cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.53q65vf
title: Data from: Estimating diversification rates on incompletely-sampled phylogenies: theoretical concerns and practical solutions

description: Molecular phylogenies are a key source of information about the tempo and
 mode of species diversification. However, most empirical phylogenies do
 not contain representatives of all species, such that diversification
 rates are typically estimated from incompletely sampled data. Most
 researchers recognize that incomplete sampling can lead to biased rate
 estimates, but the statistical properties of methods for accommodating
 incomplete sampling remain poorly known. In this point of view, we
 demonstrate theoretical concerns with the widespread use of analytical
 sampling corrections for sparsely sampled phylogenies of higher taxonomic
 groups. In particular, corrections based on “sampling fractions” can lead
 to low statistical power to infer rate variation when it is present,
 depending on the likelihood function used for inference. In the extreme,
 the sampling fraction correction can lead to spurious patterns of
 diversification that are driven solely by unbalanced sampling across the
 tree in concert with low overall power to infer shifts. Stochastic
 polytomy resolution provides an alternative to sampling fraction
 approaches that avoids some of these biases. We show that stochastic
 polytomy resolvers can greatly improve the power of common analyses to
 estimate shifts in diversification rates. We introduce a new stochastic
 polytomy resolution method (TACT: Taxonomic Addition for Complete Trees)
 that uses birth-death-sampling estimators across an ultrametric phylogeny
 to estimate branching times for unsampled taxa, with taxonomic information
 to compatibly place new taxa onto a backbone phylogeny. We close with
 practical recommendations for diversification inference under several
 common scenarios of incomplete sampling.
description: Supplemental code and
 information R notebooks used to
 conduct diversification analyses and simulations in the manuscript and
 supplemental text.
DOI: 10.5061/dryad.2h2g698
title: Data from: Clinically relevant cranio-caudal patterns of cervical cord atrophy evolution in MS

description: Objectives. To characterize the distribution and regional evolution of
 cervical cord atrophy in multiple sclerosis (MS) patients in a multicentre
 dataset. Methods. MRI and clinical evaluations were acquired from 179
 controls and 435 patients (35 clinically isolated syndromes [CIS], 259
 relapsing-remitting [RR], 99 secondary-progressive [SP] and 42
 primary-progressive [PP]MS). Sixty-nine controls and 178 patients
 underwent a one-year MRI and clinical follow-up. Patients were classified
 as clinically stable/worsened according to their disability change.
 Longitudinal changes of cord atrophy were investigated with linear
 mixed-effect models. Sample size calculations were performed using age-,
 sex- and site-adjusted annualized percentage normalized cord
 cross-sectional area (CSAn) changes..Results. Baseline CSAn was lower in
 MS patients vs controls (p&lt;0.001), but not different between
 controls and CIS or between early RRMS (disease duration&lt;5 years)
 and CIS patients. Late RRMS (disease duration&gt;5 years) showed
 significant cord atrophy vs early RRMS (p=0.02). Progressive MS patients
 had decreased CSAn (p&lt;0.001) vs RRMS. Atrophy was located between
 C1/C2 and C5 in RRMS vs CIS, and widespread along the cord in progressive
 MS vs RRMS, with an additional C5/C6 involvement in SPMS vs PPMS. At
 follow-up, CSAn decreased in all phenotypes (p&lt;0.001), except CIS.
 Cord atrophy rates were highest in early RRMS and clinically worsened
 patients, who had a more widespread cord involvement than stable patients.
 The sample size per arm required to detect a 50% treatment effect was 118
 for early RRMS patients. Conclusions. Cord atrophy increased in MS during
 one year, except for CIS. A faster atrophy contributed to explain clinical
 worsening.
description: NEUROLOGY-2018-951756-R1-Online-Supplement on DryadSupplementary methods and results
DOI: 10.5061/dryad.f81k3q7
title: Data from: Isolation, characterization, and cross-amplification of 20 microsatellite markers for the rare Conospermum undulatum (Proteaceae)

description: Premise of the study: Recent habitat fragmentation is posing a risk to the
 wavy-leaved smokebush, Conospermum undulatum, a rare plant species endemic
 to the south-western Western Australia. Microsatellites markers are
 required to characterize the genetic diversity and structure of the
 species for conservation purposes and to facilitate ecological studies.
 Methods and Results: Illumina MiSeq high-throughput sequencing was used to
 develop 20 novel microsatellite markers for C. undulatum. Polymorphism at
 each locus was assessed using 72 individuals from three natural
 populations. Nineteen markers were polymorphic, with the number of alleles
 per locus ranging from two to 21, and observed and expected heterozygosity
 ranging from 0.000 to 1.000 and 0.117 to 0.919, respectively. All markers
 successfully amplified in three congeneric species. Conclusions: The
 microsatellite markers will be useful for revealing patterns of genetic
 diversity, dispersal dynamics and hybridization events for C. undulatum to
 inform future conservation efforts.
description: Conospermum
 outputData outputs from the
 pipeline generated from NextGeneration sequencingSMA-Cu1_S55_L001_R1_001Illumina fastq file output of forward reads for Conospermum undulatum.SMA-Cu1_S55_L001_R2_001Illumina fastq file output of reverse reads for Conospermum undulatum.
DOI: 10.5061/dryad.43cp80c
title: Data from: Live-cell single particle imaging reveals the role of RNA polymerase II in histone H2A.Z eviction

description: The H2A.Z histone variant, a genome-wide hallmark of permissive chromatin,
 is enriched near transcription start sites in all eukaryotes. H2A.Z is
 deposited by the SWR1 chromatin remodeler and evicted by unclear
 mechanisms. We tracked H2A.Z in living yeast at single-molecule
 resolution, and found that H2A.Z eviction is dependent on RNA Polymerase
 II (Pol II) and the Kin28/Cdk7 kinase, which phosphorylates Serine 5 of
 heptapeptide repeats on the carboxy-terminal domain of the largest Pol II
 subunit Rpb1. These findings link H2A.Z eviction to transcription
 initiation, promoter escape and early elongation activities of Pol II.
 Because passage of Pol II through +1 nucleosomes genome-wide would
 obligate H2A.Z turnover, we propose that global transcription at yeast
 promoters is responsible for eviction of H2A.Z. Such usage of yeast Pol II
 suggests a general mechanism coupling eukaryotic transcription to erasure
 of the H2A.Z epigenetic signal.
description: H2A.Z_Halo_WT_Archive
 Halo_H2B_WT_Archive
 Swr1_Halo_WT_Archive
 Swr1_Halo_swc2del_Archive
 Halo_NLS_Archive
 H2A.Z-Halo_Swc5AA_no_RAP_Archive
 H2A.Z_Halo_Swc5AA_with_RAP_Archive
 H2A.Z_Halo_Swc5AA_Rpb1AA_with_RAP_Archive
 H2A.Z_Halo_Swc5AA_Ino80AA_with_RAP_Archive
 H2A.Z_Halo_Swc5AA_Kin28AA_withRAP_Archive
 H2A.Z_Halo_Swc5AA_Bur1AA_witRAP_Archive
 H2A.Z_Halo_Swc5AA_Ctk1AA_withRAP_Archive
 H2A.Z_Halo_Swc5AA_Cet1AA_withRAP_Archive
description: Movies with two dimensional single molecule data were analyzed by
 DiaTrack Version 3.05 (Vallotton and Olivier, 2013), which determines the
 precise position of single molecules by Gaussian intensity fitting and
 assembles particle trajectories over multiple frames. In Diatrack remove
 blur was set to 0.1, remove dim set at 70 and max jump set at 6 pixels,
 where each pixel was 107 nm. Datasets contain session files from Diatrack
 with single molecule localization, intensity of single molecules, frame
 numbers and single molecule tracking information from recorded
 videos.
DOI: 10.5061/dryad.1ft743d
title: Data from: Effects of insularity on insect leaf herbivory and chemical defences in a Mediterranean oak species

description: Aim: Research on plant-herbivore interactions has shown that islands
 typically have low abundances and diversity of herbivores because of
 barriers to dispersal, isolation, and reduced land area. Islands commonly
 have lower levels of herbivory relative to mainland regions, and, as a
 consequence, insular plants should exhibit lower levels of defences than
 their mainland counterparts. Despite these predictions, there are
 significant gaps in our understanding of insularity effects on
 plant-herbivore interactions. For instance, most work addressing the
 effects of insularity on plant-herbivore interactions have compared one or
 a few islands with a single mainland site. In addition, studies have
 measured herbivory or plant defences but not both, and the influence of
 abiotic factors has been neglected. Location: Mediterranean Basin (from
 Spain to Greece) Taxon: Quercus ilex L. Methods: We conducted a
 large-scale study to investigate whether insect leaf herbivory and plant
 chemical defences in holm oak (Quercus ilex L.) differ between insular vs.
 mainland populations. We further investigated mechanisms by which
 insularity effects on herbivory may take place by assessing the influence
 of defences and climatic variables on leaf herbivory. Results: We found
 that insular populations exhibited lower herbivory and higher defences
 (condensed tannins) than their mainland counterparts. Our analyses,
 however, suggest that these concomitant patterns of insect herbivory and
 plant defences were seemingly unrelated as island vs. mainland differences
 in defences did not account for the observed pattern in herbivory.
 Furthermore, climatic factors did not explain insularity effects on either
 herbivory or plant defences. Main conclusions: Overall, this study
 provides one of the most robust assessments to date on insularity effects
 on herbivory and builds towards a better understanding of the ecology and
 evolution of plant-insect interactions in insular ecosystems.
description: Herbivory and defences
 in Quercus ilex from insular and continental areasdata_JBI-18-0674.R1.csv
DOI: 10.5061/dryad.t8c381f
title: Data from: Human sound localization depends on sound intensity: implications for sensory coding

description: Human sound localization is an important computation performed by the
 brain. Models of sound localization commonly assume that sound
 lateralization from interaural time differences is level invariant. Here
 we observe that two prevalent theories of sound localization make opposing
 predictions. The labelled-line model encodes location through tuned
 representations of spatial location and predicts that perceived direction
 is level invariant. In contrast, the hemispheric-difference model encodes
 location through spike-rate and predicts that perceived direction becomes
 medially biased at low sound levels. Here, behavioral experiments find
 that softer sounds are perceived closer to midline than louder sounds,
 favoring rate-coding models of human sound localization. Analogously,
 visual depth perception, which is based on interocular disparity, depends
 on the contrast of the target. The similar results in hearing and vision
 suggest that the brain may use a canonical computation of location:
 encoding perceived location through population spike rate relative to
 baseline.
description: ihlefeld_alldata This folder contains the
 Matlab code for two computational models (Figure 1) and the human data
 with the statistical model, coded in R.
DOI: 10.5061/dryad.4mj8gg0
title: Data from: Genetic, morphological and ecological variation across a sharp hybrid zone between two alpine butterflies species

description: Identifying the mechanisms involved in the formation and maintenance of
 species is a central question in evolutionary biology and distinguishing
 the selective drivers of populations’ divergence from demographic
 processes is of particular interest to better understand the speciation
 process. Hybrid zones are recognized to provide ideal places to
 investigate the genetic architecture of speciation and to
 identify the mechanisms allowing diverging species to maintain
 their integrity in the face of gene flow. Here, we studied two
 alpine butterfly species in the genus Coenonympha: C.
 macromma and C. gardetta, which can be found
 flying together and hybridizing in narrow contact zones in the southern
 French Alps. We characterised the genomic composition of individuals,
 their morphology and their local habitat requirements, within and around a
 hybrid zone. Cline analysis showed that a
 significant portion of the genomic regions analysed were
 impermeable to introgression across a sharp hybrid zone (9 km wide),
 despite ongoing hybridisation between the species. We also found
 concordance between genetic, morphological and environmental variation
 across the hybrid zone, suggesting a coupling of different reproductive
 barriers. Habitat characteristics such as the presence of trees and shrubs
 and the start of the growing season were strongly associated with the
 genetic variation and we found evidence of genetic divergence at genetic
 markers associated with morphology and physiology, putatively involved in
 visual or environmental reproductive isolation. We discuss the various
 behavioural and ecological factors that might interplay to maintain
 current levels of divergence and gene flow between this species pair.
description: Landmarks_coordThe landmarks coordinates and samples information used for the geometric morphometric analysisEnv_variablesAll the environmental variables with rasters of climatic variables and a table of habitat characteristics for the sampled populationsinfos_ind_VARSSamples information and coordinatespopulations.snpsSNP resulting from the ddRADseq experiment
DOI: 10.5061/dryad.54t59r8
title: Data from: Risky behaviors and Parkinson’s disease: a Mendelian randomization study

description: Objective: To examine causal associations between risky behavior
 phenotypes on Parkinson’s disease using a Mendelian randomization
 approach. Methods: We used two-sample Mendelian randomization to generate
 unconfounded estimates using summary statistics from two independent,
 large meta-analyses of genome-wide association studies on risk taking
 behaviors (n=370,771-939,908) and Parkinson’s disease (cases: n=9581,
 controls: n = 33,245). We used inverse variance weighted as the main
 method for judging causality. Results: Our results support a strong
 protective association between the tendency to smoke and Parkinson’s
 disease (OR=0.714 per log odds of ever smoking; 95% CI=0.568-0.897;
 p-value=0.0041; Cochran Q test; p-value=0.238; I2 index=6.3%).
 Furthermore, we observed risk association trends between automobile speed
 propensity as well as the number of sexual partners and Parkinson’s
 disease after removal of overlapping loci with other risky traits
 (OR=1.986 for each standard deviation increase in normalized automobile
 speed propensity; 95% CI=1.215-3.243; p-value=0.0066, OR=1.635 for each
 standard deviation increase in number of sexual partners; 95%
 CI=1.165-2.293; p-value=0.0049). Conclusion: These findings provide
 support for a causal relationship between general risk tolerance and
 Parkinson’s disease and may provide new insights in the pathogenic
 mechanisms leading to the development of Parkinson’s disease.
description: Supplementary
 tableList of summary
 estimates used for the calculation of effect estimates for the primary MR
 analysisMR_PM_R01_D01_20190308_Neurology_SupplTable.docxe-MethodsA short introduction to Mendelian randomizationMR_PM_R01_eMethods.docx
DOI: 10.5061/dryad.v7r6v6c
title: Data from: Descriptive epidemiology of the 2018 cholera outbreak in Nigeria: implications for the global roadmap strategies

description: Introduction: The 2018 cholera outbreak in Nigeria indicates that the
 disease remains an enormous public health threat. This paper, therefore,
 provides an epidemiological description of the outbreak, with a view to
 provide current evidence for public health planning and interventions
 towards cholera elimination in the country. Methods/Principal Findings:
 This was a retrospective analysis of surveillance data from January 1st to
 November 19th, 2018. A cholera case was defined as an individual aged 2
 years or older with acute watery diarrhoea, and severe dehydration or
 dying from acute watery diarrhoea. Descriptive analyses were performed in
 terms of person, time and place. Overall, there were 43,996 cases with an
 attack rate (AR) of 127.43/100,000 population, and 836 deaths with a case
 fatality rate (CFR) of 1.90%. Individuals aged 15 years or older (47.76%)
 recorded the highest number of cases, while the proportion of males
 (49.00%) and females (51.00%) was nearly equal. The outbreak was
 characterised by four distinct epidemic waves, with higher records of
 deaths towards the end of the outbreak (296 and 295 deaths in the third
 and fourth waves, respectively). States from the north-west and north-east
 regions reported the highest ARs, while those from the north-central
 region reported the highest CFRs. Conclusion: The distribution of the 2018
 cholera outbreak in Nigeria indicates an elevated burden, especially in
 the northern part of the country, and the influence of diverse and
 interrelated drivers; thus, underlining the need to adopt a multi-sectoral
 approach to cholera prevention and control in the country as outlined in
 the Global Roadmap strategies.
description: DATASET_KEThe dataset contains variables extracted from the line-list used during the 2018 cholera outbreak which affected 20 States across Nigeria.
DOI: 10.5061/dryad.n6f068k
title: Data from: Novel track morphotypes from new tracksites indicate increased Middle Jurassic dinosaur diversity on the Isle of Skye Scotland

description: Dinosaur fossils from the Middle Jurassic are rare globally, but the Isle
 of Skye (Scotland, UK) preserves a varied dinosaur record of abundant
 trace fossils and rare body fossils from this time. Here we describe two
 new tracksites from Rubha nam Brathairean (Brothers’ Point) near where the
 first dinosaur footprint in Scotland was found in the 1980s. These sites
 were formed in subaerially exposed mudstones of the Lealt Shale Formation
 of the Great Estuarine Group and record a dynamic, subtropical, coastal
 margin. These tracksites preserve a wide variety of dinosaur track types,
 including a novel morphotype for Skye: Deltapodus which has a probable
 stegosaur trackmaker. Additionally, a wide variety of tridactyl tracks
 shows evidence of multiple theropods of different sizes and possibly hints
 at the presence of large-bodied ornithopods. Overall, the new tracksites
 show the dinosaur fauna of Skye is more diverse than previously recognized
 and give insight into the early evolution of major dinosaur groups whose
 Middle Jurassic body fossil records are currently sparse.
description: <strong>README_final </strong>
 .txt file containing usage notes and full details of the
 dataset. <strong>BP1_Model_Dataset
 </strong> .zip file containing photos and ground
 control points associated with BP1 photogrammetric model.
 <strong>BP3_Model_Dataset </strong>
 .zip file hotos and Ground Control Points Used to Construct BP3
 model <strong>Full_Tracksite_Models
 </strong> .zip folder containing whole outcrop
 photogrammetric models of BP1 and BP3
 <strong>High_Quality_Orthophotos </strong>
 .zip folder containing to photogrammetric orthophotos (.jpg
 files) of the tracksites (BP1 and BP3) described in the paper.
 <strong>Subsampled_Areas_of_Interest
 </strong> .zip folder containing smaller
 photogrammetric models associated with the portions of the outcrops at BP1
 and BP3 specifically discussed in the publication.
 <strong>Full_Tracksite_Models_Mac </strong>
 .zip folder containing whole outcrop photogrammetric models of
 BP1 and BP3 that is compatible with the Mac_OS
description: This dataset was collected by flying a UAV with a digital camera
 as a payload. The data were processed in Agisoft Photoscan
 1.2.5.2735. Additional processing and workflow details
 can be found in the associated paper and its supplement.
DOI: 10.5061/dryad.m517990
title: Data from: Profile of and risk factors for post-stroke cognitive impairment in diverse ethno-regional groups

description: OBJECTIVE: To address the variability in prevalence estimates and
 inconsistencies in potential risk factors for post-stroke cognitive
 impairment (PSCI) using a standardised approach and individual participant
 data (IPD) from international cohorts in the STROKOG consortium. METHODS:
 We harmonised data from thirteen studies based in eight countries.
 Neuropsychological test scores 2 to 6 months after stroke or TIA and
 appropriate normative data were used to calculate standardised cognitive
 domain scores. Domain-specific impairment was based on percentile cut-offs
 from normative groups, and associations between domain scores and risk
 factors were examined using one-stage IPD meta-analysis. RESULTS: In a
 combined sample of 3,146 participants admitted to hospital for stroke
 (97%) or TIA (3%), 44% were impaired in global cognition and 30–35% in
 individual domains 2 to 6 months after the index event. Diabetes and a
 history of past stroke were strongly associated with poorer cognitive
 function after covariate adjustments; hypertension, smoking and atrial
 fibrillation had weaker domain-specific associations. While there were no
 significant differences in domain impairment among ethno-racial groups,
 some inter-ethnic differences were found in the effects of risk factors on
 cognition. CONCLUSIONS: This paper confirms the high prevalence of PSCI in
 diverse populations, highlights common risk factors, in particular
 diabetes, and points to ethno-racial differences which warrant attention
 in the development of prevention strategies.
description: Profile of and risk
 factors for post-stroke cognitive impairment in diverse ethno-regional
 groups - Appendices This file contain the
 appendices to the article titled "Profile of and risk factors for
 post-stroke cognitive impairment in diverse ethno-regional groups".
 The appendices contain summary information regarding each study cohort
 which contributed data (T1 - T10), additional methods (A1 - A4),
 additional table of results (T11 - T19), flow diagram of studies included
 (F1) and additional forest plots (F2).
DOI: 10.5061/dryad.0f9m86n
title: Data from: Clinical reasoning: a 55-year-old woman presenting with ataxia and numbness 1 year after ileum resection

description: Supplemental material
description: table
 e-1Differential diagnosis
 of subacute myelopathy.
DOI: 10.5517/ccdc.csd.cc2lp95s
title: CCDC 2403745: Experimental Crystal Structure Determination

description: Related Article: Xingping Fu|2025|CSD Communication|||
description: Related Article: Xingping Fu, Qianqian Chen, Jianfeng Zhu, Weijia Su, Xiaobing Yang|2024|Chem.Eng.Journal|502|158141|doi:10.1016/j.cej.2024.158141
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2lp96t
title: CCDC 2403746: Experimental Crystal Structure Determination

description: Related Article: Xingping Fu|2025|CSD Communication|||
description: Related Article: Xingping Fu, Qianqian Chen, Jianfeng Zhu, Weijia Su, Xiaobing Yang|2024|Chem.Eng.Journal|502|158141|doi:10.1016/j.cej.2024.158141
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.