cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.s9p5c79
title: Data from: Idiopathic inflammatory myopathy: inter-rater variability in muscle biopsy reading

description: Background: Despite its importance for diagnosing idiopathic inflammatory
 myopathy (IIM) subgroups, muscle biopsy classification criteria have not
 been standardized nor validated. Objective: We sought to determine
 inter-rater variability in diagnosing individual muscle biopsy
 abnormalities. Methods: We developed a scoring tool to analyze consensus
 in muscle biopsy reading of an ad hoc workgroup of international experts.
 Twenty-four samples from suspected IIM patients were randomly selected,
 providing sections that were stained with standard histological and
 immuno-histochemical methods. Sections were made available on an online
 platform and experts were queried about myopathological features within
 four pathological domains: muscle fibers, inflammation, connective tissue
 and vasculature. A short clinical presentation of cases was included, and
 experts were asked to give a tentative diagnosis of polymyositis,
 dermatomyositis, inclusion-body myositis, anti-synthetase syndrome-related
 myositis, immune-mediated necrotizing myopathy, non-specific myositis or
 other disease. Fleiss’ Kappa values, scoring inter-rater variability,
 showed the highest agreement within the muscle fiber and connective tissue
 domains. Results: Despite overall low Kappa values, moderate agreement was
 achieved for tentative diagnosis, supporting the idea of holistic muscle
 biopsy interpretation rather than by adding up of individual features.
 Conclusion: We conclude that assessment of individual pathological
 features needs to be standardized and harmonized, and should be measured
 for sensitivity and specificity for subgroup classification. Standardizing
 the process of diagnostic muscle biopsy reading would allow identification
 of more homogeneous patient cohorts for upcoming treatment trials.
description: Supplementary
 dataComprehensive
 presentation of all data, showing questions, possible answers, and the
 calculated Fleiss’ Kappa scores.Supplement
 1.docx
DOI: 10.5061/dryad.bj486f4
title: Data from: Community-informed connectomics of the thalamocortical system in generalized epilepsy

description: OBJECTIVE. We studied the intrinsic organization of the thalamo-cortical
 circuitry in patients with generalized epilepsy with tonic-clonic seizures
 (GTCS) via resting-state fMRI (rs-fMRI) connectome analysis and evaluated
 its relation to drug-response. METHODS. In a prospectively-followed sample
 of 41 patients and 27 healthy controls, we obtained rs-fMRI and structural
 MRI. After one year of follow-up, 27 patients were classified as
 seizure-free and 14 drug-resistant. We examined connectivity within and
 between resting-state communities in cortical and thalamic subregions. In
 addition to comparing patients to controls, we examined associations to
 seizure control. We assessed reproducibility in an independent cohort of
 21 patients. RESULTS. Compared to controls, patients showed a more
 constrained network embedding of the thalamus, while frontocentral
 neocortical regions expressed increased functional diversity. Findings
 remained significant after regressing out thalamic volume and cortical
 thickness, suggesting independence from structural alterations. We
 observed more marked network imbalances in drug-resistant compared to
 seizure-free patients. Findings were similar in the reproducibility
 dataset. CONCLUSIONS. Our findings suggest a pathoconnectomic mechanism of
 generalized epilepsy with generalized tonic and clonic seizures, centered
 on diverging changes in cortical and thalamic connectivity. More
 restricted thalamic connectivity could reflect the tendency to engage in
 recursive thalamo-cortical loops, which may contribute to
 hyper-excitability. Conversely, increased connectional diversity of
 frontocentral networks may relay abnormal activity to an extended
 bilateral territory. Network imbalances were observed shortly after
 diagnosis and related to future drug-response, suggesting clinical
 utility.
description: SocioDemographicSocio-demographic and clinical information of included participantsThalamusWMD and PC values for the thalamus for the entire sampleCortex_WMDWMD values for the cortical parcels for the entire sampleCortex_PCPC values for the cortical parcels for the entire sampleAdditional Figures and TablesAdditional Figures 1-3, Additional Tables 1-2 (referenced from main manuscript)AdditionalFiguresTables.docx
DOI: 10.5061/dryad.tv4360k
title: Data from: Brain MRI features and scoring of leukodystrophy in adult-onset Krabbe disease

description: Objective: To perform a systematic analysis and scoring of brain MRI White
 Matter Hyperintensities (WMH) in adult-onset Krabbe disease. Methods: We
 retrospectively collected basic clinical data and the first available
 brain MRI from confirmed Krabbe patients with first clinical
 manifestations beyond 10 years old. Data were obtained from our reference
 center for lysosomal diseases (n=6) and from contacted authors of
 published articles describing adult-onset Krabbe patients (n=15).
 T2-weighted fluid-attenuated inversion recovery (FLAIR) images of each
 patient were analysed and scored using a radiological score of WMH in a
 single center. Results: The corticospinal tract was always affected by WMH
 (100% of patients), however with some distinctions along the tract: the
 pre-central gyrus (100%), corona radiata (95%) and posterior internal
 capsule (81%) were highly abnormal whereas the mesencephalon (57%), pons
 (52%) and medulla oblongata (5%) were less affected. WMH were also
 frequently present in the posterior lateral periventricular white matter
 (95%), optic radiations (86%), post central gyrus (71%), medial lemniscus
 (62%) and corpus callosum, especially in the isthmus (71%), whereas the
 genu was always normal. A few patients did not have the classical MRI
 pattern but extensive hyperintensities (n=3), or patchy distribution of
 hyperintensities mimicking an acquired etiology (n=2), or very subtle
 hyperintensities of the corticospinal tract (n=1). Conclusions: We
 specified the main locations of WMH, which were observed in the earliest
 stages of the disease and were also present in patients with atypical MRI
 pattern, highlighting the importance of radiological features to guide the
 diagnosis.
description: Supplementary table 1.
 Individual clinical, radiological and genetic
 characteristicsSupplementary table
 1.docxSupplementary table 2.
 Scored items and scoring methodSupplementary table
 2.docxSupplementary table 3.
 Main characteristics of subjects included in the study
 (n=21)Supplementary table
 3.docx
DOI: 10.15468/dl.twja2y
title: Occurrence Download

description: A dataset containing 704 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-1.15743 45.76707,-1.64074 45.31058,-2.21523 43.83789,-2.02464 43.22128,-1.15018 42.6383,0.48664 42.25713,3.04276 42.06654,3.80512 41.68536,4.84774 41.98806,6.98906 42.24591,7.83502 43.63812,7.64385 44.04685,7.12965 44.62038,7.12305 45.43782,7.00439 46.11683,6.79608 46.32979,6.48658 46.30349,6.258 46.20234,6.02536 46.08906,5.92017 46.18009,6.11842 46.30551,6.07796 46.34597,5.83447 46.23874,5.12696 45.76707,3.71193 45.72545,1.70037 45.35088,-1.15743 45.76707))",
 "OccurrenceStatus is Present",
 "TaxonKey is Callitriche stagnalis",
 "Year 2016-2026"
 ]
}

 The dataset includes 704 records from 118 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001766-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.3p9h20r
title: Data from: The manifold structure of limb coordination in walking Drosophila

description: Terrestrial locomotion requires animals to coordinate their limb movements
 to efficiently traverse their environment. While previous studies in
 hexapods have reported that limb coordination patterns can vary
 substantially, the structure of this variability is not yet well
 understood. Here, we characterized the symmetric and asymmetric components
 of variation in walking kinematics in the genetic model organism
 Drosophila. We found that Drosophila use a single continuum of
 coordination patterns without evidence for preferred configurations.
 Spontaneous symmetric variability was associated with modulation of a
 single control parameter—stance duration—while asymmetric variability
 consisted of small, limb-specific modulations along multiple dimensions of
 the underlying symmetric pattern. Commands that modulated walking speed,
 originating from artificial neural activation or from the visual system,
 evoked modulations consistent with spontaneous behavior. Our findings
 suggest that Drosophila employ a low-dimensional control architecture,
 which provides a framework for understanding the neural circuits that
 regulate hexapod legged locomotion.
description: Tripod gait example
 data.MATLAB version 7.3 .mat
 file, created using MATLAB 9.4.Tripod-gait.matLimb coordination model datastep_aspect_ratio_model_integrated_20181031-MatchExpDataFormat.matCanonical gait model dataMATLAB version 7.3 .mat file, created using MATLAB 9.4.20181126_CanonicalGaits-DataTable.matDataset of responses of freely-walking flies to translating random dot visual stimuli.MATLAB version 7.3 .mat file, created using MATLAB 9.4.20181025_VisualStimulus-isod1_50ms_random_dots_20180126-merged_down_downcam_Steps(_down_cam).matDataset of wild-type spontaneous behavior.MATLAB version 7.3 .mat file, created using MATLAB 9.4.20181025_20180530-20180614_IsoD1_Glass_MaskedModel_1000PCs_amplitude_phase_down_downcam_Steps(_down_cam).matDataset of responses to transient activation of moonwalker neuronsMATLAB version 7.3 .mat file, created using MATLAB 9.4.20181025_20180501-20180511_Moonwalker-8ms_Glass_MaskedModel_1000PCs_amplitude_phase_down_downcam_Steps(_down_cam).mat
DOI: 10.5061/dryad.kp07j1d
title: Data from: White matter hyperintensity load on stroke recurrence and mortality at 1 year after ischemic stroke

description: Objective: We set out to define the role and risks associated with white
 matter hyperintensity (WMH) load in a stroke population with respect to
 recurrent stroke and mortality after ischemic stroke. Methods: A total of
 7,101 patients at a network of university hospitals presenting with
 ischemic strokes were followed for one year. Multivariable Cox
 proportional-hazards model and competing risk analysis were used to
 examine the independent association between quartiles of WMH load and
 stroke recurrence and mortality at one year. Results: Overall recurrent
 stroke risk at one year was 6.7%/yr, divided between 5.6%/yr for recurrent
 ischemic and 0.5%/yr for recurrent hemorrhagic strokes. There was a
 stronger association between WMH volume and recurrent hemorrhagic stroke
 by quartile (Hazard ratios [HR] of 7.32, 14.12, and 33.52, respectively)
 than for ischemic recurrence (HR of 1.03, 1.37, and 1.61, respectively),
 but the absolute incidence of ischemic recurrence by quartile was higher
 (3.8%/yr, 4.5%, 6.3%, and 8.2% by quartiles) versus hemorrhagic recurrence
 (0.1%/yr, 0.4%, 0.6%, and 1.3%). Mortality of all-cause (10.5%) showed a
 marked association with WMH volume (HR of 1.06, 1.46, and 1.60), but this
 was attributable to non-vascular, rather than vascular causes.
 Conclusions: There is an association between WMH volume load and stroke
 recurrence, and this association is stronger for hemorrhagic than for
 ischemic stroke, although the absolute risk of ischemic recurrence remains
 higher. This data should be helpful to practitioners seeking to find the
 optimal preventative/treatment regimen for post-stroke patients and to
 individualize risk-benefit ratios.
description: Impact of WMH on Stroke
 Recurrence Supplemental Datarevised_supplemental_data.docx
DOI: 10.5061/dryad.rn288jt
title: Data from: Digit ratio (2D:4D) and prosocial behavior in economic games: no direct correlation with generosity, bargaining, or trust-related behaviors

description: Prenatal exposure to sex hormones exerts organizational effects on the
 brain which have observable behavioral correlates in adult life. There are
 reasons to expect that social behaviors—fundamental for the evolutionary
 success of humans—might be related to biological factors such as prenatal
 sex hormone exposure. Nevertheless, the existing literature is
 inconclusive as to whether and how prenatal exposure to testosterone and
 estrogen, proxied by the second-to-fourth digit ratio (2D:4D), may predict
 non-selfish behavior. Here, we investigate this question using economic
 experiments with real monetary stakes and analyze five different
 dimensions of social behavior in a comparatively large sample of Caucasian
 participants (n=560). For both males and females, our results show no
 robust association between right- or left-hand 2D:4D and generosity,
 bargaining, or trust-related behaviors. Moreover, no differences in
 behavior were found according to sex. We conclude that there is no direct
 correlation between 2D:4D and these social behaviors.
description: DR_social_behavior_dataentire dataset (DAT, STATA)
DOI: 10.5061/dryad.v1j613d
title: Data from: The spectrum of immune-mediated and inflammatory lesions of the brainstem: clues to diagnosis

description: The presentation of a patient with brainstem symptoms and signs invokes a
 number of common and less common differential diagnoses, and accurate
 diagnosis can be challenging. We review the major immune-mediated and
 inflammatory syndromes that can affect the brainstem including multiple
 sclerosis, neuromyelitis optica spectrum disorder, neuro-Behcet’s disease,
 chronic lymphocytic inflammation with pontine perivascular enhancement
 responsive to steroids, neurosarcoidosis, Susac’s syndrome and the
 histiocytic disorders. We focus on clinical features and magnetic
 resonance imaging clues that help to distinguish between the different
 brainstem conditions. Accurate diagnosis is important to guide appropriate
 treatment and limit neurological disability.
description: e-referencesSupplementary references 2.docx
DOI: 10.5061/dryad.66j57b1
title: Data from: Improving genomic prediction for two Yorkshire populations with a limited size using single-step method

description: In this study, we conducted genomic prediction for two Yorkshire purebred
 populations (Yichun and Chifeng) from two different provinces of China
 that both had a limited population size. Two growth traits (age adjusted
 to 100 kg weight, AGE; back‐fat thickness adjusted to 100 kg weight, BF)
 and one reproduction trait (total number of piglets born, TNB) were
 analyzed with four prediction strategies: one‐population BLUP, joint
 two‐population BLUP, one‐population single‐step BLUP (SSBLUP) and joint
 two‐population SSBLUP. Our results illustrate that accuracies of genomic
 estimated breeding values were improved for BF and TNB for the Yichun
 population and for BF for the Chifeng population by genomic prediction
 (one‐population SSBLUP and joint two‐population SSBLUP). The accuracy of
 TNB for the Yichun population was increased two fold when comparing the
 one‐population SSBLUP to the one‐population BLUP prediction. Meanwhile,
 prediction biases were dramatically reduced for AGE for the Yichun
 population and for TNB for the Chifeng population. The conclusions of this
 study are as follows: first, genomic prediction is useful for improving
 prediction accuracy for purebred pig breeding farms with a limited
 population size; second, joint genomic prediction for different
 populations of the same breed with certain genetic links has the trend to
 further improve prediction accuracy.
description: Self-developed swine 55K
 SNP chip-V1Information about
 self-developed swine 55K SNP chip, including marker names, chromosomes,
 positions, sequences, et al.Self-developed swine 50k
 SNP chip-V2SNP marker information
 for self-developed chip V2, including markers' name, chromosomes and
 positionsOverlap SNPs between V1
 and V2 panelsInformation about
 overlaped SNPs between V1 and V2 panels
DOI: 10.5061/dryad.t4r1n64
title: Data from: Effect of coexisting vascular disease on long-term risk of recurrent events after TIA or stroke

description: Objective:To determine whether TIA or ischemic stroke patients with
 co-existing cardiovascular disease (i.e. history of coronary or peripheral
 artery disease) are still at high risk of recurrent ischemic events
 despite current secondary prevention guideline. Methods: In a
 population-based study in Oxfordshire, United Kingdom (Oxford Vascular
 Study), we studied consecutive patients with TIA or ischemic stroke for
 2002-2014. Patients were treated according to current secondary prevention
 guidelines and we determined risks of coronary events, recurrent ischemic
 stroke, and major bleeding stratified by the presence of co-existing
 cardiovascular disease. Results: Among 2555 patients (9148 patient-years
 of follow-up), those (n=640; 25.0%) with co-existing cardiovascular
 disease (449 coronary only; 103 peripheral only; 88 both) were at higher
 10-year risk of coronary events than those without (22.8%; 95%CI
 17.4-27.9; versus 7.1%, 5.3-8.8; p&lt;0.001, age-and sex-adjusted
 HR=3.07, 2.24-4.21) and of recurrent ischemic stroke (31.5%, 25.1-37.4;
 versus 23.4%, 20.5-26.2; p=0.0049, age-and sex-adjusted HR=1.23,
 0.99-1.53), despite similar rates of use of antihrombotic and
 lipid-lowering medication. However, in patients with non-cardioembolic
 TIA/stroke, risk of extracranial bleeds was also higher in those with
 co-existing cardiovascular disease, particularly in patients aged
 &lt;75 years (8.1%, 2.8-13.0; versus 3.4%, 1.6-5.3; p=0.0050; age-and
 sex-adjusted HR=2.71, 1.16-6.30), although risk of intracerebral
 hemorrhage was not increased (age-and sex-adjusted HR=0.36, 0.04-2.99).
 Conclusions: As in older studies, TIA/stroke patients with co-existing
 cardiovascular disease still remain at high risk of recurrent ischemic
 events despite current management. More intensive lipid-lowering might
 therefore be justified, but benefit from increased antithrombotic
 treatment might be offset by the higher risk of extracranial bleeding.
description: Neurology2018941971R_Supplemental dataSupplemental data
DOI: 10.5061/dryad.rd1570s
title: Data from: Invasion origin, rapid population expansion, and the lack of genetic structure of cotton bollworm (Helicoverpa armigera) in the Americas

description: In 2013, Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) was
 officially declared as present in Brazil and, after two years, the species
 was detected in the Caribbean and North America. Information on genetic
 features and accurate distribution of pests is the basis for agricultural
 protection policies. Furthermore, such knowledge is imperative to develop
 control strategies, understand the geographical range, and genetic
 patterns of this species in the Americas. Here, we carried out the widest
 sampling of H. armigera in the South American continent and Puerto Rico,
 after we estimated the diversity, demographic parameters, and genetic
 structure. The Internal Transcribed Spacer 1 (ITS1) nuclear marker was
 used to investigate the presence of putative hybrids between H. armigera
 and H. zea and they were observed at a frequency of 1.5%. An ABC analysis,
 based in COI gene fragment, suggested Europe as the origin of South
 America specimens of H. armigera and following a movement northward
 through the Caribbean. Three mtDNA genes and three nDNA markers revealed
 high genetic diversity distributed without the defined population
 structure of H. armigera in South America. Most of the genetic variation
 is within populations with a multidirectional expansion of H. armigera
 among morphoclimatic regions. High genetic diversity, rapid population
 expansion, and hybridization have implications for pest management since
 they suggest that adaptive alleles are spread through wide areas in South
 America that favor rapid local adaptation of H. armigera to new and
 disturbed environments (e.g. in agricultural areas).
description: GenBank_accession_numbersExcel worksheet with the GenBank accession numbers, geographical locality sampled and molecular markers used from all samples collected in the field in this work. AM: Amazon Forest; AM/CE: Amazon Forest transition with Cerrado; AT: Atlantic Forest; PA: Pampas; CE/CA: Cerrado transition with Caatinga; CE: Cerrado.Scripts_used_in_ABC_analysisAll scripts used to perform the Approximate Bayesian Computation (ABC) analysis are available here. The objective of this analysis was to infer the geographical origin of Helicoverpa armigera in the Americas using COI mitochondrial molecular marker. The analyses simulated computationally were performed in the ms 20161016 coalescent sampler and the result points to an introduction coming from Europe, at least in part. The scripts and files are zipped and named (01-14) in the order they were used.
DOI: 10.5061/dryad.gn8723p
title: Data from: Kinetic study of catalytic CO2 hydration by metal-substituted biomimetic carbonic anhydrase model complexes

description: The rapid rise of the CO2 level in the atmosphere has spurred the
 development of CO2 capture methods such as the use of biomimetic complexes
 that mimic carbonic anhydrase. In this study, model complexes with
 tris(2-pyridylmethyl)amine (TPA) were synthesized using various transition
 metals (Zn2+, Cu2+ and Ni2+) to control the intrinsic proton-donating
 ability. The pKa of the water coordinated to the metal, which indicates
 its proton-donating ability, was determined by potentiometric pH titration
 and found to increase in the order [(TPA)Cu(OH2)]2+ &lt;
 [(TPA)Ni(OH2)]2+ &lt; [(TPA)Zn(OH2)]2+. The effect of pKa on the CO2
 hydration rate was investigated by stopped-flow spectrophotometry. Because
 the water ligand in [(TPA)Zn(OH2)]2+ had the highest pKa, it would be more
 difficult to deprotonate it than those coordinated to Cu2+ and Ni2+. It
 was therefore expected that the complex would have the slowest rate for
 the reaction of the deprotonated water with CO2 to form bicarbonate.
 However, it was confirmed that [(TPA)Zn(OH2)]2+ actually had the fastest
 CO2 hydration rate because the substitution of bicarbonate with water
 (bicarbonate release) occurred easily.
description: [(TPA)Ni(OH2)](SO4)Crystal structures of [(TPA)Ni(OH2)](SO4)0130B-2.cif