cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.c484g2
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Living Specimen)",
 "Country is Mexico",
 "HasCoordinate is true",
 "Issue is Occurrence status inferred from individual count",
 "Month is one of (February, March, April, May, June, July)",
 "OccurrenceStatus is Present",
 "TaxonKey is Ammodramus savannarum",
 "Year 1901-2026"
 ]
}

 The dataset includes 6 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002075-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jftz68
title: Occurrence Download

description: A dataset containing 25 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Megatherium americanum"
 ]
}

 The dataset includes 25 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002077-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.w6m905qkh
title: Data from: Examining the dynamics of Epstein-Barr virus shedding in the tonsils and the impact of HIV-1 coinfection on daily saliva viral loads

description: Epstein-Barr virus (EBV) is transmitted by saliva and is a major cause of
 cancer, particularly in people living with HIV/AIDS. Here, we describe the
 frequency and quantity of EBV detection in the saliva of Ugandan adults
 with and without HIV-1 infection and use these data to develop a novel
 mathematical model of EBV infection in the tonsils. Eligible cohort
 participants were not taking antiviral medications, and those with HIV-1
 infection had a CD4 count &gt;200 cells/mm^3. Over a 4-week period,
 participants provided daily oral swabs that we analysed for the presence
 and quantity of EBV. Compared with HIV-1 uninfected participants, HIV-1
 coinfected participants had an increased risk of EBV detection in their
 saliva (IRR=1.27, 95% CI=1.10-1.47) and higher viral loads in positive
 samples. We used these data to develop a stochastic, mechanistic
 mathematical model that describes the dynamics of EBV, infected cells, and
 immune response within the tonsillar epithelium to analyse potential
 factors that may cause EBV infection to be more severe in HIV-1 coinfected
 participants. The model, fit using Approximate Bayesian Computation,
 showed high fidelity to daily oral shedding data and matched key summary
 statistics. When evaluating how model parameters differed among
 participants with and without HIV-1 coinfection, results suggest HIV-1
 coinfected individuals have higher rates of B cell reactivation, which can
 seed new infection in the tonsils and lower rates of an EBV-specific
 immune response. Subsequently, both these traits may explain higher and
 more frequent EBV detection in the saliva of HIV-1 coinfected individuals.
description: Data on EBV shedding in adults from Kampala, Uganda and Seattle,
 Washington, USA, are included here. 
 Uganda_ebv_data.csv contains information on EBV shedding in the
 saliva, genital tract, and in the blood of Uganda cohort
 participants. Uganda_baff_cd4_hiv.csv contains
 information on the B cell activation factor amounts, CD4 T cell counts,
 and HIV RNA loads found in the blood of Uganda cohort
 participants. Seattle_ebv_data.csv contains information
 on EBV shedding in the saliva of Seattle cohort participants.
 Key for Data Labels Participant:
 unique identifying number for each participant of a cohort
 Site: site of sample collection  StudyDay:
 number of days since beginning the observation of a participant
 hiv_status: HIV-1 infection status (NEG = negative, POS =
 positive) CD4: CD4 T cell count/mm^3 in
 blood BAFF: B cell activation factor levels in pg/ml
 of serum HIV: HIV-1 RNA copies/ml of blood
 V: EBV DNA copies/ml as measured by qPCR. Note the threshold of
 detection was 150 DNA copies/ml for mucosal samples and 50 DNA copies/ml
 for serum samples
DOI: 10.5061/dryad.8931zcrm6
title: Data for: Synthesis and assessment of schwertmannite/few-layer graphene composite for the degradation of sulfamethazine in heterogeneous Fenton-like reaction

description:     Schwertmannite, an iron oxyhydrosulfate mineral, can
 catalyze Fenton-like reaction to degrade organic contaminants, but the
 reduction of Fe(III) to Fe(II) on the surface of schwertmannite is a
 limiting step for the Fenton-like process. In the present study, the
 schwertmannite/few-layer graphene composite (sch-FLG) was synthesized to
 promote the catalytic activity of schwertmannite in Fenton-like reaction.
 It was found that schwertmannite can be successfully carried by FLG in
 sch-FLG composite, mainly via the chemical bond of Fe-O-C on the surface
 of sch-FLG. The sch-FLG exhibited a much higher catalytic activity than
 schwertmannite or FLG for the degradation of SMT in the heterogeneous
 Fenton-like reaction, which resulted from that the few-layer graphene can
 pass electrons efficiently. The degradation efficiency of SMT was around
 100% under the reaction conditions of H2O2 200-500 mg L-1, sch-FLG dosage
 1-2 g L-1, temperature 28-38 °C, and initial solution pH 1-9. During the
 repeated uses of sch-FLG in Fenton-like reaction, it maintained a certain
 catalytic activity for the degradation of SMT and the mineral structure
 was not changed. In addition, SMT may be finally mineralized in
 Fenton-like reaction catalyzed by sch-FLG, and the possible degradation
 pathways were proposed. Therefore, the sch-FLG is an excellent catalyst
 for SMT degradation in heterogeneous Fenton-like reaction.
description: The morphology of sch-FLG was characterized by using
 high-resolution transmission electron microscopy (HRTEM, JEOL). The
 crystal structure of sch-FLG was characterized by using X-ray diffraction
 (XRD, Thermo Fisher XTRA) at a scanning rate of 10°
 min<sup>-1</sup> in the 2θ range of 10-70° with Cu-Kα
 radiation (λ = 1.5406 Å) at room temperature. The surface elements of
 sch-FLG were characterized by using X-ray photoelectron spectroscopy (XPS,
 Thermo Scientific ESCALAB 250Xi) system with Al Kα radiation (Energy
 1486.6 eV). The Brunauer-Emmett-Teller (BET) specific surface area and
 Barret-Joyner-Halenda (BJH) pore volume of sch-FLG were measured by using
 N<sub>2</sub> adsorption-desorption method (Tristar 3000,
 Micromeritics). The chemical structure of sch-FLG was characterized by
 using the Fourier transform infrared (FTIR, Thermo Nicolet 6700), and the
 samples were prepared with the powder pressing method in KBr pellet at
 room temperatu
description: Raw data.
DOI: 10.5061/dryad.j6q573n8r
title: Ecological and evolutionary drivers of hemoplasma infection and genotype sharing in a Neotropical bat community

description: Most emerging pathogens can infect multiple species, underscoring the
 importance of understanding the ecological and evolutionary factors that
 allow some hosts to harbor greater infection prevalence and share
 pathogens with other species. However, our understanding of pathogen jumps
 is primarily based around viruses, despite bacteria accounting for the
 greatest proportion of zoonoses. Because bacterial pathogens in bats
 (Order: Chiroptera) can have conservation and human health consequences,
 studies that examine the ecological and evolutionary drivers of bacterial
 prevalence and barriers to pathogen sharing are crucially needed. We here
 studied hemotropic Mycoplasma spp. (i.e., hemoplasmas) across a
 species-rich bat community in Belize over two years. Across 469 bats
 spanning 33 species, half of individuals and two-thirds of species were
 hemoplasma positive. Infection prevalence was higher for males and for
 species with larger body mass and colony sizes. Hemoplasmas displayed high
 genetic diversity (21 novel genotypes) and strong host specificity.
 Evolutionary patterns supported co-divergence of bats and bacterial
 genotypes alongside phylogenetically constrained host shifts. Bat species
 centrality to the network of shared hemoplasma genotypes was
 phylogenetically clustered and unrelated to prevalence, further suggesting
 rare—but detectable—bacterial sharing between species. Our study
 highlights the importance of using fine phylogenetic scales when assessing
 host specificity and suggests phylogenetic similarity may play a key role
 in host shifts for not only viruses but also bacteria. Such work more
 broadly contributes to increasing efforts to understand cross-species
 transmission and epidemiological consequences of bacterial pathogens.
DOI: 10.5061/dryad.5tb2rbp0x
title: Occupational exposure to silica and risk of heart disease: a systematic review with meta-analysis

description: Objective To search for evidence of the relationship between
 occupational silica exposure and heart disease. Design A
 systematic review and meta-analysis. Background Growing
 evidences suggest a connection between occupational silica
 exposure and heart disease; however, the link between them is less clear.
 Data sources PubMed, ScienceDirect, Springer and EMBASE were searched for
 articles published between 1 January 1995 and 20 June
 2019. Articles that investigated the effects of
 occupational silica exposure on heart disease risk were considered. Study
 selection We included cohort studies, including prospective, retrospective
 and retro-prospective studies. Data extraction and
 synthesis We extracted data by using a piloted data collection
 form and conducted random-effects meta-analysis and
 exposure-response analyses. The meta-relative risk (meta-RR), a measure of
 the average ratio of heart disease rates for those with and without silica
 exposure, was used as an inverse variance-weighted average of relative
 risks from the individual studies. The Newcastle-Ottawa Quality
 assessment Scale about cohort studies was used for study quality
 assessment. Outcome measure We calculated heart disease risks of
 pulmonary heart disease, ischaemic heart disease and other heart
 diseases. Results Twenty cohort articles were
 included. Results suggest a significant
 increase of overall heart
 disease risk (meta-RR = 1.08, 95%
 CI = 1.03, 1.13). Stronger evidences of association with
 pulmonary heart disease were found through both categories of heart
 disease risk estimate (meta-RR = 1.24, 95%
 CI = 1.08, 1.43) and exposure-response analyses
 (meta-RR = 1.39, 95% CI = 1.19, 1.62).
 Moreover, our subgroup analyses revealed that the statistical
 heterogeneity among studies could be attributed mainly to the diversities
 of reference group, occupation and study quality score.
 Conclusions Silica-exposed workers have increased risk
 of overall heart disease, especially pulmonary heart disease.
 While further research is needed to better clarify the
 relationship between occupational silica exposure and ischaemic
 heart disease.
description: <strong>1.
 Raw_data_for_meta_analysis.</strong> The
 "Raw_data_for_meta_analysis" file includes four parts: (1) data
 of "overall and categories of heart disease risk estimate"; (2)
 data of "subgroup analyses"; (3) data of "exposure-response
 analyses of ischaemic heart disease"; (4) data of
 "exposure-response analyses of pulmonary heart
 disease".
 <strong>2. Commands_for_Exposure_response_analyses.</strong> The "Commands_for_Exposure_response_analyses" file provides exposure-response analyses commands for pulmonary heart disease and ischaemic heart disease.
DOI: 10.5061/dryad.cvdncjt0m
title: Data from: Countershading enhances camouflage by reducing prey contrast

description: A 3D body shape is problematic for camouflage because overhead lighting
 produces a luminance gradient across the body’s surface. Countershading, a
 form of patterning where animals are darkest on their uppermost surface,
 is thought to counteract this luminance gradient and enhance concealment,
 but the mechanisms of protection remain unclear. Surprisingly, no study
 has examined how countershading alters prey contrast, or investigated how
 the presence of a dorso-ventral luminance gradient affects detection under
 controlled viewing conditions. It has also been suggested that the
 direction of the dorso-ventral luminance gradient (darkest or lightest on
 top) may interfere with predators’ abilities to resolve prey 3D shape, yet
 this intriguing idea has never been tested. We used live fish predators
 (western rainbowfish, Melanotaenia australis) and computer-generated prey
 images to compare the detectability of uniformly pigmented (i.e.
 non-countershaded) prey with that of optimally countershaded prey of
 varying contrasts against the background. Optimally countershaded prey
 were difficult for predators to detect, and the probability and speed of
 detection depended on prey luminance contrast with the background. In
 comparison, non-countershaded prey were always highly detectable, even
 though their average luminance closely matched the luminance of the
 background. Our findings suggest that uniformly pigmented 3D prey are
 highly conspicuous to predators, because overhead lighting increases
 luminance contrast between different body parts or between the body and
 the background. We found no evidence for the notion that countershading
 interferes with predator perception of 3D form.
DOI: 10.5061/dryad.j9kd51c7v
title: A chemically-triggered transition from conflict to cooperation in burying beetles

description: Although interspecific competition has long been recognized as a major
 driver of trait divergence and adaptive evolution, relatively little
 effort has focused on how it influences the evolution of intraspecific
 cooperation. Here we identify the mechanism by which the perceived
 pressure of interspecific competition influences the transition from
 intraspecific conflict to cooperation in a facultative cooperatively
 breeding species, the Asian burying beetle Nicrophorus
 nepalensis. We not only found that beetles are more cooperative at
 carcasses when blowfly maggots have begun to digest the tissue, but that
 this social cooperation appears to be triggered by a single chemical
 cue—dimethyl disulfide (DMDS)—emitted from carcasses consumed by
 blowflies, but not from control carcasses lacking blowflies. Our results
 provide experimental evidence that interspecific competition promotes the
 transition from intraspecific conflict to cooperation in N.
 nepalensisvia a surprisingly simple social chemical cue that is a reliable
 indicator of resource competition between species.
DOI: 10.5061/dryad.sbcc2fr2m
title: N-P utilization of Acer mono leaves at different life history stages across altitudinal gradients

description: The relationship between plants and the environment is a core area of
 research in ecology. Owing to differences in plant sensitivity to the
 environment at different life history stages, the adaptive strategies of
 plants are a cumulative result of both their life history and environment.
 Previous research on plant adaptation strategies has focused on adult
 plants, neglecting saplings or seedlings, which are more sensitive to the
 environment and largely affect the growth strategy of subsequent life
 stages. We compared leaf N and P stoichiometric traits of the seedlings,
 saplings and adult trees of Acer mono Maxim and different altitudes and
 found significant linear trends for both life history stages and altitude.
 Leaf N and P content by unit mass were greatly affected by environmental
 change, and the leaf N and P content by unit area varied greatly by life
 history stage. A. mono leaf N-P utilization showed a significant
 allometric growth trend in all life history stages and at low altitudes.
 The adult stage had higher N-use efficiency than the seedling stage and
 exhibited an isometric growth trend at high altitudes. The N-P utilization
 strategies of A. mono leaves are affected by changing environmental
 conditions but their response is further dependent upon the life history
 stage of the plant. Thus, this study provides novel insights into the
 nutrient use strategies of A. mono and how they respond to the
 environmental temperature, soil moisture content along altitude and how
 these changes differ among different life history stages, which further
 provide the scientific basis for the study of plant nutrient utilization
 strategy on regional scale.
DOI: 10.5061/dryad.2fqz612kc
title: Colonization history of the Canary Islands endemic Lavatera acerifolia, (Malvaceae) unveiled with Genotyping-by-Sequencing data and niche modeling

description: Aim Differentiation of island lineages from mainland relatives and
 radiation after initial colonization are two important processes
 generating island diversity. Both of these processes are influenced by
 colonization dynamics and contemporary connections between island species
 and their source populations. The classic island progression rule model,
 i.e., dispersal from mainland to older islands and subsequently to younger
 islands, can be considered a null hypothesis, particularly for islands
 that are geographically aligned perpendicular to the mainland coast with
 ages inversely proportional to distance from the mainland. Alterations to
 this pattern have been reported, particularly in archipelagoes that are
 geographically closely adjacent to mainland source populations. Here we
 aim to integrate genomic and environmental niche data to infer the
 colonization history of a Canary endemic species and to understand its
 current diversity patterns. Location Canary Islands. Taxon Lavatera
 acerifolia (Malvaceae). Methods We used high-throughput
 genotyping-by-sequencing (GBS) combined with species distribution
 modelling (SDM) projected onto past conditions. Genetic structure
 (clustering methods), relatedness (coalescent and ML trees), nucleotide
 diversity and differentiation (population genetics) were assessed based on
 SNPs obtained from three alternative bioinformatics pipelines. The
 influence of environmental variables over time was assessed with a GLM in
 which the response variable was amount of heterozygous sites per
 individual. Results Four genetic groups were identified arranged along a
 longitudinal gradient, and the earliest diverging coincides with the
 older, and easternmost, islands (Lanzarote and Fuerteventura). Genetic
 diversity is reduced in the westernmost islands, which are more distant
 from the mainland, host few populations and yet apparently offer more
 suitable habitats. Main conclusions The inferred colonization scenario
 generally fits the progression rule model, but suggests a more complex
 pattern for the central islands. For the westernmost islands, the contrast
 between high availability of suitable habitats and reduced genetic
 diversity and number of populations suggests a colonization front moving
 at a slow pace, rather than local extinctions, as an explanation for the
 scarcity of populations in those islands. Historical projections of SDM
 lend support to this interpretation.
description: Dataset consists of genomic data generated in vcf format.
DOI: 10.5061/dryad.h44j0zpfq
title: Data from: Nasopharyngeal microbiome profiles in rural Venezuelan children are associated with respiratory and gastrointestinal infections

description: Background: Recent research suggests that the microbiota affects
 susceptibility to both respiratory tract infections (RTIs) and
 gastrointestinal infections (GIIs). In order to optimize global treatment
 options, it is important to characterize microbiota profiles across
 different niches and geographic/socioeconomic areas where RTI and GII
 prevalences are high. Methods: We performed 16S sequencing of
 nasopharyngeal swabs from 209 Venezuelan Amerindian children aged 6
 weeks–59 months who were participating in a 13-valent pneumococcal
 conjugate vaccine (PCV13) study. Using random forest models, differential
 abundance testing, and regression analysis, we determined whether specific
 bacteria were associated with RTIs or GIIs and variation in PCV13
 response. Results: Microbiota compositions differed between
 children with or without RTIs (P = .018) or GIIs (P = .001). Several
 species were associated with the absence of infections. Some of these
 health-associated bacteria are also observed in developed regions, such as
 Corynebacterium (log2(fold change [FC]) = 3.30 for RTIs and log2(FC) =
 1.71 for GIIs), while others are not commonly observed in developed
 regions, such as Acinetobacter (log2(FC) = 2.82 and log2(FC) = 5.06,
 respectively). Klebsiella spp. presence was associ- ated with both RTIs
 (log2(FC) = 5.48) and GIIs (log2(FC) = 7.20). Conclusions: The
 nasopharyngeal microbiota of rural Venezuelan children included several
 bacteria that thrive in tropical humid climates. Interestingly,
 nasopharyngeal microbiota composition not only differed in children with
 an RTI but also in those with a GII, which suggests a reciprocal interplay
 between the 2 environments. Knowledge of region-specific microbiota
 patterns enables tailoring of preventive and therapeutic approaches.
DOI: 10.15468/dl.ybuzqd
title: Occurrence Download

description: A dataset containing 251 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Solena heterophylla",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 251 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002078-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.0rxwdbrvq
title: Illumina SNP Chip and Sequenom MassARRAY genotype data of Swedish Giant Schnauzers with and without hypothyroidism

description: In this study, we sought to identify the genetic risk factors potentially
 involved in the susceptibility to hypothyroidism in the high-risk Giant
 Schnauzer dog breed. The genotype data generated in the study (Illumina
 170k CanineHD Bead Chip, Sequenom MassARRAY high-throughput re-genotyping)
 proved to be essential for the identification and fine-mapping of a locus
 associated with protection against canine hypothyroidism.
description: See Readme file