cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7063823.v3
title: Supplemental materials for Jung et al, 2019

description: Supplemental materials for Jung <i>et al</i>, 2019<br> "Genome-wide screening for enteric colonization factors in carbapenem-resistant ST258 <i>Klebsiella pneumoniae"</i><i><br></i><i>-----------------------</i><i>-----------------------</i><i><br></i><b>Table S1.</b> List of MH258 chromosomal essential genes as identified by the EL-ARTIST pipeline (19). For the sliding window analysis, 1000 simulations, window size of 10, and p-value of 0.05 were used. 1, non-essential; 2, essential; 3, domain essential. <br><br><b>Table S2. </b>Mutants with enhanced fitness in gut colonization. Ratios of the read counts to the total read counts are listed for all the mutants that represented more than 2 percent of the total reads (highlighted in yellow) in any of the samples. <br><br><b>Table S3. </b>Average log2 fold changes in the normalized read counts for all the significant genetic loci in any of the in vivo and in vitro samples. The same color scheme to Fig. 5D was applied. Fold changes for the genes that were not significant in a given sample are not shown; they were treated as unchanged (“0”). <br><br><b>Table S4.</b> List of primers. <br><br><b>Text S1.</b> Supplemental Results <br><br><b>Text S2.</b> Supplemental methods. <br><br><b>Figure S11. </b>Genomic comparison of multiple Kp clinical strains. A circos map generated by the Proteome Comparison tool of PATRIC 3.5.27 for Table 1 is shown. <br><br><br>
DOI: 10.6084/m9.figshare.8194169.v2
title: defunct

description: practice data
DOI: 10.6084/m9.figshare.25640718.v1
title: SCZ GWAS datasets

description: Access to individual level data can be requested from the authors (Yongyong Shi, shiyongyong@gmail.com and Zhiqiang Li, lizqsjtu@gmail.com). You will need to agree to the terms of the Data Access Agreement, and send a signed copy to the authors.
DOI: 10.6084/m9.figshare.25825954.v1
title: Supplementary Material for: Predictors of early versus delayed neurological deterioration after thrombolysis for ischemic stroke: ENCHANTED study

description: Background and Purpose: We aimed to determine predictors of early (END) and delayed neurological deterioration (DND) and their association with functional outcome in patients with acute ischemic stroke (AIS) who participated in the international Enhanced Control of Hypertension and Thrombolysis Stroke Study (ENCHANTED).
Methods: END and DND were defined as scores of a ≥2 point increase on the National Institutes of Health Stroke Scale (NIHSS) or ≥1 point decrease on Glasgow coma scale, or death, from baseline to 24 hours and 24 hours to 72 hours, respectively. Multivariable logistic regression models were used to determine independent predictors of END and DND and their association with 90-day outcomes (dichotomous scores on the modified Rankin scale [mRS] of 2-6 vs 0-1 and 3-6 vs 0-2, and death).
Results: Of 4496 patients, 871 (19.4%) and 302 (8.4%) patients experienced END and DND, respectively. Higher baseline NIHSS score, older age, large artery occlusion due to significant atheroma, cardioembolic stroke subtype, hemorrhagic infarction and parenchymatous hematoma within 24 hours, were all independent predictors for both END (all P ≤0.01) and DND (all P ≤0.024). Moreover, higher baseline systolic blood pressure (BP) (odds ratio [OR] 1.07, 95% confidence interval [CI] 1.02-1.12), higher diastolic BP variability within 24 hours (OR 1.07, 95% CI 1.04-1.09), patients from Asia (OR 1.25, 95% CI 1.03-1.52) were the only independent predictors for END. However, Asian ethnicity was negatively associated with DND (OR 0.64, 95% CI 0.47-0.86). Hemorrhagic infarction and parenchymatous hematoma within 24 hours were the key predictor of END across all stroke subtypes. END and DND were all associated with a poor functional outcome at 90 days (all P&lt;0.001). 
Conclusions: We identified overlapping and unique demographic and clinical predictors of END and DND after thrombolysis for acute ischemic stroke. Both END and DND predict unfavorable outcomes at 90 days.
DOI: 10.17632/hstgh8tyxp
title: Research data for the research article "Vortex frequency locking and Shapiro steps in superconductor open nanotubes"

description: Research data underlying research article arXiv:2503.07162 "Vortex frequency locking and Shapiro steps in superconductor open nanotubes" by I. Bogush, V. M. Fomin, O. V. Dobrovolskiy, obtained in the Cryogenic Quantum Electronics Division, EMG and LENA, TU Braunschweig, as part of the CA project "3DSuper" within the EXC-2123 QuantumFrontiers 390837967 funded by the German Research Foundation (DFG)
DOI: 10.6084/m9.figshare.13473147.v1
title: Data S1

description: Body mass is one of the most important phenotypic attributes in animal ecology and life history. This trait is widely used in the fields of ecology and macroevolution, since it influences physiology, morphological functions, as well as a myriad of ecological and social interactions. In this data set, our aim was to gather a comprehensive bird and mammal body mass data set from northern South America. We report body mass, discriminated by sex, for 42,022 individual birds and 7,441 mammals representing 1317 bird species (69% of Colombia’s avifauna) and 270 mammal species (51% of Colombian mammals) from the Neotropics. The data was sourced from vouchers collected between 1942 and 2020 and from individuals captured and released at banding stations over the last two decades for birds (2000 – 2020) and the last decade for mammals (2010 – 2020), by ten research groups and institutions in Colombia. This data set fills gaps identified in other similar databases, as it focuses on northern South America, a highly diverse Neotropical region often underrepresented in morphological data sets. We provide wide taxonomic coverage for studies interested in information both at regional and local scales.
DOI: 10.6084/m9.figshare.17019836.v2
title: Dataset of automatically extracted sizes and morphologies of AuNPs from literature-mined SEM/TEM images

description: This is a dataset of automatically extracted sizes and morphologies of Gold nanoparticles, which have been obtained from the analysis of 4365 literature-mined SEM/TEM images. The dataset contains 4365 records, each of which contains extracted size/morphology information and metadata corresponding to a single microscopy image.
DOI: 10.6084/m9.figshare.22691104.v2
title: Untitled Item

description: The MIDOG++ dataset represents an extension of the data set used in the MIDOG 2021 and 2022 challenges. We provide region of interest images from 503 histological specimens of seven different tumor types with variable morphology: breast carcinoma, lung carcinoma, lymphosarcoma, neuroendocrine tumor, cutaneous mast cell tumor, cutaneous melanoma, and (sub)cutaneous soft tissue sarcoma. The human and canine samples were processed and stained at different human and veterinary pathology laboratories with standard H&E dye and digitized with different digital whole slide image scanners. We provide labels for 11,937 mitotic figures that have been differentiated against 14,351 imposter cells in a blinded consensus by two pathologists and a final decision by a third pathologist for disagreed labels.
DOI: 10.6084/m9.figshare.28600802.v1
title: Supplementary Material 1

description: Eighteen <i>Escherichia.coli</i> genomes from sepsis patients.
DOI: 10.6084/m9.figshare.7158692.v2
title: Lineage output

description: Output file from https://github.com/KyleTDavid/NGS/blob/master/get_lineage.py<br>Reports lineage for each NCBI taxa ID included in analysis, required for https://github.com/KyleTDavid/NGS/blob/master/get_plots.R
DOI: 10.6084/m9.figshare.24204750.v2
title: EPI-Clone datasets M.1-M.3: Single cell targeted DNA methylation profiling of hematopoietic stem and progenitor cells

description: This is the dataset supporting the EPI-Clone manuscript: Targeted single cell methylation profiling of hematopoietic stem and progenitor cells (HSPCs) was performed with the scTAMseq method. Three experiments are included: In M.1 and M.2 HSCs were clonally labeled with the LARRY system, transplanted to recipient mouse and profiled 4-5 months later (post-transplant hematopoiesis). In M.3 HSPCs were profiled straight from an unperturbed mouse.<b>Remaining experiments are available under different DOIs:</b>Mature cell experiment: https://doi.org/10.6084/m9.figshare.25472467Unperturbed old vs young mouse experiment: https://doi.org/10.6084/m9.figshare.25472434Human total bone marrow: https://doi.org/10.6084/m9.figshare.25526899Dataset is a seurat (v4) object with the following assays, reductions and metadata:<br><b>ASSAYS:</b>AB: Antibody expression dataDNAm: DNA methylation data, containing binary observations (0: amplicon not observed, i.e. dropout or absence of DNA methylation, 1: amplicon observed, i.e. DNA methylation). See the paper on scTAMseqintegrated: Integration of DNA methylation data performed across experimental batches.<b>DIMENSIONALITY REDUCTION</b>pca: PCA performed on the integrated dataumap: UMAP computed on the integrated dataFor strategies how to obtain dimensionality reduction that reflect clonal identity, please see the github page accompanying the manuscript.<b>METADATA</b>Experiment: The experiment that the cell is from, values are "LARRY main experiment", "LARRY replicate" and "Native hematopoiesis"ProcessingBatch: Experiments were processed in several batches.CellType: Cell type annotationLARRY: Error corrected LARRY barcodeLARRYSize: Size of the cloneGFP.or.Saphire: Identity of the donor mouse. For M.1, two donor mice were sacrificed and HSCs were labeled with LARRY constructs containing a GFP label in one case, and LARRY constructs containing a Sapphire label in the other case. Subsequently, labeled cells from each donor were transplanted into two recipient mice each. Accordingly, the data set contains cells from four mice that contain two sets of clones, labeled with GFP and Sapphire, respectively.Pseudotime: Differentiation pseudotimePerformanceNonHhaI: Performance of the control amplicons in that cell
DOI: 10.6084/m9.figshare.26225066.v1
title: Daten

description: Zufriedenheit mit der Wahl psychotherapeutischer Berufsträger_innen
DOI: 10.6084/m9.figshare.29045324.v1
title: A 3-D Vp Seismic Tomography Visualization Tool for "Unraveling the Proto-South China Sea Plate in the Mantle: New Insights from Seismic Tomography"

description: This file contains the seismic velocity model and codes for the manuscript entitled '<b>Unraveling the Proto-South China Sea Plate</b><b> in the Mantle</b><b>: N</b><b>ew</b><b> Insights from Seismic Tomography</b>' by Gou et al., including the 3-D Vp model and visualization tool based on the GMT6 scripts.
DOI: 10.17632/snf8sjg23c
title: One_erath_20-00064

description: This dataset shows the PM2.5 concentration for 367 major cities in China calculated by the reduced-form model which removes the confounding meteorological effects. The data evaluates the PM2.5 reduction for 2013-2019 and provides the future prediction for 2035 assuming that the current controlling efforts will continue.
DOI: 10.6084/m9.figshare.21552576.v1
title: In vivo detection of bile duct pre-cancer with endoscopic light scattering spectroscopy

description: Data from Douglas K. Pleskow, Mandeep S. Sawhney, Paul K. Upputuri, Tyler M. Berzin, Mark F. Coughlan, Umar Khan, Maria Glyavina, Xuejun Zhang, Liming Chen, Conor J. Sheil, Jonah M. Cohen, Edward Vitkin, Yuri N. Zakharov, Irving Itzkan, Lei Zhang, Le Qiu & Lev T. Perelman. 2022. In vivo detection of bile duct pre-cancer with endoscopic light scattering spectroscopy.
DOI: 10.6084/m9.figshare.23259329.v1
title: Eucalyptus urophylla mitochondrion, complete genome.

description: Eucalyptus urophylla mitochondrion, complete genome.
DOI: 10.6084/m9.figshare.28379579.v1
title: Prediction results for nanoparticle' stability

description: Prediction results for nanoparticle's stability.
DOI: 10.6084/m9.figshare.5563210.v1
title: H2MM analysis of simulated smFRET data

description: H2MM analysis of simulated diffusion-based smFRET data:<br>1. .csv files - input files for the analysis include a. burst data files b. timestamps - files that include all photon ID and photon timestamps of all photons in each selected burst c. BG - table of BG rates of different photon streams in the simulations per each 2s of the measurement.<br>2. Matlab files - include all the H2MM analysis variables, as is explained in https://doi.org/10.6084/m9.figshare.5401561
DOI: 10.25402/pme.24190356.v1
title: Cost-effectiveness of alternative NTRK-testing strategies and histology-independent therapy entrectinib in 3 countries - supplementary material

description: Table S1. Test groups, proportional distribution umour type distribution before NTRK gene fusion testing, NTRK prevalence and tumour type distribution in entrectinib trials.Table S2. Sensitivity and specificity of immunohistochemistry (IHC) tests by tumour type.Table S3. Number of patients and parametric distributions with the lowest AIC for overall survival (OS) and time to treatment discontinuation (TTD)Table S4. Costs of biopsy, IHC, and RNA-NGS by tumour type and country.Table S5. Standard of care treatments by cancer typeTable S6. Costs of standard of care (SoC) treatment and adverse event treatment by tumour type and country.Table S7. Probability distributions used for probabilistic sensitivity analysis (PSA)Table S8. Incremental budget impact according to time horizon of national HTA guidelinesFigure S1. Model structureFigure S2. Results of the univariate sensitivity analysis<br>
DOI: 10.6084/m9.figshare.1555009.v1
title: Distance and Comparison Between Neighboring Trees

description: The data for this lab was collected at York Universit's woodlot at 4:30 P.M and was made through a contribution of efforts by Farkhanda, Olivia, Ratiba, Huda and Reena all of who began collecting such data by walking from the edge of the woodlot to the centre in a straight line. Every instance where an adult tree was approached, the distance to the nearest tree surrounding it was measured using transect measuring tape and recorded in meters. The distance of the first tree approached and its closest neighbour both had the distance at breast height measured in meters as well. In addition, the condition of each tree was also recorded on a scale of 0 to 2 where zero is a dead tree and 2 is a full canopy. This was measured with the help of human vision. These steps were then repeated nine more times for a total of 10 tree pairs. This data allowed the observers make comparisons between two trees who are growing in close proximity to eachother in order see a pattern amongst the data and to give a direction for further research studies. The conditions during the lab were in the shaded area within the woodlot. There was a slight breeze, the ground was cool and there was not any humidity.
DOI: 10.6084/m9.figshare.28449269.v1
title: <b>Synthetic Bone Marrow </b><b>Images</b><b> Augment Real Samples in Developing Acute Myeloid Leukemia Microscopy Classification Models</b>

description: Synthetic Bone marrow Smears using GANs
DOI: 10.6084/m9.figshare.19145741.v4
title: Ferroptosis

description: 尽管血栓事件是尿毒症的主要并发症
DOI: 10.6084/m9.figshare.7867937.v1
title: Supplementary Material for: Impact of Obesity on the Metabolic Control of Type 2 Diabetes: Results of the Turkish Nationwide Survey of Glycemic and Other Metabolic Parameters of Patients with Diabetes Mellitus (TEMD Obesity Study)

description: <b><i>Background:</i></b> Obesity is the main obstacle for metabolic control in patients with type 2 diabetes. Turkey has the highest prevalence of obesity and type 2 diabetes in Europe. The effect of obesity on the metabolic control, and the macro- and microvascular complications of patients are not apparent. <b><i>Objectives:</i></b> This nationwide survey aimed to investigate the prevalence of overweight and obesity among patients with type 2 diabetes and to search for the impact of obesity on the metabolic control of these patients. We also investigated the independent associates of obesity in patients with type 2 diabetes. <b><i>Methods:</i></b> We consecutively enrolled patients who were under follow-up for at least 1 year in 69 tertiary healthcare units in 37 cities. The demographic, anthropometric, and clinical data including medications were recorded. Patients were excluded if they were pregnant, younger than 18 years, had decompensated liver disease, psychiatric disorders interfering with cognition or compliance, had bariatric surgery, or were undergoing renal replacement therapy. <b><i>Results:</i></b> Only 10% of patients with type 2 diabetes (<i>n</i> = 4,648) had normal body mass indexes (BMI), while the others were affected by overweight (31%) or obesity (59%). Women had a significantly higher prevalence of obesity (53.4 vs. 40%) and severe obesity (16.6 vs. 3.3%). Significant associations were present between high BMI levels and lower education levels, intake of insulin, antihypertensives and statins, poor metabolic control, or the presence of microvascular complications. Age, gender, level of education, smoking, and physical inactivity were the independent associates of obesity in patients with type 2 diabetes. <b><i>Conclusion:</i></b> The TEMD Obesity Study shows that obesity is a major determinant of the poor metabolic control in patients with type 2 diabetes. These results underline the importance of prevention and management of obesity to improve health care in patients with type 2 diabetes. Also, the results point out the independent sociodemographic and clinical associates of obesity, which should be the prior targets to overcome, in the national fight with obesity.
DOI: 10.17632/7fkktknnm8
title: CTCF-2

description: CTCF-RNA-seq-2
DOI: 10.17632/g638wbpg56
title: Comparative Study on the Physiological and Psychological Restorative Effects of Multisensory Combinations in Natural and Urban Landscapes

description: Participants wore wearable devices to monitor their physiological reactions, such as electroencephalography (EEG)and heart rate variability (HRV). Additionally, participants were given the Perceived Restorativeness Scale（PRS) to evaluate the restoration effects subjectively.
DOI: 10.17632/mj6xsvbfrh
title: The dataset for research of "A coastal marine spatial use layout planning model by integrating multi-stakeholder competition and cooperation of land and sea"

description: The dataset for research of "A coastal marine spatial use layout planning model by integrating multi-stakeholder competition and cooperation of land and sea"
DOI: 10.17632/t9ys89vbk2
title: A decomposition analysis of the factors contributing to the increase in cataract cases in the Chinese population from 1990 to 2021

description: The "decomposition analysis" R code conducts a decomposition analysis of the increase in cataract cases in the Chinese population from 1990 to 2021. By adjusting the relevant parameters, the analysis can be performed separately for different genders. The Excel file "population data" contains raw data for the "population" dataframe in the R code, while "Age-specific prevalence rates" provides raw data for the "cataract_data" dataframe.
DOI: 10.6084/m9.figshare.12612230.v1
title: JVASP-70621 to JVASP-74961

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.22827652.v1
title: Bayesian inference for multidimensional graded response model using Pólya-Gamma latent variables

description: In the context of both cognitive and affective tests, items are usually designed to involve more than two responses, for which polytomous models are applicable. The purpose of this paper is to propose a highly effective Pólya-Gamma Gibbs sampling algorithm based on auxiliary variables to estimate the multidimensional graded response model that has been widely used in psychological, educational, and health-related assessment. The strategy is based on the Pólya Gamma family of distributions which provides a closed-form posterior distribution for logistic-based models. With the introduction of the two latent variables, the full conditional distributions are tractable, and consequently the Gibbs sampling is easy to implement. Nice features including empirical performance of the proposed methodology are demonstrated by simulation studies. Finally, two empirical data sets were analysed to demonstrate the efficiency and utility of the proposed method.
DOI: 10.6084/m9.figshare.28580027.v2
title: Molecular Property Prediction using Pretrained-BERT and Bayesian Active Learning

description: Raw data, BERT features, and computed Morgan fingerprints used in the preparation of manuscript "Molecular Property Prediction using Pretrained-BERT and Bayesian Active Learning: A Data-Efficient Approach to Drug Design"
DOI: 10.6084/m9.figshare.11106881.v2
title: Disentangling the environmental factors that shape genetic and phenotypic leaf trait variation in the tree Qualea grandiflora across the Brazilian savanna

description: Microssatellites and leaf traits datasets generated in the work Disentangling the environmental factors that shape genetic and phenotypic leaf trait variation in the tree <i>Qualea grandiflora </i>across the Brazilian savanna.<br>If you use the dataset please citate as: Buzatti RSO, Pfeilsticker TR, Muniz AC, Ellis VA, Souza RP, Lemos-Filho JP and Lovato MB (2019). Disentangling the Environmental Factors That Shape Genetic and Phenotypic Leaf Trait Variation in the Tree <i>Qualea grandiflora</i> Across the Brazilian Savanna. Front. Plant Sci. 10:1580. doi: 10.3389/fpls.2019.01580
DOI: 10.6084/m9.figshare.13359032.v1
title: Supplementary Material for: Die Rolle von Verhaltensexperimenten in der Behandlung von Zwangsstörungen: Ein Update zur effektiven Gestaltung und Durchführung in der Praxis

description: Das Ziel des Artikels ist es, den neuesten Stand zum effektiven Einsatz von Verhaltensexperimenten im Rahmen der Psychotherapie für Zwangsstörungen darzulegen. Dazu werden im ersten Teil die evidenzbasierten Psychotherapien zur Behandlung von Zwangsstörungen vorgestellt sowie die Probleme bei der Implementierung dieser Verfahren aufgezeigt. Dabei zeigt sich, dass trotz der guten Evidenzlage die Verfahren zu selten eingesetzt werden und so die Forschungs-Praxis-Lücke fördern. Im Anschluss werden die zugrundeliegenden Rationale zur Durchführung von Verhaltensexperimenten erläutert, in Bezug zu aktuellen Forschungsarbeiten gestellt und damit die Bedeutung von Verhaltensexperimenten in der Therapie von Zwangsstörungen unterstrichen. Daraus werden Empfehlungen für die effektive Umsetzung von Verhaltensexperimenten in der Praxis abgeleitet. Die Funktionsanalyse der zwangsspezifischen Symptomatik stellt das zentrale Element im Rahmen der Behandlung von Zwangsstörungen dar. Dabei müssen die Verhaltensexperimente an die individuell befürchtete Konsequenz bei Unterlassen von Ritualen und Sicherheitsverhalten (d.h. die furchtbasierte Überzeugung) ausgerichtet sein, um eine maximale Erwartungsverletzung zu ermöglichen. Klinische Fallbeispiele werden skizziert, anhand deren effektive Verhaltensexperimente anschaulich und praxisnah dargestellt werden. Abschließend werden noch Hinweise, Tipps und Fallstricke für Praktiker zur Durchführung von effektiven Verhaltensexperimenten beleuchtet und die Grenzen von Verhaltensexperimenten benannt.