cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3ffbg79ph
title: Data from: Maintenance and expansion of genetic and trait variation following domestication in a clonal crop: Enset tGBS individual genotype data

description: Clonal propagation enables favourable crop genotypes to be rapidly
 selected and multiplied. However, the absence of sexual propagation can
 lead to low genetic diversity and accumulation of deleterious mutations,
 which may eventually render crops less resilient to pathogens or
 environmental change. To better understand this trade-off, we characterise
 the domestication and contemporary genetic diversity of Enset (Ensete
 ventricosum), an indigenous African relative of bananas (Musa) and
 principal starch staple for 20 million Ethiopians. Wild enset is strictly
 sexually outcrossing, but in cultivation is propagated clonally and
 associated with diversification and specialisation into hundreds of named
 landraces. We applied tGBS sequencing to generate genome-wide genotypes
 for 192 accessions from across enset’s cultivated distribution, and
 surveyed 1340 farmers on enset agronomic traits. Overall, reduced
 heterozygosity in the domesticated lineage was consistent with a
 domestication bottleneck that retained 37% of wild diversity. However, an
 excess of putatively deleterious missense mutations at low frequency
 present as heterozygotes suggested accumulation of mutational load in
 clonal domesticated lineages. Our evidence indicates that the major
 domesticated lineages initially arose through historic sexual
 recombination associated with a domestication bottleneck, followed by
 amplification of favourable genotypes through an extended period of clonal
 propagation. Among domesticated lineages we found significant phylogenetic
 signal for multiple farmer-identified food, nutrition and disease
 resistance traits and little evidence of contemporary recombination.
 Development of future-climate adapted genotypes may require crop breeding,
 but outcrossing risks exposing deleterious alleles as homozygotes. This
 trade-off may partly explain the ubiquity and persistence of clonal
 propagation over recent centuries of comparative climate stability.
DOI: 10.5061/dryad.fn2z34v0p
title: Seasonal changes of vomeronasal responses to chemosensory cues associated with circulating estrogen in the female muskrats (Ondatra zibethicus)

description: In numerous animals, the vomeronasal organ (VNO) is a crucial chemosensory
 organ that receives chemical signals, which is involved in
 species-specific behaviors, including social and sexual behaviors. Muskrat
 (Ondatra zibethicus) has a sensitive VNO system that detects specific
 chemicals such as pheromones and hormones and induces seasonal breeding
 behaviors. The purpose of this study is to investigate the distributions
 and expression patterns of vomeronasal receptor type-1 (V1R), vomeronasal
 receptor type-2 (V2R), estrogen receptors α and β (ERα and ERβ) in the
 female muskrats’ VNO during the different periods. V1R, V2R, ERα and ERβ
 were found in sensory epithelial cells, non-sensory epithelial cells and
 lamina propria cells of the female muskrats’ VNO. V2R and ERα mRNA levels
 in the VNO of the breeding period declined sharply, in comparison to those
 of the non-breeding period, while V1R and ERβ mRNA levels were detected
 reversely. Additionally, a transcriptomic study in the VNO identified that
 differentially expressed genes might be related to estrogen signals and
 metabolic pathways. These findings suggested that the seasonal structural
 and functional changes of VNO in the female muskrats within different
 reproductive statuses, and estrogen regulated its function through binding
 to ERα and ERβ in the female muskrats’ VNO.
DOI: 10.5061/dryad.7wm37pvz6
title: Data for: Tensile cracks can shatter classical speed limits

description: Brittle materials fail by means of rapid cracks. At their tips, tensile
 cracks dissipate elastic energy stored in the surrounding material to
 create newly fractured surfaces, precisely maintaining `energy balance’ by
 exactly equating the energy flux with dissipation. Using energy balance,
 fracture mechanics perfectly describes crack motions; accelerating from
 nucleation to their maximal speed of cR, the Rayleigh wave speed. Beyond
 cR, tensile fracture is generally considered to be impossible. By the use
 of brittle hydrogels, we experimentally demonstrate that a wholly new and
 different class of tensile cracks that move faster than the shear wave
 speed, cs, exists. The principle of energy balance no longer
 dictates their dynamics; this new branch of cracks smoothly surpasses cs
 to reach unprecedented speeds that approach the speed of dilatation waves.
 The transition from `classical’ cracks to these `supershear’ cracks takes
 place at critical values of applied strains. We, furthermore, show that
 the values of these, rather moderate (12–14%), critical strains are
 intimately related to the microscopic material structure. This new mode of
 tensile fracture represents a fundamental paradigm shift in our
 understanding of ‘how things break’.
DOI: 10.5061/dryad.12jm63z30
title: Plant productivity response to inter- and intra-symbiont diversity: mechanisms, manifestations, and meta-analyses

description: Symbiont diversity can have large effects on plant growth but the
 mechanisms generating this relationship remain opaque. We identify three
 potential mechanisms underlying symbiont diversity-plant productivity
 relationships: provisioning with complementary resources, differential
 impact of symbionts of varying quality, and interference between
 symbionts. We connect these mechanisms to descriptive representations of
 plant responses to symbiont diversity, develop analytical tests
 differentiating these patterns, and test them using meta-analysis. We find
 generally positive symbiont diversity-plant productivity relationships,
 with relationship strength varying with symbiont type. Inoculation with
 symbionts from different guilds (e.g. mycorrhizal fungi and rhizobia)
 yields strongly positive relationships, consistent with complementary
 benefits from functionally distinct symbionts. In contrast, inoculation
 with symbionts from the same guild yields weak relationships, with
 co-inoculation not consistently generating greater growth than the best
 individual symbiont, consistent with sampling effects. The statistical
 approaches we outline, along with our conceptual framework, can be used to
 further explore plant productivity and community responses to symbiont
 diversity, and we identify critical needs for additional research to
 explore context-dependency in these relationships.
DOI: 10.5061/dryad.pc866t1tq
title: Data from: It's only natural: Plant respiration in unmanaged systems

description: Respiration plays a key role in the terrestrial carbon cycle and is a
 fundamental metabolic process in all plant tissues and cells. We review
 respiration from the perspective of plants that grow in their natural
 habitat and how it is influenced by wide-ranging elements at different
 scales, from metabolic substrate availability to shifts in climate.
 Decades of field-based measurements have honed our understanding of the
 biological and environmental controls on leaf, root, stem, and
 whole-organism respiration. Despite this effort, there remain gaps in our
 knowledge within and across species and ecosystems, especially in more
 challenging-to-measure tissues like roots. Recent databases of respiration
 rates and associated leaf traits from species representing diverse biomes,
 plant functional types, and regional climates have allowed for a
 wider-lens view at modeling this important CO2 flux. We also re-analyze
 published data sets to show that maximum leaf respiration rates (Rmax) in
 species from around the globe are related both to leaf economic traits and
 environmental variables (precipitation and air temperature), but that root
 respiration does not follow the same latitudinal trends previously
 published for leaf data. We encourage the ecophysiological community to
 continue to expand their study of plant respiration in tissues that are
 difficult to measure and at the whole plant and ecosystem levels to
 address outstanding questions in the field.
description: These data are a reanalysis of data originally published in
 O'Sullivan et. (2017). Respiration temperature response curves were
 collected on a large number of species. This dataset includes the maximum
 respiration values extracted from these respiration temperature response
 curves, whereas O'Sullivan et al. (2017) published the maximum
 temperature of respiration. Full data collection methods for the
 respiration temperature response curves are available in O'Sullivan
 et al. (2017). Full data analysis methods for the extraction of maximum
 respiration are available in Schmiege et al. (2023). Full references for
 both these publications are available in the README file associated with
 this dataset.
description: The datafile is a .csv file that can be opened in most programs
 and/or software including Microsoft Excel, R and Python.
DOI: 10.5061/dryad.f7m0cfz20
title: Data for: Aspects of distribution, abundance, habitat, and life history of the Caddo Madtom (Noturus taylori), a narrow endemic of the Ouachita Highlands

description: The Caddo Madtom, Noturus taylori, is a small catfish endemic to the
 Ouachita Mountain ecoregion in Arkansas, with habitat altered by land use
 practices and reservoir dams. We examined aspects of distribution,
 abundance, habitat, and life history of N. taylori during seasonal
 sampling from winter 2016 through fall 2017. Our sampling data were
 concordant with previous studies that suggested N. taylori is more
 widespread and has higher catch per unit effort in the Caddo River
 drainage when compared to the upper Ouachita River drainage. We did not
 detect N. taylori in the Little Missouri River drainage, where it is
 presumed extirpated. A total of 370 individuals ranging from 14–76 mm
 (mean = 45.1 mm) standard length (SL) were collected during seasonal
 samples. Length-frequency analyses estimated a maximum age of 3 years for
 N. taylori, and we identified three discernable age classes with the
 emergence of young-of-year (age 0 cohort) in summer: age 0 (up to ~40 mm
 SL); age 1 (~41–60 mm SL); and age 2+ (&gt;60 mm SL). Sites where N.
 taylori was captured had an average depth of 20.6 cm, an average base
 velocity of 0.18 m/sec, and were dominated primarily by a mix of gravel,
 pebble, and cobble. Despite the relatively higher abundances of N. taylori
 in the Caddo River, we recommend that long-term, periodic monitoring of N.
 taylori would be an important conservation tool to assess potential future
 changes in distribution, habitat, occurrence, and abundance. Future
 studies that implement occupancy and habitat suitability modeling are
 needed to better understand suitable and preferred habitat of N. taylori.
description: Length data were collected for wild-caught
 <em>Noturus</em> <em>taylori</em> from sample
 sites throughout the known distribution range. Habitat variables were
 collected from each 2x2 meter plot where <em>Noturus</em>
 <em>taylori</em> was captured during seasonal
 sampling. 
description: These datasets are associated with summarized habitat variables
 and length frequency analyses for <em>Noturus</em>
 <em>taylori</em> that are presented in the published study
 above. The R scripts in the
 "R_scripts_ELEFAN_Ntaylori_McCall_Fluker_2023.txt" file are
 intended to be used in the program R with the input file
 "SL_data_Ntaylori_McCall_Fluker_2023.csv" to replicate our
 length frequency analysis of <em>Noturus</em>
 <em>taylori</em>. The analysis requires the use of R and the R
 packages "devtools" and "TropFishR". The analyses
 using these R scripts were originally conducted in R version 3.6.3 and
 were later verified to run successfully in R version 4.2.3. Data files can
 otherwise be opened with MS Excel (.xlsx) or text editor (.txt).
DOI: 10.5061/dryad.rn8pk0ph3
title: A metadata framework for electronic phenotypes

description: As many phenotyping algorithms are being created to support precision
 medicine or observational studies using electronic patient data, it is
 getting increasingly difficult to identify the right algorithm for the
 right task. A metadata framework promises to help curate phenotyping
 algorithms to facilitate more efficient and accurate retrieval. We
 recruited 20 researchers from two phenotyping communities, the eMERGE and
 the OHDSI communities, and used a mixed-methods approach to develop the
 metadata framework. Once we achieved a consensus of 39 metadata elements,
 we surveyed 47 new researchers from these communities to evaluate the
 utility of the metadata framework. Two researchers were also asked to use
 it to annotate eight type 2 diabetes mellitus phenotypes. The survey
 consisted of a series of multiple-choice questions, which allowed rating
 of the utility of each element on a scale of 1-5, and open-ended
 questions, which allowed for narrative responses. More than 90% of
 respondents rated metadata elements concerning phenotype definition and
 validation methods and metrics with a score of 4 or 5. Our thematic
 analysis of the respondents’ feedback indicates that the strengths of the
 metadata framework were its ability to capture rich descriptions,
 explicitness, compliance with data standards, comprehensiveness in
 validation metrics, and ability to enable cross-phenotype searches.
 Limitations were its complexity for data collection and entailed costs.
description: We used online third-party
 software (Qualtrics, Provo, UT) to collect the dataset. We performed
 statistical analyses in using R, version 4.1.1.
DOI: 10.5061/dryad.h18931zrm
title: Virtual prey with Lévy motion are preferentially attacked by predatory fish

description: Of widespread interest in animal behaviour and ecology is how animals
 search their environment for resources, and whether these search
 strategies are optimal. However, movement also affects predation risk
 through effects on encounter rates, the conspicuousness of prey, and the
 success of attacks. Here we use predatory fish attacking a simulation of
 virtual prey to test whether predation risk is associated with movement
 behaviour. Despite often being demonstrated to be a more efficient
 strategy for finding resources such as food, we find that prey displaying
 Lévy motion are twice as likely to be targeted by predators than prey
 utilising Brownian motion. This can be explained by the predators, at the
 moment of the attack, preferentially targeting prey that were moving with
 straighter trajectories rather than prey that were turning more. Our
 results emphasise that costs of predation risk need to be considered
 alongside the foraging benefits when comparing different movement
 strategies.
DOI: 10.5061/dryad.tht76hf43
title: Data for: Invasive brown widow spiders avoid parasitism despite high densities

description: Invasive species are sometimes less susceptible to natural enemies
 compared to native species, but the mechanism is often unclear. Here we
 tested two potential mechanisms for lower parasitism of invasive species:
 density-dependent parasitism and preference for human-dominated habitats.
 We investigated how variation in host density and habitat type affect egg
 sac parasitism in two widow spider species (family
 Theridiidae). We compared parasitism on the egg sac of the brown
 widow, Latrodectus geometricus, an urban invasive species, and
 the white widow, L. pallidus, a species native to Israel. To
 investigate variation in host and parasitoid density, we measured
 nearest-neighbor distance between spider webs and parasitism rates in 16
 sites, and in a single site monthly throughout a year. In L. pallidus,
 denser sites were more heavily parasitized (up to 55%) and parasitism rate
 increased with population density throughout the season. Extremely dense
 L. geometricus populations, however, had very low rates of parasitism
 (0-5%). We then conducted an egg sac transplant experiment in
 human-dominated and natural habitats. We found no parasitism of either
 species in the human-dominated habitat, compared to 30% parasitism of both
 species in the natural habitat. In addition, we found evidence for higher
 predation of L. pallidus than of L. geometricus egg sacs, particularly in
 the natural habitat. These combined results suggest that the
 human-dominated habitats inhabited by L. geometricus have a lower
 abundance of predators and parasites. We conclude that lower parasitism
 and predation in human-dominated habitats could contribute to the invasion
 success of L. geometricus.
description: These data were collected from field work conducted in the Negev
 Desert. The raw data of egg sacs collected and parasitism was recorded to
 Excel sheets and then was checked for accuracy.
DOI: 10.15468/dl.r3x7ks
title: Occurrence Download

description: A dataset containing 42009335 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 42009335 records from 6753 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003003-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.4121/731e56f7-fd6d-41c4-9b96-aaecf24a0008.v1
title: Replication Data for: Analyzing collaborative governance through social network analysis: a case study of River management along the Waal River in the Netherlands

description: Until recently, governmental organizations played a dominant and decisive role in natural resource management. However, an increasing number of studies indicate that this dominant role is developing towards a more facilitating role as equal partner to improve efficiency and create a leaner state. This approach is characterized by complex collaborative relationships between various actors and sectors on multiple levels. To understand this complexity in the field of environmental management, we conducted a social network analysis of floodplain management in the Dutch Rhine delta. We charted the current interorganizational relationships between 43 organizations involved in flood protection (blue network) and nature management (green network) and explored the consequences of abolishing the central actor in these networks. The discontinuation of this actor will decrease the connectedness of actors within the blue and green network and may therefore have a large impact on the exchange of ideas and decision-making processes. Furthermore, our research shows the dependence of non-governmental actors on the main governmental organizations. It seems that the Dutch governmental organizations still have a dominant and controlling role in floodplain management. This challenges the alleged shift from a dominant government towards collaborative governance and calls for detailed analysis of actual governance. (2015-09-01)
DOI: 10.5255/ukda-sn-857726
title: Islands of Innovation in Protracted Crises: A New Approach to Building Equitable Resilience From Below: Transcript Data, 2020-2023

description: Current global humanitarian initiatives around disaster risk reduction, peacebuilding, and epidemics promote a local turn (e.g. the Sendai framework, the Grand Bargain, the New Deal for Engagement in Fragile States and the International Health Regulations). However, the global humanitarian community has struggled to understand community-level dynamics and factor them into their programmes. 
These data looks at how ‘islands of innovation’ provide the basis for broader structural transformation. Political, cultural and social
histories of these communities and storytellers (e.g. customary or spiritual storytellers, music artists) are helping to create new notions and idioms of community resilience. 

These bottom-up approaches, centred on islands of innovation, emerge from long-term social learning processes, and usually as a result of multiple shocks - from disasters to epidemics and conflict. 

The result is the building of interactions between individual and community forms of resilience.
DOI: 10.15468/dl.7bksen
title: Occurrence Download

description: A dataset containing 455414 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen, Occurrence evidence)",
 "Continent is one of (South America, Africa)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Apidae"
 ]
}

 The dataset includes 455414 records from 328 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002994-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18438270
title: Supporting information for "Genomic signatures of virulence and resistance for Serratia marcescens revealed by analysis of clinical isolates from India"

description: Serratia marcescens is an opportunistic pathogen that is widely known to cause healthcare-associated infections with significant morbidity and mortality, particularly in high-risk settings. In this study, the genomic characteristics of S. marcescens isolates from an Indian tertiary care hospital outbreak of septicemia were investigated to better understand the genetic elements associated with pathogenicity and antibiotic resistance. Several mobile genetic elements, such as prophage sequences, genomic islands, and plasmid sequences, IncFIB(K), were present in the genome encoding various virulence and fitness traits, including FlhDC-ShlBA, Type Six Secretion System, pgaABCD operon, mannose-resistant (MR), and mannose-sensitive (MS) pilus. Phenotypic resistance to aminoglycoside group of antibiotics (gentamicin) was observed in 43% of the isolates analyzed, encoding aminoglycoside modifying enzymes, eight isolates that showed resistance to cefepime and aztreonam carried CTX-M-15, OXA-1, TEM-1 beta-lactamase resistance genes. Seven co-trimoxazole-resistant isolates harbored drfA14 and sul2 which confer resistance to trimethoprim and sulphonamide, respectively. None of the 16 S. marcescens isolates showed complete resistance to the fluoroquinolones tested in this study. Pan-genome analysis of 16 S. marcescens isolates identified 9601 genes, comprising 2476 core, 3488 shell, and 3637 cloud genes, demonstrating an open pan-genome shaped by horizontal gene transfer. Core genome phylogeny revealed vertical inheritance and close relatedness among isolates, while accessory gene-based clustering highlighted unit-specific adaptations and possible inter-unit transmission. Functional categorization showed core genes encoding essential metabolic functions, whereas accessory and unique genes contributed to motility, secretion, and niche-specific environmental interactions. The observations from this study highlight genetic versatility of the S. marcescens isolates.
DOI: 10.15468/dl.ardgt7
title: Occurrence Download

description: A dataset containing 174 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Parinari occidentalis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 174 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003036-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.deywgs
title: Occurrence Download

description: A dataset containing 1461 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Codonopsis pilosula"
 ]
}

 The dataset includes 1461 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003037-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.