cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sj3vp
title: Data from: Gene flow between nascent species: geographic, genotypic and phenotypic differentiation within and between Aquilegia formosa and A. pubescens.

description: Speciation can be described as a reduction, and the eventual cessation, in
 the ability to interbreed. Thus, determining how gene flow differs within
 and between nascent species can illuminate the relative stage the taxa
 have attained in the speciation process. Aquilegia formosa and A.
 pubescens are fully intercompatible yet occur in different habitats and
 have flowers specialized for pollination by hummingbirds and hawkmoths
 respectively. Using 79 SNP loci we genotyped nearly 1,000 individuals from
 populations of both species in close proximity to each other and from
 putative hybrid zones. The species shared all but one SNP polymorphism and
 on average, allele frequencies differed by only 0.14. However, the species
 were clearly differentiated using Structure and admixed individuals were
 primarily identified at putative hybrid zones. PopGraph identified a
 highly integrated network among all populations but populations of each
 species and hybrid zones occupied distinct regions in the network. Using
 either conditional graph distance (cGD) or Fst/(1-Fst) we found
 significant isolation by distance (IBD) among populations. Within species,
 IBD was strong, indicating high historic gene flow. IBD extended
 approximately 100 km in A. pubescens and 30 km in A. formosa. However, IBD
 between the species was very weak and extended only a few km beyond hybrid
 zones, suggesting little recent gene flow. The extensive sharing of SNP
 polymorphisms between these species suggests that they are very early in
 the speciation process while the low signal of IBD suggests that they have
 largely ceased gene exchange.
description: Molecular Markers
 DevelopedThis file contains the
 primers developed by the iPLEX software from Sequenom for all the SNP
 markers we have developed. We also have annotations for the markers we
 used in the current studyPhenotypes_GenotypesThis file contains the individuals we have collected from the South Sierra mountains as well as the Genotypes and Phenotypes. The Genotypes are in the format needed for Structure Software
DOI: 10.5281/zenodo.18390861
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Eduard Seler, http://www.wikidata.org/entity/Q68705. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q68705
DOI: 10.5061/dryad.7874p
title: Data from: Changes in the bacterial microbiota in gut, blood, and lungs following acute LPS instillation into mice lungs

description: Introduction: Previous reports have shown that the gastrointestinal (GI)
 bacterial microbiota can have profound effects on the lungs, which has
 been described as the “gut-lung axis”. However, whether a “lung-gut” axis
 exists wherein acute lung inflammation perturbs the gut and blood
 microbiota is unknown. Methods: Adult C57/Bl6 mice were exposed to one
 dose of LPS or PBS instillation (n = 3 for each group) directly into
 lungs. Bacterial microbiota of the bronchoalveolar lavage fluid, blood,
 and cecum were determined using 454 pyrotag sequencing and quantitative
 polymerase chain reaction (qPCR) at 4 through 168 hours post-instillation.
 We then investigated the effects of oral neomycin and streptomycin (n = 8)
 on the microbiota at 4 and 24 hours post LPS instillation versus control
 treatment (n = 5 at baseline and 4 hours, n = 7 at 24 hours). Results: At
 24 hours post LPS instillation, the total bacterial count was
 significantly increased in the cecum (P&lt;0.05); whereas the total
 bacterial count in blood was increased at 4, 48, and 72 hours
 (P&lt;0.05). Antibiotic treatment reduced the total bacteria in blood
 but not in the cecum. The increase in total bacteria in the blood
 correlated with Phyllobacteriaceae OTU 40 and was significantly reduced in
 the blood for both antibiotic groups (P&lt;0.05). Conclusion: LPS
 instillation in lungs leads to acute changes in the bacterial microbiota
 in the blood and cecum, which can be modulated with antibiotics.
description: sequence_data454 sequencing files after shhh.flows and trim,seqs commands have been implemented. No chimera removal has been done yet on these files. Their are also group files and name files associated with each respective fasta file.
DOI: 10.5281/zenodo.18390798
title: Public Perceptions and Trust in Hypnotherapy within the Context of Science and Stigma

description: This study aims to analyze the influence of public perception and social stigma on the level of trust toward hypnotherapy as a psychological treatment method in Indonesia. A quantitative approach was employed through a survey of 200 respondents familiar with hypnotherapy, analyzed using Partial Least Squares–Structural Equation Modeling (PLS-SEM). The results indicate that positive perceptions significantly increase public trust, while negative social stigma remains a barrier to acceptance. These findings align with the Risk Perception Theory and Social Stigma Theory, emphasizing that trust is shaped by individuals’ risk evaluation and socially constructed beliefs. The study suggests enhancing public education and evidence-based communication to improve perceptions, reduce stigma, and strengthen trust in hypnotherapy as a legitimate and scientific therapeutic practice.
DOI: 10.5281/zenodo.18390797
title: Public Perceptions and Trust in Hypnotherapy within the Context of Science and Stigma

description: This study aims to analyze the influence of public perception and social stigma on the level of trust toward hypnotherapy as a psychological treatment method in Indonesia. A quantitative approach was employed through a survey of 200 respondents familiar with hypnotherapy, analyzed using Partial Least Squares–Structural Equation Modeling (PLS-SEM). The results indicate that positive perceptions significantly increase public trust, while negative social stigma remains a barrier to acceptance. These findings align with the Risk Perception Theory and Social Stigma Theory, emphasizing that trust is shaped by individuals’ risk evaluation and socially constructed beliefs. The study suggests enhancing public education and evidence-based communication to improve perceptions, reduce stigma, and strengthen trust in hypnotherapy as a legitimate and scientific therapeutic practice.
DOI: 10.5061/dryad.cv0q3
title: Data from: Genes associated with ant social behavior show distinct transcriptional and evolutionary patterns

description: [No abstract entered]
description: MySQL database for gene
 expression analysisMySQL database for the
 transcriptional, network connectedness, molecular evolution, and GO term
 analysismonomorium_2014-12-08.sql.gzData tables from MySQL database for gene expression analysisseparated data tables from MySQL database as zipped .csv files for the transcriptional, network connectedness, molecular evolution, and GO term analysismonomorium tables.zipdata summary by genesummary of data listed by M. pharaonis gene in comma deliminated (.csv) format. Header line with variables: gene is the M. pharaonis gene name; SINV homolog is the identified Solenopsis invicta homolog; SINVhomologexpression is whether the identified SINVhomolg was upregulated in workers that were in the nest vs. foraging area according to Manfredini et al. 2013; dNdS is the estimate of rate of molecular evolution; kTotal, kWithin, kOut, kDiff are the estimated of network connectedness from WGCNA; behavioral cateogry is whether the gene is upregulated in foragers, nurses, or not differentially expressed (nde); fpkm is the level of expression; evalue, hit, and species describe the best BLAST hitraw behavioral scan datatable in .csv format of raw behavioral scan data showing each observation of age-marked individuals.Header line with variables: colony is whether the observation is from replicate colony b or c; date is the data of observation; age is the age of observed age-marked individual workers; behavior is the behavioral code, which is described in the Supplemental Table 1.csvtotal behavioral counts by age classtable in csv format of total counts for each age cohort. Header column with variable: age is the age cohort of individuals observed; the remaining columns are the behavioral categories that significantly changed over the course of the studyREADMEREADME description of data files
DOI: 10.5061/dryad.0p36h
title: Data from: Evolution of niche preference in Sphagnum peat mosses

description: Peat mosses (Sphagnum) are ecosystem engineers— species in boreal
 peatlands simultaneously create and inhabit narrow habitat preferences
 along two microhabitat gradients: an ionic gradient and a hydrological
 hummock-hollow gradient. In this paper we demonstrate the connections
 between microhabitat preference and phylogeny in Sphagnum. Using a dataset
 of 39 species of Sphagnum, with an 18-locus DNA alignment and an
 ecological dataset encompassing three large published studies, we tested
 for phylogenetic signal and within-genus changes in evolutionary rate of
 eight niche descriptors and two multivariate niche gradients. We find
 little to no evidence for phylogenetic signal in most component
 descriptors of the ionic gradient, but interspecific variation along the
 hummock-hollow gradient shows considerable phylogenetic signal. We find
 support for a change in the rate of niche evolution within the genus— the
 hummock-forming subgenus Acutifolia has evolved along the multivariate
 hummock-hollow gradient faster than the hollow-inhabiting subgenus
 Cuspidata. Because peat mosses themselves create some of the ecological
 gradients constituting their own habitats, the classic microtopography of
 Sphagnum-dominated peatlands is maintained by evolutionary constraints and
 the biological properties of related Sphagnum species. The patterns of
 phylogenetic signal observed here will instruct future study on the role
 of functional traits in peatland growth and reconstruction.
description: Global_Means_Ecological_DataMeans, standard deviations, and sample sizes for eight univariate niche descriptors. Values are taken from a weighted mean across sites, summarizing three major ecological surveys of Sphagnum from Scandanavia, eastern Canada, and western Canada.DNA AlignmentAlignment used to reconstruct phylogenies using BEAST v1.7 from 18 genes (8 chloroplast, 2 mitochondrial, 8 nuclear). Substitution models used for each partition are indicated in the supplemental information. Sphagnum lapazense (now Eosphagnum inretortum) and Sphagnum sericeum (now Flatbergium sericeum) used as outgroups.Sphagnum_all_genes.nexBEAST_Phylogenetic_TreesRandomly selected sample of 1000 trees from (post-burnin) posterior distribution of BEAST phylogenetic reconstruction. These 1000 trees were used to test the phylogenetic comparative hypotheses in the manuscript.Sphagnum_sample.tre
DOI: 10.5061/dryad.605v1
title: Data from: The basic keratin 10-binding domain of the virulence-associated pneumococcal serine-rich protein PsrP adopts a novel MSCRAMM fold

description: Streptococcus pneumoniae is a major human pathogen, and a leading cause of
 disease and death worldwide. Pneumococcal invasive disease is triggered by
 initial asymptomatic colonization of the human upper respiratory tract.
 The pneumococcal serine-rich repeat protein (PsrP) is a lung-specific
 virulence factor whose functional binding region (BR) binds to keratin-10
 (KRT10) and promotes pneumococcal biofilm formation through
 self-oligomerization. We present the crystal structure of the
 KRT10-binding domain of PsrP (BR187–385) determined to 2.0 Å resolution.
 BR187–385 adopts a novel variant of the DEv-IgG fold, typical for
 microbial surface components recognizing adhesive matrix molecules
 adhesins, despite very low sequence identity. An extended β-sheet on one
 side of the compressed, two-sided barrel presents a basic groove that
 possibly binds to the acidic helical rod domain of KRT10. Our study also
 demonstrates the importance of the other side of the barrel, formed by
 extensive well-ordered loops and stabilized by short β-strands, for
 interaction with KRT10.
description: DataThe data are associated
 with figures Fig. 2, Fig. 5, Fig.6, Fig. S7
DOI: 10.5281/zenodo.18390866
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Caecilie Seler-Sachs, http://www.wikidata.org/entity/Q1025362. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q1025362
DOI: 10.5281/zenodo.18390865
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Caecilie Seler-Sachs, http://www.wikidata.org/entity/Q1025362. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q1025362
DOI: 10.5061/dryad.1q0h6
title: Data from: Testing models of speciation from genome sequences: divergence and asymmetric admixture in Island Southeast Asian Sus species during the Plio-Pleistocene climatic fluctuations

description: In many temperate regions, ice ages promoted range contractions into
 refugia resulting in divergence (and potentially speciation), while warmer
 periods led to range expansions and hybridization. However, the impact
 these climatic oscillations had in many parts of the tropics remains
 elusive. Here, we investigate this issue using genome sequences of three
 pig (Sus) species, two of which are found on islands of the Sunda-shelf
 shallow seas in Island Southeast Asia (ISEA). A previous study revealed
 signatures of inter-specific admixture between these Sus species (Frantz
 et al. (2013) Genome sequencing reveals fine scale diversification and
 reticulation history during speciation in Sus. Genome biology, 14, R107).
 However, the timing, directionality and extent of this admixture remain
 unknown. Here we use a likelihood based model comparison to more finely
 resolve this admixture history and test whether it was mediated by humans
 or occurred naturally. Our analyses suggest that inter-specific admixture
 between Sunda-shelf species was most likely asymmetric and occurred long
 before the arrival of humans in the region. More precisely, we show that
 these species diverged during the late Pliocene but around 23% of their
 genomes have been affected by admixture during the later Pleistocene
 climatic transition. In addition, we show that our method provides a
 significant improvement over D-statistics which are uninformative about
 the direction of admixture.
description: Frantz_Mathematica_NoteBook500b_flt_countsMutational configurations for 500bp blocks1kb_flt_countsMutational configurations for 1kb blocks
DOI: 10.5061/dryad.g7b40
title: Data from: Does hugging provide stress-buffering social support? A study of susceptibility to upper respiratory infection and illness

description: Perceived social support has been hypothesized to protect against the
 pathogenic effects of stress. How such protection might be conferred,
 however, is not well understood. Using a sample of 404 healthy adults, we
 examined the roles of perceived social support and received hugs in
 buffering against interpersonal stress-induced susceptibility to
 infectious disease. Perceived support was assessed by questionnaire, and
 daily interpersonal conflict and receipt of hugs were assessed by
 telephone interviews on 14 consecutive evenings. Subsequently,
 participants were exposed to a virus that causes a common cold and were
 monitored in quarantine to assess infection and illness signs. Perceived
 support protected against the rise in infection risk associated with
 increasing frequency of conflict. A similar stress-buffering effect
 emerged for hugging, which explained 32% of the attenuating effect of
 support. Among infected participants, greater perceived support and
 more-frequent hugs each predicted less-severe illness signs. These data
 suggest that hugging may effectively convey social support.
description: Does Hugging Provide
 Stress-Buffering Social Support_replication data setDoes Hugging Provide
 Stress-Buffering Social Support_replication syntaxThe replication data set
 is provided as an annotated SPSS data file (.SAV), and contains all
 variables necessary to conduct the analyses reported on in the associated
 publication. Data are represented by 57 variables, which are described in
 detail in the code book that appears in the attached README.pdf document.
 The code book provides a descriptive label for each variable, as well as
 value labels for categorical and dichotomous variables (when necessary).
 Missing data are represented by empty cells. The data set includes both
 input variables and variables that were created from the input dats. The
 latter are indicated with an asterisk (*). Information on the algorithms
 used for creating computed variables is provided in the associated
 manuscript. Included alongside the data set is an SPSS syntax file (.sps)
 that includes code for all analyses reported in the manuscript’s results
 section.
DOI: 10.5878/y059-8p02
title: The Gothenburg SOM Survey 2020
title: SOM-undersökningen i Göteborg 2020

description: In the autumn of 2020, the fifth edition of the Gothenburg SOM survey was conducted. A total of 8,000 randomly selected citizens of Gothenburg answered questions about attitudes and habits in relation to society, opinion and media. Many of the questions in the Gothenburg survey are of a regional nature, and concern local politicians and infrastructure initiatives.
description: Hösten 2020 genomfördes för femte gången en SOM-undersökning i Göteborgs stad, där totalt 8 000 slumpmässigt utvalda göteborgare fick svara på frågor om attityder och vanor i relation till samhälle, opinion och medier. Många av frågorna i Göteborgsundersökningen är av regional karaktär och rör lokala politiker, infrastruktursatsningar, och bilden av Göteborg som stad.
DOI: 10.5061/dryad.gp30n
title: Data from: Variation in male reproductive longevity across traditional societies

description: Most accounts of human life history propose that women have short
 reproductive spans relative to their adult lifespans, while men not only
 remain fertile but carry on reproducing until late life. Here we argue
 that studies have overlooked evidence for variation in male reproductive
 ageing across human populations. We apply a Bayesian approach to census
 data from Agta hunter-gatherers and Gambian farmers to show that long
 post-reproductive lifespans characterise not only women but also males in
 some traditional human populations. We calculate three indices of
 reproductive ageing in men (oldest age at reproduction, male late-life
 reproduction, and post-reproductive representation) and identify a
 continuum of male reproductive longevity across eight traditional
 societies ranging from !Kung, Hadza and Agta hunter-gatherers exhibiting
 low levels of polygyny, early age at last reproduction and long
 post-reproductive lifespans, to male Gambian agriculturalists and Turkana
 pastoralists showing higher levels of polygyny, late-life reproduction and
 shorter post-reproductive lifespans. We conclude that the uniquely human
 detachment between rates of somatic senescence and reproductive decline,
 and the existence of post-reproductive lifespans, are features of both
 male and female life histories, and therefore not exclusive consequences
 of menopause.
description: Vinicus et al. BaSTA
 filesThis zip file includes
 the R code and worskpace required for replicating the Bayesian estimation
 of age-dependent curves of survival and last reproduction presented in the
 main article.
DOI: 10.5878/ggjh-v188
title: The Gothenburg SOM Survey 2020
title: SOM-undersökningen i Göteborg 2020

description: In the autumn of 2020, the fifth edition of the Gothenburg SOM survey was conducted. A total of 8,000 randomly selected citizens of Gothenburg answered questions about attitudes and habits in relation to society, opinion and media. Many of the questions in the Gothenburg survey are of a regional nature, and concern local politicians and infrastructure initiatives.
description: Hösten 2020 genomfördes för femte gången en SOM-undersökning i Göteborgs stad, där totalt 8 000 slumpmässigt utvalda göteborgare fick svara på frågor om attityder och vanor i relation till samhälle, opinion och medier. Många av frågorna i Göteborgsundersökningen är av regional karaktär och rör lokala politiker, infrastruktursatsningar, och bilden av Göteborg som stad.
DOI: 10.5061/dryad.m9160
title: Data from: FAMA is an essential component for the differentiation of two distinct cell types, myrosin cells and guard cells, in Arabidopsis

description: Brassicales plants, including Arabidopsis thaliana, have an ingenious
 two-compartment defense system, which sequesters myrosinase from the
 substrate glucosinolate and produces a toxic compound when cells are
 damaged by herbivores. Myrosinase is stored in vacuoles of idioblast
 myrosin cells. The molecular mechanism that regulates myrosin cell
 development remains elusive. Here, we identify the basic helix-loop-helix
 transcription factor FAMA as an essential component for myrosin cell
 development along Arabidopsis leaf veins. FAMA is known as a regulator of
 stomatal development. We detected FAMA expression in myrosin cell
 precursors in leaf primordia in addition to stomatal lineage cells. FAMA
 deficiency caused defects in myrosin cell development and in the
 biosynthesis of myrosinases THIOGLUCOSIDE GLUCOHYDROLASE1 (TGG1) and TGG2.
 Conversely, ectopic FAMA expression conferred myrosin cell characteristics
 to hypocotyl and root cells, both of which normally lack myrosin cells.
 The FAMA interactors ICE1/SCREAM and its closest paralog SCREAM2/ICE2 were
 essential for myrosin cell development. DNA microarray analysis identified
 32 candidate genes involved in myrosin cell development under the control
 of FAMA. This study provides a common regulatory pathway that determines
 two distinct cell types in leaves: epidermal guard cells and inner-tissue
 myrosin cells.
description: Supplemental Data.
 Shirakawa et al. (2014). Plant Cell 10.1105/tpc.114.129874_Microarray data
 of Col_vs_syp22Microarray data of
 Col_vs_syp22.Supplemental Data. Shirakawa et
 al. (2014). Plant Cell 10.1105:tpc.114.129874_Microarray data of
 Col_vs_syp22.csv