cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.n5j2m
title: Data from: Transitions in the flow patterns and aerodynamic characteristics of the flow around staggered rows of cylinders

description: A two-dimensional numerical study of flow across rows of identical square
 cylinders arranged in staggered fashion is carried out. This study will
 unreveal complex flow physics depending upon the Reynolds number (Re) and
 gap spacing (g) between the cylinders. The combined effect of Reynolds
 number and gap spacing on the flow physics around staggered rows of
 cylinders are numerically studied for 20 ≤ Re ≤ 140 and 1 ≤ g ≤ 6. We use
 the lattice Boltzmann method for numerical computations. It is found that
 with increase in gap spacing between the cylinders the critical Reynolds
 number for the onset of vortex shedding also increases. We observed a
 strong effect of Reynolds number at g = 2 and 4. Secondary cylinder
 interaction frequency disappears for large Reynolds number at g = 6 and 5
 and the flow around cylinders are fully dominated by the primary vortex
 shedding frequency. This ensures that at large gap spacing with an
 increase in the Reynolds number the wakes interaction between and behind
 the cylinders is weaken. Furthermore, it also ensures that the wake
 interaction behind the cylinders is strongly influenced by the jets in the
 gap spacing between the cylinders. We also found that g = 2 is the
 critical gap spacing for flow across rows of staggered square cylinders
 for the considered range of Reynolds number. Depending on the Reynolds
 number we observed; synchronous, quasi-periodic-I, quasi-periodic-II, and
 chaotic flow patterns. In synchronous flow pattern, an in-phase and
 anti-phase characteristics of consecutive cylinders has been observed. The
 important physical parameters are also analyzed and discussed in detail.
description: PLOS
 ONEThese are the .dat files
 of data used in the paper.
DOI: 10.5061/dryad.nt22g30
title: Data from: Modelling of ships as a source of underwater noise

description: In this paper, a methodology is presented for modelling underwater noise
 emissions from ships based on realistic vessel activity in the Baltic Sea
 region. This paper combines the Wittekind noise source model with the Ship
 Traffic Emission Assessment Model (STEAM) in order to produce regular
 updates for underwater noise from ships. This approach allows the
 construction of noise source maps, but requires parameters which are not
 commonly available from commercial ship technical databases. For this
 reason, alternative methods were necessary to fill in the required
 information. Most of the parameters needed contain information that is
 available during the STEAM model runs, but features describing propeller
 cavitation are not easily recovered for the world fleet. Baltic Sea ship
 activity data were used to generate noise source maps for commercial
 shipping. Container ships were recognized as the most significant source
 of underwater noise, and the significant potential for an increase in
 their contribution to future noise emissions was identified.
description: Underwater noise energy
 emissions from the Baltic Sea fleet during 2015A methodology was
 developed for describing the underwater noise emissions from ships. These
 files contain noise source maps in netcdf format, which contain daily
 emissions of underwater noise in three frequency bands (63, 125 and 2000
 Hz)Jalkanen_et_al_Ocean_Science_14_2018_1_Noisemaps.zip
DOI: 10.5061/dryad.kf674kb
title: Data from: Physiological and genomic signatures of evolutionary thermal adaptation in redband trout from extreme climates

description: Temperature is a master environmental factor that limits the geographical
 distribution of species, especially in ectotherms. To address challenges
 in biodiversity conservation under ongoing climate change, it is essential
 to characterize relevant functional limitations and adaptive genomic
 content at population and species levels. Here, we present evidence for
 adaptive divergence in cardiac function and genomic regions in redband
 trout (Oncorhynchus mykiss gairdneri) populations from desert and montane
 streams. Cardiac phenotypes of individual fish were measured in the field
 with a custom-built electrocardiogram apparatus. Maximum heart rate and
 its rate limiting temperature during acute warming were significantly
 higher in fish that have evolved in the extreme of a desert climate
 compared to a montane climate. Association mapping with 526,301 single
 nucleotide polymorphisms (SNPs) across the genome revealed signatures of
 thermal selection both within and among ecotypes. Among desert and montane
 populations, 413 SNPs were identified as putative outliers under natural
 selection and 20 of these loci showed significant association with average
 summer water temperatures among populations. Phenotypes for cardiac
 performance were variable within each ecotype and 207 genomic regions were
 strongly associated with either maximum heart rate or rate limiting
 temperatures among individuals. Annotation of significant loci provided
 candidate genes that underlie thermal adaptation, including pathways
 associated with cardiac function (IRX5, CASQ1, CAC1D and TITIN),
 neuroendocrine system (GPR17 and NOS) and stress response (SERPH). By
 integrating comparative physiology and population genomics, results here
 advance our knowledge on evolutionary processes of thermal adaptation in
 aquatic ectotherms.
description: genotypesA total of 526,301 SNP markers were produced using PST-I RAD sequencing. They are genotyped in 115 individuals from six redband trout populations.Genotypes of neutral loci in genepop formatThis file contains genotypes of 525,866 putative neutral loci for a total of 115 fish from six redband trout populations from southern Idahoneutral_only_6pop.genepopGenotypes of outlier loci in genepop formatThis file contains genotypes of 435 putative adaptive loci for a total of 115 fish from six redband trout populations from southern Idahooutlier_only_6pop.genepopcardiac phenotypesPhenotype data file for 114 fish from six redband trout populations. Phenotype data of one fish was not collected.cardiac phenotype.xlsx
DOI: 10.5061/dryad.056rf
title: Data from: Transcriptome profiles of sunflower reveal the potential role of microsatellites in gene expression divergence

description: The mechanisms by which natural populations generate adaptive genetic
 variation are not well understood. Some studies propose that
 microsatellites can function as drivers of adaptive variation. Here we
 tested a potentially adaptive role for transcribed microsatellites with
 natural populations of the common sunflower (Helianthus annuus L.) by
 assessing the enrichment of microsatellites in genes that show expression
 divergence across latitudes. Seeds collected from six populations at two
 distinct latitudes in Kansas and Oklahoma were planted and grown in a
 common garden. Morphological measurements from the common garden
 demonstrated that phenotypic variation among populations is largely
 explained by underlying genetic variation. An RNA–Seq experiment was
 conducted with 96 of the individuals grown in the common garden and
 differentially expressed (DE) transcripts between the two latitudes were
 identified. A total number of 825 DE transcripts were identified. DE
 transcripts and non-differentially expressed (NDE) transcripts were then
 scanned for microsatellites. The abundance of different motif lengths and
 types in both groups were estimated. Our results indicate that DE
 transcripts are significantly enriched with mononucleotide repeats and
 significantly depauperate in trinucleotide repeats. Further, the
 standardized mononucleotide repeat motif A and dinucleotide repeat motif
 AG were significantly enriched within DE transcripts while motif types, C,
 AT, ACC, and AAC in DE transcripts are significantly differentiated in
 microsatellite tract length between the two latitudes. The tract length
 differentiation at specific microsatellite motif types across latitudes
 and their enrichment within DE transcripts indicate a potential functional
 role for transcribed microsatellites in gene expression divergence in
 sunflower.
description: Gene Expression Data__95
 H annuus transcriptomesContains gene expression
 data from 58143 contigs across 95 sunflower plants from Kansas and
 Oklahoma grown in a common gardenReference_173Additional transcriptomesFasta files from five transcriptomes assembled for validating the original reference transcriptome.
DOI: 10.5061/dryad.gn6hg74q
title: Data from: QTL detection power of multi-parental RIL populations in Arabidopsis thaliana

description: A major goal of today's biology is to understand the genetic basis of
 quantitative traits. This can be achieved by statistical methods that
 evaluate the association between molecular marker variation and phenotypic
 variation in different types of mapping populations. The objective of this
 work was to evaluate the statistical power of QTL detection of various
 multi-parental mating designs as well as to assess the reasons for the
 observed differences. Our study was based on empirical data of 20
 Arabidopsis thaliana accessions which have been selected to capture the
 maximum genetic diversity. The examined mating designs differed strongly
 with respect to the statistical power to detect QTL. We observed the
 highest power to detect QTL for the diallel cross with random mating
 design. The results of our study suggested that performing sibling mating
 within subpopulations of joint linkage mapping populations has the
 potential to considerably increase the power for QTL detec tion. Our
 results, however, revealed that using designs in which more than two
 parental alleles segregate in each subpopulation increases the power even
 more.
description: simulation_5000.tarsimulation_2500.tarsimulation_1250.tareffects_25.tareffects_50.tareffects_100.tarhaplotype_mapposition_map
DOI: 10.5061/dryad.9089
title: Data from: Rapid development and screening of microsatellite loci for Artibeus lituratus and their utility for six related species within Phyllostomidae

description: Microsatellites are often the marker of choice for population genetic
 studies at intermediate spatial and temporal scales. Developing large
 numbers of markers has traditionally been technically difficult and this
 has limited our ability to investigate evolutionary phenomena that emerge
 across short temporal scales. Moreover, few markers tend to successfully
 amplify across species boundaries. As rapid advancements in
 high-throughput sequencing make microsatellite development cost and
 time-effective, new avenues for evolutionary, population genetic, and
 chromosome linkage mapping research are emerging. We used a published PERL
 script and second-generation sequencing to rapidly and affordably develop
 microsatellite loci for a widespread phyllostomid bat, Artibeus lituratus,
 for which no markers were previously available. We used Roche FLX
 (Titanium) Genome Sequencing to randomly sequence ~101 Mb (255,065 unique
 reads) of genomic DNA for A. lituratus, within which we discovered 30100
 microsatellite loci. We designed primers for 19395 loci that contained
 suitable flanking regions. We ordered primers for 96 loci, 90 of which
 produced a single PCR product in A. lituratus. We genotyped 52 loci, and
 45 were polymorphic in A. lituratus. We tested cross-species amplification
 for 96 loci in six additional phyllostomid species: A. planirostris, A.
 fimbriatus, A. phaeotis, Enchisthenes hartii, Sturnira lilium, and
 Carollia perspicillata. Cross-species amplification was successful for at
 least one species for 87 loci (A. fimbriatus), and in all species at least
 66 loci amplified. These markers will facilitate future work on these
 seven species, but also illustrate the utility of this high-throughput
 method for development of primers across many species simultaneously.
description: S1_Alituratus_SeqFile containing the sequences obtained for Artibeus lituratus from Roche FLX (Titanium) genome sequencing (~1/8th plate).S1_Alituratus_SeqQualityFile of quality data associated with sequence output file from Roche FLX (Titanium) genome sequencing for Artibeus lituratus.S2_Alituratus_AllPrimersAn excel table with details on every microsatellite locus for which forward and reverse priming sites could be developed.
DOI: 10.5061/dryad.sq227
title: Data from: Naked mole rats exhibit metabolic but not ventilatory plasticity following chronic sustained hypoxia

description: Naked mole rats are among the most hypoxia-tolerant mammals identified and
 live in chronic hypoxia throughout their lives. The mechanisms underlying
 this tolerance, however, are poorly understood. Most vertebrates
 hyperventilate in acute hypoxia and exhibit an enhanced hyperventilation
 following acclimatization to chronic sustained hypoxia (CSH). Conversely,
 naked mole rats do not hyperventilate in acute hypoxia and their response
 to CSH has not been examined. In this study we explored mechanisms of
 plasticity in the control of the hypoxic ventilatory response (HVR) and
 hypoxic metabolic response (HMR) of freely behaving naked mole rats
 following 8-10 days of chronic sustained normoxia (CSN) or CSH.
 Specifically, we investigated the role of the major inhibitory
 neurotransmitter γ-amino butyric acid (GABA) in mediating these responses.
 Our study yielded three important findings. First, naked mole rats did not
 exhibit ventilatory plasticity following CSH, which is unique among adult
 animals studied to date. Second, GABA receptor (GABAR) antagonism altered
 breathing patterns in CSN and CSH animals and modulated the acute HVR in
 CSN animals. Third, naked mole rats exhibited GABAR-dependent metabolic
 plasticity following long-term hypoxia, such that the basal metabolic rate
 was ~25% higher in normoxic CSH animals than CSN animals, and GABAR
 antagonists modulated this increase.
description: Raw data for
 ProceedingsThis file contains raw
 LabChart files documenting changes ventilation and metabolism during an
 acute hypoxic exposure in naked mole rats acclimated to 8-10 day of either
 chronic sustained normoxia or chronic sustained hypoxia
DOI: 10.5061/dryad.tg5f2hp
title: Data from: Population-specific genetic modification of Huntington's disease in Venezuela

description: Modifiers of Mendelian disorders can provide insights into disease
 mechanisms and guide therapeutic strategies. A recent genome-wide
 association (GWA) study discovered genetic modifiers of Huntington's
 disease (HD) onset in Europeans. Here, we performed whole genome
 sequencing and GWA analysis of a Venezuelan HD cluster whose families were
 crucial for the original mapping of the HD gene defect. The Venezuelan HD
 subjects develop motor symptoms earlier than their European counterparts,
 implying the potential for population-specific modifiers. The main
 Venezuelan HD family inherits HTT haplotype hap.03, which differs subtly
 at the sequence level from European HD hap.03, suggesting a different
 ancestral origin but not explaining the earlier age at onset in these
 Venezuelans. GWA analysis of the Venezuelan HD cluster suggests both
 population-specific and population-shared genetic modifiers. Genome-wide
 significant signals at 7p21.2-21.1 and suggestive association signals at
 4p14 and 17q21.2 are evident only in Venezuelan HD, but genome-wide
 significant association signals at the established European chromosome 15
 modifier locus are improved when Venezuelan HD data are included in the
 meta-analysis. Venezuelan-specific association signals on chromosome 7
 center on SOSTDC1, which encodes a bone morphogenetic protein antagonist.
 The corresponding SNPs are associated with reduced expression of SOSTDC1
 in non-Venezuelan tissue samples, suggesting that interaction of reduced
 SOSTDC1 expression with a population-specific genetic or environmental
 factor may be responsible for modification of HD onset in Venezuela.
 Detection of population-specific modification in Venezuelan HD supports
 the value of distinct disease populations in revealing novel aspects of a
 disease and population-relevant therapeutic strategies.
description: vz2018.association.analysis.result.summaryResults of a genome-wide association study to identify genetic modifiers of Huntington's disease in Venezuelans.
DOI: 10.5061/dryad.364qh
title: Data from: Phylogenomics offers resolution of major tunicate relationships

description: Tunicata, a diverse clade of approximately 3,000 described species of
 marine, filter-feeding chordates, is of great interest to researchers
 because tunicates are the closest living relatives of vertebrates and they
 facilitate comparative studies of our own biology. The group also includes
 numerous invasive species that cause considerable economic damage and some
 species of tunicates are edible. Despite their diversity and importance,
 relationships among major lineages of Tunicata are not completely
 resolved. Here, we supplemented public data with transcriptomes from seven
 species spanning the diversity of Tunicata and conducted phylogenomic
 analyses on data sets of up to 798 genes. Sensitivity analyses were
 employed to examine the influences of reducing compositional heterogeneity
 and branch-length heterogeneity. All analyses maximally supported a
 monophyletic Tunicata within Olfactores (Vertebrata + Tunicata). Within
 Tunicata, all analyses recovered Appendicularia sister to the rest of
 Tunicata and confirmed (with maximal support) that Thaliacea is nested
 within Ascidiacea. Stolidobranchia is the sister taxon to all other
 tunicates except Appendicularia. In most analyses, phlebobranch tunicates
 were recovered paraphyletic with respect to Aplousobranchia. Support for
 this topology varied but was strong in some cases. However, when only the
 50 best genes based on compositional heterogeneity were analysed, we
 recovered Phlebobranchia and Aplousobranchia reciprocally monophyletic
 with strong support, consistent with most traditional morphology-based
 hypotheses. Examination of internode certainty also cast doubt on results
 of phlebobranch paraphyly, which may be due to limited taxon sampling.
 Taken together, these results provide a higher-level phylogenetic
 framework for our closest living invertebrate relatives.
description: Supplementary
 DataData matrices, trees and
 related files, assembled transcriptomes, translated transcriptomes, HaMStR
 output, script, and RCFV and LB data.
DOI: 10.5061/dryad.mc7c1
title: Data from: Global transcriptome changes in perennial ryegrass during early infection by pink snow mould

description: Lack of resistance to pink snow mould (Microdochium nivale) is a major
 constraint for adaptation of perennial ryegrass (Lolium perenne L.) to
 continental regions with long-lasting snow cover at higher latitudes.
 Almost all investigations of genetic variation in resistance have been
 performed using cold acclimated plants. However, there may be variation in
 resistance mechanisms that are functioning independently of cold
 acclimation. In this study our aim was to identify candidate genes
 involved in such resistance mechanisms. We first characterized variation
 in resistance to M. nivale among non-acclimated genotypes from the
 Norwegian cultivar ‘Fagerlin’ based on relative regrowth and fungal
 quantification by real-time qPCR. One resistant and one susceptible
 genotype were selected for transcriptome analysis using paired-end
 sequencing by Illumina Hiseq 2000. Transcriptome profiles, GO enrichment
 and KEGG pathway analysis indicate that defense response related genes are
 differentially expressed between the resistant and the susceptible
 genotype. A significant up-regulation of defense related genes, as well as
 genes involved in cell wall cellulose metabolic processes and aryl-alcohol
 dehydrogenase (NADP+) activity, was observed in the resistant genotype.
 The candidate genes identified in this study might be potential molecular
 marker resources for breeding perennial ryegrass cultivars with improved
 resistance to pink snow mould.
description: Snowmould_Resistant_genotype_Trinity_transcriptomeSnow mould resistant genotype of Lolium perenne denovo assembly by Trinity programSnowmould_Susceptible_genotype_Trinity_transcriptomeSnow mould susceptible genotype of Lolium perenne de novo assembly generated by Trinity programEST_candidategenes_snowmouldSequences of potential candidate genes for snow mould resistance detected in this studysignificant_GO_Terms_fisherstestSequences of the genes under significant gene ontology (GO) terms which are over represented in snow mould resistant (R) genotype.
DOI: 10.5061/dryad.b3ng3
title: Data from: Pupillometry reveals perceptual differences that are tightly linked to autistic traits in typical adults

description: The pupil is primarily regulated by prevailing light levels, but is also
 modulated by perceptual and attentional factors. We measured pupil-size in
 typical adult humans viewing a bistable-rotating cylinder, constructed so
 the luminance of the front surface changes with perceived direction of
 rotation. In some participants, pupil diameter oscillated in phase with
 the ambiguous perception, more dilated when the black surface was in
 front. Importantly, the magnitude of oscillation predicts autistic traits
 of participants, assessed by the Autism-Spectrum Quotient AQ. Further
 experiments suggest that these results are driven by differences in
 perceptual styles: high AQ participants focus on the front surface of the
 rotating cylinder, while those with low AQ distribute attention to both
 surfaces in a more global, holistic style. This is the first evidence that
 pupillometry reliably tracks inter-individual differences in perceptual
 styles; it does so quickly and objectively, without interfering with
 spontaneous perceptual strategies.
description: License
 FileLicense.txtRaw Data and Analysis functions29-09-2017-RA-eLife-32399R2.zip
DOI: 10.5061/dryad.3g19f
title: Data from: Linking transcriptomic and genomic variation to growth in brook charr hybrids (Salvelinus fontinalis, Mitchill)

description: Hybridization can lead to phenotypic differences arising from changes in
 gene expression patterns or new allele combinations. Variation in gene
 expression is thought to be controlled by differences in transcription
 regulation of parental alleles, either through cis or trans regulatory
 elements. A previous study among brook charr hybrids from different
 populations (Rupert, Laval, and domestic) showing distinct length at age
 during early life stages also revealed different patterns in transcription
 regulation inheritance of transcript abundance. In the present study,
 transcript abundance by means of RNA-seq and qRT-PCR, SNP genotypes and
 allelic imbalance were assessed in order to understand the molecular
 mechanisms underlying the observed transcriptomic and differences in
 length at age among domestic × Rupert hybrids and Laval × domestic
 hybrids. We found 198 differentially expressed genes between the two
 hybrid crosses and allelic imbalance could be analyzed for 69 of them.
 Among these 69 genes, 36 genes exhibited cis acting regulatory effects in
 both of the two crosses, thus confirming the prevalent role of cis acting
 regulatory elements in the regulation of differentially expressed genes
 among intraspecific hybrids. In addition, we detected a significant
 association between SNP genotypes of three genes and length at age. Our
 study is thus one of the few that have highlighted some of the molecular
 mechanisms potentially involved in the differential phenotypic expression
 in intraspecific hybrids for non-model species.
description: Data_filesData of 454 sequencing, phenotypes, Kaspar analysis, qPCR analysis for all experiments used in manuscriptdata_files.tar