cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/m7nz2jk8wb
title: Clonal dynamics after allogeneic haematopoietic cell transplantation using genome-wide somatic mutations

description: These are large files need to reproduce analysis in the manuscript "Clonal dynamics after allogeneic haematopoietic cell transplantation using genome-wide somatic mutations". These files are to be used alongside the code and smaller data files available at:
https://github.com/mspencerchapman/Clonal_dynamics_of_HSCT
The folders 'annot_files' and 'annot_files_no_dups' should be placed in the 'data' folder from the github repository.
The contents of the folder 'Targeted_sequencing_data' should be placed in the 'data/Targeted_sequencing_data' folder from the github repository. Note that the 'raw_model_output' data is not essential for most analyses as the 'posterior_cell_fracs.Rds' object is a combined and processed list of this data. To reproduce the phylogeny-aware targeted sequencing results from the Gibb's sampler, you will need to download the compressed data in 'Targeted_sequencing_data/data_by_baitset'.
The HDP_multi_chain.Rdata file should be placed in the data/HDP folder
The folder 'genomic_loci_reference_files' (which is 8.5Gb when uncompressed) is only needed for one analysis to create Extended Data Fig. 5c. and therefore need only be downloaded if trying to reproduce this analysis. If used, it should again be place in the 'data' folder of the github repository.
DOI: 10.6084/m9.figshare.28381112.v2
title: Dataset for Exploring terrain-precipitation relationships with interpretable AI for advancing future climate projections

description: Dataset for <b>Exploring terrain-precipitation relationships with interpretable AI for advancing future climate projections</b>, including the terrain and precipitation dataset in Asia.
DOI: 10.6084/m9.figshare.5459299.v4
title: PPG-BP Database

description: The peer-reviewed paper associated with this dataset has now been published in Scientific Data, and can be accessed here: https://www.nature.com/articles/sdata201820. Please cite this when using the<br> dataset. <br> Open clinical trial data provide a valuable opportunity for researchers worldwide to assess new hypotheses, validate published results, and collaborate for scientific advances in medical research. Here, we present a health dataset for the non-invasive detection of cardiovascular disease (CVD), containing 657 data records from 219 subjects. The dataset covers an age range of 20–89 years and records of diseases including hypertension and diabetes. Data acquisition was carried out under the control of standard experimental conditions and specifications. This dataset can be used to carry out the study of photoplethysmograph (PPG) signal quality evaluation and to explore the intrinsic relationship between the PPG waveform and cardiovascular disease to discover and evaluate latent characteristic information contained in PPG signals. These data can also be used to study early and noninvasive screening of common CVD such as hypertension and other related CVD diseases such as diabetes.
DOI: 10.6084/m9.figshare.25033916.v1
title: <b>The demographic basis of population growth: a 32-year transient life table response experiment </b>

description: This data set was used to examine changes in demographic rates and population size in a population of Columbian ground squirrels (<i>Urocitellus columbianus</i>) studied over 32 years (1992-2023), in Alberta, Canada. The data stems from a long-term research project initiated by Jan O Murie and later maintained by F Stephen Dobson and Vincent A Viblanc. The study is now part of the long-term Studies in Ecology and Evolution (SEE-Life) program of the CNRS.
DOI: 10.17632/5btz7hh399
title: Radiative view factor correlations in particulate media from ray tracing simulations and data-driven modeling

description: Datasets for figures included in the results section in our recently accepted publication at International Journal of Heat and Mass Transfer: https://doi.org/10.1016/j.ijheatmasstransfer.2023.124250
DOI: 10.17632/89yn2xtm4s
title: Raw data for: GRADE and CINeMA showed moderate to substantial concordance in the evaluation of certainty of the evidence

description: Since 2014, two approaches have been developed to assess the certainty of the evidence of network meta-analysis results: the approach developed by the Grading of Recommendations Assessment, Development and Evaluation (GRADE) and the Confidence in Network Meta-Analysis (CINeMA) approach, inspired by the methodology developed by the GRADE Working Group.
GRADE and CINeMA were applied to four networks of different sizes and structures related to different outcomes in different clinical conditions and settings by 13 evaluators.
All domains in CINeMA have three levels of ratings (i.e. no concern, some concerns or major concerns). GRADE has also three levels of ratings (i.e. not serious, serious and very serious) except for two domains: publication bias has two (i.e. undetectable versus strongly detectable), and imprecision has four ratings (i.e. not serious, serious, very serious and very very serious).
DOI: 10.17632/bjgghsp5gn
title: Development of Morphea in Patients on Biologic Therapies: A Systematic Review

description: Supplemental File 1: Search Strategy Supplemental File 2: PRISMA Checklist
DOI: 10.17632/jc4mmnvcdk
title: Yoga for all: A Comprehensive Collection of Yoga Images and Videos dataset

description: The dataset comprises both images and videos depicting right and wrong postures for a variety of Yoga asanas. The focus of the dataset is on 10 specific Yoga postures, namely Anantasana, Ardhakati Chakrasana, Bhujangasana, Kati Chakrasana, Marjariasana, Parvatasana, Sarvangasana, Tadasana, Vajrasana, and Viparita Karani.

The Image dataset comprises a total of 11,344 compressed images (256 × 256 dimension) and is organized into 10 subfolders, each corresponding to a specific Yoga asana. Within each subfolder, there are two additional folders labeled "Right Steps" and "Wrong Steps". The "Right Steps" folder contains several subfolders, each representing a specific step in the right sequence of the Yoga asana and displaying the corresponding images. On the other hand, the "Wrong Steps" folder includes multiple subfolders, each showing images of an wrong steps in the sequence of the Yoga asana.

The Yoga asana video dataset consists of 8 videos for each posture, comprising 4 videos demonstrating the right posture from 4 different angles and 4 videos exhibiting the wrong posture from 4 different angles. This dataset includes a total of 80 compressed videos for 10 Yoga asanas, with 40 videos demonstrating the right postures captured from 4 different angles, and 40 videos illustrating the wrong postures from 4 different angles.

The dataset has advantages for various groups, such as app developers, machine learning researchers, Yoga instructors, and Yoga practitioners. Machine learning researchers can utilize this dataset to train computer vision algorithms in recognizing and categorizing various yoga postures automatically. App developers can use the dataset to generate yoga apps that present users with visual guidance on executing each posture and keeping track of their progress.
DOI: 10.17632/nddrc4wkcc
title: Systemic_risk_ports_datasets

description: This data + Jupyter Notebook allows one to reproduce the results + plots of the paper "Verschuur, Koks and Hall (2023), Systemic risks from climate-related disruptions at ports, Nature Climate Change". It includes:
-Jupyter notebook to read data, perform analysis, reproduce plots in paper, and perform additional analysis for specific countries and ports 
-Input data to perform analysis
-Output data of analysis that can be used without re-running the notebook

In general all data are structured according to the systemic risks analysed: maritime transport network, maritime trade network, global supply chain network. 

For any questions or comments: jasper.verschuur@eci.ox.ac.uk
DOI: 10.6084/m9.figshare.11787243.v2
title: Genotypic distribution of three polymorphisms of IL-10 in patients with PEX, PEXG, and POAG.xlsx

description: Genotypic distribution of three polymorphisms -592C/A (rs1800872), -819C/T (rs1800871) and -1082A/G (rs1800896) of IL-10 gene promoter in patients with pseudoexfoliation syndrome (PEX), pseudoexfoliative glaucoma (PEXG), and primary open-angle glaucoma (POAG)
DOI: 10.6084/m9.figshare.29146361.v1
title: 基于动态土地利用变化的改进SWAT模型对秦江流域水土流失的模拟

description: 本研究旨在提高 SWAT 模型在土地利用和土地覆盖 （LULC） 快速变化下对秦江流域 （QJRB） 径流和泥沙负荷的模拟能力。
DOI: 10.6084/m9.figshare.5948416.v1
title: Noheteroafter filter.hmp.txt

description: SNP sequence data - Nebraska Wheat Lines
DOI: 10.17632/6xg5b8yrxn
title: Hypoglycemia Promotes Breakdown of the Blood-Retinal Barrier and Retinal Vascular Leakage in Diabetic Mice

description: RNAseq, Western blotting raw data
DOI: 10.17632/9ns6gmtz3j
title: Which decentralised trial activities are reported in clinical trial protocols of drug trials initiated in 2019-2020? A cross-sectional study in ClinicalTrials.gov

description: This Excel file contains data used for the research that is described in the manuscript entitled: "Which decentralised trial activities are reported in clinical trial protocols of drug trials initiated in 2019-2020? A cross-sectional study in ClinicalTrials.gov" by Amos J. de Jong,1 Renske J. Grupstra,1 Yared Santa-Ana-Tellez,1 Mira G.P. Zuidgeest,2 Anthonius de Boer,1,3 Helga Gardarsdottir,1,4,5 On behalf of the Trials@Home Consortium6

1 Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
2 Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands
3 Dutch Medicines Evaluation Board, Utrecht, the Netherlands
4 Department of Clinical Pharmacy, Division Laboratory and Pharmacy, University Medical Center Utrecht, Utrecht, The Netherlands
5 Faculty of Pharmaceutical Sciences, University of Iceland, Reykjavik, Iceland
6 trialsathome.com

Data content: 
The file contains data on the reporting of decentralised and on-site conduct of predefined trial activities (i.e., participant outreach, pre-screening, pre-screening through medical records, screening, consenting, asynchronous communication with the participant, participant training, investigational medicinal product supply, investigational medicinal product adherence monitoring, clinical trial monitoring, and data collection) and general clinical trial characteristics of the 254 analysed protocols. 

The methodology and search strategy are explained in the manuscript text.
DOI: 10.17632/9sxjgcfwjc
title: Dataset: IP Address Geographic Profiles

description: This dataset provides geolocation information for a collection of randomly generated IPv4 addresses. Each entry includes city, region, country, postal code, latitude, longitude, time zone, ISP, organization, and autonomous system. This dataset offers insights into the geographic distribution and diversity of IP addresses across the globe, making it valuable for various analytical and research purposes, including network analysis, cybersecurity, and geographical data exploration.
DOI: 10.6084/m9.figshare.27322671.v1
title: Timetable

description: This is a Excel spreadsheet of Thonya Monkhe's weekly timetable
DOI: 10.6084/m9.figshare.12858122.v1
title: R0186_20170901a_videos

description: Rat 0186, skilled reaching data collected on 9/1/2017 in Leventhal laboratory by Alexandra Bova
DOI: 10.17632/48m4scp8jx
title: Climate uncertainty in climate impact studies

description: These data allow the full reproduction of Schwarzwald and Lenssen, "The Importance of Internal Climate Variability in Climate Impact Projections," currently accepted at PNAS. All code used in this study is available at https://github.com/ks905383/iv_impacts. All data used in this study are either available from this repository, or can be generated from the code itself.

Uncertainty in climate projections is driven by three components: scenario uncertainty, inter-model uncertainty, and internal variability. Although socioeconomic climate impact studies increasingly take into account the first two components, little attention has been paid to the role of internal variability, though underestimating this uncertainty may lead to underestimating the socioeconomic costs of climate change. Using large ensembles from seven Coupled General Circulation Models with a total of 414 model runs, we partition the climate uncertainty in classic dose-response models relating county-level corn yield, mortality, and per-capita GDP to temperature in the continental United States. The partitioning of uncertainty depends on the time frame of projection, the impact model, and the geographic region. Internal variability represents more than 50% of the total climate uncertainty in certain projections, including mortality projections for the early 21st century, though its relative influence decreases over time. We recommend including uncertainty due to internal variability for many projections of temperature-driven impacts, including early- and mid-century projections, projections in regions with high internal variability such as the Upper Midwest United States, and for impacts driven by non-linear relationships.
DOI: 10.17632/52z36kyt4g
title: Improving the quality of atopic dermatitis epidemiological research in the United States - A systematic review of disease definitions and related content in national surveys

description: Background: Epidemiologic study of atopic dermatitis has been critical to improve our understanding of disease burden and to identify numerous atopic and non-atopic comorbidities. Despite widespread use, atopic dermatitis case definitions and related content in population-based surveys have not been comprehensively evaluated. Objective: To characterize the state of population-based health-related surveys in the United States that include atopic dermatitis or eczema. Methods: We conducted a systematic review searching Ovid MEDLINE for population-based surveys to study atopic dermatitis in the United States from database inception through February 23, 2024. Results: Of 916 articles screened, 24 articles were included for analysis which included 11 independent surveys. Most surveys relied on self-report of physician diagnosis of atopic dermatitis or the International Study of Asthma and Allergies in Childhood (ISAAC) criteria, including a modified version of the ISAAC criteria which has not been validated. National surveys yielded the largest samples and were typically repeated annually, but some national surveys did not include questions on atopic dermatitis in recent years. Conclusion: National surveys do not use standardized definitions to identify atopic dermatitis and do not adequately capture key aspects of atopic dermatitis burden. Future population-based surveys should be designed to fill these important gaps.
DOI: 10.6084/m9.figshare.25917628.v1
title: snRNA-seq, Primary-Recurrent GBM (Mikolajewicz Cohort)

description: <b>Summary.</b><br>10 primary GBM and 8 recurrent GBM samples (14/18 matched) profiled using single nucleus RNA- sequencing (sci-RNA-seq3 protocol).<br><b>Data Format.</b><br>Data is provided as preprocessed dataset, stored in Seurat Object.<br><b>Sample processing, sci-RNA-seq3 library generation, and sequencing</b><br>Snap-frozen patient pGBM and rGBM tissues were chopped with a razor blade or scissors before nucleus isolation. Nuclei extraction and fixation were performed as previously described (Cao 2019), except for the use of a modified CST lysis buffer50 plus 1% of SUPERase-In RNase Inhibitor (Invitrogen, #AM2696). Lysis time and washing steps were further optimized based on human GBM tissue. Nuclei quality was checked with DAPI and Wheat Germ Agglutinin (WGA) staining. Sci-RNA-seq3 libraries were generated as previously described49 using three-level combinatorial indexing. The final libraries were sequenced on Illumina NovaSeq as follows: read 1: 34bp, read 2: &gt;=69bp, index 1: 10bp, index 2: 10bp.<br><b>Demultiplexing and read alignments.</b><br>Raw sequencing reads were first demultiplexed based on i5/i7 PCR barcodes. FASTQ files were then processed using the sci-RNA-Seq3 pipeline. After barcodes and unique molecular identifiers (UMIs) were extracted from the read1 of FASTQ files, read alignment was performed using STAR short-read aligner (v2.5.2b) with the human genome (hg19) and Gencode v24 gene annotations. After removing duplicate reads based on UMI, barcode, chromosome and alignment position, reads were summarized into a count matrix of M genes × N nuclei.<br><b>Filtering, normalization, integration, and dimensional reduction.</b><br>Raw count matrices were loaded into a Seurat object (version 4.0.1) and filtered to retain cells with (i) 200 – 9000 recovered genes per cell, (ii) less than 60% mitochondrial content, and (iii) unmatched rate within 3 median absolute deviations of the median. To normalize count matrix, we adopted the modeling framework previously described and implemented in sctransform (R Package, version 0.3.2). In brief, count data were modelled by regularized negative binomial regression, using sequencing depth as a model covariate to regress out the influence of technical effects, and Pearson residuals were used as the normalized and variance stabilized biological signal for downstream analysis. Data from each patient were integrated with the reciprocal PCA method (Seurat) using the top 2000 variable features. PCA was performed on the integrated dataset, and the top N components that accounted for 90% of the observed variance were used for UMAP embedding, RunUMAP(max_components = 2, n_neighbours = 50, min_dist = 01, metric = cosine).<br><b>Contact.</b><br>Contact Dr. Nicholas Mikolajewicz regarding any questions about the data or analysis (n.mikolajewicz@utoronto.ca)
DOI: 10.17632/hc5rj27m8m
title: Anxiety sensitivity and heart rate variability study

description: This data was collected for Dr. Bethany Gourley's dissertation to examine the relationship between anxiety sensitivity and heart rate variability. Participants were assessed for anxiety sensitivity via ASI-3 during online screening and the in-person appointment. Their heart rate was measured at baseline and during three counterbalanced behavioral stress paradigms: physical (hyperventilation), cognitive (PASAT), and social (Trier Social Stress Task).

Attached is an Excel with the cleaned participant-level data used by the dissertation, with outputs from the Kubios HRV software. Two R Markdown files (code used for the manuscript, in Word doc form) are also attached, one detailing the power/sensitivity analysis and the other detailing the full code used for the Tu et al. (2023) paper.

For the raw heart rate Polar data, please email Joseph at jtu@emich.edu
DOI: 10.6084/m9.figshare.13720660.v1
title: Supplementary Material for: What Are the Most Challenging Aspects of Inflammatory Bowel Disease? An International Survey of Gastroenterologists Comparing Developed and Developing Countries

description: <b><i>Background and Aims:</i></b> As inflammatory bowel disease (IBD) becomes more prevalent, the challenges that gastroenterologists face in managing these patients evolve. We aimed to describe the most important challenges facing gastroenterologists from around the world and compare these between those working in developed and developing countries. <b><i>Methods:</i></b> An online questionnaire was developed, and a link distributed to gastroenterologists. Data were analyzed descriptively using Friedman and Wilcoxon matched-pair signed rank tests to compare rankings for responses. Mann-Whitney <i>U</i> tests were used to compare rankings between responses from gastroenterologists from developed and developing countries. Lower scores reflected greater challenges. <b><i>Results:</i></b> Of 872 who started, 397 gastroenterologists (45.5%) completed the survey. Respondents represented 65 countries (226 [56.9%] from developed countries). Overall, the challenge ranked most important (smallest number) was increasing IBD prevalence (13.6%). There were significant differences in mean ranking scores for many simple aspects of care for those from developing countries compared to providers from developed countries, such as access to simple IBD treatments (5.52 vs. 6.02, <i>p</i> = 0.01), access to anti-TNF drugs including dose escalation (3.33 vs. 3.93, <i>p</i> &lt; 0.01), access to good stoma care (2.57 vs. 3.03, <i>p</i> &lt; 0.001), access to therapeutic drug monitoring (1.47 vs. 1.84, <i>p</i> &lt; 0.001), and access to care for people from low socioeconomic status (2.77 vs. 3.37, <i>p</i> &lt; 0.001). <b><i>Conclusions:</i></b> Increasing IBD prevalence is seen by gastroenterologists as the greatest challenge facing them. There are significant differences between the IBD challenges facing gastroenterologists from developed and developing countries that reflect inequities in access to health care.
DOI: 10.6084/m9.figshare.1593083.v1
title: Effect of Crowding and Plant Height on Insect Abundance

description: This experiment was done at the grasslands at york university, Toronto Canada over the course of two days between the hours of 2:30 PM and 5:30 PM. On day one the weather was approximately 13 Degrees C and mostly sunny and day 2 was partly cloudy and approximately 10 Degrees C. In this experiment 40 plastic bowls (each day totaling 80 bowls), all of the same colour were placed randomly within the grasslands and filled at least one quarter the way full with soapy water. After all bowls were placed a 1m by 1m quadrat was placed around each bowl and the crowding of living or dead plant matter within the quadrat was estimated from 0-4 (0 meaning no plant biomass 4 meaning no ground could be seen through the plants). Afterwards, the average plant height was estimated with the use of a transect. The tallest and shortest plants were measured, the estimation was made based upon how much area the talest and shortest plants took up within the quadrat and the measurement was recorded in inches. after all measurements had been taken, the bowls were left for 2 hours. When the 2 hours were up the bowls were collected and the number of insects caught in the bowls were counted and recorded. This experiment was conducted to see how the abundance of insects were effected by plant height and plant crowding. This data can be useful to see which, crowding or height, effects insect abundance more. It is also interesting to note that even though the temperatures for both days of the experiment were close, only 3 degree difference, there were significantly fewer insects on the second day of testing.
DOI: 10.17632/27fcgy62fy
title: Data for: Measurement invariance of the Positive Gains Scale in families of children with and without disabilities

description: Combined dataset of mothers of children with and without disabilities.
DOI: 10.17632/32f7nxc32j
title: Floating car data 201805Fuzhou

description: Floating car DatA in an area of the Gulou Zone in Fuzhou, China. The area is the core center of Fuzhou and is densely populated. Floating car trajectories were collected from May 5th, 2018 and the data contain 6,402,027 GPS sample points of 7073 taxes (Dataset, 2020). The trajectories comprise from 10s to 60s sample points with an average sample rate of 20s.