2_monkeyAxData for Figure 2 - supplement 2, monkey AxFigure2_S2_monkeyBaData for Figure 2 - supplement 2, monkey BaFigure3_A_monkeyBa_lateralBicepsData for Figure 3A, monkey Ba, lateral BicepsFigure3_B_monkeyBa_trapeziusData for Figure 3B, monkey Ba, trapeziusFigure3_D_monkeyAx_medialBicepsData for Figure 3D, monkey Ax, medial bicepsFigure3_C_monkeyBa_medialDeltoidData for Figure 3C, monkey Ba, medial deltoidFigure3_E_monkeyAx_anteriorDeltoidFigure 3E, monkey Ax, anterior deltoidFigure3_F_monkeyAx_medialDeltoidData for Figure 3F, medial deltoidFigure3_S1Datat for Figure 3 - supplement 1Figure4EMG data for Figure 4Figure4_S1Data for Figure 4 - supplement 1Figure4_S2Data for Figure 4 - supplement 2Figure5_A_neuron88Data for Figure 5A, neuron 88Figure5_B_neuron105Data for Figure 5B, neuron 105Figure5_C_neuron110Data for Figure 5C, neuron 110Figure7_CDData for Figure 7CDFigure8Data for Figure 8Figure8_S1Data for Figure 8 - supplement 1Figure9Data for Figure 9Figure10_and10_S1Data for Figure 10 and supplement 1Figure10_S2Data for Figure 10 - supplement 2Figure11_ABData for Figure 11ABFigure11_CDData for Figure 11CDFigure11_S1Data for Figure 11 - supplement 1
DOI: 10.5061/dryad.js408
title: Data from: The complex contributions of genetics and nutrition to immunity in Drosophila melanogaster

description: Both malnutrition and undernutrition can lead to compromised immune
 defense in a diversity of animals, and “nutritional immunology” has been
 suggested as a means of understanding immunity and determining strategies
 for fighting infection. The genetic basis for the effects of diet on
 immunity, however, has been largely unknown. In the present study, we have
 conducted genome-wide association mapping in Drosophila melanogaster to
 identify the genetic basis for individual variation in resistance, and for
 variation in immunological sensitivity to diet (genotype-by-environment
 interaction, or GxE). D. melanogaster were reared for several generations
 on either high-glucose or low-glucose diets and then infected with
 Providencia rettgeri, a natural bacterial pathogen of D. melanogaster.
 Systemic pathogen load was measured at the peak of infection intensity,
 and several indicators of nutritional status were taken from uninfected
 flies reared on each diet. We find that dietary glucose level
 significantly alters the quality of immune defense, with elevated dietary
 glucose resulting in higher pathogen loads. The quality of immune defense
 is genetically variable within the sampled population, and we find genetic
 variation for immunological sensitivity to dietary glucose
 (genotype-by-diet interaction). Immune defense was genetically correlated
 with indicators of metabolic status in flies reared on the high-glucose
 diet, and we identified multiple genes that explain variation in immune
 defense, including several that have not been previously implicated in
 immune response but which are confirmed to alter pathogen load after RNAi
 knockdown. Our findings emphasize the importance of dietary composition to
 immune defense and reveal genes outside the conventional “immune system”
 that can be important in determining susceptibility to infection.
 Functional variation in these genes is segregating in a natural
 population, providing the substrate for evolutionary response to pathogen
 pressure in the context of nutritional environment.
description: GWAS results for immune
 defense when data from both diets pooledColumns are: SNP
 position, factor, denominator DF, numerator DF, F, P,
 Chromosomeall.snps.csvGWAS for interaction between diet and SNP for immune responseColumns are: SNP, factor, denominator DF, numerator DF, F, P, chromosomeall.interact.csvGWAS for immune response on high glucose dietColumns are: SNP, factor, denominator DF, numerator DF, F, P, chromosomeallhigh.dpt.snpsGWAS for immune response on low glucose dietColumns are: SNP, factor, denominator DF, numerator DF, F, P, chromosomealllow.dpt.snpsLine means for all phenotypes from studyColumns are self-explanatory with all values for nutritional indices being mg/fly, bacterial load is natural log load per fly, weight is in mg. Data from linear models as described in manuscript.allnutrients.csv
DOI: 10.13140/rg.2.2.17029.41444
title: RHtestV2 User Manual
DOI: 10.5061/dryad.j68v0
title: Data from: Nucleus reuniens of the thalamus contains head direction cells

description: Discrete populations of brain cells signal heading direction, rather like
 a compass. These ‘head direction’ cells are largely confined to a
 closely-connected network of sites. We describe, for the first time, a
 population of head direction cells in nucleus reuniens of the thalamus in
 the freely-moving rat. This novel subcortical head direction signal
 potentially modulates the hippocampal CA fields directly and, thus,
 informs spatial processing and memory.
description: Dryad_NRe_cells_and_histology