cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.39c3k
title: Data from: Genome-wide associations identify novel candidate loci associated with genetic susceptibility to tuberculosis in wild boar

description: Tuberculosis (TB) affects a wide range of host species worldwide.
 Understanding host-pathogen co-evolution remains a global challenge owing
 to complex interactions among host genetic factors, pathogen traits and
 environmental conditions. We used an endemic wild boar population that had
 undergone a huge increase in Mycobacterium bovis infection prevalence,
 from 45% in 2002/06 to 83% in 2009/12, to understand the effects of host
 genetics on host TB outcomes and disease dynamics. Host genomic variation
 was characterized using a high-density single nucleotide polymorphism
 (SNP) array, while host TB phenotype was assessed using both gross
 pathology and mycobacterial culture. Two complementary genome-wide
 association (GWAS) analyses were conducted: (i) infected-uninfected; and
 (ii) 2002/06–2009/12. The SNPs with the highest allelic frequency
 differences between time-periods and TB outcomes were identified and
 validated in a large dataset. In addition, we quantified the expression
 levels of some of their closest genes. These analyses highlighted various
 SNPs (i.e. rs81465339, rs81394585, rs81423166) and some of the closest
 genes (i.e. LOC102164072, BDNF/NT-3, NTRK2, CDH8, IGSF21) as candidates
 for host genetic susceptibility. In addition to TB-driven selection, our
 findings outline the putative role of demographic events in shaping
 genomic variation in natural populations and how population crashes and
 drift may impact host genetic susceptibility to TB over time.
description: Raw_SNP_dataStructure_SNP_data64_ind_29504_SNPsDataset used for calculating genome diversity parameters44_ind_29504_SNPsDataset applied in the genome-wide association studies76_ind_8_SNPsDataset used in the validation of genome-wide association studiesGWAS_TB_standard_44GWAS summary statistics for infected vs infected MTC individualsGWAS_TB_stratified_44GWAS summary statistics for stratified analysis of infected vs. uninfected MTC individualsGWAS_TB_standard_76GWAS summary statistics for the validation test between infected vs. uninfected MTC individualsGWAS_TB_stratified_76GWAS summary statistics for the validation test, stratified analysis, between infected vs. uninfected MTC individualsGWAS_Season_standard_44GWAS summary statistics of 2002/06 vs. 2009/12 seasonsGWAS_Season_stratified_44GWAS summary statistics of stratified analysis for 2002/06 vs. 2009/12 seasons.GWAS_Season_standard_76GWAS summary statistics for the validation test between 2002/06 vs. 2009/12 seasons.GWAS_Season_stratified_76GWAS summary statistics for the validation test, stratified analysis, between 2002/06 vs. 2009/12 seasons.
DOI: 10.5061/dryad.86922
title: Data from: How many dinosaur species were there? Fossil bias and true richness estimated using a Poisson sampling model

description: The fossil record is a rich source of information about biological
 diversity in the past. However, the fossil record is not only incomplete
 but has also inherent biases due to geological, physical, chemical and
 biological factors. Our knowledge of past life is also biased because of
 differences in academic and amateur interests and sampling efforts. As a
 result, not all individuals or species that lived in the past are equally
 likely to be discovered at any point in time or space. To reconstruct
 temporal dynamics of diversity using the fossil record, biased sampling
 must be explicitly taken into account. Here, we introduce an approach that
 uses the variation in the number of times each species is observed in the
 fossil record to estimate both sampling bias and true richness. We term
 our technique TRiPS (True Richness estimated using a Poisson Sampling
 model) and explore its robustness to violation of its assumptions via
 simulations. We then venture to estimate sampling bias and absolute
 species richness of dinosaurs in the geological stages of the Mesozoic.
 Using TRiPS, we estimate that 1936 (1543–2468) species of dinosaurs roamed
 the Earth during the Mesozoic. We also present improved estimates of
 species richness trajectories of the three major dinosaur clades: the
 sauropodomorphs, ornithischians and theropods, casting doubt on the
 Jurassic–Cretaceous extinction event and demonstrating that all dinosaur
 groups are subject to considerable sampling bias throughout the Mesozoic.
description: TRiPS_Dryad_2016R scripts, functions and data needed to perform TRiPS and reproduce analysis and figures in main article.
DOI: 10.5061/dryad.dh371
title: Data from: Analysis of protein phosphorylation in nerve terminal reveals extensive changes in active zone proteins upon exocytosis

description: Neurotransmitter release is mediated by the fast, calcium-triggered fusion
 of synaptic vesicles with the presynaptic plasma membrane, followed by
 endocytosis and recycling of the membrane of synaptic vesicles. While many
 of the proteins governing these processes are known, their regulation is
 only beginning to be understood. Here we have applied quantitative
 phosphoproteomics to identify changes in phosphorylation status of
 presynaptic proteins in resting and stimulated nerve terminals isolated
 from the brains of Wistar rats. Using rigorous quantification, we
 identified 252 phosphosites that are either up- or downregulated upon
 triggering calcium-dependent exocytosis. Particularly pronounced were
 regulated changes of phosphosites within protein constituents of the
 presynaptic active zone, including bassoon, piccolo, and RIM1.
 Additionally, we have mapped kinases and phosphatases that are activated
 upon stimulation. Overall, our study provides a snapshot of
 phosphorylation changes associated with presynaptic activity and provides
 a foundation for further functional analysis of key phosphosites involved
 in presynaptic plasticity.
description: Supplementary file 1.
 Complete List of identified Proteins in Proteome StudySupplementary file 2.
 Complete list of phosphosites quantified in the three stimulation
 comparisonsSupplementary file 3.
 List of the previously reported phosphosite with the related
 publications
DOI: 10.5061/dryad.0643c
title: Data from: Shape analysis of moss (Bryophyta) sporophytes: insights into land plant evolution

description: PREMISE OF THE STUDY: The alternation of generations life cycle represents
 a key feature of land-plant evolution and has resulted in a diverse array
 of sporophyte forms and modifications in all groups of land plants. We
 test the hypothesis that evolution of sporangium (capsule) shape of the
 mosses—the second most diverse land-plant lineage—has been driven by
 differing physiological demands of life in diverse habitats. This study
 provides an important conceptual framework for analyzing the evolution of
 a single, homologous character in a continuous framework across a deep
 expanse of time, across all branches of the tree of life. METHODS: We
 reconstruct ancestral sporangium shape and ancestral habitat on the
 largest phylogeny of mosses to date, and use phylogenetic generalized
 least squares regression to test the association between habitat and
 sporangium shape. In addition, we examine the association between shifts
 in sporangium shape and species diversification. RESULTS: We demonstrate
 that sporangium shape is convergent, under natural selection, and
 associated with habitat type, and that many shifts in speciation rate are
 associated with shifts in sporangium shape. CONCLUSIONS: Our results
 suggest that natural selection in different microhabitats results in the
 diversity of sporangium shape found in mosses, and that many increasing
 shifts in speciation rate result in changes in sporangium shape across
 their 480 million year history. Our framework provides a way to examine if
 diversification shifts in other land plants are also associated with
 massive changes in sporophyte form, among other morphological traits.
description: phylogram_bootstrapphylogram of mosses, liverworts, and hornworts with support values based on 500 bootstrap replicatesmoss_chronochronogram of bryophytescontrolcontrol file for BAMMfractionfraction file for BAMMalignments21 gene alignments plus concatenated alignment
DOI: 10.15468/dl.wqs2th
title: Occurrence Download

description: A dataset containing 5105 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is one of (Centralisation des observations floristiques dans le cadre du SINP - Observations floristiques - plateforme SINP régionale SILENE PACA, Centralisation des observations floristiques - Observations floristiques issues de la base de données du Conservatoire botanique national alpin, INPN - Données flore des CBN agrégées par la FCBN, 16 - Inventaire général de la flore et de la fonge - GENTIANA - Inventaire de la flore de l'Isère, FloraCAT: Banco de datos de los cormófitos de Cataluña, Observations faune et flore du Parc national des Écrins, Pl@ntNet automatically identified occurrences, Centralisation des observations floristiques - Observations floristiques floutées issues de la base de données flore du Conservatoire botanique national alpin, 16 - Inventaire général de la flore et de la fonge - CBNA - inventaire général de la flore et de la fonge réalisé sur le terrain)",
 "Geometry POLYGON((-1.15743 45.76707,-1.64074 45.31058,-2.21523 43.83789,-2.02464 43.22128,-1.15018 42.6383,0.48664 42.25713,3.04276 42.06654,3.80512 41.68536,4.84774 41.98806,6.98906 42.24591,7.83502 43.63812,7.64385 44.04685,7.12965 44.62038,7.12305 45.43782,7.00439 46.11683,6.79608 46.32979,6.48658 46.30349,6.258 46.20234,6.02536 46.08906,5.92017 46.18009,6.11842 46.30551,6.07796 46.34597,5.83447 46.23874,5.12696 45.76707,3.71193 45.72545,1.70037 45.35088,-1.15743 45.76707))",
 "OccurrenceStatus is Present",
 "TaxonKey is Aconitum anthora"
 ]
}

 The dataset includes 5105 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001438-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57826/agimo/kdihja
title: MATSim Dresden GitHub

description: See Metadata→Related Publication
DOI: 10.15468/dl.ce9mas
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "ScientificName is Euphorbia adiantoides",
 "BasisOfRecord is Specimen"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001440-260126135527185/datasets/export for details.
DOI: 10.5061/dryad.5890r
title: Data from: Ecomorphological diversifications of Mesozoic marine reptiles: the roles of ecological opportunity and extinction

description: Mesozoic marine ecosystems were dominated by several clades of reptiles,
 including sauropterygians, ichthyosaurs, crocodylomorphs, turtles, and
 mosasaurs, that repeatedly invaded ocean ecosystems. Previous research has
 shown that marine reptiles achieved great taxonomic diversity in the
 Middle Triassic, as they broadly diversified into many feeding modes in
 the aftermath of the Permo-Triassic mass extinction, but it is not known
 whether this initial phase of evolution was exceptional in the context of
 the entire Mesozoic. Here, we use a broad array of disparity, morphospace,
 and comparative phylogenetic analyses to test this. Metrics of
 ecomorphology, including functional disparity in the jaws and dentition
 and skull-size diversity, show that the Middle to early Late Triassic
 represented a time of pronounced phenotypic diversification in marine
 reptile evolution. Following the Late Triassic extinctions, diversity
 recovered, but disparity did not, and it took over 100 Myr for comparable
 variation to recover in the Campanian and Maastrichtian. Jurassic marine
 reptiles generally failed to radiate into vacated functional roles. The
 signatures of adaptive radiation are not seen in all marine reptile
 groups. Clades that diversified during the Triassic biotic recovery, the
 sauropterygians and ichthyosauromorphs, do show early diversifications,
 early high disparity, and early burst, while less support for these models
 is found in thalattosuchian crocodylomorphs and mosasaurs. Overall, the
 Triassic represented a special interval in marine reptile evolution, as a
 number of groups radiated into new adaptive zones.
description: Supplementary
 DataImage sources for
 functional character measurements, Skull size data specimens and sources,
 z transformed functional character data , Time bin assignments, PCOa
 scores for all taxa - primary analysis, PCA scores for all taxa -
 sensitivity analyses, First and last appearance dates for all taxa, PCOa
 scores from individual clade analysesSupplementary_Data_revised.xlsxSupplementary TextAdditional methodsSupplementary_Text_revised.docxSupplementary Figure 1Supplementary_Figure_1.pdfSupplementary Figure 2Supplementary_Figure_2.pdfSupplementary Figure 3Supplementary_Figure_3.pdfSupplementary Figure 4Supplementary_Figure_4.pdfSupplementary Figure 5Supplementary_Figure_5.pdfSupplementary Figure 6Supplementary_Figure_6.pdfSupplementary Figure 7Supplementary_Figure_7.pdfSupplementary Table 1Supplementary_Table_1.docxSupplementary Table 2Supplementary_Table_2.docxSupplementary Table 3Supplementary_Table_3.docxSupplementary Table 4Supplementary_Table_4.docx
DOI: 10.5061/dryad.5nk70
title: Data from: A gradiometric version of contactless inductive flow tomography: theory and first applications

description: The contactless inductive flow tomography (CIFT) is a measurement
 technique that allows reconstructing the flow of electrically conducting
 fluids by measuring the flow-induced perturbations of one or various
 applied magnetic fields and solving the underlying inverse problem. One of
 the most promising application fields of CIFT is the continuous casting of
 steel, for which the online monitoring of the flow in the mould would be
 highly desirable. In previous experiments at a small-scale model of
 continuous casting, CIFT has been applied to various industrially relevant
 problems, including the sudden changes of flow structures in case of argon
 injection and the influence of a magnetic stirrer at the submerged entry
 nozzle. The application of CIFT in the presence of electromagnetic brakes,
 which are widely used to stabilize the flow in the mould, has turned out
 to be more challenging due to the extreme dynamic range between the strong
 applied brake field and the weak flow-induced perturbations of the
 measuring field. In this paper, we present a gradiometric version of CIFT,
 relying on gradiometric field measurements, that is capable to overcome
 those problems and which seems, therefore, a promising candidate for
 applying CIFT in the steel casting industry.
description: Data
 ArchiveInduced magnetic field
 over time for all experimental figures.access.zip
DOI: 10.5061/dryad.9m8ff
title: Data from: RClone: a package to identify MultiLocus Clonal Lineages and handle clonal datasets in R

description: Partially clonal species are common in the Tree of Life. And yet,
 population genetics models still mostly focus on the extremes: strictly
 sexual versus purely asexual reproduction. Here we present an R package
 built upon GenClone software including new functions and several
 improvements. The RClone package includes functions to handle clonal
 datasets, allowing (i) checking for dataset reliability to discriminate
 multi-locus genotypes (MLG), (ii) ascertainment of MLG and semi-automatic
 determination of clonal lineages (MLL), (iii) genotypic richness and
 evenness indices calculation based on MLGs or MLLs, and (iv) describing
 several spatial components of clonality. RClone allows the one shot
 analysis of multi-population datasets without size limitation, suitable
 for datasets now increasingly produced through Next Generation Sequencing.
 A major improvement compared to existing software is the ability to
 determine the threshold to cluster similar MLGs into MLLs, based on
 implemented simulations of sexual events. Several functions allow data
 importation, conversion and exportation with adegenet, Genetix or
 Arlequin. RClone is provided with two vignettes to handle analysis on one
 (RClone_quickmanual) or several populations (RClone_qmsevpops).
description: synthetic_04Generated in silico pseudo-observed population (here called synthetic population) using a simulation program written with Python 2.7 (Foundation Python Software, available on: http://wwz.ifremer.fr/clonix/Logiciels/SimulatorClonix). The simulation was conducted among 10000 generations, with meiotic mutation rate of 10-3 and somatic mutation rate of 10-6. Population was of 1000 individuals with c = 0.4. Each population was of 100 loci, 10 alleles possible per loci.synthetic_09999Generated in silico pseudo-observed population (here called synthetic population) using a simulation program written with Python 2.7 (Foundation Python Software, available on: http://wwz.ifremer.fr/clonix/Logiciels/SimulatorClonix). The simulation was conducted among 10000 generations, with meiotic mutation rate of 10-3 and somatic mutation rate of 10-6. Population was of 10000 individuals with a clonality rate (c) of 0.9999. Each population was of 100 loci, 10 alleles possible per loci.
DOI: 10.5061/dryad.1d2c6
title: Data from: Manipulation of light spectral quality disrupts host location and attachment by parasitic plants in the genus Cuscuta

description: Parasitic plants in the genus Cuscuta (dodders) make their living by
 extracting resources from other plants. While relatively few dodder
 species are agricultural pests, those that are can be challenging to
 control, in part due to their intimate physical and physiological
 association with host plants. Consequently, dodders remain pervasive and
 economically damaging pests in a variety of crop systems. The development
 of improved management strategies would be facilitated by greater
 understanding of the ecological and environmental factors that influence
 the establishment and perpetuation of dodder infestations. Light cues play
 an important role in dodder host location and attachment. To better
 understand the influence of light conditions on parasite ecology, and
 potential implications for management, we examined how manipulating the
 ratio of red to far-red wavelengths (R:FR), via both passive filtering of
 natural sunlight and active spectral manipulation using LEDs, affects host
 location and host attachment by two dodder species (C. campestris on
 tomato hosts and C. gronovii on jewelweed). For both host-parasite
 combinations, host location and subsequent attachment by dodder parasites
 was dramatically reduced in high R:FR environments compared to control
 conditions (with R:FR characteristic of sunlight) and low R:FR conditions.
 Circumnutation by dodder seedlings was also significantly faster under
 high R:FR. We observed short-term effects of high R:FR on the height and
 dry mass of tomato host plants (immediately following 7-day exposure), as
 well as changes in tomato volatile emissions. However, preliminary
 investigation of long-term effects on host plants suggests that short-term
 exposure to high R:FR (i.e. during the critical period when dodder
 seedlings emerge and attach to hosts) has little or no effect on host
 plant size or fruit yield at the time of harvest. Synthesis and
 applications. Our findings suggest that spectral manipulation during the
 early stages of crop plant growth (e.g. via light-filtering row covers),
 may have significant potential to augment existing methods for managing or
 preventing dodder infestations in agricultural crops. We discuss potential
 obstacles to the realization of its potential, as well as next steps
 toward the development and optimization of spectral manipulation methods
 for use in agroecosystems.
description: AttachmentAssayCcampestrisELVISCgronoviiJewelweedELVIS_LightSettingsELVIScircumnutationEndofSeasonStatsForagingAssayPhytohormonesPlantEffectsFromLightVolatiles
DOI: 10.15468/dl.vudg6b
title: Occurrence Download

description: A dataset containing 9488 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Ochlerotatus taeniorhynchus, Culex quinquefasciatus)"
 ]
}

 The dataset includes 9488 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001439-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17360120
title: Dataset for Publication "Unlocking Bio-Based Potential: Assessing Biomass and Nutrient Availability for Sustainable Development"

description: These are datasets of the following publication:

Mihajloska, Emilija, Pavlina Zdraveva, Vladimir Gjorgievski, Natasa Markovska, and Alajdin Abazi. "Unlocking Bio-Based Potential: Assessing Biomass and Nutrient Availability for Sustainable Development." Journal of Sustainable Development of Energy, Water and Environment Systems 13, no. 2 (2025): 1-17.

The publication can be accessed here: https://www.sdewes.org/jsdewes/pid13.0562.
DOI: 10.5281/zenodo.17360121
title: Dataset for Publication "Unlocking Bio-Based Potential: Assessing Biomass and Nutrient Availability for Sustainable Development"

description: These are datasets of the following publication:

Mihajloska, Emilija, Pavlina Zdraveva, Vladimir Gjorgievski, Natasa Markovska, and Alajdin Abazi. "Unlocking Bio-Based Potential: Assessing Biomass and Nutrient Availability for Sustainable Development." Journal of Sustainable Development of Energy, Water and Environment Systems 13, no. 2 (2025): 1-17.

The publication can be accessed here: https://www.sdewes.org/jsdewes/pid13.0562.