cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tq5f0
title: Data from: Genome-wide meta-analysis of sciatica in Finnish population

description: Sciatica or the sciatic syndrome is a common and often disabling low back
 disorder in the working-age population. It has a relatively high
 heritability but poorly understood molecular mechanisms. The Finnish
 population is a genetic isolate where small founder population and
 bottleneck events have led to enrichment of certain rare and low frequency
 variants. We performed here the first genome-wide association (GWAS) and
 meta-analysis of sciatica. The meta-analysis was conducted across two GWAS
 covering 291 Finnish sciatica cases and 3671 controls genotyped and
 imputed at 7.7 million autosomal variants. The most promising loci
 (p&lt;1x10-6) were replicated in 776 Finnish sciatica patients and
 18,489 controls. We identified five intragenic variants, with relatively
 low frequencies, at two novel loci associated with sciatica at genome-wide
 significance. These included chr9:14344410:I (rs71321981) at 9p22.3 (NFIB
 gene; p=1.30x10-8, MAF=0.08) and four variants at 15q21.2: rs145901849,
 rs80035109, rs190200374 and rs117458827 (MYO5A; p=1.34x10-8, MAF=0.06;
 p=2.32x10-8, MAF=0.07; p=3.85x10-8, MAF=0.06; p=4.78x10-8, MAF=0.07,
 respectively). The most significant association in the meta-analysis, a
 single base insertion rs71321981 within the regulatory region of the
 transcription factor NFIB, replicated in an independent Finnish population
 sample (p=0.04). Despite identifying 15q21.2 as a promising locus, we were
 not able to replicate it. It was differentiated; the lead variants within
 15q21.2 were more frequent in Finland (6-7%) than in other European
 populations (1-2%). Imputation accuracies of the three significantly
 associated variants (chr9:14344410:I, rs190200374, and rs80035109) were
 validated by genotyping. In summary, our results suggest a novel locus,
 9p22.3 (NFIB), which may be involved in susceptibility to sciatica. In
 addition, another locus, 15q21.2, emerged as a promising one, but failed
 to replicate.
description: Results of genome-wide
 meta-analysis of sciaticaRaw result data of the
 genome-wide meta-analysis of sciaticaMeta_GWAS_sciatica_results
DOI: 10.5061/dryad.253p6
title: Data from: Modeling of kidney hemodynamics: probability-based topology of an arterial network

description: Through regulation of the extracellular fluid volume, the kidneys provide
 important long-term regulation of blood pressure. At the level of the
 individual functional unit (the nephron), pressure and flow control
 involves two different mechanisms that both produce oscillations. The
 nephrons are arranged in a complex branching structure that delivers blood
 to each nephron and, at the same time, provides a basis for an interaction
 between adjacent nephrons. The functional consequences of this interaction
 are not understood, and at present it is not possible to address this
 question experimentally. We provide experimental data and a new modeling
 approach to clarify this problem. To resolve details of microvascular
 structure, we collected 3D data from more than 150 afferent arterioles in
 an optically cleared rat kidney. Using these results together with
 published micro-computed tomography (μCT) data we develop an algorithm for
 generating the renal arterial network. We then introduce a mathematical
 model describing blood flow dynamics and nephron to nephron interaction in
 the network. The model includes an implementation of electrical signal
 propagation along a vascular wall. Simulation results show that the renal
 arterial architecture plays an important role in maintaining adequate
 pressure levels and the self-sustained dynamics of nephrons.
description: 3D data stack
 (superficial renal vasculature)Dimensions are
 1640x1640x69, corresponding to 850x850x497 micrometers.Nyre_5-1_Strep_100_DBE_500_mikro.czi3D data stack 2 (superficial renal vasculature)Dimensions 1708x1708x150, corresponding to 850x850x1018 micrometers1 mm stack online finger printing.czi
DOI: 10.5061/dryad.82vm4
title: Data from: Recent selection for self-compatibility in a population of Leavenworthia alabamica

description: The evolution of self-compatibility (SC) is the first step in the
 evolutionary transition in plants from outcrossing enforced by
 self-incompatibility (SI) to self-fertilization. In the Brassicaceae, SI
 is controlled by alleles of two tightly linked genes at the S-locus.
 Despite permitting inbreeding, mutations at the S-locus leading to SC may
 be selected if they provide reproductive assurance and/or gain a
 transmission advantage in a population when SC plants self- and outcross.
 Positive selection can leave a genomic signature in the regions physically
 linked to the focus of selection when selection has occurred recently.
 From an SC population of Leavenworthia alabamica with a known
 nonfunctional mutation at the S-locus, we collected sequence data from a
 ∼690 Kb region surrounding the S-locus, as well as from regions not linked
 to the S-locus. To test for recent positive selection acting at the
 S-locus, we examined polymorphism and the site-frequency spectra. Using
 forward simulations, we demonstrate that recent selection of the strength
 expected for SC at a locus formerly under balancing selection can generate
 patterns similar to those seen in our empirical data.
description: Individual bam files
 used in population genomic analysesThe data consist of
 MIseq amplicon reads mapped to the file available in 'A2 reference
 for read mapping'.a2_bams.zipA2 reference for read mappingThis reference consists of 2 fasta entries: s_region and unlinked. The s_region is concatenated sequence from all S-linked contigs/scaffolds from the reference assembly (A2 reference genome assembly) for which we had amplicon data. The same is true for the unlinked entry, except these contigs/scaffolds were not physically linked to the S-locusa2_pseudoS_genome_2chroms.txtHatton variants in A2 read mapping referenceThis file is a version of the A2 read mapping reference file with the Hatton SNP variants inserted. This file served as our ancestral sequence for polarizing the SFS.a2_hatton_insert_2chroms.txtA2 reference genome assemblyThe A2 genome assembly that was used to determine contigs/scaffolds homologous to the S-locus region from the well-assembled Russellville reference (http://grandiflora.eeb.utoronto.ca:8190/cgi-bin/hgGateway).LA_A2_ray31_sdn_61scafSeq.faHatton reference genome assemblyThis is the reference assembly for the Hatton (SI) population of L. alabamica.LalSRKrun2_41_61.scafSeq
DOI: 10.5061/dryad.9f2p5
title: Data from: Genome-wide effects of selenium and translational uncoupling on transcription in the termite gut symbiont Treponema primita

description: When prokaryotic cells acquire mutations, encounter translation-inhibiting
 substances, or experience adverse environmental conditions that limit
 their ability to synthesize proteins, transcription can become uncoupled
 from translation. Such uncoupling is known to suppress transcription of
 protein-encoding genes in bacteria. Here we show that the trace element
 selenium controls transcription of the gene for the
 selenocysteine-utilizing enzyme formate dehydrogenase (fdhFSec) through a
 translation-coupled mechanism in the termite gut symbiont Treponema
 primitia, a member of the bacterial phylum Spirochaetes. We also evaluated
 changes in genome-wide transcriptional patterns caused by selenium
 limitation and by generally uncoupling translation from transcription via
 antibiotic-mediated inhibition of protein synthesis. We observed that
 inhibiting protein synthesis in T. primitia influences transcriptional
 patterns in unexpected ways. In addition to suppressing transcription of
 certain genes, the expected consequence of inhibiting protein synthesis,
 we found numerous examples in which transcription of genes and operons is
 truncated far downstream from putative promoters, is unchanged, or is even
 stimulated overall. These results indicate that gene regulation in
 bacteria allows for specific post-initiation transcriptional responses
 during periods of limited protein synthesis, which may depend both on
 translational coupling and on unclassified intrinsic elements of
 protein-encoding genes.
description: minus_selplus_selplus_tetTreponema_primitia_zas2_genomeFASTA File of T. primitia azs2 Genomic SequenceTreponema_primitia_zas2.fas
DOI: 10.5061/dryad.j82k4
title: Data from: Sex differences in social focus across the lifecycle in humans

description: Age and gender are two important factors that play crucial roles in the
 way organisms allocate their social effort. In this study, we analyse a
 large mobile phone dataset to explore the way life history influences
 human sociality and the way social networks are structured. Our results
 indicate that these aspects of human behaviour are strongly related to age
 and gender such that younger individuals have more contacts and, among
 them, males more than females. However, the rate of decrease in the number
 of contacts with age differs between males and females, such that there is
 a reversal in the number of contacts around the late 30s. We suggest that
 this pattern can be attributed to the difference in reproductive
 investments that are made by the two sexes. We analyse the inequality in
 social investment patterns and suggest that the age- and gender-related
 differences we find reflect the constraints imposed by reproduction in a
 context where time (a form of social capital) is limited.
description: Egocentric_File_RSOSThe file Egocentric_File_RSOS.csv contains data corresponding to egocentric networks of 3,106,293 individuals derived from anonymized call detail records for a single month in the year 2007 from a mobile phone service provider in a European country.
DOI: 10.5061/dryad.ph75c
title: Data from: Feeding capability in the extinct giant Siamogale melilutra and comparative mandibular biomechanics of living Lutrinae

description: At 50 kg in estimated weight, the extinct Siamogale melilutra is larger
 than all living otters, and ranks among the largest fossil otters. The
 biomechanical capability of S. melilutra jaws as related to their large
 size is unknown but crucial to reconstructing the species’ potentially
 unique ecological niche. Here we compare the mandibular biomechanics of S.
 melilutra using engineering-based performance measures against ten extant
 otter biomechanical models. Despite a wide range of feeding preferences
 from durophagy to piscivory, living otter species exhibit a linear
 relationship between mandible stiffness and volume, as expected in
 isometric model scaling. In contrast, S. melilutra models exhibit a
 six-fold increase in stiffness from expected stiffness-volume
 relationships calculated from extant species models. Unlike stiffness,
 mechanical efficiency of biting is conserved among living otters and in S.
 melilutra. These findings indicate that although similar to living
 bunodont otters in morphology and biting efficiency, jaw strength in S.
 melilutra far surpasses molluscivores such as sea otters and Cape clawless
 otters, even after accounting for size. Therefore, Siamogale represents a
 feeding ecomorphology with no living analog, and its giant size and high
 mandibular strength confer shell-crushing capability matched only by other
 extinct molluscivores such as the marine bear Kolponomos.
description: Tsengetal_Siamogale_FEA_modelsFinite element models of otter mandibles in Strand7 file format.
DOI: 10.5061/dryad.6365v
title: Data from: "De novo assembly transcriptome for the rostrum dace (Leuciscus burdigalensis, Cyprinidae: fish) naturally infected by a copepod ectoparasite" in Genomic Resources Notes accepted 1 December 2014 to 31 January 2015

description: The emergence of pathogens represents substantial threats to public
 health, livestock, domesticated animals, and biodiversity. How wild
 populations respond to emerging pathogens has generated a lot of interest
 in the last two decades. With the recent advent of high-throughput
 sequencing technologies it is now possible to develop large transcriptomic
 resources for non-model organisms, hence allowing new research avenues on
 the immune responses of hosts from a large taxonomic spectra. We here
 focused on a wild population of the rostrum dace (Leuciscus burgiladensis)
 that is infected by Tracheliastes polycolpus, an emerging freshwater
 ectoparasite copepod. We used next generation Illumina sequencing
 technology to sequence the transcriptome of eight L. burdigalensis adult
 individuals collected in natura from the same sampling site. Four
 individuals were non-infected and four individuals were infected by T.
 polycolpus. We specifically focused on the spleen, the head kidney and
 epithelial cells and mucus from the fins, three tissues known to be
 involved in the immune response of fish. We used the Trinity methodology
 to reconstruct a de novo full-length transcriptome for L. burdigalensis.
 The resulting transcriptome will serve as an important broad-scale genomic
 resource for further studying the response of local population of L.
 burdigalensis to T. polycolpus pressures.
description: Lburdigalensis_transcriptome_assembyBest blast hits of each contig from the de novo assembly of L. burdigalensis to Danio rerio cDNA databaseThis excel file contains all the best blast hits of each contigs from the de novo assembly of Leuciscus burdigalensis to Danio rerio cDNA database (Danio_rerio.Zv9.73.cdna.all.fasta available at: ftp://ftp.ensembl.org/pub/release-77/fasta/danio_rerio/cdna/) using a 1e-10 e-value threshold. The excel file contains four sheets.Blast_Lburdigalensis_Drerio_cDNA.xls
DOI: 10.5061/dryad.p15m6
title: Data from: Comparison of gene coexpression profiles and construction of conserved gene networks to find functional modules

description: Background: Computational approaches toward gene annotation are a
 formidable challenge, now that many genome sequences have been determined.
 Each gene has its own function, but complicated cellular functions are
 achieved by sets of genes. Therefore, sets of genes with strong functional
 relationships must be identified. For this purpose, the similarities of
 gene expression patterns and gene sequences have been separately utilized,
 although the combined information will provide a better solution. Result
 & Discussion: We propose a new method to find functional modules,
 by comparing gene coexpression profiles among species. A coexpression
 pattern is represented as a list of coexpressed genes with each guide
 gene. We compared two coexpression lists, one from a human guide gene and
 the other from a homologous mouse gene, and defined a measure to evaluate
 the similarity between the lists. Based on this coexpression similarity,
 we detected the highly conserved genes, and constructed human gene
 networks with conserved coexpression between human and mouse. Some of the
 tightly coupled genes (modules) showed clear functional enrichment, such
 as immune system and cell cycle, indicating that our method could identify
 functionally related genes without any prior knowledge. We also found a
 few functional modules without any annotations, which may be good
 candidates for novel functional modules. All of the comparisons are
 available at the http://v1.coxsimdb.info web database.
description: data-repositorycoexpression-conservation-between-human-and-mouse.zipTurning-PointThe list of turning points in coexpression conservation.Enriched-GO-TermsThe list of all enriched GO terms when SCS = 3, 4 and 5
DOI: 10.5061/dryad.m1s4p
title: Data from: A multimodal image guiding system for Navigated Ultrasound Bronchoscopy (EBUS): a human feasibility study

description: Background: Endobronchial ultrasound transbronchial needle aspiration
 (EBUS-TBNA) is the endoscopic method of choice for confirming lung cancer
 metastasis to mediastinal lymph nodes. Precision is crucial for correct
 staging and clinical decision-making. Navigation and multimodal imaging
 can potentially improve EBUS-TBNA efficiency. Aims: To demonstrate the
 feasibility of a multimodal image guiding system using electromagnetic
 navigation for ultrasound bronchoschopy in humans. Methods: Four patients
 referred for lung cancer diagnosis and staging with EBUS-TBNA were
 enrolled in the study. Target lymph nodes were predefined from the
 preoperative computed tomography (CT) images. A prototype convex probe
 ultrasound bronchoscope with an attached sensor for position tracking was
 used for EBUS-TBNA. Electromagnetic tracking of the ultrasound
 bronchoscope and ultrasound images allowed fusion of preoperative CT and
 intraoperative ultrasound in the navigation software. Navigated EBUS-TBNA
 was used to guide target lymph node localization and sampling. Navigation
 system accuracy was calculated, measured by the deviation between lymph
 node position in ultrasound and CT in three planes. Procedure time,
 diagnostic yield and adverse events were recorded. Results: Preoperative
 CT and real-time ultrasound images were successfully fused and displayed
 in the navigation software during the procedures. Overall navigation
 accuracy (11 measurements) was 10.0 ± 3.8 mm, maximum 17.6 mm, minimum 4.5
 mm. An adequate sample was obtained in 6/6 (100%) of targeted lymph nodes.
 No adverse events were registered. Conclusions: Electromagnetic navigated
 EBUS-TBNA was feasible, safe and easy in this human pilot study. The
 clinical usefulness was clearly demonstrated. Fusion of real-time
 ultrasound, preoperative CT and electromagnetic navigational bronchoscopy
 provided a controlled guiding to level of target, intraoperative overview
 and procedure documentation.
description: Patient EBUS
 01Patient 01 - CT and
 UltrasoundPatient EBUS
 02Patient 02 - CT and
 UltrasoundPatient EBUS
 03Patient 03 - CT and
 UltrasoundPatient EBUS
 04Patient 04 - CT and
 Ultrasound
DOI: 10.5061/dryad.94ms3
title: Data from: Development, validation and high-throughput analysis of sequence markers in nonmodel species

description: DNA sequences derived from multiple regions of the nuclear genome are
 essential for historical inferences in the fields of phylogeography and
 phylogenetics. The appropriate markers should be single-copy, variable,
 easy to amplify from multiple samples and easy to sequence using
 high-throughput technologies. This may be difficult to achieve for species
 lacking sequenced genomes and particularly challenging for species
 possessing large genomes, which consist mostly of repetitive sequences.
 Here, we present a cost-effective, broadly applicable framework for
 designing, validating and high-throughput sequencing of multiple markers
 in nonmodel species without sequenced genomes. We demonstrate its utility
 in two closely related species of newts, representatives of urodeles, a
 vertebrate group characterized by large genomes. We show that over 80
 markers, c. 600 bp each, developed mainly from 3′ untranslated transcript
 regions (3′UTR) may be effectively multiplexed and sequenced. Data are
 further processed using standard, freely available bioinformatic tools,
 producing phase-resolved sequences. The approach does not require barcoded
 PCR primers, and the cost of library preparation is independent of the
 number of markers investigated. We hope that this approach will be of
 broad interest for researchers working at the interface of population
 genetics and phylogenetics, exploring deep intraspecific genetic
 structure, species boundaries and phylogeographies of closely related
 species.
description: SAM_filesReconstructed_sequencesReference_contigsScriptTranslation_table_for_individualsTranslation_table.xlsxVCF_filesGenotype dataGenotype data for Lissotriton montandoni from Eastern Carpathians region, provided in GENEPOP format for tests of Hardy-Weinberg equilibrium.Genotypes
DOI: 10.5061/dryad.b70pn
title: Data from: Measuring ectomycorrhizal fungal dispersal: macroecological patterns driven by microscopic propagules

description: Dispersal plays a prominent role in most conceptual models of community
 assembly. However, direct measurement of dispersal across a whole
 community is difficult at ecologically relevant spatial scales. For
 cryptic organisms, such as fungi and bacteria, the scale and importance of
 dispersal limitation has become a major point of debate. We use an
 experimental island biogeographic approach to measure the effects of
 dispersal limitation on the ecological dynamics of an important group of
 plant symbionts, ectomycorrhizal fungi. We manipulated the isolation of
 uncolonized host seedlings across a natural landscape and used a range of
 molecular techniques to measure dispersal rates of ectomycorrhizal
 propagules and host colonization. Some species were prolific dispersers,
 producing annual spore loads on the order of trillions of spores per km2.
 However, fungal propagules reaching host seedlings decreased rapidly with
 increasing distance from potential spore sources, causing a concomitant
 reduction in ectomycorrhizal species richness, host colonization, and host
 biomass. There were also strong differences in dispersal ability across
 species, which correlated well with the predictable composition of
 ectomycorrhizal communities associated with establishing pine forest. The
 use of molecular tools to measure whole community dispersal provides a
 direct confirmation for a key mechanism underlying island biogeography
 theory and has the potential to make microbial systems a model for
 understanding the role of dispersal in ecological theory.
description: dataArchive_26Apr2012Site level variables measured in experiment.Representative ITS1 sequences for OTUsIncludes the extracted ITS1 sequences for each operational taxonomic unit resulting from OTU picking as described in the text.rep_seqs_ITS1.fnaGPV8ECL01_SFF454 image file for 1/4 plate Run 1 of 2.GPV8ECL01.sffGPV8ECL02_SFF454 image file for 1/4 plate run 2 of 2.GPV8ECL02.sff
DOI: 10.5061/dryad.36h28
title: Data from: Extracellular space preservation aids the connectomic analysis of neural circuits

description: Dense connectomic mapping of neuronal circuits is limited by the time and
 effort required to analyze 3D electron microscopy (EM) datasets.
 Algorithms designed to automate image segmentation suffer from substantial
 error rates and require significant manual error correction. Any
 improvement in segmentation error rates would therefore directly reduce
 the time required to analyze 3D EM data. We explored preserving
 extracellular space (ECS) during chemical tissue fixation to improve the
 ability to segment neurites and to identify synaptic contacts. ECS
 preserved tissue is easier to segment using machine learning algorithms,
 leading to significantly reduced error rates. In addition, we observed
 that electrical synapses are readily identified in ECS preserved tissue.
 Finally, we determined that antibodies penetrate deep into ECS preserved
 tissue with only minimal permeabilization, thereby enabling correlated
 light microscopy (LM) and EM studies. We conclude that preservation of ECS
 benefits multiple aspects of the connectomic analysis of neural circuits.
description: Figure3 - Source Data
 1Raw
 data for 3D SBEM High ECS dataset. Viewable in Knossos
 (www.knossostool.org)Figure3_sourcedata1_M0007_33_mag1_subvol.zipFigure 3 - Source Data 2Raw data for 3D SBEM Low ECS dataset. Viewable in Knossos (www.knossostool.org)Figure3_sourcedata2_M0027_11_mag1_subvol.zip