cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9n6q6
title: Data from: Drechslerella stenobrocha genome ilustrates the mechanism of constricting rings and the origin of nematode predation in fungi

description: Background: Nematode-trapping fungi are a unique group of organisms that
 can capture nematodes using sophisticated trapping structures. The genome
 of Drechslerella stenobrocha, a constricting-ring-forming fungus, has been
 sequenced and reported, and provided new insights into the evolutionary
 origins of nematode predation in fungi, the trapping mechanisms, and the
 dual lifestyles of saprophagy and predation. Results: The genome of the
 fungus Drechslerella stenobrocha, which mechanically traps nematodes using
 a constricting ring, was sequenced. The genome was 29.02 Mb in size and
 was found rare instances of transposons and repeat induced point
 mutations, than that of Arthrobotrys oligospora. The functional proteins
 involved in nematode-infection, such as chitinases, subtilisins, and
 adhesive proteins, underwent a significant expansion in the A. oligospora
 genome, while there were fewer lectin genes that mediate fungus-nematode
 recognition in the D. stenobrocha genome. The carbohydrate-degrading
 enzyme catalogs in both species were similar to those of efficient
 cellulolytic fungi, suggesting a saprophytic origin of nematode-trapping
 fungi. In D. stenobrocha, the down-regulation of saprophytic enzyme genes
 and the up-regulation of infection-related genes during the capture of
 nematodes indicated a transition between dual life strategies of
 saprophagy and predation. The transcriptional profiles also indicated that
 trap formation was related to the protein kinase C (PKC) signal pathway
 and regulated by Zn(2)-C6 type transcription factors. Conclusions: The
 genome of D. stenobrocha provides support for the hypothesis that nematode
 trapping fungi evolved from saprophytic fungi in a high carbon and low
 nitrogen environment. It reveals the transition between saprophagy and
 carnivory of these fungi and also proves new insights into the mechanisms
 of mechanical trapping.
description: Phylogenetic
 treeThe phylogeny tree was
 constructed using RAxML.finalAln.nex
DOI: 10.5061/dryad.4n3d1
title: Data from: Persistence of the mitochondrial lineage responsible for the Irish potato famine in extant New World Phytophthora infestans

description: The plant pathogen Phytophthora infestans emerged in Europe in 1845,
 triggering the Irish potato famine and massive European potato crop losses
 that continued until effective fungicides were widely employed in the 20th
 century. Today the pathogen is ubiquitous, with more aggressive and
 virulent strains surfacing in recent decades. Recently, complete P.
 infestans mitogenome sequences from 19th-century herbarium specimens were
 shown to belong to a unique lineage (HERB-1) predicted to be rare or
 extinct in modern times. We report 44 additional P. infestans mitogenomes:
 four from 19th-century Europe, three from 1950s U.K. and 34 from modern
 populations across the New World. We use phylogenetic analyses to identify
 the HERB-1 lineage in modern populations from both Mexico and South
 America, and to demonstrate distinct mitochondrial haplotypes were present
 in 19th-century Europe, with this lineage initially diversifying 75 years
 before the first reports of potato late blight.
description: FASTA alignment of
 assembled mtDNA genome sequences used in ML analysis (excluding reference
 genomes Ia,Ib, IIa and IIb)FASTA alignment of whole
 mitogenome sequences for Phytophthora infestans samples considered in our
 ML analysismitogenome sequences
 alignments.fasta
DOI: 10.5061/dryad.jf150
title: Data from: To keep on track during flight, fruitflies discount the skyward view

description: When small flying insects go off their intended course, they use the
 resulting pattern of motion on their eye, or optic flow, to guide
 corrective steering. A change in heading generates a unique, rotational
 motion pattern and a change in position generates a translational motion
 pattern, and each produces corrective responses in the wingbeats. Any
 image in the flow field can signal rotation, but owing to parallax, only
 the images of nearby objects can signal translation. Insects that fly near
 the ground might therefore respond more strongly to translational optic
 flow that occurs beneath them, as the nearby ground will produce strong
 optic flow. In these experiments, rigidly tethered fruitflies steered in
 response to computer-generated flow fields. When correcting for unintended
 rotations, flies weight the motion in their upper and lower visual fields
 equally. However, when correcting for unintended translations, flies
 weight the motion in the lower visual fields more strongly. These results
 are consistent with the interpretation that fruitflies stabilize by
 attending to visual areas likely to contain the strongest signals during
 natural flight conditions.
description: l_r_wbaTwo files zipped together. "l_r_wba_1.npy" contains the wing beat amplitudes that produced figure 2, i--iix, in the free numerical python array format. The numerical python command "d = load("l_r_wba.npy") will instantiate "d" with a four dimensional array 2x8x143x6900. The first dimension indexes the left and right wing beat amplitudes, the second one indexes the eight different experiments, the third one indexes each of 143 repetitions, and the fourth dimension indexes time, with samples taken at 1kHz. "l_r_wba_2.npy" contains the wing beat data for figure 2, ix-x, and will load into a 2x2x88x6900 array. The indexes are similar, but it contains only two different experiments and 88 repetitions. In each case the stimulus each fly viewed moved left and right with a triangular waveform, "t = -arcsin(sin(linspace(0, 8*pi, 6900)))"
DOI: 10.5061/dryad.kr154
title: Data from: Epidemiology of injuries in elite taekwondo athletes: two Olympic periods cross-sectional retrospective study

description: Objective: Taekwondo injuries differ according to the characteristics of
 the athletes and the competition. This analytical cross-sectional
 retrospective cohort study aimed to describe reported taekwondo injuries
 and to determine the prevalence, characteristics and possible risk factors
 for injuries sustained by athletes of the Spanish national team. In
 addition, we compared each identified risk factor—age, weight category,
 annual quarter, injury timing and competition difficulty level—with its
 relation to injury location and type. Settings: Injury occurrences in
 taekwondo athletes of the Spanish national team during two Olympic periods
 at the High Performance Centre in Barcelona were analysed. Participants:
 48 taekwondo athletes (22 male, 26 female; age range 15–31 years) were
 studied; 1678 injury episodes occurred. Inclusion criteria were: (1)
 having trained with the national taekwondo group for a minimum of one
 sports season; (2) being a member of the Spanish national team. Results:
 Independently of sex or Olympic period, the anatomical sites with most
 injury episodes were knee (21.3%), foot (17.0%), ankle (12.2%), thigh
 (11.4%) and lower leg (8.8%). Contusions (29.3%) and cartilage (17.6%) and
 joint (15.7%) injuries were the prevalent types of injury. Chronological
 age, weight category and annual quarter can be considered risk factors for
 sustaining injuries in male and female elite taekwondists according to
 their location and type (p≤0.001). Conclusions: This study provides
 epidemiological information that will help to inform future injury
 surveillance studies and the development of prevention strategies and
 recommendations to reduce the number of injuries in taekwondo competition.
description: Figure
 1Figure
 2
DOI: 10.5061/dryad.fg679
title: Data from: Postmarket safety in Canada: are significant therapeutic advances and biologics less safe than other drugs? A cohort study

description: Objectives: Examine the probability of new active substances (NASs)
 approved in Canada between 1 January 1997 and 31 March 2012 acquiring a
 serious postmarket safety warning. Design: Cohort study. Data sources:
 Annual reports of the Therapeutic Products Directorate and the Biologic
 and Genetic Therapies Directorate; evaluations of therapeutic innovation
 from the Patented Medicine Prices Review Board and Prescrire
 International; MedEffect Canada website. Interventions: Postmarket
 regulatory safety warning or withdrawal from market due to safety reasons.
 Primary and secondary outcome measures: Compare the probability of
 acquiring a postmarket safety warning in Canada in four different groups
 of drugs: (1) traditional medications versus biologics; (2) medications
 that offer significant new therapeutic benefits versus those that do not.
 Determine how well the type of review that an NAS received from Health
 Canada predicted the product's postmarket therapeutic value. Results:
 The probability of a traditional NAS acquiring a serious safety warning
 and/or being withdrawn was 29.9% (95% CI 21.8% to 40.2%) vs 27.3% (95% CI
 18.2% to 39.7%) for an NAS of biological origin (p=0.47, log-rank test).
 For medications that were significant therapeutic advances the probability
 was 40.2% (95% CI 24.5% to 60.9%) vs 33.9% (95% CI 26.4% to 42.7%) for
 those that were not (p=0.18, log-rank test). Health Canada was 77.4%
 accurate in predicting the therapeutic importance of an NAS. Conclusions:
 There was no difference in postmarket regulatory safety action between
 traditional medications and biologics and no difference between drugs with
 significant therapeutic benefits and those without. Although these results
 draw on Canadian data, they are likely to be relevant internationally.
 Further research should assess whether the current level of premarket
 safety evaluation is acceptable.
description: Main table - NAS
 databaseDatabase listing all new
 active substances approved by Health Canada from January 1, 1995 to March
 31, 2013 along with dates and nature of serious safety warnings (dates in
 bold)Therapeutic rating
 scoresDatabase contains the
 therapeutic rating scores for new active substances from the Patented
 Medicine Prices Review Board and from Prescrire
 International.NAS - PMPRB & Prescrire
 ratings.xlsx
DOI: 10.5061/dryad.2cs4g
title: Data from: Genotyping-by-sequencing for Populus population genomics: an assessment of genome sampling patterns and filtering approaches

description: Continuing advances in nucleotide sequencing technology are inspiring a
 suite of genomic approaches in studies of natural populations. Researchers
 are faced with data management and analytical scales that are increasing
 by orders of magnitude. With such dramatic advances comes a need to
 understand biases and error rates, which can be propagated and magnified
 in large-scale data acquisition and processing. Here we assess genomic
 sampling biases and the effects of various population-level data filtering
 strategies in a genotyping-by-sequencing (GBS) protocol. We focus on data
 from two species of Populus, because this genus has a relatively small
 genome and is emerging as a target for population genomic studies. We
 estimate the proportions and patterns of genomic sampling by examining the
 Populus trichocarpa genome (Nisqually-1), and demonstrate a pronounced
 bias towards coding regions when using the methylation-sensitive ApeKI
 restriction enzyme in this species. Using population-level data from a
 closely related species (P. tremuloides), we also investigate various
 approaches for filtering GBS data to retain high-depth, informative SNPs
 that can be used for population genetic analyses. We find a data filter
 that includes the designation of ambiguous alleles resulted in metrics of
 population structure and Hardy-Weinberg equilibrium that were most
 consistent with previous studies of the same populations based on other
 genetic markers. Analyses of the filtered data (27,910 SNPs) also resulted
 in patterns of heterozygosity and population structure similar to a
 previous study using microsatellites. Our application demonstrates that
 technically and analytically simple approaches can readily be developed
 for population genomics of natural populations.
description: HapMap.hmc.txt.tarHapMap hmc files generated by UNEAK (Universal Network Enabled Analysis Kit) filter with default settings.HapMap.hmp.txt.tarHapMap hmp file generated by UNEAK (Universal Network Enabled Analysis Kit) filter with default settings
DOI: 10.15468/dl.5eaq6z
title: Occurrence Download

description: A dataset containing 2159 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Atlas de la Biodiversité Communale de Breuillet-ABC Breuillet"
 ]
}

 The dataset includes 2159 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001611-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.5ds40
title: Data from: Sex uncovered special issue: selective maintenance of recombination between the sex chromosomes

description: A hallmark of many sex chromosomes is the dramatically reduced rate of
 recombination between them in the heterogametic sex (e.g., between the X
 and Y). Sexually antagonistic selection is thought to be the main
 selective driver of this reduced recombination, with tighter linkage
 strengthening the association between alleles favourable to females and
 the X, as well as alleles favourable to males and the Y. Nevertheless,
 many sex chromosomes retain substantial levels of recombination over
 millions of years, and some old sex chromosomes remain homomorphic with
 few signs of recombination suppression and the chromosomal degradation
 expected to follow. This paper explores the selective factors that can
 maintain recombination between the sex chromosomes. Specifically, by
 analysing the dynamics of genes that modify the rate of recombination, I
 present results demonstrating that certain forms of selection – all
 involving overdominance in males – can positively maintain recombination
 in the pseudo-autosomal region. To understand these cases, one has to
 revise our standard view of sexual antagonistic selection as involving two
 partners (males and females) to three partners (the X in females, the X in
 males, and the Y).
description: Analysis (Mathematica
 file)Mathematica 8.0 (Wolfram
 Research, Inc. 2010) package detailing the recursion equations, analyses,
 and simulations conducted.RecModifier.nbAnalysis (PDF)PDF of a Mathematica 8.0 (Wolfram Research, Inc. 2010) package detailing the recursion equations, analyses, and simulations conducted.RecModifier.pdf
DOI: 10.5061/dryad.42ph0
title: Data from: The environmental structure of trilobite morphological disparity

description: Despite the mounting evidence that taxonomic diversity dynamics are
 patterned environmentally and that taxonomic diversity and morphological
 disparity are decoupled both temporally and spatially in many clades, very
 little work has been done to assess whether disparity is also influenced
 by environment. Here I investigate whether trilobite disparity shows
 environmental patterning through time. I used the method developed by
 Simpson and Harnik (2009) for estimating latitudinal, substrate, and
 bathymetric affinities from fossil occurrence data, downloaded from the
 Paleobiology Database. This method has the advantages that the biological
 null hypothesis is explicitly separated from the expectation due to
 sampling, and that the posterior probability can be used to infer degree
 of preference for one habitat compared to another. To measure morphology,
 I used a data set of outlines of the trilobite cranidium from Foote
 (1993). Many of the species in this data set are not represented in the
 Paleobiology Database in sufficient numbers to assess species-level
 affinity for these taxa, but species-level affinity could be estimated
 with high fidelity by using genus-level affinities. Results show that
 cranidial morphological diversity was structured by environmental
 preferences of the taxa but the structure was complex and changed through
 time. In particular, there was little differentiation in morphospace
 around latitudinal, substrate, or bathymetric affinity during the
 Cambrian. In contrast, both diversification and expansion into previously
 unoccupied areas of morphospace during the Ordovician were dominated by
 tropical, deeper-water taxa.
description: Hopkins-SupplementaryTable1See Hopkins_tables-description.pdf for explanation of tableHopkins-SupplementaryTable2See Hopkins_tables-description.pdf for explanation of tableHopkins-SupplementaryTable3See Hopkins_tables-description.pdf for explanation of tableHopkins-SupplementaryTable4See Hopkins_tables-description.pdf for explanation of tableHopkins-SupplementaryTable5See Hopkins_tables-description.pdf for explanation of tableHopkins-SupplementaryTable6See Hopkins_tables-description.pdf for explanation of tableHopkins-SupplementaryTable7See Hopkins_tables-description.pdf for explanation of tableHopkins_tables-descriptionMetadata for supplementary tables
DOI: 10.5061/dryad.bv4k7
title: Data from: Gut microbiota signatures predict host and microbiota responses to dietary interventions in obese individuals

description: Background: Interactions between the diet and intestinal microbiota play a
 role in health and disease, including obesity and related metabolic
 complications. There is great interest to use dietary means to manipulate
 the microbiota to promote health. Currently, the impact of dietary change
 on the microbiota and the host metabolism is poorly predictable and highly
 individual. We propose that the responsiveness of the gut microbiota may
 depend on its composition, and associate with metabolic changes in the
 host. Methodology: Our study involved three independent cohorts of obese
 adults (n = 78) from Belgium, Finland, and Britain, participating in
 different dietary interventions aiming to improve metabolic health. We
 used a phylogenetic microarray for comprehensive fecal microbiota analysis
 at baseline and after the intervention. Blood cholesterol, insulin and
 inflammation markers were analyzed as indicators of host response. The
 data were divided into four training set – test set pairs; each
 intervention acted both as a part of a training set and as an independent
 test set. We used linear models to predict the responsiveness of the
 microbiota and the host, and logistic regression to predict responder vs.
 non-responder status, or increase vs. decrease of the health parameters.
 Principal Findings: Our models, based on the abundance of several, mainly
 Firmicute species at baseline, predicted the responsiveness of the
 microbiota (AUC = 0.77–1; predicted vs. observed correlation = 0.67–0.88).
 Many of the predictive taxa showed a non-linear relationship with the
 responsiveness. The microbiota response associated with the change in
 serum cholesterol levels with an AUC of 0.96, highlighting the involvement
 of the intestinal microbiota in metabolic health. Conclusion: This
 proof-of-principle study introduces the first potential microbial
 biomarkers for dietary responsiveness in obese individuals with impaired
 metabolic health, and reveals the potential of microbiota signatures for
 personalized nutrition.
description: HITChip microarray
 dataThe file contains
 phylogenetic microarray signal intensities for 1037 species and uncultured
 phylotypes, and for 130 genus-like group (≥ 90% sequence similarity in the
 16S rRNA gene). More information about the phylogenetic design of the
 HITChip can be found at
 http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.01900.x/full
 The data are extracted with using min/max normalisation and
 log-transformed (not subjected to between-study normalization; for details
 see the publication).PLoS1MicrobiotaResponsetoDiet.txt
DOI: 10.5061/dryad.3n010
title: Data from: The clock gene Period1 regulates innate routine behaviour in mice

description: Laboratory mice are well capable of performing innate routine behaviour
 programmes necessary for courtship, nest-building and exploratory
 activities although housed for decades in animal facilities. We found that
 in mice inactivation of the clock gene Period1 profoundly changes innate
 routine behaviour programmes like those necessary for courtship, nest
 building, exploration and learning. These results in wild-type and Period1
 mutant mice, together with earlier findings on courtship behaviour in
 wild-type and period-mutant Drosophila melanogaster, suggest a conserved
 role of Period-genes on innate routine behaviour. Additionally, both
 per-mutant flies and Period1-mutant mice display spatial learning and
 memory deficits. The profound influence of Period1 on routine behaviour
 programmes in mice, including female partner choice, may be independent of
 its function as a circadian clock gene, since Period1-deficient mice
 display normal circadian behaviour.
description: Raw data Bechstein et al
 2014 PRSBAll numerical data for
 the main figures
DOI: 10.7927/z7jc-8164
title: IPCC AR6 Synthesis Report LR Figure 3.6 (c): Timing of reaching net-zero GHG and CO2 emissions for global modelled pathways that limit warming

description: Total GHG and CO2 emissions timing of reaching net-zero in different mitigation pathways. The Panel shows median (vertical line), likely (bar) and very likely (thin lines) timing of reaching net-zero GHG and CO2 emissions for global modelled pathways that limit warming to 1.5°C (&gt;50%) with no or limited overshoot (C1) (left) or 2°C (&gt;67%) (C3) (right).
DOI: 10.5061/dryad.r458n
title: Data from: ExcaliBAR: a simple and fast software utility to calculate intra- and interspecific distances from DNA barcodes

description: In the context of DNA Barcoding, sequences of standard marker genes for
 thousands and potentially millions of individuals and species are becoming
 available, requiring ever more efficient bioinformatic environments and
 software algorithms for analysis. We here present ExcaliBAR (Extraction,
 Calculation, Barcoding), a user-friendly software utility to facilitate
 one important initial step in DNA barcoding analyses, namely the
 determination of the barcoding gap between pairwise genetic distances
 among and within species, based on original distance matrices computed by
 MEGA software. In addition, the software is able to rename sequences
 downloaded via the standard user interfaces of public databases such as
 GenBank, without the need of developing and applying specific scripts for
 this purpose.
description: ExCaliBAR