cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.cb2d2
title: Data from: Density-dependent vulnerability of forest ecosystems to drought

description: Climate models predict increasing drought intensity and frequency for many
 regions, which may have negative consequences for tree recruitment,
 growth, and mortality, as well as forest ecosystem services. Furthermore,
 practical strategies for minimizing vulnerability to drought are limited.
 Tree population density, a metric of tree abundance in a given area, is a
 primary driver of competitive intensity among trees, which influences tree
 growth and mortality. Manipulating tree population density may be a
 mechanism for moderating drought-induced stress and growth reductions,
 although the relationship between tree population density and tree drought
 vulnerability remains poorly quantified, especially across climatic
 gradients. In this study, we examined three long-term forest ecosystem
 experiments in two widely-distributed North American pine species,
 ponderosa pine Pinus ponderosa (Lawson & C. Lawson) and red pine
 Pinus resinosa (Aiton), to better elucidate the relationship between tree
 population density, growth, and drought. These experiments span a broad
 latitude and aridity range and include tree population density treatments
 that have been purposefully maintained for several decades. We
 investigated how tree population density influenced resistance (growth
 during drought) and resilience (growth after drought compared to
 pre-drought growth) of stand-level growth during and after documented
 drought events. Our results show that relative tree population density was
 negatively related to drought resistance and resilience, indicating that
 trees growing at lower densities were less vulnerable to drought. This
 result was apparent in all three forest ecosystems, and was consistent
 across species, stand age, and drought intensity. Synthesis and
 applications. Our results highlighted that managing pine forest ecosystems
 at low tree population density represents a promising adaptive strategy
 for reducing the adverse impacts of drought on forest growth in coming
 decades. Nonetheless, the broader applicability of our findings to other
 types of forest ecosystems merits additional investigation.
description: BHEF_ALLThis file contains individual tree ring records, in Tucson format, for each tree sampled at the Black Hill Experimental Forest thinning experiment included in the study.CEF_allThis file contains individual tree ring records, in Tucson format, for each tree sampled at the Cutfoot Experimental Forest thinning experiment included in the study.FVEF_ALLThis file contains individual tree ring records, in Tucson format, for each tree sampled at the Fort Valley Experimental Forest thinning experiment included in the study.
DOI: 10.5061/dryad.3t423
title: Data from: Phylogeny of xerophilic aspergilli (subgenus Aspergillus) and taxonomic revision of section Restricti

description: Aspergillus section Restricti together with sister sect. Aspergillus
 (formerly Eurotium) comprises osmophilic species, that are able to grow on
 substrates with low water activity and in extreme environments. We
 adressed the monophyly of both sections within subgenus Aspergillus and
 applied a multidisciplinary approach for definition of species boundaries
 in sect. Restricti. The monophyly of sections Aspergillus and Restricti
 was tested on a set of 102 taxa comprising all currently accepted species
 and was strongly supported by Maximum likelihood (ML) and Bayesian
 inferrence (BI) analysis based on coding regions of β-tubulin (benA),
 calmodulin (caM) and RNA polymerase II second largest subunit (RPB2) loci.
 More than 300 strains belonging to sect. Restricti from various isolation
 sources and four continents were characterized by DNA sequencing, and 193
 isolates selected for phylogenetic analyses and phenotypic studies.
 Species delimitation methods based on multispecies coalescent model were
 employed on DNA sequences from four loci, i.e., ID region of rDNA (ITS +
 LSU), caM, benA and RPB2, and supported recognition of 21 species,
 including 14 new. All these species were also strongly supported in ML and
 BI analyses. All recognized species can be reliably identified by all four
 examined genetic loci. Phenotype analysis was performed to support the
 delimitation of new species, it comprised colony characteristics on seven
 cultivation media incubated at several temperatures, growth on an osmotic
 gradient (six media with NaCl concentration from 0 to 25%) and analysis of
 morphology including scanning electron microscopy. The micromorphology of
 conidial heads, vesicle dimensions, temperature profiles and growth
 parameters in osmotic gradient were useful criteria for species
 identification.
description: beta-tubulin alignmnent
 of sect. Restricticalmodulin alignmnent of
 sect. RestrictirDNA ID region
 alignmnent of sect. RestrictiRNA polymerase beta
 alignmnent of sect. Restricticoncatenated alignmnent
 of sect. Restricticoncatenated alignmnent
 of subg. Aspergilluspartitioned analysis of
 sect. Restricti treepartitioned analysis of
 subg. Aspergillus treeStacey (penicillioides
 clade)Stacey (restrictus,
 conicus, vitricola clades)starBEAST
DOI: 10.5061/dryad.275d4
title: Data from: A randomized synbiotic trial to prevent sepsis among infants in rural India

description: Sepsis in early infancy results in one million annual deaths worldwide,
 most of them in developing countries. No efficient means of prevention is
 currently available. Here we report on a randomized, double-blind,
 placebo-controlled trial of an oral synbiotic preparation (Lactobacillus
 plantarum plus fructooligosaccharide) in rural Indian newborns. We
 enrolled 4,556 infants that were at least 2,000 g at birth, at least 35
 weeks of gestation, and with no signs of sepsis or other morbidity, and
 monitored them for 60 days. We show a significant reduction in the primary
 outcome (combination of sepsis and death) in the treatment arm (risk ratio
 0.60, 95% confidence interval 0.48–0.74), with few deaths (4 placebo, 6
 synbiotic). Significant reductions were also observed for culture-positive
 and culture-negative sepsis and lower respiratory tract infections. These
 findings suggest that a large proportion of neonatal sepsis in developing
 countries could be effectively prevented using a synbiotic containing L.
 plantarum ATCC-202195.
description: RCT Protocol for: A
 randomized synbiotic trial to prevent sepsis among infants in rural
 IndiaStudy protocol: A
 double-blind, randomized, placebo-controlled study to test the
 effectiveness of a prophylactic oral administration of a L. plantarum +
 FOS preparation to community-born neonates in reducing the incidence of
 neonatal sepsis.Panigrahi_et_al._RCT_Protocol_Synbiotic_study.pdfData from: A Randomized Synbiotic Trial to Prevent Sepsis Among Infants in Rural IndiaDeidentified SEPSISF clean data set from randomized Synbiotic Trial with all variables used in SAS analysis. Reference file: Data dictionary, please click on the appended "Readme file" below for study codes used in this analysis.Panigrahi et al.SEPSSIF.CSV
DOI: 10.5061/dryad.53b58
title: Data from: A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: testing co-localization among outlier markers, candidate genes, and QTLs for production traits

description: Comparative genome scans can be used to identify chromosome regions, but
 not traits, that are putatively under selection. Identification of
 targeted traits may be more likely in recently domesticated populations
 under strong artificial selection for increased production. We used a
 North American Atlantic salmon 6K SNP dataset to locate genome regions of
 an aquaculture strain (Saint John River) that were highly diverged from
 that of its putative wild founder population (Tobique River). First,
 admixed individuals with partial European ancestry were detected using
 STRUCTURE and removed from the dataset. Outlier loci were then identified
 as those showing extreme differentiation between the aquaculture
 population and the founder population. All Arlequin methods identified an
 overlapping subset of 17 outlier loci, 3 of which were also identified by
 BayeScan. Many outlier loci were near candidate genes and some were near
 published quantitative trait loci (QTLs) for growth, appetite, maturity,
 or disease-resistance. Parallel comparisons using a wild, non-founder
 population (Stewiacke River) yielded only one overlapping outlier locus as
 well as a known maturity QTL. We conclude that genome scans comparing a
 recently domesticated strain with its wild founder population can
 facilitate identification of candidate genes for traits known to have been
 under strong artificial selection.
description: TOB VS STW
 populations_textraw dataset with 3980
 SNP genotypes for two wild Atlantic salmon populations from the Tobique
 River and the Stewiacke River in the Bay of Fundy,
 Canada.
DOI: 10.5061/dryad.jv280
title: Data from: Petiolate wings: effects on the leading-edge vortex in flapping flight

description: The wings of many insect species including crane flies and damselflies are
 petiolate (on stalks), with the wing planform beginning some distance away
 from the wing hinge, rather than at the hinge. The aerodynamic impact of
 flapping petiolate wings is relatively unknown, particularly on the
 formation of the lift-augmenting leading-edge vortex (LEV): a key flow
 structure exploited by many insects, birds and bats to enhance their lift
 coefficient. We investigated the aerodynamic implications of petiolation P
 using particle image velocimetry flow field measurements on an array of
 rectangular wings of aspect ratio 3 and petiolation values of P = 1–3. The
 wings were driven using a mechanical device, the ‘Flapperatus’, to produce
 highly repeatable insect-like kinematics. The wings maintained a constant
 Reynolds number of 1400 and dimensionless stroke amplitude Λ* (number of
 chords traversed by the wingtip) of 6.5 across all test cases. Our results
 showed that for more petiolate wings the LEV is generally larger, stronger
 in circulation, and covers a greater area of the wing surface,
 particularly at the mid-span and inboard locations early in the wing
 stroke cycle. In each case, the LEV was initially arch-like in form with
 its outboard end terminating in a focus-sink on the wing surface, before
 transitioning to become continuous with the tip vortex thereafter. In the
 second half of the wing stroke, more petiolate wings exhibit a more
 detached LEV, with detachment initiating at approximately 70% and 50% span
 for P = 1 and 3, respectively. As a consequence, lift coefficients based
 on the LEV are higher in the first half of the wing stroke for petiolate
 wings, but more comparable in the second half. Time-averaged LEV lift
 coefficients show a general rise with petiolation over the range tested.
description: Vectormap
 DataVectormap data behind
 Figures 3 - 6, and 9. All variables are in SI units.VectormapData.zip
DOI: 10.5061/dryad.4p55b
title: Data from: Outcomes of cataract surgery in urban and rural population in the South Indian State of Andhra Pradesh: Rapid Assessment of Visual Impairment (RAVI) Project

description: Objective: To assess the visual outcomes after cataract surgery among
 urban and rural population aged ?40 years in the South India state of
 Andhra Pradesh. Methods: A population based cross-sectional study was
 conducted in which 7800 subjects were sampled from two rural and one urban
 location. Visual Acuity was assessed and eye examination were performed by
 trained personnel. A questionnaire was used to collect personal and
 demographic information, and history of cataract surgery. Blindness and
 moderate Visual Impairment (MVI) was defined as presenting VA &lt;6/60
 and &lt;6/18 to 6/60 in the better eye respectively. Results: In
 total, 7378 (94.6%) were examined. Of these, 1228 eyes of 870 individuals
 were operated for cataract. The mean age of operated subjects was 63.7
 years (SD: 10.7 years). In total, 56.3% of those operated were women, 76%
 were illiterate and 42% of them were using spectacles after cataract
 surgery. Even after surgery, 12.2% of the operated eyes had MVI and
 blindness was seen in 14.7% of the eyes. A significantly higher proportion
 of subjects in urban area had good outcome as compared to those in the
 rural area (p=0.01). Uncorrected refractive error (58.7%) was the leading
 cause of MVI, and posterior segment disease (34.3%) was the leading cause
 of blindness. On applying multiple logistic regression, risk factors for
 poor outcomes were age ? 70 years (OR: 1.9, 95% CI: 1.3 - 2.8), rural
 residence (OR: 1.3, 95% CI:1.0 - 1.8) and presence of aphakia ( OR: 8.9,
 95% CI: 5.7 - 13.8). Conclusions: Post cataract surgery, refractive errors
 remain an important correctable cause of MVI, in the south Indian state of
 Andhra Pradesh. The correction of refractive errors is required to provide
 good visual recovery and achieve the benefit of cataract surgery.
description: AP
 RAVI_Outcomes_gee
DOI: 10.5061/dryad.728hn
title: Data from: Tropical ancient DNA reveals relationships of the extinct Bahamian giant tortoise Chelonoidis alburyorum

description: Ancient DNA of extinct species from the Pleistocene and Holocene has
 provided valuable evolutionary insights. However, these are largely
 restricted to mammals and high latitudes because DNA preservation in warm
 climates is typically poor. In the tropics and subtropics, non-avian
 reptiles constitute a significant part of the fauna and little is known
 about the genetics of the many extinct reptiles from tropical islands. We
 have reconstructed the near-complete mitochondrial genome of an extinct
 giant tortoise from the Bahamas (Chelonoidis alburyorum) using an
 approximately 1 000-year-old humerus from a water-filled sinkhole (blue
 hole) on Great Abaco Island. Phylogenetic and molecular clock analyses
 place this extinct species as closely related to Galápagos (C. niger
 complex) and Chaco tortoises (C. chilensis), and provide evidence for
 repeated overseas dispersal in this tortoise group. The ancestors of
 extant Chelonoidis species arrived in South America from Africa only after
 the opening of the Atlantic Ocean and dispersed from there to the
 Caribbean and the Galápagos Islands. Our results also suggest that the
 anoxic, thermally buffered environment of blue holes may enhance DNA
 preservation, and thus are opening a window for better understanding
 evolution and population history of extinct tropical species, which would
 likely still exist without human impact.
description: Assemblies of
 mitochondrial genomes of Chelonoidis alburyorum, C. carbonarius, C.
 chilensis, C. denticulatus, C. vicina, Geochelone
 sulcata.Text files created with
 Tablet 1.15.09.1.
DOI: 10.5061/dryad.s0k3h
title: Data from: Photovoltage field-effect transistors

description: It is of intense interest to extend the excellent performance of silicon
 photodetectors into the infrared spectrum beyond silicon’s bandgap.
 Detection of infrared radiation is at the base of applications such as
 night vision, health monitoring, and optical commuincations. Silicon is
 the workhorse of modern electronics, but its electronic bandgap prevents
 detection of light at wavlengths longer than ~ 1100 nm. Here we present
 the photovoltage field effect transitor (PVFET) that uses silicon for
 charge transport, but adds infrared sensitization via a quantum dot light
 absorber. Using the photovoltage generated at the silicon:quantum dot
 heterointerface, combined with the high transconductance provided by the
 silicon device, we demonstrate high gain (&gt;104 electrons/photon at
 1500 nm), fast time response (&lt; 10 s), and widely tunable spectral
 response. The PVFET shows a responsivity 5 orders of magnitude higher at
 1500 nm wavelength than prior IR-sensitized silicon detectors. The
 sensitization is achieved using a room temperature solution process and
 does not rely on traditional high temperature epitaxial growth
 semiconductors, as per germanium and III-V compounds. Our results
 demonsrate, for the first time, colloidal quantum dots as an efficient
 platform for silicon based infrared detection, competitive with
 state-of-the-art epitaxial semiconductors.
description: Published_dataData published in the manuscript and supplementary information
DOI: 10.5061/dryad.r7s04
title: Data from: Prevalence of depression, anxiety, adjustment disorders, and somatoform disorders in patients with age-related macular degeneration in Germany

description: Aims: The purpose of this study was to analyze the prevalence of
 depression, anxiety, adjustment disorders, and somatoform disorders in
 patients diagnosed with age-related macular degeneration (AMD) in Germany.
 Methods: This study included 7,580 patients between the ages of 40 and 90
 diagnosed with AMD between January 2011 and December 2014 in 1,072 primary
 care practices (index date). The last follow-up was in July 2016. We also
 included 7,580 controls without AMD, which were matched (1:1) to the AMD
 cases by age, sex, type of health insurance (private or statutory),
 physician, and Charlson comorbidity score as a generic marker of
 comorbidity. The outcome of the study was the prevalence of depression,
 anxiety, adjustment disorders, and somatoform disorders recorded in the
 database between the index date and the end of follow-up. Results: The
 mean age among subjects was 75.7 years (SD=10.1 years), 34.0% were men,
 and 7.8% had private health insurance coverage. The Charlson comorbidity
 index was 2.0 (SD=1.8). Depression was the most frequent disease (33.7% in
 AMD patients versus 27.3% in controls), followed by somatoform disorders
 (19.6% and 16.7%), adjustment disorders (14.8% and 10.5%), and anxiety
 disorders (11.7% and 8.2%). Depression (OR=1.37, 95% CI: 1.27–1.47),
 anxiety (OR=1.50, 95% CI: 1.35–1.67), adjustment disorders (OR=1.50, 95%
 CI: 1.36–1.65), and somatoform disorders (OR=1.22, 95% CI: 1.12–1.32) were
 all positively associated with AMD. Conclusion: Overall, a significant
 association was found between AMD and depression, anxiety, adjustment
 disorders, and somatoform disorders.
description: maculaPatients with and
 without macula degeneration diagnosis in the time 2011-2014 from general
 practitioner offices in Germany. Age, gender, diagnoses of depression;
 anxiety; adjustment disorder; somatoform disorder are
 included.
DOI: 10.5061/dryad.34c1r
title: Data from: Measures of biologically relevant environmental heterogeneity improve prediction of regional plant species richness

description: Aim:Relatively few models of species richness explicitly consider aspects
 of environmental heterogeneity, other than topographic heterogeneity. We
 hypothesized that environmental heterogeneity is an important determinant
 of species richness, especially in ancient climatically stable
 environments. Location: South Africa, which accommodates a range of biomes
 that differ strongly in species richness.Methods: We included measures of
 climatic, edaphic and biotic variables and their spatial heterogeneities
 in boosted regression tree models of vascular plant species richness.
 Species richness was assessed using herbarium records per quarter degree
 square (QDS). To avoid autocorrelation and problems of variable collection
 rates we iteratively randomly subsampled 20% of the available QDS. We also
 verified estimates of species richness using an independent data source.
 Results: The models predicted 68% of QDS species richness and 95% of biome
 richness. Spatial variability in diurnal temperature range was the
 strongest predictor of species richness, and inclusion of edaphic and
 biotic terms as well as spatial heterogeneities increased the explanatory
 power of the model considerably. Heterogeneity variables featured strongly
 (8 of 13) as predictors of species richness, but several resource
 variables (e.g. precipitation, seasonality and evapotranspiration) were
 also important. The spatial heterogeneities of some variables (e.g. water
 availability, fire) were related to their mean values, possibly explaining
 why some global models that have not explicitly included heterogeneity
 (other than topographic) perform well. Main conclusions: Environmental
 heterogeneities are important predictors of species richness, yielding
 accurate predictions even in the absence of any consideration of
 diversification rates or environmental stability. Greater heterogeneity of
 some resource variables when limiting, contributed to modelled species
 richness, adding to understanding of why species richness of some
 resource-poor Mediterranean-ecosystems is high. We suggest that species
 richness in ancient, climatically stable Mediterranean-ecosystems is
 contingent on resource and environmental heterogeneity that has enabled
 both the diversification and maintenance of regional species richness.
description: Modelled vascular plant
 species richness of South Africa and neighbouring
 territoriesA raster in GeoTiff
 format at 0.0417° resolution (coordinate reference systems EPSG: 4326) of
 vascular plant species richness in South Africa, Swaziland and Lesotho,
 predicted from the full boosted regression tree model. The modelled output
 includes prediction to areas for which species richness was not included
 in the data used for model construction (Swaziland and Lesotho). Species
 richness is expressed as counts per quarter degree
 square.species_map.tif
DOI: 10.5061/dryad.9kp7d
title: Data from: The origin of floral organ identity quartets

description: The origin of flowers has puzzled plant biologists ever since Darwin
 referred to their sudden appearance in the fossil record as an abominable
 mystery. Flowers are considered to be an assembly of protective,
 attractive and reproductive male and female leaf-like organs. Their origin
 cannot be understood by a morphological comparison to gymnosperms, their
 closest relatives, which develop separate male or female cones. Despite
 these morphological differences, gymnosperms and angiosperms possess a
 similar genetic toolbox consisting of phylogenetically related MADS-domain
 proteins. Using ancestral MADS-domain protein reconstruction, we trace the
 evolution of organ identity quartets along the stem lineage of crown
 angiosperms. We provide evidence that current floral quartets specifying
 male organ identity, which consist of four types of subunits, evolved from
 ancestral complexes of two types of subunits through gene duplication and
 integration of SEPALLATA proteins just before the origin of flowering
 plants. Our results suggest that protein interaction changes underlying
 this compositional shift were the result of a gradual and reversible
 evolutionary trajectory. Modelling shows that such compositional changes
 may have facilitated the evolution of the perfect, bisexual flower.
description: Supplemental Data Set
 1List
 of accessions of SEPALLATA-like, APETALA3- and PISTILLATA-like, AGAMOUS-
 and SEEDSTICK-like genes used for dating the E-class
 duplication.SupplementalDataSet1.xlsxSupplemental Data Set 2Multiple alignment of AP3/PI used for estimating time of diversification.SupplementalDataSet2Supplemental Data Set 3Multiple alignment of AG/STK used for estimating time of diversification.SupplementalDataSet3Supplemental Data Set 4Multiple alignment of SEP3/SEP1 used for estimating time of diversification.SupplementalDataSet4Supplemental Data Set 5List of accession numbers of APETALA3- and PISTILLATA-like proteins, AG- and STK-like proteins, and SEPALLATA-like proteins used for ancestral sequence reconstruction.SupplementalDataSet5.xlsxSupplemental Data Set 6Multiple alignment of AP3/PI used for ancestral protein reconstruction.SupplementalDataSet6Supplemental Data Set 7Multiple alignment of AG/STK used for ancestral protein reconstruction.SupplementalDataSet7Supplemental Data Set 8Multiple alignment of SEP3/SEP1 used for ancestral protein reconstruction.SupplementalDataSet8