cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17876520
title: SHM_120832_HST_3D

description: Photogrammetric 3D model of a black earthenware jug from the Early or High Middle Ages, collected from Kalmar, Sweden and currently held in the collections of the National Historical Museums in Stockholm.

 

Link to the Dynamic Collection platform 

https://dyncolldev.ht.lu.se/plus/artifact_view.php?item=512

Link to Sök I Samlingarna  

https://samlingar.shm.se/object/2C5D7084-B615-4DCF-A163-5C3C0517D84A
DOI: 10.5061/dryad.p72k5
title: Data from: Modelling the area of occupancy of habitat types with remote sensing

description: 1. A current challenge of biodiversity and conservation is the estimation
 of the spatial extent of habitat types across broad territories. In the
 absence of fine-resolution maps, predictive modelling helps in assessing
 the spatial distribution of vegetation cover. However, such approaches are
 still uncommon in regional planning and management. Here, we present a
 framework for mapping the area of occupancy (AOO) of habitat types that
 allows highly suitable estimates at different scales. 2. We model the
 potential AOO with abiotic variables related to topography and climate,
 resulting in broad AOO estimates that are subsequently downscaled to the
 local AOO with remote sensing. The combination of individual local AOO
 estimates allows the defining of the realized AOO, comprising locations
 with a high likelihood of occurrence and low uncertainty for each habitat.
 We applied this framework to mapping 24 protected habitat types of Natura
 2000 sites in northern Spain. 3. Local and realized AOO were highly
 accurate, with a 70% overall accuracy for the realized AOO. Remote sensing
 data, and especially LiDAR, were the most important predictors in habitat
 types related to forests and shrubs, followed by rock outcrops and
 pastures. Environmental variables were also relevant for specific habitats
 subject to abiotic constraints. 4. The combination of ecological modelling
 with remote sensing offers multiple advantages over traditional field
 surveys and image interpretation, allowing the harmonization of habitat
 maps across large regions and through time. This is particularly useful
 for implementing conservation actions under Natura 2000 principles or
 assessing IUCN criteria for ecosystems.
description: Predictor layers and
 occurrence data for habitat mappingSpatial database
 collected from official sources; Field data obtained from vegetation maps
 and fieldwork; ETRS89 UTM30NData.rar
DOI: 10.5061/dryad.k7c40
title: Data from: Local adaptation interacts with expansion load during range expansion: maladaptation reduces expansion load

description: The biotic and abiotic factors that facilitate or hinder species range
 expansions are many and complex. We examine the impact of two genetic
 processes and their interaction on fitness at expanding range edges: local
 maladaptation resulting from the presence of an environmental gradient and
 expansion load resulting from increased genetic drift at the range edge.
 Results from spatially explicit simulations indicate that the presence of
 an environmental gradient during range expansion reduces expansion load;
 conversely, increasing expansion load allows only locally adapted
 populations to persist at the range edge. Increased maladaptation reduces
 the speed of range expansion, resulting in less genetic drift at the
 expanding front and more immigration from the range center, therefore
 reducing expansion load at the range edge. These results may have
 ramifications for species being forced to shift their ranges because of
 climate change or other anthropogenic changes. If rapidly changing climate
 leads to faster expansion as populations track their shifting climatic
 optima, populations may suffer increased expansion load beyond previous
 expectations.
description: MakeNemoInputs_NormalDispR script to generate Nemo input files for simulations with Gaussian dispersal kernels.MakeNemoInputs_KurtoticDispR script to generate Nemo input files for simulations with leptokurtic dispersal kernels.MakeNemoInputs_NormalDisp_lowerFecundity_mimicMutationLoadR script to generate Nemo input files for simulations with lower fecundity to mimic the presence of mutation load.PopulationSizesSummarized simulation results data of population sizesPopulationFitnessesSummarized simulation results data of population fitnessExpansionSpeedResultsSummarized simulation results data for speed of expansion across simulations.EdgeLocation-FitnessResultsSummarized simulation results data for the location of the range edge in space across time points for simulations.SummaryFilesSummarized simulation result files for deleterious mutations. Row 1 of each file contains column headers, row 2 contains the heterozygous of homozygous state effect sizes for each mutation, respectively, and rows 3 onward give the frequency of mutations across the landscape. Data is across generation times, as indicated by the file names.
DOI: 10.5061/dryad.b84nh
title: Data from: First diagnosis of septic arthritis in a dinosaur

description: Identification and interpretation of pathologies in the fossil record
 allows for unique insights into the life histories of extinct organisms.
 However, the rarity of such finds limits not only the sample size for
 palaeopathologic studies, but also the types of analyses that may be
 performed. In this study, we present the first occurrence of a
 palaeopathology in a vertebrate from the Mesozoic of the East Coast of
 North America (Appalachia), a pathologic ulna and radius of an
 indeterminate hadrosaur from the Navesink Formation (New Jersey). X-ray
 microtomography allowed for both detailed and more accurate diagnosis of
 the pathologic condition as well as virtual conservation of the specimen.
 Based on extant archosaurian comparisons, the hadrosaur was diagnosed with
 severe septic arthritis affecting the proximal ulna and radius. Diagnosis
 was based on erosion of the joint and highly reactive periosteal bone
 growth and fusion of the elements. To the best of our knowledge, this is
 the first recorded account of septic arthritis in dinosaurs. The severity
 of the pathology suggests the animal suffered with this condition for some
 time before death. Unfortunately, only the ulna and radius were found.
 Thus, the extent to which the condition spread to other parts of the body
 is unknown.
description: Radius VGL
 fileCan be opened with
 vgsutiomax for reconstruction of the radius.Hedrick_Bone1.vglRadius MCS fileRadius file that can be opened in using the mimics software. Can use to scroll through individual slices.EdmontosaurRadius.mcsRadius Scanning ParametersScanning parameters for the radius to be used in conjunction with CT reconstructive softwareHedrick_Bone1_01.xtekctRadius STL fileReconstructed 3D model of the radius that can be opened using the freeware, MeshLab.ProxRadiusSTL.stlUlna VGL fileCan be opened with vgsutiomax for reconstruction of the ulna.Hedrick_Bone4.vglUlna STL fileReconstructed 3D model of the ulna that can be opened using the freeware, MeshLab.UlnaEdmontosaur.stlUlna MCS fileUlna file that can be opened in using the mimics software. Can use to scroll through individual slices.EdmontoUlna.mcsUlna Scanning ParametersScanning parameters for the ulna to be used in conjunction with CT reconstructive software.Hedrick_Bone4.xtekctUlna JPEG StackUlna JPEG stacks representing individual CT slices.UlnajpgsStack.zipRadius JPEG StackUlna JPEG stacks representing individual CT slices.RadiusjpgsStack.zip
DOI: 10.5061/dryad.76n6f7c
title: Data from: Slower environmental change hinders adaptation from standing genetic variation

description: Evolutionary responses to environmental change depend on the time
 available for adaptation before environmental degradation leads to
 extinction. Explicit tests of this relationship are limited to microbes
 where adaptation usually depends on the sequential fixation of de novo
 mutations, excluding standing variation for genotype-by-environment
 fitness interactions that should be key for most natural species. For most
 natural species evolving from standing genetic variation, adaptation at
 slower rates of environmental change may be impeded since the best
 genotypes at the most extreme environments can be lost during evolution
 due to genetic drift or founder effects. To address this hypothesis, we
 perform experimental evolution with self-fertilizing populations of the
 nematode Caenorhabditis elegans and develop an inference model to describe
 natural selection on extant genotypes under environmental change. Under a
 sudden environmental change, we find that selection rapidly increases the
 frequency of genotypes with high fitness in the most extreme environment.
 In contrast, under a gradual environmental change selection first favors
 genotypes that are worse at the most extreme environment. We demonstrate
 with a second set of evolution experiments that, as a consequence of
 slower environmental change and thus longer periods to reach the most
 extreme environments, genetic drift and founder effects can lead to the
 loss of the most beneficial genotypes. We further find that maintenance of
 standing genetic variation can retard the fixation of the best genotypes
 in the most extreme environment because of interference between them.
 Taken together, these results show that slower environmental change can
 hamper adaptation from standing genetic variation and they support
 theoretical models indicating that standing variation for
 genotype-by-environment fitness interactions critically alters the pace
 and outcome of adaptation under environmental change.
description: READMEinput_data-genotp_data_NaClanalysis_code-genotp_data_NaClinput_data-growth_rate_data_NaClanalysis_code-growth_rate_data_NaClanalysis_code-inferring_RWH_paramsanalysis_resultsinput_data-genotp_data_NaCl_continuationanalysis_code-genotp_data_NaCl_continuation
DOI: 10.5061/dryad.4q08q
title: Data from: The Near East as a cradle of biodiversity: a phylogeography of banded newts (genus Ommatotriton) reveals extensive inter- and intraspecific genetic differentiation

description: The banded newt (genus Ommatotriton) is widely distributed in the Near
 East (Anatolia, Caucasus and the Levant) – an understudied region from the
 perspective of phylogeography. The genus is polytypic, but the number of
 species included and the phylogenetic relationships between them are not
 settled. We sequenced two mitochondrial and two nuclear DNA markers
 throughout the range of Ommatotriton. For mtDNA we constructed
 phylogenetic trees, estimated divergence times using fossil calibration,
 and investigated changes in effective population size with Bayesian
 skyline plots and mismatch analyses. For nuDNA we constructed phylogenetic
 trees and haplotype networks. Species trees were constructed for all
 markers and nuDNA only. Species distribution models were projected on
 current and Last Glacial Maximum climate layers. We confirm the presence
 of three Ommatotriton species: O. nesterovi, O. ophryticus and O.
 vittatus. These species are genetically distinct and their most recent
 common ancestor was dated at ∼25 Ma (Oligocene). No evidence of recent
 gene flow between species was found. The species show deep intraspecific
 genetic divergence, represented by geographically structured clades, with
 crown nodes of species dated ∼8-13 Ma (Miocene to Early Quaternary);
 evidence of long-term in situ evolution and survival in multiple glacial
 refugia. While a species tree based on nuDNA suggested a sister species
 relationship between O. vittatus and O. ophryticus, when mtDNA was
 included, phylogenetic relationships were unresolved, and we refrain from
 accepting a particular phylogenetic hypothesis at this stage. While
 species distribution models suggest reduced and fragmented ranges during
 the Last Glacial Maximum, we found no evidence for strong population
 bottlenecks. We discuss our results in in the light of other
 phylogeographic studies from the Near East. Our study underlines the
 important role of the Near East in generating and sustaining biodiversity.
description: FP_ABI_filesRaw sequence data for KIAA, SACS, COI and CytB for the genus Ommatotriton in ABI formatFP_Bayesian_skylineInput and output data for Bayesian Skyline analysesFP_ENMEcological Niche Modeling in- and output dataFP_jModelTestjModelTest in- and output dataFP_Mismatch_analysisIn- and output data for mismatch analysesFP_PhylogeneticsIn- and output data for phylogenetic analyses (RAxML, MrBayes, BEAST)FP_SPF_filesContig files of sequence data for KIAA, SACS, COI and CytB for genus Ommatotriton.
DOI: 10.5281/zenodo.18385743
title: Data for "FLNB and TTC26 regulate ciliary Hedgehog signaling to maintain intervertebral disc matrix homeostasis in adolescent idiopathic scoliosis"
DOI: 10.5281/zenodo.18385744
title: Data for "FLNB and TTC26 regulate ciliary Hedgehog signaling to maintain intervertebral disc matrix homeostasis in adolescent idiopathic scoliosis"
DOI: 10.5061/dryad.q7mk04m
title: Data from: Spatial and topical imbalances in biodiversity research

description: The rapid erosion of biodiversity is among the biggest challenges human
 society is facing. Concurrently, major efforts are in place to quantify
 changes in biodiversity, to understand the consequences for ecosystem
 functioning and human wellbeing, and to develop sustainable management
 strategies. Based on comprehensive bibliometric analyses covering 134,321
 publications, we report systematic spatial biases in biodiversity-related
 research. Research is dominated by wealthy countries, while major research
 deficits occur in regions with disproportionately high biodiversity as
 well as a high share of threatened species. Similarly, core scientists,
 who were assessed through their publication impact, work primarily in
 North America and Europe. Though they mainly exchange and collaborate
 across locations of these two continents, the connectivity among them has
 increased with time. Finally, biodiversity-related research has primarily
 focused on terrestrial systems, plants, and the species level, and is
 frequently conducted in Europe and Asia by researchers affiliated with
 European and North American institutions. The distinct spatial imbalances
 in biodiversity research, as demonstrated here, must be filled, research
 capacity built, particularly in the Global South, and spatially-explicit
 biodiversity data bases improved, curated and shared.
description: Bibliometric Analysis
 BiodiversityThis data base was used
 for the analyses described in the publication "Spatial and Topical
 Imbalances in Biodiversity Research" by Tydecks, Laura, Jeschke,
 Jonathan, Wolf, Max, Singer, Gabriel, Tockner, Klement. The data were
 derived from Web of Science (WoS). These terms were used to set up the
 data base: biodiversity, biological diversity, species richness, species
 evenness, genetic diversity, species diversity, ecosystem diversity, alpha
 diversity, beta diversity, gamma diversity, taxonomic diversity,
 phylogenetic diversity, behavio(u)ral diversity, functional diversity. All
 articles in English from 1945 to 2014 are included (download date: May 12,
 2015). pid = publication ID py = publication year ti = title ab = abstract
 auid = author ID an = author name cc = country tc = times
 citedSpatial and Topical Imbalances
 in Biodiversity Research_DB.txt
DOI: 10.5061/dryad.jn400
title: Data from: Does adaptive radiation of a host lineage promote ecological diversity of its bacterial communities? A test using gut microbiota of Anolis lizards

description: Adaptive radiations provide unique opportunities to test whether and how
 recent ecological and evolutionary diversification of host species
 structures the composition of entire bacterial communities. We used 16S
 rRNA gene sequencing of faecal samples to test for differences in the gut
 microbiota of six species of Puerto Rican Anolis lizards characterized by
 the evolution of distinct ‘ecomorphs’ related to differences in habitat
 use. We found substantial variation in the composition of the microbiota
 within each species and ecomorph (trunk-crown, trunk-ground, grass-bush),
 but no differences in bacterial alpha diversity among species or
 ecomorphs. Beta diversity analyses revealed subtle but significant
 differences in bacterial composition related to host phylogeny and
 species, but these differences were not consistently associated with
 Anolis ecomorph. Comparison of a trunk-ground species from this clade (A.
 cristatellus) with a distantly related member of the same ecomorph class
 (A. sagrei) where the two species have been introduced and are now
 sympatric in Florida revealed pronounced differences in the alpha
 diversity and beta diversity of their microbiota despite their ecological
 similarity. Comparisons of these populations with allopatric conspecifics
 also revealed geographic differences in bacterial alpha diversity and beta
 diversity within each species. Finally, we observed high intraindividual
 variation over time and strong effects of a simplified laboratory diet on
 the microbiota of A. sagrei. Collectively, our results indicate that
 bacterial communities are only weakly shaped by the diversification of
 their lizard hosts due to the strikingly high levels of bacterial
 diversity and variation observed within Anolis species.
description: all_lizard_partA.fastaFasta file containing the sequences for lizard fecal 16S rRNA V1-V3 region. Sequencing was performed on MiSeq platform, and fasta files are generated after QC. Sequence ID contains sampleID (see metadata file for details) followed by sequence number. This file needs to be combined with partB.all_lizard_partA.fnaall_lizard_partB.fastaFasta file containing the sequences for lizard fecal 16S rRNA V1-V3 region. Sequencing was performed on MiSeq platform, and fasta files are generated after QC. Sequence ID contains sampleID (see metadata file for details) followed by sequence number. This file needs to be combined with partA.all_lizard_partB.fnalizard_metadata.xlsxThis is the metadata file contains information concerning the lizard samples used in analyses.all.xlsx
DOI: 10.5061/dryad.4931c
title: Data from: Machine learning for characterization of insect vector feeding

description: Insects that feed by ingesting plant and animal fluids cause devastating
 damage to humans, livestock, and agriculture worldwide, primarily by
 transmitting pathogens of plants and animals. The feeding processes
 required for successful pathogen transmission by sucking insects can be
 recorded by monitoring voltage changes across an insect-food source
 feeding circuit. The output from such monitoring has traditionally been
 examined manually, a slow and onerous process. We taught a computer
 program to automatically classify previously described insect feeding
 patterns involved in transmission of the pathogen causing citrus greening
 disease. We also show how such analysis contributes to discovery of
 previously unrecognized feeding states and can be used to characterize
 plant resistance mechanisms. This advance greatly reduces the time and
 effort required to analyze insect feeding, and should facilitate
 developing, screening, and testing of novel intervention strategies to
 disrupt pathogen transmission affecting agriculture, livestock and human
 health.
description: Data1Part 1 of Labelled EPG
 data from recordings of Asian Citrus Psyllid (Diaphorina citri) feeding on
 citrus cultivars.Data2Part 2 of Labelled EPG
 recordings of Asian Citrus Psyllid (Diaphorina citri) feeding on citrus
 cultivars.
DOI: 10.5061/dryad.ff051
title: Data from: Beyond animals and plants: dynamic maternal effects in the fungus Neurospora crassa

description: Maternal effects are widely documented in animals and plants, but not in
 fungi or other eukaryotes. A principal cause of maternal effects is
 asymmetrical parental investment in a zygote, creating greater maternal
 versus paternal influence on offspring phenotypes. Asymmetrical
 investments are not limited to animals and plants, but are also prevalent
 in fungi and groups including apicomplexans, dinoflagellates, and red
 algae. Evidence suggesting maternal effects among fungi is sparse and
 anecdotal. In an experiment designed to test for maternal effects across
 sexual reproduction in the model fungus Neurospora crassa, we measured
 offspring phenotypes from crosses of all possible pairs of 22 individuals.
 Crosses encompassed reciprocals of 11 mating-type “A” and 11 mating-type
 “a” wild strains. After controlling for the genetic and geographic
 distances between strains in any individual cross, we found strong
 evidence for maternal control of perithecia (sporocarp) production, as
 well as maternal effects on spore numbers and spore germination. However,
 both parents exert equal influence on the percentage of spores that are
 pigmented, and size of pigmented spores. We propose a model linking the
 stage-specific presence or absence of maternal effects to cellular
 developmental processes: effects appear to be mediated primarily through
 the maternal cytoplasm, and, after spore cell walls form, maternal
 influence on spore development is limited. Maternal effects in fungi, thus
 far largely ignored, are likely to shape species’ evolution and ecologies.
 Moreover, the association of anisogamy and maternal effects in a fungus
 suggests maternal effects may also influence the biology of other
 anisogamous eukaryotes.
description: All summarized flow
 cytometry data and strain informationThis csv contains the
 summarized flow cytometry data for each cross (each row is a different
 cross). The descriptions of the columns are included in the readme
 file.ncrassa_maternal_effects_data_dryad.csvImages of crosses for perithecia countingThis zip file contains images of all crosses along with the imageJ .xml files corresponding to each cross in which perithecia are marked for counting.Perithecia_counting.zipSpore Flow Cytometry (fcs) filesThese are the raw flow cytometry data files. See readme for description of contents.Spore_FlowCytometry_Files.zipMitochondrial genome variant and non variant callsThis is a .vcf file of all variant and non-variant sites called across 10 or more of the 21 N. crassa strains.2mm_joint_genotype_filtered_select10_all.vcf
DOI: 10.5061/dryad.543pp71
title: Data from: Empty conformers of HLA-B preferentially bind CD8 and regulate CD8+ T cell function

description: When complexed with antigenic peptides, human leukocyte antigen (HLA)
 class I (HLA-I) molecules initiate CD8+ T cell responses via interaction
 with the T cell receptor (TCR) and co-receptor CD8. Peptides are generally
 critical for the stable cell surface expression of HLA-I molecules.
 However, for HLA-I alleles such as HLA-B35:01, peptide-deficient (empty)
 heterodimers are thermostable and detectable on the cell surface.
 Additionally, peptide-deficient HLA-B35:01 tetramers preferentially bind
 CD8 and to a majority of blood-derived CD8+ T cells via a CD8-dependent
 binding mode. Further functional studies reveal that peptide-deficient
 conformers of HLA-B35:01 do not directly activate CD8+ T cells, but
 accumulate at the immunological synapse in antigen-induced responses, and
 enhance cognate peptide-induced cell adhesion and CD8+ T cell activation.
 Together, these findings indicate that HLA-I peptide occupancy influences
 CD8 binding affinity, and reveal a new set of regulators of CD8+ T cell
 activation, mediated by the binding of empty HLA-I to CD8.
description: Fig 1CFig 2Fig 3Fig 4 Fig Supplement
 1Fig 4Fig 5 Fig Supplement
 1Fig 5Fig 6 Fig Supplement
 1Fig 6