cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7272/q6gf0rqd
title: Survey Dataset: UDLI, LLRC. NLRC

description: ABSTRACT
             Statements about building walls, deportation and denying services to undocumented immigrants made by the US president may induce fear in Latino populations and create barriers to their health care access. To assess the impact of these statements on undocumented Latino immigrants’ (UDLI) and Latino legal residents/citizens’ (LLRC) perceptions of safety and their presentations for emergency care, we conducted surveys of adult patients at three county emergency departments (EDs) in California from June 2017 to December 2018. Of 1,684 patients approached, 1,337 (79.4%) agreed to participate: 34.3% UDLI, 36.9% LLRC, and 29.8% non-Latino legal residents/citizens (NLRC). The vast majority of UDLI (95%), LLRC (94%), and NLRC (85%) had heard statements about immigrants by President Trump. Most UDLI (89%), LLRC (88%), and NLRC (87%) either thought that these measures were being enacted now or will be enacted in the future. Most UDLI and LLRC reported that these statements made them feel unsafe living in the US, 75% (95% CI 70 to 80%) and 51% (95% CI 47 to 56%), respectively. More UDLI reported that these statements made them afraid to come to the ED (24% 95% CI 20 to 28%) vs LLRC (4.4% [95% CI 3 to 7%]) and NLRC (3.5% [95% CI 2 to 6%]); 55% of UDLI with this fear stated it caused them to delay coming to the ED (median delay 2-3 days). The vast majority of patients in our California EDs have heard statements about immigrants by the US president, which have induced worry and safety concerns in both UDLI and LLRC patients. These statements may also act as a barrier to some UDLI’s access of emergency care. Given California’s sanctuary state status, these safety concerns and ED access fears may be greater in a nationwide population of Latinos.
DOI: 10.5061/dryad.r6h8dr2
title: Data from: Long-lived metabolic enzymes in the crystalline lens identified by pulse-labeling of mice and mass spectrometry

description: The lenticular fiber cells are comprised of extremely long-lived proteins
 while still maintaining an active biochemical state. Dysregulation of
 these activities has been implicated in age-related cataracts, and other
 lens diseases. However, the lenticular protein dynamics underlying health
 and disease is unclear. We sought to measure the global protein turnover
 rates in the eye using dietary nitrogen-15 (15N)-labeling of mice between
 3 and 15 weeks of age. By performing mass spectrometry we measured the
 14N- to 15N-peptide ratios of 248 lens proteins, including Crystallin,
 Aquaporin, Collagen and Laminin of the lens capsule, and enzymes that
 catalyze glycolysis as well as oxidation and reduction reactions.
 Unexpectedly, like the crystallin proteins, many of these enzymes are also
 exceedingly long-lived. The slow replacement of these enzymes in spite of
 young age of the mice suggests their potential roles in age-related
 metabolic changes in the lens.
description: Supplementary dataset: A
 complete list of lens, vitreoretina and sclera/choroid proteins identified
 by mass spectrometryA complete list of lens,
 vitreoretina and sclera/choroid proteins identified by mass spectrometry
 from nitrogen-15 (15N)-labeled mice.Supplementary
 dataset.xlsx
DOI: 10.5061/dryad.443s9p4
title: Data from: Prevalence of afebrile malaria and development of risk-scores for gradation of villages: a study from a hot-spot in Odisha

description: Introduction: Malaria is a public health emergency in India and Odisha.
 The national malaria elimination programme aims to expedite early
 identification, treatment and follow-up of malaria cases in hot-spots
 through a robust health system, besides focusing on efficient vector
 control. This study, a result of mass screening conducted in a hot-spot in
 Odisha, aimed to assess prevalence, identify and estimate the risks and
 develop a management tool for malaria elimination. Methods: Through a
 cross-sectional study and using WHO recommended Rapid Diagnostic Test
 (RDT), 13221 individuals were screened. Information about age, gender,
 education and health practices were collected along with blood sample (5
 µl) for malaria testing. Altitude, forestation, availability of a village
 health worker and distance from secondary health center were captured
 using panel technique. A multi-level poisson regression model was used to
 analyze association between risk factors and prevalence of malaria, and to
 estimate risk scores. Results: The prevalence of malaria was 5.8% and
 afebrile malaria accounted for 79 percent of all confirmed cases. Higher
 proportion of Pv infections were afebrile (81%). We found the prevalence
 to be 1.38 (1.1664 - 1.6457) times higher in villages where the Accredited
 Social Health Activist (ASHA) didn’t stay; the risk increased by 1.38
 (1.0428 - 1.8272) and 1.92 (1.4428 - 2.5764) times in mid- and
 high-altitude tertiles. With regard to forest coverage, villages falling
 under mid- and highest-tertiles were 2.01 times (1.6194 - 2.5129) and 2.03
 times (1.5477 - 2.6809), respectively, more likely affected by malaria.
 Similarly, villages of mid tertile and lowest tertile of education had
 1.73 times (1.3392 - 2.2586) and 2.50 times (2.009 - 3.1244) higher
 prevalence of malaria. Conclusion: Presence of ASHA worker in villages,
 altitude, forestation, and education emerged as principal predictors of
 malaria infection in the study area. An easy-to-use risk-scoring system
 for ranking villages based on these risk factors could facilitate resource
 prioritization for malaria elimination.
description: individual_screeningThis file contains characteristics and screening results of individuals.individual.csv
DOI: 10.5061/dryad.v652k70
title: Data from: Unraveling independent origins of two tetraploid Achillea species by amplicon sequencing

description: Allopolyploidy is a significant mechanism of plant speciation, and many
 allopolyploid species have arisen recurrently. However, the probability
 that allopolyploidization between the same two parental species may lead
 to the origin of different taxa has received little attention. Here we
 used a new progenitor-specific amplicon sequencing method to demonstrate
 the independent origins of two yarrow species, Achillea alpina and A.
 wilsoniana, via allotetraploidy from the same diploid progenitor species
 pair, A. acuminata and A. asiatica. Based on the sequences of 17 nuclear
 genes from 21 wild populations of the four Achillea species investigated,
 a clear view of  genetic structure and demographic history was
 obtained with each species. Significant genetic differentiation was
 evident between the two tetraploid species. Two genetically
 distinguishable groups were detected within one of the progenitor, A.
 acuminata, and ancestors belonging to those two groups contributed to the
 two tetraploid species, respectively. Excluding fixed heterozygosity, we
 detected extremely low genetic diversity in many populations of both
 tetraploid species. Approximate Bayesian computation indicated that both
 tetraploid species originated before the Last Glacial Maximum, and nearly
 all diploid lineages went through population declines after the
 allopolyploidization events. Our study demonstrates that independent
 allopolyploidization events between the same Achillea parental species
 have generated two genetically and ecologically distinct taxa.
description: <strong>SNP</strong> SNP statistics based
 on transcriptomes of three species
 SNP.xlsx 
 <strong>structure_c</strong> STRUCTURE input file
 for the c-subset structure_Hap17_c.txt
 
 <strong>structure_s</strong> STRUCTURE input file
 for the s-subset structure_Hap17_s.txt
 
 <strong>allele_types</strong> allele
 types/sequences for each fragment allele
 types.fas 
 <strong>allele_statistics</strong> allele statistics
 for each amplicon allele statistics.xlsx
 
 <strong>resample_SNP_c</strong> 100 resampled SNP
 files for the c-subset resample_SNP_c.rar
 
 <strong>resample_SNP_s</strong> 100 resampled SNP
 files for the s-subset resample_SNP_s.rar
 
 <strong>alp_unigene</strong> unigenes in A.
 alpina from transcriptome assembly
 alp-unigene.fas 
 <strong>abc_c</strong> - DIYABC input file
 (DNA sequence file of introns) for the c-subset
 abc_c.mss 
 <strong>abc_s</strong> DIYABC input file
 (DNA sequence file of introns) for the s-subset
 abc_s.mss 
 <strong>acu_unigene</strong> unigenes in A.
 acuminate from transcriptome assembly
 acu-unigene.fas 
 <strong>asi_unigene</strong> unigenes in A.
 asiatica from transcriptome assembly
 asi-unigene.fas
DOI: 10.5061/dryad.mn15f80
title: Data from: Old lake vs. young taxa: a comparative phylogeographic perspective on the evolution of Caspian Sea gastropods (Neritidae: Theodoxus)

description: The Caspian Sea has been a highly dynamic environment throughout the
 Quaternary and witnessed major oscillations in lake level, which were
 associated with changes in salinity and habitat availability. Such
 environmental pressures are considered to drive strong phylogeographic
 structure in species by forcing populations into suitable refugia.
 However, little is actually known on the effect of lake level fluctuations
 in the Caspian Sea on its aquatic biota. We compared the phylogeographic
 patterns of the aquatic neritid snail genus Theodoxus across the
 Pontocaspian region with refugial populations in southern Iran. Three gene
 fragments were used to determine relationships and divergence times
 between sampled populations in both groups. A dated phylogeny and
 statistical haplotype networks were generated in conjunction with analyses
 of molecular variance and calculations of isolation by distance using
 distance-based redundancy analyses. Extended Bayesian skyline plots were
 constructed to assess demographic history. Compared to the Iranian
 populations, we found little phylogeographic structure for the
 Pontocaspian Theodoxus group, with more recent diversification,
 homogeneity of haplotypes across the Pontocaspian region and a relatively
 stable demographic history since the Middle Pleistocene. Our results argue
 against a strong influence of Caspian Sea low stands on population
 structure post the early Pleistocene, whereas high stands may have
 increased the dispersal possibilities and homogenisation of haplotypes
 across the Pontocaspian region during this time. However, prior to this
 period a more dramatic low stand in the Caspian Sea around a million years
 ago may have had caused reduction of Theodoxus diversity to a single
 lineage in the region. In addition, our results provide new insights into
 Theodoxus taxonomy and outlooks for regional conservation.
description: Nucleotide sequence
 alignmentsAll nucleotide sequence
 alignments used for the various analyses with
 explanations.IBD_distance based
 redundancy analysis (db-RDA)Input files and R-script
 of the distance based redundancy analyses (db-RDA) for calculations of
 isolation by distance.IBD_distance based redundancy
 analysis.zipExtended Bayesian
 skyline plot dataOutput data of extended
 Bayesian skyline plot analyses used to plot the the
 graphs.EBSP
 results.xlsx
DOI: 10.5061/dryad.2gg2300
title: Data from: Intracranial atherosclerosis on 7T MRI and cognitive functioning – the SMART-MR study

description: Objective: To investigate the association between intracranial
 atherosclerosis (ICAS) and cognitive functioning in patients with a
 history of vascular disease. Methods: Within the SMART-MR study
 cross-sectional analyses were performed in 130 patients (mean±SD age 68±9
 years) with 7T vessel wall–magnetic resonance imaging data. Vessel wall
 lesions were rated according to established criteria and summed into a
 circulatory and artery-specific ICAS burden. Associations between ICAS
 burden and Z-scores of memory, executive functioning, working memory and
 processing speed, were estimated using linear regression analyses adjusted
 for age, sex, education, reading ability, and vascular risk factors.
 Results: A total of 125 patients (96%) had ≥1 vessel wall
 lesions; the mean ICAS burden was 8.5±5.7. A statistically non-significant
 association was found between total ICAS burden and memory (b = -0.03 per
 +1 lesion; 95% CI -0.05 to 0.00). No associations were found for the other
 domains. A statistically significant association was found for ICAS burden
 of the posterior cerebral artery (PCA) and memory (b= -0.12 per +1 lesion;
 95%CI -0.23 to -0.01) and executive functioning (b= -0.10 per +1 lesion;
 95%CI -0.19 to -0.01). Statistically non-significant associations were
 found for the anterior cerebral artery (ACA) burden and memory (b= -0.13
 per +1 lesion; 95%CI -0.26 to 0.01) and executive functioning (b= -0.11
 per +1 lesion; 95%CI -0.22 to 0.01). Additional adjustments for large
 infarcts, white matter hyperintensities, lacunes and ≥50% carotid
 stenosis, produced similar results. Conclusions: Our results
 suggest an artery-specific vulnerability of memory and executive
 functioning to ICAS, possibly due to strategic brain regions involved with
 these cognitive domains, which are located in the arterial territory of
 the PCA and ACA.
description: Supplemental Figure e-1: Adjusted mean domain-specific cognitive
 functioning Z-scores per aproximate quartile (or tertile) of
 artery-specific ICAS burden.<br>
DOI: 10.5061/dryad.pd0ks46
title: Data from: Phylogeography of sand-burrowing amphipods (Haustoriidae) supports an ancient suture zone in the Gulf of Mexico

description: AIM: To evaluate the impact of a proposed ancient suture zone in the Gulf
 of Mexico on the distribution and molecular diversity of
 dispersal-limited, sand-burrowing amphipods of the genera Haustorius and
 Lepidactylus (Haustoriidae: Amphipoda). LOCATION: Gulf of Mexico, U.S.A.
 and Mexico. METHODS: Phylogenetic and population genetic analyses were
 performed using mitochondrial (COI and 16S) and nuclear (18S and 28S) data
 from 93 amphipod individuals from 16 sites across the Gulf of Mexico.
 Bayesian and ML phylogenies were constructed for all genes, divergence
 times were estimated using a molecular clock for COI (0.007–0.013
 subs./site per My), and four species delimitation methods were used to
 identify operational taxonomic units (OTUs) within each amphipod species.
 The mitochondrial COI gene was used to construct haplotype networks and
 estimate population genetic parameters to evaluate historical changes in
 effective population sizes. RESULTS: Deep divergences (most estimated to
 be &gt;4 Mya) were uncovered between sister clades of both amphipod
 genera on either side of the Mississippi River as well as within
 Lepidactylus triarticulatus where each sample site was found to harbor a
 unique genetic lineage. Two cryptic OTUs of L. triarticulatus were
 identified living sympatrically at Pass Christian, Mississippi. Two
 distinct OTUs representing western and eastern Haustorius galvezi clades
 were identified along the Texas and Mexico coastlines with abutting
 ranges. Population genetic results show some support for recent population
 expansions for western Gulf OTUs, while eastern Gulf OTUs may have
 suffered population bottlenecks in the past. MAIN CONCLUSIONS: Divergences
 between sister species of sand-burrowing amphipods exceeds the timing of
 previous vicariant hypotheses. The split appears to be consistent with
 Miocene sedimentation levels from the Mississippi River acting as an
 east-west barrier to gene flow in the Gulf of Mexico. Given their strong
 population structure and cryptic diversity, haustoriid amphipods are ideal
 model organisms for studying open coast biogeography.
description: StarBeast_LogNormClock*BEAST XML fileSequence file: 16S16SfileSequence file: 18S18SfileSequence file: 28S28SfileSequence file: COICO1file
DOI: 10.15468/dl.dckgdn
title: Occurrence Download

description: A dataset containing 24794414 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Machine Observation, Human Observation, Specimen)",
 "OccurrenceStatus is Present",
 "TaxonKey is Aves",
 "Year 2025-2025"
 ]
}

 The dataset includes 24794414 records from 248 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001874-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.g108557
title: Data from: Assessing the effects of quantitative host resistance on the life-history traits of sporulating parasites with growing lesions

description: Assessing life-history traits of parasites on resistant hosts is crucial
 in evolutionary ecology. In the particular case of sporulating pathogens
 with growing lesions, phenotyping is difficult because one needs to
 disentangle properly pathogen spread from sporulation. By considering
 Phytophthora infestans on potato, we use mathematical modelling to tackle
 this issue and refine the assessment pathogen response to quantitative
 host resistance. We elaborate a parsimonious leaf-scale model by
 convolving a lesion growth model and a sporulation function, after a
 latency period. This model is fitted to data obtained on two isolates
 inoculated on three cultivars with contrasted resistance level. Our
 results confirm a significant host-pathogen interaction on the various
 estimated traits, and a reduction of both pathogen spread and spore
 production, induced by host resistance. Most interestingly, we highlight
 that quantitative resistance also changes the sporulation function, whose
 mode is significantly time-lagged.This alteration of the infectious period
 distribution on resistant hosts may have strong impacts on the dynamics of
 parasite populations, and should be considered when assessing the
 durability of disease control tactics based on plant resistance
 management. This inter-disciplinary work also supports the relevance of
 mechanistic models for analysing phenotypic data of plant-pathogen
 interactions.
description: Phenotypic
 dataPhenotypic data used for
 the study. Columns names are similar to the notations used in the
 manuscript (See Table 1).data.csvR_code_lesion_modelR script for fitting lesion growth and sporulation models to destructive phenotypic data.
DOI: 10.5061/dryad.gt43p25
title: Data from: Genomic and phenotypic effects of inbreeding across two different hatchery management regimes in Chinook salmon

description: Genomic approaches permit direct estimation of inbreeding and its effect
 on fitness. We used genomic-based estimates of inbreeding to investigate
 their relationship with eight adult traits in a captive-reared Pacific
 salmonid that is released into the wild. Estimates were also used to
 determine whether alternative broodstock management approaches reduced
 risks of inbreeding. Specifically, 1,100 unlinked restriction-site
 associated (RAD) loci were used to compare pairwise relatedness, derived
 from a relationship matrix, and individual inbreeding, estimated by
 comparing observed and expected homozygosity, across four generations in
 two hatchery lines of Chinook salmon that were derived from the same
 source. The lines are managed as “integrated” with the founding wild
 stock, with ongoing gene flow, and as “segregated” with no gene flow.
 While relatedness and inbreeding increased in the first generation of both
 lines, possibly due to population subdivision caused by hatchery
 initiation, the integrated line had significantly lower levels in some
 subsequent generations (relatedness: F2-F4; inbreeding F2). Generally,
 inbreeding was similar between the lines despite large differences in
 effective numbers of breeders. Inbreeding did not affect fecundity,
 reproductive effort, return timing, fork length, weight, condition factor,
 and daily growth coefficient. However, it delayed spawn timing by 1.75
 days per one standard deviation increase in F (~0.16). The results
 indicate that integrated management may reduce inbreeding but also suggest
 that it is relatively low in a small, segregated hatchery population that
 maximized number of breeders. Our findings demonstrate the utility of
 genomics to monitor inbreeding under alternative management strategies in
 captive breeding programs.
description: Code to analyze effect
 of inbreeding on phenotypes This is the R code used
 to quantify the effect of individual inbreeding coefficient, F, on each of
 eight fitness-related traits. The file also contains code used to estimate
 post-hoc power of the coefficients. Effects of F on
 phenotypes.R Data file used by R code
 to analyze effects of F on phenotypes Data file used by the R
 code to quantify the effect of individual inbreeding coefficient on each
 of eight fitness-related traits. Missing values and genotypes are coded as
 NA. Data
 file for effects of F on phenotypes.csv
description: Returning adult Chinook salmon were sampled for DNA and sequenced
 using restriction-site associated (RAD) sequencing methods.
DOI: 10.5061/dryad.bt6rj5g
title: Data from: Anthropogenic noise does not surpass land cover in explaining habitat selection of Greater Prairie-Chicken (Tympanuchus cupido)

description: Over the last century, increasing human populations and conversion of
 grassland to agriculture have had severe consequences for numbers of
 Greater Prairie-Chickens (Tympanuchus cupido). Understanding Greater
 Prairie-Chicken response to human disturbance, including the effects of
 anthropogenic noise and landscape modification, is vital for conserving
 remaining populations because these disturbances are becoming more common
 in grassland systems. Here, we evaluate the effect of low-frequency noise
 emitted from a wind energy facility on habitat selection. We used the
 Normalized Difference Soundscape Index, a ratio of human-generated and
 biological acoustic components, to determine the impact of the dominant
 acoustic characteristics of habitat relative to physical landscape
 features known to influence within-home range habitat selection. Female
 Greater Prairie-Chickens avoided wooded areas and row crops but showed no
 selection or avoidance of wind turbines based on the availability of these
 features across their home range. Although the acoustic environment near
 the wind energy facility was dominated by anthropogenic noise, our results
 show that acoustic habitat selection is not evident for this species. In
 contrast, our work highlights the need to reduce the presence of trees
 which have been historically absent from the region, as well as decrease
 the conversion of grassland to row crop agriculture. Our findings suggest
 physical landscape changes surpass altered acoustic environments in
 mediating Greater Prairie-Chicken habitat selection.
description: Whole Study Area Greater
 Prairie-Chicken (Tympanuchus cupido) used and available resource
 dataThis file contains
 resource/habitat data for all 49 study individual female Greater
 Prairie-Chicken (Tympanuchus cupido) tracked near Ainsworth, Nebraska,
 2013-2014.WholeStudyAreaGRPCdata.csvAcoustic Surface Study Area Greater Prairie-Chicken (Tympanuchus cupido) used and available resource dataThis file contains Resource/Habitat data for 26 tracked Greater Prairie-Chicken (Tympanuchus cupido) near Ainsworth, Nebraska, 2013-2014AcousticSurfaceGRPCdata.csv