cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.646v2r1
title: Data from: A systems toxicology approach for the prediction of kidney toxicity and its mechanisms in vitro

description: The failure to predict kidney toxicity of new chemical entities early in
 the development process before they reach humans remains a critical issue.
 Here, we used primary human kidney cells and applied a systems biology
 approach that combines multidimensional datasets and machine learning to
 identify biomarkers that not only predict nephrotoxic compounds but also
 provide hints towards their mechanism of toxicity. Gene expression and
 high content imaging phenotypical data from 46 diverse kidney toxicants
 were analyzed using Random Forest machine learning. Imaging features
 capturing changes in cell morphology and nucleus texture along with mRNA
 levels of HMOX1 and SQSTM1 were identified as the most powerful predictors
 of toxicity. These biomarkers were validated by their ability to
 accurately predict kidney toxicity of 4 out of 6 candidate therapeutics
 that exhibited toxicity only in in late stage preclinical/clinical
 studies. Network analysis of similarities in toxic phenotypes was
 performed based on live-cell high-content image analysis at seven time
 points. Using compounds with known mechanism as reference, we could infer
 potential mechanisms of toxicity of candidate therapeutics. In summary, we
 report an approach to generate a multidimensional biomarker panel for
 mechanistic de-risking and prediction of kidney toxicity in vitro for new
 therapeutic candidates and chemical entities.
description: systox.tarAll necessary code and data is housed within this archive. The archive should have an md5 checksum d56eabd45e46af9f28d7936bd7390899. The code is version controlled and any updates can be found at https://github.com/pvtodorov/systox . The data is also stored on synapse.org as syn11697964. The code and data within this repo are released under the CC Zero license.
DOI: 10.5061/dryad.m55c932
title: Data from: Drought effects on the stability of forest-grassland ecotones under gradual climate change

description: Plant communities in forest-grassland ecotones of the European Alps are
 already suffering from gradual climate change and will likely be exposed
 to more frequent and intense drought periods in the future. Yet, how
 gradual climate change and extreme drought will affect the stability of
 these plant communities is largely unknown. Here, we investigated how
 drought modulates the effects of gradual climate change on the long-term
 structural stability of these ecotone communities using a multidimensional
 approach. Using a spatially explicit landscape vegetation model, we
 simulated three drought scenarios, on top of gradual changes of climate
 variables, and their impacts on the dynamics of 24 plant functional
 groups, distinguishing between forests and grasslands, as well as
 different land uses. We then used n-dimensional hypervolumes to define
 community states under the different drought scenarios, and compared them
 to initial conditions to assess changes in community structural stability.
 In general, added drought effects did not counteract the long-term
 consequences of gradual climate changes, although they resulted in
 quantitatively different effects. Importantly, drought and climate change
 had non-negligible consequences for taxonomic and functional structure
 that differed between communities and land-use regimes. For instance,
 forest taxonomic structure was more overall more stable than grassland’s,
 despite the observed functional shifts towards more warm-adapted species
 compositions. Conversely, unmanaged grasslands were the least stable,
 suffering the loss of characteristic alpine species. Also, while frequent
 and severe drought regimes caused forests to become more variable in time,
 they had the opposite effect on grasslands. Our results agree with
 observations of drought- and climate-driven changes in mountain
 communities of the Alps, and we discuss their relevance for ecosystem
 management. Importantly, we demonstrate the utility of this
 multidimensional approach to study community stability for analysing
 cross-community and cross-disturbance responses to global change.
description: DRYAD
DOI: 10.5061/dryad.s2405
title: Data from: Less is more: extreme genome complexity reduction with ddRAD using Ion Torrent semiconductor technology

description: Massively parallel sequencing a small proportion of the whole genome at
 high coverage enables answering a wide range of questions from molecular
 evolution and evolutionary biology to animal and plant breeding and
 forensics. In this study, we describe the development of restriction-site
 associated DNA (RAD) sequencing approach for Ion Torrent PGM platform. Our
 protocol results in extreme genome complexity reduction using two
 rare-cutting restriction enzymes and strict size selection of the library
 allowing sequencing of a relatively small number of genomic fragments with
 high sequencing depth. We applied this approach to a common freshwater
 fish species, the Eurasian perch (Perca fluviatilis L.), and generated
 over 2.2 MB of novel sequence data consisting of ~17 000 contigs,
 identified 1259 single nucleotide polymorphisms (SNPs). We also estimated
 genetic differentiation between the DNA pools from freshwater (Lake
 Peipus) and brackish water (the Baltic Sea) populations and identified
 SNPs with the strongest signal of differentiation that could be used for
 robust individual assignment in the future. This work represents an
 important step towards developing genomic resources and genetic tools for
 the Eurasian perch. We expect that our ddRAD sequencing protocol for
 semiconductor sequencing technology will be useful alternative for
 currently available RAD protocols.
description: Raw
 filesRaw files.rar contains
 the following files: 1) perch_pddRAD_map5_out.ace; 2)
 pop1_lttrim_filt_trimmed_seq_split_V2.fastq; 3)
 pop2_lttrim_filt_trimmed_seq_split_V2.fastq. Pop1 and pop2 stands for
 Baltic Sea and Lake Peipus pool, respectively.PythonCodesPythonCodes.zip - custom Python scripts used in the study.SNP primer sequencesList of 12 markers that were individually validated using seven individuals by PCR and Sanger sequencing.AlignmentsSanger sequencing alignments are in BioEdit (*.bio) and Fasta format (*.fas).
DOI: 10.5061/dryad.94r9s
title: Data from: Cell signaling-based classifier predicts response to induction therapy in elderly patients with acute myeloid leukemia

description: Single-cell network profiling (SCNP) data generated from multi-parametric
 flow cytometry analysis of bone marrow (BM) and peripheral blood (PB)
 samples collected from patients &gt;55 years old with non-M3 AML were
 used to train and validate a diagnostic classifier (DXSCNP) for predicting
 response to standard induction chemotherapy (complete response [CR] or CR
 with incomplete hematologic recovery [CRi] versus resistant disease [RD]).
 SCNP-evaluable patients from four SWOG AML trials were randomized between
 Training (N = 74 patients with CR, CRi or RD; BM set = 43; PB set = 57)
 and Validation Analysis Sets (N = 71; BM set = 42, PB set = 53). Cell
 survival, differentiation, and apoptosis pathway signaling were used as
 potential inputs for DXSCNP. Five DXSCNP classifiers were developed on the
 SWOG Training set and tested for prediction accuracy in an independent BM
 verification sample set (N = 24) from ECOG AML trials to select the final
 classifier, which was a significant predictor of CR/CRi (area under the
 receiver operating characteristic curve AUROC = 0.76, p = 0.01). The
 selected classifier was then validated in the SWOG BM Validation Set
 (AUROC = 0.72, p = 0.02). Importantly, a classifier developed using only
 clinical and molecular inputs from the same sample set (DXCLINICAL2)
 lacked prediction accuracy: AUROC = 0.61 (p = 0.18) in the BM Verification
 Set and 0.53 (p = 0.38) in the BM Validation Set. Notably, the DXSCNP
 classifier was still significant in predicting response in the BM
 Validation Analysis Set after controlling for DXCLINICAL2 (p = 0.03),
 showing that DXSCNP provides information that is independent from that
 provided by currently used prognostic markers. Taken together, these data
 show that the proteomic classifier may provide prognostic information
 relevant to treatment planning beyond genetic mutations and traditional
 prognostic factors in elderly AML.
description: READMESamples to File
 MappingMapping information
 between Sample IDs, modulation condition to FCS and Gating image
 files.Mapping_Samples_to_Files.csvFlow Cytometry Data (FCS FIles) and Gating Image FilesFor each sample data is include for three wells: unmodulated (UM) condition at 15 min timepoint, unmodulated condition at 24 hour timepoint and AraC+Daunorubicin treated condition at 24 hour timepoint. For each well the zipped archive file consists of one FCS files and one gating image file.FCSFiles.zip
DOI: 10.15139/s3/r0yn2m
title: Data Management and Sharing Plan for: Targeting EBV-associated lymphomas

description: The Data Management and Sharing Plan describes the scientific data to be generated and/or used in the research and outlines a strategy for managing and sharing project data.
description: Data Management and Sharing Plan
DOI: 10.5061/dryad.v9t5h
title: Data from: Genetic structure in village dogs reveals a Central Asian domestication origin

description: Dogs were the first domesticated species, originating at least 15,000 y
 ago from Eurasian gray wolves. Dogs today consist primarily of two
 specialized groups—a diverse set of nearly 400 pure breeds and a far more
 populous group of free-ranging animals adapted to a human commensal
 lifestyle (village dogs). Village dogs are more genetically diverse and
 geographically widespread than purebred dogs making them vital for
 unraveling dog population history. Using a semicustom 185,805-marker
 genotyping array, we conducted a large-scale survey of autosomal,
 mitochondrial, and Y chromosome diversity in 4,676 purebred dogs from 161
 breeds and 549 village dogs from 38 countries. Geographic structure shows
 both isolation and gene flow have shaped genetic diversity in village dog
 populations. Some populations (notably those in the Neotropics and the
 South Pacific) are almost completely derived from European stock, whereas
 others are clearly admixed between indigenous and European dogs.
 Importantly, many populations—including those of Vietnam, India, and
 Egypt—show minimal evidence of European admixture. These populations
 exhibit a clear gradient of short-range linkage disequilibrium consistent
 with a Central Asian domestication origin.
description: Genotype file for Canine
 HD semi custom array (bed)ShannonBoyko_All.bedMarker file for Canine HD semi custom array (bim)ShannonBoyko_All.bimSample file for Canine HD semi custom array (fam)ShannonBoyko_All.nopheno.famIdentification for individuals genotyped on the Canine HD semi custom arrayShannonBoyko_All.nopheno.txtGenotype file for merged Illumina and Affymetrix array data (bed)ShannonBoyko_Merged.bedMarker file for merged Illumina and Affymetrix array data (bim)ShannonBoyko_Merged.bimSample file for merged Illumina and Affymetrix array data (fam)ShannonBoyko_Merged.famIdentification for individuals included in merged Illumina and Affymetrix dataShannonBoyko_Merged.indMt Marker locationsShannonBoyko_Mt.mapGenotypes for Mt haplotypesShannonBoyko_MtHaplotypeGenotypesMt haplotype calls for indvidualsShannonBoyko_MtHaplotypesY marker locationsShannonBoyko_Y.mapGenotypes for Y haplotypesShannonBoyko_YHaplotypeGenotypes.pedY haplotype calls for indvidualsShannonBoyko_YHaplotypes
DOI: 10.5061/dryad.18sg7
title: Data from: Ancestry-specific methylation patterns in admixed offspring from an experimental coyote and gray wolf cross

description: Reduced fitness of admixed individuals is typically attributed to genetic
 incompatibilities. Although mismatched genomes can lead to fitness
 changes, in some cases the reduction in hybrid fitness is subtle. The
 potential role of transcriptional regulation in admixed genomes could
 provide a mechanistic explanation for these discrepancies, but evidence is
 lacking for non-model organisms.Here, we explored the intersection of
 genetics and gene regulation in admixed genomes derived from an
 experimental cross between a western gray wolf and western coyote. We
 found a significant positive association between methylation and wolf
 ancestry, and identified outlier genes that have been previously
 implicated in inbreeding-related, or otherwise deleterious, phenotypes. We
 describe a pattern of site-specific, rather than genome-wide, methylation
 driven by inter-specific hybridization. Epigenetic variation is thus
 suggested to play a non-trivial role in both maintaining and combating
 mismatched genotypes through putative transcriptional mechanisms. We
 conclude that the regulation of gene expression is an underappreciated key
 component of hybrid genome functioning, but could also act as a potential
 source of novel and beneficial adaptive variation in hybrid offspring.
description: wyoteMeth_10x_3mil_sites_MFThis file contains the methylation frequency (MF, number of cytosines out of the total read coverage) per site for a coyote, wolves, and their hybrid offspring. This dataset contains ~3 million cytosines.Wyotes_15733_GBS_SNPsThis file contains SNP genotypes for 15,733 sites generated by GBS for a coyote, wolves, and their hybrid offspring.
DOI: 10.5061/dryad.mq2q9
title: Data from: A phylogenomic analysis of Marek's disease virus (MDV) reveals independent paths to virulence in Eurasia and North America

description: Virulence determines the impact a pathogen has on the fitness of its host,
 yet current understanding of the evolutionary origins and causes of
 virulence of many pathogens is surprisingly incomplete. Here, we explore
 the evolution of Marek's disease virus (MDV), a herpesvirus commonly
 afflicting chickens and rarely other avian species. The history of MDV in
 the 20th century represents an important case study in the evolution of
 virulence. The severity of MDV infection in chickens has been rising
 steadily since the adoption of intensive farming techniques and
 vaccination programs in the 1950s and 1970s respectively. It has remained
 uncertain, however, which of these factors is causally more responsible
 for the observed increase in virulence of circulating viruses. We
 conducted a phylogenomic study to understand the evolution of MDV in the
 context of dramatic changes to poultry farming and disease control. Our
 analysis reveals evidence of geographical structuring of MDV strains, with
 reconstructions supporting the emergence of virulent viruses independently
 in North America and Eurasia. Of note, the emergence of virulent viruses
 appears to coincide approximately with the introduction of comprehensive
 vaccination on both continents. The time-dated phylogeny also indicated
 that MDV has a mean evolutionary rate of ~1.6 x 10-5 substitutions / site
 / year. An examination of gene-linked mutations did not identify a strong
 association between mutational variation and virulence phenotypes,
 indicating that MDV may evolve readily and rapidly under strong selective
 pressures, and that multiple genotypic pathways may underlie virulence
 adaptation in MDV.
description: phylogenetic
 analysisContains whole genome
 alignments, BEAST and PhyML filesmutation
 analysisContains FastML output
 files and ORF mutation informationR code
 fileContains R code and
 paths to relevant files in the data packagecode.R
DOI: 10.5061/dryad.dm690
title: Data from: Loss of sexual recombination and segregation is associated with increased diversification in evening primroses

description: The loss of sexual recombination and segregation in asexual organisms has
 been portrayed as an irreversible process that commits
 asexually-reproducing lineages to reduced diversification. We test this
 hypothesis by estimating rates of speciation, extinction, and transition
 between sexuality and functional asexuality in the evening primroses.
 Specifically, we estimate these rates using the recently developed BiSSE
 (Binary State Speciation and Extinction) phylogenetic comparative method,
 which employs maximum likelihood and Bayesian techniques. We infer that
 net diversification rates (speciation minus extinction) in functionally
 asexual evening primrose lineages are roughly eight times faster than
 diversification rates in sexual lineages, largely due to higher speciation
 rates in asexual lineages. We further reject the hypothesis that a loss of
 recombination and segregation is irreversible because the transition rate
 from functional asexuality to sexuality is significantly greater than
 zero.and in fact exceeded the reverse rate. These results provide the
 first empirical evidence in support of the alternative theoretical
 prediction that asexual populations should instead diversify more rapidly
 than sexual populations because they are free from the homogenizing
 effects of sexual recombination and segregation. Although asexual
 reproduction may often constrain adaptive evolution, our results show that
 the loss of recombination and segregation need not be an evolutionary
 dead-end in terms of diversification of lineages.
description: Onagraceae TREEBASE
 fileML_analysesThis zip directory gives the BiSSE maximum likelihood analyses reported in Table S3.MCMC_analysesThis zip directory gives the full MCMC results and the R code that generated the data underlying Figure 3, Figure S1, Figure S3, Table 1, and Table S2.
DOI: 10.5061/dryad.4qf2h
title: Data from: Gene expression under thermal stress varies across a geographic range expansion front

description: Many ectothermic species are currently expanding their distributions
 polewards due to anthropogenic global warming. Molecular genetic
 mechanisms facilitating range expansion under these conditions are largely
 unknown, but understanding these could help mitigate expanding pests and
 disease vectors, or help explain why some species fail to track changing
 climates. Here, using RNA-seq data, we examine genome-wide changes in gene
 expression under heat and cold stress in the range-expanding damselfly
 Ischnura elegans in northern Europe. We find that both the number of genes
 involved and levels of gene expression under heat stress have become
 attenuated during the expansion, consistent with a previously-reported
 release from selection on heat tolerances as species move polewards. Genes
 upregulated under cold stress differed between core and edge populations,
 corroborating previously-reported rapid adaptation to cooler climates at
 the expansion front. Expression of sixty-nine genes exhibited a region x
 treatment effect; these were primarily upregulated in response to heat
 stress in core populations but in response to cold stress at the range
 edge, suggesting that some cellular responses originally adapted to heat
 stress may switch to cold stress functionality upon encountering novel
 thermal selection regimes during range expansion. Transcriptional
 responses to thermal stress involving heat shock and neural function genes
 were largely geographically conserved, while retrotransposon, regulatory,
 muscle function and defence gene expression patterns were more variable.
 Flexible mechanisms of cold stress response and the ability of some genes
 to shift their function between heat and cold stress might be key
 mechanisms facilitating rapid poleward expansion in insects.
description: AssemblyThe file contains fasta sequence of high quality transcripts obtained after three step of stringent filtering.annotationsThe file contains annotations for high quality transcripts by BLASTX, InterProScan, GO and Enzymes terms.RSEM.tarThe folder contains RSEM output files for each sample.differential_expression.tarThe folder contains files for differential expression analysis between heat and cold treatments from two regions (hoje and nora).
DOI: 10.5061/dryad.r31js91
title: Data from: Shifts in selective pressures on snake phototransduction genes associated with photoreceptor transmutation and dim-light ancestry

description: The visual systems of snakes are heavily modified relative to other
 squamates, a condition often thought to reflect their fossorial origins.
 Further modifications are seen in caenophidian snakes, where evolutionary
 transitions between rod and cone photoreceptors, termed photoreceptor
 transmutations, have occurred in many lineages. Little previous work,
 however, has focused on the molecular evolutionary underpinnings of these
 morphological changes. To address this, we sequenced seven snake eye
 transcriptomes and utilized new whole genome and targeted capture
 sequencing data. We used this data to analyze gene loss and shifts in
 selection pressures in phototransduction genes that may be associated with
 snake evolutionary origins and photoreceptor transmutation. We identified
 the surprising loss of rhodopsin kinase (GRK1), despite a low degree of
 gene loss overall and a lack of relaxed selection early during snake
 evolution. These results provide some of the first evolutionary genomic
 corroboration for a dim-light ancestor that lacks strong fossorial
 adaptations. Our results also indicate that snakes with photoreceptor
 transmutation experienced significantly different selection pressures from
 other reptiles. Significant positive selection was found primarily in
 cone-specific genes, but not rod-specific genes, contrary to our
 expectations. These results reveal potential molecular adaptations
 associated with photoreceptor transmutation, and also highlight
 unappreciated functional differences between rod- and cone-specific
 phototransduction proteins. This intriguing example of snake visual system
 evolution illustrates how the underlying molecular components of a complex
 system can be reshaped in response to changing selection pressures.
description: Draft Genome
 CDSSequences extracted from
 various draft genomes used in the selection analyses.FDR Control
 ResultsResults of analyses to
 control the false discovery rate (FDR).PAML
 FilesAlignment and tree files
 needed to run the PAML analyses.PAML Results
 TablesDetailed results and
 summary tables of each of the PAML analyses.Sequence
 AlignmentsMultiple sequence
 alignments for each gene.Transcriptome
 AssembliesDe novo Trinity
 assemblies of the colubrid snake eye transcriptomes.