cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.35cs5
title: Data from: A cross-lingual similarity measure for detecting biomedical term translations

description: Bilingual dictionaries for technical terms such as biomedical terms are an
 important resource for machine translation systems as well as for humans
 who would like to understand a concept described in a foreign language.
 Often a biomedical term is first proposed in English and later it is
 manually translated to other languages. Despite the fact that there are
 large monolingual lexicons of biomedical terms, only a fraction of those
 term lexicons are translated to other languages. Manually compiling
 large-scale bilingual dictionaries for technical domains is a challenging
 task because it is difficult to find a sufficiently large number of
 bilingual experts. We propose a cross-lingual similarity measure for
 detecting most similar translation candidates for a biomedical term
 specified in one language (source) from another language (target).
 Specifically, a biomedical term in a language is represented using two
 types of features: (a) intrinsic features that consist of character
 n-grams extracted from the term under consideration, and (b) extrinsic
 features that consist of unigrams and bigrams extracted from the
 contextual windows surrounding the term under consideration. We propose a
 cross-lingual similarity measure using each of those feature types. First,
 to reduce the dimensionality of the feature space in each language, we
 propose prototype vector projection (PVP)—a non-negative lower-dimensional
 vector projection method. Second, we propose a method to learn a mapping
 between the feature spaces in the source and target language using partial
 least squares regression (PLSR). The proposed method requires only a small
 number of training instances to learn a cross-lingual similarity measure.
 The proposed PVP method outperforms popular dimensionality reduction
 methods such as the singular value decomposition (SVD) and non-negative
 matrix factorization (NMF) in a nearest neighbor prediction task.
 Moreover, our experimental results covering several language pairs such as
 English–French, English–Spanish, English–Greek, and English–Japanese show
 that the proposed method outperforms several other feature projection
 methods in biomedical term translation prediction tasks.
description: plos_medpred_datasetDataset used in the experiments described in the paper.
DOI: 10.5061/dryad.br0h8
title: Data from: Biofilm morphotypes and population structure among Staphylococcus epidermidis from commensal and clinical samples

description: Bacterial species comprise related genotypes that can display divergent
 phenotypes with important clinical implications. Staphylococcus
 epidermidis is a common cause of nosocomial infections and, critical to
 its pathogenesis, is its ability to adhere and form biofilms on surfaces,
 thereby moderating the effect of the host’s immune response and
 antibiotics. Commensal S. epidermidis populations are thought to differ
 from those associated with disease in factors involved in adhesion and
 biofilm accumulation. We quantified the differences in biofilm formation
 in 98 S. epidermidis isolates from various sources, and investigated
 population structure based on ribosomal multilocus typing (rMLST) and the
 presence/absence of genes involved in adhesion and biofilm formation. All
 isolates were able to adhere and form biofilms in in vitro growth assays
 and confocal microscopy allowed classification into 5 biofilm morphotypes
 based on their thickness, biovolume and roughness. Phylogenetic
 reconstruction grouped isolates into three separate clades, with the
 isolates in the main disease associated clade displaying diversity in
 morphotype. Of the biofilm morphology characteristics, only biofilm
 thickness had a significant association with clade distribution. The
 distribution of some known adhesion-associated genes (aap and sesE) among
 isolates showed a significant association with the species clonal frame,
 with the exception of. These data challenge the assumption that
 biofilm-associated genes, such as those on the ica operon, are genetic
 markers for less invasive S. epidermidis isolates, and suggest that
 phenotypic characteristics, such as adhesion and biofilm formation, are
 not fixed by clonal descent but are influenced by the presence of various
 genes that are mobile among lineages.
description: Isolate
 ListDryad
 data.xlsxGenome
 assembliesAssembled genomes used
 in this study to identify rMLST, virulence and biofilm-associated gene
 sequences.Dryad
 seq.zip
DOI: 10.5061/dryad.985s5
title: Data from: Point process models for presence-only analysis

description: 1. Presence-only data are widely used for species distribution modelling,
 and point process regression models are a exible tool that has
 considerable potential for this problem, when data arise as point events.
 2. In this paper we review point process models, some of their advantages,
 and some common methods of fitting them to presence-only data. 3.
 Advantages include (and are not limited to): clarification of what the
 response variable is that is modelled; a framework for choosing the number
 and location of quadrature points (commonly referred to as pseudoabsences
 or \background points”) objectively; clarity of model assumptions and
 tools for checking them; models to handle spatial dependence between
 points when it is present; ways forward regarding difficult issues such as
 accounting for sampling bias. 4. Point process models are related to some
 common approaches to presenceonly species distribution modelling, which
 means that a variety of different software tools can be used to fit these
 models, including MAXENT or generalised linear modelling software.
description: Environmental data for
 Blue Mountains regionRData file with
 environmental and soil covariates at 100m resolution for locations within
 the Greater Blue Mountains World Heritage Area. See ReadMe.txt file for a
 description of these covariates.Quad100m.RData
DOI: 10.5061/dryad.125p3
title: Data from: Known mutator alleles do not markedly increase mutation rate in clinical Saccharomyces cerevisiae strains

description: Natural selection has the potential to act on all phenotypes, including
 genomic mutation rate. Classic evolutionary theory predicts that in
 asexual populations, mutator alleles, which cause high mutation rates, can
 fix due to linkage with beneficial mutations. This phenomenon has been
 demonstrated experimentally and may explain the frequency of mutators
 found in bacterial pathogens. By contrast, in sexual populations,
 recombination decouples mutator alleles from beneficial mutations,
 preventing mutator fixation. In the facultatively sexual yeast
 Saccharomyces cerevisiae, segregating alleles of MLH1 and PMS1 have been
 shown to be incompatible, causing a high mutation rate when combined.
 These alleles had never been found together naturally, but were recently
 discovered in a cluster of clinical isolates. Here we report that the
 incompatible mutator allele combination only marginally elevates mutation
 rate in these clinical strains. Genomic and phylogenetic analyses provide
 no evidence of a historically elevated mutation rate. We conclude that the
 effect of the mutator alleles is dampened by background genetic modifiers.
 Thus, the relationship between mutation rate and microbial pathogenicity
 may be more complex than once thought. Our findings provide rare
 observational evidence that supports evolutionary theory suggesting that
 sexual organisms are unlikely to harbour alleles that increase their
 genomic mutation rate.
description: Mutation rate
 dataData on genomic mutation
 rate measured for the paper.mutators_supp_data.txtStatistical analyses of mutation rate dataR script to analyze mutation rate data.mutation_rate_statistical_analysis.RFigure 2R script to make Figure 2.make_figure2.Rgenome analysis zip archiveZip archive for genome analysis data and scriptsmutators_genome_analysis.zipREADMEReadme for all files in this repository.
DOI: 10.5061/dryad.m56c1
title: Data from: The contribution of marine aggregate-associated bacteria to the accumulation of pathogenic bacteria in oysters: an agent-based model

description: Bivalves process large volumes of water, leading to their accumulation of
 bacteria, including potential human pathogens (e.g., vibrios). These
 bacteria are captured at low efficiencies when freely suspended in the
 water column, but they also attach to marine aggregates, which are
 captured with near 100% efficiency. For this reason, and because they are
 often enriched with heterotrophic bacteria, marine aggregates have been
 hypothesized to function as important transporters of bacteria into
 bivalves. The relative contribution of aggregates and unattached bacteria
 to the accumulation of these cells, however, is unknown. We developed an
 agent-based model to simulate accumulation of vibrio-type bacteria in
 oysters. Simulations were conducted over a realistic range of
 concentrations of bacteria and aggregates and incorporated the dependence
 of pseudofeces production on particulate matter. The model shows that the
 contribution of aggregate-attached bacteria depends strongly on the
 unattached bacteria, which form the colonization pool for aggregates and
 are directly captured by the simulated oysters. The concentration of
 aggregates is also important, but its effect depends on the concentration
 of unattached bacteria. At high bacterial concentrations, aggregates
 contribute the majority of bacteria in the oysters. At low concentrations
 of unattached bacteria, aggregates have a neutral or even a slightly
 negative effect on bacterial accumulation. These results provide the first
 evidence suggesting that the concentration of aggregates could influence
 uptake of pathogenic bacteria in bivalves and show that the tendency of a
 bacterial species to remain attached to aggregates is a key factor for
 understanding species-specific accumulation.
description: Transport of bacteria
 into oysters by aggregates Data and CodeData and code needed to
 run models and generate manuscript figures.
DOI: 10.5281/zenodo.18351678
title: Follow-up of young adults from a rural northern Pakistani village

description: These data come from a follow-up to a 1989-1996 study of diarrhea and pneumonia in children under age 5 years. The aim was to examine individual-level associations between childhood health and family socioeconomic indicators of early life adversity with adolescent health and development.
DOI: 10.5281/zenodo.18380867
title: Follow-up of young adults from a rural northern Pakistani village

description: These data come from a follow-up to a 1989-1996 study of diarrhea and pneumonia in children under age 5 years. The aim was to examine individual-level associations between childhood health and family socioeconomic indicators of early life adversity with adolescent health and development.
DOI: 10.5061/dryad.pq608
title: Data from: Identification of sex-specific molecular markers using restriction site associated DNA sequencing (RAD-seq)

description: A major barrier to evolutionary studies of sex determination and sex
 chromosomes has been a lack of information on the types of sex-determining
 mechanisms that occur among different species. This is particularly
 problematic in groups where most species lack visually heteromorphic sex
 chromosomes, such as fish, amphibians and reptiles, because cytogenetic
 analyses will fail to identify the sex chromosomes in these species. We
 describe the use of restriction site associated DNA (RAD) sequencing, or
 RAD-seq, to identify sex-specific molecular markers and subsequently
 determine whether a species has male or female heterogamety. To test the
 accuracy of this technique we examined the lizard Anolis carolinensis. We
 performed RAD-seq on seven male and ten female A. carolinensis and found
 one male-specific molecular marker. Anolis carolinensis has previously
 been shown to possess male heterogamety and the recently published A.
 carolinensis genome facilitated characterization of the sex-specific
 RAD-seq marker. We validated the male specificity of the new marker using
 PCR on additional individuals and also found that it is conserved in some
 other Anolis species. We discuss the utility of using RAD-seq to identify
 sex determining mechanisms in other species with cryptic or homomorphic
 sex chromosomes and the implications for the evolution of male
 heterogamety in Anolis.
description: Gamble_Zarkower_Supp_File1Supplementary File 1. RADtools output – full datasetGamble_Zarkower_Supp_File2Supplementary File 2. Fasta file with male-specific RAD lociGamble_Zarkower_Supp_File3Supplementary File 3. RADtools output – sub-sampled datasets
DOI: 10.5061/dryad.q1m7t
title: Data from: Ranking and characterization of established BMI and lipid associated loci as candidates for gene-environment interactions

description: Phenotypic variance heterogeneity across genotypes at a single nucleotide
 polymorphism (SNP) may reflect underlying gene-environment (G·E) or
 gene-gene interactions. We modeled variance heterogeneity for blood lipids
 and BMI in up to 44,211 participants and investigated relationships
 between variance effects (Pv), G·E interaction effects (with smoking and
 physical activity), and marginal genetic effects (Pm). Correlations
 between Pv and Pm were stronger for SNPs with established marginal effects
 (Spearman's ρ=0.401 for triglycerides, and ρ=0.236 for BMI) compared
 to all SNPs. When Pv and Pm were compared for all pruned SNPs, only BMI
 was statistically significant (Spearman's ρ=0.010). Overall, SNPs
 with established marginal effects were overrepresented in the nominally
 significant part of the Pv distribution (Pbinomial&lt;0.05). SNPs from
 the top 1% of the Pm distribution for BMI had more significant Pv values
 (PMann-Whitney=1.46E-5), and the odds ratio of SNPs with nominally
 significant (&lt;0.05) Pm and Pv was 1.33 (95% CI: 1.12, 1.57) for
 BMI. Moreover, BMI SNPs with nominally significant G·E interaction
 P-values (Pint&lt;0.05) were enriched with nominally significant Pv
 values (Pbinomial=8.63E-9 and 8.52E-7 for SNP·smoking and SNP·physical
 activity, respectively). We conclude that some loci with strong marginal
 effects may be good candidates for G·E, and variance-based prioritization
 can be used to identify them.
description: Levenes test P
 valuesThe zip file contains 10
 plain txt files - each of the 10 files have 2 columns, rsID SNP identifier
 and P values obtained from Levene's test for trait variance
 heterogeneity between genotypes. The files cover 5 cardiometabolic traits
 (body mass index, high density lipoprotein cholesterol, low density
 lipoprotein cholesterol, triglycerides, total cholesterol), 2 files for
 each trait. One contains a pruned subset of SNPs and the other one all
 SNPs as described in the main text of the publication.LevenePvalues.zip
DOI: 10.5061/dryad.372sq
title: Data from: HyDe: a Python package for genome-scale hybridization detection

description: The analysis of hybridization and gene flow among closely related taxa is
 a common goal for researchers studying speciation and phylogeography. Many
 methods for hybridization detection use simple site pattern frequencies
 from observed genomic data and compare them to null models that predict an
 absence of gene flow. The theory underlying the detection of hybridization
 using these site pattern probabilities exploits the relationship between
 the coalescent process for gene trees within population trees and the
 process of mutation along the branches of the gene trees. For certain
 models, site patterns are predicted to occur in equal frequency (i.e.,
 their difference is 0), producing a set of functions called
 textit{phylogenetic invariants}. In this paper we introduce HyDe, a
 software package for detecting hybridization using phylogenetic invariants
 arising under the coalescent model with hybridization. HyDe is written in
 Python, and can be used interactively or through the command line using
 pre-packaged scripts. We demonstrate the use of HyDe on simulated data, as
 well as on two empirical data sets from the literature. We focus in
 particular on identifying individual hybrids within population samples and
 on distinguishing between hybrid speciation and gene flow. HyDe is freely
 available as an open source Python package under the GNU GPL v3 on both
 GitHub (https://github.com/pblischak/HyDe) and the Python Package Index
 (PyPI: https://pypi.python.org/pypi/phyde).
description: Data files and notebook
 for HyDeThis is a zipped folder
 containing all of the simulated data and the output files for our analyses
 using HyDe. The Jupyter Notebook (HyDe_SysBio.ipynb) that is included has
 code to analyze all of the data.hyde-sims.zipJupyter notebook for analyses with HyDeThis repository has the Jupyter notebook for simulating, processing, and analyzing all data sets used for the description of. Code for the simulations, as well as code for processing results, are all part of the notebook.hyde-sims-R1.zip
DOI: 10.5061/dryad.p13s2
title: Data from: Modeling connectivity to identify current and future anthropogenic barriers to movement of large carnivores: a case study in the American Southwest

description: This study sought to identify critical areas for puma (Puma concolor)
 movement across the state of Arizona in the American Southwest and to
 identify those most likely to be impacted by current and future human land
 uses, particularly expanding urban development and associated increases in
 traffic volume. Human populations in this region are expanding rapidly,
 with the potential for urban centers and busy roads to increasingly act as
 barriers to demographic and genetic connectivity of large-bodied,
 wide-ranging carnivores such as pumas, whose long-distance movements are
 likely to bring them into contact with human land uses and whose low
 tolerance both for and from humans may put them at risk unless
 opportunities for safe passage through or around human-modified landscapes
 are present. Brownian bridge movement models based on global positioning
 system collar data collected during bouts of active movement and linear
 mixed models were used to model habitat quality for puma movement, then a
 wall-to-wall application of circuit theory models was used to produce a
 continuous statewide estimate of connectivity for puma movement and to
 identify pinch points, or bottlenecks, that may be most at risk of impacts
 from current and future traffic volume and expanding development. Rugged,
 shrub- and scrub-dominated regions were highlighted as those offering high
 quality movement habitat for pumas, and pinch points with the greatest
 potential impacts from expanding development and traffic, though widely
 distributed, were particularly prominent to the north and east of the city
 of Phoenix and along interstate highways in the western portion of the
 state. These pinch points likely constitute important conservation
 opportunities, where barriers to movement may cause disproportionate loss
 of connectivity, but also where actions such as placement of wildlife
 crossing structures or conservation easements could enhance connectivity
 and prevent detrimental impacts before they occur.
description: Habitat quality,
 conductance, and connectivity for puma movement across
 ArizonaThe data file contains
 raster datasets in geotiff format representing: 1) puma habitat quality
 for movement, 2) conductance of the landscape to puma movement, and 3)
 connectivity for puma across the state of Arizona. Each dataset is
 accompanied by a layer file providing symbology matching the figures in
 the accompanying publication.McClureetal2017_EE.zip
DOI: 10.5061/dryad.q8j5k80
title: Data from: Genome-specific histories of divergence and introgression between an allopolyploid unisexual salamander lineage and two ancestral sexual species

description: Quantifying introgression between sexual species and polyploid lineages
 traditionally thought to be asexual is an important step in understanding
 what drives the longevity of putatively asexual groups. Here, we
 capitalize on three recent innovations—ultraconserved element (UCE)
 sequencing, bioinformatic techniques for identifying genome-specific
 variation in polyploids, and model-based methods for evaluating historical
 gene flow—to measure the extent and tempo of introgression over the
 evolutionary history of an allopolyploid lineage of all-female salamanders
 and two ancestral sexual species. Our analyses support a scenario in which
 the genomes sampled in unisexual salamanders last shared a common ancestor
 with genomes in their parental species ~3.4 million years ago, followed by
 a period of divergence between homologous genomes. Recently, secondary
 introgression has occurred at different times with each sexual species
 during the last 500,000 years. Sustained introgression of sexual genomes
 into the unisexual lineage is the defining characteristic of their
 reproductive mode, but this study provides the first evidence that
 unisexual genomes have undergone long periods of divergence without
 introgression. Unlike other sperm-dependent taxa in which introgression is
 rare, the alternating periods of divergence and introgression between
 unisexual salamanders and their sexual relatives could explain why these
 salamanders are among the oldest described unisexual animals.
description: Phrapl input, analyses,
 and resultsThis directory includes
 all Phrapl input, control files, and analysis output. All folders indicate
 a different model detailed in the manuscript, and general scripts are
 included in the top directory._Dryad.Evol.18-0238.zip