cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2sp72
title: Data from: Autoantibody prevalence in active tuberculosis: reactive or pathognomonic?

description: Objectives: To evaluate the autoantibody in patients without corresponding
 symptoms, whether these autoantibody are pathognomonic or not. We
 hypothesised that autoantibody may be reactive to chronic infection, such
 as tuberculosis (TB). Design: Randomised, case–control cohort study.
 Setting: A tertiary centre in Taiwan. Participants: We randomly chose 100
 patients out of the data bank of patients with TB in a tertiary medical
 centre. All patients completed the sera sampling. We chose 100 patients
 according to autoantibody prevalence in previous literature. We also chose
 100 medical staff as control group. Interventions: We tested anti-SSA,
 anti-SSB, anti-Sm, anti ribonucleoprotein, anti-Scl 70, anticentromere,
 anti-double-stranded DNA, anticardiolipin IgG and IgM in all patient and
 control groups. The clinical symptoms and the underlying disease were all
 recorded. Primary and secondary outcome measures: The result of sera
 antibody titre was recorded. For those with specific positive serology
 results, following examination was carried out after a 3-month anti-TB
 medication. Results: Anticardiolipin IgG titre was significantly higher in
 patients with TB than in control group. We compared the result with
 previous population study and found that anti-Scl70 is also significantly
 higher in patients with TB. The following up data in anti-Scl70 revealed
 decreased titre after treatment. No correlation between sera titre and
 clinical conditions was observed. Conclusions: In TB endemic areas, a
 significant proportion (32%) of patients with TB have elevated
 autoantibody titres, especially anticardiolipin IgG and anti-Scl-70.
 Mycobacterial studies should be performed in patients with elevated serum
 autoantibody titres but without the typical or multiple manifestations of
 autoimmune diseases. Trial registration: The study was approved by the
 Institutional Review Board of the hospital (NTUH REC: 9561707008) after
 informed consent had been obtained from the patients.
description: Primary data
 數字resultThe ELISA result of
 autoantibodies of active TB patientsNormal population ENA
 primary resultThe ELISA result of
 autoantibodies from control population
DOI: 10.5061/dryad.mn17p
title: Data from: A 1,000-year-old antimicrobial remedy with antistaphylococcal activity

description: Plant-derived compounds and other natural substances are a rich potential
 source of compounds that kill or attenuate pathogens that are resistant to
 current antibiotics. Medieval societies used a range of these natural
 substances to treat conditions clearly recognizable to the modern eye as
 microbial infections, and there has been much debate over the likely
 efficacy of these treatments. Our interdisciplinary team, comprising
 researchers from both sciences and humanities, identified and
 reconstructed a potential remedy for Staphylococcus aureus infection from
 a 10th century Anglo-Saxon leechbook. The remedy repeatedly killed
 established S. aureus biofilms in an in vitro model of soft tissue
 infection and killed methicillin-resistant S. aureus (MRSA) in a mouse
 chronic wound model. While the remedy contained several ingredients that
 are individually known to have some antibacterial activity, full efficacy
 required the combined action of several ingredients, highlighting the
 scholarship of premodern doctors and the potential of ancient texts as a
 source of new antimicrobial agents.
description: Effect of Bald's
 eyesalve and its constituent ingredients on S. aureus in vitro and in
 vivo.Data presented in Figs
 2-5 and Fig S1 of Harrison et al, mBio 2015. Each worksheet contains a)
 raw data and b) annotated R code for a single figure.Harrison_mBio2015.xls
DOI: 10.5061/dryad.ff868
title: Data from: Kin selection, not group augmentation, predicts helping in an obligate cooperatively breeding bird

description: Kin selection theory has been the central model for understanding the
 evolution of cooperative breeding, where non-breeders help bear the cost
 of rearing young. Recently the dominance of this idea has been questioned;
 particularly in obligate cooperative breeders where breeding without help
 is uncommon and seldom successful. In such systems, the direct benefits
 gained through augmenting current group size have been hypothesised to
 provide a tractable alternative (or addition) to kin selection. However,
 clear empirical tests of the opposing predictions are lacking. Here, we
 provide convincing evidence to suggest that kin selection and not group
 augmentation accounts for decisions of whether, where and how often to
 help in an obligate cooperative breeder, the chestnut-crowned babbler
 (Pomatostomus ruficeps). We found no evidence that group members base
 helping decisions on the size of breeding units available in their social
 group, despite both correlational and experimental data showing
 substantial variation in the degree to which helpers affect productivity
 in units of different size. By contrast, 98% of group members with kin
 present helped, 100% directed their care towards the most related brood in
 the social group and those rearing half/full-sibs helped approximately 3
 times harder than those rearing less/non-related broods. We conclude that
 kin selection plays a central role in the maintenance of cooperative
 breeding in this species, despite the apparent importance of living in
 large groups.
description: breeding
 successThese data were used to
 analyse the effect of the number of individuals present in each unit on
 the number of fledglings produced per unit per year.group feeding
 rateThese data were used to
 analyse the effect of experimentally enlarged and reduced broods on the
 per capita feeds (feeds/chick/hour) provided by the
 unit.individual
 contributionsThese data were used to
 analyse the effect of relatedness to recipient and breeding unit size on
 individual feeding rates.
DOI: 10.5061/dryad.79gq3
title: Data from: Saturating effects of species diversity on life-history evolution in bacteria

description: Species interactions can play a major role in shaping evolution in new
 environments. In theory, species interactions can either stimulate
 evolution by promoting coevolution or inhibit evolution by constraining
 ecological opportunity. The relative strength of these effects should vary
 as species richness increases, and yet there has been little evidence for
 evolution of component species in communities. We evolved bacterial
 microcosms containing between 1 and 12 species in three different
 environments. Growth rates and yields of isolates that evolved in
 communities were lower than those that evolved in monocultures, consistent
 with recent theory that competition constrains species to specialize on
 narrower sets of resources. This effect saturated or reversed at higher
 levels of richness, consistent with theory that directional effects of
 species interactions should weaken in more diverse communities. Species
 varied considerably, however, in their responses to both environment and
 richness levels. Mechanistic models and experiments are now needed to
 understand and predict joint evolutionary dynamics of species in diverse
 communities.
description: FiegnaEvoAssayTable of data from assays of the growth of bacterial isolates over 96 hours. Species gives a number for the focal isolate, mix is the community composition, replicate indicates 3 experimental replicates, diversity is the number of species in the starting culture of the community, environment indicates the growth medium, survival indicates whether the focal isolate could be extracted from the final community or not, sp2 to sp63 indicate which other species were present in the final community, T0 to T96 are the number of cells per ml of each isolate during the growth assays, Div.end is the final number of species recovered from each community.
DOI: 10.5061/dryad.vf71t
title: Data from: Divergence and molecular variation in common whelk Buccinum undatum (Buccinidae) in Iceland: a trans-Atlantic comparison

description: The dispersal and history of species affects their genetic population
 structure at both small and large geographical scales. The common whelk,
 Buccinum undatum, is a widespread subtidal gastropod in the North Atlantic
 that has no planktonic larvae and has thus limited dispersal capacity. The
 snail, which has been harvested by humans for centuries, is highly
 variable in morphology. To evaluate the population structure in the rich
 fishing grounds in western Iceland and its divergence from samples across
 the Atlantic, genetic patterns based on sequence variation in two mtDNA
 genes (COI and 16S) and five microsatellites were studied and compared to
 variation in populations from both sides of the Atlantic. Significant
 differences in allele and haplotype frequencies were found among samples
 separated by short distances along the coast of Iceland. Partition of the
 variation showed larger variance among samples obtained from distant
 regions than from neighbouring sites and genetic distances were correlated
 with geographical distance among populations in Europe. Phylogeographic
 patterns in mtDNA reveal different monophyletic lineages on both sides of
 the Atlantic, which predate the onset of the Ice-age and which may
 constitute cryptic species. Similar micro- and macrogeographic patterns
 were observed for the mtDNA and microsatellite markers despite high
 frequencies of null alleles. Bayesian skyline reconstructions of the
 demographic history and mismatch distributions suggest that while sizes of
 some populations were unaffected by Ice Age glaciations others show signs
 of expansion after the last glacial maximum. These phylogeographic
 patterns are consistent with patterns expected for low dispersal species
 that have survived in allopatric glacial refugial populations on both
 sides of the Atlantic and in deep-sea refugia within each continent. The
 observed genetic structure has implications for conservation and
 sustainable management of the harvested populations.
description: Microsatellites in
 Common whelkGenepop format, five
 loci: bu67, bu119, bu122, bu145, bu151. Populations: Britain (BR), Faeroe
 Islnds (FE), Greenland (GR1-4), Canada (CA), Iceland: Faxafloi (FA),
 Hempill (HE), Hruteyjar (HR), Oddbjarnarsker (OD), Hunafloi
 (HF)bk2.datmtDNA_haplfreqfrequencies of mtDNA (COI and 16S) haplotypes with genbank accession numbers
DOI: 10.5061/dryad.45sp7nr
title: Data from: The sickle cell trait affects contact dynamics and endothelial cell activation in Plasmodium falciparum-infected erythrocytes

description: Sickle cell trait, a common hereditary blood disorder, protects carriers
 from severe disease in infections with the human malaria parasite
 Plasmodium falciparum. Protection is associated with a reduced capacity of
 parasitized erythrocytes to cytoadhere to the microvascular endothelium
 and cause vaso-occlusive events. However, the underpinning cellular and
 biomechanical processes are only partly understood and the impact on
 endothelial cell activation is unclear. Here, we show, by combining
 quantitative flow chamber experiments with multiscale computer simulations
 of deformable cells in hydrodynamic flow, that parasitized erythrocytes
 containing the sickle cell haemoglobin displayed altered adhesion
 dynamics, resulting in restricted contact footprints on the endothelium.
 Main determinants were cell shape, knob density and membrane bending. As a
 consequence, the extent of endothelial cell activation was decreased. Our
 findings provide a quantitative understanding of how the sickle cell trait
 affects the dynamic cytoadhesion behavior of parasitized erythrocytes and,
 in turn, endothelial cell activation.
description: Data for
 10.1038/s42003-018-0223-3This excel file contains
 the original data underlying the display items presented in the manuscript
 and the supplementary information.COMMSBIO-18-0696A
 (1).xlsx
DOI: 10.5061/dryad.p6130
title: Data from: Reduced incompatibility in the production of second generation hybrids between two Magnolia species revealed by Bayesian gene dispersal modeling

description: PREMISE OF THE STUDY: Hybrid zones are areas where gene flow between
 related species is currently occurring, so information on the
 compatibility between related species and their hybrids is essential for
 predicting the dynamics of such zones generated by introgressive
 hybridization. In this study, we quantified the compatibility among
 Magnolia stellata, M. salicifolia and their hybrids in a hybrid zone using
 gene dispersal modeling. METHODS: After determining the genealogical
 classes of adult trees in the hybrid zone, a paternity analysis of 574
 open pollinated seeds from 37 known maternal trees was performed with
 microsatellite markers. A neighborhood-based Bayesian gene dispersal model
 developed by us for estimating compatibility was then applied to the
 paternity data. KEY RESULTS: When M. stellata or M. salicifolia were
 mothers, interspecific mating to produce F1 hybrids yielded significant
 incompatibility but backcrossing with F1 hybrids did not. Furthermore,
 when F1 hybrids became mothers, no significant incompatibility resulted
 from backcrossing to parental species or intra-F1 mating to produce F2
 hybrids. The estimated proportion of F1 hybrids in the outcrossed seeds
 (1.7%) in the hybrid zone was much lower than that in the adult trees
 (14.0%). CONCLUSIONS: While it is difficult to obtain F1 hybrids, their
 low incompatibility makes it easy to produce advanced generation hybrids,
 once they have been successfully obtained. Although the production of F1
 seeds is rare, heterosis and/or weak selection pressure in an empty niche
 between the parental species' niches may have contributed to the
 increased proportion of adult F1 hybrids in the hybrid zone.
description: Data_and_script_for_AJB_IT170914Genotype and ecological data sets, and R scripts used in this study
DOI: 10.5061/dryad.hn11m
title: Data from: Unexpected population genetic structure of European roe deer in Poland: an invasion of the mtDNA genome from Siberian roe deer

description: Introgressive hybridization is a widespread evolutionary phenomenon which
 may lead to increased allelic variation at selective-neutral loci and to
 transfer of fitness-related traits to introgressed lineages. We inferred
 the population genetic structure of the European roe deer (Capreolus
 capreolus) in Poland from mitochondrial (CR and cyt b) and sex-linked
 markers (ZFX, SRY, DBY4 and DBY8). Analyses of CR mtDNA sequences from 452
 individuals indicated widespread introgression of Siberian roe deer (C.
 pygargus) mtDNA in the European roe deer genome, 2000 km from the current
 distribution range of C. pygargus. Introgressed individuals constituted
 16.6% of the deer studied. Nearly 75% of them possessed haplotypes
 belonging to the group which arose 23 kyr ago and have not been detected
 within the natural range of Siberian roe deer, indicating that majority of
 present introgression has ancient origin. Unlike the mtDNA results,
 sex-specific markers did not show signs of introgression. Species
 distribution modelling analyses suggested that C. pygargus could have
 extended its range as far west as Central Europe after LGM. The main
 hybridization event was probably associated with range expansion of the
 most abundant European roe deer lineage from western refugia and took
 place in Central Europe after the Younger Dryas (10.8–10.0 ka BP).
 Initially introgressed mtDNA variants could have spread out on the wave of
 expansion through the mechanism of gene surfing, reaching high frequencies
 in European roe deer populations and leading to observed asymmetrical gene
 flow. Human-mediated introductions of C. pygargus had minimal effect on
 the extent of mtDNA introgression.
description: DISTLM_input_filesDISTLM input filesDISTLM_Forward_input_filesDISTLM Forward input filesSex-linked_markers_-_alignmentAlignment files for sex-linked markers: ZFX gene intron 9; concatenated sequences of SRY, DBY4 and DBY8mtDNA_-_alignment_and_tree_filesAlignment files for mtDNA: Control Region, cytochrome b and concatenated sequences of CR and cytb. Tree files are provided with additional Supporting information.
DOI: 10.5061/dryad.231b9
title: Data from: Ecological speciation by temporal isolation in a population of the stonefly Leuctra hippopus (Plecoptera, Leuctridae)

description: Stream dwelling invertebrates are ideal candidates for the study of
 ecological speciation as they are often adapted to particular
 environmental conditions within a stream and inhabit only certain reaches
 of a drainage basin, separated by unsuitable habitat. We studied an
 atypical population of the stonefly Leuctra hippopus at a site in central
 Norway, the Isterfoss rapids, in relation to three nearby and two remote
 conspecific populations. Adults of this population emerge about a month
 earlier than those of nearby populations, live on large boulders emerging
 from the rapids, and are short-lived. This population also has distinct
 morphological features and was studied earlier during the period
 1975–1990. We reassessed morphological distinctness with new measurements
 and added several analyses of genetic distinctness based on mitochondrial
 and nuclear sequence markers, as well as AFLP fingerprinting and SNPs
 mined from RAD sequences. The Isterfoss population is shown to be most
 closely related to its geographical neighbors, yet clearly morphologically
 and genetically distinct and homogeneous. We conclude that this population
 is in the process of sympatric speciation, with temporal isolation being
 the most important direct barrier to gene flow. The shift in reproductive
 season results from the particular temperature and water level regime in
 the Isterfoss rapids. The distinct adult body shape and loss of flight are
 hypothesized to be an adaptation to the unusual habitat. Ecological
 diversification on small spatial and temporal scales is one of the likely
 causes of the high diversity of aquatic insects.
description: Data from: Ecological
 speciation by temporal isolation in a population of the stonefly Leuctra
 hippopus (Plecoptera, Leuctridae)Data from the paper
 "Ecological speciation by temporal isolation in a population of the
 stonefly Leuctra hippopus (Plecoptera, Leuctridae)", by Boumans,
 Hogner, Brittain & Johnsen. Ecology and Evolution: xxx. DOI: xxx.
 Included are the following files: Files used in the software program
 STRUCTURE, for different subsets of the data (see paper): -AFLP_data.csv
 -RAD matrix 1.csv -RAD matrix 1a.csv -RAD matrix 2.csv -RAD matrix 2a.csv
 Samples sorted by % missing data for the above four RAD matrices: -Samples
 sorted by missing data.csv Stacks sumstats output files for Matrix 1a and
 2a: -Stacks_sumstats_output_RAD_data_matrix 1a.csv
 -Stacks_sumstats_output_RAD_data_matrix 2a.csvLeuctra_hippopus.zip
DOI: 10.5061/dryad.b1k0v
title: Data from: How well are national guidelines relating to the general sales of aspirin and paracetamol, adhered to by retail stores: a mystery shopper study

description: Objective: To determine whether non-pharmaceutical retail outlets are
 aboding to the current Medicines and Healthcare products Regulatory Agency
 (MHRA) national guidelines for over-the-counter (OTC) sales of aspirin and
 paracetamol. Methods: Stages 1 and 2 of the study deployed eight and four
 medical students, respectively, to undertake a mystery shopper style
 investigation. Stage 1: eight medical students attempted to buy ≥96
 tablets/capsules aspirin or paracetamol in one transaction in 62 shops.
 Stage 2: four medical students attempted to purchase 32 paracetamol 500 mg
 along with a ‘flu remedy preparation also containing paracetamol, in 54
 shops. Results: Stage 1 data revealed that 58% and 57% retailers sold more
 than the MHRA guidelines recommended for paracetamol and aspirin,
 respectively. We observed that 23% and 28% retailers were willing to sell
 ≥96 tablets of paracetamol or aspirin with no questions asked. Stage 2
 results showed that 57% retailers sold 32×500 mg paracetamol in
 conjunction with a paracetamol-containing ‘flu preparation; while 98%
 shops sold 16×paracetamol 500 mg along with a paracetamol-containing ‘flu
 remedy, with no questions asked of the shopper or advice given.
 Discussion: MHRA national guidelines for OTC medicines sales appear to be
 poorly adhered to in non-pharmacy shops. Sales of aspirin and paracetamol
 OTC must be better regulated in the UK to ultimately reduce morbidity and
 mortality rates of deliberate and accidental overdoses.
description: Average quantity of
 paracetamol and aspirin purchased in one transactionTables 1 and
 2.docx
DOI: 10.5061/dryad.224hj
title: Data from: Adaptive credible intervals on stratigraphic ranges when recovery potential is unknown

description: Numerous methods exist for estimating the true stratigraphic range of a
 fossil taxon based on the stratigraphic positions of its fossil
 occurrences. Many of these methods require the assumption of uniform
 fossil recovery potential—that fossils are equally likely to be found at
 any point within the taxon's true range. This assumption is
 unrealistic, because factors such as stratigraphic architecture, sampling
 effort, and the taxon's abundance and geographic range affect
 recovery potential. Other methods do not make this assumption, but they
 instead require a priori quantitative knowledge of recovery potential that
 may be difficult to obtain. We present a new Bayesian method, the Adaptive
 Beta method, for estimating the true stratigraphic range of a taxon that
 works for both uniform and non-uniform recovery potential. In contrast to
 existing methods, we explicitly estimate recovery potential from the
 positions of the occurrences themselves, so that a priori knowledge of
 recovery potential is not required. Using simulated datasets, we compare
 the performance of our method with existing methods. We show that the
 Adaptive Beta method performs well in that it achieves or nearly achieves
 nominal coverage probabilities and provides reasonable point estimates of
 the true extinction in a variety of situations. We demonstrate the method
 using a dataset of the Cambrian mollusc Anabarella.
description: Version of Fig. 5
 accessible to color-deficient readersBlack-and-white version
 of Figure 5.fig5bw.pdfVersion of Fig. 6 accessible to color-deficient readersBlack and white version of Figure 6.fig6bw.pdfR codeR code for Adaptive Beta Method (v38.0)Wang et al 2015 ABM code.txt