cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19518483.v1
title: Additional file 4 of Genomic epidemiology of the Los Angeles COVID-19 outbreak and the early history of the B.1.43 strain in the USA

description: Additional file 4: Table S4. B.1.43 lineages found among the GISAID and UCLA Health SARS-CoV-2 genomes.
DOI: 10.6084/m9.figshare.19518225
title: Additional file 2 of The effectiveness of governmental nonpharmaceutical interventions against COVID-19 at controlling seasonal influenza transmission: an ecological study

description: Additional file 2: Table S4. Confidence intervals (Median (P0.025, P0.975)) of the spearman correlation coefficients of NPIs with different lag days and the influenza suppression index.
DOI: 10.6084/m9.figshare.19518474
title: Additional file 1 of Genomic epidemiology of the Los Angeles COVID-19 outbreak and the early history of the B.1.43 strain in the USA

description: Additional file 1: Table S1. Collection dates and quality control for 260 patient samples.
DOI: 10.6084/m9.figshare.19518474.v1
title: Additional file 1 of Genomic epidemiology of the Los Angeles COVID-19 outbreak and the early history of the B.1.43 strain in the USA

description: Additional file 1: Table S1. Collection dates and quality control for 260 patient samples.
DOI: 10.6084/m9.figshare.19518477.v1
title: Additional file 2 of Genomic epidemiology of the Los Angeles COVID-19 outbreak and the early history of the B.1.43 strain in the USA

description: Additional file 2: Table S2. Lineage assignment for 142 high quality patient samples from UCLA health.
DOI: 10.6084/m9.figshare.19518483
title: Additional file 4 of Genomic epidemiology of the Los Angeles COVID-19 outbreak and the early history of the B.1.43 strain in the USA

description: Additional file 4: Table S4. B.1.43 lineages found among the GISAID and UCLA Health SARS-CoV-2 genomes.
DOI: 10.6084/m9.figshare.19518641
title: Additional file 10 of Proteomic landscape subtype and clinical prognosis of patients with the cognitive impairment by Japanese encephalitis infection

description: Additional file 10: Table S4. Upregulated proteins in JE2 comparing with JE1.
DOI: 10.5281/zenodo.10117944
title: Cine and real-time free-breathing CMR at rest and under exercise stress of healthy volunteers

description: The dataset consists of cine and real-time images from 15 healthy volunteers (7 males; 8 females). All images were acquired in supine position using a 32-channel cardiac surface receiver coil at 3 T (Skyra, Siemens Healthineers, Germany).
Conventional imaging at rest included a balanced steady-state free precession (bSSFP) ECG-gated cine sequence to create a short-axis stack covering the entire heart including both ventricles and atria. Real-time CMR data acquisition was performed during free-breathing and without ECG-synchronization at rest and under two different levels of exercise stress.
The dataset includes automatically created contours (comDL) using Medis (version 4.0.56.4, QMass® 8.1, Medical Imaging Systems, Leiden, Netherlands) for all images, as well as manually corrected (mc) contours based on the comDL contours for all cine and real-time measurements at rest and under exercise stress for end-diastolic (ED) and end-systolic phases (ES).
The dataset also includes segmentation masks in NIfTI format for cine and real-time CMR at rest and under exercise stress created with nnU-Net (DOI:10.1038/s41592-020-01008-z) with freely available weights based trained on the dataset of the cardiac segmentation challenge "Automated Cardiac Segmentation Challenge" (ACDC) (DOI:10.1109/TMI.2018.2837502).
To minimize the influence of respiratory motion on clinical measures, images in the ED and ES phase of the cardiac cycle during end-expiration were manually selected for each slice. The dataset includes indices for these images for real-time CMR measurements at rest and under exercise stress. For intra-observer variability, manually corrected contours for the derivation of the clinical measures were created three to six months after the initial segmentation. Single images in the ED and ES phase during end-expiration were once again chosen from each slice.
Image data is provided in a file format used by the BART toolbox. DOI:10.5281/zenodo.7110562
DOI: 10.6084/m9.figshare.19518644
title: Additional file 11 of Proteomic landscape subtype and clinical prognosis of patients with the cognitive impairment by Japanese encephalitis infection

description: Additional file 11: Table S5. Downregulated proteins in JE2 comparing with JE1
DOI: 10.5281/zenodo.10639198
title: 6-ton wheel loader short Y-cycle data for 440 seconds loading of gravel

description: The data contains pressures, flow rates, hydraulic cylinder piston positions, diesel engine RPM and fuel rate, machine speed and bunch of derived variables for a 6-ton wheel loader like machine. The work cycle is short Y-cycle for loading gravel, and the measurement lasts 440 seconds. Data is described in a separate PDF file. Data can be opened by Matlab 2006b or later.
DOI: 10.5281/zenodo.10639199
title: 6-ton wheel loader short Y-cycle data for 440 seconds loading of gravel

description: The data contains pressures, flow rates, hydraulic cylinder piston positions, diesel engine RPM and fuel rate, machine speed and bunch of derived variables for a 6-ton wheel loader like machine. The work cycle is short Y-cycle for loading gravel, and the measurement lasts 440 seconds. Data is described in a separate PDF file. Data can be opened by Matlab 2006b or later.
DOI: 10.6084/m9.figshare.19518225.v1
title: Additional file 2 of The effectiveness of governmental nonpharmaceutical interventions against COVID-19 at controlling seasonal influenza transmission: an ecological study

description: Additional file 2: Table S4. Confidence intervals (Median (P0.025, P0.975)) of the spearman correlation coefficients of NPIs with different lag days and the influenza suppression index.
DOI: 10.6084/m9.figshare.19518641.v1
title: Additional file 10 of Proteomic landscape subtype and clinical prognosis of patients with the cognitive impairment by Japanese encephalitis infection

description: Additional file 10: Table S4. Upregulated proteins in JE2 comparing with JE1.
DOI: 10.6084/m9.figshare.19518671
title: Additional file 8 of Proteomic landscape subtype and clinical prognosis of patients with the cognitive impairment by Japanese encephalitis infection

description: Additional file 8: Table S2. Upregulated proteins related with JE.
DOI: 10.6084/m9.figshare.19518671.v1
title: Additional file 8 of Proteomic landscape subtype and clinical prognosis of patients with the cognitive impairment by Japanese encephalitis infection

description: Additional file 8: Table S2. Upregulated proteins related with JE.
DOI: 10.6084/m9.figshare.19518674
title: Additional file 9 of Proteomic landscape subtype and clinical prognosis of patients with the cognitive impairment by Japanese encephalitis infection

description: Additional file 9: Table S3. Downregulated proteins related with JE.
DOI: 10.5281/zenodo.10117943
title: Cine and real-time free-breathing CMR at rest and under exercise stress of healthy volunteers

description: The dataset consists of cine and real-time images from 15 healthy volunteers (7 males; 8 females). All images were acquired in supine position using a 32-channel cardiac surface receiver coil at 3 T (Skyra, Siemens Healthineers, Germany).

Conventional imaging at rest included a balanced steady-state free precession (bSSFP) ECG-gated cine sequence to create a short-axis stack covering the entire heart including both ventricles and atria. Real-time CMR data acquisition was performed during free-breathing and without ECG-synchronization at rest and under two different levels of exercise stress.

The dataset includes automatically created contours (comDL) using Medis (version 4.0.56.4, QMass® 8.1, Medical Imaging Systems, Leiden, Netherlands) for all images, as well as manually corrected (mc) contours based on the comDL contours for all cine and real-time measurements at rest and under exercise stress for end-diastolic (ED) and end-systolic phases (ES).

The dataset also includes segmentation masks in NIfTI format for cine and real-time CMR at rest and under exercise stress created with nnU-Net (DOI:10.1038/s41592-020-01008-z) with freely available weights based trained on the dataset of the cardiac segmentation challenge "Automated Cardiac Segmentation Challenge" (ACDC) (DOI:10.1109/TMI.2018.2837502).

To minimize the influence of respiratory motion on clinical measures, images in the ED and ES phase of the cardiac cycle during end-expiration were manually selected for each slice. The dataset includes indices for these images for real-time CMR measurements at rest and under exercise stress. For intra-observer variability, manually corrected contours for the derivation of the clinical measures were created three to six months after the initial segmentation. For inter-observer variability, manually corrected contours for the derivation of the clinical parameters were created for the first five volunteers by a second reader with experience in cardiac segmentation. Single images in the ED and ES phase during end-expiration were once again chosen from each slice.

Image data is provided in a file format used by the BART toolbox. DOI:10.5281/zenodo.7110562
DOI: 10.5281/zenodo.10639392
title: Cine and real-time free-breathing CMR at rest and under exercise stress of healthy volunteers

description: The dataset consists of cine and real-time images from 15 healthy volunteers (7 males; 8 females). All images were acquired in supine position using a 32-channel cardiac surface receiver coil at 3 T (Skyra, Siemens Healthineers, Germany).

Conventional imaging at rest included a balanced steady-state free precession (bSSFP) ECG-gated cine sequence to create a short-axis stack covering the entire heart including both ventricles and atria. Real-time CMR data acquisition was performed during free-breathing and without ECG-synchronization at rest and under two different levels of exercise stress.

The dataset includes automatically created contours (comDL) using Medis (version 4.0.56.4, QMass® 8.1, Medical Imaging Systems, Leiden, Netherlands) for all images, as well as manually corrected (mc) contours based on the comDL contours for all cine and real-time measurements at rest and under exercise stress for end-diastolic (ED) and end-systolic phases (ES).

The dataset also includes segmentation masks in NIfTI format for cine and real-time CMR at rest and under exercise stress created with nnU-Net (DOI:10.1038/s41592-020-01008-z) with freely available weights based trained on the dataset of the cardiac segmentation challenge "Automated Cardiac Segmentation Challenge" (ACDC) (DOI:10.1109/TMI.2018.2837502).

To minimize the influence of respiratory motion on clinical measures, images in the ED and ES phase of the cardiac cycle during end-expiration were manually selected for each slice. The dataset includes indices for these images for real-time CMR measurements at rest and under exercise stress. For intra-observer variability, manually corrected contours for the derivation of the clinical measures were created three to six months after the initial segmentation. For inter-observer variability, manually corrected contours for the derivation of the clinical parameters were created for the first five volunteers by a second reader with experience in cardiac segmentation. Single images in the ED and ES phase during end-expiration were once again chosen from each slice.

Image data is provided in a file format used by the BART toolbox. DOI:10.5281/zenodo.7110562
DOI: 10.6084/m9.figshare.25196030.v1
title: Supplementary Material for: Exploring the methodological approaches of studies on radiographic databases used in cariology to feed AI: A Systematic Review

description: Introduction: A growing number of studies on diagnostic imaging show superior efficiency and accuracy of computer-aided diagnostic systems compared to certified dentists. This methodological systematic review aims to evaluate the different methodological approaches used by studies focusing on machine learning and deep learning and that have used radiographic databases to classify, detect, and segment dental caries.
Methods: The protocol was registered in PROSPERO before data collection (CRD42022348097). Literature research was performed in MEDLINE, Embase, IEEE Xplore, and Web of Science until December 2022, without language restrictions. Studies and surveys using a dental radiographic database for the classification, detection, or segmentation of carious lesions were sought. Records deemed eligible were retrieved and further assessed for inclusion by two reviewers who resolved any discrepancies through consensus. A third reviewer was consulted when any disagreements or discrepancies persist between the two reviewers.
After data extraction, the same reviewers assessed the methodological quality using the CLAIM and QUADAS-AI checklists. 
Results: After screening 325 articles, 35 studies were eligible and included. The bitewing was the most commonly used radiograph (n=17) at the time when detection (n=15) was the most explored computer vision task. The sample sizes used ranged from 95 to 38437, while the augmented training set ranged from 300 to 315786. Convolutional neural network (CNN) was the most commonly used model. The mean completeness of CLAIM items was 49 % (SD ± 34%). The applicability of the CLAIM checklist items revealed several weaknesses in the methodology of the selected studies: most of the studies were monocentric, and only 9% of them used an external test set when evaluating the model’s performance. The QUADAS-AI tool revealed that only 43% of the studies included in this systematic review were at low risk of bias concerning the standard reference domain. 
Conclusion: This review demonstrates that the overall scientific quality of studies conducted to feed AI algorithms is low. Some improvement in the design and validation of studies can be made with the development of a standardized guideline for the reproducibility and generalizability of results and, thus, their clinical applications.
DOI: 10.6084/m9.figshare.19518644.v1
title: Additional file 11 of Proteomic landscape subtype and clinical prognosis of patients with the cognitive impairment by Japanese encephalitis infection

description: Additional file 11: Table S5. Downregulated proteins in JE2 comparing with JE1
DOI: 10.6084/m9.figshare.19518674.v1
title: Additional file 9 of Proteomic landscape subtype and clinical prognosis of patients with the cognitive impairment by Japanese encephalitis infection

description: Additional file 9: Table S3. Downregulated proteins related with JE.
DOI: 10.5281/zenodo.10639877
title: Data and code - Emergence of a resource acquisition tradeoff at the community scale during environmental change

description: Data and code for reproducing statistical results and generating figures in Emergence of a resource acquisition tradeoff at the community scale during environmental change submitted in 2024
DOI: 10.5281/zenodo.10639878
title: Data and code - Emergence of a resource acquisition tradeoff at the community scale during environmental change

description: Data and code for reproducing statistical results and generating figures in Emergence of a resource acquisition tradeoff at the community scale during environmental change submitted in 2024
DOI: 10.6084/m9.figshare.23714082
title: Additional file 2 of Integrative analysis of the ST6GALNAC family identifies GATA2-upregulated ST6GALNAC5 as an adverse prognostic biomarker promoting prostate cancer cell invasion

description: Additional file 2: Table S2. The sequences of siRNAs.
DOI: 10.6084/m9.figshare.23714097
title: Additional file 7 of Integrative analysis of the ST6GALNAC family identifies GATA2-upregulated ST6GALNAC5 as an adverse prognostic biomarker promoting prostate cancer cell invasion

description: Additional file 7: Table S3. The antibody list.
DOI: 10.6084/m9.figshare.23714100.v1
title: Additional file 8 of Integrative analysis of the ST6GALNAC family identifies GATA2-upregulated ST6GALNAC5 as an adverse prognostic biomarker promoting prostate cancer cell invasion

description: Additional file 8: Table S4. The list of reagents and kits.
DOI: 10.6084/m9.figshare.12177858
title: Additional file 1 of BAMscale: quantification of next-generation sequencing peaks and generation of scaled coverage tracks

description: Additional file 1: Table S1. Detailed list of processed samples. Table S2. Colocalization statistics of ATAC-seq peaks with &gt; 3x opening and &lt; 3x opening induced by camptothecin (CPT) treatment in human leukemia CCRF-CEM SLFN11 wild type and KO. Table S3. Differential expression analysis results between Top1mt wild type and knockout murine liver tumor samples.
DOI: 10.6084/m9.figshare.12177858.v1
title: Additional file 1 of BAMscale: quantification of next-generation sequencing peaks and generation of scaled coverage tracks

description: Additional file 1: Table S1. Detailed list of processed samples. Table S2. Colocalization statistics of ATAC-seq peaks with &gt; 3x opening and &lt; 3x opening induced by camptothecin (CPT) treatment in human leukemia CCRF-CEM SLFN11 wild type and KO. Table S3. Differential expression analysis results between Top1mt wild type and knockout murine liver tumor samples.
DOI: 10.6084/m9.figshare.12703701.v1
title: Additional file 12 of Long non-coding RNA H19 promotes colorectal cancer metastasis via binding to hnRNPA2B1

description: Additional file 12: Table S4. Identifed the proteins binding to H19 by LC-MS
DOI: 10.6084/m9.figshare.23714097.v1
title: Additional file 7 of Integrative analysis of the ST6GALNAC family identifies GATA2-upregulated ST6GALNAC5 as an adverse prognostic biomarker promoting prostate cancer cell invasion

description: Additional file 7: Table S3. The antibody list.
DOI: 10.6084/m9.figshare.23714079.v1
title: Additional file 1 of Integrative analysis of the ST6GALNAC family identifies GATA2-upregulated ST6GALNAC5 as an adverse prognostic biomarker promoting prostate cancer cell invasion

description: Additional file 1: Table S1. The primers for plasmid construction, qRT-PCR and ChIP.
DOI: 10.5281/zenodo.10639901
title: A dataset of regressions in web applications detected by end‑to‑end tests - reproduction package

description: Reproduction package for the paper "A dataset of regressions in web applications detected by end‑to‑end tests" publised in the Software Quality Journal.
DOI: 10.5281/zenodo.10639902
title: A dataset of regressions in web applications detected by end‑to‑end tests - reproduction package

description: Reproduction package for the paper "A dataset of regressions in web applications detected by end‑to‑end tests" publised in the Software Quality Journal.
DOI: 10.6084/m9.figshare.23714079
title: Additional file 1 of Integrative analysis of the ST6GALNAC family identifies GATA2-upregulated ST6GALNAC5 as an adverse prognostic biomarker promoting prostate cancer cell invasion

description: Additional file 1: Table S1. The primers for plasmid construction, qRT-PCR and ChIP.
DOI: 10.6084/m9.figshare.23714082.v1
title: Additional file 2 of Integrative analysis of the ST6GALNAC family identifies GATA2-upregulated ST6GALNAC5 as an adverse prognostic biomarker promoting prostate cancer cell invasion

description: Additional file 2: Table S2. The sequences of siRNAs.
DOI: 10.6084/m9.figshare.23714100
title: Additional file 8 of Integrative analysis of the ST6GALNAC family identifies GATA2-upregulated ST6GALNAC5 as an adverse prognostic biomarker promoting prostate cancer cell invasion

description: Additional file 8: Table S4. The list of reagents and kits.
DOI: 10.6084/m9.figshare.20046012.v1
title: Additional file 2 of Identification of different proteins binding to Na, K-ATPase α1 in LPS-induced ARDS cell model by proteomic analysis

description: Additional file 2.
DOI: 10.6084/m9.figshare.23714266.v1
title: Additional file 4 of Identification of cell subpopulations associated with disease phenotypes from scRNA-seq data using PACSI

description: Additional file 4. Table with differential expression genes in PACSI-identified cells associated with good immunotherapy response versus all other cells. Table with Hallmark pathways enrichment of differential expression genes between PACSI-identified cells associated with good immunotherapy response versus all other cells. Table with full list of genes in PACSI-derived signature associated with good immunotherapy response. Table with the specificity scores of regulons in PACSI-identified cells associated with good immunotherapy response.
DOI: 10.6084/m9.figshare.12703445
title: Additional file 2 of Integrated epigenetic biomarkers in circulating cell-free DNA as a robust classifier for pancreatic cancer

description: Additional file 2: Supplementary Table 1. Mapping summary of cfDNA 5mC sequencing data. Supplementary Table 2. Mapping summary of cfDNA 5hmC sequencing results. Supplementary Table 3. Differentially methylated peaks identified by t test. Supplementary Table 4. List of 5mC markers used in model construction. Supplementary Table 5. Wd-scores of PDAC patients derived from distinct models. Supplementary Table 6. Differentially hydroxymethylated peaks identified by t test. Supplementary Table 7. List of 5hmC markers used in model construction.
DOI: 10.6084/m9.figshare.23714266
title: Additional file 4 of Identification of cell subpopulations associated with disease phenotypes from scRNA-seq data using PACSI

description: Additional file 4. Table with differential expression genes in PACSI-identified cells associated with good immunotherapy response versus all other cells. Table with Hallmark pathways enrichment of differential expression genes between PACSI-identified cells associated with good immunotherapy response versus all other cells. Table with full list of genes in PACSI-derived signature associated with good immunotherapy response. Table with the specificity scores of regulons in PACSI-identified cells associated with good immunotherapy response.
DOI: 10.15468/dl.dkqm8f
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pavetta lasiocalyx Bremek."
 ]
}

 The dataset includes 6 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0067905-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ycm8fm
title: Occurrence Download

description: A dataset containing 21 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Peperomia elmeri C.DC."
 ]
}

 The dataset includes 21 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0067906-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3f3xyg
title: Occurrence Download

description: A dataset containing 145 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pedicularis lineata Franch. ex Maxim."
 ]
}

 The dataset includes 145 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0067907-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ykwc5v
title: Occurrence Download

description: A dataset containing 341 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pavetta lasioclada (K.Krause) Mildbr. ex Bremek."
 ]
}

 The dataset includes 341 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0067908-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.