cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6086/d1566z
title: Unequal reproduction early in a social transition

description: In eusocial insects, nestmate queens can differ in their reproductive
 output, causing asymmetries in the distribution of mutual benefits.
 However, little is known about how reproductive success is partitioned in
 incipiently polygynous species, which would provide clues about the
 evolutionary forces shaping the emergence of polygyny. Here, we leverage a
 recent transition from predominantly single-queen (monogyne) to
 multiple-queen (polygyne) colonies in an invasive yellowjacket to
 investigate whether queens in incipiently polygyne colonies invest equally
 in reproductive effort or vary in their relative investment in each caste.
 We excavated nine polygyne Vespula pensylvanica colonies in Hawaii and
 used RAD-sequencing to infer the parentage of worker, male, and gyne
 (daughter queen) pupae from each nest comb.  In four colonies
 with at least eight gyne pupae, a single queen produced most or all gynes.
 These queens had no male offspring and few worker offspring, suggesting
 that a subset of nestmate queens might exploit the collective benefits of
 newly polygyne societies. In contrast to most queens, gyne-producers had
 offspring distributed non-randomly across nest combs.  Nestmate
 queens generally exhibited low relatedness levels. Our results suggest
 that rapid, ecologically driven transitions to polygyny among unrelated
 queens may, at their onset, be vulnerable to reproductive asymmetries that
 are likely evolutionarily unstable. More broadly, this study contributes
 to the understanding of social evolution by uncovering asymmetric
 partitioning of reproduction in a population with newly evolved polygyny
 and raises questions about the future trajectories of introduced
 populations.
DOI: 10.15468/dl.ssce7b
title: Occurrence Download

description: A dataset containing 273 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((159.00094 -48.95058,200.03306 -48.95058,200.03306 -32.54476,159.00094 -32.54476,159.00094 -48.95058))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Rhynchostegium muriculatum"
 ]
}

 The dataset includes 273 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002461-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.fbg79cnsc
title: Predation risk in relation to brain size in alternative prey of pygmy owls varies depending on the abundance of main prey

description: Large brains in prey may allow adoption of anti-predator behavior that
 facilitates escape. Prey species with relatively large brains have been
 shown to be less likely to fall prey to predators. This leads to the
 hypothesis that individuals that have been captured by predators on
 average should have smaller brains than sympatric individuals. We
 exploited the fact that Eurasian pygmy owls  Glaucidium
 passerinum hoard small mammals and birds in cavities and nest-boxes for
 over-winter survival, allowing for comparison of the phenotype of prey
 with that of live conspecifics. In Northern Europe, main prey of pygmy
 owls are voles of the genera  Myodes and  Microtus ,
 while forest birds and shrews are the most important alternative prey.
 Large fluctuations (amplitude 100-200-fold) in vole populations induce
 rapid numerical responses of pygmy owls in response to main prey
 populations, which in turn results in varying predation pressure on small
 birds. We found, weighed and measured 153 birds in food-stores of pygmy
 owls and mist-netted, weighed and measured 333 live birds of 12 species in
 central-western Finland during two autumns with low (2017) and high (2018)
 pygmy owl risk. In two autumns, individuals with large brains survived
 longer compared to individuals with small brains. Avian prey of pygmy owls
 had smaller heads than live birds in autumn 2018 when predation risk by
 pygmy owl was high, while a similar difference was not significant in 2017
 when predation risk by pygmy owls was reduced.  Finally,
 avian survivors were in better body condition than avian prey individuals.
 These findings are consistent with the hypothesis that pygmy owls
 differentially prey on small birds that are in poor body condition and
 have small brains, and that predation risk imposed by pygmy owls on small
 birds in boreal forests varies depending on the abundance of the main prey
 (voles).
description: Fieldwork. Analysed with JMP (https://www.jmp.com/)
DOI: 10.15468/dl.gty8a6
title: Occurrence Download

description: A dataset containing 77 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Brenierea insignis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 77 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002462-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.h44j0zph8
title: Demographic history shaped geographical patterns of deleterious mutation load in a broadly distributed Pacific Salmon

description: A thorough reconstruction of historical processes is essential for a
 comprehensive understanding the mechanisms shaping patterns of genetic
 diversity. Indeed, past and current conditions influencing effective
 population size have important evolutionary implications for the efficacy
 of selection, increased accumulation of deleterious mutations, and loss of
 adaptive potential. Here, we gather extensive genome-wide data that
 represent the extant diversity of the Coho salmon (Oncorhynchus kisutch)
 to address two objectives. We demonstrate that a single glacial refugium
 is the source of most of the present-day genetic diversity, with
 detectable inputs from a putative secondary micro-refugium. We found
 statistical support for a scenario whereby ancestral populations located
 south of the ice sheets expanded in postglacial time, swamping out most of
 the diversity from other putative micro-refugia. Demographic inferences
 revealed that genetic diversity was also affected by linked selection in
 large parts of the genome. Moreover, we demonstrate that the recent
 demographic history of this species generated regional differences in the
 load of deleterious mutations among populations, a finding that mirrors
 recent results from human populations and provides increased support for
 models of expansion load. We propose that insights from these historical
 inferences should be better integrated in conservation planning of wild
 organisms, which currently focuses largely on neutral genetic diversity
 and local adaptation, with the role of potentially maladaptive variation
 being generally ignored.
description: vcf generated from stacks after aligning reads on the v1 coho
 genome with bwa-mem
DOI: 10.15151/esrf-es-2313058686
title: Macromolecular Crystallography in Bordeaux/Lyon/Toulouse : IECB IBGC CBMN / IBCP-MMSB ICBMS / IPBS LMGM

description: The different research teams who are part of this BAG are located in Bordeaux, Lyon and Toulouse. They are mainly working on worldwide health concerns or biotechnological relevant projects. In more details, infectiology, molecular assemblies, biosynthetic pathways or glycobiology are their main research axises. Important results have been obtained so far regarding the development of new therapeutic strategies against several infectious diseases or regarding plastic bioremediation. In order to go further into details of all these studies, access to ESRF facilities is a requirement.
DOI: 10.15151/esrf-es-2318079171
title: IBS BAG

description: The IBS BAG includes teams from IBS (Grenoble) and external groups from CEA-Cadarache (St Paul lez Durance) and IRBA (Brétigny-sur-Orge). We study the structure-function relationships of proteins with a focus on human health, biotechnology and methodology. Most of the projects are a continuation of the MX-2586 proposal and can be grouped under the following themes: host-pathogen interaction, new therapeutic targets, fundamental cellular mechanisms, membrane proteins, biotechnological applications and methodology. Some of these projects use integrative approaches (X-ray crystallography, cryo-EM, SAXS and NMR) together with other biophysical and biochemical studies and, more recently, the use of AI (AlphaFold) to fully understand the complexity of the biological macromolecular systems under study.
DOI: 10.5061/dryad.3ffbg79g4
title: Efficient production of few-layer black phosphorus by liquid-phase exfoliation

description: Phosphorene is a new 2D material that has recently attracted much
 attention owing to its fascinating electrical, optical, thermal, and
 chemical properties. Here, we report on high-quality exfoliation of black
 phosphorus nanosheets, with controllable size produced in large quantities
 by liquid phase exfoliation using N-methyl-2-pyrrolidone (NMP) as a
 solvent under ambient conditions. The as-synthesized few layers show a
 great potential for solar energy conversion based on the optical results
 shown in this work.
description: This data was collected from Raman spectroscopy measurements of
 all the samples, and the UV/visible absorption spectra for bulk, 13000 rpm
 and 15000 rpm samples.
DOI: 10.5061/dryad.1jwstqjs8
title: Supplementary figures for: Respiratory trajectories in type 2 and 3 Spinal muscular atrophy in the iSMAC cohort study

description: Objective. To describe the respiratory trajectories and their correlation
 with motor function in an international paediatric cohort of patients with
 type 2 and non-ambulant type 3 spinal muscular atrophy (SMA). Methods.
 Eight-year retrospective observational study of patients in the iSMAc
 natural history study. We retrieved anthropometrics, forced vital capacity
 (FVC) absolute, FVC% predicted (FVC%P.), Non-Invasive ventilation (NIV)
 requirement. Hammersmith functional motor scale (HFMS) and Revised
 performance of upper limb (RULM) were correlated with respiratory
 function. We excluded patients in interventional clinical trials and on
 Nusinersen commercial therapy. Results. There were 437 patients with SMA:
 348 type 2, 89 non-ambulant type 3. Mean age at first visit was 6.9(±4.4)
 and 11.1(±4) years. In SMA type 2 FVC%P declined by 4.2%/year from 5 to 13
 years, followed by a slower decline (1.0%/year). In type 3 FVC%P declined
 by 6.3%/year between 8 and 13 years, followed by a slower decline
 (0.9%/year). 39% SMA type 2 and 9% type 3 required NIV at median age
 5.0(1.8-16.6) and 15.1(13.8-16.3) years. 84% SMA type 2 and 80% type 3 had
 scoliosis, 54% and 46% required surgery, which did not significantly
 affect respiratory decline. FVC%P positively correlated with HFMS and RULM
 in both subtypes. Conclusions. In SMA type 2 and non-ambulant type 3 lung
 function declines differently, with a common levelling after age 13 years.
 Lung and motor function correlated in both subtypes. Our data further
 defines the milder SMA phenotypes and provides novel information to
 benchmark the long-term efficacy of new treatments for SMA.
description: Supplementary Figures (eFigure1-eFigure3).
DOI: 10.5061/dryad.5mkkwh73p
title: Data from: Characteristics of Narcondam Hornbill Rhyticeros narcondami nest trees

description: The global distribution of the Narcondam Hornbill is restricted to the
 small Narcondam Island spread over an area of 6.8 sq. km in the Andaman
 Sea. In this study, we describe the nest site characteristics, and
 abundance of the Narcondam Hornbill nest tree species based on 33 nests
 (active and potential) that we observed during our study period. We
 describe nests that we found in 13 tree species including some species
 which have not been reported in the past literature. The nest trees varied
 in girth from 103 – 380 cm, and the nest height varied from 4 – 31 m.
 Abundance of most of the nest tree species was highest in the low (0 – 200
 m above mean sea level (ASL)) and mid (200 – 400 m ASL) elevations. The
 overall density of large trees decreased from lower to higher elevations
 pointing towards potential reduced nesting opportunities in higher
 elevations. While more than 57% of cavities were between north-west and
 north-east facing, 21% of the cavities were south-west and west facing. We
 have also compiled the list of known Narcondam Hornbill nest tree species
 based on this and previous studies. 
description: This data was
 collected as part of a larger project on the Narcondam Hornbill ecology.
 We conducted field work on Narcondam Island between December 2019 and
 February 2020. During the field work, we found nests of Narcondam Hornbill
 which were confirmed by revisits at most nests and by determining their
 status prior to our end of field work in February. Many nests were active
 by the time we left the island. For active and potential nests, we
 measured girth at breast height (1.4 m) using a measuring tape for
 non-buttressed trees. For trees with buttress, girth was visually
 estimated at a point of the trunk from where the buttresses emerge. Nest
 height and tree height were measured using a rangefinder. Nest orientation
 was determined using a Garmin eTrex 30 GPS.
description: Readme file has been provided that gives additional details of
 the study.
DOI: 10.5061/dryad.8931zcrnh
title: Data from: Tradeoffs with growth limit host range in complex life cycle helminths

description: Parasitic worms with complex life cycles have several developmental
 stages, with each stage creating opportunities to infect additional host
 species. Using a dataset for 973 species of trophically transmitted
 acanthocephalans, cestodes, and nematodes, we confirmed that worms with
 longer life cycles (i.e. more successive hosts) infect a greater diversity
 of host species and taxa (after controlling for study effort). Generalism
 at the stage level was highest for ‘middle’ life stages, the second and
 third intermediate hosts of long life cycles. By simulating life cycles in
 real food webs, we found that middle stages had more potential host
 species to infect, suggesting that opportunity constrains generalism.
 However, parasites usually infected fewer host species than expected from
 simulated cycles, suggesting generalism also has costs. There was no
 tradeoff in generalism from one stage to the next, but worms spent less
 time growing and developing in stages where they infected more
 taxonomically diverse hosts. Our results demonstrate that life cycle
 complexity favors high generalism, and host use across life stages is
 determined by both ecological opportunity and life history tradeoffs.
description: Data on the host generalism of complex life cycle helminths was
 compiled from literature sources and databases. We compared helminth
 generalism to that from life cycles simulated in empirical food webs. More
 details on how data were compiled, processed, and analysed can be found in
 our manuscript (Benesh et al. 2020. Tradeoffs with growth limit host range
 in complex life cycle helminths. The American Naturalist), in the metadata
 associated with the data files, and in this GitHub repository:
 https://github.com/dbenesh82/clc_generalism.
description: The data are divided into 5 zip archives. Three contain the raw
 data used to calculate parasite generalism:
 "<strong>lc_database.zip</strong>",
 "<strong>host_records_taxonomy.zip</strong>", and
 "<strong>study_effort.zip</strong>". They include
 life cycle, host association, and study effort data, respectively. From
 these data, we calculated parasite generalism (and other variables) at the
 parasite species and stage levels. Those tables were used in the main
 analyses and are contained in
 "<strong>compiled_data_at_species_stage_level.zip</strong>". An additional archive, "<strong>simulated_life_cycles.zip</strong>", has generalism data for parasite life cycles that were simulated in real food webs. Each archive contains a "<strong>METADA.txt</strong>" describing contents of the data files.
DOI: 10.5061/dryad.cnp5hqc2r
title: Factors associated with COVID-19 infections and mortality in Africa: A cross-sectional study using publicly available data

description: Introduction The current COVID-19 pandemic is a global threat. This
 elicits questions on the level of preparedness and capacity of health
 systems to respond to emergencies. Relative to other parts of the world,
 Africa has poorly developed health systems with limited capacity to
 respond to health crises. Africa is particularly disadvantaged. Methods
 This cross-sectional study uses publicly available core health data for 53
 African countries, to determine risk factors for cumulative COVID-19
 deaths and cases per million in all countries in the continent.
 Descriptive statistics were determined for the indicators and a negative
 binomial regression was used for modelling the risk factors. Results In
 Sub-Saharan Africa, an increase in the number of nursing and midwifery
 personnel decreased the risk of COVID-19 deaths (p=0.0178) while a unit
 increase in UHC index of service coverage and prevalence of insufficient
 physical activity among adults increased the risk of COVID-19 deaths
 (p=0.0432 and p=0.0127). An increase in the proportion of infants
 initiating breastfeeding reduced the number of cases per million
 (p&lt;0.0001) while an increase in higher healthy life expectancy at
 birth increased the number of cases per million (p=0.0340). Conclusion
 Despite its limited resources, Africa’s preparedness and response to the
 COVID-19 pandemic can be improved by identifying and addressing specific
 gaps in the funding of health services delivery. These gaps impact
 negatively on service delivery but appear to have received limited funding
 and policy priority.
description: Data for
 selected indicators were extracted from the 2018 Global Reference List of
 100 Core Health Indicators. The 12 thematic areas are Mortality by Age and
 Sex, Mortality by Cause, Morbidity, Nutrition, Environmental Risk Factors,
 Non-Communicable Diseases, Immunization, Essential health services,
 Utilization and access, Health workforce, Health Information and Health
 financing. Data were extracted
 in .xls format for each variable and imported into STATA 15.0 software
 (StataCorp LLC College Station, TX). For each variable, the most recent
 data for all countries included in the study was retained with the
 corresponding year and country name and saved in .dta format. The
 different variables were merged using the country name as the unique
 identifier to obtain the final data set used for the analysis. The
 countries were further categorized into their assigned WHO region and
 World Bank income group.
description: The data is freely available and COVID-19 cases and deaths are
 changing by the day.
DOI: 10.5061/dryad.4b8gtht9n
title: Ictal source imaging in epilepsy patients - Supplementary Data

description: Objective Localization of seizure onset zone in focal epilepsy patients is
 a crucial step prior to surgical planning. Noninvasively achieving this
 goal would have a tremendous impact on clinical management of intractable
 seizure. Methods In a total of 39 focal epilepsy patients, we recorded and
 extracted 138 seizures and 1,325 interictal epileptic discharges using
 high-density EEG. We have investigated a novel approach for directly
 imaging sources of seizures and interictal spikes from high density EEG
 recordings, and rigorously validated it for noninvasive localization of
 seizure onset zone (SOZ) determined from intracranial EEG findings and
 surgical resection volume. Conventional source imaging analyses were also
 performed for comparison. Results Ictal source imaging showed a
 concordance rate of 95% when compared to intracranial EEG or resection
 results. The average distance from estimation to seizure onset
 (intracranial) electrodes is 1.35 cm in patients with concordant results,
 and 0.74 cm to surgical resection boundary in patients with successful
 surgery. About 41% of the patients were found to have multiple types of
 interictal activities; coincidentally, a lower concordance rate and a
 significantly worse performance in localizing SOZ were observed in these
 patients. Interpretation Noninvasive ictal source imaging with
 high-density EEG recording can provide highly concordant results with
 clinical decisions obtained by invasive monitoring or confirmed by
 resective surgery. By means of direct seizure imaging using high-density
 scalp EEG recordings, the added value of ictal source imaging is
 particularly high in patients with complex interictal activity patterns,
 who may represent the most challenging cases with poor
 prognosis.
DOI: 10.5061/dryad.280gb5mnk
title: Data from: Variant files for genotypic and sex-reversed males

description: X and Y chromosomes are usually derived from a pair of homologous
 autosomes, which then diverge from each other over time. Although
 Y-specific features have been characterized in sex chromosomes of various
 ages, the earliest stages of Y chromosome evolution remain elusive. In
 particular, we do not know whether early stages of Y chromosome evolution
 consist of changes to individual genes or happen via chromosome-scale
 divergence from the X. To address this question, we quantified divergence
 between young proto-X and proto-Y chromosomes in the house
 fly, Musca domestica. We compared proto-sex chromosome sequence
 and gene expression between genotypic (XY) and sex-reversed (XX) males. We
 find evidence for sequence divergence between genes on the proto-X and
 proto-Y, including five genes with mitochondrial functions. There is also
 an excess of genes with divergent expression between the proto-X and
 proto-Y, but the number of genes is small. This suggests that individual
 proto-Y genes, but not the entire proto-Y chromosome, have diverged from
 the proto-X. We identified one gene, encoding an axonemal dynein assembly
 factor (which functions in sperm motility), that has higher expression in
 XY males than XX males because of a disproportionate contribution of the
 proto-Y allele to gene expression. The up-regulation of the proto-Y allele
 may be favored in males because of this gene’s function in
 spermatogenesis. The evolutionary divergence between proto-X and proto-Y
 copies of this gene, as well as the mitochondrial genes, is consistent
 with selection in males affecting the evolution of individual genes during
 early Y chromosome evolution.