cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j4h65
title: Data from: Life-stage associated remodeling of lipid metabolism regulation in Atlantic salmon

description: Atlantic salmon migrates from rivers to sea to feed, grow and develop
 gonads before returning to spawn in freshwater. The transition to marine
 habitats is associated with dramatic changes in the environment, including
 water salinity, exposure to pathogens, and shift in dietary lipid
 availability. Many anticipatory changes in physiology occur before
 migration to sea, but little is known about the molecular nature of these
 changes. Here we use a long term feeding experiment to study
 transcriptional regulation of lipid metabolism in Atlantic salmon gut and
 liver in both fresh- and saltwater. We find that lipid metabolism is
 highly plastic in response to differences in dietary lipid composition in
 freshwater, but then undergoes a marked shift when salmon transitions to
 the marine life-stage. Expression of genes in liver relating to
 lipogenesis and lipid transport decrease overall and become less
 responsive to diet, while genes for lipid uptake in gut become more highly
 expressed. Finally, analyses of evolutionary consequences of the salmonid
 specific whole-genome duplication on lipid metabolism reveals several
 pathways with significantly different (p&lt;0.05) duplicate retention
 or duplicate regulatory conservation. We also find a limited number of
 cases where the whole genome duplication has resulted in an increased gene
 dosage. Our results demonstrate the presence of a life-stage associated
 remodeling of lipid metabolism at the gene regulatory level, suggesting an
 evolved preparatory optimization of lipid metabolism
description: Supplementary_files_Harvey_et_al_MEC-17-0821This zip file contains 10 supplementary files associated to Harvey et al. "Life-stage associated remodeling of lipid metabolism regulation in Atlantic salmon".
DOI: 10.15468/dl.9r6sc2
title: Occurrence Download

description: A dataset containing 81203 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Duttaphrynus melanostictus"
 ]
}

 The dataset includes 81203 records from 131 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001476-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8bp05
title: Data from: Unravelling the immune signature of Plasmodium falciparum transmission-reducing immunity

description: Infection with Plasmodium can elicit antibodies that inhibit parasite
 survival in the mosquito, when they are ingested in an infectious blood
 meal. Here, we determine the transmission-reducing activity (TRA) of
 naturally acquired antibodies from 648 malaria-exposed individuals using
 lab-based mosquito-feeding assays. Transmission inhibition is
 significantly associated with antibody responses to Pfs48/45, Pfs230, and
 to 43 novel gametocyte proteins assessed by protein microarray. In
 field-based mosquito-feeding assays the likelihood and rate of mosquito
 infection are significantly lower for individuals reactive to Pfs48/45,
 Pfs230 or to combinations of the novel TRA-associated proteins. We also
 show that naturally acquired purified antibodies against key
 transmission-blocking epitopes of Pfs48/45 and Pfs230 are mechanistically
 involved in TRA, whereas sera depleted of these antibodies retain
 high-level, complement-independent TRA. Our analysis demonstrates that
 host antibody responses to gametocyte proteins are associated with reduced
 malaria transmission efficiency from humans to mosquitoes.
description: Protein microarray
 serological dataBackground corrected and
 normalised microarray median florescence intensity data, for all
 individuals in the study (n=648). Data from IVTT protein targets are
 presented along with control targets in tab 1 and 2 (n=762). Data from the
 gametocyte IVTT protein targets only are presented in tab 3
 (n=528).Data
 file.xlsxMetadata for the protein
 micro-array serological analysisMetadata for the protein
 microarray serological analysis. Full description of the variables
 provided is in tab 2 (key).Sample
 file.xlsx
DOI: 10.5061/dryad.qm419
title: Data from: Greater pollination generalization is not associated with reduced constraints on corolla shape in Antillean plants

description: Flowers show important structural variation as reproductive organs but the
 evolutionary forces underlying this diversity are still poorly understood.
 In animal-pollinated species, flower shape is strongly fashioned by
 selection imposed by pollinators, which is expected to vary according to
 guilds of effective pollinators. Using the Antillean subtribe Gesneriinae
 (Gesneriaceae), we tested the hypothesis that pollination specialists
 pollinated by one functional type of pollinator have maintained more
 similar corolla shapes through time due to more constant and stronger
 selection constraints compared to species with more generalist pollination
 strategies. Using geometric morphometrics and evolutionary models, we
 showed that the corolla of hummingbird specialists, bat specialists, and
 species with a mixed-pollination strategy (pollinated by hummingbirds and
 bats; thus a more generalist strategy) have distinct shapes and that these
 shapes have evolved under evolutionary constraints. However, we did not
 find support for greater disparity in corolla shape of more generalist
 species. This could be because the corolla shape of more generalist
 species in subtribe Gesneriinae, which has evolved multiple times, is
 finely adapted to be effectively pollinated by both bats and hummingbirds.
 These results suggest that ecological generalization is not necessarily
 associated with relaxed selection constraints.
description: Supplementary
 InformationSupplementary Tables and
 Figures for the manuscriptJoly_Evolution_FlowerShape_SI.pdfR scripts and associated dataR script used to analyse the data and all associated datasets required to run the analyses.scriptsAndData.zipInteractive FiguresInteractive figures representing the floral morphospaces (Principal Component Analyses; PCA), providing the opportunity to identify the position of species and individual pictures on the plot and to zoom in for better visualization.Joly&al_Evolution_InteractiveFigures.htmlPicture thumbnailsThis archive contains picture thumbnails of all the flowers analyzed in the study. Note that they are not the original files used for the analysis.PictureThumbnails.zip
DOI: 10.5061/dryad.n4k45
title: Data from: Diversity change during the rise of tetrapods and the impact of the ‘Carboniferous rainforest collapse’

description: The Carboniferous and early Permian were critical intervals in the
 diversification of early four-limbed vertebrates (tetrapods), yet the
 major patterns of diversity and biogeography during this time remain
 unresolved. Previous estimates suggest that global tetrapod diversity rose
 continuously across this interval and that habitat fragmentation following
 the ‘Carboniferous rainforest collapse’ (CRC) drove increased endemism
 among communities. However, previous work failed to adequately account for
 spatial and temporal biases in sampling. Here, we reassess early tetrapod
 diversity and biogeography with a new global species-level dataset using
 sampling standardization and network biogeography methods. Our results
 support a tight relationship between observed richness and sampling,
 particularly during the Carboniferous. We found that subsampled species
 richness initially increased into the late Carboniferous, then decreased
 substantially across the Carboniferous/Permian boundary before slowly
 recovering in the early Permian. Our analysis of biogeography does not
 support the hypothesis that the CRC drove endemism; instead, we found
 evidence for increased cosmopolitanism in the early Permian. While a
 changing environment may have played a role in reducing diversity in the
 earliest Permian, our results suggest that the CRC was followed by
 increased global connectivity between communities, possibly reflecting
 both reduced barriers to dispersal and the diversification of amniotes.
description: Global occurrences of
 Tetrapoda (Carboniferous–early Permian)This file is a direct
 download from the Paleobiology Database which contains global occurrences
 for Tetrapodomorpha from the Carboniferous to early
 Permian.Supplementary data
 X.csv
DOI: 10.5061/dryad.qq586
title: Data from: Information criteria for comparing partition schemes

description: When inferring phylogenies, one important decision is whether and how
 nucleotide substitution parameters should be shared across different
 subsets or partitions of the data. One sort of partitioning error occurs
 when heterogeneous subsets are mistakenly lumped together and treated as
 if they share parameter values. The opposite kind of error is mistakenly
 treating homogeneous subsets as if they result from distinct sets of
 parameters. Lumping and splitting errors are not equally bad. Lumping
 errors can yield parameter estimates that do not accurately reject any of
 the subsets that were combined whereas splitting errors yield estimates
 that did not benefit from sharing information across partitions.
 Phylogenetic partitioning decisions are often made by applying information
 criteria such as the Akaike Information Criterion (AIC). As with other
 information criteria, the AIC evaluates a model or partition scheme by
 combining the maximum log-likelihood value with a penalty that depends on
 the number of parameters being estimated. For the purpose of selecting an
 optimal partitioning scheme, we derive an adjustment to the AIC that we
 refer to as the AICP and that is motivated by the idea that splitting
 errors are less serious than lumping errors. We also introduce a similar
 adjustment to the Bayesian Information Criterion (BIC) that we refer to as
 the BICP. Via simulation and empirical data analysis, we contrast AIC and
 BIC behavior to our suggested adjustments. We discuss these results and
 also emphasize why we expect the probability of lumping errors with the
 AICP and the BICP to be relatively robust to model parameterization.
description: ray-finned-fishonline appendix and data files for ray-finned fish taxa
DOI: 10.17632/6vhwdwfkv4.1
title: Gig Worker poor psychological health Thematic Analyses Coding File

description: This file contains the coding generated by the thematic analyses performed on 36 papers identified through a systematic literature review. The coding is performed to identify the various themes of gig worker that cause poor psychological health.
DOI: 10.5061/dryad.m7f8n
title: Data from: Determination of sulfonamides in milk by capillary electrophoresis with PEG@MoS2 as a dispersive solid-phase extraction sorbent

description: A synthetic polyethylene glycol-molybdenum disulfide (PEG@MoS2) composite
 was prepared using a simple method, and the application of this material
 in dispersive solid-phase extraction (DSPE) was investigated for the
 enrichment of eight sulfonamides (SAs) in milk samples. The composite was
 characterized by energy dispersive spectroscopy, scanning electron
 microscopy, transmission electron microscopy, Fourier transform infrared
 spectroscopy and Brunner-Emmett-Teller measurements. The results showed
 that the MoS2 synthesized in the presence of PEG has the advantage of a
 larger surface area and that the adsorption effect of this MoS2 was
 enhanced. After extraction, the eight SAs were separated by capillary zone
 electrophoresis with a good linear relationship (R2 &gt; 0.9902) in
 the range of 0.3-30 µg/mL and good precision (between 0.32% and 9.83%).
 Additionally, good recoveries (between 60.52% and 110.91%) were obtained
 for the SAs in the milk samples. The developed PEG@MoS2-based DSPE method
 could be applied for the enrichment of SAs in real milk samples.
description: RSOS
DOI: 10.17632/h26xkghdvd
title: Metabolomics Data- ACBP: a poor-prognosis biomarker in sepsis and a target for disease mitigation

description: Mass spectrometry-based metabolomics performed in spleen, heart, plasma, liver and kidney of C57Bl/6J mice.
DOI: 10.5061/dryad.5jm7b
title: Data from: Basic description and some notes on the evolution of seven sympatric morphs of Dolly Varden Salvelinus malma from the Lake Kronotskoe Basin

description: The paper examines the basic morphological and ecological features of
 Dolly Varden from Lake Kronotskoe (Russia, Kamchatka). Seven valid morphs
 different in head proportions, feeding, timing and place of spawning have
 been determined in this ecosystem. The basic morphometric characteristics
 clearly separate Lake Kronotskoe morphs from each other, as well as from
 its potential ancestor (Dolly Varden). According to CVA analysis, the most
 notable morphological characteristics determining the mouth position are:
 the length of a lower jaw and rostrum. Furthermore, five of seven morphs
 inhabit different depth zones of the lake and feed on different food
 resources. Our data suggest that reproductive isolation may be maintained
 by temporal/spatial isolation for two morphs with lacustrine spawning, and
 by spatial isolation only for the rest of the morphs with riverine
 spawning. The sympatric diversity of the Lake Kronotskoe charrs is
 exceptionally wide and there are no other examples for seven sympatric
 morphs of genus Salvelinus to coexist within a single ecosystem. This
 study puts forward a three-step hypothetical model of charr divergence in
 Lake Kronotskoe as a potential ground for future studies.
description: LMM_schemeThis scheme (side view) was used for land-marks digitizing. Landmarks in the Tps-files are given according this order. Here also some addition land-marks that can be used for the linear measurements calculations i.e. fin length and width etc.landarks BBTps file for Bigmouth (B-) morphlandmarks_SSTps file for Smallmouth (S-) morphWW_landmarksTps file for White (W-) morphLL_landmarksTps file for Longhead (L-) morphNN1_landmarksTps file for Nosed1 (N1-) morph (side view)NN2_landmarksTps file for Nosed2 (N2-) morph (side view)NN3_landmarksTps file for Nosed3 (N3-) morph (side view)LLM_scheme_bottom viewThis scheme (bottom view) was used for land-marks digitizing. Landmarks in the Tps-files are given according this order (for NN morphs only).NN1_bottom_landmarksTps file for Nosed1 (N1-) morph (bottom view)NN2_bottom_landmarksTps file for Nosed2 (N2-) morph (bottom view)NN3_bottom_landmarksTps file for Nosed1 (N3-) morph (bottom view)
DOI: 10.17632/h26xkghdvd.2
title: Metabolomics Data- ACBP: a poor-prognosis biomarker in sepsis and a target for disease mitigation

description: Mass spectrometry-based metabolomics performed in spleen, heart, plasma, liver and kidney of C57Bl/6J mice.
DOI: 10.5061/dryad.b4v22
title: Data from: Patterns of activity and body temperature of Aldabra giant tortoises in relation to environmental temperature

description: We studied the temperature relations of wild and zoo Aldabra giant
 tortoises (Aldabrachelys gigantea) focusing on: 1) the relationship
 between environmental temperature and tortoise activity patterns (n=8 wild
 individuals), and 2) on tortoise body temperature fluctuations, including
 how their core and external body temperatures vary in relation to
 different environmental temperature ranges (seasons; n=4 wild, and n=5 zoo
 individuals). In addition, we surveyed the literature to review the effect
 of body mass on core body temperature range in relation to environmental
 temperature in the Testudinidae. Diurnal activity of tortoises was
 bimodally distributed, and influenced by environmental temperature and
 season. The mean air temperature at which activity is maximised was
 27.9˚C, with a range of 25.8–31.7˚C. Furthermore, air temperature
 predicted changes in the core body temperature better than did mass, and
 only during the coldest trial did tortoises with higher mass show more
 stable temperatures. Our results, together with the overall Testudinidae
 overview, suggest that, once variation in environmental temperature has
 been taken into account, there is little effect of mass on the temperature
 stability of tortoises. Moreover, the presence of thermal inertia in an
 individual tortoise depends on the environmental temperatures, and we
 found no evidence for inertial homeothermy. Finally, patterns of core and
 external body temperatures in comparison to environmental temperatures
 suggest that Aldabra giant tortoises act as mixed conformer-regulators.
 Our study provides a baseline to manage the thermal environment of wild
 and rewilded populations of an important island ecosystem engineer species
 in an era of climate change.
description: Falcon et al 2018 Giant
 tortoise activity and thermoregulationData used for the
 analysis done for the article. It is divided in 1) patterns of activity in
 relation to environmental temperature and 2) patterns of body temperature
 in relation to environmental temperatures.Falcon et al 2018
 dataset.xlsx
DOI: 10.17632/mz7y54p86v
title: Original data on 《A Multi-Epitope Vaccine Targeting the WbkC Protein Confers Protection against Brucella Challenge in BALB/c Mice 》

description: Brucellosis, a globally prevalent zoonosis caused by Brucella species, currently lacks an approved subunit vaccine. By integrating immunoinformatics approaches with in vivo experiments, this study developed a multi-epitope vaccine against Brucella with high immunogenicity and protective efficacy, which provides a novel strategic avenue for the development of Brucella subunit vaccines and accelerates the research and development process of such vaccines.
DOI: 10.5061/dryad.78h27
title: Data from: Evolutionary dynamism in bryophytes: phylogenomic inferences confirm rapid radiation in the moss family Funariaceae

description: Rapid diversifications of plants are primarily documented and studied in
 angiosperms, which are perceived as evolutionarily dynamic. Recent studies
 have, however, revealed that bryophytes have also undergone periods of
 rapid radiation. The speciose family Funariaceae, including the model
 taxon Physcomitrella patens, is one such lineage. Here, we infer
 relationships among major lineages within the Entosthodon-Physcomitrium
 complex from virtually complete organellar exomes (i.e., 123 genes)
 obtained through high throughput sequencing of genomic libraries enriched
 in these loci via targeted locus capture. Based on these extensive exonic
 data we (1) reconstructed a robust backbone topology of the Funariaceae,
 (2) confirmed the monophyly of Funaria and the polyphyly of Entosthodon,
 Physcomitrella, and Physcomitrium, and (3) argue for the occurrence of a
 rapid radiation within the Entosthodon-Physcomitrium complex that began 28
 mya and gave rise more than half of the species diversity of the family.
 This diversification may have been triggered by a whole genome duplication
 and coincides with global Eocene cooling that continued through the
 Oligocene and Miocene. The Funariaceae join a growing list of bryophyte
 lineages whose history is marked by at least one burst of diversification,
 and our study thereby strengthens the view that bryophytes are
 evolutionarily dynamic lineages and that patterns and processes
 characterizing the evolution of angiosperms may be universal among land
 plants.
description: Plastid
 alignmentAlignment of the 79
 plastid genes obtained from 91 accessions of Funariaceae and outgroups via
 targeted enrichmentFunariaceaePlastidAlignment.nexMitochondrial alignmentAlignment of the 38 genes obtained from 91 accessions of Funariaceae and outgroups obtained via targeted enrichmentFunariaceaeMitochondrialAlignment.nexFunariaceae_plastidCompressed file with the single-gene sequence lists for the plastid genomeFunariaceae_mitochondrialCompressed file with the single-gene sequence lists for the mitochondrial genomeVoucher tableInformation about the vouchers of the samples used for the study. Some old ID numbers and their equivalence to the final ID numbers are included. Samples present in the single-gene sequence list not used in the study were discarded after failing the barcode test with psbA-trnH (see Materials and Methods)Vouchers.xlsx
DOI: 10.17632/mz7y54p86v.1
title: Original data on 《A Multi-Epitope Vaccine Targeting the WbkC Protein Confers Protection against Brucella Challenge in BALB/c Mice 》

description: Brucellosis, a globally prevalent zoonosis caused by Brucella species, currently lacks an approved subunit vaccine. By integrating immunoinformatics approaches with in vivo experiments, this study developed a multi-epitope vaccine against Brucella with high immunogenicity and protective efficacy, which provides a novel strategic avenue for the development of Brucella subunit vaccines and accelerates the research and development process of such vaccines.
DOI: 10.5061/dryad.2ff46
title: Data from: Agriculture shapes the trophic niche of a bat preying on multiple pest arthropods across Europe: evidence from DNA metabarcoding

description: The interaction between agricultural production and wildlife can shape,
 and even condition, the functioning of both systems. In this study we i)
 explored the degree to which a widespread European bat, namely the common
 bent-wing bat Miniopterus schreibersii, consumes crop-damaging insects at
 a continental scale, and ii) tested whether its dietary niche is shaped by
 the extension and type of agricultural fields. We employed a dual-primer
 DNA metabarcoding approach to characterise arthropod 16S and COI DNA
 sequences within bat faecal pellets collected across 16 Southern European
 localities, to first characterise the bat species’ dietary niche, secondly
 measure the incidence of agricultural pests across their ranges, and
 thirdly assess whether geographical dietary variation responds to
 climatic, landscape diversity, agriculture type and vegetation
 productivity factors. We detected 12 arthropod orders, among which
 lepidopterans were predominant. We identified &gt;200 species, 44 of
 which are known to cause agricultural damage. Pest species were detected
 at all but one sampling site and in 94% of the analysed samples.
 Furthermore, the dietary diversity of M. schreibersii exhibited a negative
 linear relation with the area of intensive agricultural fields, thus
 suggesting crops restrict the dietary niche of bats to prey taxa
 associated with agricultural production within their foraging range.
 Overall our results imply that M. schreibersii might be a valuable asset
 for biological pest suppression in a variety of agricultural productions,
 and highlight the dynamic interplay between wildlife and agricultural
 systems.
description: Zeale
 sequencesSequences filtered by
 DAMe using 2/3 filtering strategy and a minimum copy number of
 2.zeale_sequences.zipEpp sequencesSequences filtered by DAMe using 2/3 filtering strategy and a minimum copy number of 2.epp_sequences.zip
DOI: 10.17632/gjnghs5pzc
title: The Distributional Effects of Carbon Pricing Across Countries - Replication Package

description: This replication package contains all data and code required to reproduce the results of the paper “The Distributional Effects of Carbon Pricing Across Countries”, from Mathilde Le Moigne, Simon Lepot, Marcos Ritel and Dora Simon.
DOI: 10.5066/p13j6xwz
title: Data acquired in laboratory experiments conducted to characterize Ag bioaccumulation kinetics in Daphnia magna after exposures to polystyrene microplastics and Ag nanoparticles

description: Microplastics (MPs) are an environmental concern. They can interact with other contaminants and pose new threats to organisms. We assessed the effect MPs on silver (Ag) bioaccumulation in the filter-feeding zooplankton Daphnia magna exposed to Ag nanoparticles at environmentally relevant concentrations.
DOI: 10.17632/gjnghs5pzc.1
title: The Distributional Effects of Carbon Pricing Across Countries - Replication Package

description: This replication package contains all data and code required to reproduce the results of the paper “The Distributional Effects of Carbon Pricing Across Countries”, from Mathilde Le Moigne, Simon Lepot, Marcos Ritel and Dora Simon.