cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.agt9db
title: Occurrence Download

description: A dataset containing 8527 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "Country is Ukraine",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "IucnRedListCategory is one of (CR, EN, VU)",
 "OccurrenceStatus is Present",
 "TaxonKey is Tracheophyta"
 ]
}

 The dataset includes 8527 records from 161 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002927-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.bvq83bk96
title: Sugar and nitrogen digestive processing does not explain the specialized relationship between euphonias and low quality fruits

description: In the Neotropical region, euphonias (Euphonia spp., Fringillidae) are the
 quintessential example of specialized bird frugivores, making the bulk of
 feeding visits to certain mistletoes (Phoradendron spp., Santalaceae) and
 epiphytes in the genus Rhipsalis (Cactaceae), whose fruits have high water
 and low sugar and protein concentrations. Surprisingly, a mechanistic
 explanation for such specialized, otherwise rare, relationships is
 lacking. Using captive birds and artificial diets, we contrasted euphonias
 with frugivorous tanagers in the genus Thraupis (Thraupidae), which rarely
 eats Rhipsalis fruits, to test the hypothesis that the digestive capacity
 of euphonias entails them to exploit such low-energy fruits. We expected
 that compensatory feeding in response to decreasing energy density would
 occur only in euphonias, whose higher reliance on fruits would entail a
 lower nitrogen requirement than the tanagers. Euphonias and tanagers were
 both able to compensate energy intake as sugar density decreased, and both
 species had the same mass-corrected energy intake at any given sugar
 concentration. Similarly, euphonias and tanagers did not differ in
 mass-corrected maintenance nitrogen requirement. Therefore, the
 physiological traits we investigated do not explain euphonia´s
 specialization on Rhipsalis fruits. The fast rates of fruit passage
 typical of specialized avian frugivores as euphonias that entail the
 processing of a large volume of fruits, and the putative better abilities
 of such birds to deal with secondary compounds likely present in Rhipsalis
 fruits are other possible mechanisms that should be considered in future
 studies to unveil the mechanisms underlying the intriguing specialized
 relationships between euphonias and certain fruits.
description: Please, refer to the associated article.
DOI: 10.5061/dryad.d51c5b045
title: Weight stability in adults with obesity initiating medical marijuana treatment

description: Few studies have evaluated weight change in patients who initiate medical
 marijuana treatment to address diagnosed health concerns. The objective of
 this study was to examine whether patients initiating medical marijuana
 use for a qualifying health condition experienced changes in health and
 biopsychosocial functioning over time, including weight gain or loss.
 Specifically, this observational, longitudinal study evaluated changes in
 the Body Mass Index (BMI) of adults with co-morbid obesity (Body Mass
 Index [BMI] ≥ 30 kg/m2) and severe obesity (BMI ≥ 40 kg/m2) who were
 starting medical marijuana treatment for any of the 23 qualifying medical
 conditions at one of three dispensaries in Pennsylvania. Height and weight
 measurements were collected at baseline (prior to medical marijuana use)
 and then 90 days (± 14 days) later. Participants included in analyses (n =
 52, M = 55.0 ± 13.6 years, 59.6% female) had a mean baseline BMI of 36.2 ±
 5.4 kg/m2 and the majority sought medical marijuana for chronic pain
 (73.1%). No significant change in BMI was observed from baseline to month
 three (p &gt; 0.05) in the sample. Additionally, no significant change
 in BMI was observed in the subset of patients with severe obesity (n = 12,
 p &gt; 0.05). Our findings are limited by low follow-up rates and
 convenience sampling methodology but may help to mitigate weight gain
 concerns in the context of medical marijuana use.
description: After participants provided informed consent, staff collected
 their demographic information along with their height (inches) and weight
 (lbs.) (SECA 813, SECA Corp., Chino, CA) with no shoes and light clothing.
 Participants returned in 90 days (± 14 days) to complete a follow-up
 assessment that included weight measurement. To be included in the
 analytic sample, individuals had to meet the established definition of
 obesity (i.e., BMI ≥ 30.0 kg/m2). Data were managed
 using PCOM's REDCap and analyzed using SPSS v. 24.0.
DOI: 10.6071/m3r08x
title: Data associated with: Minor genetic consequences of a major mass mortality: Short-term effects in Pisaster ochraceus

description: Mass mortality events (MMEs) are increasing globally in frequency and
 magnitude, largely due to human-induced change. The effects of these MMEs,
 both in the long- and short-term, are of imminent concern because of their
 ecosystem impacts. Genomic data can be used to reveal some of the
 population-level changes associated with MMEs. Here, we use
 reduced-representation sequencing to identify potential short-term genetic
 impacts of an MME associated with a sea star wasting (SSW) outbreak. We
 tested for changes in the population for genetic differentiation,
 diversity, and effective population size between pre-SSW versus post-SSW
 populations of Pisaster ochraceus — a species that suffered high
 SSW-associated mortality (75–100% at 80% of sites). We detected no
 significant population-based genetic differentiation over the spatial
 scale sampled, however, the post-SSW population tended toward more
 differentiation across sites than the pre-SSW population. Genetic
 estimates of effective population size (Ne) did not detectably change,
 consistent with theoretical expectations; however, rare alleles were lost.
 While we were unable to detect significant population-based genetic
 differentiation or changes in Ne over this short time period, the genetic
 burden of this MME may be borne by future generations, unless widespread
 recruitment mitigates the population decline. Prior results from P.
 ochraceus indicated natural selection played a role in altering allele
 frequencies following this MME. In addition to the role of selection found
 in a previous study on the genomic impacts of SSW on P. ochraceus, our
 current study highlights the potential role the stochastic loss of many
 individuals plays in altering how genetic variation is structured across
 the landscape. Future genetic monitoring is needed to determine long-term
 genetic impacts in this long-lived species. Given the increased frequency
 of MMEs, it is important to implement demographic and genetic monitoring
 strategies that capture baselines and background dynamics to better
 contextualize species’ responses to large perturbations.
description: See publication.
DOI: 10.5061/dryad.nk98sf7v6
title: Data used in: Social status does not predict in-camp integration among egalitarian hunter-gatherer men

description: In the last few decades, there has been much research regarding the
 importance of social prestige in shaping the social structure of
 small-scale societies. While recent studies show that social prestige may
 have important health consequences, little is known about the extent to
 which prestige translates into actual in-person interactions and
 proximity, even though the level of integration into such real-life social
 networks has been shown to have important health consequences. Here, we
 determine the extent to which two different domains of social prestige,
 popularity (being perceived as a friend by others) and hunting reputation
 (being perceived as a good hunter), translate into GPS-derived in- and
 out-of-camp proximity networks in a group of egalitarian hunter-gatherer
 men, the Hadza. We show that popularity and hunting reputation differ in
 the extent to which they are translated into time spent physically close
 to each other. Moreover, our findings suggest that in-camp proximity
 networks, which are commonly applied in studies of small-scale societies,
 do not show the full picture of Hadza men’s social preferences. While men
 are in camp, neither popularity nor hunting reputation is associated with
 being central in the proximity network; however, when out of camp, Hadza
 men who are popular are more integrated in the proximity networks while
 men with better hunting reputations are less integrated. Overall, our
 findings suggest that, in order to fully understand social preferences
 among hunter-gatherers, both in-camp and out-of-camp proximity networks
 should be considered.  
description: The description of the data is in the Method section of following
 manuscript: Fedurek et al. Social Status Does Not Predict In-Camp
 Integration Among Egalitarian Hunter-gatherer Men.
description: The description of the data is in the Method section of following
 manuscript: Fedurek et al. Social Status Does Not Predict In-Camp
 Integration Among Egalitarian Hunter-gatherer Men as well as in the R
 codes file. 'aa' from the left-top of the
 matrices has to removed before running the analyses (Dryad does not allow
 to upload data with unlabelled columns of the datasets.
DOI: 10.5061/dryad.r2280gbdq
title: Gene expression of neurotransmitter receptors over reproductive cycle of Nicrophorus vespilloides

description: Understanding genetic influences of traits in non-model organisms is
 crucial to understanding how novel traits arise. Do new traits require new
 genes, or are old genes repurposed? How predictable is this process? Here
 we examine this question for gene expression influencing parenting
 behavior in a beetle, Nicrophorus vespilloides. Parental care, produced
 from many individual behaviors, should be influenced by changes of
 expression of multiple genes and one suggestion is that the genes can be
 predicted based on knowledge of behavior expected to be precursors to
 parental care, such as, aggression, resource defense, and mating on a
 resource. Thus, testing gene expression during parental care allows us to
 test expectations of this “precursor hypothesis” for multiple genes and
 traits. We tested for changes of the expression of serotonin,
 octopamine/tyramine, and dopamine receptors, as well as, one glutamate
 receptor, predicting that these gene families would be differentially
 expressed during social interactions with offspring and associated
 resource defense. We found that serotonin receptors were strongly
 associated with social and aggression behavioral transitions. Octopamine
 receptors produced a complex picture of gene expression over a
 reproductive cycle. Dopamine was not associated with the behavioral
 transitions sampled here, while the glutamate receptor was most consistent
 with a behavioral change of resource defense/aggression. Our results
 generate new hypotheses, refine candidate lists for further studies, and
 inform the genetic mechanisms that are co-opted during the evolution of
 parent-offspring interactions, a likely evolutionary path for many
 lineages that become fully social. The precursor hypothesis, while not
 perfect, does provide a starting point for identifying candidate genes.
DOI: 10.5061/dryad.ksn02v74z
title: Data from: Fractal triads efficiently sample ecological diversity and processes across spatial scales

description: The relative influence of ecological assembly processes, such as
 environmental filtering, competition, and dispersal, vary across spatial
 scales. Changes in phylogenetic and taxonomic diversity across
 environments provide insight into these processes, however, it is
 challenging to assess the effect of spatial scale on these metrics. Here,
 we outline a nested sampling design that fractally spaces sampling
 locations to concentrate statistical power across spatial scales in a
 study area. We test this design in northeast Utah, at a study site with
 distinct vegetation types (including sagebrush steppe and mixed conifer
 forest), that vary across environmental gradients. We demonstrate the
 power of this design to detect changes in community phylogenetic diversity
 across environmental gradients and assess the spatial scale at which the
 sampling design captures the most variation in empirical data. We find
 clear evidence of broad-scale changes in multiple features of phylogenetic
 and taxonomic diversity across aspect. At finer scales, we find additional
 variation in phylodiversity, highlighting the power of our fractal
 sampling design to efficiently detect patterns across multiple spatial
 scales. Thus, our fractal sampling design and analysis effectively
 identify important environmental gradients and spatial scales that drive
 community phylogenetic structure. We discuss the insights this gives us
 into the ecological assembly processes that differentiate plant
 communities found in northeast Utah.
description: See methods in Oikos manuscript, <em>Fractal triads
 efficiently sample ecological diversity and processes across spatial
 scales, </em>DOI: 10.111/oik.08272 for detail about how the data was
 collected and processed via the code submitted along with it. 
description: See README and metadata files associated with each set of
 collected data along with notes in the code for how to process and clean
 the data.
DOI: 10.5061/dryad.p5hqbzkqb
title: Mitonuclear interactions and introgression genomics of macaque monkeys (Macaca) highlight the influence of behaviour on genome evolution

description: In most macaques, females are philopatric and males migrate from their
 natal ranges, which results in pronounced divergence of mitochondrial
 genomes within and among species. We therefore predicted that some nuclear
 genes would have to acquire compensatory mutations to preserve
 compatibility with diverged interaction partners from the mitochondria. We
 additionally expected that these sex-differences would have distinctive
 effects on gene flow in the X and autosomes. Using new genomic data from
 29 individuals from eight species of Southeast Asian macaque, we
 identified evidence of natural selection associated with mitonuclear
 interactions, including extreme outliers of interspecies differentiation
 and metrics of positive selection, low intraspecies polymorphism, and
 atypically long runs of homozygosity associated with nuclear-encoded genes
 that interact with mitochondria-encoded genes. In one individual with
 introgressed mitochondria, we detected a small but significant enrichment
 of autosomal introgression blocks from the source species of her
 mitochondria that contained genes that interact with mitochondria-encoded
 loci. Our analyses also demonstrate that sex-specific demography sculpts
 genetic exchange across multiple species boundaries. These findings show
 that behaviour can have profound but indirect effects on genome evolution
 by influencing how interacting components of different genomic
 compartments (mitochondria, the autosomes, the sex chromosomes) move
 through time and space.
description: This dataset includes vcf files generated by mapping whole genome
 shotgun sequences to the MacaM reference genome and with genotyping and
 filtering as described in the main text of the paper.  I have also
 included various scripts that were used in the paper.
description: Please see README file for (very) brief description of this
 repository.
DOI: 10.5061/dryad.6t1g1jx06
title: Genetics of mercury accumulation in Stickleback, genotypes and metal accumulation phenotypes

description: Anthropogenic stressors, such as pollutants, act as selective factors that
 can leave measurable changes in allele frequencies in the
 genome.  Metals are of particular concern among pollutants,
 because of interference with vital biological pathways. We use the
 three-spined stickleback as a model for adaptation to mercury pollution in
 natural populations. We collected sticklebacks from 21 locations in
 Flanders (Belgium), measured the accumulated levels of mercury in the
 skeletal muscle tissue, and genotyped the fish by sequencing (GBS). The
 spread of muscle mercury content across locations was considerable,
 ranging from 21.5 to 327 ng/g dry weight (DW). We then conducted a genome
 wide association study (GWAS) between 28,450 SNPs and the accumulated
 levels of mercury, using different approaches. Based on a linear mixed
 model analysis, the GWAS yielded multiple hits with a single top hit on
 Chromosome 4, with eight more SNPs (Single Nucleotide
 Polymorphism)  suggestive of association. A second approach, a
 latent factor mixed model analysis, highlighted one single SNP on
 Chromosome 11. Finally, an outlier test identified one additional SNP on
 chromosome 4 that appeared under selection. Out of all ten SNPs we
 identified as associated with mercury in muscle, three SNPs all located on
 Chromosome 4 and positioned within a 2.5 kbp distance of an annotated
 gene. Based on these results and the genome coverage of our SNPs, we
 conclude that the selective effect of mercury pollution in Flanders causes
 a significant association with at least one locus on Chromosome 4 in
 three-spined stickleback.
description: Please see description in the paper
description: The data comes as a R data file.  The objects in the file
 correspond to the phenotype, genotype, population, and genetic map.  The
 data dictionary is as: fish25: an object with the
 genetic data coded as 0/1/2 (following the PLINK 1.9 convention -- see the
 PLINK 1.9 documentation), each line corresponding to a fish, each column
 corresponding to a SNP bim25: an object containing the
 genotype map (corresponding to the BIM file used by PLINK). The first
 column is the chromosome name, the second column the SNP name, the third
 column the position in cM (unknown for all SNPs), the fourth column is the
 position in base pairs, the fifth and sixth columns are the two
 alleles. fam25: an object containing the family data
 (corresponding to the FAM file used by PLINK).  The first column is the
 population information, the second column is the individual ID. 
 phenos2: an object with phenotype data.  The first column is the
 fish ID, the second is the code for the drainage basin, the third is the
 sampling location code, the fourth the sampling location name, the fifth
 and sixth are the coordinates, the seventh is the mercury in muscle, the
 eighth is the individuals' length, and the final column is the
 individuals' sex.
DOI: 10.5281/zenodo.18398091
title: COVID-19-Todesfälle in Deutschland

description: Im Datensatz "COVID-19-Todesfälle in Deutschland" des Robert Koch-Instituts werden täglich aktualisierte Informationen zu COVID-19-bedingten Todesfällen in Deutschland bereitgestellt. Die Datenerhebung erfolgt im Rahmen des Infektionsschutzgesetzes (IfSG). Der Datensatz umfasst aggregierte Todesfallzahlen nach Berichtsdatum, Altersgruppen und Bundesländern und wird ergänzt durch den Fall-Verstorbenen-Anteil. Der Datensatz ermöglicht fundierte Analysen zur Bewertung der Krankheitsschwere und Verbreitung von COVID-19 in Deutschland.
DOI: 10.5061/dryad.tqjq2bw0j
title: Does salinization impact long-term Daphnia assemblage dynamics? Evidence from the sediment egg bank in a small hard-water lake

description: Salinization of freshwater ecosystems threatens global aquatic
 biodiversity. There is a need for studies that follow populations in situ
 during salinization to understand the effects on species and ecosystems.
 We follow 170 years of Daphnia dynamics in the sediment ephippia archive
 of a small urban lake near St. Paul, Minnesota, to characterize effects of
 severe recent salinization on lake Daphnia. We found modest changes in the
 flux of ephippia in this lake; all three key Daphnia functional groups
 remained in the assemblage throughout the period of salinization.
 Reconstruction of the size distribution of D. pulicaria demonstrated that
 predation pressure by fish may not have increased for the largest and most
 susceptible member of the assemblage despite cultural meromixis. Our
 findings highlight that in hardwater lakes, the effects of salinization
 are nuanced and require further investigation to better understand overall
 impacts of salinization on lake Daphnia assemblages.
description: Ephippia were collected from sediments of Tanners lake. Counts of
 ephippia were made and converted to fluxes based on the sediment
 accumulation model.  Ephippia were measured on their
 dorsal axis. 
description: Analysis were conducted in R.
DOI: 10.5281/zenodo.18396913
title: Concordance results for the corpus-based study of translator's voice

description: 1. How these results were generated in the corpus concordance/retrieval process:

txt file "antconc_results1_we (L0_R3) collocates": This is the corpus concordance results generated after searching for the key word "we" in the "Collocates" section of the corpus tool AntConc (v.3.5.7).

txt file "antconc_results2_we have": This is the corpus concordance results generated after clicking "have" on the interface of AntConc's "Collocates" search for "we".

 

2. About the screenshots:  

screenshot "antconc concordance screenshot1_we" : This is the corpus concordance interface while searching for the key word "we" in the "Collocates" section of the corpus tool AntConc (v.3.5.7).

screenthot "antconc concordance screenshot2_we have" : This is the corpus concordance interface while clicking "have" on the interface of AntConc's "Collocates" search for "we".
DOI: 10.5281/zenodo.18396914
title: Concordance results for the corpus-based study of translator's voice

description: 1. How these results were generated in the corpus concordance/retrieval process:

txt file "antconc_results1_we (L0_R3) collocates": This is the corpus concordance results generated after searching for the key word "we" in the "Collocates" section of the corpus tool AntConc (v.3.5.7).

txt file "antconc_results2_we have": This is the corpus concordance results generated after clicking "have" on the interface of AntConc's "Collocates" search for "we".

 

2. About the screenshots:  

screenshot "antconc concordance screenshot1_we" : This is the corpus concordance interface while searching for the key word "we" in the "Collocates" section of the corpus tool AntConc (v.3.5.7).

screenthot "antconc concordance screenshot2_we have" : This is the corpus concordance interface while clicking "have" on the interface of AntConc's "Collocates" search for "we".