cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.smm75h
title: Occurrence Download

description: A dataset containing 3454 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Leontodon tuberosus"
 ]
}

 The dataset includes 3454 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035782-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jc73hq
title: Occurrence Download

description: A dataset containing 699 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Allium stellerianum"
 ]
}

 The dataset includes 699 records from 39 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035780-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jnncwu
title: Occurrence Download

description: A dataset containing 110651 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pyrola minor"
 ]
}

 The dataset includes 110651 records from 799 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035663-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wxjd2u
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Dendrocygna autumnalis (Linnaeus, 1758)",
 "Year is less than or equal to 2024",
 "Year is greater than or equal to 2021",
 "Continent is North America"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012989-250515123054153/datasets/export for details.
DOI: 10.14288/1.0397586
title: Data for: Coevolution fails to maintain genetic variation in a host-parasite model with constant finite population size

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;Coevolutionary negative frequency-dependent selection has been hypothesized to maintain genetic variation in host and parasites.  &lt;br&gt; Despite the extensive literature pertaining to host-parasite coevolution, the dynamics of genetic variation has not been examined in a matching-alleles model (MAM) with a finite population size relative to the expectation under neutral genetic drift alone.  The dynamics of the MA coevolution in an infinite population, in fact, suggests that genetic variation in these coevolving populations behaves neutrally.   By comparing host heterozygosity to the expectation in a single-species model of neutral genetic drift we find that while this is also largely true in finite populations two additional phenomena arise.  First, reciprocal natural selection acting on stochastic perturbations in host and pathogen allele frequencies results in a slight increase or decrease in genetic variation depending on the parameter conditions. Second, following the fixation of an allele in the parasite, selection in the MAM becomes directional, which then rapidly erodes genetic variation in the host.  Hence, rather than maintain it, we find that, on average, matching-alleles coevolution depletes genetic variation.&lt;/p&gt;
DOI: 10.14288/1.0395421
title: CapnoBase InVivo Dataset

description: The in-vivo dataset contains capnography signals that were recorded during real clinical cases. Information that could possibly identify the source of the data has been removed.
DOI: 10.14288/1.0395422
title: CapnoBase Respiratory Event Benchmark

description: The CapnoBase benchmark dataset contains 44 scenarios that were recorded in the same manner as the in-vivo dataset. The scenarios contain very typical capnography and spirometry signals or patient conditions that may arise during anesthesia. The benchmark dataset is used by researchers to test and compare algorithms. &lt;br&gt;&lt;b&gt;This dataset is a benchmark and should not be used to train or tune an algorithm as it may bias the performance results.&lt;/b&gt; For training use the inVivo dataset.
DOI: 10.14288/1.0395426
title: CapnoBase Simulation Dataset

description: The simulation dataset was produced with a computer model that simulates the behavior of the human cardio-respiratory system. Producing artificial capnography signals is useful when signals that are otherwise hard to obtain are required, or when the condition or change in state of the patient must to be precisely known.
DOI: 10.14288/1.0397881
title: Patterns, predictors, and consequence of dominance in hybrids

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;Compared to those of their parents, are the traits of first-generation (F&lt;sub&gt;1&lt;/sub&gt;) hybrids typically intermediate, biased toward one parent, or mismatched for alternative parental phenotypes? And how does hybrid trait expression affect fitness? To address this empirical gap, we compiled data from 198 studies in which traits were measured in a common environment for two parent taxa and their F&lt;sub&gt;1&lt;/sub&gt; hybrids. We find that individual traits in F&lt;sub&gt;1&lt;/sub&gt;s are, on average, halfway between the parental midpoint and one parental value (e.g., hybrid trait values are 0.75 if parents'values are 0 &amp;1). When considering pairs of traits together, a hybrid's bivariate phenotype tends to resemble one parent (pairwise parent-bias) about 50 % more than the other while also exhibiting a similar magnitude of mismatch due to different traits having dominance in conflicting directions. We detect no phylogenetic signal nor an effect of parental genetic distance on dominance or mismatch. Using data from an experimental field planting of recombinant hybrid sunflowers, we illustrate that pairwise parent-bias improves fitness whereas pairwise mismatch reduces fitness. In sum, our study has three major conclusions. First, hybrids between ecologically divergent natural populations are not phenotypically intermediate but rather exhibit substantial mismatch while also resembling one parent more than the other. Second, dominance and mismatch do not seem to be governed by general rules but rather by the idiosyncratic evolutionary trajectories of individual traits in individual populations or species. Finally, selection against hybrids likely results from selection against both intermediate and mismatched phenotypes.&lt;/p&gt;
DOI: 10.14288/1.0397786
title: Comparative gene expression analysis reveals mechanism of Pinus contorta response to the fungal pathogen Dothistroma septosporum

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;Many conifers have distributions that span wide ranges in both biotic and abiotic conditions, but the basis of response to biotic stress has received much less attention than response to abiotic stress. In this study,&lt;span style="background-color:#ffffff;"&gt; w&lt;/span&gt;e investigated the gene expression response of lodgepole pine (&lt;i&gt;Pinus contorta&lt;/i&gt;) to attack by the fungal pathogen &lt;i&gt;Dothistroma septosporum&lt;/i&gt;, which causes &lt;i&gt;Dothistroma &lt;/i&gt;needle blight (DNB), a disease that has caused severe climate-related outbreaks in northwestern British Columbia. We inoculated tolerant and susceptible pines with two &lt;i&gt;D. septosporum&lt;/i&gt; isolates and analyzed the differentially expressed genes, differential exon usage, and co-expressed gene modules using RNA-seq data. We found a rapid and strong transcriptomic response in tolerant lodgepole pine samples inoculated with one &lt;i&gt;D. septosporum&lt;/i&gt; isolate, and a late and weak response in susceptible samples inoculated with another isolate. We mapped 43 of the DEG- or gene-module-identified genes to the reference plant-pathogen interaction pathway deposited in KEGG database. These genes are present in PAMP-triggered and effector-triggered immunity pathways, including genes encoding mitogen-activated protein kinase and disease resistance protein. Genes comprising pathways and gene modules had signatures of strong selective constraint, while the highly expressed genes in tolerant samples appear to have been favored by selection to counterattack the pathogen. We identified candidate resistance genes that may respond to &lt;i&gt;D. septosporum&lt;/i&gt; effectors. Taken together, our results show that gene expression response to &lt;i&gt;D. septosporum&lt;/i&gt; infection in lodgepole pine varies both among tree genotypes and pathogen strains, and involves both known candidate genes and a number of genes with previously unknown functions.&lt;/p&gt;
DOI: 10.14288/1.0395036
title: Replication Data for: Current Surgical Treatment of Intermediate Risk Differentiated Thyroid Cancer: A Systematic Review

description: Surgical treatment of thyroid cancer has become less aggressive but for many patients, the threshold for performing total thyroidectomy (TT), as opposed to thyroid lobectomy (TL), has remained unclear. Current American Thyroid Association (ATA) guidelines encourage more individualization of treatment options, which necessitates explicit review of the pros and cons of the different options with patients. This review focuses on the extent of surgery for treatment of intermediate-risk differentiated thyroid cancer, restricted to relevant literature available after publication of the 2015 ATA guidelines.
DOI: 10.15468/dl.zhzgsk
title: Occurrence Download

description: A dataset containing 1123 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is LACM Malacology",
 "TaxonKey is Gastropoda",
 "Year is 1933"
 ]
}

 The dataset includes 1123 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000472-250424135625364/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.14288/1.0447184
title: Standard Operating Procedures for Sepsis CoLab Administrators: Dataverse Operations

description: Simple step by step instructions for CoLab administrators on operating and maintaining the CoLab Dataverse.
DOI: 10.14288/1.0397826
title: Data from: Beyond a single patch: local and regional processes explain diversity patterns in a seagrass epifaunal metacommunity

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;Ecological communities are jointly structured by dispersal, density-independent responses to environmental conditions and density-dependent biotic interactions. Metacommunity ecology provides a framework for understanding how these processes combine to determine community seagrass meadows along the British Columbia coast, we tested the hypothesis that eelgrass (&lt;i&gt;Zostera marina&lt;/i&gt; L.) epifaunal invertebrate assemblages are influenced by local environmental conditions, but that high dispersal rates at larger spatial scales dampen effects of environmental differences. We used hierarchical joint species distribution modelling to understand the contribution of environmental conditions, spatial distance between meadows, and species co-occurrences to epifaunal invertebrate abundance and distribution across the region. We found that patterns of taxonomic compositional similarity among meadows were inconsistent with dispersal limitation, and meadows in the same region were often no more similar to each other than meadows over 1000 km away. Abiotic environmental conditions (temperature, dissolved oxygen) explained a small fraction of variation in taxonomic abundances patterns across the region. We found novel co-occurrence patterns among taxa that could not be explained by shared responses to environmental gradients, suggesting the possibility that interspecific interactions influence seagrass invertebrate abundance and distribution. Our results suggest that biodiversity and ecosystem functions provided by seagrass meadows reflect ecological processes occurring both within meadows and across seascapes, and that management of eelgrass habitat for biodiversity may be most effective when both local and regional processes are considered.&lt;/p&gt;
DOI: 10.14288/1.0397945
title: Phylogenetic analysis of the distribution of deadly amatoxins among the little brown mushrooms of the genus Galerina

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;Some but not all of the species of 'little brown mushrooms' in the genus &lt;i&gt;Galerina&lt;/i&gt; contain deadly amatoxins at concentrations equaling those in the death cap, &lt;i&gt;Amanita&lt;/i&gt; &lt;i&gt;phalloides.&lt;/i&gt; However, &lt;i&gt;Galerina&lt;/i&gt;'s ~300 species are notoriously difficult to identify by morphology and the identity of toxin-containing specimens has not been verified with DNA barcode sequencing. This left open the question of which &lt;i&gt;Galerina&lt;/i&gt; species contain toxins and which do not. We selected specimens for toxin analysis using a preliminary phylogeny of the fungal DNA barcode region, the ribosomal internal transcribed spacer (ITS) region. Using liquid chromatography/mass spectrometry, we analyzed amatoxins from 70 samples of &lt;i&gt;Galerina&lt;/i&gt; and close relatives, collected in western British Columbia, Canada. To put the presence of toxins into a phylogenetic context, we included the 70 samples in maximum likelihood analyses of 438 taxa, using ITS, RNA polymerase II second largest subunit gene (&lt;i&gt;RPB2&lt;/i&gt;), and nuclear large subunit ribosomal RNA (LSU) gene sequences. We sequenced barcode DNA from types where possible to aid with applications of names. We detected amatoxins only in the 24 samples of the &lt;i&gt;G. marginata&lt;/i&gt; s.l. complex in the &lt;i&gt;Naucoriopsis&lt;/i&gt; clade. We delimited 56 putative &lt;i&gt;Galerina&lt;/i&gt; species using Automatic Barcode Gap Detection software. Phylogenetic analysis showed moderate to strong support for &lt;i&gt;Galerina&lt;/i&gt; infrageneric clades &lt;i&gt;Naucoriopsis&lt;/i&gt;, &lt;i&gt;Galerina&lt;/i&gt;, &lt;i&gt;Tubariopsis&lt;/i&gt;, and&lt;i&gt; Sideroides&lt;/i&gt;. &lt;i&gt;Mycenopsis &lt;/i&gt;appeared paraphyletic and included &lt;i&gt;Gymnopilus&lt;/i&gt;. Amatoxins were not detected in 46 samples from &lt;i&gt;Galerina&lt;/i&gt; clades outside of &lt;i&gt;Naucoriopsis&lt;/i&gt; or from outgroups. Our data show significant quantities of toxin in all mushrooms tested from the &lt;i&gt;G. marginata&lt;/i&gt; s.l. complex. DNA barcoding revealed consistent accuracy in morphology-based identification of specimens to &lt;i&gt;G.&lt;/i&gt; &lt;i&gt;marginata &lt;/i&gt;s.l. complex. Prompt and careful morphological identification of ingested &lt;i&gt;G.&lt;/i&gt; &lt;i&gt;marginata &lt;/i&gt;s.l. has the potential to improve patient outcomes by leading to fast and appropriate treatment.&lt;/p&gt;
DOI: 10.14288/1.0397550
title: Data for: Feedback between coevolution and epidemiology can help or hinder the maintenance of genetic variation in host-parasite models

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;Antagonistic coevolution has long been suggested to help maintain host genetic variation. While, ecological and epidemiological feedbacks are known to have important consequences on coevolutionary allele frequency dynamics, their effects on the maintenance of genetic variation remains poorly understood.Here, we extend our previous work on the maintenance of genetic variation in a classic matching-alleles coevolutionary model by exploring the effects of ecological and epidemiological feedbacks, where both allele frequencies and population sizes are allowed to vary over time.  We find that coevolution rarely maintains more host genetic variation than expected under neutral genetic drift alone.  When and if coevolution maintains or depletes genetic variation relative to neutral drift is  determined, predominantly, by two factors: the deterministic stability of the Red Queen allele frequency cycles and the chance of allele fixation in the pathogen, as this results in directional selection and depletion of genetic variation in the host. Compared to purely coevolutionary models with constant host and pathogen population sizes, ecological and epidemiological feedbacks stabilize Red Queen cycles deterministically, but population fluctuations in the pathogen increase the rate of allele fixation in the pathogen, especially in epidemiological models.  Our results illustrate the importance of considering the ecological and epidemiological context in which coevolution occurs when examining the impact of Red Queen cycles on genetic variation.&lt;/p&gt;
DOI: 10.14288/1.0397848
title: Genomic analyses of phenotypic differences between native and invasive populations of diffuse knapweed (Centaurea diffusa)

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p style="margin-bottom:13px;"&gt;Invasive species represent excellent opportunities to study the evolutionary potential of traits important to success in novel environments. Although some ecologically-important traits have been identified in invasive species, little is typically known about the genetic mechanisms that underlie invasion success in non-model species. Here, we use a genome-wide association (GWAS) approach to identify the genetic basis of trait variation in the non-model, invasive, diffuse knapweed (&lt;i&gt;Centaurea diffusa &lt;/i&gt;Lam.&lt;i&gt; &lt;/i&gt;[Asteraceae]). To assist with this analysis, we have assembled the first draft genome reference and fully annotated plastome assembly for this species, and the one of the first from this large, weedy, genus, which is of major ecological and economic importance. We collected phenotype data from 372 individuals from four native and four invasive populations of &lt;i&gt;C. diffusa &lt;/i&gt;grown in a common environment. Using these individuals, we produced reduced-representation genotype-by-sequencing (GBS) libraries and identified 7058 SNPs. We identify two SNPs associated with leaf width in these populations, a trait which significantly varies between native and invasive populations. In this rosette forming species, increased leaf width is a major component of increased biomass, a common trait in invasive plants correlated with increased fitness. Finally, we use annotations from &lt;i&gt;Arabidopsis thaliana&lt;/i&gt; to identify 98 candidate genes that are near the associated SNPs and highlight several good candidates for leaf width variation.&lt;/p&gt;
DOI: 10.14288/1.0397972
title: Phylogenomics reveals novel relationships among Neotropical crocodiles (Crocodylus spp.)

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;Extant species in the order Crocodylia are remnants of an ancient lineage of large-bodied archosaur reptiles. Despite decades of systematic studies, phylogenetic relationships among members of the genus &lt;i&gt;Crocodylus&lt;/i&gt; (true crocodiles) in the Neotropics are poorly understood. Here we estimated phylogenomic relationships among the four extant &lt;i&gt;Crocodylus &lt;/i&gt;species in the Americas. Species-tree reconstructions using genotypic data from 17,538 SNPs collected for 33 individuals spanning six &lt;i&gt;Crocodylus &lt;/i&gt;species (four ingroup and two outgroup) revealed novel relationships for all Neotropical species. For the first time, &lt;i&gt;C. acutus&lt;/i&gt;, the American crocodile, was recovered as monophyletic when individuals from Antillean and continental populations were analyzed together. Our results also contradict previous inferences based on mitochondrial DNA data and a limited number of nuclear markers by robustly grouping Morelet's crocodile (&lt;i&gt;C. moreletii&lt;/i&gt;) as the sister species to &lt;i&gt;C. acutus&lt;/i&gt;., suggesting a novel phylogeographic hypothesis for the group. The present study punctuates the importance of using nuclear genome-wide information and representative sampling for resolving phylogenetic relationships, especially in broadly distributed species and those with complex evolutionary histories.&lt;/p&gt;
DOI: 10.14288/1.0395197
title: Economic evaluation of the Smart Discharges program in Uganda

description: Data was collected from September to December 2019 via a mixed-methods approach to: 1) Identify cost drivers 2) Estimate out-of-pocket costs 3) Conduct a cost-effectiveness analysis of the Smart Discharge program.
DOI: 10.14288/1.0397631
title: Data from: Divergence of Arctic shrub growth associated with sea ice decline

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p style="border:none;margin-top:16px;margin-bottom:4px;text-align:justify;"&gt;&lt;span style="page-break-after:avoid;"&gt;Arctic sea ice extent (SIE) is declining at an accelerating rate with a wide range of ecological consequences. However, determining sea ice effects on tundra vegetation remains a challenge. In this study, we examined the universality or lack thereof in tundra shrub growth responses to changes in SIE and summer climate across the Pan-Arctic, taking advantage of 23 tundra shrub-ring chronologies from 19 widely distributed sites (56⁰-83⁰N). &lt;/span&gt;&lt;/p&gt;
DOI: 10.14288/1.0397858
title: Fitness maps to a large-effect locus in introduced stickleback populations

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;Mutations of small effect underlie most adaptation to new environments, but beneficial variants with large fitness effects are expected to contribute under certain conditions. Genes and genomic regions having large effects on phenotypic differences between populations are known from numerous taxa, but fitness effect sizes have rarely been estimated. We mapped fitness over a generation in an F2 intercross between a marine and a lake stickleback population introduced to a freshwater pond. A QTL map of the number of surviving offspring per F2 female detected a single, large-effect locus near &lt;i&gt;Ectodysplasin&lt;/i&gt; (&lt;i&gt;Eda&lt;/i&gt;), a gene having an ancient freshwater allele causing reduced bony armor and other changes. F2 females homozygous for the freshwater allele had twice the number of surviving offspring as homozygotes for the marine allele, producing a large selection coefficient, &lt;i&gt;s&lt;/i&gt; = 0.50 ± 0.09 SE. Correspondingly, the frequency of the freshwater allele increased from 0.50 in F2 mothers to 0.58 in surviving offspring. We compare these results to observed allele frequency changes at the &lt;i&gt;Eda&lt;/i&gt; gene in an Alaskan lake population colonized by marine stickleback in the 1980’s. The frequency of the freshwater &lt;i&gt;Eda&lt;/i&gt; allele rose steadily over multiple generations and reached 95% within 20 years, yielding a similar estimate of selection, &lt;i&gt;s&lt;/i&gt; = 0.49 ± 0.05. These findings are consistent with other studies suggesting strong selection on this gene (and/or linked genes) in fresh water. Selection on ancient genetic variants carried by colonizing ancestors is likely to increase the prevalence of large-effect fitness variants in adaptive evolution.&lt;/p&gt;
DOI: 10.14288/1.0395366
title: UBC Farm Land Use Map - GIS Files

description: This dataset contains shape files and supporting files for the most up-to-date (as of the published date) land use map at the UBC Farm. The best uses of these maps are: 1) to visualize locations of field codes in other UBC Farm datasets; 2) to visualize field codes for UBC Farm research projects, and 3) to understand the general layout of the Farm.