cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fb5hk394
title: Data from: Types, levels, and patterns of low-copy DNA sequence divergence, and phylogenetic implications, for Gossypium genome types

description: To explore types, levels, and patterns of genetic divergence among diploid
 Gossypium (cotton) genomes, 780 cDNA, genomic DNA, and SSR loci were
 re-sequenced in Gossypium herbaceum (A1 genome), G. arboreum (A2), G.
 raimondii (D5), G. trilobum (D8), G. sturtianum (C1) and an outgroup,
 Gossypioides kirkii. Divergence among these genomes ranged from 7.32
 polymorphic base pairs per 100 between G. kirkii and G. herbaceum (A1) to
 only 1.44 between G. herbaceum (A1) and G. arboreum (A2). SSR loci are
 least conserved with 12.71 polymorphic base pairs and 3.77 polymorphic
 sites per 100 base pairs, while ESTs are most conserved with 3.96
 polymorphic base pairs and 2.06 sites. SSR loci also exhibit the highest
 percentage of 'extended polymorphisms' (spanning multiple
 consecutive nucleotides). The A genome lineage was particularly rapidly
 evolving, with the D genome also showing accelerated evolution relative to
 the C genome. Unexpected asymmetry in mutation rates was found, with much
 more transition than transversion mutation in the D genome after its
 divergence from a common ancestor shared with the A genome. This large
 quantity of orthologous DNA sequence strongly supports a phylogeny in
 which A-C divergence is more recent than A-D divergence, a subject that is
 of much importance in view of A-D polyploid formation being key to the
 evolution of the most productive and finest-quality cottons. Loci that are
 monomorphic within A or D genome types, but polymorphic between genome
 types, may be of practical importance for identifying locus-specific DNA
 markers in tetraploid cottons including leading cultivars.
description: Supplemental
 FiguresThis file includes three
 supplemental figures which are related to the paper. The figure legends
 are given below each figure.Spplemental
 Figure.docSpplemental
 Figure.pdfSupplemental
 TablesThis file includes four
 supplemental tables which are relevant to the paper. The supplemental
 table 1 lists the locus name, GenBank accession number, primer sequence
 and annealing temperature for all loci studied in this research.
 Supplemental table 2 is about the diversities revealed in the pair wise
 comparison including extended and single deletion, insertion, SNP,
 polymorphic sites, and polymorphic base pairs. Supplemental table 3 is
 about SNPs, polymorphic sites, and polymorphic base pairs between A and D
 ancestral genomes. Supplemental table 4 is about diversities revealed in
 the three way comparison including extended and single deletion,
 insertion, SNP, polymorphic sites, and polymorphic base
 pairs.
DOI: 10.5061/dryad.br760
title: Data from: Transmission of multidrug-resistant and drug-susceptible tuberculosis within households: a prospective cohort study

description: Background: The “fitness” of an infectious pathogen is defined as the
 ability of the pathogen to survive, reproduce, be transmitted, and cause
 disease. The fitness of multidrug-resistant tuberculosis (MDRTB) relative
 to drug-susceptible tuberculosis is cited as one of the most important
 determinants of MDRTB spread and epidemic size. To estimate the relative
 fitness of drug-resistant tuberculosis cases, we compared the incidence of
 tuberculosis disease among the household contacts of MDRTB index patients
 to that among the contacts of drug-susceptible index patients. Methods and
 Findings: This 3-y (2010–2013) prospective cohort household follow-up
 study in South Lima and Callao, Peru, measured the incidence of
 tuberculosis disease among 1,055 household contacts of 213 MDRTB index
 cases and 2,362 household contacts of 487 drug-susceptible index cases. A
 total of 35/1,055 (3.3%) household contacts of 213 MDRTB index cases
 developed tuberculosis disease, while 114/2,362 (4.8%) household contacts
 of 487 drug-susceptible index patients developed tuberculosis disease. The
 total follow-up time for drug-susceptible tuberculosis contacts was 2,620
 person-years, while the total follow-up time for MDRTB contacts was 1,425
 person-years. Using multivariate Cox regression to adjust for confounding
 variables including contact HIV status, contact age, socio-economic
 status, and index case sputum smear grade, the hazard ratio for
 tuberculosis disease among MDRTB household contacts was found to be half
 that for drug-susceptible contacts (hazard ratio 0.56, 95% CI 0.34–0.90, p
 = 0.017). The inference of transmission in this study was limited by the
 lack of genotyping data for household contacts. Capturing incident disease
 only among household contacts may also limit the extrapolation of these
 findings to the community setting. Conclusions: The low relative fitness
 of MDRTB estimated by this study improves the chances of controlling
 drug-resistant tuberculosis. However, fitter multidrug-resistant strains
 that emerge over time may make this increasingly difficult.
description: Transmission of
 Multidrug-Resistant and Drug Susceptible Tuberculosis Within Households: A
 Prospective Cohort StudyStudy
 DatabaseHousehold_Study_Database.xlsx
DOI: 10.5061/dryad.6356f
title: Data from: Hidden shift of the ionome of plants exposed to elevated CO2 depletes minerals at the base of human nutrition

description: Mineral malnutrition stemming from undiversified plant-based diets is a
 top global challenge. In C3 plants (e.g., rice, wheat), elevated
 concentrations of atmospheric carbon dioxide (eCO2) reduce protein and
 nitrogen concentrations, and can increase the total nonstructural
 carbohydrates (TNC; mainly starch, sugars). However, contradictory
 findings have obscured the effect of eCO2 on the ionome - the mineral and
 trace-element composition - of plants. Consequently, CO2-induced shifts in
 plant quality have been ignored in the estimation of the impact of global
 change on humans. This study shows that eCO2 reduces the overall mineral
 concentrations (-8%, 95% confidence interval: -9.1 to -6.9, p
 carbon:minerals in C3 plants. The meta-analysis of 7,761 observations,
 including 2,264 observations at state of the art FACE centers, covers 130
 species/cultivars. The attained statistical power reveals that the shift
 is systemic and global. Its potential to exacerbate the prevalence of
 'hidden hunger' and obesity is discussed.
description: CO2 Dataset (CSV
 format)The dataset of elevated
 CO2 effects on the concentration of chemical elements in foliar and edible
 tissues of crops and wild plants. This file is in CSV format and
 made-ready for analysis with statistical package such as R. The same data
 can also be found in XLSX format for easy viewing (decreases are blue,
 increases are red) as another file posted here.co2df.csvCO2 Dataset (XLSX format)The dataset of elevated CO2 effects on the concentration of chemical elements in foliar and edible tissues of crops and wild plants. This file is in XLSX format for easy viewing (decreases are blue, increases are red). The same data can also be found in CSV format made-ready for analysis with statistical package such as R.CO2 Dataset.xlsxTable S1This table provides supportive data for Figures 1-8 and contains the outcomes of statistical analyses of various data subsets. It consists of two sheets: Results and ReadMe.R Code for the CO2 datasetpwr.boot.R
DOI: 10.5061/dryad.7p1r30q5
title: Data from: Efficacy and safety of four weeks’ treatment with combined fluticasone furoate/vilanterol in a single inhaler given once daily in COPD: a placebo-controlled randomised trial

description: BACKGROUND: Fluticasone furoate/vilanterol (FF/VI) is a novel once-daily
 (OD) inhaled corticosteroid/long-acting β2 agonist combination in
 development for chronic obstructive pulmonary disease (COPD) and asthma.
 TRIAL DESIGN: A multicentre, randomised, double-blind, parallel-group,
 placebo-controlled study. METHODS: Participants were patients with
 moderate-to-severe COPD treated with placebo or FF/VI 400/25 μg OD for 4
 weeks. Study objectives were to assess the safety and efficacy of FF/VI
 400/25 μg OD administered for 4 weeks via a novel dry powder inhaler.
 Co-primary end points were change from baseline in weighted mean (wm)
 heart rate 0–4 h postdose at day 28 and the incidence of adverse events
 (AEs). Secondary end points included change from baseline in trough forced
 expiratory volume in one second (FEV1) (23–24 h postdose; day 29) and wm
 FEV1 (0–4 h postdose; day 28). Patients were randomised to receive FF/VI
 400/25 μg or placebo in a 2:1 ratio; all patients and investigators were
 blinded to active or placebo treatment. RESULTS: 60 patients (mean age 64
 years) were randomised (FF/VI: n=40; placebo: n=20), and all contributed
 data to the analysis. Mean screening post-bronchodilator FEV1 per cent
 predicted was comparable between groups (FF/VI: 58.5%; placebo: 60.1%).
 The wm heart rate 0–4 h postdose was similar between groups (difference:
 0.6 beats per minute; 95% CI −3.9 to 5.1). More on-treatment AEs were
 reported in the FF/VI group (68%) compared with the placebo group (50%).
 The most common drug-related AEs in the FF/VI group were oral candidiasis
 (8%) and dysphonia (5%). There were no clinically relevant effects on
 laboratory values, including glucose and potassium, or on vital signs or
 ECGs/Holters. The FF/VI group had statistically greater improvements
 compared with placebo in trough FEV1 (mean difference 183 ml) and 0–4 h
 postdose wm FEV1 (mean difference 236 ml). CONCLUSION: FF/VI has a good
 safety and tolerability profile and improves lung function compared with
 placebo in patients with COPD.
description: FF-VI_348_study_Dryad-DATA
DOI: 10.5061/dryad.2pf35
title: Data from: Rapid morphological changes, admixture and invasive success in populations of Ring-necked parakeets (Psittacula krameri) established in Europe

description: The Ring-necked parakeet (Psittacula krameri), native of Asia and Africa,
 is a very successful invasive species in Europe: it has been present there
 for over 50 years. A recent study showed that European invasive
 populations occupy a colder climatic niche than in their native range but
 the establishment of this tropical species in temperate regions remains
 unexplained. Two main hypotheses may explain the success of Ring-necked
 parakeet in Europe: admixture between individuals from different origins
 and/or rapid adaptation to new environmental conditions. In this study, we
 investigated with molecular data the origin of European populations of
 Ring-necked parakeets to assess whether these populations result from
 admixture between individuals from different source populations. We also
 investigated the morphology of individuals from European populations and
 from the native range to assess whether the invasive populations have
 morphologically diverged from their source and could have become adapted
 to European conditions. We found evidence of admixture in some of the
 European populations but not all of them. Admixture between individuals
 from different origins within European populations thus cannot explain
 alone their invasive success. Conversely, we found that the morphology of
 the individuals from European populations has diverged from the morphology
 of native individuals, in a similar direction. Rapid adaptation to
 European environmental conditions via phenotypic plasticity or natural
 selection could thus be a factor explaining the invasive success of
 Ring-necked parakeets in Europe.
description: list of the samples used
 in the phylogenyGives for each sample
 used in the phylogeny, its ID number, species, subspecies, country and
 locality of capture, and the Genbank access number of the sequence
 used.list_of_samples_phylogeny.xlsxCytB sequences psittacula krameriGives the cytB sequences that were used in the phylogeny.CytB_sequences_psittacula_krameri.xlsxmicrosatellite data setGives the microsatellite profiles of each individuals used in the population genetics analyses.msat_data_set_psittacula_krameri.xlsxtraditional morphometric measurementsGives the raw morphological measurements taken on individuals from the native and invasive ranges and used in the traditional morphometric analysis.morphometric_data_traditional_psittacula_krameri.xlsxgeometric morphometric dataGives the morphological variables taken on individuals from the native and invasive ranges and used in the geometric morphometric analysis.morphometric_data_geometric_psittacula_krameri.xlsx
DOI: 10.15468/dl.jmj8j3
title: Occurrence Download

description: A dataset containing 108351 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Orchis militaris"
 ]
}

 The dataset includes 108351 records from 624 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000552-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15482/usda.adc/26877439
title: Data from: Tracking Individual <i>Bactrocera tryoni </i>(Diptera: Tephritidae): Wind Effects and Natural Movement

description: Determining the natural movement parameters of pest insects, such as tephritid fruit flies, is critical to developing models that can be used to increase the effectiveness of control and surveillance strategies. In this study, two experiments were conducted using harmonic radar to track wild-caught male Queensland fruit flies (Qflies), <i>Bactrocera tryoni</i>, a major horticultural pest in Australia. Experiment 1 continuously tracked individual flies which were prodded to induce movement in a high-density papaya field. Experiment 2 was conducted in a field with lower papaya density and tracked flies were allowed to move without disturbance. This latter natural movement experiment showed that Qfly move at a rate of 19 ± 3 m/h. In both experiments, overall and between-tree flight directions were found to be correlated with wind direction while within-tree movement directions were not. Further, the effect of wind direction on fly trajectories varied by step-distance but not strongly with wind speed while step-distance distributions were consistent with Lévy walks. Qfly movements were well fitted by two-state hidden Markov models further supporting the observation that Qflies move differently within (short steps with random direction) and between (longer more directional steps) trees. Data on flight directionality, step-distances, and movement speed determined in this study provide parameters that may help enhance current surveillance, control, and eradication methods, such as optimizing trap placements and pesticide applications, determining release sites for parasitoids, and setting quarantine boundaries after incursions.
DOI: 10.15482/usda.adc/26877439.v1
title: Data from: Tracking Individual <i>Bactrocera tryoni </i>(Diptera: Tephritidae): Wind Effects and Natural Movement

description: Determining the natural movement parameters of pest insects, such as tephritid fruit flies, is critical to developing models that can be used to increase the effectiveness of control and surveillance strategies. In this study, two experiments were conducted using harmonic radar to track wild-caught male Queensland fruit flies (Qflies), <i>Bactrocera tryoni</i>, a major horticultural pest in Australia. Experiment 1 continuously tracked individual flies which were prodded to induce movement in a high-density papaya field. Experiment 2 was conducted in a field with lower papaya density and tracked flies were allowed to move without disturbance. This latter natural movement experiment showed that Qfly move at a rate of 19 ± 3 m/h. In both experiments, overall and between-tree flight directions were found to be correlated with wind direction while within-tree movement directions were not. Further, the effect of wind direction on fly trajectories varied by step-distance but not strongly with wind speed while step-distance distributions were consistent with Lévy walks. Qfly movements were well fitted by two-state hidden Markov models further supporting the observation that Qflies move differently within (short steps with random direction) and between (longer more directional steps) trees. Data on flight directionality, step-distances, and movement speed determined in this study provide parameters that may help enhance current surveillance, control, and eradication methods, such as optimizing trap placements and pesticide applications, determining release sites for parasitoids, and setting quarantine boundaries after incursions.
DOI: 10.5061/dryad.44nd5
title: Data from: The roles of contact conformity, temperature and displacement amplitude on the lubricated fretting wear of a steel-on-steel contact

description: This paper investigates the effect of contact geometry, temperature and
 displacement amplitude on the fretting behaviour of an aero-turbo oil
 lubricated cylinder-on-flat contact. To be effective, the lubricant needed
 both to penetrate the contact and then offer protection. Lubricant
 penetration into the fretting contact is found to be controlled by two
 physical parameters, namely (i) the width of the contact that remains
 covered throughout the fretting test and (ii) the lubricant viscosity. The
 protection offered by the lubricant (assuming that it has successfully
 penetrated the contact) is influenced by four physical parameters, namely
 (i) lubricant viscosity, (ii) traverse velocity, (iii) nominal contact
 pressure, and (iv) chemical effects. The relationship between the three
 experimental parameters which were varied in the programme of work
 (temperature, fretting displacement and cylinder radius) and physical
 parameters which influence the protection offered by the lubricant film
 can be competing, and therefore complex wear behaviour is observed. The
 roles of the various parameters in controlling the wear behaviour are
 presented in a coherent physical framework.
description: Figure
 DataContains the data on
 which the figures in the paper have been built
DOI: 10.5281/zenodo.18381695
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Timothy Andrew Hammer, https://orcid.org/0000-0003-3816-7933. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
DOI: 10.5061/dryad.2503h
title: Data from: Food provisioning alters infection dynamics in populations of a wild rodent

description: While pathogens are often assumed to limit the growth of wildlife
 populations, experimental evidence for their effects is rare. A lack of
 food resources has been suggested to enhance the negative effects of
 pathogen infection on host populations, but this theory has received
 little investigation. We conducted a replicated two-factor enclosure
 experiment, with introduction of the bacterium Bordetella bronchiseptica
 and food supplementation, to evaluate the individual and interactive
 effects of pathogen infection and food availability on vole populations
 during a boreal winter. We show that prior to bacteria introduction, vole
 populations were limited by food availability. Bordetella bronchiseptica
 introduction then reduced population growth and abundance, but contrary to
 predictions, primarily in food supplemented populations. Infection
 prevalence and pathological changes in vole lungs were most common in food
 supplemented populations, and are likely to have resulted from increased
 congregation and bacteria transmission around feeding stations. Bordetella
 bronchiseptica-infected lungs often showed protozoan co-infection
 (consistent with Hepatozoon erhardovae), together with more severe
 inflammatory changes. Using a multidisciplinary approach, this study
 demonstrates a complex picture of interactions and underlying mechanisms,
 leading to population-level effects. Our results highlight the potential
 for food provisioning to markedly influence disease processes in wildlife
 mammal populations.
description: Vole monitoring
 dataVole data for each
 trapping occasion, inlcuding individual characterisitcs, population
 density, haematological indices and survival.Forbes_VoleData.xlsxVole infection dataVole data for euthanised individuals. Inlcudes infection and co-infection status, and pathological changes.Forbes_InfectionData.xlsx
DOI: 10.15468/dl.uan2zw
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Panochthus greslebini"
 ]
}

 The dataset includes 4 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000584-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.3661174
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Timothy Andrew Hammer, https://orcid.org/0000-0003-3816-7933. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
DOI: 10.5061/dryad.1f6m9
title: Data from: Critical analysis of forest degradation in the southern Eastern Ghats of India: comparison of satellite imagery and soil quality index

description: India has one of the largest assemblages of tropical biodiversity, with
 its unique floristic composition of endemic species. However, current
 forest cover assessment is performed via satellite-based forest surveys,
 which have many limitations. The present study, which was performed in the
 Eastern Ghats, analysed the satellite-based inventory provided by forest
 surveys and inferred from the results that this process no longer provides
 adequate information for quantifying forest degradation in an empirical
 manner. The study analysed 21 soil properties and generated a forest soil
 quality index of the Eastern Ghats, using principal component analysis.
 Using matrix modules and geospatial technology, we compared the forest
 degradation status calculated from satellite-based forest surveys with the
 degradation status calculated from the forest soil quality index. The
 Forest Survey of India classified about 1.8% of the Eastern Ghats’ total
 area as degraded forests and the remainder (98.2%) as open, dense, and
 very dense forests, whereas the soil quality index results found that
 about 42.4% of the total area is degraded, with the remainder (57.6%)
 being non-degraded. Our ground truth verification analyses indicate that
 the forest soil quality index along with the forest cover density data
 from the Forest Survey of India are ideal tools for evaluating forest
 degradation.
description: Soil Quality Index
 DataSoil Parameters used to
 prepare soil quality indexSQI_publish.xlsSpecies diversity in the Eastern GhatsList of species recorded in different hills in the Eastern Ghats of TamilNadurevised species_upload.doc