cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pb1d5
title: Data from: Adjunctive use of modified Yunu-Jian in the non-surgical treatment of male smokers with chronic periodontitis: a randomized double-blind, placebo-controlled clinical trial

description: Background: Yunu-Jian (YJ) is a Chinese medicine (CM) heat purging
 formula, which is used to reduce wei huo (stomach-heat, SH) and enrich
 shen yin (kidney-yin, KY). This formula is also commonly used to manage
 diabetes mellitus and gum/oral inflammation. The activity of YJ can be
 modified or refined by the addition of other CM herbs and/or minor changes
 to one of its five key ingredients. The aim of this study was to evaluate
 the adjunctive use of modified YJ (mYJ) or YJ containing additional
 osteoblast-stimulating and inflammation-modulating CM herbs in the
 non-surgical periodontal treatment of smokers with chronic periodontitis
 in a randomized, double-blind, prospective, placebo-controlled study.
 Methods: Healthy adult male smokers with untreated chronic periodontitis
 who showed CM syndrome of SH and KY deficiency (KYD) whilst attending a
 dental teaching hospital from October to December, 2005, were invited to
 participate in a randomized double-blind, placebo-controlled clinical
 trial. The trial itself involved the once-daily oral administration of a
 placebo or mYJ for 3 months as an adjunct to non-surgical periodontal
 therapy. Several periodontal parameters, including radiographic alveolar
 bone density, were measured by computer-assisted densitometric image
 analysis (CADIA) on selected sites, and CM signs of SH and KYD were
 followed from their baseline values to various time points up to 12 months
 or the end of study. Results: Twenty-five smokers (consumed 25.0 ± 15.3
 smoking-pack years, ranged 7.5–80; aged 46.3 ± 6.8 years) with
 periodontitis and SH and KYD were recruited (Placebo, n = 14; mYJ, n =
 11). All of the participants showed good tolerance towards the CM recipe.
 All of the periodontal parameters had improved after 12-month follow-up,
 and no statistically significant differences were detected between the
 control group and test group, except for the higher CADIA values observed
 compared with the baseline at 12 months for test sites (P = 0.025). 4/3/3
 test vs 14/13/13 control participants had persisting SH and KYD at 6, 9
 and 12 months (P &lt; 0.001), respectively. Conclusions: The
 adjunctive use of mYJ preserved the post-treatment increases in the
 radiographic alveolar bone density at the study sites and led to an
 overall improvement in SH and KYD compared with the controls.
description: Clinical data of test
 and control groupClinical data of test
 and control groupdata.xlsx
DOI: 10.5281/zenodo.18381906
title: Dataset for the paper "Unsupervised Discovery and Analysis of the Vocal Repertoires and Patterns of Select Corvid Species".

description: This dataset accompanies the paper "Unsupervised Discovery and Analysis of the Vocal Repertoires and Patterns of Select Corvid Species".

It contains calls from 5 corvid species.

 

The data is provided as compressed tar.gz files.
DOI: 10.5061/dryad.19fg1
title: Data from: Increasing procaspase 8 expression using repurposed drugs to induce HIV infected cell death in ex vivo patient cells

description: HIV persists because a reservoir of latently infected CD4 T cells do not
 express viral proteins and are indistinguishable from uninfected cells.
 One approach to HIV cure suggests that reactivating HIV will activate
 cytotoxic pathways; yet when tested in vivo, reactivating cells do not die
 sufficiently to reduce cell-associated HIV DNA levels. We recently showed
 that following reactivation from latency, HIV infected cells generate the
 HIV specific cytotoxic protein Casp8p41 which is produced by HIV protease
 cleaving procaspase 8. However, cell death is prevented, possibly due to
 low procaspase 8 expression. Here, we tested whether increasing procaspase
 8 levels in CD4 T cells will produce more Casp8p41 following HIV
 reactivation, causing more reactivated cells to die. Screening 1277 FDA
 approved drugs identified 168 that increased procaspase 8 expression by at
 least 1.7-fold. Of these 30 were tested for anti-HIV effects in an acute
 HIVIIIb infection model, and 9 drugs at physiologic relevant levels
 significantly reduced cell-associated HIV DNA. Primary CD4 T cells from
 ART suppressed HIV patients were treated with one of these 9 drugs and
 reactivated with αCD3/αCD28. Four drugs significantly increased Casp8p41
 levels following HIV reactivation, and decreased total cell associated HIV
 DNA levels (flurbiprofen: p = 0.014; doxycycline: p = 0.044; indomethacin:
 p = 0.025; bezafibrate: P = 0.018) without effecting the viability of
 uninfected cells. Thus procaspase 8 levels can be increased
 pharmacologically and, in the context of HIV reactivation, increase
 Casp8p41 causing death of reactivating cells and decreased HIV DNA levels.
 Future studies will be required to define the clinical utility of this or
 similar approaches.
description: Caspase 8 expression
 dataProcaspase 8 ELISA
 results of FDA-approved drug screen.Copy of FDA-IN drugs_Plate map
 (96-well-format).xlsx
DOI: 10.5281/zenodo.18381905
title: Dataset for the paper "Unsupervised Discovery and Analysis of the Vocal Repertoires and Patterns of Select Corvid Species".

description: This dataset accompanies the paper "Unsupervised Discovery and Analysis of the Vocal Repertoires and Patterns of Select Corvid Species".

It contains calls from 5 corvid species.

 

The data is provided as compressed tar.gz files.
DOI: 10.5061/dryad.c96j0
title: Data from: Unexpected but welcome. Artificially selected traits may increase fitness in wild boar

description: Artificial selection affects phenotypes differently by natural selection.
 Domestic traits, which pass into the wild, are usually negatively
 selected. Yet, exceptionally, this axiom may fail to apply if genes, from
 the domestic animals, increase fertility in the wild. We studied a rare
 case of a wild boar population under the framework of Wright's
 interdemic selection model, which could explain gene flow between wild
 boar and pig, both considered as demes. We analysed the MC1R gene and
 microsatellite neutral loci in 62 pregnant wild boars as markers of
 hybridization, and we correlated nucleotide mutations on MC1R (which are
 common in domestic breeds) to litter size, as an evaluation of fitness in
 wild sow. Regardless of body size and phyletic effects, wild boar sows
 bearing nonsynonymous MC1R mutations produced larger litters. This
 directly suggests that artificially selected traits reaching wild
 populations, through interdemic gene flow, could bypass natural selection
 if and only if they increase the fitness in the wild.
description: MC1R alignment_Fulgione
 et al. 2016.fastaMC1R sequences of
 pregnant wild boar samples collectedmtDNA alignment_Fulgione
 et al. 2016mtDNA sequences of
 pregnant wild boar samples collected
DOI: 10.15468/vmdzin
title: Winter Bird Census

description: Censuses cover all observed bird species. Annual counts have been done in the winter time since 1957. Methodology is explained in link: 
http://www.luomus.fi/seurannat/methods.htm
Data quality: From year 2019, 390 documents are incorrectly missing MY.taxonCensus: aves -key/value, which tell that all observed birds have been recorded during the census.
DOI: 10.5061/dryad.569j0
title: Data from: Low prevalence of methicillin-resistant Staphylococcus aureus among men who have sex with men attending an STI clinic in Amsterdam, a cross-sectional study

description: Objective: Community-associated methicillin-resistant Staphylococcus
 aureus (CA-MRSA) is common among men who have sex with men (MSM) in the
 USA. It is unknown whether this is also the case in Amsterdam, the
 Netherlands. Design: Cross-sectional study. Setting: Sexually transmitted
 infection outpatient low- threshold clinic, Amsterdam, the Netherlands.
 Participants: Between October 2008 and April 2010, a total of 211 men were
 included, in two groups: (1) 74 MSM with clinical signs of a skin or soft
 tissue infection (symptomatic group) and (2) 137 MSM without clinical
 signs of such infections (asymptomatic group). Primary outcome measures: S
 aureus and MRSA infection and/or colonisation. Swabs were collected from
 the anterior nasal cavity, throat, perineum, penile glans and, if present,
 from infected skin lesions. Culture for S aureus was carried out on blood
 agar plates and for MRSA on selective chromagar plates after enrichment in
 broth. If MRSA was found, the spa- gene was sequenced. Secondary outcome
 measures: Associated demographic characteristics, medical history, risk
 factors for colonisation with S aureus and high-risk sexual behaviour were
 collected through a self- completed questionnaire. Results: The prevalence
 of S aureus colonisation in the nares was 37%, the pharynx 11%, the
 perianal region 12%, the glans penis 10% and in skin lesions 40%. In
 multivariable analysis adjusting for age, anogenital S aureus colonisation
 was significantly associated with the symptomatic group (p=0.01) and
 marginally with HIV ( p=0.06). MRSA was diagnosed in two cases: prevalence
 0.9% (95% CI 0.1% to 3.4%)). Neither had CA-MRSA strains. Conclusions:
 CA-MRSA among MSM in Amsterdam is rare. Genital colonisation of S aureus
 is not associated with high-risk sexual behaviour.
description: Methicillin-resistant
 Staphylococcus aureus among men who have sex with men attending an STI
 clinic in AmsterdamMRSA among MSM Amsterdam key
 data final.xls
DOI: 10.5061/dryad.85pr1
title: Data from: Inferring the degree of incipient speciation in secondary contact zones of closely related lineages of Palearctic green toads (Bufo viridis subgroup)

description: Reproductive isolation between lineages is expected to accumulate with
 divergence time, but the time taken to speciate may strongly vary between
 different groups of organisms. In anuran amphibians, laboratory crosses
 can still produce viable hybrid offspring &gt;20 My after separation,
 but the speed of speciation in closely related anuran lineages under
 natural conditions is poorly studied. Palearctic green toads (Bufo viridis
 subgroup) offer an excellent system to address this question, comprising
 several lineages that arose at different times and form secondary contact
 zones. Using mitochondrial and nuclear markers, we previously demonstrated
 that in Sicily, B. siculus and B. balearicus developed advanced
 reproductive isolation after Plio-Pleistocene divergence (2.6 My,
 3.3–1.9), with limited historic mtDNA introgression, scarce nuclear
 admixture, but low, if any, current gene flow. Here, we study genetic
 interactions between younger lineages of early Pleistocene divergence
 (1.9 My, 2.5–1.3) in northeastern Italy (B. balearicus, B. viridis). We
 find significantly more, asymmetric nuclear and wider, differential mtDNA
 introgression. The population structure seems to be molded by geographic
 distance and barriers (rivers), much more than by intrinsic genomic
 incompatibilities. These differences of hybridization between zones may be
 partly explained by differences in the duration of previous isolation.
 Scattered research on other anurans suggests that wide hybrid zones with
 strong introgression may develop when secondary contacts occur
 &lt;2 My after divergence, whereas narrower zones with restricted gene
 flow form when divergence exceeds 3 My. Our study strengthens support for
 this rule of thumb by comparing lineages with different divergence times
 within the same radiation.
description: Microsatellite genotypes
 and mitochondrial D-loop haplogroups datasetThe file includes
 microsatellite genotypes (12 markers) and mitochondrial D-loop haplogroups
 of Bufo viridis/balearicus green toads sampled in the Po valley.
 "NA" indicates missing data. Microsatellites null alleles
 (estimated with MICROCHECKER) are indicated as "0". For details
 on the mitochondrial D-loop haplogroups, please refer to the
 paper.Microsat_D-loopHaplogroups_Dataset.xls
DOI: 10.5061/dryad.dr9712v
title: Data from: Asymmetric competitive effects during species range expansion: an experimental assessment of interaction strength between ‘equivalent’ grazer species at their range overlap

description: 1. Biotic interactions are central to the development of theory and
 concepts in community ecology; experimental evidence has shown their
 strong effects on patterns of population and community organization and
 dynamics over local spatial scales. The role of competition in determining
 range limits and preventing invasions at biogeographic scales is more
 controversial, partly because of the complexity of processes involved in
 species colonization of novel habitats and the difficulties in performing
 appropriate manipulations and controls. 2. We examined experimentally
 whether competition is likely to affect poleward range expansion hindering
 or facilitating the establishment of the limpet Scurria viridula along the
 southeastern Pacific rocky shore (30°S, Chile) in the region occupied by
 the congeneric S. zebrina. We also assessed whether competition with the
 “invader” or range expanding species could reduce individual performance
 of the ‘native’ S. zebrina and depress local populations 3. Geographic
 field surveys were conducted to characterize the abundance and identity of
 limpets along the south-eastern Pacific coast from 18°S to 41°S, and the
 micro-scale (few cm) spatial distribution across the range overlap of the
 two species. Field-based competition experiments were conducted at the
 southern leading edge of the range of S. viridula (33°S) and at the
 northern limit of S. zebrina (30°S). 4. Field surveys showed poleward
 range expansion of S. viridula of ca. 210 km since year 2000, with an
 expansion rate of 13.1 km year -1. No range shift was detected for S.
 zebrina. The resident S. zebrina had significant negative effects on the
 growth rate of the invading juvenile S. viridula, while no effect of the
 latter was found on S. zebrina. Spatial segregation between species was
 found at the scale of cms. 5. Our results provide novel evidence of an
 asymmetric competitive effect of a resident species on an invader, which
 may hamper further range expansion. No negative effect of the invader on
 the resident species was detected. This study highlights the complexities
 of evaluating the role of species interactions in setting range limits of
 species, but showed how interspecific competition might slow the advance
 of an invader by reducing individual performance and overall population
 size at the advancing front.
description: data_scurria_densData species abundance at different geographic ranges (18°S to 42°S)
DOI: 10.5061/dryad.g26k9
title: Data from: Behavioural isolation may facilitate homoploid hybrid speciation in cichlid fish

description: Hybrid speciation is constrained by the homogenizing effects of gene flow
 from the parental species. In the absence of post-mating isolation due to
 structural changes in the genome, or temporal or spatial premating
 isolation, another form of reproductive isolation would be needed for
 homoploid hybrid speciation to occur. Here, we investigate the potential
 of behavioural mate choice to generate assortative mating among hybrids
 and parental species. We made three-first-generation hybrid crosses
 between different species of African cichlid fish. In three-way
 mate-choice experiments, we allowed hybrid and nonhybrid females to mate
 with either hybrid or nonhybrid males. We found that hybrids generally
 mated nonrandomly and that hybridization can lead to the expression of new
 combinations of traits and preferences that behaviourally isolate hybrids
 from both parental species. Specifically, we find that the phenotypic
 distinctiveness of hybrids predicts the symmetry and extent of their
 reproductive isolation. Our data suggest that behavioural mate choice
 among hybrids may facilitate the establishment of isolated hybrid
 populations, even in proximity to one or both parental species.
description: Selz et al.
 2013See ReadMe
 file.
DOI: 10.5061/dryad.215sn
title: Data from: Revisiting the provenance delineation of a widespread shrub, Frangula alnus—the role of spatial, temporal and environmental patterns

description: Including population genetic aspects into the selection of planting
 material within the framework of conservation and restoration measures is
 of vital importance for the long-term persistence of populations. This is
 especially true facing climate change since genetic diversity and the
 spread of potentially beneficial alleles are important for the
 adaptability of populations. Therefore, knowledge about genetic
 variability within and between populations is a critical aspect when
 determining provenance regions. In our study, we investigated the
 population genetic structure of a widespread, insect-pollinated and mainly
 bird-dispersed shrub species, Frangula alnus, on the basis of seven
 microsatellites and two chloroplast DNA markers throughout Germany. The
 aim was to determine the spatial, temporal and ecological processes
 genetically structuring populations to critically revise existing
 provenance regions. Therefore, we conducted analyses on different spatial
 scales (country-wide, regional and local) using the two different marker
 sets in addition to environmental variables. We detected distinct patterns
 on all spatial scales which indicated influences of historic
 recolonization processes, regional differences of seed dispersal across
 the landscape, as well as small-scale spatial genetic structures
 attributable to local dispersal processes. No relation of underlying
 environmental gradients such as temperature or precipitation and genetic
 patterns was found. We conclude that different aspects of historic and
 more recent gene flow shape population genetic structures and that a
 thorough analysis on a variety of spatial, temporal and environmental
 scales is necessary to appropriately select planting material for
 conservation and restoration measures. Correspondingly, management advice
 regarding provenance delineations will be provided.
description: Franugla_Microsat_DatMikrosatellite data: alleles (fragment sizes in bp) of 7 loci from 576 individuals of 30 populations (as described in Materials & Methods, Table 1 and Supplementary Material).Franugla_cpDNA_DatcpDNA data: nucleotide sequences at 8 differentiating loci in two chloroplast regions observed in 236 individuals from 30 populations (as described in Methods & Materials, Table 1, Fig. 6 and Supplementary Material).
DOI: 10.5061/dryad.s0054
title: Data from: Color vision varies more among populations than among species of live-bearing fish from South America

description: Background: Sensory Bias models for the evolution of mate preference place
 a great emphasis on the role of sensory system variation in mate
 preferences. However, the extent to which sensory systems vary across-
 versus within-species remains largely unknown. Here we assessed whether
 color vision varies in natural locations where guppies (Poecilia
 reticulata) and their two closest relatives, Poecilia parae and Poecilia
 picta, occur in extreme sympatry and school together. All three species
 base mate preferences on male coloration but differ in the colors
 preferred. Results: Measuring opsin gene expression, we found that within
 sympatric locations these species have similar color vision and that color
 vision differed more across populations of conspecifics. In addition, all
 three species differ across populations in the frequency of the same opsin
 coding polymorphism that influences visual tuning. Conclusions: Together,
 this shows sensory systems vary considerably across populations and
 supports the possibility that sensory system variation is involved in
 population divergence of mate preference.
description: R
 analysesFile of all analyses
 carried out on opsin expression data.Proportional Opsin
 Expression DataOpsin expression data
 for each individual.GuySymPropOps.csvRelative to housekeeping measure of opsin expressionOpsin expression for each individual.GuySymRelHouse.csvLWS-1 genotypesAlleles of the LWS-1 for each individual.Sample log.xlsx
DOI: 10.5061/dryad.vs97g
title: Data from: Vertebrate community composition and diversity declines along a defaunation gradient radiating from rural villages in Gabon

description: Anthropocene defaunation is the global phenomenon of human-induced animal
 biodiversity loss. Understanding the patterns and process of defaunation
 is critical to predict outcomes for wildlife populations and cascading
 consequences for ecosystem function and human welfare. We investigated a
 defaunation gradient in northeastern Gabon by establishing 24 transects at
 varying distances (2–30 km) to rural villages and surveying the abundance
 and composition of vertebrate communities. Distance from village was
 positively correlated with observations of hunting (shotgun shells,
 campfires, hunters), making it a good proxy for hunting pressure. Species
 diversity declined significantly with proximity to village, with mammal
 richness increasing by roughly 1.5 species every 10 km travelled away from
 a village. Compared to forest far from villages, the wildlife community
 near villages consisted of higher abundances of large birds and rodents
 and lower abundances of large mammals like monkeys and ungulates. Distance
 to nearest village emerged as a key driver of the relative abundance of
 five of the six taxonomic guilds, indicating that the top–down force of
 hunting strongly influences large vertebrate community composition and
 structure. Several measures of vegetation structure also explained animal
 abundance, but these varied across taxonomic guilds. Forest elephants were
 the exception: no measured variable or combination of variables explained
 variation in elephant abundances. Synthesis and applications. Hunting is
 concentrated within 10 km around villages, creating a hunting halo
 characterized by heavily altered animal communities composed of relatively
 small-bodied species. Although the strongest anthropogenic effects are
 relatively distance-limited, the linear increase in species richness shown
 here even at distances 30 km from villages suggests that hunting may have
 altered vertebrate abundances across the entire landscape. Central African
 forests store &gt;25% of the carbon in tropical forests and are home
 to 3000 endemic species, but roughly 53% of the region lies within the
 village hunting halo. Resource management strategies should take into
 account this hunting-induced spatial variation in animal communities. Near
 villages, resource management should focus on sustainable community-led
 hunting programs that provide long-term supplies of wild meat to rural
 people. Resource management far from villages should focus on law
 enforcement and promoting industry practices that maintain remote tracts
 of land to preserve ecosystem services like carbon storage and
 biodiversity.
description: IvindoData_DryadVersionLarge vertebrate community data and environmental characteristics for 24 2-km transects with varying hunting intensities in the Ivindo landscape in northeast Gabon.
DOI: 10.15468/dl.bpffte
title: Occurrence Download

description: A dataset containing 483 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Brunfelsia pauciflora",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 483 records from 88 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000848-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.