cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.828nn
title: Data from: The clinical significance and molecular features of the spatial tumor shapes in breast cancers

description: Each breast cancer has its unique spatial shape, but the clinical
 importance and the underlying mechanism for the three-dimensional tumor
 shapes are mostly unknown. We collected the data on the three-dimensional
 tumor size and tumor volume data of invasive breast cancers from 2,250
 patients who underwent surgery between Jan 2000 and Jul 2007. The degree
 of tumor eccentricity was estimated by using the difference between the
 spheroid tumor volume and ellipsoid tumor volume (spheroid-ellipsoid
 discrepancy, SED). In 41 patients, transcriptome and exome sequencing data
 obtained. Estimation of more accurate tumor burden by calculating
 ellipsoid tumor volumes did not improve the outcome prediction when
 compared to the traditional longest diameter measurement. However, the
 spatial tumor eccentricity, which was measured by SED, showed significant
 variation between the molecular subtypes of breast cancer. Additionally,
 the degree of tumor eccentricity was associated with well-known prognostic
 factors of breast cancer such as tumor size and lymph node metastasis.
 Transcriptome data from 41 patients showed significant association between
 MMP13 and spatial tumor shapes. Network analysis and analysis of TCGA gene
 expression data suggest that MMP13 is regulated by ERBB2 and S100A7A. The
 present study validates the usefulness of the current tumor size method in
 determining tumor stages. Furthermore, we show that the tumors with high
 eccentricity are more likely to have aggressive tumor characteristics.
 Genes involved in the extracellular matrix remodeling can be candidate
 regulators of the spatial tumor shapes in breast cancer.
description: SED vs Transcriptome
 ProfileRNA-Seq Analysis
 Results: Read counts, correlation with SED values, and final filtered
 genesExome
 ProfileExome Analysis Results:
 Copy number variations inferred by absCN-seq, clonality analysis by
 sciClone, and somatic mutations by VarScan.
DOI: 10.5061/dryad.239sm
title: Data from: Using the Phenoscape Knowledgebase to relate genetic perturbations to phenotypic evolution

description: The abundance of phenotypic diversity among species can enrich our
 knowledge of development and genetics beyond the limits of variation that
 can be observed in model organisms. The Phenoscape Knowledgebase (KB) is
 designed to enable exploration and discovery of phenotypic variation among
 species. Because phenotypes in the KB are annotated using standard
 ontologies, evolutionary phenotypes can be compared with phenotypes from
 genetic perturbations in model organisms. To illustrate the power of this
 approach, we review the use of the KB to find taxa showing evolutionary
 variation similar to that of a query gene. Matches are made between the
 full set of phenotypes described for a gene and an evolutionary profile,
 the latter of which is defined as the set of phenotypes that are variable
 among the daughters of any node on the taxonomic tree. Phenoscape’s
 semantic similarity interface allows the user to assess the statistical
 significance of each match and flags matches that may only result from
 differences in annotation coverage between genetic and evolutionary
 studies. Tools such as this will help meet the challenge of relating the
 growing volume of genetic knowledge in model organisms to the diversity of
 phenotypes in nature. The Phenoscape KB is available at
 http://kb.phenoscape.org.
description: Semantic Similarity
 ResultsSemanticSimilarityResults.tsv.gzOntologytbox-hierarchy-only.owl.zipPhenotype profilesprofiles.ttl.zip
DOI: 10.5061/dryad.4tv57
title: Data from: Modulation of the cutaneous silent period in the upper-limb with whole-body instability

description: The silent period induced by cutaneous electrical stimulation of the
 digits has been shown to be task-dependent, at least in the grasping
 muscles of the hand. However, it is unknown if the cutaneous silent period
 is adaptable throughout muscles of the entire upper limb, in particular
 when the task requirements are substantially altered. The purpose of the
 present study was to examine the characteristics of the cutaneous silent
 period in several upper limb muscles when introducing increased whole-body
 instability. The cutaneous silent period was evoked in 10 healthy
 individuals with electrical stimulation of digit II of the right hand when
 the subjects were seated, standing, or standing on a wobble board while
 maintaining a background elbow extension contraction with the triceps
 brachii of ~5% of maximal voluntary contraction (MVC) strength. The first
 excitatory response (E1), first inhibitory response (CSP), and second
 excitatory response (E2) were quantified as the percent change from
 baseline and by their individual durations. The results showed that the
 level of CSP suppression was lessened (47.7 ± 7.7% to 33.8 ± 13.2% of
 baseline, p = 0.019) and the duration of the CSP inhibition decreased (p =
 0.021) in the triceps brachii when comparing the seated and wobble board
 tasks. For the wobble board task the amount of cutaneous afferent
 inhibition of EMG activity in the triceps brachii decreased; which is
 proposed to be due to differential weighting of cutaneous feedback
 relative to the corticospinal drive, most likely due to presynaptic
 inhibition, to meet the demands of the unstable task.
description: AA_MVCAA_StandingAA_WobbleAZ_MVCAZ_SeatedAZ_StandingAZ_WobbleCM_MVCCM_SeatedCM_StandingCM_WobbleDW_MVCDW_SeatedDW_StandingDW_WobbleKC_MVCKC_SeatedKC_StandingKC_WobbleKK_MVCKK_SeatedKK_StandingKK_WobbleMD_MVCMD_SeatedMD_StandingMD_WobbleMM_MVCMM_SeatedMM_StandingMM_WobbleNE_MVCNE_SeatedNE_StandingNE_WobbleRR_MVCRR_SeatedRR_StandingRR_WobbleWO_MVCWO_SeatedWO_StandingWO_WobbleREADMEThis includes information about how the data was collected and with what methods
DOI: 10.5061/dryad.33243
title: Data from: X-ray micro-CT scanning reveals temporal separation of male harm and female kicking during traumatic mating in seed beetles

description: In the seed beetle Callosobruchus maculatus, the male intromittent organ
 is covered in sharp spines that pierce the female copulatory tract wall
 during mating. Although the fitness consequences of traumatic mating are
 well studied in this species, we know much less about how the male and
 female genitalia interact during mating. This is partly due to the fact
 that genital interactions occur primarily inside the female, and so are
 difficult to observe. In this study, we use X-ray micro-CT scanning to
 examine the proximate mechanisms of traumatic mating in C. maculatus in
 unprecedented detail. We show that this technique can be used to identify
 female tissue damage before the melanization of wound sites. We visualize
 the positioning of the male intromittent organ inside the female
 copulatory tract during mating, and show how this relates to tract
 wounding in three dimensions. By scanning pairs flash-frozen at different
 times during mating, we show that significant tract wounding occurs before
 the onset of female kicking. There is thus some degree of temporal
 separation between the onset of wounding and the onset of kicking, which
 supports recent suggestions that kicking is not an effective female
 counter-adaptation to reduce copulatory wounding in this species. We also
 present evidence that the sharp teeth protruding from the female tract
 wall are able to pierce the spermatophore as it is deposited, and may thus
 function to aid sperm release.
description: Dougherty_Simmons_all_dataData on degree of copulatory wounding for all pairs scannedVideo S13D volume rendering showing a male aedeagus partly everted inside a female during the early stages of mating (pair frozen in copula after 60 seconds of mating, female not shown). The colour represents the relative X-Ray attenuation (brightness) of the tissue, with red representing highest density and blue representing lowest density.Video S23D volume rendering showing a fully everted male aedeagus inside a female during the early stages of mating (pair frozen in copula after 60 seconds of mating, female not shown). The colour represents the relative X-Ray attenuation (brightness) of the tissue, with red representing highest density and blue representing lowest density.Video S33D volume rendering showing the interaction between the male aedeagus (colour) and female copulatory tract (greyscale) during the early stages of mating (pair frozen in copula after 60 seconds of mating), viewed from the side. The colours represent the relative X-Ray attenuation (brightness) of the tissue, with red/white representing highest density and blue/dark grey representing lowest density for male and female traits respectively.
DOI: 10.5061/dryad.pj25h
title: Data from: New records of the late Pliensbachian to early Toarcian (Early Jurassic) gladius-bearing coleoid cephalopods from the Ya Ha Tinda Lagerstätte, Canada

description: The Ya Ha Tinda Lagerstätte from Alberta, Canada, is the first Jurassic
 marine Konservat-Lagerstätte from North America and hosts a substantial
 collection of exceptionally preserved fossil Vampyropoda specimens.
 Vampyropods are soft-bodied cephalopods (coleoids) characterized by eight
 arms and an internalized chitinous shell (gladius). Due to their lack of
 hard parts, Vampyropoda have a fragmentary fossil record, largely limited
 to exceptional Lagerstätten deposits. Excavations at Ya Ha Tinda have
 uncovered sixteen vampyropod fossils from Pliensbachian and Toarcian
 strata, making it the largest deposit of Vampyropoda found outside of the
 Tethys Ocean (Europe and the Middle East) for the Jurassic. Here, we
 present a taxonomic analysis of the Ya Ha Tinda Vampyropoda specimens and
 the first comprehensive study of Early Jurassic vampyropods from North
 America. In total, fourteen specimens have sufficient morphological
 details preserved on the gladius for taxonomic descriptions. Two specimens
 are identifiable only to the suborder Loligosepiina (one to the family
 Geopeltidae), while the remaining twelve specimens are identified to the
 genus level; six Paraplesioteuthis, three Loligosepia, one Geopeltis, one
 Parabelopeltis, and one Jeletzkyteuthis. The discovery of Loligosepia cf.
 aalensis within Pliensbachian strata pushes back the earliest occurrence
 of this taxon from the early Toarcian to the late Pliensbachian. With the
 exception of Paraplesioteuthis, this is the first time these genera have
 been found outside of Europe for the Jurassic; therefore, this study
 significantly expands their palaeogeographic range. Furthermore, with
 established high-resolution bio and chemostratigraphy, specimens can be
 assigned to ammonite zones and placed in context of the global Toarcian
 Oceanic Anoxic Event.
description: Marroquín et al. 2017
 SupplementIncluded in this
 supplement are: (1) Fifteen supplemental figures (S1–S15) of part and
 counterpart of each vampyropod specimen discovered at the Ya Ha Tinda
 Lagerstätte shown in various lighting techniques and (2) a word document
 with the figure captions for all supplemental figures
 (S1–S15).
DOI: 10.15468/dl.9wxz7e
title: Occurrence Download

description: A dataset containing 84390 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Biodiversity of Luiz Saldanha Marine Park"
 ]
}

 The dataset includes 84390 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000366-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/14630639
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5061/dryad.f468j
title: Data from: Selection biases the prevalence and type of epistasis along adaptive trajectories

description: The contribution to an organism's phenotype from one genetic locus
 may depend upon the status of other loci. Such epistatic interactions
 among loci are now recognized as fundamental to shaping the process of
 adaptation in evolving populations. Although little is known about the
 structure of epistasis in most organisms, recent experiments with
 bacterial populations have concluded that antagonistic interactions abound
 and tend to de-accelerate the pace of adaptation over time. Here, we use
 the NK model of fitness landscapes to examine how natural selection biases
 the mutations that substitute during evolution based on their epistatic
 interactions. We find that, even when beneficial mutations are rare, these
 biases are strong and change substantially throughout the course of
 adaptation. In particular, epistasis is less prevalent than the neutral
 expectation early in adaptation and much more prevalent later, with a
 concomitant shift from predominantly antagonistic interactions early in
 adaptation to synergistic and sign epistasis later in adaptation. We
 observe the same patterns when re-analyzing data from a recent microbial
 evolution experiment. These results show that when the order of
 substitutions is not known, standard methods of analysis may suggest that
 epistasis retards adaptation when in fact it accelerates it.
description: Code, scripts, and data
 filesArchive of C code, R
 scripts, and data files.Dryad_files.zip
DOI: 10.5061/dryad.1p888
title: Data from: Conservation and divergence of gene expression plasticity following c. 140 million years of evolution in lodgepole pine (Pinus contorta) and interior spruce (Picea glauca × Picea engelmannii)

description: Species respond to environmental stress through a combination of genetic
 adaptation and phenotypic plasticity, both of which may be important for
 survival in the face of climatic change. By characterizing the molecular
 basis of plastic responses and comparing patterns among species, it is
 possible to identify how such traits evolve. Here, we use de novo
 transcriptome assembly and RNA-seq to explore how patterns of gene
 expression differ in response to temperature, moisture, and light regime
 treatments in lodgepole pine (Pinus contorta) and interior spruce (a
 natural hybrid population of Picea glauca and Picea engelmannii). We found
 wide evidence for an effect of treatment on expression within each
 species, with 6,413 and 11,658 differentially expressed genes identified
 in spruce and pine, respectively. Comparing patterns of expression among
 these species, we found that 74% of all orthologs with differential
 expression had a pattern that was conserved in both species, despite 140
 million years of evolution. We also found that the specific treatments
 driving expression patterns differed between genes with conserved vs.
 diverged patterns of expression. We conclude that natural selection has
 likely played a role in shaping plastic responses to environment in these
 species.
description: data for: Conservation
 and divergence of gene expression plasticity following ~140 million years
 of evolution in lodgepole pine (Pinus contorta) and interior spruce (Picea
 glauca and Picea engelmannii)This archive includes
 raw data and scripts used for the paper. .dat files contain annotation
 information in blast2go format.lodgepole_pine_interior_spruce_RNAseq_archive.tar.gz
DOI: 10.5061/dryad.43t60
title: Data from: Sequence capture and next-generation sequencing of ultraconserved elements in a large-genome salamander

description: Amidst the rapid advancement in next-generation sequencing (NGS)
 technology over the last few years, salamanders have been left behind.
 Salamanders have enormous genomes – up to 40 times the size of the human
 genome – and this poses challenges to generating NGS data sets of quality
 and quantity similar to those of other vertebrates. However, optimization
 of laboratory protocols is time-consuming and often cost prohibitive, and
 continued omission of salamanders from novel phylogeographic research is
 detrimental to species facing decline. Here, we use a salamander endemic
 to the southeastern US, Plethodon serratus, to test the utility of an
 established protocol for sequence capture of ultraconserved elements
 (UCEs) in resolving intraspecific phylogeographic relationships and
 delimiting cryptic species. Without modifying the standard laboratory
 protocol, we generated a data set consisting of over 600 million reads for
 85 P. serratus samples. Species delimitation analyses support recognition
 of seven species within P. serratus sensu lato, and all phylogenetic
 relationships among the seven species are fully resolved under a
 coalescent model. Results also corroborate previous data suggesting
 non-monophyly of the Ouachita and Louisiana regions. Our results
 demonstrate that established UCE protocols can successfully be used in
 phylogeographic studies of salamander species, providing a powerful tool
 for future research on evolutionary history of amphibians and other
 organisms with large genomes.
description: RAxML-20percent-allConcatenated phylip alignment for RAxML: all samples, up to 20 percent missing samples per locusmafft-nexus-80-all.phylipRAxML-60percent-allConcatenated phylip alignment for RAxML: all samples, up to 40 percent missing samples per locusmafft-nexus-60-all.phylipRAxML-20percent-1kConcatenated phylip alignment for RAxML: 1k-samples, up to 20 percent missing samples per locusmafft-nexus-80-1k.phylipRAxML-40percent-1kConcatenated phylip alignment for RAxML: 1k-samples, up to 40 percent missing samples per locusmafft-nexus-60-1k.phylipStarbeast_BPP_informative70Alignments (nexus) for *Beast and BPP analyses: 70 most informative lociStarbeast_informative100Alignments (nexus) for *Beast analysis: 100 most informative lociStarbeast_informative50Alignments (nexus) for *Beast analysis: 50 most informative lociStarbeast_informative20Alignments (nexus) for *Beast analysis: 20 most informative lociStarbeast_BPP_random70_1Alignments (nexus) for *Beast and BPP analyses: 70 random loci, set 1Starbeast_random70_2Alignments (nexus) for *Beast analysis: 70 random loci, set 2Starbeast_random70_3Alignments (nexus) for *Beast analysis: 70 random loci, set 3Starbeast_random70_4Alignments (nexus) for *Beast analysis: 70 random loci, set 4Starbeast_random70_5Alignments (nexus) for *Beast analysis: 70 random loci, set 5Structure_random_allpopsSNP file for Structure analyses. Population in second column.
DOI: 10.5061/dryad.f3r35
title: Data from: Detection of SNPs based on transcriptome sequencing in Norway spruce (Picea abies (L.) Karst)

description: A novel set of SNPs was derived from transcriptome data of ten Norway
 spruce (Picea abies) trees from the Bavarian Forest National Park in
 Germany (BaFoNP). SNPs were identified by mapping against a de-novo
 transcriptome assembly and against pre-mRNAs of predicted genes of the
 reference genome assembly. This resulted in 111,849 and 366,577 SNPs,
 respectively. Out of these, 311 were either randomly selected or chosen
 because of their pronounced divergence between sampling sites and
 genotyped in 218 trees with an Illumina Infinium HD iSelect BeadChip.
description: Pabies1.0-all.phase.changed.gff3gene feature format (gff3) file from Picea abies v1.0 with phase informationcont_plastids_mito_plants_ribosome_dnachloroplast genomes, mitochondrial genomes and ribosomal DNA sequences for NGS data filtering combined and obtained from NCBI
DOI: 10.5061/dryad.mq7rh
title: Data from: Evaluating the role of Pleistocene refugia, rivers and environmental variation in the diversification of central African duikers (genera Cephalophus and Philantomba)

description: Background: This study aims to assess the role that Pleistocene refugia,
 rivers and local habitat conditions may have played in the evolutionary
 diversification of three central African duiker species (Cephalophus
 dorsalis, C. callipygus and Philantomba monticola). Genetic data from
 geo-referenced feces were collected from a wide range of sites across
 Central Africa. Historical patterns of population genetic structure were
 assessed using a ~ 650 bp fragment of the mitochondrial control region and
 contemporary patterns of genetic differentiation were evaluated using 12
 polymorphic microsatellite loci. Results: Mitochondrial analyses revealed
 that populations of C. callipygus and P. monticola in the Gulf of Guinea
 refugium are distinct from other populations in west central Africa. All
 three species exhibit signatures of past population expansion across much
 of the study area consistent with a history of postglacial expansion.
 There was no strong evidence for a riverine barrier effect in any of the
 three species, suggesting that duikers can readily cross major rivers.
 Generalized dissimilarity models (GDM) showed that environmental variation
 explains most of the nuclear genetic differentiation in both C. callipygus
 and P. monticola. The forest-savanna transition across central Cameroon
 and the Plateaux Batéké region in southeastern Gabon show the highest
 environmentally-associated turnover in genetic variability. A pattern of
 genetic differentiation was also evident between the coast and forest
 interior that may reflect differences in precipitation and/or vegetation.
 Conclusions: Findings from this study highlight the historical impact of
 Pleistocene fragmentation and current influence of environmental variation
 on genetic structure in duikers. Conservation efforts should therefore
 target areas that harbor as much environmentally-associated genetic
 variation as possible in order to maximize species’ capacity to adapt to
 environmental change.
description: Duiker_dataMicrosatellite data, sampling locations and pairwise FST values for GDM analysis of three species of duiker: Cephalophus dorsalis, C. callipygus and Philantomba monticola. Geographic locations of sampling points for MAXENT modeling of all three species.Environmental variables for DryadEnvironmental data layers used in MAXENT and GDM modeling.Env Vars for Dryad.zipResistance_distancesResistance distances based on Circuitscape for all three species GDMs.Supplementary_data_filesSupplementary data files from Ntie et al. (2017) in both Microsoft Office and OpenOffice formats.