cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7pc00
title: Data from: Mosaic VSGs and the scale of Trypanosoma brucei antigenic variation

description: A main determinant of prolonged Trypanosoma brucei infection, and hence
 transmission and success of the parasite, is the interplay between host
 acquired immunity and antigenic variation of the parasite variant surface
 glycoprotein (VSG) coat. About 0.1% of trypanosome divisions produce a
 switch to a different VSG through differential expression of an archive of
 hundreds of silent VSG genes and pseudogenes, but the patterns and extent
 of the trypanosome diversity phenotype, particularly in chronic infection,
 are unclear. We applied longitudinal VSG cDNA sequencing to estimate
 variant richness and test whether pseudogenes contribute to antigenic
 variation. We show that individual growth peaks can contain at least 15
 distinct variants, are estimated computationally to comprise many more,
 and that antigenically distinct ‘mosaic’ VSGs arise from segmental gene
 conversion between donor VSG genes or pseudogenes. The potential for
 trypanosome antigenic variation is probably much greater than VSG archive
 size; mosaic VSGs are core to antigenic variation and chronic infection.
description: Alignments of expressed
 VSG sequencesPlease see
 Hall2013_ReadMe.txt for details.Hall2013_ExpressedAlignments.zipBasic copy VSG sequences associated with expressed VSGsPlease see Hall2013_ReadMe.txt for details.Hall2013_ExpressedBasicCopies.zipDetails of expressed VSG sequencesPlease see Hall2013_ReadMe.txt for details.Hall2013_ExpressedClones.xlsxHall2013_ReadMe.txtReadMe file for associated data files.
DOI: 10.5061/dryad.1ns7n
title: Data from: Complex relationships between competing guilds along large-scale environmental gradients

description: Despite much research over the past 30 years, there is still little
 general understanding of how the outcomes of interactions vary along
 environmental gradients, particularly at large geographic scales. A simple
 expectation is that decreasing environmental quality should reduce
 densities of competitors and hence the effects of competition should
 weaken in poorer environments. A counterintuitive consequence is that
 associations between densities of competitors might change from negative
 to positive as environments decrease in quality. Here we test these
 predictions in a set of vascular plant communities where perennial species
 share space and resources with less competitive annuals. We surveyed nine
 gray dune communities annually for 5 years along a cross-European
 latitudinal gradient of habitat quality. We find that densities of annual
 and perennial species are negatively correlated at the high-quality end of
 the gradient, while at the low-quality end, guild densities are
 uncorrelated or positively correlated, consistent with a weakening of
 competition linked to increasing environmental limitations. Our results
 suggest that even simple interactions can give rise to nonobvious changes
 in species associations along environmental gradients. They highlight that
 understanding the outcome of species interactions may require explicit
 characterization of their changing intensity with environmental quality
 and that the factors limiting species’ codistribution can vary along
 environmental gradients.
description: Raw annual and perennial
 abundance dataThis data set contains
 annual abundances for all sites and all years (2008-2012) as well as
 perennial heights in cms (2009-2012) and perennial ground covers as
 percentages (2008-2012). It also contains a column called
 "relationship" which shows the type of relationship found
 between annual abundances and perennial heights (one of positive, negative
 or quadratic) according to the method described in the paper. This data
 was used to produce figures 4, 5, 6, B2 and B4.annual_perennial_abundance.csvEnvironmental data along the latitudinal gradientThis file contains data on the abiotic and biotic conditions experienced by both annual and perennial guilds along the sampled latitudinal gradient. Variables include mean rainfall in mm, temperatures in degree celcius (mean monthly maximum, mean monthly minimum, mean daily), mean sunshine hours in autumn, spring and winter, mean number of rabbit faecal pellets (a proxy for grazing intensity), mean soil nitrogen concentration, as well as mean bryophyte ground cover and mat thickness, and mean correlation between annual abundances and bryophyte ground cover. This data was used to produce figures 3, B1 and B3.environmental_data.csv
DOI: 10.5061/dryad.gj318
title: Data from: Associations among antibiotic and phage resistance phenotypes in natural and clinical Escherichia coli isolates

description: The spread of antibiotic resistance is driving interest in new approaches
 to control bacterial pathogens. This includes applying multiple
 antibiotics strategically, using bacteriophages against
 antibiotic-resistant bacteria, and combining both types of antibacterial
 agents. All these approaches rely on or are impacted by associations among
 resistance phenotypes (where bacteria resistant to one antibacterial agent
 are also relatively susceptible or resistant to others). Experiments with
 laboratory strains have shown strong associations between some resistance
 phenotypes, but we lack a quantitative understanding of associations among
 antibiotic and phage resistance phenotypes in natural and clinical
 populations. To address this, we measured resistance to various
 antibiotics and bacteriophages for 94 natural and clinical Escherichia
 coli isolates. We found several positive associations between resistance
 phenotypes across isolates. Associations were on average stronger for
 antibacterial agents of the same type (antibiotic-antibiotic or
 phage-phage) than different types (antibiotic-phage). Plasmid profiles and
 genetic knockouts suggested that such associations can result from both
 colocalization of resistance genes and pleiotropic effects of individual
 resistance mechanisms, including one case of antibiotic-phage
 cross-resistance. Antibiotic resistance was predicted by core genome
 phylogeny and plasmid profile, but phage resistance was predicted only by
 core genome phylogeny. Finally, we used observed associations to predict
 genes involved in a previously uncharacterized phage resistance mechanism,
 which we verified using experimental evolution. Our data suggest that
 susceptibility to phages and antibiotics are evolving largely
 independently, and unlike in experiments with lab strains, negative
 associations between antibiotic resistance phenotypes in nature are rare.
 This is relevant for treatment scenarios where bacteria encounter multiple
 antibacterial agents.
description: Data
 Files
DOI: 10.5061/dryad.gm2sm
title: Data from: Historical retreat of alpine glaciers in the Ahklun Mountains, western Alaska

description: The Ahklun Mountains support the only extant glaciers in western Alaska.
 The glaciers were originally mapped by the U.S. Geological Survey using
 photogrammetry methods based on 1972 - 1973 aerial photos. We surveyed for
 presence or absence of the glaciers by fixed-wing aircraft in 2006. Of 109
 glaciers originally mapped, 10 (9%) had disappeared. Using aerial imagery
 of a subset of 76 glaciers at three time steps between 1957 - 2009, we
 determined the average rate of areal loss was 45% over 52 years. At this
 rate, it is likely that all Ahklun Mountain glaciers will be extinguished
 by the end of the current century.
description: Ahklun Mountain glacier
 status in 2009Ahklun Mountain glacier
 status in 2009, area, and mapping confidence at three time steps for a
 subset of 76 glaciers.Table
 A1.docMapping confidence of
 Ahklun Mountain glacier filesMapping confidence at
 three time steps for 76 Ahklun Mountain glaciers, southwestern
 Alaska.Table
 A2.doc
DOI: 10.15468/dl.xapng9
title: Occurrence Download

description: A dataset containing 42 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Distribution of Undaria pinnatifida along the Atlantic coast of the Iberian Peninsula in 2024"
 ]
}

 The dataset includes 42 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000622-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.gv940
title: Data from: The role of geography and ecology in shaping repeated patterns of morphological and genetic differentiation between European minnows (Phoxinus phoxinus) from the Pyrenees and the Alps

description: Neutral and selective processes can drive repeated patterns of evolution
 in different groups of populations experiencing similar ecological
 gradients. In this paper, we used a combination of nuclear and
 mitochondrial DNA markers, as well as geometric morphometrics, to
 investigate repeated patterns of morphological and genetic divergence of
 European minnows in two mountain ranges: the Pyrenees and the Alps.
 European minnows (Phoxinus phoxinus) are cyprinid fish inhabiting most
 freshwater bodies in Europe, including those in different mountain ranges
 that could act as major geographical barriers to gene flow. We explored
 patterns of P. phoxinus phenotypic and genetic diversification along a
 gradient of altitude common to the two mountain ranges, and tested for
 isolation by distance (IBD), isolation by environment (IBE) and isolation
 by adaptation (IBA). The results indicated that populations from the
 Pyrenees and the Alps belong to two well differentiated, reciprocally
 monophyletic mtDNA lineages. Substantial genetic differentiation due to
 geographical isolation within and between populations from the Pyrenees
 and the Alps was also found using rapidly evolving AFLPs markers
 (isolation by distance or IBD), as well as morphological differences
 between mountain ranges. Also, morphology varied strongly with elevation
 and so did genetic differentiation to a lower extent. Despite moderate
 evidence for IBE and IBA, and therefore of repeated evolution, substantial
 population heterogeneity was found at the genetic level, suggesting that
 selection and population specific genetic drift act in concert to affect
 genetic divergence.
description: aflpdata_Pyrenees_Collin_FumagalliThis table contains 1930 AFLP markers from Phoxinus phoxinus from the Pyrenees. Population number, and individual ID are indicated. Individual IDs correspond to the first 2 letters of the population name, followed by the individual number. AFLP data are coded as: 0=recessive allele, 1= dominant allelemitochondiral_alignement_PphoxinusNexus alignement file containing partial mitochondrial DNA control region sequences
DOI: 10.5061/dryad.440n9
title: Data from: Modification of plant-induced responses by an insect ecosystem engineer influences the colonization behaviour of subsequent shelter-users

description: Herbivores that modify plant morphology, such as gall forming insects, can
 disproportionately impact arthropod community on their host plants by
 providing novel habitats and shelters from biotic and abiotic stresses.
 These ecosystem engineers could also modify plant chemical properties, but
 how such changes in plant quality affect the behaviour of subsequent
 colonizers has rarely been investigated. We explored how an initial
 infestation of the tall goldenrod (Solidago altissima) by an ecosystem
 engineer, the rosette gall-midge (Rhopalomyia solidaginis), affects
 colonization behaviour of a shelter-using beetle (Microrhopala vittata)
 through plant-induced responses in the field. Beetles preferentially
 colonized plants with galls and exhibited a clumped distribution on those
 plants, which suggested a possible advantage for aggregating on galled
 plants. Accordingly, we found that beetles remained longer on galled
 plants with previous beetle damage than those without beetle damage. No
 such effect of beetle damage was found on plants without a gall. Similar
 interactions between galler-infestation and beetle damage were found in
 beetle's feeding choice, leaf diterpene and serine protease inhibitor
 production, and volatile organic compound (VOC) emission. These plant
 metabolic induction and herbivore response patterns indicated that the
 gall-midge can alter how plants respond to the beetle damage, and that
 gall presence coupled with beetle damage improves leaf palatability for
 the beetle. Finally, we found reciprocal effects of beetles on gall-midge
 performance to be neutral to slightly positive, suggesting that the
 observed field association of the two herbivores could be formed by
 plant-mediated facilitation. Synthesis: Our study suggests that an
 ecosystem engineer could have significant impact on herbivore community
 not only by changing plant morphology, but also by altering host quality
 and modifying plant induced responses to subsequent herbivory. As such, R.
 solidaginis also functions as a keystone herbivore that has
 disproportionate effects on community dynamics and composition meditated
 by induced plant growth and metabolic responses.
description: field_lab_
 experimentsfield and laboratory
 experiments for "Field survey of beetle distribution pattern",
 and "Beetle preferences and plant induced
 responses"chemistryChemistry data including diterpene acids, SPIs and VOCs.
DOI: 10.5061/dryad.3jq14
title: Data from: Phylogeography and population differentiation in the Psittacanthus calyculatus (Loranthaceae) mistletoe: a complex scenario of climate-volcanism interaction along the Trans-Mexican Volcanic Belt

description: Aim The formation of the Trans-Mexican Volcanic Belt (TMVB) played an
 important role in driving inter- and intraspecific diversification at high
 elevations. However, Pleistocene climate changes and ecological factors
 might also contribute to plant genetic structuring along the volcanic
 belt. Here, we analysed phylogeographic patterns of the parrot-mistletoe
 Psittacanthus calyculatus to determine the relative contribution of these
 different factors. Location Trans-Mexican Volcanic Belt Methods Using
 nuclear and chloroplast DNA sequence data for 370 individuals, we
 investigate the genetic differentiation of 35 populations across the
 species range. We conducted phylogenetic, population and spatial genetic
 analyses of P. calyculatus sequences along with ecological niche modelling
 and Bayesian inference methods to gain insight into the structuring of
 genetic variation of these populations. Results Our analyses revealed
 population structure with three genetic groups corresponding to
 individuals from Oaxaca and those from the central-eastern and western
 TMVB regions. A significant genetic signal of demographic expansion, an
 east-to-west expansion predicted by species distribution modelling, and
 approximate Bayesian computation analyses strongly supported a scenario of
 habitat isolation and invasion of TMVB by P. calyculatus during the
 late-Pleistocene. Main conclusions The genetic differentiation of P.
 calyculatus may be explained by the combined effects of (i) geographical
 isolation linked to the effects of the glacial/interglacial cycles and
 environmental factors, driving genetic differentiation from congeners into
 more xeric vegetation and (ii) the invasion of TMVB from east to west,
 suggesting a role for both colonization and glacial/interglacial cycles
 models.
description: Pérez-Crespo et
 al_MAXENT_Psittacanthus_calyculatusPsittacanthus_calyculatus_MAXENT_File: coordinates longitude and latitude of Psittacanthus calyculatus.Pérez-Crespo et al_ITSITS_File: Psittacanthus calyculatus sequences of the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA (nrDNA) sequences.Pérez-Crespo et al_trnL-FtrnL-F_File: Psittacanthus calyculatus sequences of the trnL-F intergenic spacer region from the chloroplast genome (cpDNA).
DOI: 10.5061/dryad.447b022
title: Data from: Improved mould-resistance and antibacterial activity of bamboo coated with ZnO/graphene

description: Bamboo is easier to mould and attack by fungi because of its higher
 content of starch and sugar. To make bamboo-based outdoor materials，a new
 type bamboo timber with improved mould-resistance and antibacterial
 activity, coated with reduced graphene oxide and nano crystal ZnO
 (abbreviated as RGO@ZnOBT), was fabricated by two steps of dip-dry and
 hydro-thermal process. A possible synthesis mechanism of RGO@ZnOBT making
 were discussed by X-ray diffraction, scanning electron microscopy,
 transmission electron microscope, energy-dispersal X-ray analysis, X-ray
 photo-electron spectroscopy, and Fourier transform infrared spectroscopy.
 According to the China standard test method, the Aspergillus niger mould
 resistance of RGO@ZnOBT is grade 2, meanwhile the Trichoderma virideduring
 ang Penicillium citrinum mould resistance of RGO@ZnOBT are grade 0, which
 are better than the grade 4 of original bamboo timber (abbreviated as BT).
 The Escherichia coli resistance test showed that antibacterial circle of
 RGO@ZnOBT is 3 mm, which is greatly higher than BT (0 mm). The
 antibacterial activity of treated bamboo is greatly significantly
 improved.
description: FTIRCharacterization results
 of FTIRmould
 recordMould resistant test
 resultsXPSCharacterization results
 of XPSXRD.zipCharacterization results of XRD
DOI: 10.5061/dryad.73250
title: Data from: Association between preoperative anaemia with length of hospital stay among patients undergoing primary total knee arthroplasty in Singapore: a single-centre retrospective study

description: OBJECTIVES: Studies in western healthcare settings suggest that
 preoperative anaemia is associated with poor outcomes after elective
 orthopaedic surgery. We investigated the prevalence of preoperative
 anaemia among patients with primary unilateral total knee arthroplasty
 (TKA) in Singapore and its association with length of hospital stay (LOS),
 perioperative blood transfusion and hospital readmission rates. METHODS:
 Retrospective cohort study performed in a tertiary academic medical centre
 in Singapore, involving patients who underwent primary unilateral TKA
 between January 2013 and June 2014. Demographics, comorbidities,
 preoperative haemoglobin (Hb) level, LOS and 30-day readmission data were
 collected. Anaemia was classified according to WHO definition. Prolonged
 LOS was defined as more than 6 days, which corresponds to &gt;75th
 centile LOS of the data. RESULTS: We analysed 2394 patients. The
 prevalence of anaemia was 23.7%. 403 patients (16.8%) had mild anaemia and
 164 patients (6.8%) had moderate to severe anaemia. Overall mean LOS was
 5.4±4.8 days. Based on multivariate logistic regression, preoperative
 anaemia significantly increased LOS (mild anaemia, adjusted OR (aOR) 1.71,
 p&lt;0.001; moderate/severe anaemia, aOR 2.29, p&lt;0.001).
 Similar effects were seen when preoperative anaemia was defined by Hb
 level below 13 g/dL, regardless of gender. Transfusion proportionately
 increased prolonged LOS (1 unit: aOR 2.12, p=0.006; 2 or more units: aOR
 6.71, p&lt;0.001). Repeat operation during hospital stay, previous
 cerebrovascular accidents, general anaesthesia and age &gt;70 years
 were associated with prolonged LOS. Our 30-day related readmission rate
 was 1.7% (42) cases. CONCLUSION: Anaemia is common among patients
 undergoing elective TKA in Singapore and is independently associated with
 prolonged LOS and increased perioperative blood transfusion. We suggest
 measures to correct anaemia prior to surgery, including the use of
 non-gender-based Hb cut-off for establishing diagnosis.
description: Dryad TKR Dataset
 without datesThis is a dataset of
 2600 patients who underwent primary TKR between Jan 2013 to Jun 2014 in
 Singapore General Hospital. The purpose of this dataset was to investigate
 the relationship between preoperative anaemia, hospital length of stay,
 perioperative blood transfusion rate and 30-day readmission rate among
 patients who had undergone primary TKA.
DOI: 10.5061/dryad.j380c
title: Data from: Characterization of microsatellite primers in the endangered orchid Phaius australis and cross-amplification to P. bernaysii (Orchidaceae)

description: Premise of the study: The swamp orchid, Phaius australis (Orchidaceae), is
 nationally endangered due to illegal collection and habitat loss and
 fragmentation, resulting in a disjunct distribution in spring and coastal
 wetland ecotones along Australia's east coast. Polymorphic
 microsatellite markers were developed to study genetic diversity and
 population structure for conservation and restoration purposes. Methods
 and Results: Illumina HiSeq high-throughput sequencing was used to develop
 15 nuclear microsatellite markers, including 10 polymorphic markers for P.
 australis. Polymorphism at each marker was evaluated using 90 individuals
 from four natural populations. The number of alleles per locus ranged from
 one to three, and the observed and expected heterozygosity varied from
 0.036 to 0.944 and from 0.035 to 0.611, respectively. These markers
 transferred successfully to congener P. bernaysii. Conclusions: The
 microsatellite markers will be useful for revealing levels of genetic
 diversity and gene flow for P. australis and may inform future
 conservation efforts.
description: Phaius
 OutputData outputs from the
 QDDv2b pipeline generated from NextGeneration
 sequencing.