cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3v3m7fk
title: Data from: Development, characterization and comparisons of targeted and non-targeted metabolomics methods

description: The potential of a metabolomics method to detect statistically significant
 perturbations in the metabolome of an organism is enhanced by excellent
 analytical precision, unequivocal identification, and broad metabolomic
 coverage. While the former two metrics are usually associated with
 targeted metabolomics and the latter with non-targeted metabolomics, a
 systematic comparison of the performance of both approaches has not yet
 been carried out. The present work reports on the development and
 performance evaluation of separate targeted and non-targeted metabolomics
 methods. The targeted approach facilitated determination of 181
 metabolites (quantitative analysis of 18 amino acids, 10 biogenic amines,
 5 neurotransmitters, 5 nucleobases and semi-quantitative analysis of 50
 carnitines, 83 phosphotidylcholines, and 9 sphingomyelins) using
 ultra-performance liquid chromatography-tandem mass spectrometry
 (UPLC-MS/MS) and flow injection-tandem mass spectrometry (FI-MS/MS).
 Method accuracy and/or precision were assessed using replicate samples of
 NIST SRM1950 as well as fish liver and brain tissue from Gilthead Bream
 (Sparus aurata). The non-target approach involved UPLC-high resolution
 (Orbitrap) mass spectrometry (UPLC-HRMS). Testing of ionization mode and
 stationary phase revealed that a combination of positive electrospray
 ionization and HILIC chromatography produced the largest number of
 chromatographic features during non-target analysis. Furthermore, an
 evaluation of 4 different sequence drift correction algorithms, and
 combinations thereof, revealed that batchCorr produced the best precision
 in almost every test. However, even following correction of non-target
 data for signal drift, the precision of targeted data was better,
 confirming our existing assumptions about the strengths of targeted
 metabolomics. Finally, the accuracy of the online MS2-library mzCloud was
 evaluated using reference standards for 38 different metabolites. This is
 among the few studies that have systematically evaluated the performance
 of targeted and non-targeted metabolomics and provides new insight into
 the advantages and disadvantages of each approach.
description: TNTmetabolomicsRawDataThe raw chromatographical data (peak areas) after integration from Orbitrap and triple quad analysis.
DOI: 10.5061/dryad.8vs569h
title: Data from: Spatial heterogeneity in species composition constrains plant community responses to herbivory and fertilization

description: Environmental change can result in substantial shifts in community
 composition. The associated immigration and extinction events are likely
 constrained by the spatial distribution of species. Still, studies on
 environmental change typically quantify biotic responses at single spatial
 (time series within a single plot) or temporal (spatial beta-diversity at
 single time points) scales, ignoring their potential interdependence.
 Here, we use data from a global network of grassland experiments to
 determine how turnover responses to two major forms of environmental
 change – fertilization and herbivore loss – are affected by species pool
 size and spatial compositional heterogeneity. Fertilization led to higher
 rates of local extinction whereas turnover in herbivore exclusion plots
 was driven by species replacement. Overall, sites with more spatially
 heterogeneous composition showed significantly higher rates of annual
 turnover, independent of species pool size and treatment. Taking into
 account spatial biodiversity aspects will therefore improve our
 understanding of consequences of global and anthropogenic change on
 community dynamics.
description: composition-dataThe file contains information on sample ID (site_code, block, plot), number of years since the first treatment application (0 = year before treatment application), treatment (Control = control, NPK = nutrient addition, Fence = herbivore exclusion, NPK+Fence = combined treatment of nutrient addition and herbivore exclusion), species identity (Taxon) and % cover of each speciesEnvironmental parameters measured in Y0The file contains information on sample ID (site_code, block, plot), treatment (Control = control, NPK = nutrient addition, Fence = herbivore exclsuion, NPK+Fence = combiend treatment of nutrient addition and herbivore exclusion), soil measurements, ambient light measurement (Ambient_PAR), annual temperature variability (TEMP_VAR) and annual rainfall variability (MAP_VAR). All measurements were taken before the first application of treatments.env-param-Y0.csv
DOI: 10.5061/dryad.f6t39kj
title: Data from: Traits of lizards of the world: variation around a successful evolutionary design

description: Motivation – over the last 12 years I have been collecting trait and
 geographic data on lizards. These data could be useful for scientists
 studying this remarkable reptilian radiation. Furthermore, as published
 data for some of the less well known species are scarce, I hope this study
 can initiate a community effort to fill in data gaps. I present
 geographical, morphological, ecological, physiological and life history
 data for the 6657 known species of lizards. I further indicate whether
 there are phylogenetic data associated with them, and their threat
 assessment, if they have one. I present descriptive statistics regarding
 these traits and point to avenues for future research using the dataset.
 Main types of variable contained – body size, ecological, thermal biology,
 geographic, phylogenetic and life history data Spatial location - global
 Time period – data are for species known from living, or recently extinct
 species. Most underlying data were collected during the 20th and 21st
 centuries. Major taxa – Reptilia, Sauria (Squamata, including Amphisbaenia
 but excluding Serpentes) Level of measurement - species Software format –
 csv.
description: Appendix S1 - Lizard
 data version 1.0traits of the lizards of
 the worldAppendix S2 -
 metadatametadata for data
 file
DOI: 10.5061/dryad.8nc444t
title: Data from: The microstructure of white feathers predicts their visible and near-infrared reflectance properties

description: Research on the optical properties of animal integuments, including fur,
 feather, skin and cuticle, has focussed almost exclusively on
 animal-visible wavelengths within the narrow range of 300 - 700 nm. By
 contrast, the near-infrared (NIR) portion of direct sunlight, spanning 700
 - 2600 nm, has been largely ignored despite its potentially important
 thermal consequences. We quantified variation in visible and NIR
 reflectance and transmission for white body contour feathers of 50 bird
 species, and examined how well they are predicted by feather macro- and
 micro-structural morphology. Both visible and NIR reflectance of the
 feathers varied substantially across species. Larger, thicker, and sparser
 feathers that are characteristic of larger species, and feathers with
 rounder barbs and more closely spaced barbules, had high average
 reflectance, particularly within avian-visible wavelengths (300 - 700 nm).
 Feathers with rounder barbs and more closely situated barbules also had
 high average reflectance, particularly for NIR wavelengths. Barb roundness
 and barbule density were the only predictors of NIR reflectance after
 accounting for variation in visible reflectance and body size. Our results
 highlight the potential for adaptive variation in NIR reflectance mediated
 by feather structure, which may inform the design of functional materials
 to control light and heat.
description: reflectance and
 transmission spec measurementsThis file is the raw
 reflectance and transmission measurements taken of the feathers of the 50
 species listed in the publication.data for comparative
 analysesmodels and model
 outputs
DOI: 10.5061/dryad.bd55173
title: Data from: Experimental study on permeability characteristics for containing-gas raw coal under different stress conditions

description: The experimental study on permeability characteristics for raw coal under
 different stress state is implemented by applying the triaxial self-made
 "THM coupled with servo-controlled seepage apparatus for
 containing-gas coal", the result indicates: The flow rate of coal
 sample gradually decreases with the nonlinear loading of axial pressure
 and increases with the nonlinear unloading of axial stress and confining
 pressure. The flow rate, axial stress and confining pressure curves all
 satisfy the negative exponential function relation. When the sample
 reaches the peak intensity, the sample will be destroyed and the stress
 will drop rapidly, then the flow rate of the sample will increase rapidly.
 At this stage, the flow rate and axial strain show an oblique
 "v" pattern. The flow rate of coal sample increases nonlinear
 with the increase of gas pressure, the relation curve between flow rate
 and gas pressure satisfies power function relation. Under the condition of
 same confining pressure and gas pressure, the larger the axial stress is,
 the flow rate of coal sample will be smaller. Under the condition of same
 axial stress and gas pressure, as confining pressure decreases, the flow
 rate of coal sample will firstly decrease, but then increase. During the
 loading and unloading process post-peak, the flow rate of coal sample will
 decrease with the loading of confining pressure but increase with the
 unloading of confining pressure, and it will increase in wave shape with
 the increase of axial strain. The flow rate of each loading and unloading
 confining pressure is higher than that of the previous loading and
 unloading confining pressure. At the post-peak stage, the relation curve
 between the flow rate of coal sample and confining pressure satisfies the
 power function relation in the process of loading and unloading confining
 pressure.
description: original test
 dataThe data is the original
 data of the test process, which can be opened by Excel
 software.
DOI: 10.5061/dryad.37628q6
title: Data from: Valproic acid is protective in cellular and worm models of oculopharyngeal muscular dystrophy

description: Objective: To explore valproic acid (VPA) as a potentially beneficial drug
 in cellular and worm models of oculopharyngeal muscular dystrophy (OPMD).
 Methods: Using a combination of live cell imaging and biochemical
 measures, we evaluated the potential protective effect of VPA in a stable
 C2C12 muscle cell model of OPMD, in lymphoblastoid cell lines derived from
 patients with OPMD and in a transgenic Caenorhabditis elegans OPMD model
 expressing human mutant PABPN1. Results: We demonstrated that VPA protects
 against the toxicity of mutant PABPN1. Of note, we found that VPA confers
 its long-term protective effects on C2C12 cell survival, proliferation,
 and differentiation by increasing the acetylated level of histones.
 Furthermore, VPA enhances the level of histone acetylation in
 lymphoblastoid cell lines derived from patients with OPMD. Moreover,
 treatment of nematodes with moderate concentrations of VPA significantly
 improved the motility of the PABPN-13 Alanines worms. Conclusions: Our
 results suggest that VPA helps to counteract OPMD-related phenotypes in
 the cellular and C elegans disease models.
description: Valproic acid is
 protective in cellular and worm models of oculopharyngeal muscular
 dystrophy (Supplementary Figures)Supplementary Figures:
 figure e-1, figure e-2, figure e-3, figure e-4, figure e-5, figure e-6,
 figure e-7, figure e-8, figure e-9, figure e-10, figure e-11, figure e-12,
 figure e-13.Supplementary
 Figures.pdf
DOI: 10.5061/dryad.97c7v3k
title: Data from: An integrated data resource for genomic analysis of cutaneous T-cell lymphoma

description: Recently, several groups have conducted sequencing studies of cutaneous
 T-cell lymphoma (CTCL) in order to identify disease driving mutations. An
 integrated genomic dataset that combines multiple cohorts may facilitate
 more comprehensive studies of disease pathways and genomic classification
 of CTCL, but currently no such resource is available. In this study we
 compiled and analyzed one such dataset that included matched genomic
 mutations and copy number alterations of 139 CTCL cases. Using this
 dataset, we studied mutual exclusivity of mutations in the most frequently
 mutated pathways and survival curves depending on mutation load and other
 parameters. We found that mutations in the NFkB pathway genes PLCG1,
 CARD11 and TNFRSF1B were mutually exclusive. Mutations in the NFkB pathway
 genes and those in p53 were also mutually exclusive. No significant
 difference in overall survival was seen between SS cases with or without
 mutations in p53 or the NFkB pathway genes. There was a difference in
 overall survival between SS cases with the most and the fewest mutations
 in the genome. These results suggest the possibility of classifying CTCL
 by underlying pathogenic pathways and the potential for selective
 targeting of CTCL by patient-specific mutations in order to personalize
 CTCL therapies.
description: Supplemental_tables_Chang_et_al
DOI: 10.5061/dryad.jt07145
title: Data from: Counting with DNA in metabarcoding studies: how should we convert sequence reads to dietary data?

description: Advances in DNA sequencing technology have revolutionised the field of
 molecular analysis of trophic interactions and it is now possible to
 recover counts of food DNA sequences from a wide range of dietary samples.
 But what do these counts mean? To obtain an accurate estimate of a
 consumer’s diet should we work strictly with datasets summarising
 frequency of occurrence of different food taxa, or is it possible to use
 relative number of sequences? Both approaches are applied to obtain
 semi-quantitative diet summaries, but occurrence data is often promoted as
 a more conservative and reliable option due to taxa-specific biases in
 recovery of sequences. We explore representative dietary metabarcoding
 datasets and point out that diet summaries based on occurrence data often
 overestimate the importance of food consumed in small quantities
 (potentially including low-level contaminants) and are sensitive to the
 count threshold used to define an occurrence. Our simulations indicate
 that using relative read abundance (RRA) information often provide a more
 accurate view of population-level diet even with moderate recovery biases
 incorporated; however, RRA summaries are sensitive to recovery biases
 impacting common diet taxa. Both approaches are more accurate when the
 mean number of food taxa in samples is small. The ideas presented here
 highlight the need to consider all sources of bias and to justify the
 methods used to interpret count data in dietary metabarcoding studies. We
 encourage researchers to continue addressing methodological challenges,
 and acknowledge unanswered questions to help spur future investigations in
 this rapidly developing area of research.
description: R-code used to run
 simulations outlined in the paperSee README
 fileSimulations.rR code for figures and dataThe data used to produce figures in the paper
DOI: 10.5061/dryad.p2p7j6g
title: Data from: Uncertainty in geographic estimates of performance and fitness

description: 1. Thermal performance curves (TPCs) have become key tools for predicting
 geographic distributions of performance by ectotherms. Such TPC-based
 predictions, however, may be sensitive to errors arising from diverse
 sources. 2. We analyzed potential errors that arise from common choices
 faced by biologists integrating TPCs with climate data by constructing
 case studies focusing on experimental sets of TPCs and simulating
 geographic patterns of mean performance. We first analyzed differences in
 geographic patterns of performance derived from two pairs of commonly used
 TPCs. Mean performance differed most (up to 30%) in regions with
 relatively constant mean temperatures similar to those at which the TPCs
 diverged the most. 3. We also analyzed the effects of thermal history by
 comparing geographic estimates derived from (1) a broad TPC based on
 short-term measurements of insect larvae (Manduca sexta) with a history of
 exposure to thermal variation versus (2) a narrow TPC based on long-term
 measurements of larvae held at constant temperatures. Estimated mean
 performance diverged by up to 40%, and differences were magnified in
 simulated future climates. 4. Finally, to quantify geographic error
 arising from statistical error in fitted TPCs, we propose and illustrate a
 bootstrapping technique for establishing 95% prediction intervals on mean
 performance at each location (pixel). 5. Collectively, our analyses
 indicate that error arising from several underappreciated sources can
 significantly affect the mean performance values derived from TPCs, and we
 suggest that the magnitudes of these errors should be estimated routinely
 in future studies.
description: Figure2_a_rasterRaster layer of data presented in Figure 2a saved as geotiff.Figure2_b_rasterRaster layer of data presented in Figure 2b saved as a geotiffFigure2_d_rasterRaster layer of data presented in Figure 2d saved as a geotiffFigure2_e_rasterRaster layer of data presented in Figure 2e saved as a geotiffFigure3_a_rasterRaster layer of data presented in Figure 3a saved as a geotiffFigure3_b_rasterRaster layer of data presented in Figure 3b saved as a geotiffFigure3_d_rasterRaster layer of data presented in Figure 3d saved as a geotiffFigure3_e_rasterRaster layer of data presented in Figure 3e saved as a geotiffFigure4_a_rasterRaster layer of data presented in Figure 4a saved as a geotiffFigure4_b_rasterRaster layer of data presented in Figure 4b saved as a geotiffFigure4_d_rasterRaster layer of data presented in Figure 4d saved as a geotiffFigure4_e_rasterRaster layer of data presented in Figure 4e saved as a geotiff
DOI: 10.5061/dryad.28fg251
title: Data from: Sequence capture phylogenomics of eyeless Cicurina spiders from Texas caves, with emphasis on US federally-endangered species from Bexar County (Araneae, Hahniidae)

description: We combined morphological, mitochondrial, and nuclear phylogenomic data to
 address phylogenetic and species delimitation questions in cave-limited
 Cicurina spiders from central Texas. We focused special effort on
 specimens and cave locations in the San Antonio region (Bexar County),
 home to four eyeless species listed as US Federally Endangered. Our
 sequence capture experiments resulted in the recovery of ~ 200-400
 homologous ultra-conserved element (UCE) nuclear loci across taxa, and
 nearly complete COI mitochondrial DNA sequences from the same set of
 individuals. Some of these nuclear and mitochondrial sequences were
 recovered from "standard" museum specimens without special
 preservation of DNA material, including museum specimens preserved in the
 1990s. Multiple phylogenetic analyses of the UCE data agree in the
 recovery of two major lineages of eyeless Cicurina in Texas. These
 lineages also differ in mitochondrial clade membership, female genitalic
 morphology, degree of troglomorphy (as measured by relative leg length),
 and are mostly allopatric across much of Texas. Rare sympatry was
 confirmed in Bexar County, where members of the two major clades sometimes
 co-exist in the same karst feature. Both nuclear phylogenomic and
 mitochondrial data indicate the existence of undescribed species from the
 San Antonio region, although further sampling and collection of adult
 specimens is needed to explicitly test these hypotheses. Our data support
 the two following species synonymies (Cicurina venii Gertsch 1992 =
 Cicurina madla Gertsch 1992; Cicurina loftini Cokendolpher 2004 = Cicurina
 vespera Gertsch 1992), formally proposed here. Overall, our
 taxonomy-focused research has many important conservation implications,
 and again highlights the fundamental importance of robust taxonomy in
 conservation research.
description: Cicurina_COI_wUCECOI sequence alignmentCicurina_399UCE_5050% occupancy nuclear UCE matrixCicurina_238UCE_7070% occupancy nuclear UCE matrixCicurina_COI_RAxML_bipartitionsCOI RAxML treeCicurina_399UCEloci_50_RAxML50% occupancy nuclear UCE RAxML treeCicurina_238UCEloci_70_RAxML70% occupancy nuclear UCE RAxML treeCicurina_399UCEloci_ASTRAL_5050% occupancy nuclear UCE ASTRAL treeCicurina_238UCEloci_ASTRAL_7070% occupancy nuclear UCE ASTRAL treeCicurina_238UCEloci_70_SVD70% occupancy nuclear UCE SVDQuartets treeCicurina_238UCEloci_70_BEAST_concat70% occupancy nuclear UCE BEAST tree
DOI: 10.5061/dryad.0vt7nt0
title: Data from: Social behavior in bees influences the abundance of Sodalis (Enterobacteriaceae) symbionts

description: Social interactions can facilitate transmission of microbes between
 individuals, reducing variation in gut communities within social groups.
 Thus, the evolution of social behaviors and symbiont community composition
 have the potential to be tightly linked. We explored this connection by
 characterizing the diversity of bacteria associated with both eusocial and
 solitary bee species within the behaviorally variable family Halictidae
 using 16S amplicon sequencing. Contrary to expectations, we found few
 differences in bacterial abundance or variation between social forms; most
 halictid species appear to share similar gut bacterial communities.
 However, several strains of Sodalis, a genus described as a symbiont in a
 variety of insects but yet to be characterized in bees, differ in
 abundance between eusocial and solitary bees. Phylogenetic reconstructions
 based on whole-genome alignments indicate that Sodalis has independently
 colonized halictids at least three times. These strains appear to be
 mutually exclusive within individual bees, although they are not
 host-species-specific and no signatures of vertical transmission were
 observed, suggesting that Sodalis strains compete for access to hosts. The
 symbiosis between halictids and Sodalis therefore appears to be in its
 early stages.
description: Genome assembly and
 annotations for Sodalis lineage SAL1Genome was assembled
 using metagenomic techniques and annotated using the RAST
 server.SAL1.tar.gzGenome assembly and annotations for Sodalis lineage SAL2Genome was assembled using metagenomic techniques and annotated using the RAST server.SAL2.tar.gzGenome assembly and annotations for Sodalis lineage SLEUGenome was assembled using metagenomic techniques and annotated using the RAST server.SLEU.tar.gzRepresentative sequences for 16S OTUs identified in this study.Sequences with names beginning with "denovo" are less than 97% similar to Greengenes representative sequences at this similarity level. All other sequences are those from Greengenes release 13_8.qiime_rep_set.fa.gz