cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pc866t1qv
title: Cross-seasonal effects in the American Woodcock: conditions prior to fall migration relate to migration strategy and its implications for conservation

description: How post-breeding habitat quality and body composition of migratory birds
 carry over to influence fall migration strategies and residency merits
 consideration when creating cross-seasonal conservation plans, especially
 in breeding populations that are partial migrants. We assessed the
 influence of post-breeding habitat quality on departure body composition
 and fall migration patterns in a southern New England breeding population
 of American Woodcock (Scolopax minor). Woodcock that overwintered near
 breeding areas (n=5) had less fat upon capture in fall and used lower
 quality habitat during the fall than birds that eventually departed on
 migration (n=17). Woodcock that departed earlier were long-distance
 migrants that had inhabited higher-quality landscapes prior to migration,
 departed with less fat or similar fat stores, stopped over for shorter
 periods on migration, and arrived earlier on their more southerly
 wintering areas. In contrast, woodcock that departed later were
 short-distance migrants that had inhabited lower quality landscapes prior
 to migration yet stored similar or more fat upon departure, stopped over
 for longer periods on migration, and arrived relatively late to their more
 northerly wintering areas. These differences in migration strategies were
 evident under the same fall environmental conditions and did not appear
 related to individuals responding to their own condition as would be
 expected if they were class condition-based carry-over effects. As such,
 the southern New England breeding population of woodcock are best
 categorized as non-facultative partial migrants (i.e., includes residents,
 short-distance migrants, and long-distance migrants) that demonstrate weak
 connectivity between life stages; such populations are excellent for the
 study of the costs and benefits of migration. The stopover and wintering
 areas used by woodcock in the coastal mid-Atlantic deserve conservation
 and management attention in order to preserve critical habitat throughout
 their wintering range.
DOI: 10.5281/zenodo.18399812
title: Dataset for paper "Design rules for doped transition metal dichalcogenides heterostructures" (https://doi.org/10.1103/PhysRevMaterials.8.106001)
DOI: 10.5061/dryad.g4f4qrfsd
title: Source data for: Soluble MAC is primarily released from MAC-resistant bacteria that potently convert complement component C5

description: The Membrane Attack Complex (MAC or C5b-9) is an important effector of the
 immune system to kill invading microbes. MAC is formed when complement
 enzymes on the bacterial surface convert complement component C5 into C5b.
 Although the MAC is a membrane-inserted complex, soluble forms of MAC
 (sMAC, or terminal complement complex (TCC)) are often detected in sera of
 patients suffering from infections. Consequently, sMAC has been proposed
 as a biomarker, but it remains unclear when and how it is formed during
 infections. Here, we studied mechanisms of MAC formation on
 different Gram-negative and Gram-positive bacteria and found that
 sMAC is primarily formed in human serum by bacteria resistant to
 MAC-dependent killing. Surprisingly, C5 was converted into C5b more
 potently by MAC-resistant compared to MAC-sensitive Escherichia coli
 strains. In addition, we found that MAC precursors are released from the
 surface of MAC-resistant bacteria during MAC assembly. Although the
 release of MAC precursors from bacteria induced lysis of bystander human
 erythrocytes, serum regulators vitronectin (Vn) and clusterin (Clu) can
 prevent this. Combining size exclusion chromatography with mass
 spectrometry profiling, we show that sMAC released from bacteria in serum
 is a heterogeneous mixture of complexes composed of C5b-8, up to 3 copies
 of C9 and multiple copies of Vn and Clu. Altogether, our data provide
 molecular insight into how sMAC is generated during bacterial infections.
 This fundamental knowledge could form the basis for exploring the use of
 sMAC as a biomarker.
description: The file "Underlying data points graphs (Fig 1 until Fig 6
 supplement 1a)" contain the underlying data for all graphs in Figure
 1 up and until Figure 5 (including supplements), Figure 6ab, and Fig 6
 supplement 1a. Descriptions of the experimental procedure for these data
 and what the data points represent are in the README file. Data underlying
 Figure 6c-f, Figure 6 - supplement 1b-e, and Figure 7 have been deposited
 to the ProteomeXchange partner MassIVE database and assigned the
 identifier MSV000088560 available at https://doi.org/10.25345/C5QW00.<br><br>The dataset "flow cytometry.zip" contains the supporting raw data (.fsc or .mqd files) used to analyze binding of complement components to bacteria by flow cytometry. Data have been organized in a folder underlying the figure for which they have been used and placed in a subfolder for each individual experiment (sorted by date, YYYY-MM-DD). FlowJo can be used to open and analyze the .fcs and .mqd. files. Also, .xlsx files have been added to indicate which sample corresponds with which .fsc or .mqd file. The dataset "Gels.zip" contains complete images of all SDS-PAGE or BN-PAGE gels (after subsequent Western blotting, Silver staining or fluorescence imaging) used in this study. Lanes that were discussed in this study have been indicated in the image.
DOI: 10.5281/zenodo.18399811
title: Dataset for paper "Design rules for doped transition metal dichalcogenides heterostructures" (https://doi.org/10.1103/PhysRevMaterials.8.106001)
DOI: 10.15468/dl.uxgdna
title: Occurrence Download

description: A dataset containing 73 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((105 20,170 20,170 70,105 70,105 20))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Rubia hexaphylla"
 ]
}

 The dataset includes 73 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003068-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.sxksn035b
title: Climate and non-native herbivores influence reproductive investment by Greater Sage-grouse

description: Highly seasonal environments can increase competition among herbivores for
 nutrients, leading to consequences affecting rates of reproduction and
 survival. There is concern about the impacts of non-native ungulates on
 Greater Sage-grouse in the Great Basin of North America. We estimated
 nesting propensity, the annual proportion of females attempting a nest,
 for Greater Sage-grouse in relation to the abundance of ungulates using 7
 years of data from the northwestern Great Basin, USA. We focused on
 nesting because it is the necessary first major investment required for
 the production of new recruits. We used a Bayesian multi-stratum model to
 investigate the effects of weather and sympatric non-native herbivores,
 free-roaming horses and domestic cattle, on reproductive rates and female
 survival of adult and yearling sage-grouse. Adults nested at a higher rate
 (0.931, 95% CI, 0.904 – 0.953) than yearlings (0.867, 95% CI, 0.802 –
 0.922) under average conditions of all other covariates. If the first nest
 failed, renesting rates were similar between adults (0.349, 95% CI, 0.292
 – 0.410) and yearlings (0.353, 95% CI, 0.217 – 0.507). Females in better
 body condition at the start of the season nested at higher rates, and
 moderately snowy winters led to the highest nesting propensity during the
 following spring. Drier conditions led to low rates of nesting,
 particularly in areas with dense cattle grazing. Female survival was lower
 for nesting females, indicating a survival cost of reproduction. Areas
 with abundant free-roaming horses had slightly higher nesting propensity,
 though other research suggests negative impacts later in the breeding
 cycle. Sage-grouse face life-history trade-offs that may be shifting due
 to changing climatic conditions. Our work suggests that the effects of
 competition with non-native ungulates on sage-grouse life-histories may be
 exacerbated by adverse weather.
description: Greater Sage-grouse data was collected by trapping and radio
 collaring female birds. Birds were monitored using ground telemetry. Other
 variables were collected from Bureau of Land Management reports and PRISM
 climate data.
description: Code was originally run with R version 4.0.3 using R Studio.
 Required packages are noted in each code file and the README.
DOI: 10.5061/dryad.2547d7wsd
title: Population genetics reveals bidirectional fish movement across the Continental Divide via an interbasin water transfer

description: Interbasin water transfers are becoming an increasingly common tool to
 satisfy municipal and agricultural water demand, but their impacts on
 movement and gene flow of aquatic organisms are poorly understood. The
 Grand Ditch is an interbasin water transfer that diverts water from
 tributaries of the upper Colorado River on the west side of the
 Continental Divide to the upper Cache la Poudre River on the east side of
 the Continental Divide. We used single nucleotide polymorphisms to
 characterize population genetic structure in cutthroat trout (Oncorhynchus
 clarkii) and determine if fish utilize the Grand Ditch as a movement
 corridor. Samples were collected from two sites on the west side and three
 sites on the east side of the Continental Divide. We identified two or
 three genetic clusters, and relative migration rates and spatial
 distributions of admixed individuals indicated that the Grand Ditch
 facilitated bidirectional fish movement across the Continental Divide, a
 major biogeographic barrier. Previous studies have demonstrated ecological
 impacts of interbasin water transfers, but our study is one of the first
 to use genetics to understand how interbasin water transfers affect
 connectivity between previously isolated watersheds. We also discuss
 implications on native trout management and balancing water demand and
 biodiversity conservation. 
description: This is the SNP dataset for the article: Population genetics
 reveals bidirectional fish movement across the Continental Divide via an
 interbasin water transfer. We genotyped 229 cutthroat
 trout at a panel of 125 single nucleotide polymorphisms developed by
 Houston et al. 2012. This dataset includes all individuals (229) and all
 SNPs (125). For additional details on sampling, genotyping, and how data
 was subsequently filtered for analysis, see corresponding methods in the
 associated manuscript published in <em>Conservation
 Genetics</em>.
description: The dataset contains 127 columns--one for population
 (Population), individual name (Sample.Name), and 125 SNP genotypes
 (columns 3-127). Each SNP genotype column contains both allele calls
 separated by a semicolon. Missing genotypes are designated by
 NA.
DOI: 10.34740/kaggle/dsv/14648886
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5061/dryad.msbcc2g0z
title: Data from: Chromosome scale genome assemblies and annotations for Poales species Carex cristatella, Carex scoparia, Juncus effusus and Juncus inflexus

description: The majority of sequenced genomes in the Monocots are from species
 belonging to the Poaceae, which includes many commercially important
 crops. Here, we expand the number of sequenced genomes from the Monocots
 to include the genomes of four related Cyperids: Carex cristatella and
 Carex scoparia from Cyperaceae and Juncus effusus and Juncus inflexus from
 Juncaceae. The high-quality, chromosome-scale genome sequences from these
 four Cyperids were assembled by combining whole-genome shotgun sequencing
 of Nanopore long reads, Illumina short reads, and Hi-C sequencing data.
 Some members of the Cyperaceae and Juncaceae are known to possess
 holocentric chromosomes.  We examined the repeat landscapes in
 our sequenced genomes to search for potential repeats associated with
 centromeres. Several large satellite repeat families, comprising 3.2% to
 9.5% of our sequenced genomes, showed dispersed distribution of large
 repeat clusters across all Carex chromosomes, with few instances of these
 repeats clustering in the same chromosomal regions. In contrast, most
 large Juncus satellite repeats were clustered in a single location on each
 chromosome, with sporadic instances of large satellite repeats throughout
 the Juncus genomes. Recognizable transposable elements account for about
 20% of the assemblies, with the Carex genomes containing more DNA
 transposons than retrotransposons while the converse is true for the
 Juncus genomes. These genome sequences and annotations will facilitate
 better comparative analysis within monocots.
description: Genome assemblies for <em>Carex cristatella</em>,
 <em>Carex scoparia</em>, <em>Juncus effusus</em>,
 and <em>Juncus inflexus</em> were generated using Nanopore
 long read data.  Assemblies were polished using Illumina short read
 DNA-seq data.  Scaffolding was performed with HiC Illumina sequencing. 
 Annotation was performed using the MAKER pipeline with Nanopore cDNA
 sequence and protein alignments used as evidence.  Functional descriptions
 were assigned based on homology to genes with functional annotation or by
 protein domain analysis using Pfam domain homology.
DOI: 10.5061/dryad.jwstqjqbh
title: Tropical plant–hummingbird interactions withstand short-term experimental removal of a common flowering plant

description: In this study, we simulated the extirpation of a hummingbird-pollinated
 understory plant, Heliconia tortuosa, from tropical
 forest fragments using a replicated Before-After-Control-Impact
 (BACI) experimental design while quantifying hummingbird space use, foral
 visitation rates, and plant pollination success. Each response variable
 was measured during each experimental period (pre and post) in sites with
 and without H. tortuosa removal (treatment and control).
description: These datasets were collected in the landscape surrounding the
 Las Cruces Biological Research Station in southern Costa Rica
 (2016–2018). Details for each dataset are provided in
 the README file. Datasets included:
 1) Hummingbird captures in mist nets 
 Number of hummingbirds captured per capture session
 Recapture rate (proportion of birds captured during
 'pre' period that were recaptured during 'post'
 period) Body mass measurements for captured
 hummingbirds (mass and wing length) 2)
 Hummingbird radio-telemetry Proportion of
 observation time spent in focal area where bird was originally
 captured 3) Plant-hummingbird interactions
 quantified through trail camera observations 
 Visitation rates for <em>Heliconia </em>and
 non-<em>Heliconia </em>flowers (all birds)
 Visitation rates for <em>Heliconia </em>and
 non-<em>Heliconia </em>flowers (individual marked birds,
 2017-2018 only) Visit durations
 4) Pollination success 
 Proportion of flowers (styles) with pollen tubes
 5) Site and replicate characteristics (elevation,
 <em>Heliconia </em>density, and <em>Heliconia
 </em>calories removed/ha) 6) Data related to
 percentage of calories removed Relative
 visitation rates to 35 plant species (i.e., weights used to tailor
 estimate of floral resource availability to hummingbird
 perspective) Estimated percentage of calories removed
 by experimental <em>Heliconia </em>removal
 Missing values are denoted by NA. Additional details
 are available in the README file.
DOI: 10.5061/dryad.xsj3tx9hd
title: Genome-wide DNA methylation analysis in monozygotic twins identifies potential biomarkers of fasting plasma glucose

description: Purpose: An epigenome-wide association study (EWAS) was conducted to
 detect specific epigenetic variants potentially related to fasting plasma
 glucose (FPG) in middle-aged and elderly Chinese monozygotic twins.
 Methods: Association between DNA methylation (DNAm) of single CpG and FPG
 was tested by applying generalized estimation equation in 52 twin pairs.
 Differentially methylated regions (DMRs) were identified by comb-P
 approach. Inference about Causation through Examination of Familial
 Confounding (ICE FALCON) was utilized to perform the causal inference.
 Candidate CpGs were quantified using Sequenom MassARRAY platform in a
 community population. Weighted gene co-expression network analysis (WGCNA)
 was conducted using gene expression data. Results: The relationship
 between DNAm of 30 top CpGs and FPG reached P-value&lt;1×10-6 level.
 Thirty-two DMRs within 24 genes, such as TLCD1, MRPS31P5, CASZ1 and
 CXADRP3, were identified. Causal relationship of 20 top CpGs within TLCD1,
 MZF1, PTPRN2, SLC6A18, ASTN2, IQCA1, GRIN1, and PDE2A with FPG were
 further identified. Pathways related to FPG such as mitogen-activated
 protein kinase p38 binding were found. Three CpGs mapped to SLC6A18 were
 validated in a community population, with a hypermethylated direction in
 type 2 diabetes cases. The gene expression levels of 18 genes where the
 top CpGs and DMRs located, such as SLC6A18 and TLCD1, were positively
 correlated with FPG. Besides, common biological pathways, such as dopamine
 binding, regulation of biosynthetic process, and neuron fate
 specification, were found in methylation and gene expression analyses.
 Conclusion: Our findings showed that multiple methylated CpGs and regions,
 crucial genes, and biological pathways were underlyingly associated with
 FPG and diabetes.
DOI: 10.5061/dryad.q573n5tkw
title: Experimental data testing CO2 × heatwave effects in Pacific herring offspring including data on vital rates and experimental conditions

description: Forage fish tend to respond strongly to environmental variability and
 therefore may be particularly sensitive to marine climate stressors. We
 used controlled laboratory experiments to assess the vulnerability of
 Pacific herring (Clupea pallasii) embryos to the combined effects of high
 pCO2 and a simulated marine heatwave. The two pCO2 treatments reflected
 current conditions (~550 µatm) and a future extreme level (~2,300 µatm).
 The dynamics of heatwave (i.e., rate of onset: ~0.85°C d-1; maximum
 intensity: +4.4°C) were modeled from the most extreme events detected by a
 long-term regional temperature dataset. Simultaneous exposure to these
 potential stressors did not affect embryo survival. However, the heatwave
 did elicit significant metabolic effects that included higher rates of
 routine metabolism (Q10 = 1.15 - 1.72), growth (Q10 = 1.87), rate of
 development to hatch (Q10 = 3.01), and yolk consumption (Q10 = 3.21) as
 well as a significant reduction in production efficiency (-10.8%) and a
 three-fold increase in the rate of developmental anomalies. By contrast,
 high pCO2 conditions produced comparatively small effects to vital rates,
 including a significant increase in time to hatch (+0.88 d) and a
 reduction in routine metabolic rate (-6.3%) under the ambient temperature
 regime only. We found no evidence that high pCO2 increased routine
 metabolic rate at either temperature. These results indicate that Pacific
 herring embryos possess sufficient physiological plasticity to cope with
 extreme seawater acidification under optimal and heatwave temperature
 conditions, although lingering metabolic inefficiencies induced by the
 heatwave may lead to important carry-over effects in later life-stages.
DOI: 10.5061/dryad.k0p2ngf9z
title: Morphometry of the pedipalp patella provides new characters for species-level taxonomy in whip spiders (Arachnida, Amblypygi): A test case with description of a new species of Phrynus

description: Whip spiders (Amblypygi Thorell, 1883) are easily distinguished from their
 spider relatives (Araneae Clerck, 1757) by their raptorial pedipalps, the
 second pair of appendages, which are covered in spines and used to grasp
 and impale prey. Among other characters, the number, distribution, and
 size differences among the pedipalp spines continue to be important for
 whip spider systematics at different levels in the taxonomic hierarchy.
 However, traditional meristic and qualitative characters used to describe
 the pedipalp spines often limit their use for species-level taxonomy, as
 character states are invariant or overlapping. The present study employs
 landmark-based morphometrics to map the morphospace comprising the
 retrolateral surface of the pedipalp patella and its dorsal spines in a
 group of Neotropical whip spiders of the genus Phrynus Lamarck, 1801, all
 of which share an inconspicuous spine on the prolateral surface of the
 pedipalp tarsus, i.e., “group B” proposed by Quintero (1983). The analysis
 presented demonstrates that the relative pedipalp patella lengths and
 spine to pedipalp patella width ratios are of similar use for species
 diagnosis as the commonly employed relative length of leg femur I.
 Importantly, the analysis reveals that, beyond the traditional approach of
 qualitatively reporting relative pedipalp patella dorsal spine lengths
 (e.g., P3 &gt; P5 &gt; P2 &gt; P4 &gt; P6 &gt; P1),
 the ratios between spine lengths are useful morphometric characters for
 species-level taxonomy in Phrynus. New morphometric ratios are provided
 for the species of Phrynus group B and used, together with traditional
 characters, to describe Phrynus guarionexi sp. nov. from the Dominican
 Republic. Finally, new morphological data are provided concerning the
 cerotegument, frontal process and prolateral surface of the pedipalp tibia
 in the species of group B.
description: Complete dataset and scripts required to reproduce the analyses
 of the study “Morphometry of the pedipalp patella provides new characters
 for species-level taxonomy in whip spiders (Arachnida, Amblypygi): A test
 case with description of a new species of Phrynus”. A usage guide is
 provided as a README file.
DOI: 10.5061/dryad.x0k6djhmp
title: eDNA from archived leaves reveals no losses of α-diversity, but widespread community turnover and biotic homogenization as drivers of forest insect decline

description: A major limitation of current reports on insect declines is the lack of
 standardized, long-term, and taxonomically broad time series. Here, we
 demonstrate the utility of environmental DNA from archived leaf material
 to characterize plant-associated arthropod communities. We base our work
 on several multi-decadal leaf time series from tree canopies in four land
 use types, which were sampled as part of a long-term environmental
 monitoring program across Germany. Using these highly standardized and
 well-preserved samples, we analyze temporal changes of diversity and
 relative biomass in communities of several thousand arthropod species
 belonging to 23 orders using multilocus metabarcoding and quantitative
 PCR. Our data do not support widespread declines of α-diversity or genetic
 diversity within species. Instead, we find a gradual community turnover,
 which results in temporal and spatial biotic homogenization. Colonization
 by novel widespread taxa and loss of range-restricted taxa cause spatial
 diversity loss. At the same time, increasingly similar species occurrences
 between consecutive sampling years cause a temporal decline of diversity.
 These effects are independent of land use and observed for all arthropod
 orders. Our results suggest that insect decline is more complex than mere
 α-diversity loss, but can be driven by β-diversity decay across space and
 time.