cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pm7p6
title: Data from: A method for deducing neck mobility in plesiosaurs, using the exceptionally preserved Nichollssaura borealis

description: The elongate-necked aquatic plesiosaurs existed for 135 million years
 during the Mesozoic. The function of this elongate neck is a point of
 debate. Using computed tomography (CT) and 3-dimensional (3D) modelling,
 the range of motion (ROM) of the plesiosaur *Nichollssaura borealis* neck
 was assessed. To quantify the ROM, the intervertebral mobility was
 measured along the cervical vertebral column. This was done by
 manipulating the 3D models in the lateral and dorso-ventral directions
 during two trials. The first assessed the mean intervertebral ROM between
 pairs of cervical vertebrae along the entire column, and the second
 assessed ROM with reduced intervertebral spaces. The results suggest that
 there may be preference for lateral neck movements in *N. borealis*, which
 could correspond to an ecological function related to prey capture. This
 study demonstrates that 3D modelling is an effective tool for assessing
 function morphology for structures where no good modern analogue exists.
description: Dryad Upload
 Nborealis
DOI: 10.5061/dryad.3jg57
title: Data from: How little data is enough? Phase-diagram analysis of sparsity-regularized X-ray computed tomography

description: We introduce phase-diagram analysis, a standard tool in compressed sensing
 (CS), to the X-ray computed tomography (CT) community as a systematic
 method for determining how few projections suffice for accurate
 sparsity-regularized reconstruction. In CS, a phase diagram is a
 convenient way to study and express certain theoretical relations between
 sparsity and sufficient sampling. We adapt phase-diagram analysis for
 empirical use in X-ray CT for which the same theoretical results do not
 hold. We demonstrate in three case studies the potential of phase-diagram
 analysis for providing quantitative answers to questions of undersampling.
 First, we demonstrate that there are cases where X-ray CT empirically
 performs comparably with a near-optimal CS strategy, namely taking
 measurements with Gaussian sensing matrices. Second, we show that, in
 contrast to what might have been anticipated, taking randomized CT
 measurements does not lead to improved performance compared with standard
 structured sampling patterns. Finally, we show preliminary results of how
 well phase-diagram analysis can predict the sufficient number of
 projections for accurately reconstructing a large-scale image of a given
 sparsity by means of total-variation regularization.
description: article_dataCode and data to reproduce all figures of the article. In addition, information about where one can find additional code to run all simulations producing the data supplied here.
DOI: 10.5061/dryad.v089t
title: Data from: Almost a spider: a 305-million-year-old fossil arachnid and spider origins

description: Spiders are an important animal group, with a long history. Details of
 their origins remain limited, with little knowledge of their stem group,
 and no insights into the sequence of character acquisition during spider
 evolution. We describe a new fossil arachnid, Idmonarachne brasieri gen.
 et sp. nov. from the late Carboniferous (Stephanian, ca. 305–299 Ma) of
 Montceau-les-Mines, France. It is three-dimensionally preserved within a
 siderite concretion, allowing both laboratory- and synchrotron-based
 phase-contrast computed tomography (CT) reconstruction. The latter is a
 first for siderite-hosted fossils, and has allowed us to investigate fine
 anatomical details. Although distinctly spider-like in habitus, this
 remarkable fossil lacks a key diagnostic character of Araneae: spinnerets
 on the underside of the opisthosoma. It also lacks a flagelliform telson
 found in the recently recognised, spider-related, Devonian–Permian
 Uraraneida. Cladistic analysis resolves our new fossil as sister group to
 the spiders: the spider stem-group comprises the uraraneids and I.
 brasieri. Whilst we are unable to demonstrate the presence of spigots in
 this fossil, the recovered phylogeny suggests the earliest character to
 evolve on the spider stem-group is the secretion of silk. This would have
 been followed by the loss of a flagelliform telson, and then the ability
 to spin silk using spinnerets. This last innovation defines the true
 spiders, significantly postdates the origins of silk, and may be key to
 the group’s success. The Montceau-les-Mines locality has previously
 yielded a mesothele spider (with spinnerets). Evidently, late Palaeozoic
 spiders lived alongside Palaeozoic arachnid grades which approached the
 spider condition, but did not express the full suite of crown-group
 autapomorphies.
description: Garwood et al 2016, SI
 File 1.A 3D model of I.
 brasieri - provided in the VAXML interchange format [39]. Can be open with
 the freely available software SPIERS
 (spiers-software.org).Garwood_et_al_SI_File_01_scan.zipGarwood et al 2016, SI File 2.A video showing the 3D model of I. brasieri from both laboratory and synchrotron scans, plus slices from synchrotron scans demonstrating the lack of ventral opisthosomal spinnerets.Garwood_et_al_SI_File_02.avi
DOI: 10.5061/dryad.r55m2
title: Data from: Effects of seal predation on a modelled marine fish community and consequences for a commercial fishery

description: We constructed a size- and trait-based dynamic marine community model of
 the Celtic Sea/Biologically Sensitive Area, including grey seals
 Halichoerus grypus (Fabricius 1791) and harbour seals Phoca vitulina
 vitulina (Linnaeus 1758) to examine potential resource conflict between
 seals and commercial trawl fisheries. The model incorporates seal diet
 preference, population size and commercial fishery catch, with survey data
 to quantify ecological interactions between seals and fisheries. Total
 annual consumption by seals was an order of magnitude less than the catch
 of the modelled trawl fishery. Increasing fishing pressure reduced fish
 spawning stock biomass (SSB) much more than a proportionally equivalent
 increase in seal predation. For most fish species, quadrupling seal
 predation showed little effect on the predicted fishery catch. These
 results arise from relatively low seal abundance and partial niche
 partitioning. The fishery harvested a wider range of fish lengths and
 species than seals consumed. The fish community was dominated by small
 fish lengths and seals predated on these more than suggested by their
 calculated diet preference. Seal predation disproportionately affected
 several fish species not targeted by the fishery, but seal predation did
 not significantly affect the SSB of any of the species that constitute 90%
 of the total landings of the fishery. Synthesis and applications.
 Predation of fish by grey and harbour seals is unlikely to harm commercial
 trawl fisheries in south-west Irish waters. This conclusion differs from
 those of some model-based studies of other North Atlantic systems,
 demonstrating the need for ecosystem-specific evidence in considering such
 conflicts. In systems with low niche overlap between seals and fisheries,
 the two are largely decoupled in effect, leaving fishing pressure as the
 overwhelming determinant of targeted fish stock status.
description: Houle_etal_ScriptsMatlab code for the simulation model. The main model file is food_mul.m
DOI: 10.5061/dryad.fc71cp4
title: Data from: An inverse latitudinal gradient in speciation rate for marine fishes

description: Far more species of organisms are found in the tropics than in temperate
 and polar regions, but the evolutionary and ecological causes of this
 pattern remain controversial1,2. Tropical marine fish communities are much
 more diverse than cold-water fish communities found at higher
 latitudes3,4, and several explanations for this latitudinal diversity
 gradient propose that warm reef environments serve as evolutionary
 ‘hotspots’ for species formation5,6,7,8. Here we test the relationship
 between latitude, species richness and speciation rate across marine
 fishes. We assembled a time-calibrated phylogeny of all ray-finned fishes
 (31,526 tips, of which 11,638 had genetic data) and used this framework to
 describe the spatial dynamics of speciation in the marine realm. We show
 that the fastest rates of speciation occur in species-poor regions outside
 the tropics, and that high-latitude fish lineages form new species at much
 faster rates than their tropical counterparts. High rates of speciation
 occur in geographical regions that are characterized by low surface
 temperatures and high endemism. Our results reject a broad class of
 mechanisms under which the tropics serve as an evolutionary cradle for
 marine fish diversity and raise new questions about why the coldest oceans
 on Earth are present-day hotspots of species formation.
description: Analysis scripts and
 dataIncludes phylogenetic
 trees, evolutionary rate estimates, geographic data, and scripts to repeat
 all analyses from article.Archive.zip
DOI: 10.5061/dryad.vn342
title: Data from: Fundamental activity constraints lead to specific interpretations of the connectome

description: The continuous integration of experimental data into coherent models of
 the brain is an increasing challenge of modern neuroscience. Such models
 provide a bridge between structure and activity, and identify the
 mechanisms giving rise to experimental observations. Nevertheless,
 structurally realistic network models of spiking neurons are necessarily
 underconstrained even if experimental data on brain connectivity are
 incorporated to the best of our knowledge. Guided by physiological
 observations, any model must therefore explore the parameter ranges within
 the uncertainty of the data. Based on simulation results alone, however,
 the mechanisms underlying stable and physiologically realistic activity
 often remain obscure. We here employ a mean-field reduction of the
 dynamics, which allows us to include activity constraints into the process
 of model construction. We shape the phase space of a multi-scale network
 model of the vision-related areas of macaque cortex by systematically
 refining its connectivity. Fundamental constraints on the activity, i.e.,
 prohibiting quiescence and requiring global stability, prove sufficient to
 obtain realistic layer- and area-specific activity. Only small adaptations
 of the structure are required, showing that the network operates close to
 an instability. The procedure identifies components of the network
 critical to its collective dynamics and creates hypotheses for structural
 data and future experiments. The method can be applied to networks
 involving any neuron model with a known gain function.
description: data_submission_v3This archive contains all Python scripts necessary to reproduce the figures of the manuscript as well as the underlying data. See README file for the required Python packages.
DOI: 10.5061/dryad.k543p
title: Data from: Mapping of craniofacial traits in outbred mice identifies major developmental genes involved in shape determination

description: The vertebrate cranium is a prime example of the high evolvability of
 complex traits. While evidence of genes and developmental pathways
 underlying craniofacial shape determination is accumulating, we are still
 far from understanding how such variation at the genetic level is
 translated into craniofacial shape variation. Here we used 3D geometric
 morphometrics to map genes involved in shape determination in a population
 of outbred mice (Carworth Farms White, or CFW). We defined shape traits
 via principal component analysis of 3D skull and mandible measurements. We
 mapped genetic loci associated with shape traits at ~80,000 candidate
 single nucleotide polymorphisms in ~700 male mice. We found that
 craniofacial shape and size are highly heritable, polygenic traits.
 Despite the polygenic nature of the traits, we identified 17 loci that
 explain variation in skull shape, and 8 loci associated with variation in
 mandible shape. Together, the associated variants account for 11.4% of
 skull and 4.4% of mandible shape variation, however, the total additive
 genetic variance associated with phenotypic variation was estimated in
 ~45%. Candidate genes within the associated loci have known roles in
 craniofacial development; this includes 6 transcription factors and
 several regulators of bone developmental pathways. One gene, Mn1, has an
 unusually large effect on shape variation in our study. A knockout of this
 gene was previously shown to affect negatively the development of
 membranous bones of the cranial skeleton, and evolutionary analysis shows
 that the gene has arisen at the base of the bony vertebrates
 (Eutelostomi), where the ossified head first appeared. Therefore, Mn1
 emerges as a key gene for both skull formation and within-population shape
 variation. Our study shows that it is possible to identify important
 developmental genes through genome-wide mapping of high-dimensional shape
 features in an outbred population.
description: RcodeThis folder contains
 four Rcode files necessary to reproduce our analyses. map.qtls.gemma.PCs.R
 is the master code that requires functions from other.code.R, run.gemma.R,
 and analyses.PCs.R.Eigenvectors_PCAThis folder contains two files with the eigenvectors of the PCA done with skull shape and mandible shape data. These files can be used to project new shape data into our PCA.Eigenvector_PCA.zipPhenotype fileThis file contains skull and mandible shape principal component (PC) scores for each mouse. PC scores were normalized to mean 0 and std of 1. Mandible PC scores were calculated from the regression residuals of shape ~ BMD. Skull and mandible centroid size (CS) data is also included.pheno.mandskull.csvGenotype dataThis files contains genotype (SNP) data for each mouse.geno.dosage.RData
DOI: 10.5061/dryad.6j13r
title: Data from: Virtual reconstruction of endocast anatomy in early ray-finned fishes (Osteichthyes: Actinopterygii)

description: Cranial endocasts, infillings of the skeletal void that once contained the
 brain and associated soft tissues, represent detailed anatomical
 structures that have long been the focus of paleontological investigation.
 We applied computed tomographics (CTs) in order to generate endocast
 models for the Paleozoic actinopterygian fishes Mimipiscis and Kentuckia,
 which serve as key representatives of anatomically primitive, early ray
 fins in analyses of early vertebrate relationships. The resultant
 endocranial models generally corroborate existing accounts of endocranial
 anatomy in these genera, drawn from descriptions of the inner face of the
 brain cavity. However, the endocasts also provide new anatomical details,
 the most significant of which are the presence in Mimipiscis of widely
 divergent olfactory tracts, small optic lobes, and anterior and posterior
 semicircular canals that extend dorsal to the roof of the endocranial
 chamber. By contrast, Kentuckia possesses a single, straight olfactory
 tract, wide optic lobes, and anterior and posterior semicircular canals
 that do not reach the dorsal surface of the endocast. In each of these
 features, Kentuckia resembles stratigraphically younger actinopterygians
 such as Lawrenciella and Kansasiella, whereas Mimipiscis more closely
 resembles sarcopterygians and other outgroups. This character distribution
 provides further support for earlier phylogenetic interpretations of these
 genera.
description: Supplemental Data
 1Table giving key
 references for endocranial descriptions of Paleozoic jawed fishes.
 Regional divisions of the stratigraphic record given as age estimates in
 individual descriptions have been replaced with global equivalents where
 possible following Gradstein et al. (2012).Supplemental_Data_1.docxSupplemental Data 2Workflow of segmentation method described for Avizo.Supplemental_Data_2.docxSupplemental Data 3Animation of the endocast of Mimipiscis toombsi NHMUK PV P.53247.Supplemental_Data_3.gifSupplemental Data 4Animation of the endocast of Kentuckia deani MCZ 8361.Supplemental_Data_4.gifSupplemental Data 5PLY 3D file of the endocast of Mimipiscis toombsi NHMUK PV P.53247.Supplemental_Data_5.plySupplemental Data 6PLY 3D file of the endocast of of Kentuckia deani MCZ 8361.Supplemental_Data_6.plySupplemental Data 7PLY 3D file of the partial endocast of of Kentuckia deani MCZ 5226.Supplemental_Data_7.ply
DOI: 10.5061/dryad.b21r5
title: Data from: "Transcriptome sequencing of the Queensland fruit fly, Bactrocera tryoni (Diptera: Tephritidae)" in Genomic Resources Notes accepted 1 December 2013 to 31 January 2014

description: [No abstract filled]
description: Contigs from Library
 1An
 unannotated version of the trascriptome assembly (contigs and unigenes) is
 presented here.F-Contig.faContigs from Library 2An unannotated version of the trascriptome assembly (contigs and unigenes) is presented here.UF-Contig.faAll-UnigeneAn unannotated version of the trascriptome assembly (contigs and unigenes) is presented here.Sequence assembly and Contig annotationThe raw reads were used to generate a de novo assembly. High quality reads were then assembled into contigs and tese contigs were then further assembled into unigenes using paired end information to combine contigs that arose from the same transcript.annotation.xlsBlast hitsAll unigenes were screened against protein databases Nr, SwissProt, KEGG and COG using BLASTx (e-value&lt;10-5) and against nucleotide database Nt using BLASTn (e-value&lt;10-5). The best hits were used to determine the sequence direction of the unigenes.All-Unigene.blast.cds.fa
DOI: 10.5061/dryad.nn18gb7
title: Data from: Predicting the spread of an invasive tree pest: the pine wood nematode in Southern Europe

description: 1. Invasive tree pests are increasingly threatening forest ecosystems.
 Understanding and controlling their spread presents a major challenge for
 managers, researchers, and policy makers. In 1999, the pine wood nematode
 Bursaphelenchus xylophilus, causal agent of pine wilt disease and native
 to North America, was first detected in Europe, more precisely in south
 western Portugal. Since then, it has spread to more than 30% of the
 country, producing large-scale damages in Portuguese forests. 2. We
 applied a new spatio-temporal network-based model to predict, at yearly
 intervals, the natural spread of the pine wood nematode on the Iberian
 Peninsula, as dispersed by the longhorn beetle Monochamus
 galloprovincialis, its only known vector in Europe. We compared the model
 predictions with independent observations of the natural spread of pine
 wilt disease in Portugal between 2005 and 2015. We simulated the effect of
 potential containment measures on the disease spread. 3. The model
 predicted the status (infected or non-infected) of forest areas with 93%
 accuracy, had 93% sensitivity and specificity, and AUC=0.96 (averages for
 8 years with validation data). 4. Simulated clear-cut belts stopped the
 spread only if they were wider than 30 km, although thinner belts delayed
 invasion. Furthermore, clear-cuts were much more effective in slowing down
 the invasion when reinforced, in the adjacent areas, by the reduction of
 the vector beetle population through mass trapping and by the early
 detection and removal of infected trees. 5. Model projections identified
 areas through which the nematode is most likely to invade, by natural
 means, the phytosanitary buffer zone established along the Portuguese
 border, and Spain. 6. Synthesis and applications. In the absence of
 effective containment measures, the pine wood nematode may naturally
 spread into Spain in about 5 years. In less than 10 years, it may reach
 the major forest and climatic corridors that provide a gateway for
 subsequent expansion towards the rest of the Iberian Peninsula and, in the
 longer term, towards other European countries. Our model can considerably
 support management efforts by forecasting when areas are at highest risk
 of vector-mediated invasion as well as the effects of specific control
 measures on the disease spread.
description: Data
 layersThe file indicates the
 spatial layers that were used as inputs for the pine wood nematode spread
 modelling and provides the URLs at which they can be
 accessed.Predictions of future
 PWN spreadThis is a spatial layer
 in vector format (shapefile) providing the predictions of the pine wood
 nematode natural spread for years 2018, 2022, 2026 and 2028. All the 8
 files of the spatial layer (shapefile format) are zipped in a single
 compressed file. Please see the attached README.pdf file for a description
 of the content of the spatial layer and of the different fields in its
 attribute table.Predictions_PWN_spread_outwards_2018_2022_2026_2028.zip
DOI: 10.5061/dryad.h54d699
title: Data from: High-throughput sequencing of the T-cell receptor beta chain gene distinguishes two subgroups of cutaneous T-cell lymphoma

description: [No abstract entered]
description: HTS of the TCR beta
 chain distinguishes two subgroups of CTCLT-cell repertoire
 characterization data are provided herein as a supplement to:
 High-Throughput Sequencing of the T-cell receptor beta chain gene
 distinguishes two subgroups of cutaneous T-cell lymphoma By Jie Wang, MD,
 Bryan Rea, MD, Paul Haun, MD, Ryan Emerson, PhD, Ilan Kirsch, MD, and Adam
 Bagg, MD
DOI: 10.5061/dryad.hf93c
title: Data from: Bulk genotyping of biopsies can create spurious evidence for heterogeneity in mutation content

description: When multiple samples are taken from the neoplastic tissues of a single
 patient, it is natural to compare their mutation content. This is often
 done by bulk genotyping of whole biopsies, but the chance that a mutation
 will be detected in bulk genotyping depends on its local frequency in the
 sample. When the underlying mutation count per cell is equal, homogenous
 biopsies will have more high-frequency mutations, and thus more detectable
 mutations, than heterogeneous ones. Using simulations, we show that bulk
 genotyping of data simulated under a neutral model of somatic evolution
 generates strong spurious evidence for non-neutrality, because the pattern
 of tissue growth systematically generates differences in biopsy
 heterogeneity. Any experiment which compares mutation content across
 bulk-genotyped biopsies may therefore suggest mutation rate or selection
 intensity variation even when these forces are absent. We discuss
 computational and experimental approaches for resolving this problem.
description: sampled genotypes from
 simulation of Barrett's esophagusSimulated data for
 biopsies from Barrett's esophagus with no selection or variation in
 mutation rate. 5 cases x 500 data sets. Each data set contains 10
 simulated biopsies of 100 crypts.kostadinov.tgz