cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.57745/g7lrkg
title: P638251001_projection_datasheet.pdf
DOI: 10.57745/h4pswb
title: P207002002_projection_datasheet.pdf
DOI: 10.57745/iwcpho
title: P248402001_projection_datasheet.pdf
DOI: 10.57745/jce5le
title: P081402001_projection_datasheet.pdf
DOI: 10.57745/jpihdn
title: P138000000_projection_datasheet.pdf
DOI: 10.57745/kz1joj
title: P177000101_projection_datasheet.pdf
DOI: 10.57745/lhs5hh
title: P801251001_projection_datasheet.pdf
DOI: 10.57745/lpuxfg
title: P613402002_projection_datasheet.pdf
DOI: 10.57745/lscfaz
title: P411401001_projection_datasheet.pdf
DOI: 10.57745/m09eq0
title: P178052000_projection_datasheet.pdf
DOI: 10.57745/mbkwax
title: P231502001_projection_datasheet.pdf

description: :unav
DOI: 10.57745/n3ggpg
title: P171291001_projection_datasheet.pdf
DOI: 10.57745/ohevn8
title: P009000201_projection_datasheet.pdf
DOI: 10.57745/pnyelc
title: P071401001_projection_datasheet.pdf
DOI: 10.57745/qo77af
title: P616151101_projection_datasheet.pdf
DOI: 10.57745/qpdhrg
title: P231502001_projection_datasheet.pdf
DOI: 10.57745/qyvnox
title: P616151001_projection_datasheet.pdf
DOI: 10.57745/r0w0ub
title: P839431001_projection_datasheet.pdf
DOI: 10.57745/r73gap
title: P065000101_projection_datasheet.pdf
DOI: 10.57745/r8mgt7
title: P816252001_projection_datasheet.pdf
DOI: 10.57745/ryxowf
title: P712151001_projection_datasheet.pdf
DOI: 10.57745/rz4ka1
title: P313102001_projection_datasheet.pdf
DOI: 10.57745/sfiefo
title: P726151001_projection_datasheet.pdf
DOI: 10.57745/sfospx
title: P196291001_projection_datasheet.pdf
DOI: 10.57745/sn7hrn
title: P335252001_projection_datasheet.pdf
DOI: 10.57745/t2v5pn
title: Notice_fiche_synthÃ¨se_Explore2.pdf
DOI: 10.57745/t6zsh6
title: P810251001_projection_datasheet.pdf
DOI: 10.57745/ttdbbf
title: P174401003_projection_datasheet.pdf
DOI: 10.57745/ufjbjz
title: P205401001_projection_datasheet.pdf
DOI: 10.57745/vqvmbw
title: P327401001_projection_datasheet.pdf
DOI: 10.57745/wejiq4
title: P152000101_projection_datasheet.pdf
DOI: 10.57745/wernpi
title: P248401001_projection_datasheet.pdf
DOI: 10.57745/wsh0bo
title: P927401001_projection_datasheet.pdf
DOI: 10.57745/wwr8cz
title: P504401001_projection_datasheet.pdf
DOI: 10.57745/xbvfik
title: P178051001_projection_datasheet.pdf
DOI: 10.57745/xort9o
title: P714401001_projection_datasheet.pdf
DOI: 10.57745/xus6dn
title: P700151001_projection_datasheet.pdf
DOI: 10.57745/y4phfw
title: P088501001_projection_datasheet.pdf
DOI: 10.57745/yuldrb
title: P230001001_projection_datasheet.pdf
DOI: 10.57745/z7jmte
title: P135001002_projection_datasheet.pdf
DOI: 10.57745/z97uby
title: P392252001_projection_datasheet.pdf
DOI: 10.57745/zclqto
title: P165001001_projection_datasheet.pdf
DOI: 10.14288/1.0421187
title: Data for Strong relationships between urbanization, landscape structure, and ecosystem service multifunctionality in urban forest fragments

description: Data on multiple ecosystem services provided by 21 forest fragments along an urban-to-rural gradient in Maple Ridge, British Columbia, Canada.
DOI: 10.57745/0ks8uc
title: P831252001_projection_datasheet.pdf
DOI: 10.57745/1myega
title: P636251001_projection_datasheet.pdf
DOI: 10.57745/3snmgv
title: P427101001_projection_datasheet.pdf
DOI: 10.57745/4wibyl
title: P323401001_projection_datasheet.pdf
DOI: 10.57745/94unyb
title: P500000201_projection_datasheet.pdf
DOI: 10.57745/abxzmt
title: P828401001_projection_datasheet.pdf
DOI: 10.57745/epuqlu
title: P320101001_projection_datasheet.pdf
DOI: 10.57745/glk958
title: P820401001_projection_datasheet.pdf
DOI: 10.57745/h3fhfp
title: P540401001_projection_datasheet.pdf
DOI: 10.57745/ihgdgu
title: P246401001_projection_datasheet.pdf
DOI: 10.57745/lico9f
title: P320102001_projection_datasheet.pdf
DOI: 10.57745/ooroun
title: P634251001_projection_datasheet.pdf
DOI: 10.57745/oy0ugg
title: P335251001_projection_datasheet.pdf
DOI: 10.57745/qoa2ha
title: P532001001_projection_datasheet.pdf
DOI: 10.57745/tgcx66
title: P555001001_projection_datasheet.pdf
DOI: 10.57745/tt2ek0
title: P401501001_projection_datasheet.pdf
DOI: 10.57745/vlicjl
title: P316401001_projection_datasheet.pdf
DOI: 10.57745/xo6coa
title: P400101001_projection_datasheet.pdf
DOI: 10.14288/1.0416318
title: Pleiotropic opposing dominance within a color gene block contributes to a nascent species boundary via its influence on hybrid male territorial behavior

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;The divergence of plumage color genes contributes to songbird radiation. However, the mechanisms by which color gene divergence counteracts gene flow to maintain reproductive isolation during the formation of new species boundaries remain elusive. The hybrid zone between Setophaga occidentalis (SOCC) and S. townsendi (STOW) in the Cascade Range provides a natural observatory to investigate potential behavioral mechanisms underlying divergent selection on color genes. Recently, we found that selection within a single gene block associated with plumage color variation has maintained a stable and narrow hybrid zone. Here, we investigated the potential role of plumage signals in moderating a behavioral mechanism of selection. Specifically, we assessed whether two plumage traits are associated with body size among breeding males and if trait mismatch predicted aggressive behavior within hybrid and parental individuals in response to simulated territorial intrusion. The two plumage signals, cheek and flank coloration, though associated with the same gene block, reflect opposing dominance of SOCC and STOW alleles. We found that both plumage traits significantly predict the body size in the territorial sex (i.e. males). The opposing dominance of the single color gene block resulted in plumage signal discordance in heterozygotes, which in turn was associated with reduced hybrid territorial performance, an important proxy of fitness in this system. Taken together, these observations point to a single-locus-two-alleles mechanism of incompatibility in shaping a natural species boundary in the early stage of speciation.&lt;/p&gt;
DOI: 10.14288/1.0426564
title: Replication Data for: The effect of placement and group size on the use of a mechanical brush by groups of lactating dairy cattle

description: Mechanical brushes are often provided on dairy farms to facilitate grooming. However, current brush designs do not provide data on their use and little is known about the effects of group size and placement of brushes within the pen. The objectives of this study were to automatically detect brush use in cow groups and investigate the influence of (1) group size and the corresponding cow-to-brush ratio and (2) brush placement in relation to the lying stalls and the feeding and drinking areas. We measured brush use in groups of 60, 48, 36, and 24 cows with the brush placed either in the alley adjacent to the feed bunk and water trough or in the back alley. Cows used the brush longer when placed in the feed/water alley compared to when placed in the back alley. Average brush use per cow increased when cows were housed in smaller groups but the brush was never in use more than 50% of the day regardless of group size. We conclude that brush use in-creases when availability is increased and when the brush is placed closer to feed and water.
DOI: 10.14288/1.0416391
title: The effect of air purifiers and curtains on aerosol dispersion and removal in multi-patient hospital rooms

description: &lt;p&gt; Airborne transmission of disease is of concern in many indoor spaces. Here, aerosol dispersion and removal in an unoccupied 4-bed hospital room was characterized using a transient aerosol tracer experiment for 38 experiments covering 4 configurations of air purifiers and 3 configurations of curtains. NaCl particle (mass mean aerodynamic diameter ∼3μm) concentrations were measured around the room following an aerosol release. Particle transport across the room was 1.5 - 4 minutes which overlaps with the characteristic times for significant viral deactivation and gravitational settling of larger particles. Concentrations were close to spatially uniform except very near the source. Short curtains had no consistent effects on concentrations at the non-source patient locations while floor-length curtains reduced concentrations slightly depending on the purifier configuration. The aerosol decay rate was in most cases higher than expected from the clean air delivery rate, but the reduction in steady-state concentrations resulting from air purifiers was less than suggested by the decay rates. Apparently a substantial (and configuration-dependent) fraction of the aerosol is removed immediately and this effect is not captured by the decay rate. Overall, the combination of curtains and purifiers is likely to reduce disease transmission in multipatient hospital rooms. &lt;/p&gt;
DOI: 10.14288/1.0432650
title: Single-strain behavior predicts responses to environmental pH and osmolality in the gut microbiota

description: Abstract Changes to gut environmental factors such as pH and osmolality due to disease or drugs correlate with major shifts in microbiome composition; however, we currently cannot predict which species can tolerate such changes or how the community will be affected. Here, we assessed the growth of 92 representative human gut bacterial strains spanning 28 families across multiple pH values and osmolalities in vitro. The ability to grow in extreme pH or osmolality conditions correlated with the availability of known stress response genes in many cases, but not all, indicating that novel pathways may participate in protecting against acid or osmotic stresses. Machine learning analysis uncovered genes or subsystems that are predictive of differential tolerance in either acid or osmotic stress. For osmotic stress, we corroborated the increased abundance of these genes in vivo during osmotic perturbation. The growth of specific taxa in limiting conditions in isolation in vitro correlated with survival in complex communities in vitro and in an in vivo mouse model of diet-induced intestinal acidification. Our data show that in vitro stress tolerance results are generalizable and that physical parameters may supersede interspecies interactions in determining the relative abundance of community members. Importantly, we provide an extensive resource for predicting shifts in microbial composition and gene abundance in complex perturbations. Furthermore, this work highlights the physical environment as a major driver of bacterial composition and the importance of performing physical measurements in animal and clinical studies to elucidate the drivers of shifts in microbiota abundance.
DOI: 10.14288/1.0417548
title: Data from: Genotyping-in-Thousands by Sequencing panel development and application for high-resolution monitoring of introgressive hybridization within sockeye salmon

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;Stocking programs have been widely implemented to re-establish extirpated fish species to their historical ranges; when employed in species with complex life histories, such management activities should include careful consideration of resulting hybridization dynamics with resident stocks and corresponding outcomes on recovery initiatives. Genetic monitoring can be instrumental for quantifying the extent of introgression over time, however, conventional markers typically have limited power for the identification of advanced hybrid classes, especially at the intra-specific level. Here, we demonstrate a workflow for developing, evaluating, and deploying a Genotyping-in-Thousands by Sequencing (GT-seq) SNP panel with the power to detect advanced hybrid classes to assess the extent and trajectory of intra-specific hybridization, using the sockeye salmon (&lt;em&gt;Oncorhynchus nerka)&lt;/em&gt; stocking program in Skaha Lake, British Columbia, as a case study. Previous analyses detected significant levels of hybridization between the anadromous (sockeye) and freshwater resident (kokanee) forms of &lt;em&gt;O. nerka&lt;/em&gt;, but were restricted to assigning individuals to pure-stock or “hybrid”. Simulation analyses indicated our GT-seq panel had high accuracy, efficiency and power (&gt; 94.5%) of assignment to pure-stock sockeye salmon/kokanee, F&lt;sub&gt;1&lt;/sub&gt;, F&lt;sub&gt;2&lt;/sub&gt;, and B&lt;sub&gt;2&lt;/sub&gt; backcross-sockeye/kokanee. Re-analysis of 2016/2017 spawners previously analyzed using TaqMan&lt;span style="font-size:13.3333px;"&gt; &lt;/span&gt;assays and otolith microchemistry revealed shifts in assignment of some hybrids to adjacent pure-stock or B&lt;sub&gt;2&lt;/sub&gt;-backcross classes, while new assignment of 2019 spawners revealed hybrids comprised 31% of the population, ~74% of which were B&lt;sub&gt;2&lt;/sub&gt;-backcross or F&lt;sub&gt;2&lt;/sub&gt;. Overall, the GT-seq panel development workflow presented here could be applied to virtually any system where genetic stock identification and intra-specific hybridization are important management parameters.&lt;/p&gt;
DOI: 10.14288/1.0429372
title: Replication Data for: Crowd sourcing remote comparative lameness assessments for dairy cattle

description: Lameness assessments are rarely conducted routinely on dairy farms and when completed typically underestimate lameness prevalence, hampering early diagnosis and treatment. A well-known feature of many perceptual tasks is that relative assessments are more accurate than absolute assessments, suggesting that creating methods that allow for the relative scoring of ‘which cow is more lame’ will allow for reliable lameness assessments. Here we developed and tested a remote comparative lameness assessment method: we recruited non-experienced crowd workers via an online platform and asked them to watch two videos side-by-side, each showing a cow walking, and to identify which cow was more lame and by how much (on a scale of -3 to 3). We created 11 tasks, each with 10 video pairs for comparison, and recruited 50 workers per task. All tasks were also completed by 5 experienced cattle lameness assessors. We evaluated data filtering and clustering methods based on worker responses and determined the agreement among workers, among experienced assessors, and between these groups. A moderate to high interobserver reliability was observed (intraclass correlation coefficient, ICC=0.46 to 0.77) for crowd workers and agreement was high among the experienced assessors (ICC=0.87). Average crowd worker responses showed excellent agreement with the average of experienced assessor responses (ICC= 0.89 to 0.91), regardless of data processing method. To investigate if we could use fewer workers per task while still retaining high agreement with experienced assessors, we randomly sub-sampled 2 to 43 (1 less than the minimum number of workers retained per task after data cleaning) workers from each task. The agreement with experienced assessors increased substantially as we increased the number of workers from 2 to 10, but little increase was observed after 10 or more workers were used (ICC&gt;0.80). The proposed method provides a fast and cost-effective way to assess lameness in commercial herds. In addition, this method allows for large-scale data collection useful for training computer vision algorithms that could be used to automate lameness assessments on farm.
DOI: 10.14288/1.0417547
title: Population genomics of an emergent tri-species hybrid zone

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;Isolating barriers that drive speciation are commonly studied in the context of two-species hybrid zones. There is however evidence that more complex introgressive relationships are common in nature. Here, we use field observations and genomic analysis, including the sequencing and assembly of a novel reference genome, to study an emergent hybrid zone involving two colliding hybrid zones of three woodpecker species: red-breasted, red-naped, and yellow-bellied sapsuckers (&lt;em&gt;Sphyrapicus ruber&lt;/em&gt;, &lt;em&gt;S. nuchalis&lt;/em&gt;, and &lt;em&gt;S. varius&lt;/em&gt;). Surveys of the area surrounding Prince George, British Columbia, Canada, show that all three species are sympatric, and Genotyping-by-Sequencing identifies hybrids from each species pair and birds with ancestry from all three species. Observations of phenotypes and genotypes of mated pairs provide evidence for assortative mating, though there is some heterospecific pairing. Hybridization is more extensive in this tri-species hybrid zone than in two di-species hybrid zones. However, there is no evidence of a hybrid swarm, and admixture is constrained to contact zones, so we classify this region as a tension zone and invoke selection against hybrids as a likely mechanism maintaining species boundaries. Analysis of sapsucker age classes does not show disadvantages in hybrid survival to adulthood, so we speculate the selection upholding the tension zone may involve hybrid fecundity. Gene flow among all sapsuckers in di-species hybrid zones suggests introgression likely occurred before the formation of this tri-species hybrid zone and might result from bridge hybridization, vagrancies, or other three-species interactions. &lt;/p&gt;
DOI: 10.14288/1.0417593
title: Dataset for the Canadian Institutes of Health Research (CIHR) Research Quality Assurance Program 2019 to 2021

description: This dataset contains 3 years of quality assurance data (2019-2021) from peer reviewer performance assessments conducted by Peer Review Committee leaders in the Canadian Institutes of Health Research (CIHR) Project Grant Competition. The dataset contains separate sheets for each of the 4 project grant competitions completed during the 3-year study period, plus all raw data. There is also an aggregate dashboard sheet to display overall summary data. A copy of the Reviewer Quality Feedback Form, which was used to collect the performance data contained in the dataset, is available from: https://cihr-irsc.gc.ca/e/51654.html.
DOI: 10.15468/dl.vamuh7
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Willughbeia sarawacensis (Pierre) K.Schum.",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Human Observation, Living Specimen, Occurrence evidence)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000490-250424135625364/datasets/export for details.
DOI: 10.14288/1.0417549
title: Phylogenomics shows unique traits in Noctilucales are derived rather than ancestral

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;&lt;span lang="EN-US"&gt;Dinoflagellates are a diverse group of protists that possess many unique traits. These include (but are not limited to) expansive genomes packaged into permanently condensed chromosomes, photosynthetic or cryptic plastids acquired vertically or horizontally in serial endosymbioses, and a ruffle-like transverse flagellum attached along its length to the cell. When reconstructing &lt;/span&gt;&lt;span lang="EN-US"&gt;character evolution, early branching lineages with unusual features that distinguish them from the rest of the group have proven useful for inferring ancestral states. The Noctilucales are one such lineage, possessing relaxed chromosomes in some life stages and a trailing, thread-like transverse flagellum. However, most of the cellular and molecular data for the entire group come from a single cultured species, &lt;/span&gt;&lt;em&gt;&lt;span lang="IT"&gt;Noctiluca scintillans&lt;/span&gt;&lt;/em&gt;&lt;span lang="EN-US"&gt;, and because its phylogenetic position is unresolved, it remains unclear if these traits are ancestral or derived. Here, we use single cell transcriptomics to characterize three diverse&lt;/span&gt;&lt;span lang="ES-TRAD"&gt; Noctilucales genera: &lt;/span&gt;&lt;em&gt;&lt;span lang="EN-US"&gt;Spatulodinium&lt;/span&gt;&lt;/em&gt;&lt;span lang="EN-US"&gt;, &lt;em&gt;Kofoidinium&lt;/em&gt;, and a new lineage, &lt;em&gt;Fabadinium&lt;/em&gt; gen. nov. We also provide transcriptomes for undescribed species in &lt;em&gt;Amphidinium&lt;/em&gt;&lt;/span&gt;&lt;span lang="DE"&gt; and Abediniales&lt;/span&gt;&lt;span lang="EN-US"&gt;, critical taxa for clarifying the phylogenetic position of &lt;/span&gt;&lt;span lang="ES-TRAD"&gt;Noctilucales&lt;/span&gt;&lt;span lang="EN-US"&gt;. Phylogenomic analyses suggest that the Noctilucales are sister to &lt;em&gt;Amphidinium&lt;/em&gt; rather than an independent branch outside the core dinoflagellates. This topology is consistent with observations of shared characteristics between some members of Noctilucales and &lt;em&gt;Amphidinium&lt;/em&gt; and provides the most compelling evidence to date that the unusual traits within this group are derived rather than ancestral. We also confirm that &lt;em&gt;Spatulodinium&lt;/em&gt; &lt;/span&gt;&lt;span lang="ES-TRAD"&gt;plastids are photosynthetic and of ancestral origin&lt;/span&gt;&lt;span lang="EN-US"&gt;, and show that all non-photosynthetic Noctilucales retain plastid &lt;/span&gt;&lt;span lang="ES-TRAD"&gt;genes&lt;/span&gt;&lt;span lang="EN-US"&gt; indicating a cryptic organelle.&lt;/span&gt;&lt;/p&gt;
DOI: 10.14288/1.0418473
title: Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets

description: There is a growing collection of genomics data sets generated for identifying the gene targets under control of transcription regulators (TRs). TR ChIP-seq and RNA expression experiments that perturb TR activity are the most common strategies for mapping TRs to genes at a genomic scale. However, the collection, preprocessing, summarization, and integration of these data sets requires a non-trivial degree of bioinformatics experience. In this study, we set out a framework to accomplish these tasks. We focus on eight TRs in both mouse and human, encompassing nearly 500 experiments, with two main objectives. The first is a detailed examination of the properties of the contributing experiments, to better learn of potential biases and pitfalls when aggregating diverse data sets. The second is to provide summarized, transparent, and convenient TR-target rankings based upon these genomic data sets for community use. Our work thus catalogues the state of the literature for a subset of important mammalian TRs, prioritizes gene targets based upon available empirical evidence, and provides a framework for ready expansion to more TR data sets.