cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7k048
title: Data from: A reliability study of colour-Doppler sonography for the diagnosis of chronic cerebrospinal venous insufficiency shows low inter-rater agreement

description: Objective: Chronic cerebrospinal venous insufficiency (CCSVI) has been
 extremely variable associated with multiple sclerosis in color-Doppler
 sonographic studies. We aimed to evaluate inter-rater agreement in color
 doppler sonograpy venous examination. Design: Inter-rater agreement study.
 Setting: First-referral multiple sclerosis centre. Participants:
 thirty-eight multiple sclerosis patients, and 55 age-matched (± 5 years)
 controls. Intervention: sonography was carried out in accordance with
 Zamboni's five criteria by 8 sonographers with different expertise,
 blinded to the status of cases and controls. Each subject was evaluated by
 two operators. Primary and secondary outcome measures: inter-rater
 agreement was measured through the Kappa statistics and the Intraclass
 Correlation Coefficient. Results: The agreement was no higher than chance
 for criterion 2-reflux in the deep cerebral veins (Kappa=-0.02) and 4-flow
 not Doppler-detectable in one or both the internal jugular (IJVs) or
 vertebral veins (VVs) (-0.09). It was substantially low for criterion
 1-reflux in the IJVs and/or VVs (0.29), criterion 3-IJV stenosis or
 malformations (0.23), and criterion 5-absence of IJV diameter increase
 when passing from sitting to supine position (0.22). The Kappa value for
 CCSVI as a whole was 0.20 (95% confidence limits=-0.01 - 0.42). Intraclass
 Correlation Coefficients for the measure of cross-sectional area ranged
 from 0.05 to 0.25. Inter-rater agreement was low for CCSVI experts (kappa=
 0.24; -0.11 to 0.59), and non-experts (0.20; -0.33 to 0.73); neurologists
 (0.21; -0.06 to 0.47) and non neurologists (0.18; -0.20 to 0.56); cases
 (0.19; -0.14 to 0.52) and controls (0.21; -0.08 to 0.49). Zamboni-trained
 neurosonographers ascertained CCSVI more frequently than non-trained.
 Conclusions: Agreement was unsatisfactory for the diagnosis of CCSVI as a
 whole, for each of its five criteria, and according to different
 subgroups. Standardization of the method is urgently needed prior to its
 further application in studies of patients with multiple sclerosis or
 other neurological diseases.
description: Leone_CCSVIThe filke contains data about 38 multiple sclerosis patients and 55 age-matched (± 5 years) controls. Each subject (case or control) has been evaluated with color-Doppler sonography by two operators (column headline= alpha or beta) in accordance with Zamboni's five criteria (column headline=criterion1 to criterion5). The file contains additional data on smoke and the presence of varicous veins at lower limbs.
DOI: 10.5061/dryad.4r34459
title: Data from: Petrophysical characterization of high-rank coal by nuclear magnetic resonance: a case study of the Baijiao coal reservoir, SW China

description: To better apply nuclear magnetic resonance (NMR) to evaluate the
 petrophysical characterization of high-rank coal, six anthracite samples
 from the Bajiao coal reservoir were measured by NMR. The porosity, T2
 cutoff value, permeability, and pore type were analysed using the
 transverse relaxation time (T2) spectrum before and after centrifugation.
 The results show that the T2 spectrum of water-saturated anthracite can be
 divided into a discontinuous and continuous trimodal distribution.
 According to the connectivity among pores, three T2 spectrum peaks were
 identified at the relaxation times of 0.01-1.7 ms, 1.7-65 ms, and
 &gt;65 ms, which correspond to the micropores (&lt;100 nm),
 mesopores (100-1000 nm), and macropores (&gt;1000 nm), respectively.
 Based on the T2 cutoff value, we divided the T2 spectrum into two parts:
 bound fluid and free fluid. By comparing two classic permeability models,
 we proposed a permeability model to calculate the permeability of
 anthracite. This result demonstrates that NMR has a great significance to
 the exploration of coal reservoirs and to the understanding of the
 development of coalbed methane.
description: T2 curve of coal
 samplesThe data is the original
 data of the test process, which can be opened by Excel
 software.
DOI: 10.5061/dryad.jm57v
title: Data from: Increased dietary intake of saturated fatty acid heptadecanoic acid (C17:0) associated with decreasing ferritin and alleviated metabolic syndrome in dolphins

description: Similar to humans, bottlenose dolphins (Tursiops truncatus) can develop
 metabolic syndrome and associated high ferritin. While fish and fish-based
 fatty acids may protect against metabolic syndrome in humans, findings
 have been inconsistent. To assess potential protective factors against
 metabolic syndrome related to fish diets, fatty acids were compared
 between two dolphin populations with higher (n = 30, Group A) and lower (n
 = 19, Group B) mean insulin (11 ± 12 and 2 ± 5 μIU/ml, respectively; P
 &lt; 0.0001) and their dietary fish. In addition to higher insulin,
 triglycerides, and ferritin, Group A had lower percent serum heptadecanoic
 acid (C17:0) compared to Group B (0.3 ± 0.1 and 1.3 ± 0.4%, respectively;
 P &lt; 0.0001). Using multivariate stepwise regression, higher percent
 serum C17:0, a saturated fat found in dairy fat, rye, and some fish, was
 an independent predictor of lower insulin in dolphins. Capelin, a common
 dietary fish for Group A, had no detectable C17:0, while pinfish and
 mullet, common in Group B’s diet, had C17:0 (41 and 67 mg/100g,
 respectively). When a modified diet adding 25% pinfish and/or mullet was
 fed to six Group A dolphins over 24 weeks (increasing the average daily
 dietary C17:0 intake from 400 to 1700 mg), C17:0 serum levels increased,
 high ferritin decreased, and blood-based metabolic syndrome indices
 normalized toward reference levels. These effects were not found in four
 reference dolphins. Further, higher total serum C17:0 was an independent
 and linear predictor of lower ferritin in dolphins in Group B dolphins.
 Among off the shelf dairy products tested, butter had the highest C17:0
 (423mg/100g); nonfat dairy products had no detectable C17:0. We
 hypothesize that humans’ movement away from diets with potentially
 beneficial saturated fatty acid C17:0, including whole fat dairy products,
 could be a contributor to widespread low C17:0 levels, higher ferritin,
 and metabolic syndrome.
description: Metabolic Syndrome and
 Fatty Acids in Dolphins - Venn-Watson et al. 2015 - PLOS ONE
 16JUN2015Blood-based metabolic
 and iron indices and percent fatty acids in bottlenose dolphins, including
 comparisons between two populations and changes among six dolphins on a
 modified diet over six months; levels of heptadecanoic acid in various
 fish and dairy food types
DOI: 10.5061/dryad.08507r35
title: Data from: Two highly informative dinucleotide SSR multiplexes for the conifer Larix decidua (European larch)

description: We have designed two highly polymorphic microsatellite multiplexes for
 Larix decidua Mill. (European larch), a coniferous tree species with a
 fragmented distribution across Europe. The multiplexes combine
 microsatellites previously designed for the sister species L. kaempferi
 and newly identified microsatellites obtained by pyrosequencing of an
 enriched microsatellite library and subsequent marker candidate selection.
 As we wanted to target highly polymorphic markers, only microsatellite
 motifs with a high number of repeats (≥12) were selected. An important
 proportion of the marker candidates presented multiple bands, bad
 amplification or insufficient polymorphism. Such difficulties were
 expected owing to the large genome size of the studied species. Our
 strategy for marker validation followed most recent recommendations for
 microsatellite development, e.g. verifying marker quality in terms of
 polymorphism and accurate allele binning before multiplexing. The most
 promising loci were combined in two multiplexes, a 7-plex and a 6-plex.
 These were tested on a sample of 413 individuals from 18 populations
 distributed across the natural range. The 13 loci had from 9 to 36
 alleles. Markers were successfully tested in another laboratory,
 confirming robustness of the marker protocols. We also tested
 transferability on six other larch species from Asia and North America.
 Overall, this study shows that, even in species with large genome size and
 relatively low overall polymorphism, microsatellites can be successfully
 developed using next-generation sequencing technologies provided that some
 additional precautions are taken compared to species lacking these
 characteristics.
description: Larix_decidua_sample_infoThis data file contains information about sampling location individual genotype information for 18 Larix decidua populations from across the natural distribution range. Columns 1-3: Population ID and corresponding geographical coordinates. Columns 4-30: 413 Individual genotypes of 18 populations, each composed of 13 loci. Missing data value: 0
DOI: 10.5061/dryad.546rd
title: Data from: Tracing the trans-Pacific evolutionary history of a domesticated seaweed (Gracilaria chilensis) with archaeological and genetic data

description: The history of a domesticated marine macroalga is studied using
 archaeological, phylogeographic and population genetic tools.
 Phylogeographic and population genetic analyses demonstrated that the
 cultivated red alga Gracilaria chilensis colonised the Chilean coast from
 New Zealand. Combining archaeological observations with phylogeographic
 data provided evidence that exchanges between New Zealand and Chile have
 occurred at least before the Holocene, likely at the end of the Last
 Glacial Maximum (LGM) and we suggest that migration probably occurred via
 rafting. Furthermore, the remarkably low microsatellite diversity found in
 the Chilean populations compared to those in New Zealand is consistent
 with a recent genetic bottleneck as a result of over-exploitation of
 natural populations and/or the process of domestication. Therefore, the
 aquaculture of this seaweed, based essentially on clonal propagation, is
 occurring from genetically depressed populations and may be driving the
 species to an extinction vortex in Chile.
description: Microsatellite genotypes
 of Gracilaria chilensis from New Zealand and ChileThis readme file
 describes the microsatellites genotypes for a red algae: Gracilaria
 chilensis. The file include data for 187 individuals collected from eight
 natural populations from New Zealand (including the Chatham Islands) and
 410 individuals collected along the Chilean coast. G. chilensis is
 extensively cultivated in Chile for agar production, however, only natural
 populations (i.e. non cultivated ones) are reported in this data set. The
 five microsatellite loci are named according to Guillemin et al. (2005,
 Development of microsatellites DNA markers in the cultivated seaweed
 Gracilaria chilensis (Gracilariales Rhodophyta). Mol Ecol Notes 5,
 155–157.). All individuals are diploids. “0” correspond to missing data.
 For any further queries please contact
 marielaure.guillemin@gmail.comGracilariachilensis-Chile-NewZealand-Guillemin.txt
DOI: 10.5061/dryad.qf488
title: Data from: Stocking impacts the expression of candidate genes and physiological condition in introgressed brook charr (Salvelinus fontinalis) populations

description: Translocation of plants and animal populations between environments is one
 of the major forms of anthropogenic perturbation experienced by pristine
 populations, and consequently, human mediated hybridization by stocking
 practices between wild and exogenous conspecifics is of increasing
 concern. In this study, we compared the expression of seven candidate
 genes involved in multifactorial traits and regulatory pathways for growth
 as a function of level of introgressive hybridization between wild and
 domestic brook charr to test the null hypothesis of no effect of
 introgression on wild fish. Our analyses revealed that the expression of
 two of the genes tested, cytochrome c oxidase VIIa and the growth hormone
 receptor isoform I, was positively correlated with the level of
 introgression. We also observed a positive relationship between the extent
 of introgression and physiological status quantified by the Fulton’s
 condition index. The expression of other genes was influenced by other
 variables, including year of sampling (reflecting different thermal
 conditions), sampling method and lake of origin. This is the first
 demonstration in nature that introgression from stocked populations has an
 impact on the expression of genes playing a role in important biological
 functions that may be related with fitness in wild introgressed
 populations.
description: Microsatellites
 dataThe 23 microsatellites
 used for the Bayesian clustering analyses. The populations, refere to
 Méthot Lake (MET), Petit Saint-Bernard Lake (BER), Lac des Écorces
 aquaculture facility (LDE), Bourassa Lake (BOU) and Jacques Cartier
 aquaculture facility (JC).Genotype.csv
DOI: 10.5061/dryad.4gr1h
title: Data from: Indication for selfing in geographically separated populations and evidence for Pleistocene survival within the Alps: the case of Cylindrus obtusus (Pulmonata: Helicidae)

description: Background: Cylindrus obtusus is one of the most prominent endemic snail
 species of the Eastern Alps. It is restricted to alpine meadows and
 calcareous rocky habitats above 1500 m. Its genital tract shows a peculiar
 intraspecific difference: in the eastern populations the two mucus glands
 associated with the love dart sac are highly variable, while almost no
 variation was observed in the western populations. This raises the
 question whether the mode and success of reproduction of the respective
 populations are different. To find out whether these anatomical
 differences reflect a genetic differentiation, which might be an
 indication for distinct glacial refugia, we investigated a 650 bp fragment
 of the mitochondrial cytochrome oxidase subunit 1 gene (COI) (280
 individuals) and 9 microsatellite loci (487 individuals from 29
 populations) from samples covering the whole distribution range of the
 species. Results: The COI sequences show a geographic differentiation
 between eastern, central and western populations. The westernmost
 localities, which were covered under ice sheets during glacial periods,
 are characterized by extreme low variability. Overall genetic distances
 among all individuals are small (max. 1.7 % p-distance). The
 microsatellite analysis reveals a high differentiation between
 populations, implying restriction of gene flow. The highest genetic
 variability was found in the central populations. Remarkably, nearly all
 individuals from the eastern populations, which are more variable in their
 genital morphology, are homozygous in all microsatellite loci, although
 different alleles were found within populations. Conclusions: The most
 peculiar outcome of the study is the strong evidence of selfing in C.
 obtusus as indicated by the microsatellite data in the easternmost
 populations. This finding is supported by the deformation of the mucus
 glands in the same populations. Since mucus glands play an important role
 in sexual reproduction, it seems plausible that in selfing organisms these
 structures are reduced. The phylogeographic structure revealed by COI
 sequences implies at least three refugia during the last ice ages. The
 small genetic distances among all individuals (max. 1.7 %), suggest that
 C. obtusus has experienced severe bottlenecks in the past.
description: cylindrus obtusus
 microsatellite dataMicrosatellite data for
 9 loci of 486 individuals of Cylindrus obtusus
 (Gastropoda)cylindrus_dryas.xlsx
DOI: 10.5061/dryad.pk14p
title: Data from: Sex-chromosome turnovers induced by deleterious mutation load

description: In sharp contrast with mammals and birds, many cold-blooded vertebrates
 present homomorphic sex chromosomes. Empirical evidence supports a role
 for frequent turnovers, which replace non-recombining sex chromosomes
 before they have time to decay. Three main mechanisms have been proposed
 for such turnovers, relying either on neutral processes, sex-ratio
 selection, or intrinsic benefits of the new sex-determining genes (due
 e.g. to linkage with sexually antagonistic mutations). Here we suggest an
 additional mechanism, arising from the load of deleterious mutations that
 accumulate on non-recombining sex chromosomes. In the absence of dosage
 compensation, this load should progressively lower survival rate in the
 heterogametic sex. Turnovers should occur when this cost outweighs the
 benefits gained from any sexually antagonistic genes carried by the
 non-recombining sex chromosome. We use individual-based simulations of a
 Muller’s ratchet process to test this prediction, and investigate how the
 relevant parameters (effective population size, strength and dominance of
 deleterious mutations, size of non-recombining segment, and strength of
 sexually antagonistic selection) are expected to affect the rate of
 turnovers.
description: Evolution_12-0102Zip file containing a ReadMe file and all input files needed for the simulations.
DOI: 10.5061/dryad.db2dd
title: Data from: Vaccination method affects immune response and bacterial growth but not protection in the Salmonella Typhimurium animal model of typhoid

description: Understanding immune responses elicited by vaccines, together with immune
 responses required for protection, is fundamental to designing effective
 vaccines and immunisation programs. This study examines the effects of the
 route of administration of a live attenuated vaccine on its interactions
 with, and stimulation of, the murine immune system as well as its ability
 to increase survival and provide protection from colonisation by a
 virulent challenge strain. We assess the effect of administration method
 using the murine model for typhoid, where animals are infected with S.
 Typhimurium. Mice were vaccinated either intravenously or orally with the
 same live attenuated S. Typhimurium strain and data were collected on
 vaccine strain growth, shedding and stimulation of antibodies and
 cytokines. Following vaccination, mice were challenged with a virulent
 strain of S. Typhimurium and the protection conferred by the different
 vaccination routes was measured in terms of challenge suppression and
 animal survival. The main difference in immune stimulation found in this
 study was the development of a secretory IgA response in orally-vaccinated
 mice, which was absent in IV vaccinated mice. While both strains showed
 similar protection in terms of challenge suppression in systemic organs
 (spleen and liver) as well as survival, they differed in terms of
 challenge suppression of virulent pathogens in gut-associated organs. This
 difference in gut colonisation presents important questions around the
 ability of vaccines to prevent shedding and transmission. These findings
 demonstrate that while protection conferred by two vaccines can appear to
 be the same, the mechanisms controlling the protection can differ and have
 important implications for infection dynamics within a population.
description: All
 dataData for all
 figures
DOI: 10.5061/dryad.v21k1
title: Data from: Echinorhynchus salmonis Müller, 1784 (Acanthocephala: Echinorhynchidae) from the Bothnian Bay, Baltic Sea: morphological variability and radial asymmetry of proboscis hooks

description: Echinorhynchus salmonis is a common parasite of salmoniform and other
 fishes, occurring in fresh and brackish waters throughout the Holarctic.
 Presented here is the first analysis of the morphometric and meristic
 variation in a Palaearctic population of E. salmonis, collected from
 whitefish Coregonus lavaretus L. and smelt Osmerus eperlaus (L.) from the
 Bothnian Bay, northern Baltic Sea. Morphological data were compared with
 published descriptions of congeneric taxa. Nearctic populations of
 salmonid echinorhynchids considered by some to represent a distinct
 species, E. coregoni Linkins in Van Cleave, 1919, did not show any
 morphological divergence from Palaearctic populations, indicating that the
 name E. coregoni should be suppressed. Similarly, E. alpinus Linstow, 1901
 has been considered to be a junior synonym of E. salmonis. However, E.
 alpinus should be regarded as a valid species, because it has a longer and
 more elongate body. The armature of the acanthocephalan proboscis
 typically displays radial symmetry. However, in E. salmonis the hooks on
 the dorsal surface of the proboscis are smaller than those on the ventral
 surface. Size differences between dorsal and ventral hooks are most
 pronounced at the base of the proboscis. The systematic and functional
 significance of radial asymmetry of proboscis hooks is discussed.
description: Egg and acanthor
 dimensions of Echinorhynchus salmonisMeasurements of 135 eggs
 (3 from each of 45 acanthocephalans) in micrometres.Echinorhynchus_salmonis_egg_dimensions.csvMorphometric and meristic data from female Echinorhynchus salmonisMorphometric and meristic data for 122 specimens of female Echinorhynchus salmonis from the Bothnian Bay, Baltic Sea. All measurements in micrometres.morphometric_and_meristic_data_for_female_Echinorhynchus_salmonis.csvMorphometric and meristic data from male Echinorhynchus salmonisMorphometric and meristic data from 17 specimens of Echinorhynchus salmonis from the Bothnian Bay, Baltic Sea. All measurements in micrometres.morphometric_and_meristic_data_for_male_Echinorhynchus_salmonis.csvHook measurements from female Echinorhynchus_salmonisHook measurements from 36 female specimens of Echinorhynchus salmonis from the Bothnian Bay, Baltic Sea. All measurements in micrometres.Hook_measurements_from_female_Echinorhynchus_salmonis.csvHook measurements from male Echinorhynchus salmonisHook measurements from six specimens of male Echinorhynchus salmonis from the Bothnian Bay, Baltic Sea. All measurements in micrometres.Hook_measurements_from_male_Echinorhynchus_salmonis.csv
DOI: 10.15468/dl.geytxv
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Japan",
 {
 "or" : [
 "Geometry POLYGON((140.43142 37.23724,141.44481 37.23724,141.44481 37.64242,140.43142 37.64242,140.43142 37.23724))",
 "Geometry POLYGON((140.02644 37.6593,141.99097 37.6593,141.99097 38.62764,140.02644 38.62764,140.02644 37.6593))"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Cuculus canorus",
 "Year 2020-2026"
 ]
}

 The dataset includes 32 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001056-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.