cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.57vvna
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Opisthoproctus Vaillant, 1888",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((43.4313 -17.5054,43.9059 -19.9421,43.0686 -21.0649,42.7023 -21.9969,43.1619 -23.5254,43.213 -24.5373,43.6164 -25.1504,44.9648 -25.1504,44.9648 -16.1504,43.978 -16.1504,43.9239 -16.5407,43.4313 -17.5054))"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011102-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15209912
title: Training and testing Datasets for the paper VANER2: Towards more general biomedical named entity recognition using multi-task large language model encoders
DOI: 10.5281/zenodo.15209913
title: Training and testing Datasets for the paper VANER2: Towards more general biomedical named entity recognition using multi-task large language model encoders
DOI: 10.5281/zenodo.15559649
title: Training and testing Datasets for the paper VANER2: Towards more general biomedical named entity recognition using multi-task large language model encoders
DOI: 10.5281/zenodo.15559674
title: THE IMPORTANCE OF AUTHENTIC MATERIALS IN FRENCH LANGUAGE LEARNING
DOI: 10.5281/zenodo.15559675
title: THE IMPORTANCE OF AUTHENTIC MATERIALS IN FRENCH LANGUAGE LEARNING
DOI: 10.15468/dl.rcvm2b
title: Occurrence Download

description: A dataset containing 42467 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Asclepias tuberosa L."
 ]
}

 The dataset includes 42467 records from 198 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011106-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u4ptzz
title: Occurrence Download

description: A dataset containing 508 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "OccurrenceStatus is Present",
 "TaxonKey is Aquilegia bertolonii Schott"
 ]
}

 The dataset includes 508 records from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011104-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8m7nkf
title: Occurrence Download

description: A dataset containing 743 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Casuarina glauca Sieber)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 743 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011103-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uf4z26
title: Occurrence Download

description: A dataset containing 46363 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rapistrum rugosum (L.) All."
 ]
}

 The dataset includes 46363 records from 777 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011105-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25326/vr5p-f526
title: spark soot + None - Aerosol study - physical properties - 1999-10-11

description: Publication of the dataset
DOI: 10.48689/mn9g-pr12
title: Tsunami Hazard Line (Victoria)
DOI: 10.48689/38cw-e560
title: Tsunami Hazard Lines (White Rock)
DOI: 10.48689/x0hp-4v71
title: Tsunami Studies (2009 ongoing)
DOI: 10.48689/me5p-8560
title: Tufted Puffin Colonies
DOI: 10.5061/dryad.bk3j9kdbk
title: Data from: Latitudinal embryonic thermal tolerance and plasticity shape the vulnerability of oviparous species to climate change

description: Heat tolerance at the immobile embryonic stage is expected to be critical
 in determining species vulnerability to climate change. However, how the
 mean and developmental plasticity of embryonic heat tolerance vary
 geographically, and how these geographic variations affect species’
 vulnerability under climate change remain unknown. We experimentally
 determined the mean and developmental plasticity of embryonic acute heat
 tolerance (EAHT, i.e., heat shock temperature at which embryonic
 heartbeats ceased) for three latitudinally-distributed populations of an
 oviparous lacertid lizard. The experimental results suggested that the
 mean EAHT decreased with decreasing latitude and that the reaction norms
 of EAHT in relation to developmental temperatures showed ‘flat’,
 ‘bell-shaped’, and ‘decreasing’ patterns at high, medium, and low
 latitudes, respectively. Based on the means and plasticity of EAHT and
 weather data across China, we project that the heat stress frequency would
 increase from present to the future and increase towards low latitudes.
 Furthermore, heat stress becomes more extensive with the incorporation of
 developmental plasticity. Incorporating the mean EAHT during the embryonic
 development season, heat stress frequency, and climate variables in a
 species distribution model projects that suitable habitats could move
 northward in response to ongoing climate change and shrink due to the loss
 of southern habitat. Moreover, even lizards within the areas that are
 predicted to remain highly suitable are expected to experience increases
 in heat stress over time, particularly at medium and low latitudes. Our
 study reveals geographic variation in the mean and developmental
 plasticity of EAHT and highlights its importance for predicting species
 vulnerability and range shifts in response to climate change.
description: Air temperatures are collected by iButton hourly;
 Heat tolerance are collected by Egg buddy and thermal couple
 synchronously; Egg incubation were conducted at 24℃,
 26℃, 28℃, 30℃, 32℃; Heat stress frequency were
 calculated by soil temperatures and EAHT, with the code of heat stress we
 developed in R. Others see details in materials and
 methods in the paper
description: The dataset contains five excel files and two codes in
 R.  The details for method and analysis are provided in
 the main text of the paper. The description for each
 item in excels are provided separately in each sheet of file, or you can
 see details in readme file.
DOI: 10.48689/mq6n-yn88
title: Tug and Service Vessel Hours 2010
DOI: 10.5061/dryad.5mkkwh75h
title: The different fates of two Asian horseshoe crab species with different dispersal abilities

description: Impending anthropogenic climate change will severely impact coastal
 organisms at unprecedented speed. Knowledge on organisms’ evolutionary
 responses to past sea level fluctuations and estimation of their
 evolutionary potential is therefore indispensable in efforts to mitigate
 the effects of future climate change. We sampled tens of thousands of
 genomic markers of ~300 individuals in two of the four extant horseshoe
 crab species across the complex archipelagic Singapore Straits.
 Carcinoscorpius rotundicauda Latreille, a less mobile mangrove species,
 has finer population structure and lower genetic diversity compared to the
 dispersive deep-sea Tachypleus gigas Müller. Even though the source
 populations of both species during the Last Glacial Maximum exhibited
 comparable effective population sizes, the less dispersive C. rotundicauda
 seems to lose genetic diversity much more quickly because of population
 fragmentation. Contra previous studies’ results, we predict that the more
 commonly sighted C. rotundicauda faces a more uncertain conservation
 plight, with a continuing loss in evolutionary potential and higher
 vulnerability to future climate change. Our study provides important
 genomic baseline data for the redirection of conservation measures in the
 face of climate change, and can be used as a blueprint for assessment and
 mitigation of the adverse effects of impending sea level rise in other
 systems.
description: The datasets are single nucleotide polymorphism collected from
 two horseshoe crab species across the Singapore Straits using
 double-digest RAD sequencing.
description: The datasets are STACKS file for the SNP calling. Please see
 ReadMe for details.
DOI: 10.48689/khep-k997
title: Turbidity Reduces Predation on Migrating Juvenile Pacific Salmon
DOI: 10.48689/v1nj-5b81
title: Two Decades of Fish Habitat Restoration and Bioengineering on the Fraser River Estuary, British Columbia, Canada
DOI: 10.5061/dryad.9s4mw6mg6
title: Fruit abundance and trait matching determine diet type and body condition across frugivorous bird populations

description: Research on seed-dispersal mutualisms has been highly unbalanced towards
 the plants, largely overlooking the fitness effects of fruit resources on
 frugivorous animals. Moreover, despite morphological mismatches like gape
 limitation may reduce the abundance of fruits that are actually accessible
 to a frugivore species, there is very little evidence on the
 trait-matching implications from a frugivore’s perspective. Here, we
 refine recent resource-provisioning models to comprehensively test the
 joint effects of fruit abundance and trait matching on diet type and body
 condition (a surrogate of fitness) across frugivorous bird populations:
 Sardinian warblers (Curruca melanocephala) inhabiting ten Mediterranean
 forests differing in the abundance and composition of fleshy fruits. We
 hypothesised the abundance of fruit resources to have positive effects on
 the degree of frugivory and body condition of warblers, and such effects
 to be more pronounced when accounting for both trait matching (accessible
 fruits) and resource provisioning (energy in accessible fruits). We found
 a sharp threshold over which warblers shifted from a diet with very little
 or even no fruits to a predominantly frugivorous diet with increasing the
 local abundance of accessible fruits. We also found a strong positive
 relationship between the abundance of accessible fruits and the body
 condition of warblers (body mass and residual body mass), an effect that
 was more pronounced in females than in males. Although diet type and body
 condition were much better predicted when accounting for trait matching,
 accounting for resource provisioning did not improve the explanatory power
 of fruit resources. The fact that we detected strong and sex-dependent
 effects of fruit resources on body condition just a few weeks before the
 breeding season suggests that fruit resources likely affect the timing and
 success of reproduction, a question that deserves further research. Our
 findings provide new insight into the fitness consequences of
 seed-dispersal mutualisms for frugivorous animals.
description: All the methods are described in detail in the scientific paper
 associated to this dataset: González-Varo et al. 2021 Oikos 10.1111/oik.08106
DOI: 10.48689/nmr6-fs31
title: U.S. JGOFS Data System (1988-2005)
DOI: 10.48689/d6h3-5g69
title: UBC Herbarium - Bryophytes, Fungi and Lichens
DOI: 10.48689/mz72-js45
title: UBC Herbarium - Fungi and Lichens
DOI: 10.48689/bame-er96
title: UBC Herbarium- Algae
DOI: 10.48689/5kxj-5r18
title: UBC Herbarium- Bryophytes
DOI: 10.48689/4cj0-tt50
title:  UBC Herbarium-Vascular Plants (1912 ongoing)
DOI: 10.5061/dryad.jq2bvq88b
title: Supplementary mass spectonomy data to analyse generation of spliced mutant Kras/RAC2 epitopes

description: In vitro proteasome processing of neo-splicetopes does not
 predict their presentation in vivo Proteasome catalyzed peptide
 splicing (PCPS) of cancer-driving antigens could generate attractive
 neoepitopes to be targeted by TCR-based adoptive T cell therapy. Based on
 a spliced peptide prediction algorithm TCRs were generated against
 putative KRASG12V and RAC2P29L derived neo-splicetopes
 with high HLA-A*02:01 binding affinity. TCRs generated
 in mice with a diverse human TCR repertoire specifically recognized the
 respective target peptides with high efficacy. However, we failed to
 detect any neo-splicetope specific T cell response when testing
 the in vivo neo-splicetope generation and obtained no
 experimental evidence that the putative KRASG12V- and RAC2P29L-derived
 neo-splicetopes were naturally processed and presented. Furthermore, only
 the putative RAC2P29L-derived neo-splicetopes was generated by in
 vitro PCPS.  Our experiments pose severe
 questions on the notion that available algorithms or the in
 vitro PCPS reaction reliably simulate in
 vivo splicing and argue against the general applicability of an
 algorithm-driven “reverse immunology” pipeline for the identification of
 cancer-specific neo-splicetopes.
DOI: 10.48689/1mvt-bv24
title: Underwater Video Point Descriptions (CRD)
DOI: 10.48689/nxda-eh08
title: Universal Length of Day
DOI: 10.48689/w4zz-6t72
title: Upper Ocean Processes Group - Data Archives
DOI: 10.48689/a48d-vd49
title: Upper Ocean Sub Regions
DOI: 10.15468/dl.fqmcb6
title: Occurrence Download

description: A dataset containing 168 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Correlophus ciliatus"
 ]
}

 The dataset includes 168 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002841-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48689/cmrs-dv92
title: Upwelling Indices
DOI: 10.5061/dryad.1c59zw3v6
title: Temperature‐associated decreases in demographic rates of Afrotropical bird species over 30 years

description: Tropical mountains harbor globally significant levels of biodiversity and
 endemism. Climate change threatens many tropical montane species, yet
 little research has assessed the effects of climate change on the
 demographic rates of tropical species, particularly in the Afrotropics.
 Here, we report on the demographic rates of 21 Afrotropical bird species
 over 30 years in montane forests in Tanzania. We used mark-recapture
 analyses to model rates of population growth, recruitment, and apparent
 survival as functions of annual mean temperature and annual precipitation.
 For over one-half of focal species, decreasing population growth rates
 were associated with increasing temperature. Due to the trend in
 temperature over time, we substituted a time covariate for the temperature
 covariate in top-ranked population growth rate models. Temperature was a
 better explanatory covariate than time for 6 of the 12 species, or 29% of
 all focal species. Population growth rates were also lower for species
 found further below their elevational midpoint and for smaller-bodied
 species. Changes in population growth rates were more closely tied to
 changes in recruitment than to changes in apparent survival. There were no
 consistent associations between demographic rates and precipitation. This
 study demonstrates temperature-associated demographic impacts for 6 (29%)
 of 21 focal species in an Afrotropical understory bird community and
 highlights the need to incorporate the impacts of climate change on
 demographic rates into conservation planning across the tropics.
description: See the published paper for full details on methods. Over 30
 years (1987-2016) understory forest birds were caught in mist nets and
 banded in two forest blocks in the Usambara Mountains of Tanzania. We
 provide the capture histories for 21 focal understory bird species in the
 East and West Usambara Mountains. There is a text file per species, and
 each file contains the capture histories of each uniquely-banded
 individual. There is also a column for the banding location:
 "East" or "West". The file name is a species code; for
 full species names see Table 1.
DOI: 10.48689/q6s4-4p89
title: Upwelling Indices (1946- ongoing)
DOI: 10.48689/61q1-1130
title: Use of SLICE (1996-2014)
DOI: 10.48689/1620-e506
title: Use of Therapeutants (1995-2014)
DOI: 10.6084/m9.figshare.30578940
title: Generalizable features of pegRNA design for prime editing of inherited retinal diseases

description: The variety of ocular cell types involved in inherited retinal disease (IRD) necessitates the use of gene editing therapeutics which have generalizable components. In our study, we investigate the generalizable characteristics of non-engineered pegRNA design (PE2) for efficient, proof-in-principle gene correction of over 21 genes implicated in IRDs and associated syndromes. We use a single-transgene oligopool approach, comprising approximately 12,000 uniquely barcoded pegRNAs that target a synthetically integrated, 50 bp sequence motif, which faithfully recapitulate the disease context of their various counterpart IRDs. Using this approach, we perform a high throughput, pooled analysis of pegRNA characteristics across non- and ocular cell types to propose a cell-line agnostic set of pegRNA design guidelines. Briefly, we find that non-engineered pegRNA 3′ extensions should mediate substitution-type edits and that the desired edit should be placed within five nucleotides upstream of the nick site induced by the Cas-endonuclease. Further, PBS and RTT lengths of at least 12 and 14 nucleotides, respectively, should be used and each non-engineered pegRNA 3′ extension should obviate an initial templating cytosine nucleotide. We establish a set of recommendations for the generalizable design of the non-engineered pegRNA 3′ extension for the correction of several IRDs, enabling overall simplification of design parameters for PE2-based systems.
DOI: 10.6084/m9.figshare.30578940.v1
title: Generalizable features of pegRNA design for prime editing of inherited retinal diseases

description: The variety of ocular cell types involved in inherited retinal disease (IRD) necessitates the use of gene editing therapeutics which have generalizable components. In our study, we investigate the generalizable characteristics of non-engineered pegRNA design (PE2) for efficient, proof-in-principle gene correction of over 21 genes implicated in IRDs and associated syndromes. We use a single-transgene oligopool approach, comprising approximately 12,000 uniquely barcoded pegRNAs that target a synthetically integrated, 50 bp sequence motif, which faithfully recapitulate the disease context of their various counterpart IRDs. Using this approach, we perform a high throughput, pooled analysis of pegRNA characteristics across non- and ocular cell types to propose a cell-line agnostic set of pegRNA design guidelines. Briefly, we find that non-engineered pegRNA 3′ extensions should mediate substitution-type edits and that the desired edit should be placed within five nucleotides upstream of the nick site induced by the Cas-endonuclease. Further, PBS and RTT lengths of at least 12 and 14 nucleotides, respectively, should be used and each non-engineered pegRNA 3′ extension should obviate an initial templating cytosine nucleotide. We establish a set of recommendations for the generalizable design of the non-engineered pegRNA 3′ extension for the correction of several IRDs, enabling overall simplification of design parameters for PE2-based systems.
DOI: 10.5061/dryad.1vhhmgqsh
title: Ecological genomics of distinct bleaching tolerances among cryptic coral species

description: Reef-building coral species are experiencing an unprecedented decline due
 to increasing frequency and intensity of marine heatwaves and associated
 bleaching-induced mortality. Closely related species of reef building
 corals from the Acropora hyacinthus species complex differ in heat
 tolerance and in their association with heat-tolerant symbionts, as well
 as growth rate, colony morphology and skeletal density. We used
 low-coverage full genome sequencing of 114 colonies monitored across the
 2015 bleaching event in American Samoa to determine the genetic
 differences among four cryptic species (termed HA, HC, HD, and HE) that
 have diverged in these species traits. Cryptic species differed strongly
 at thousands of single nucleotide polymorphisms across the genome that are
 enriched for amino acid changes in the bleaching-resistant species HE. In
 addition, HE also showed two particularly divergent regions with strong
 signals of differentiation. One approximately 220-kilobase locus, HES1,
 contained the majority of fixed differences in HE. A second locus, HES2,
 was fixed in HE but polymorphic in the other cryptic species, in which
 HE-like genotypes were associated with increased bleaching sensitivity. At
 both loci, HE showed particular sequence similarity to a congener, A.
 millepora. This trans-species similarity could reflect introgression or
 deep ancestral polymorphism. Between these closely related species,
 differentiated loci show strong signatures of selective sweeps,
 introgression or long-term balancing selection, and a possible role for
 epistasis. Overall, resilience to bleaching during the third global
 bleaching event was strongly structured by host cryptic species, buoyed by
 differences in symbiont associations between these species.
DOI: 10.48689/6v1q-7t76
title: Zoning (Saanich)
DOI: 10.6084/m9.figshare.30134530
title: Multimodal imaging and electrophysiological features in bradyopsia associated with homozygous variants (c.895T&gt;C) in Regulator of G-protein Signaling 9 (<i>RGS9</i>)

description: To report multimodal imaging findings and natural history of clinical features in two probands with bradyopsia harboring homozygous variants (c.895T&gt;C) in Regulator of G-protein Signaling 9 (RGS9). Ophthalmic history, clinical examination, fundus autofluorescence (FAF), optical coherence tomography (OCT), microperimetry, flood-illuminated adaptive optics (AO) imaging, and electroretinogram (ERG) were obtained. A 37-year-old male and a 67-year-old female from non-consanguineous parents had normal fundus examination, FAF, and OCT. ERGs for the male case between the age of 4 and 38 years showed no progression. Both probands had flat International Society for Clinical Electrophysiology of Vision (ISCEV) Standard full-field ERG light-adapted (LA) responses but dark-adapted (DA) red x-wave and S-cone responses were present. DA 30 Hz flicker was present after 2 but not after 10 seconds. The reduced amplitude and b:a ratio of the DA10 response improved with increasing interstimulus interval. AO and microperimetry demonstrated preservation of foveal cone density and subnormal retinal sensitivity, respectively. Both measures remained stable over 3 years. The c.895T&gt;C variant was classified as pathogenic. Bradyopsia associated with homozygous RGS9 c.895T&gt;C variants is characterized by normal retinal structure but subnormal macular sensitivity. Extended ERG protocols can be used to confirm delayed phototransduction recovery.