cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15139/s3/mravsg
title: Data Management and Sharing Plan for: Phase-controlled hybrid magnonics enabled by synergistic interfacial spin-spin interactions

description: The Data Management and Sharing Plan describes the scientific data to be generated and/or used in the research and outlines a strategy for managing and sharing project data.
description: Data Management and Sharing Plan
DOI: 10.5061/dryad.02v6wwq04
title: Data from: Phylogenetics and seed morphology of African Nymphoides (Menyanthaceae)

description: We evaluated the boundaries among Nymphoides (Menyanthaceae) species in
 Africa, a region where the genus has received relatively little study. We
 gathered morphological data from seeds using light and scanning electron
 microscopy, and we conducted molecular phylogenetic analyses using nuclear
 sequence data from the internal transcribed spacer (ITS) region.
 Morphological and molecular features distinguished six species and
 affirmed their respective geographic ranges. No African specimens were
 attributable to Nymphoides indica, even though this paleotropical species
 previously had been understood to grow in Africa. We establish the new
 combination Nymphoides senegalensis (G. Don) Tippery, based on an
 established African basionym, to accommodate the specimens formerly
 identified as N. indica. Phylogenetic analyses resolved two distinct
 clades containing African species. The majority of African species are
 closely related to neotropical species, with which they share similar
 petal ornamentation. The morphologically distinct N. ezannoi shares floral
 and phylogenetic similarity with species from North America and Asia.
 Results presented here support prior hypotheses that allopolyploid species
 in the Americas may have originated from one or more parental lineages in
 Africa. Seed morphological characters remain some of the most reliable
 features for identifying species, particularly for herbarium specimens
 lacking observable floral characters.
DOI: 10.7941/d18907
title: Current limits on determination of protonation state using neutron macromolecular crystallography

description: Neutron diffraction is a technique used to locate hydrogen and and
 deuterium atoms at medium data resolution in macromolecular
 structures. Typically, the structures are not determined de novo; instead,
 the structure has been previously determined with X-ray diffraction. The
 Protein Data Bank (PDB) was parsed to find homologue models for all
 neutron structures. The data table lists PDB IDs for
 X-ray structures that are similar to neutron
 models deposited  in the PDB (as of October
 2019).  
description: The
 homologue protein sequences were obtained with the program BLAST. The
 X-ray model with the highest sequence identity and highest resolution
 (cut-offs: minimum sequence identity of 90% and minimum data resolution of
 2Å) was considered as homologue. The BLAST search
 provided 156 homologues for all 161 neutron models.
DOI: 10.3886/e206781v1-198150
title: Data and code for: Targeting Impact versus Deprivation

description: A large literature has examined how best to target anti-poverty programs to those most deprived in some sense (e.g., consumption). We examine the potential tradeoff between this objective and targeting those most impacted by such programs. We work in the context of an NGO cash transfer program in Kenya, employing recent advances in machine learning methods and dynamic outcome data to learn proxy means tests that jointly target both objectives. Targeting solely on the basis of deprivation is not attractive in this setting under standard social welfare criteria unless the planner’s preferences are extremely redistributive.<br>This repository provides data and code accompanying the article.<br><br>
description: The analysis uses household sampling weights
description: Response Rates: See Egger et al. (2022) for full survey response rate details.
description: Households were randomly sampled within study villages, stratified by cash transfer eligibility status. See Egger et al. (2022) for full details.
description: Households in 653 villages in Siaya County, Kenya taking part in an NGO cash transfer experiment<br>. Smallest Geographic Unit: household
description: computer-assisted personal interview (CAPI);
DOI: 10.15139/s3/miajpf
title: Data Management and Sharing Plan for: The Clinical Genome Resource - Advancing genomic medicine through biocuration and expert assessment of genes and variants at scale

description: The Data Management and Sharing Plan describes the scientific data to be generated and/or used in the research and outlines a strategy for managing and sharing project data.
description: Data Management and Sharing Plan
DOI: 10.5061/dryad.k98sf7m3c
title: Cascading effects of climate change on plankton community structure

description: Plankton communities account for at least half of global primary
 production and play a key role in the global carbon cycle. Warming and
 acidification may alter the interaction chains in these communities from
 the bottom and top of the food web. Yet, the relative importance of these
 potentially complex interactions has not yet been quantified. Here we
 examine the isolated and combined effects of warming, acidification, and
 reductions in phytoplankton and predator abundances in a series of
 factorial experiments. We find that warming directly impacts the top of
 the food web, but that the intermediate trophic groups are more strongly
 influenced by indirect effects mediated by altered top-down interactions.
 Direct manipulations of predator and phytoplankton abundance reveal
 similar strong top-down interactions following top predator decline. A
 meta-analysis of published experiments further support the conclusion that
 warming has stronger direct impacts on the top and bottom of the food web
 rather than the intermediate trophic groups, with important differences
 between freshwater and marine plankton communities. Our results reveal
 that the trophic effect of warming cascading down from the top of the
 plankton food web is a powerful agent of global change.
description: This data is supplement to: Murphy et al. Cascading effects of
 climate change on plankton community structure. Ecology and
 Evolution.
DOI: 10.5061/dryad.15dv41nt9
title: Data from: BCI training to move a virtual hand reduces phantom limb pain: a randomized crossover trial

description: Objective: To determine whether training with a brain–computer interface
 (BCI) to control an image of a phantom hand, which moves based on cortical
 currents estimated from magnetoencephalographic signals, reduces phantom
 limb pain. Methods: Twelve patients with chronic phantom limb pain of the
 upper limb due to amputation or brachial plexus root avulsion participated
 in a randomized single-blinded crossover trial. Patients were trained to
 move the virtual hand image controlled by the BCI with a real decoder,
 which was constructed to classify intact hand movements from motor
 cortical currents, by moving their phantom hands for 3 days (“real
 training”). Pain was evaluated using a visual analogue scale (VAS) before
 and after training, and at follow-up for an additional 16 days. As a
 control, patients engaged in the training with the same hand image
 controlled by randomly changing values (“random training”). The two
 trainings were randomly assigned to the patients. This trial is registered
 at UMIN-CTR (UMIN000013608). Results: VAS at day 4 was significantly
 reduced from the baseline after real training (45.3 [24.2] to 30.9 [20.6],
 1/100mm, mean [SDs]; P=0.009&lt;0.025), but not after random training
 (P=0.047&gt;0.025). Compared to VAS at day 1, VAS at days 4 and 8 was
 significantly reduced by 32% and 36%, respectively, after real training
 and was significantly lower than VAS after random training
 (P&lt;0.01). Conclusion: Three-day training to move the hand images
 controlled by BCI significantly reduced pain for one week. Classification
 of evidence: This study provides Class &#8546; evidence that BCI
 reduces phantom limb pain.  
description: These are the supplementary information for the manuscript
 entitled "BCI training to move a virtual hand reduces phantom limb
 pain: A randomized crossover trial" published in Neurology.
DOI: 10.5061/dryad.g1jwstqn0
title: Multiple-batch spawning as a bet-hedging strategy in highly stochastic environments: an exploratory analysis of Atlantic cod

description: Stochastic environments shape life-history traits and can promote
 selection for risk-spreading strategies, such as bet-hedging. Although the
 strategy has often been hypothesised to exist for various species,
 empirical tests providing firm evidence have been rare, mainly due to the
 challenge in tracking fitness across generations. Here, we take a ‘proof
 of principle’ approach to explore whether the reproductive strategy of
 multiple-batch spawning constitutes a bet-hedging. We used Atlantic cod
 (Gadus morhua) as the study species and parameterised an eco-evolutionary
 model, using empirical data on size-related reproductive and survival
 traits. To evaluate the fitness benefits of multiple-batch spawning
 (within a single breeding period), the mechanistic model separately
 simulated multiple-batch and single-batch spawning populations under
 temporally varying environments. We followed the arithmetic and geometric
 mean fitness associated with both strategies and quantified the mean
 changes in fitness under several environmental stochasticity levels. We
 found that, by spreading the environmental risk among batches,
 multiple-batch spawning increases fitness under fluctuating environmental
 conditions. The multiple-batch spawning trait is, thus, advantageous and
 acts as a bet-hedging strategy when the environment is exceptionally
 unpredictable. Our research identifies an analytically flexible,
 stochastic, life-history modelling approach to explore the fitness
 consequences of a risk-spreading strategy and elucidates the importance of
 evolutionary applications to life-history diversity. 
description: Data for this study was simulated with the eco-evolutionary model
 parameterised for Atlantic cod (.R code is provided). The process is
 described in the method sections.
description: There are two types of data sets: 1) A
 simulation code to drive the eco-evolutionary dynamics of multiple-batch
 and single-batch spawning cod populations. The code is an extended version
 of the code developed by https://doi.org/10.1111/j.1752-4571.2011.00215.x  2) Last-year transcripts of populations that have been preadapted to each scenario of environmental pressure. These transcripts serve as import files or initial populations that are needed to run the simulation code.
DOI: 10.15468/dl.u5vm5h
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "PublishingOrg is one of (c2ecae57-6701-485e-9ebd-5f87b2945cb2, f9b67ad0-9c9b-11d9-b9db-b8a03c50a862, 6ea87510-0561-11d8-b851-b8a03c50a862)",
 "TaxonKey is Melanoplus comanche",
 "Year 1900-2026"
 ]
}

 The dataset includes 17 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002161-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.r7sqv9s7v
title: Variation in body size and sexual size dimorphism in the most widely-ranging lizard: testing the effects of reproductive mode and climate

description: Reproductive mode, ancestry, and climate are hypothesized to determine
 body-size variation in reptiles but their effects have rarely been
 estimated simultaneously, especially at the intraspecific level. The
 common lizard (Zootoca vivipara) occupies almost the entire Northern
 Eurasia and includes viviparous and oviparous lineages, thus representing
 an excellent model for such studies. Using body length data for
 &gt;10,000 individuals from 72 geographically distinct populations
 over the species’ range we analysed how sex-specific adult body size and
 sexual size dimorphism (SSD) is associated with reproductive mode, lineage
 identity, and several climatic variables. Variation in male size was low
 and poorly explained by our predictors. In contrast, female size and SSD
 varied considerably, demonstrating significant effects of reproductive
 mode and particularly seasonality. Populations of the western oviparous
 lineage (northern Spain, south-western France) exhibited a smaller female
 size and less female-biased SSD than those of the western viviparous
 (France to Eastern Europe) and the eastern viviparous (Eastern Europe to
 Far East) lineages; this pattern persisted even after controlling for
 climatic effects. The phenotypic response to seasonality was complex:
 across the lineages, as well as within the Eastern Viviparous lineage,
 female size and SSD increase with increasing seasonality, whereas the
 Western Viviparous lineage followed the opposing trends. Altogether,
 viviparous populations seem to follow a saw-tooth geographic cline, which
 might reflect the non-monotonic relationship of body size at maturity in
 females with the length of activity season. This relationship is predicted
 to arise in perennial ectotherms as a response to environmental
 constraints caused by seasonality of growth and reproduction. 
 The SSD allometry followed the converse of Rensch's rule, a rare
 pattern for amniotes. Our results provide the first evidence of opposing
 body-size—climate relationships in intraspecific units.
description: See Methods and Appendices 1,  and 3 in Roitberg et al. 2020, as
 well as the Readme files in datadryad for details
DOI: 10.5061/dryad.qv9s4mwb3
title: Nucleotide diversity of functionally different groups of immune response genes in Old World camels based on newly annotated and reference-guided assemblies

description: Background Immune-response (IR) genes have an important role in the
 defense against highly variable pathogens, and therefore, genetic
 diversity in these genomic regions is essential for species’ survival and
 adaptation. Although current genome assemblies from Old World camelids are
 very useful for investigating genome-wide diversity, demography and
 population structure, they have inconsistencies and gaps that limit
 analyses at local genomic scales. Improved and more accurate genome
 assemblies and annotations are needed to study complex genomic regions
 like adaptive and innate IR genes. Results In this work, we improved the
 genome assemblies in the three Old World camel species – domestic
 dromedary and Bactrian camel, and the two-humped wild camel – via
 different computational methods. The newly annotated dromedary genome
 assembly CamDro3 served as reference to scaffold the NCBI RefSeq genomes
 of domestic Bactrian and wild camels. These upgraded assemblies were then
 used to assess nucleotide diversity of IR genes within and between
 species, and to compare the diversity found in immune genes and the rest
 of the genes in the genome. We detected differences in the nucleotide
 diversity among the three Old World camelid species and between IR gene
 groups, i.e., innate versus adaptive. Among the three species, domestic
 Bactrian camels showed the highest mean nucleotide diversity. Among the
 functionally different IR gene groups, the highest mean nucleotide
 diversity was observed in the major histocompatibility complex.
 Conclusions The new camel genome assemblies were greatly improved in terms
 of contiguity and increased size with fewer scaffolds, which is of general
 value for the scientific community. This allowed us to perform in-depth
 studies on genetic diversity in immunity-related regions of the genome.
 Our results suggest that differences of diversity across classes of genes
 appear compatible with being caused by a combination of population history
 coupled with possible distinct exposures to pathogens and consequent
 different selective pressures.
description: See attached old-world-camel-genomes-readme-all-revision.txt for
 additional information.
DOI: 10.25934/pr00012551.0
title: Available datapackage for study 'Bridging the Evidence-to-Practice Gap: Evaluating Practice Facilitation as a Strategy to Accelerate Translation of a Systems-Level Adherence Intervention into Safety Net Practices / Project EVIDENCE'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.5061/dryad.3n5tb2rcz
title: Intrinsic post-ejaculation sperm ageing does not affect offspring fitness in Atlantic salmon

description: Postmeiotic sperm ageing, both before and after ejaculation, has been
 shown to negatively affect offspring fitness by lowering the rate of
 embryonic development, reducing embryonic viability, and decreasing
 offspring condition. These negative effects are thought to be caused by
 intrinsic factors such as oxidative stress and ATP depletion or extrinsic
 factors such as temperature and osmosis. Effects of post-ejaculation sperm
 ageing on offspring fitness have so far almost exclusively been tested in
 internal fertilisers. Here, we tested whether intrinsic post-ejaculation
 sperm ageing affects offspring performance in an external fertiliser, the
 Atlantic salmon Salmo salar. We performed in vitro fertilisations with a
 split clutch design where sperm were subjected to four post-ejaculation
 ageing treatments. We varied the duration between sperm activation and
 fertilisation while minimising extrinsic stress factors and tested how
 this affected offspring fitness. We found no evidence for an effect of our
 treatments on embryo survival, hatching time, larval standard length,
 early larval survival or larval growth rate, indicating that intrinsic
 post-ejaculation sperm ageing may not occur in Atlantic salmon. One reason
 may be the short lifespan of salmon sperm after ejaculation. Whether our
 findings are true in other external fertilisers with extended sperm
 activity remains to be tested.
DOI: 10.5061/dryad.mcvdncjwq
title: Stable flies, Stomoxys calcitrans L. (Diptera: Muscidae), improve offspring fitness by avoiding oviposition substrates with competitors or parasites

description: Oviposition site selection by gravid female insects is an important
 determinant in species distribution, abundance, and population dynamics.
 Females may assess the suitability of a potential oviposition substrate by
 using cues from conspecific or heterospecific individuals already present.
 Here, we assessed whether the presence of conspecific or heterospecific
 larvae and parasites influenced oviposition decisions by the stable fly,
 Stomoxys calcitrans (Linneaus). Using dual and multiple-choice oviposition
 bioassays, we found that gravid female S. calcitrans avoided substrates
 with conspecific larvae, the larvae of house flies, Musca domestica
 (Linneaus), and the mite Macrocheles muscaedomesticae (Scopoli). Avoidance
 of conspecific and heterospecific larvae persisted in the dark, suggesting
 that this behaviour is mediated by chemical rather than visual cues. When
 we reared S. calcitrans in the presence of conspecific larvae and the
 larvae of house flies at different densities we found that this negatively
 affected emergence time, larval weight, larval survival, pupal weight,
 pupal survival, and adult weight. We also demonstrated that individuals of
 S. calcitrans developed in the presence of mites exhibited low egg
 hatchability, and poor larval and adult survival. Our study provides
 additional support for the “preference-performance” hypothesis in S.
 calcitrans, with gravid females preferring to lay eggs on a substrate that
 will enhance offspring fitness. We recommend that the  chemical
 cues involved in avoidance by gravid female S. calcitrans of substrates
 with conspecific and heterospecific larvae should be elucidated. This
 could lead to the discovery of repellent chemicals important for S.
 calcitrans management.
description: See data description file and manuscript for more details.
DOI: 10.5061/dryad.4qrfj6q6j
title: Data for: Convergent evolution of tail spines in squamate reptiles driven by microhabitat use

description: The repeated evolution of convergent or analogous traits is often used as
 evidence for adaptive evolution. Squamate reptiles show a high degree of
 convergence in a variety of morphological traits; however, the
 evolutionary mechanisms driving these patterns are not fully understood.
 Here we investigate the evolution of tail spines, a trait that evolved
 multiple times in evolutionarily independent clades of lizards. Taking a
 comparative phylogenetic approach, we use 2877 squamate species to
 demonstrate that the evolution of spiny tails is correlated with
 microhabitat use, with species that live in rocky habitats significantly
 more likely to have evolved spiny tails. In light of previous behavioural
 observations, our results suggest that spiny-tailed lizards have an
 advantage in rocky habitats through predation avoidance, where tail spines
 are used to prevent extraction from rocky crevices. In concordance with
 previous research on lizard body armour, our results suggest that the
 evolution of tail spines is coupled to both a rock-dwelling lifestyle and
 predator avoidance strategies, and highlight a complex interplay between
 different selective pressures on the evolution of defensive morphologies
 in reptiles.
description: <b>Supplementary
 Figure 1</b> Distinction of the SPINY and the
 SPINY STRICT datasets   <b>Supplementary Table
 1</b> Data Body size, microhabitat and spiny
 tail data of the 2877 squamate species used in the study   <b>Supplementary Table
 2</b> Results of the fitPagel
 funtion Results
 of the fitPagel function, testing for correlations between the evolution
 of spiny tails and microhabitat use   <b>Supplementary Table
 3</b> Results of the HiSSE
 models Results of
 the hidden state-dependent speciation and extinction models (HiSSE),
 testing for changes in diversification rates associated with spiny
 tails  
 <b>Supplementary
 Table 4</b> Results of the D
 statistic Results
 of the D statistic, testing for a phylogenetic signal of the spiny tail
 trait  
 <b>Supplementary
 Table 5</b> Phylogenetic ANOVA results (spiny
 tails vs microhabitat) Results of the phylogenetic
 ANOVA, testing if there are differences in the number of spiny-tailed
 species in different microhabitats   <b>Supplementary Table
 6</b> Phylogenetic ANOVA results (spiny
 tails vs. body size) Results of the phylogenetic
 ANOVA, testing if there are differences in body size between spiny-tailed
 and non-spiny-tailed species   <b>Supplementary Table
 7</b> Phylogenetic ANOVA results
 (microhabitat vs body size) Results of the phylogenetic
 ANOVA, testing if there are differences in body size between squamates
 occupying different microhabitats   <b>Supplementary Table
 8</b> Phylogenetic logistic regression
 results Results
 of the phylogenetic logistic regression, testing for correlations between
 the spiny tail trait and body size   <b>Supplementary
 references</b> Literature list used for coding
 the spiny tail and microhabitat traits   <b>Tree
 file</b> Dated tree used for the
 analyses