cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7p05v
title: Data from: Comparative landscape genetic analysis of three Pacific salmon species from subarctic North America

description: We examined the assumption that landscape heterogeneity similarly
 influences the spatial distribution of genetic diversity in closely
 related and geographically overlapping species. Accordingly, we evaluated
 the influence of watershed affiliation and nine habitat variables from
 four categories (spatial isolation, habitat size, climate, and ecology) on
 population divergence in three species of Pacific salmon (Oncorhynchus
 tshawytscha, O. kisutch, and O. keta) from three contiguous watersheds in
 subarctic North America. By incorporating spatial data we found that the
 three watersheds did not form the first level of hierarchical population
 structure as predicted. Instead, each species exhibited a broadly similar
 spatial pattern: a single coastal group with populations from all
 watersheds and one or more inland groups primarily in the largest
 watershed. These results imply that the spatial scale of conservation
 should extend across watersheds rather than at the watershed level which
 is the scale for fishery management. Three independent methods of
 multivariate analysis identified two variables as having influence on
 population divergence across all watersheds: precipitation in all species
 and subbasin area (SBA) in Chinook. Although we found general broad-scale
 congruence in the spatial patterns of population divergence and evidence
 that precipitation may influence population divergence in each species, we
 also found differences in the level of population divergence (coho
 &gt; Chinook and chum) and evidence that SBA may influence population
 divergence only in Chinook. These differences among species support a
 species-specific approach to evaluating and planning for the influence of
 broad-scale impacts such as climate change.
description: Landscape genetics of
 Alaska salmonThe nine files contain
 genotypic and environmental data for Chinook, Coho, and Chum Salmon (three
 files per species). For more detail see the README.pdf
 file.LG.zip
DOI: 10.1594/pangaea.917953
title: Oceanographic profile of CTD cast K180528_TowYo_001_Cast_016
DOI: 10.1594/pangaea.917965
title: Oceanographic profile of CTD cast K180528_TowYo_001_Cast_028
DOI: 10.1594/pangaea.917943
title: Oceanographic profile of CTD cast K180528_TowYo_001_Cast_007
DOI: 10.1594/pangaea.917954
title: Oceanographic profile of CTD cast K180528_TowYo_001_Cast_017
DOI: 10.1594/pangaea.885708
title: Climate records from different places in black cherry - pine forests in the Havelland, north-eastern Germany

description: The data has been gathered in order to investigate the influence of the invasive black cherry (Prunus serotina Ehrh.) on bats (Chiroptera: Verpertilionidae) in Scots pine (Pinus sylvestris) forest ecosystems. The bat calls were recorded using automated recording devices (batcorders) in pine forest stands with three different black cherry densities (pine monoculture, light and dense black cherry) for a period of 60 survey nights between the end of July and late September 2016. Three plots per forest type were sampled with a repetition of 20 survey nights per plot. A total of 3888 bat call recordings were made during the study period, from which eight bat species could be identified to species level.Additionally to the bat calls, climate data (temperature and humidity) was collected with the same sampling design as the bat call recording.
description: This dataset has been carefully reviewed and curated in accordance with PANGAEA's exceptionally high quality standards. However, due to discontinued communication from the authors' side, it did not receive the usual formal approval by the authors and therefore lacks final scientific validation.
DOI: 10.1594/pangaea.917952
title: Oceanographic profile of CTD cast K180528_TowYo_001_Cast_015
DOI: 10.5061/dryad.0k27q21
title: Data from: Risk factors for possible REM sleep behavior disorder: a CLSA population-based cohort study

description: Objective: Idiopathic REM sleep behavior disorder (RBD) is a powerful
 marker of prodromal neurodegenerative synucleinopathy, with 80% of
 patients ultimately phenoconverting to defined disease. Several
 environmental risk factors for RBD have been suggested, but associations
 vary between studies. We assessed sociodemographic, socioeconomic and
 clinical correlates of RBD in a 30,000-subject national cohort. Methods:
 Subjects aged 45-85 years in Canada were collected as part of the Canadian
 Longitudinal Study on Aging. Possible RBD (pRBD) was screened with the
 RBD-1Q, a questionnaire with 94% specificity and 87% sensitivity. To
 improve diagnostic reliability, subjects screening positive for apnea or
 non-REM parasomnia (young onset pRBD), and subjects self-reporting
 dementia or Parkinson’s disease were excluded. A series of
 sociodemographic, life style and mental health variables were analysed
 cross-sectionally. Potential correlates were assessed via multivariable
 logistic regression. Results: Of 30,097 subjects, 958 (3.2%) had pRBD.
 Male sex (OR=2.14 ,95%CI=[1.84, 2.49]) and lower education (OR=0.95 [0.92,
 0.98] were associated with pRBD. pRBD subjects had smoked more (total
 smoking years OR=1.006 [1.010, 1.011]) and were more likely to be
 moderate-heavy drinkers (OR=1.25 [1.03, 1.50]). There was a strong
 association between pRBD and self-reported antidepressant treatment for
 depression (OR=2.76 [2.22, 3.44]), psychological distress (OR=1.52 [1.37,
 1.69]), mental illness (OR=2.08 [1.79, 2.41]), and post-traumatic stress
 disorder (OR=2.84 [2.55, 3.54]). Conclusions: Our study replicated
 previous reported associations between pRBD and smoking, low education and
 male sex, and found previously-unreported links with alcohol use and
 psychological distress. The risk factors for pRBD differ from those
 previously defined for neurodegenerative synucleinopathies.
description: RBD Paper 2018-4-30
 Supplementary
DOI: 10.1594/pangaea.833178
title: CTD measurements from the Mediterranean Sea during the MicroB3 Summer School in May 2014

description: This dataset has been carefully reviewed and curated in accordance with PANGAEA's exceptionally high quality standards. However, due to discontinued communication from the authors' side, it did not receive the usual formal approval by the authors and therefore lacks final scientific validation.
DOI: 10.1594/pangaea.917957
title: Oceanographic profile of CTD cast K180528_TowYo_001_Cast_020
DOI: 10.1594/pangaea.885937
title: Ages and magnetic susceptibility of Lake Lungo, Italy
DOI: 10.1594/pangaea.925083
title: Carbon and nitrogen geochemistry of IODP Site 353-U1445
DOI: 10.5061/dryad.bt36t
title: Data from: Durations and delays in care seeking, diagnosis and treatment initiation in uncomplicated pulmonary tuberculosis patients in Mumbai, India

description: Background: Timely diagnosis and treatment initiation are critical to
 reduce the chain of transmission of Tuberculosis (TB) in places like
 Mumbai, where almost 60% of the inhabitants reside in overcrowded slums.
 This study documents the pathway from the onset of symptoms suggestive of
 TB to initiation of TB treatment and examines factors responsible for
 delay among uncomplicated pulmonary TB patients in Mumbai. Methods: A
 population-based retrospective survey was conducted in the slums of 15
 high TB burden administrative wards to identify 153 self-reported TB
 patients. Subsequently in-depth interviews of 76 consenting patients that
 fit the inclusion criteria were undertaken using an open-ended interview
 schedule. Mean total, first care seeking, diagnosis and treatment
 initiation duration and delays were computed for new and retreatment
 patients. Patients showing defined delays were divided into outliers and
 non-outliers for all three delays using the median values. Results: The
 mean duration for the total pathway was 65 days with 29% of patients being
 outliers. Importantly the mean duration of first care seeking was similar
 in new (24 days) and retreatment patients (25 days). Diagnostic duration
 contributed to 55% of the total pathway largely in new patients. Treatment
 initiation was noted to be the least among the three durations with mean
 duration in retreatment patients twice that of new patients. Significantly
 more female patients experienced diagnostic delay. Major shift of patients
 from the private to public sector and non-allopaths to allopaths was
 observed, particularly for treatment initiation. Conclusion: Achieving
 positive behavioural changes in providers (especially non-allopaths) and
 patients needs to be considered in TB control strategies. Specific
 attention is required in counselling of TB patients so that timely care
 seeking is effected at the time of relapse. Prioritizing improvement of
 environmental health in vulnerable locations and provision of point of
 care diagnostics would be singularly effective in curbing pathway delays.
description: Data for Durations and
 delays in TB patients, MumbaiData for Durations and
 delays in TB patients, MumbaiFor
 repository.xlsx
DOI: 10.1594/pangaea.918734
title: Geochemistry and biomarker of sediment core PS97/056-1

description: Calendar Years AD 1830-1880; 1780-1875 and 1823-1876 are extrapolated based on the prior sedimentation rate.
DOI: 10.1594/pangaea.918736
title: Geochemistry and biomarker of sediment core PS97/072-2

description: Calendar Years AD 1823-1871 are extrapolated based on the prior sedimentation rate.
DOI: 10.1594/pangaea.918735
title: Geochemistry and biomarker of sediment core PS97/068-2

description: Calendar Years AD 1780-1875 are extrapolated based on the prior sedimentation rate.
DOI: 10.1594/pangaea.918806
title: Geochemistry of sediment core PS97/072-1TC
DOI: 10.1594/pangaea.925082
title: Inorganic analyses of major, trace, and rare earth element concentrations for 30 bulk sediment samples at Site U1445 and additional samples from other sites in the Bay of Bengal
DOI: 10.5061/dryad.j2n46
title: Data from: Variation in the post-mating fitness landscape in fruitflies

description: Sperm competition is pervasive and fundamental to determining a male’s
 overall fitness. Sperm traits and seminal fluid proteins (Sfps) are key
 factors. However, studies of sperm competition may often exclude females
 that fail to remate during a defined period. Hence, the resulting datasets
 contain fewer data from the potentially fittest males that have most
 success in preventing female remating. It is also important to consider a
 male’s reproductive success before entering sperm competition, which is a
 major contributor to fitness. The exclusion of these data can both hinder
 our understanding of the complete fitness landscapes of competing males
 and lessen our ability to assess the contribution of different
 determinants of reproductive success to male fitness. We addressed this
 here, using the Drosophila melanogaster model system, by (i) capturing a
 comprehensive range of intermating intervals that define the fitness of
 interacting wild type males, and (ii) analysing outcomes of sperm
 competition using selection analyses. We conducted additional tests using
 males lacking the sex peptide (SP) ejaculate component versus genetically
 matched (SP+) controls. This allowed us to assess the comprehensive
 fitness effects of this important Sfp on sperm competition. The results
 showed a signature of positive, linear selection in wild type and SP+
 control males on the length of the intermating interval and on male sperm
 competition defense. However, the fitness surface for males lacking SP was
 distinct, with local fitness peaks depending on contrasting combinations
 of remating intervals and offspring numbers. The results suggest that
 there are alternative routes to success in sperm competition and provide
 an explanation for the maintenance of variation in sperm competition
 traits.
description: Raw data for Fricke
 & Chapman_DRYAD SP variation msAll the raw data for the
 MS.
DOI: 10.1594/pangaea.917948
title: Oceanographic profile of CTD cast K180528_TowYo_001_Cast_012
DOI: 10.1594/pangaea.917958
title: Oceanographic profile of CTD cast K180528_TowYo_001_Cast_021
DOI: 10.1594/pangaea.917951
title: Oceanographic profile of CTD cast K180528_TowYo_001_Cast_014
DOI: 10.1594/pangaea.925084
title: Hydrogen isotopes and carbon isotope analyses of leaf wax fatty acids extracted from samples at IODP Site 353-U1445
DOI: 10.5061/dryad.2m3k7v74
title: Data from: The effect of variable frequency of sexual reproduction on the genetic structure of natural populations of a cyclical parthenogen

description: Cyclical parthenogens are a valuable system in which to empirically test
 theoretical predictions as to the genetic consequences of sexual
 reproduction in natural populations, particularly if the frequency of
 sexual relative to asexual reproduction can be quantified. In this study
 we utilized a series of lake populations of the cyclical parthenogen,
 Daphnia pulicaria, that vary consistently in their investment in sexual
 reproduction, to address the questions of whether the ecological variation
 in investment in sex is detectable at the genetic level, and if so,
 whether the genetic patterns seen are consistent with theoretical
 predictions. We show that there is variation in the genetic structure of
 these populations in a manner consistent with their investment in sexual
 reproduction. Populations engaging in a high frequency of sex were in
 Hardy-Weinberg and gametic phase equilibrium, and showed little genotypic
 differentiation across sampled years. In contrast, populations with a
 lower frequency of sex deviated widely from equilibrium, had reduced
 multi-locus clonal diversity, and showed significant temporal genotypic
 deviation.
description: AllenLynch Population
 GenotypesList of microsatellite
 genotypes for ten loci for each of the 17 samples described in the
 article. (5 populations x 3 years, 1 population x 2 years). All data were
 generated using an ABI 3730 sequencer. Population abreviations are:
 CD-Cloverdale, LL-Little Long, BR-Bristol, W-Warner, P-Pine, B-Baker. The
 population name (eg CD0434) consists of the population abreviation (CD),
 the year of sampling (04) and the individual identifier (34). Data is
 stored as an Excel file.
DOI: 10.1594/pangaea.917936
title: Oceanographic profile of CTD cast K180528_TowYo_001_Cast_001
DOI: 10.1594/pangaea.917945
title: Oceanographic profile of CTD cast K180528_TowYo_001_Cast_009
DOI: 10.1594/pangaea.917921
title: Oceanographic profile of CTD cast K180528_Towed001_20180531
DOI: 10.1594/pangaea.917964
title: Oceanographic profile of CTD cast K180528_TowYo_001_Cast_027
DOI: 10.1594/pangaea.917947
title: Oceanographic profile of CTD cast K180528_TowYo_001_Cast_011
DOI: 10.1594/pangaea.917959
title: Oceanographic profile of CTD cast K180528_TowYo_001_Cast_022
DOI: 10.5061/dryad.q5s51
title: Data from: Intestinal Ralstonia pickettii augments glucose intolerance in obesity

description: An altered intestinal microbiota composition has been implicated in the
 pathogenesis of metabolic disease including obesity and type 2 diabetes
 mellitus (T2DM). Low grade inflammation, potentially initiated by the
 intestinal microbiota, has been suggested to be a driving force in the
 development of insulin resistance in obesity. Here, we report that
 bacterial DNA is present in mesenteric adipose tissue of obese but
 otherwise healthy human subjects. Pyrosequencing of bacterial 16S rRNA
 genes revealed that DNA from the Gram-negative species Ralstonia was most
 prevalent. Interestingly, fecal abundance of Ralstonia pickettii was
 increased in obese subjects with pre-diabetes and T2DM. To assess if R.
 pickettii was causally involved in development of obesity and T2DM, we
 performed a proof-of-concept study in diet-induced obese (DIO) mice.
 Compared to vehicle-treated control mice, R. pickettii-treated DIO mice
 had reduced glucose tolerance. In addition, circulating levels of
 endotoxin were increased in R. pickettii-treated mice. In conclusion, this
 study suggests that intestinal Ralstonia is increased in obese human
 subjects with T2DM and reciprocally worsens glucose tolerance in DIO mice.
description: DryadPlosOneUdayappanGraphPad Prism file containing data belonging to Udayappan et al, Intestinal Ralstonia pickettii augments glucose intolerance in obesity, MS #: PONE-D-17-01669 DOI: 10.1371/journal.pone.0181693
DOI: 10.1594/pangaea.885938
title: XRF analysis of sediments of Lake Lungo, Italy
DOI: 10.1594/pangaea.917960
title: Oceanographic profile of CTD cast K180528_TowYo_001_Cast_023
DOI: 10.1594/pangaea.863962
title: TV-MUC video at station PS92/047-20

description: TV-MUC video at station PS92-047 Transsiz Expedition Polarstern 2015. Video shows the descent of phytodetritus aggregates through the &gt;2000m thick water column.
DOI: 10.1594/pangaea.982631
title: The raw µ-XRD data of Formation Mechanism and Gemological Characteristics of "Yellow-Skinned" Nanhong Agate in Northeastern Yunnan, China: Evidence from Mineralogy and Geochemistry

description: This dataset contains raw micro-X-ray diffraction (μ-XRD) patterns of 8 yellow-skinned Nanhong Agate samples collected from Northeastern Yunnan, China. Data acquisition was performed using a Malvern PANalytical EMPYREAN diffractometer(Malvern-Panalytical, UK) with Cu-Kα radiation (λ = 1.54056 Å), operating at 40 kV and 40 mA. The measurements were performed on a defined microarea using a 0.5-mm X-ray beam collimator. The sample was scanned over a 2θ range of 5° to 90° with a step size of 0.02°. The data acquisition time for each step was 140.25 s, and the scan speed was 0.048°/s. The total time spent at each test site was 30 min and 53 s, ensuring adequate counting statistics. The obtained diffraction patterns were analyzed using Rietveld refinement. The analyses were performed at the Kunming University of Science and Technology Analysis and Testing Research Center on June 25, 2024.
description: Laboratory Instruments：The X-ray diffraction measurements were performed using an EMPYREAN multifunctional X-ray diffractometer (Malvern-Panalytical, UK) equipped with a PIXCEL 3D detector and copper target. The instrument configuration included advanced optical path control modules: a BBHD filter, parallel beam mirror, and double cross slit system. This setup enabled flexible switching between focused and parallel beam modes, with precise control of micro-focused beam spot size (adjustable down to 0.1 mm minimum dimension through slit optimization). The parallel beam configuration achieved an ultra-low grazing incidence angle of 0.1°, while the double cross slit assembly maintained a minimum effective aperture of ≥0.1 mm during measurements.2θ (degrees): Diffraction angle range (5° to 90°).Intensity (counts): Measured intensity of the diffracted X-rays.Step size (degrees): 0.02°.Acquisition time per step (seconds): 140.25 s.Scan speed (degrees/second): 0.048°/s.Total measurement time per site (minutes:seconds): 30:53.Additional Notes:The dataset includes raw μ-XRD patterns for eight samples.The data files contain columns for 2θ (degrees) and corresponding intensity (counts).Non-common abbreviations (e.g., μ-XRD, Cu-Kα) are explained in the metadata.
DOI: 10.5061/dryad.3g824
title: Data from: Population structure of sea-type and lake-type sockeye salmon and kokanee in the Fraser River and Columbia River drainages

description: Population structure of three ecotypes of Oncorhynchus nerka (sea-type
 Sockeye Salmon, lake-type Sockeye Salmon, and Kokanee) in the Fraser River
 and Columbia River drainages was examined with microsatellite variation,
 with the main focus as to whether Kokanee population structure within the
 Fraser River drainage suggested either a monophyletic or polyphyletic
 origin of the ecotype within the drainage. Variation at 14 microsatellite
 loci was surveyed for sea-type and lake-type Sockeye Salmon and Kokanee
 sampled from 121 populations in the two river drainages. An index of
 genetic differentiation, FST, over all populations and loci was 0.087,
 with individual locus values ranging from 0.031 to 0.172. Standardized to
 an ecotype sample size of 275 individuals, the least genetically diverse
 ecotype was sea-type Sockeye Salmon with 203 alleles, whereas Kokanee
 displayed the greatest number of alleles (260 alleles), with lake-type
 Sockeye Salmon intermediate (241 alleles). Kokanee populations from the
 Columbia River drainage (Okanagan Lake, Kootenay Lake), the South Thompson
 River (a major Fraser River tributary) drainage populations, and the
 mid-Fraser River populations all clustered together in a neighbor-joining
 analysis, indicative of a monophyletic origin of the Kokanee ecotype in
 these regions, likely reflecting the origin of salmon radiating from a
 refuge after the last glaciation period. However, upstream of the
 mid-Fraser River populations, there were closer relationships between the
 lake-type Sockeye Salmon ecotype and the Kokanee ecotype, indicative of
 the Kokanee ecotype evolving independently from the lake-type Sockeye
 Salmon ecotype in parallel radiation. Kokanee population structure within
 the entire Fraser River drainage suggested a polyphyletic origin of the
 ecotype within the drainage. Studies employing geographically restricted
 population sampling may not outline accurately the phylogenetic history of
 salmonid ecotypes.
description: Baseline Allele
 FrequenciesBaseline Allele
 Frequencies by Locus and Population - Sockeye and Kokanee
 combinedS+K_250814_AF.csv
DOI: 10.5061/dryad.td997
title: Data from: The influence of locus number and information content on species delimitation: an empirical test case in an endangered Mexican salamander

description: Perhaps the most important recent advance in species delimitation has been
 the development of model-based approaches to objectively diagnose species
 diversity from genetic data. Additionally, the growing accessibility of
 next-generation sequence datasets provides powerful insights into
 genome-wide patterns of divergence during speciation. However, applying
 complex models to large datasets is time consuming and computationally
 costly, requiring careful consideration of the influence of both
 individual and population sampling, as well as the number and
 informativeness of loci on species delimitation conclusions. Here, we
 investigated how locus number and information content affect species
 delimitation results for an endangered Mexican salamander species,
 Ambystoma ordinarium. We compared results for an eight-locus,
 137-individual dataset and an 89-locus, seven-individual dataset. For both
 datasets, we used species discovery methods to define delimitation models
 and species validation methods to rigorously test these hypotheses. We
 also used integrated demographic model selection tools to choose among
 delimitation models, while accounting for gene flow. Our results indicate
 that while cryptic lineages may be delimited with relatively few loci,
 sampling larger numbers of loci may be required to ensure that enough
 informative loci are available to accurately identify and validate
 shallow-scale divergences. These analyses highlight the importance of
 striking a balance between dense sampling of loci and individuals,
 particularly in shallowly-diverged lineages. They also confirm the
 presence of a currently unrecognized, endangered species in the western
 part of A. ordinarium's range.
description: Gene alignments for 8L
 and 89L data sets from Ambystoma ordinariumOrdinarium_Data.zip