cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6086/d1fh6j
title: Grain nutritional profiles of a cowpea MAGIC population

description: This dataset includes nutritional and agronomic traits collected from a
 multi-parent advanced generation intercross (MAGIC) population of cowpea
 grown in California during 2016–2017. The data were used in QTL mapping
 and genomic prediction as part of the manuscript entitled
 "Quantitative trait loci and genomic prediction for grain sugar and
 mineral  concentrations of cowpea [Vigna unguiculata (L.)
 Walp.]"
description: Grain sugar concentrations were assayed using high-performance
 liquid chromatography. Grain mineral concentrations were determined by
 inductively coupled plasma–optical emission spectrometry and
 combustion.
description: Microsoft Excel is required to open this data file.
DOI: 10.6084/m9.figshare.30821443
title: Optimizing Pediatric Dose Finding: A Phase I/II Design Integrating Adult Data

description: Precision dose selection in pediatric trials is imperative given children’s distinct profiles, yet constrained by ethical barriers and recruitment challenges that could be strategically mitigated through adult trial data integration. To address the limitations of existing methods, we propose the pp-BOIN12 and pp-TITE-BOIN12 designs based on the Power prior framework to identify optimal biological dose (OBD) and address delayed outcomes. These designs adaptively quantify dose-level similarity between adult and pediatric cohorts using Hellinger distance to calibrate real-time borrowing weights. Numerical simulations demonstrate that pp-BOIN12 improves the percentage of correct OBD selection while reducing patient assignments to doses above maximum tolerated dose (MTD). pp-TITE-BOIN12 maintains comparable accuracy with minimal performance degradation while significantly shortening trial duration. This work provides an adaptive and safe method for incorporating adult data into pediatric extrapolation trials.
DOI: 10.5061/dryad.37pvmcvqf
title: Environmental parameters and DCF rates in Yangtze Estuary and coastal waters

description: Environmental parameters and DCF rates in Yangtze estuary and coastal
 waters --- The uploaded dataset consists of seven files, as follows:
 Environmental parameters.csv DCF rates of temperature gradients.csv Annual
 DCF rates.csv Increase of DCF rates under 2.0 °C and 4.0 °C warming
 scenarios.csv Increase of DCF rates under different warming scenarios.csv
 DCF rate in August under current and 4.0 °C warming scenario and the
 inhibition percentage DCF rates of ammonium gradients.csv Among them,
 environmental parameters and DCF rate of 5–40°C are measured data, and the
 rest data are simulated by polynomial fitting in Origin 2022.
DOI: 10.6084/m9.figshare.31169588
title: Genomic analyses of globally distributed <i>Rhizopus microsporus</i> populations indicate clinical isolates derived from environmental diversity reservoirs

description: Mucormycosis is a group of diseases that is increasing in frequency. A common opportunistic human fungal pathogen in this group is <i>Rhizopus microsporus</i>, which is a globally distributed species present in soil-associated environments. A subset of isolates in this species host endobacteria that are hypothesized to influence fungal pathogenicity in both clinical and environmental settings. We have limited understanding of how clinically and environmentally derived isolates are related or how physiological attributes, including thermotolerance and endosymbiosis, are correlated with population structure. Traditional molecular barcodes used to assess intraspecific relationships, such as ribosomal DNA internal transcribed spacer (ITS-rDNA)–based markers, do not provide species-level resolution, necessitating analyses of whole genome data. In this study, we generated novel whole genome sequencing data for six <i>R. microsporus</i> isolates and combined these data with publicly available whole genome sequences of 46 <i>R. microsporus</i> isolates. We evaluated these sequences to understand the evolutionary relationships among clinical and environmental isolates using phylogenomic and single nucleotide polymorphism (SNP)-based population genomics methods. We further studied their relationships by quantifying and comparing potential physiological differences and endosymbiont presence in a subset of 16 isolates with live cultures. We found that clinical isolates that originate from environmental settings contain higher molecular diversity than subpopulations isolated from clinical settings. We observed that environmental isolates grow faster than clinical isolates at temperatures between 22 and 37 C and that 7 of 16 (44%) contain endobacteria in the genus <i>Mycetohabitans</i> (Burkholderiales). Lastly, we observed that genome assembly size in <i>R. microsporus</i> is variable and that long-read sequencing technologies greatly enhance our ability to investigate the underlying genomic features. Our study provides a valuable backdrop for probing the basic biology and applied biomedical importance of <i>Rhizopus</i> and related fungi that cause mucormycosis.
DOI: 10.6084/m9.figshare.31169588.v1
title: Genomic analyses of globally distributed <i>Rhizopus microsporus</i> populations indicate clinical isolates derived from environmental diversity reservoirs

description: Mucormycosis is a group of diseases that is increasing in frequency. A common opportunistic human fungal pathogen in this group is <i>Rhizopus microsporus</i>, which is a globally distributed species present in soil-associated environments. A subset of isolates in this species host endobacteria that are hypothesized to influence fungal pathogenicity in both clinical and environmental settings. We have limited understanding of how clinically and environmentally derived isolates are related or how physiological attributes, including thermotolerance and endosymbiosis, are correlated with population structure. Traditional molecular barcodes used to assess intraspecific relationships, such as ribosomal DNA internal transcribed spacer (ITS-rDNA)–based markers, do not provide species-level resolution, necessitating analyses of whole genome data. In this study, we generated novel whole genome sequencing data for six <i>R. microsporus</i> isolates and combined these data with publicly available whole genome sequences of 46 <i>R. microsporus</i> isolates. We evaluated these sequences to understand the evolutionary relationships among clinical and environmental isolates using phylogenomic and single nucleotide polymorphism (SNP)-based population genomics methods. We further studied their relationships by quantifying and comparing potential physiological differences and endosymbiont presence in a subset of 16 isolates with live cultures. We found that clinical isolates that originate from environmental settings contain higher molecular diversity than subpopulations isolated from clinical settings. We observed that environmental isolates grow faster than clinical isolates at temperatures between 22 and 37 C and that 7 of 16 (44%) contain endobacteria in the genus <i>Mycetohabitans</i> (Burkholderiales). Lastly, we observed that genome assembly size in <i>R. microsporus</i> is variable and that long-read sequencing technologies greatly enhance our ability to investigate the underlying genomic features. Our study provides a valuable backdrop for probing the basic biology and applied biomedical importance of <i>Rhizopus</i> and related fungi that cause mucormycosis.
DOI: 10.5061/dryad.f1vhhmh22
title: Data from: Hominin fossils from Kromdraai and Drimolen inform Paranthropus robustus craniofacial ontogeny

description: Growth and development provide critical information about the evolutionary
 history of early hominin adult morphology. Using fossils from the southern
 African site of Kromdraai, we herein present the digital models of three
 juvenile specimens that are especially valuable because they shed light on
 how the distinct adult craniofacial characteristics of Paranthropus
 robustus developed. We find significant differences in the development of
 P. robustus and Australopithecus africanus. Additionally, some features of
 the P. robustus specimens suggest that the iconic SK 54 juvenile calvaria
 from the southern African site of Swartkrans is more likely an
 early Homo specimen rather than Paranthropus. The results of this study
 shed light on the evolutionary relationships between different early
 hominin species and could help to identify the closest relative to the
 Paranthropus/Homo clade.
description: Specimens
 The three
 <em>Paranthropus robustus</em> infant specimens numbered KW
 6420, KW 9000/9600 and KW 10840 from Kromdraai are curated at the
 Evolutionary Studies Institute, University of the Witwatersrand in
 Johannesburg, South Africa. Researchers may apply for access through the
 University Fossil Access Advisory Committee by contacting the University
 Curator for Fossil and Rock Collections: Bernhard Zipfel, PhD, University
 Curator of Fossil and Rock Collections, Evolutionary Studies Institute,
 University of the Witwatersrand, Johannesburg (e-mail: Bernhard.Zipfel@wits.ac.za) X-ray micro-computed tomography and 3-D digital (.stl) models The X-ray micro-computed tomography scanning was performed at the University of the Witwatersrand (Johannesburg, South Africa) using the Nikon Metrology XTH 225/320 LC dual source industrial CT system, and at the South African Nuclear Energy Corporation (Pelinbada, South Africa) using the Metris X-Tek XT H225L. The specimens were scanned at a voltage of 120kV and current of 130μA with isometric voxel dimensions ranging from 10 to 36 µm. An ‘.stl’ file (or digital model) of each specimen was obtained in Avizo Standard 8.1.1 (www.thermofisher.com) from micro-CT data.
description: The three data files can be
 opened using ‘MeshLab’, a free and open-source software (version 2 or
 later) that is dedicated to the processing of meshes (or digital models).
 For more information, please visit: https://en.wikipedia.org/wiki/MeshLab
DOI: 10.5061/dryad.70rxwdc3f
title: Beyond the usual climate? Factors determining flowering and fruiting phenology across a genus over 117 years

description: Premise: Although changes in plant phenology are largely attributed to
 changes in climate, the roles of other factors, such as genetic
 constraints, competition, and self-compatibility, are
 underexplored.  Methods: We compiled &gt;900 herbarium
 records spanning 117 years for all 8 nominal species of the winter-annual
 genus Leavenworthia (Brassicaceae). We used linear regression to determine
 the rate of phenological change across years and phenological sensitivity
 to climate. Using a variance partitioning analysis, we assessed the
 relative influence of climatic and non-climatic factors
 (self-compatibility, range overlap, latitude, and year) on Leavenworthia
 reproductive phenology.  Key Results: Flowering advanced by ~2.0
 days and fruiting ~1.3 days per decade. For every 1°C increase in spring
 temperature, flowering advanced ~2.3 days and fruiting ~3.3 days. For
 every 100 mm decrease in spring precipitation, each advanced ~6-7 days.
 The best models explained 35.4% of flowering variance and 33.9% of
 fruiting. Spring precipitation accounted for 51.3% of explained variance
 in flowering date and 44.6% in fruiting. Mean spring temperature accounted
 for 10.6% and 19.3%, respectively. Year accounted for 16.6% of flowering
 variance and 5.4% of fruiting, and latitude 2.3% and 15.1%, respectively.
 Non-climatic variables combined accounted for &lt;11% of the variance
 across phenophases. Conclusions: Spring precipitation, alongside other
 climate and climatically-related factors, were dominant predictors of
 phenological variance. Our results emphasize the strong effect of
 precipitation on phenology, especially in moisture-limited habitats
 preferred by Leavenworthia. Amongst the many factors that determine
 phenology, climate is the dominant influence, indicating the effects of
 climate change on phenology are expected to increase.
DOI: 10.25338/b8td2t
title: Approaching a thermal tipping point in the Eurasian boreal forest at its southern margin

description: Climate change is increasing the intensity and frequency of extreme heat
 events. Ecological responses to extreme heat will depend on vegetation
 physiology and thermal tolerance. Here we report that Larix sibirica, a
 foundation species across boreal Eurasia, is vulnerable to extreme heat at
 its southern range margin due to its low thermal tolerance (Tcrit of
 photosynthesis: ~ 37–48 °C). Projections from CMIP6 Earth System Models
 (ESMs) suggest that leaf temperatures might exceed the 25th percentile of
 Larix sibirica’s Tcrit by two to three days per year within the next two
 to three decades (by 2050) under high emission scenarios (SSP3-7.0 and
 SSP5-8.5). This degree of warming will threaten the biome’s continued
 ability to assimilate and sequester carbon. This work highlights that
 under high emission trajectories, we may approach an abrupt ecological
 tipping point in southern boreal Eurasian forests substantially sooner
 than ESM estimates that do not consider plant thermal tolerance traits.
description: Ecophysiological data were collected using a Jr. PAM Chlorophyll
 Fluorometer and a mass spectrometer. Climate model data
 comes from CMIP6.
description: Data can be opened using a text editor or Microsoft
 Excel. Codes can be opened using a mix of R, Matlab,
 and Python.
DOI: 10.5061/dryad.fqz612jx0
title: Activity of a freshwater turtle varies across a latitudinal gradient: implications for the success of assisted colonisation

description: The value of assisted colonisation as a response to climate change can
 only be realised if focal species are well suited to their new habitats.
 For ectotherms, new habitats must offer microclimates that promote crucial
 behaviours such as thermoregulation and foraging. The Western Swamp Turtle
 (Pseudemydura umbrina), a Critically Endangered species from southwestern
 Australia, serves as a global case-study of assisted colonisation in
 action. Initial trials where juvenile P. umbrina were released into wetter
 and cooler climates found that individuals spent considerable time at body
 temperatures that apparently limited their growth. Using high-resolution
 biologging data (temperature and depth), here we tested if turtle activity
 is thermally constrained in cooler latitudes by releasing 48 juveniles
 into seasonal swamps at three sites. One site was core natural habitat,
 and the other sites were wetlands 380 km apart that offered either warmer
 or cooler microclimates. Generalised additive mixed models were used to
 evaluate behaviours and time spent at optimal temperatures for
 approximately one month following release, and growth rates were measured
 and analysed after release until the end of the hydroperiod 4-5 months
 later. We found that turtles released into the most poleward (southern)
 wetland spent significantly less time active and basking and grew
 significantly less compared to turtles released further north. When
 analysed together, behavioural and growth datasets showed that activity
 was positively correlated with growth rates. We conclude that poor growth
 of turtles in the southern wetland was likely a result of lower body
 temperatures, stemming from a reduced ability to thermoregulate in water.
 Consequently, for assisted colonisation of P. umbrina to be successful,
 recipient wetlands must offer aquatic microclimates that are sufficiently
 warm to promote foraging activity that leads to growth, and ultimately to
 maturation.
description: Data was collected by attaching Data Storage Tags to turtles that
 recorded temperature and depth.
description: The dataset can be analysed using R-program and
 Microsoft-Excel.
DOI: 10.5061/dryad.h9w0vt4nw
title: Management intensity affects insect pests and natural pest control on Arabica coffee in its native range

description: Agroforestry systems provide opportunities to reduce the trade-off between
 agricultural production and biodiversity, for example by enhancing a
 diverse community of species potentially acting as natural pest control
 agents. While management of agroforestry systems is intensifying across
 the globe, we lack insights into the impact of management intensity on
 pest levels and natural pest control, especially along broad management
 gradients and as compared with natural forests. We assessed the impact of
 management intensity on major insect pests (the coffee blotch miner, the
 serpentine leaf miner, the coffee leaf skeletonizer, and damage by other
 free-feeding herbivores) and natural pest control by parasitoid wasps
 across sixty sites in the center of origin of Arabica coffee in
 southwestern Ethiopia. Within this region, coffee is growing along a broad
 management gradient ranging from little or no management in the natural
 forest to intensively managed commercial plantations. In the wet season,
 pest levels were largely similar in the natural forest, semi-forest, and
 semi-plantation systems, whereas pests reached outbreak densities in the
 most intensively managed plantation system. In contrast, management
 intensity did not significantly affect pest levels in the dry season. The
 insect pests differed in their seasonal dynamics, consistently declined
 with elevation, and were largely unaffected by shade levels. Parasitism
 rate of the coffee blotch miner was lower, and the parasitoid community
 was distinct, in the most intensively managed plantation system. Synthesis
 and applications: Our findings support the hypothesis that the weaker
 top-down control by parasitoids in the intensively managed plantation
 sites leads to higher pest levels, and that – at least for some pest
 species – there is a threshold in the effect of management intensity on
 pest levels and natural pest control. It is important to consider such
 non-linear relationships to maintain or enhance the sustainability of
 agroforestry systems during management intensification. Overall, our
 findings highlight that ecological knowledge of natural pest control can
 be used to intensify production to improve the livelihood of smallholders
 without jeopardizing natural pest control, at least up to a certain point.
DOI: 10.15468/dl.z43vqx
title: Occurrence Download

description: A dataset containing 602 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "TaxonKey is Crambe tataria"
 ]
}

 The dataset includes 602 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003485-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.xpnvx0kkz
title: Introgression between highly divergent fungal sister species

description: To understand how species evolve and adapt to changing environments, it is
 important to study gene flow and introgression due to their influence on
 speciation and radiation events. Here, we apply a novel experimental
 system for investigating these mechanisms using natural populations. The
 system is based on two fungal sister species with morphological and
 ecological similarities occurring in overlapping habitats. We examined
 introgression between these species by conducting whole genome sequencing
 of individuals from populations in North America and Europe. We assessed
 genome-wide nucleotide divergence and performed crossing experiments to
 study reproductive barriers. We further used ABBA-BABA statistics together
 with a network analysis to investigate introgression, and conducted
 demographic modelling to gain insight into divergence times and
 introgression events. The results revealed that the species are highly
 divergent and incompatible in vitro. Despite this, small regions of
 introgression were scattered throughout the genomes and one introgression
 event likely involves a ghost population (extant or extinct). This study
 demonstrates that introgression can be found among divergent species and
 that population histories can be studied without collections of all the
 populations involved. Moreover, the experimental system is shown to be a
 useful tool for research on reproductive isolation in natural populations.
DOI: 10.6084/m9.figshare.31169584
title: Gradient Wild Bootstrap for Instrumental Variable Quantile Regressions with Weak and Few Clusters

description: We study the gradient wild bootstrap-based inference for instrumental variable quantile regressions in the framework of a small number of large clusters in which the number of clusters is viewed as fixed, and the number of observations for each cluster diverges to infinity. We illustrate the good finite-sample performance of the new inference methods using simulations and provide an empirical application to a well-known dataset about US local labor markets.
DOI: 10.6084/m9.figshare.31169584.v1
title: Gradient Wild Bootstrap for Instrumental Variable Quantile Regressions with Weak and Few Clusters

description: We study the gradient wild bootstrap-based inference for instrumental variable quantile regressions in the framework of a small number of large clusters in which the number of clusters is viewed as fixed, and the number of observations for each cluster diverges to infinity. We illustrate the good finite-sample performance of the new inference methods using simulations and provide an empirical application to a well-known dataset about US local labor markets.
DOI: 10.5061/dryad.1zcrjdfx7
title: The supplementary animations, results and the codes of the green-beard simulation study

description: This dataset includes the Supplementary Animations, simulation codes and
 results of the article "The role of recognition error in the
 stability of green-beard genes" in Evolution Letters. This
 dataset contains the MATLAB simulation code based on game-theoretic and
 green-beard aspects of the yeast interactions. The parameters of the
 simulation results (the relative fitness in each condition) are presented
 in the paper. The precise description is provided in the
 ‘Simulation_code_and_dataset_guide.docx.’ The visualizations of the
 simulation results are presented with Supplementary Animations.
description: The methods of the simulation code is included.
description: MATLAB was used.
DOI: 10.15468/dl.vgja4z
title: Occurrence Download

description: A dataset containing 1012 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lethe verma"
 ]
}

 The dataset includes 1012 records from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003486-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.