cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.78b22
title: Data from: Severity of mitral valve degeneration is associated with chromosome 15 loci in Whippet dogs

description: Mitral valve degeneration (MVD) is the most common form of heart disease
 in dogs, frequently leading to left-sided congestive heart failure and
 cardiac mortality. Although breed-specific disease characteristics and
 overrepresentation point towards a genetic origin for MVD, a causative
 mutation and complete molecular pathogenesis are unknown. Whippet dogs are
 overrepresented in incidence of MVD, suggesting an inherited component in
 this breed. Expressivity of this condition is variable with some dogs
 showing evidence of more severe disease at earlier ages than other dogs.
 This phenomenon makes a traditional case versus control genetic study
 prone to phenotyping error. This study sought to avoid these common
 pitfalls by identifying genetic loci associated with severity of MVD in
 Whippets through a genome-wide association study (GWAS). 138 Whippet dogs
 were characterized for MVD by echocardiographic examination and a novel
 disease severity score was developed and adjusted for age in each subject.
 Single nucleotide polymorphism (SNP) genotype data (170k Illumina CanineHD
 SnpChip) was obtained for DNA isolated from blood of each study subject.
 Continuous variable genome wide association was performed after correction
 for population stratification by efficient mixed model association
 expedited (EMMAX) in 130 dogs. A genome wide significant association was
 identified on chromosome 15 (peak locus 57,770,326; Padj = 0.049) and
 secondary loci of suggestive association were identified on chromosome 2
 (peak locus 37,628,875; Padj = 0.079). Positional candidate genes were
 identified within the primary and secondary loci including
 follistatin-related protein 5 precursor (FSTL5) and Rho GTPase-activating
 protein 26 (ARHGAP26). These results support the hypothesis that severity
 of MVD in whippets has a genetic basis and warrants further study by
 either candidate gene sequencing or next-generation techniques.
description: Illumina CanineHD
 Beadchip dataIllumina CanineHD
 Beadchip data of whippets - traditional ped based format for
 PLINKSTERNetal.txt
DOI: 10.5061/dryad.01f6p
title: Data from: Minimally invasive estimation of ventricular dead space volume through use of Frank-Starling curves

description: This paper develops a means of more easily and less invasively estimating
 ventricular dead space volume (Vd), an important, but difficult to measure
 physiological parameter. Vd represents a subject and condition dependent
 portion of measured ventricular volume that is not actively participating
 in ventricular function. It is employed in models based on the time
 varying elastance concept, which see widespread use in haemodynamic
 studies, and may have direct diagnostic use. The proposed method involves
 linear extrapolation of a Frank-Starling curve (stroke volume vs
 end-diastolic volume) and its end-systolic equivalent (stroke volume vs
 end-systolic volume), developed across normal clinical procedures such as
 recruitment manoeuvres, to their point of intersection with the y-axis
 (where stroke volume is 0) to determine Vd. To demonstrate the broad
 applicability of the method, it was validated across a cohort of six
 sedated and anaesthetised male Pietrain pigs, encompassing a variety of
 cardiac states from healthy baseline behaviour to circulatory failure due
 to septic shock induced by endotoxin infusion. Linear extrapolation of the
 curves was supported by strong linear correlation coefficients of R = 0.78
 and R = 0.80 average for pre- and post- endotoxin infusion respectively,
 as well as good agreement between the two linearly extrapolated
 y-intercepts (Vd) for each subject (no more than 7.8% variation). Method
 validity was further supported by the physiologically reasonable Vd values
 produced, equivalent to 44.3-53.1% and 49.3-82.6% of baseline end-systolic
 volume before and after endotoxin infusion respectively. This method has
 the potential to allow Vd to be estimated without a particularly
 demanding, specialised protocol in an experimental environment. Further,
 due to the common use of both mechanical ventilation and recruitment
 manoeuvres in intensive care, this method, subject to the availability of
 multi-beat echocardiography, has the potential to allow for estimation of
 Vd in a clinical environment.
description: Pig1MATLAB .mat file Column
 1: Left Ventricular Pressure @200Hz Column 2: Left Ventricular Volume
 @200Hz Column 3: Aortic Pressure @200Hz Column 4: Femoral Pressure
 @200HzPig2MATLAB .mat file Column
 1: Left Ventricular Pressure @200Hz Column 2: Left Ventricular Volume
 @200Hz Column 3: Aortic Pressure @200Hz Column 4: Femoral Pressure
 @200HzPig3MATLAB .mat file Column
 1: Left Ventricular Pressure @200Hz Column 2: Left Ventricular Volume
 @200Hz Column 3: Aortic Pressure @200Hz Column 4: Femoral Pressure
 @200HzPig4MATLAB .mat file Column
 1: Left Ventricular Pressure @200Hz Column 2: Left Ventricular Volume
 @200Hz Column 3: Aortic Pressure @200Hz Column 4: Femoral Pressure
 @200HzPig5MATLAB .mat file Column
 1: Left Ventricular Pressure @200Hz Column 2: Left Ventricular Volume
 @200Hz Column 3: Aortic Pressure @200Hz Column 4: Femoral Pressure
 @200Hz
DOI: 10.5061/dryad.4gk80
title: Data from: Molecular study of bacterial diversity within the trophosome of the vestimentiferan tubeworm Ridgeia piscesae

description: A large proportion of the faunal biomass in hydrothermal vent ecosystems
 relies on symbiotic relationships, with bacteria as a source of nutrition.
 Whereas multiple symbioses have been observed in diverse vent hosts,
 siboglinid tubeworms have been thought to harbour a single endosymbiont
 phylotype affiliated to the Gammaproteobacteria. In the case of the
 Northeast Pacific vestimentiferan Ridgeia piscesae, two previous studies
 suggested the presence of more than one symbiont. The possibility of
 multiple, and possibly habitat-specific, symbionts in R. piscesae provided
 a potential explanation for the tubeworm's broad ecological niche,
 compared with other hydrothermal vent siboglinids. This study further
 explored the diversity of trophosome bacteria in R. piscesae using two
 methodological approaches not yet applied to this symbiosis. We carried
 out 454-pyrosequencing on trophosome samples from 46 individual worms and
 used catalyzed reporter deposition-fluorescence in situ hybridization
 (CARD-FISH) to verify the presence of the major groups detected in the
 pyrotag data. Both methods yielded inconsistent and sometimes
 contradictory results between sampling sites, and neither provided
 irrefutable evidence for the presence of symbionts other than the expected
 Gammaproteobacteria. We therefore conclude that the other adaptive
 mechanisms must be considered to explain the broad physico-chemical niche
 occupied by the different growth forms of R. piscesae.
description: Sanger sequencing fasta
 file from bacterial communities associated with the trophosome of Ridgeia
 piscesae - A Canadian Healthy Oceans Network Population Connectivity
 project, PC-11Near-complete SSU rRNA
 gene sequences obtained from the trophosome Ridgeia piscesae in
 hydrothermal habitats contrasted by flow regime. This data was obtained
 from Sanger sequencing.CHONe_PC-11_ForgetN_data(1).fasGroup file for the pyrosequencing fasta file - A Canadian Healthy Oceans Network Population Connectivity project, PC-11Group file required in order to perform analysis on the pyrosequencing fasta file. This file was obtained from the software mothur.CHONe_PC-11_ForgetN_data(3).groupsPyrosequencing fasta file from bacteria associated with the trophosome of Ridgeia piscesae - A Canadian Healthy Oceans Network Population Connectivity project, PC-11Partial SSU rRNA gene sequences obtained from the trophosome of Ridgeia piscesae in hydrothermal habitats contrasted by flow regime. This data was obtained from pyrosequencing.CHONe_PC-11_ForgetN_data(2).fas
DOI: 10.5061/dryad.453f3
title: Data from: Free-living bacterial communities associated with tubeworm (Ridgeia piscesae) aggregations in contrasting diffuse flow hydrothermal vent habitats at the Main Endeavour Field, Juan de Fuca Ridge

description: We systematically studied free-living bacterial diversity within
 aggregations of the vestimentiferan tubeworm Ridgeia piscesae sampled from
 two contrasting flow regimes (High Flow and Low Flow) in the Endeavour
 Hydrothermal Vents Marine Protected Area (MPA) on the Juan de Fuca Ridge
 (Northeast Pacific). Eight samples of particulate detritus were recovered
 from paired tubeworm grabs from four vent sites. Most sequences (454 tag
 and Sanger methods) were affiliated to the Epsilonproteobacteria, and the
 sulfur-oxidizing genus Sulfurovum was dominant in all samples.
 Gammaproteobacteria were also detected, mainly in Low Flow sequence
 libraries, and were affiliated with known methanotrophs and decomposers.
 The cooccurrence of sulfur reducers from the Deltaproteobac- teria and the
 Epsilonproteobacteria suggests internal sulfur cycling within these
 habitats. Other phyla detected included Bacteroidetes, Actinobacteria,
 Chloroflexi, Firmicutes, Planctomycetes, Verrucomicrobia, and
 Deinococcus–Thermus. Statisti- cally significant relationships between
 sequence library composition and habitat type suggest a predictable
 pattern for High Flow and Low Flow environments. Most sequences
 significantly more represented in High Flow libraries were related to
 sulfur and hydrogen oxidizers, while mainly heterotrophic groups were more
 represented in Low Flow libraries. Differences in temperature, avail- able
 energy for metabolism, and stability between High Flow and Low Flow
 habitats potentially explain their distinct bacterial communities.
description: Sanger sequencing fasta
 file from free-living bacterial communities associated with Ridgeia
 piscesae - A Canadian Healthy Oceans Network Population Connectivity
 project, PC-11Near-complete SSU rRNA
 gene sequences obtained from particulate detritus associated with Ridgeia
 piscesae in hydrothermal habitats contrasted by flow regime. This data was
 obtained from Sanger sequencing.CHONe_PC-11_ForgetN_data(1).fasPyrosequencing fasta file from free-living bacteria associated with Ridgeia piscesae - A Canadian Healthy Oceans Network Population Connectivity project, PC-11Partial SSU rRNA gene sequences obtained from particulate detritus associated with Ridgeia piscesae in hydrothermal habitats contrasted by flow regime. This data was obtained from pyrosequencing.CHONe_PC-11_ForgetN_data(2).fasGroup file for the pyrosequencing fasta file - A Canadian Healthy Oceans Network Population Connectivity project, PC-11Group file required in order to perform analysis on the pyrosequencing fasta file. This file was obtained from the software mothur.CHONe_PC-11_ForgetN_data(3).groups
DOI: 10.5061/dryad.j2dj4
title: Data from: Genetics of plasminogen activator inhibitor-1 (PAI-1) in a Ghanaian population

description: Plasminogen activator inhibitor 1 (PAI-1), a major modulator of the
 fibrinolytic system, is an important factor in cardiovascular disease
 (CVD) susceptibility and severity. PAI-1 is highly heritable, but the few
 genes associated with it explain only a small portion of its variation.
 Studies of PAI-1 typically employ linear regression to estimate the
 effects of genetic variants on PAI-1 levels, but PAI-1 is not normally
 distributed, even after transformation. Therefore, alternative statistical
 methods may provide greater power to identify important genetic variants.
 Additionally, most genetic studies of PAI-1 have been performed on
 populations of European descent, limiting the generalizability of their
 results. We analyzed &gt;30,000 variants for association with PAI-1 in
 a Ghanaian population, using median regression, a non-parametric
 alternative to linear regression. Three variants associated with median
 PAI-1, the most significant of which was in the gene arylsulfatase B
 (ARSB) (p = 1.09 x 10−7). We also analyzed the upper quartile of PAI-1,
 the most clinically relevant part of the distribution, and found 19 SNPs
 significantly associated in this quartile. Of note an association was
 found in period circadian clock 3 (PER3). Our results reveal novel
 associations with median and elevated PAI-1 in an understudied population.
 The lack of overlap between the two analyses indicates that the genetic
 effects on PAI-1 are not uniform across its distribution. They also
 provide evidence of the generalizability of the circadian pathway’s effect
 on PAI-1, as a recent meta-analysis performed in Caucasian populations
 identified another circadian clock gene (ARNTL).
description: HeART_Rinput_allcommonSNPsQZData for study in txt format
DOI: 10.5061/dryad.4qc06
title: Data from: The impact of variable degrees of freedom and scale parameters in Bayesian methods for genomic prediction in Chinese Simmental beef cattle

description: Three conventional Bayesian approaches (BayesA, BayesB and BayesCπ) have
 been demonstrated to be powerful in predicting genomic merit for complex
 traits in livestock. A priori, these Bayesian models assume that the
 non-zero SNP effects (marginally) follow a t-distribution depending on two
 fixed hyperparameters, degrees of freedom and scale parameters. In this
 study, we performed genomic prediction in Chinese Simmental beef cattle
 and treated degrees of freedom and scale parameters as unknown with
 inappropriate priors. Furthermore, we compared the modified methods
 (BayesFA, BayesFB and BayesFCπ) with their corresponding counterparts
 using simulation datasets. We found that the modified methods with
 distribution assumed to the two hyperparameters were beneficial for
 improving the predictive accuracy. Our results showed that the predictive
 accuracies of the modified methods were slightly higher than those of
 their counterparts especially for traits with low heritability and a small
 number of QTLs. Moreover, cross-validation analysis for three traits,
 namely carcass weight, live weight and tenderloin weight, in 1136
 Simmental beef cattle suggested that predictive accuracy of BayesFCπ
 noticeably outperformed BayesCπ with the highest increase (3.8%) for live
 weight using the cohort masking cross-validation.
description: dataThe resource populations
 were established in Ulgai, Xilingole League, Inner Mongolia of China. All
 the young Simmental beef cattle were born between 2008 and 2013. After
 weaning, Simmental cattle were moved to Beijing Jinweifuren cattle farm
 for fattening and put under the same feeding and management conditions.
 Each animal was measured for growth and developmental traits on time until
 its slaughter when they were 18 to 24 months of age. Live weight was
 measured after 24 hours of fasting. During the period of slaughter,
 carcass traits and meat quality traits were measured according to the
 Institutional Meat Purchase Specification for fresh beef
 guidelines.
DOI: 10.5061/dryad.gv595
title: Data from: Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms

description: Genomic analyses of microbial populations in their natural environment
 remain limited by the difficulty to assemble full genomes of individual
 species. Consequently, the chromosome organization of microorganisms has
 been investigated in a few model species, but the extent to which the
 features described can be generalized to other taxa remains unknown. Using
 controlled mixes of bacterial and yeast species, we developed meta3C, a
 metagenomic chromosome conformation capture approach that allows
 characterizing individual genomes and their average organization within a
 mix of organisms. Not only can meta3C be applied to species already
 sequenced, but a single meta3C library can be used for assembling,
 scaffolding and characterizing the tridimensional organization of unknown
 genomes. By applying meta3C to a semi-complex environmental sample, we
 confirmed its promising potential. Overall, this first meta3C study
 highlights the remarkable diversity of microorganisms chromosome
 organization, while providing an elegant and integrated approach to
 metagenomic analysis. - See more at:
 http://elifesciences.org/content/3/e03318#sthash.Yx6nSY4J.dpuf
description: mix_bacteriaFiles associated to the Figure 1.mix_11yeastsFiles associated with the figure 2.mix_environmental_sampleFiles associated with the figure 3.
DOI: 10.5061/dryad.mn8k0
title: Data from: The genetic architecture of novel trophic specialists: higher effect sizes are associated with exceptional oral jaw diversification in a pupfish adaptive radiation

description: The genetic architecture of adaptation is fundamental to understanding the
 mechanisms and constraints governing diversification. However, most case
 studies focus on loss of complex traits or parallel speciation in similar
 environments. It is still unclear how the genetic architecture of these
 local adaptive processes compares to the architecture of evolutionary
 transitions contributing to morphological and ecological novelty. Here we
 identify quantitative trait loci (QTL) between two trophic specialists in
 an excellent case study for examining the origins of ecological novelty: a
 sympatric radiation of pupfishes endemic to San Salvador Island, Bahamas
 containing a large-jawed scale-eater and a short-jawed molluscivore with a
 skeletal nasal protrusion. These specialized niches and trophic traits are
 unique among over 2,000 related species. Measurements of the fitness
 landscape on San Salvador demonstrate multiple fitness peaks and a larger
 fitness valley isolating the scale-eater from the putative ancestral
 intermediate phenotype of the generalist, suggesting that more
 large-effect QTL should contribute to its unique phenotype. We evaluated
 this prediction using an F2 intercross between these specialists. We
 present the first linkage map for pupfishes and detect significant QTL for
 sex and eight skeletal traits. Larger-effect QTL contributed more to
 enlarged scale-eater jaws than the molluscivore nasal protrusion,
 consistent with predictions from the adaptive landscape. The
 microevolutionary genetic architecture of larger-effect QTL for oral jaws
 parallels the exceptional diversification rates of oral jaws within the
 San Salvador radiation observed over macroevolutionary timescales and may
 have facilitated exceptional trophic novelty in this system.
description: Input data files for
 R/qtl including genotypes and phenotypesInput data files for
 R/qtl including genotypes and phenotypes.genotype and phenotype raw data
 files.zipstacks pipeline scripts
 catalog and parental filesStacks pipeline scripts,
 catalog files, and parental files.
DOI: 10.5061/dryad.fj594
title: Data from: "Transcriptome resources for three hybrid sunflower species (Helianthus anomalus, H. deserticola, H paradoxus)" in Genomic Resources Notes accepted 1 February 2013–31 March 2013

description: This article documents the public availability of three transcriptome
 sequences. These genomic resources were developed for the following
 species: Helianthus anomalus, Helianthus deserticola and Helianthus
 paradoxus.
description: snp_table_anomalusList of SNPs for H.anomalus. Column 1 refers to the reference sequence. Column 2 to the position were the SNP is located. Column 3 and after are the genotypes per individualsnp_table_deserticolaList of SNPs for H.deserticola. Column 1 refers to the reference sequence. Column 2 to the position were the SNP is located. Column 3 and after are the genotypes per individualIlluminaContaminantsList of possible Illumina adaptor contaminants used in read trimming.coverage_per_gene_individualsCoverage (Number of reads aligned) per individuals and per gene.snp_table_paradoxusList of SNPs for H.paradoxus. Column 1 refers to the reference sequence. Column 2 to the position were the SNP is located. Column 3 and after are the genotypes per individual
DOI: 10.5061/dryad.270gs
title: Data from: The fossil Osmundales (Royal Ferns)—a phylogenetic network analysis, revised taxonomy, and evolutionary classification of anatomically preserved trunks and rhizomes

description: The Osmundales (Royal Fern order) originated in the late Paleozoic and is
 the most ancient surviving lineage of leptosporangiate ferns. In contrast
 to its low diversity today (less than 20 species in six genera), it has
 the richest fossil record of any extant group of ferns. The structurally
 preserved trunks and rhizomes alone are referable to more than 100 fossil
 species that are classified in up to 20 genera, four subfamilies, and two
 families. This diverse fossil record constitutes an exceptional source of
 information on the evolutionary history of the group from the Permian to
 the present. However, inconsistent terminology, varying formats of
 description, and the general lack of a uniform taxonomic concept renders
 this wealth of information poorly accessible. To this end, we provide a
 comprehensive review of the diversity of structural features of
 osmundalean axes under a standardized, descriptive terminology. A novel
 morphological character matrix with 45 anatomical characters scored for 15
 extant species and for 114 fossil operational units (species or specimens)
 is analysed using networks in order to establish systematic relationships
 among fossil and extant Osmundales rooted in axis anatomy. The results
 lead us to propose an evolutionary classification for fossil Osmundales
 and a revised, standardized taxonomy for all taxa down to the rank of
 (sub)genus. We introduce several nomenclatural novelties: (1) a new
 subfamily Itopsidemoideae (Guaireaceae) is established to contain
 Itopsidema, Donwelliacaulis, and Tiania; (2) the thamnopteroid genera
 Zalesskya, Iegosigopteris, and Petcheropteris are all considered
 synonymous with Thamnopteris; (3) 12 species of Millerocaulis and
 Ashicaulis are assigned to modern genera (tribe Osmundeae); (4) the
 hitherto enigmatic Aurealcaulis is identified as an extinct subgenus of
 Plenasium; and (5) the poorly known Osmundites tuhajkulensis is assigned
 to Millerocaulis. In addition, we consider Millerocaulis stipabonettiorum
 a possible member of Palaeosmunda and Millerocaulis estipularis as
 probably constituting the earliest representative of the
 (Todea-)Leptopteris lineage (subtribe Todeinae) of modern Osmundoideae.
description: Raw data and results
 filesBomfleur_et_al_FossilOsmundales-SDA.zip