cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.5910897
title: Prolonged Hypoxic Exposure May Improve Left Ventricular Function in Patients with Prior Myocardial Infarction

description: This dataset was acquired at DLR, Cologne, Germany. The study complied with the Declaration of Helsinki, and was approved by the local ethics committee. All subjects gave written informed consent. <strong>Data acquisition</strong><br> <em>MRI data</em> All MR images were acquired on a Siemens 3T mMR Biograph a using cardiac and spine coils. The scanning protocol consisted of the following sequences. <strong>mpi70_FOV_320_16x6mm_33ms_SA20</strong>: cardiac realtime MRI of the short axis (TR=2.56 ms; TE=1.62 ms; 1.6x1.6 mm; 6 mm slice thickness; 20 slices; FoV320x320 mm; radial spokes 13) <strong>CINE_FL2D7_RETRO_14SLICES_EPAT</strong>: conventional CINE cardiac short axis (TR= 40.32 ms; TE= 2.41 ms, 1.77x1.77 mm; 8 mm slice thickness; FA= 15°; FoV 340x276 mm) Cinematic real time MRI of the short axis view was acquired at the time points V1 to V3 in three subjects and V1 to V4 in one subject. Conventional cinematic short axis MRI was acquired at time point V3 in all subjects and V4 in one subject. Video files: 0MF_V1_Series_027_mpi70_FOV320_16x6mm_33ms_SA20 0MF_V2_Series_027_mpi70_FOV320_16x6mm_33ms_SA20 0MF_V3_Series_027_mpi70_FOV320_16x6mm_33ms_SA20 0MF_V4_Series_027_mpi70_FOV320_16x6mm_33ms_SA20 Cinematic real time MRI of the short axis view at the time points V1 to V4 in 1 subject. <strong>Transthoracic Echocardiography (TTE)</strong> All TTE images were acquired on a GE Vivid iq with GE M5Sc probe. Imaging contained apical 2-, 3- and 4 chamber views. These images were used to obtain global longitudinal strain (GLS), biplane left ventricular ejection fraction (LVEF) (Simpson Method), systolic pulmonary artery pressure (SPAP), basal right ventricular diameter, and tricuspid annular plane systolic excursion (TAPSE). The presented data were conducted at baseline (series 1), 0.118 FiO2/hypoxia (series 2-5), recovery (series 6,7) and 12 week follow-up (subject 0MF, series 8).
DOI: 10.5281/zenodo.5910896
title: Prolonged Hypoxic Exposure May Improve Left Ventricular Function in Patients with Prior Myocardial Infarction

description: This dataset was acquired at DLR, Cologne, Germany. The study complied with the Declaration of Helsinki, and was approved by the local ethics committee. All subjects gave written informed consent. <strong>Data acquisition</strong><br> <em>MRI data</em> All MR images were acquired on a Siemens 3T mMR Biograph a using cardiac and spine coils. The scanning protocol consisted of the following sequences. <strong>mpi70_FOV_320_16x6mm_33ms_SA20</strong>: cardiac realtime MRI of the short axis (TR=2.56 ms; TE=1.62 ms; 1.6x1.6 mm; 6 mm slice thickness; 20 slices; FoV320x320 mm; radial spokes 13) <strong>CINE_FL2D7_RETRO_14SLICES_EPAT</strong>: conventional CINE cardiac short axis (TR= 40.32 ms; TE= 2.41 ms, 1.77x1.77 mm; 8 mm slice thickness; FA= 15°; FoV 340x276 mm) Cinematic real time MRI of the short axis view was acquired at the time points V1 to V3 in three subjects and V1 to V4 in one subject. Conventional cinematic short axis MRI was acquired at time point V3 in all subjects and V4 in one subject. Video files: 0MF_V1_Series_027_mpi70_FOV320_16x6mm_33ms_SA20 0MF_V2_Series_027_mpi70_FOV320_16x6mm_33ms_SA20 0MF_V3_Series_027_mpi70_FOV320_16x6mm_33ms_SA20 0MF_V4_Series_027_mpi70_FOV320_16x6mm_33ms_SA20 Cinematic real time MRI of the short axis view at the time points V1 to V4 in 1 subject. <strong>Transthoracic Echocardiography (TTE)</strong> All TTE images were acquired on a GE Vivid iq with GE M5Sc probe. Imaging contained apical 2-, 3- and 4 chamber views. These images were used to obtain global longitudinal strain (GLS), biplane left ventricular ejection fraction (LVEF) (Simpson Method), systolic pulmonary artery pressure (SPAP), basal right ventricular diameter, and tricuspid annular plane systolic excursion (TAPSE). The presented data were conducted at baseline (series 1), 0.118 FiO2/hypoxia (series 2-5), recovery (series 6,7) and 12 week follow-up (subject 0MF, series 8).
DOI: 10.5281/zenodo.7583555
title: GPAM: Genetic Programming with Associative Memory - datasets for symbolic regression

description: This collection contains five data sets for symbolic regression generated using functions known as Koza-1, Nguyen-7, Nguyen-10, Korns-1, and Korns-4. In each function, we replaced some data points with randomly generated values from interval [−10, 10].
DOI: 10.5281/zenodo.7583554
title: GPAM: Genetic Programming with Associative Memory - datasets for symbolic regression

description: This collection contains five data sets for symbolic regression generated using functions known as Koza-1, Nguyen-7, Nguyen-10, Korns-1, and Korns-4. In each function, we replaced some data points with randomly generated values from interval [−10, 10].
DOI: 10.5281/zenodo.7584055
title: Data management table for PhD project:Reconquering the city: Pastoral agency and spatial impact of workers' parishes in Belgium (1884-1914)

description: In this data management table I organized additional information on all the sorts of data I am or will be using in the course of my research project. The content of the table sheds a light on why, how and for who I work on these different kinds of data.
DOI: 10.5281/zenodo.7584054
title: Data management table for PhD project:Reconquering the city: Pastoral agency and spatial impact of workers' parishes in Belgium (1884-1914)

description: In this data management table I organized additional information on all the sorts of data I am or will be using in the course of my research project. The content of the table sheds a light on why, how and for who I work on these different kinds of data.
DOI: 10.5519/qd.k8hti37l
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.6084/m9.figshare.21975611
title: Supplementary Material for: Independent Predictive Value of Elevated YKL-40 in Ischemic Stroke Prognosis: Findings from a Nationwide Stroke Registry

description: <b><i>Introduction:</i></b> Elevated circulatory concentrations of YKL-40 have been reported in patients with ischemic stroke. This study further investigated the association of plasma YKL-40 concentrations at admission and short, long-term prognosis after ischemic stroke. <b><i>Methods:</i></b> Based on a prospective, nationwide multicenter registry focusing consecutive patients of ischemic stroke and transient ischemic attack, plasma YKL-40 levels were detected by enzyme-linked immunosorbent assay at admission, and patients were stratified into percentile according to the plasma YKL-40 concentrations. The multivariate Cox or logistic regression model was used to investigate the association of YKL-40 concentration with death and functional outcomes at 3 months, 6 months, and 12 months after ischemic stroke, with potential confounders adjusted. <b><i>Results:</i></b> A total of 8,006 first-ever ischemic stroke patients, with the age of 61.7 ± 11.5, were included in this study. The mortality of 0–33%, 34–66%, 67–90%, and 91–100% groups at 12 months follow-up was 0.9%, 2.2%, 4.4%, and 9.4%, respectively (<i>p</i> &lt; 0.0001), and the modified Rankin Scale 3–6 ratio was 6.8%, 10.5%, 15.7%, and 24.0%, respectively (<i>p</i> &lt; 0.0001). In the multivariate regression, after adjusting for potential confounders, 91–100% group had higher risk of death (hazard ratio 2.99, 95% confidence interval 1.75–5.11)and modified Rankin Scale 3–6 (odds ratio 1.42, 95% confidence interval 1.08–1.88) at 12 months since onset of ischemic stroke compared to the 0–33% group. <b><i>Conclusions:</i></b> The elevated YKL-40 at admission can potentially help predict death, functional prognosis after ischemic stroke, which may help further studies to explore the potential physiological and pathological mechanism including the effects of vulnerable plaque and collateral circulation.
DOI: 10.5519/qd.0n8ycqpk
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.6084/m9.figshare.21964535
title: Acinetobacter T4aP phylogenetic profile

description: The following files can be used to display the phylogenetic profile of type IVa pilus proteins in the software PhyloProfile. This tool can be used to interactively inspect proteins and compare annotated features with the respective orthologs. <br> To use ths data, the following steps are required. Installation of PhyloProfile (https://github.com/BIONF/PhyloProfile) Run the software via R library("PhyloProfile") runPhyloProfile() Upload the input file type_IV_pilus.phyloprofile A message will appear, stating that the taxon IDs are not recognized. Select Function - NCBI taxonomy data - Import taxonomy DB files. Select the provided files within the taxonomy_data directory. In the Input & settings tab, upload: Additional input data - type_IV_pilus.domains Fasta files - type_IV_pilus.fa Order taxa by user defined tree - type_IV_pilus.nwk Select A. baumannii as the reference, and Plot. Datapoints represent the orthologs and their feature architecture can be inspected by clicking on them. <br>
DOI: 10.5281/zenodo.7584228
title: B-cell receptor data from intratumoural B cells in melanoma patients

description: This record contains data used in the Crescioli et al. analysis of B-cell response in melanoma, specifically analysis concerning high-throughput BCR repertoire. Files: "Visium_all_Aug22_comboDatBoth.txt": IMGT/HighV-Quest output of the high-throughput intratumoural BCR repertoire from n=5 melanoma tumours. In tab-separated text file format. "HV_EB_COV_MEL_comb_Oct22.RDS": A R data object (readable into R with "readRDS(...)") containing combined data from the melanoma (MEL) data with analogous high-throughput BCR repertoire data from healthy volunteers (HV), Ebola convalescent patients (EB) and hospitalised COVID-19 patients (COV). HV, EB and COV data are taken from https://dx.doi.org/10.5281/zenodo.5146019. Here the sequences are filtered to contain only unique combinations of isotype and IMGT-numbered V-domain DNA sequence (to remove redundancies due to e.g. capturing BCR transcripts from plasma cells).
DOI: 10.5281/zenodo.7584206
title: Detection of the Fire Drill anti-pattern: 15 real-world projects with ground truth, issue-tracking data, source code density, models and code

description: This package contains artifacts for <strong>15</strong> real-world software projects. The data is supposed to aid the detection of the presence of the Fire Drill anti-pattern. We include original data, ground truth, code (experimental setups and models), and notebooks. The data supports two distinct methods of detecting the AP: a) through issue-tracking data, and b) through the underlying source code. This version of the dataset corresponds to <strong>v8</strong> of the technical report and the GitHub repository. The package includes the following: Original data: For each project, its <strong>original</strong> artifacts (e.g., wikis, meeting minutes, mentor's notes, etc.) Evaluation of raters' notes by the assessor Fire Drill in issue-tracking data: <strong>Ground truth</strong> for whether and how strong each project exhibits the Fire Drill AP, on a scale from [0,10]. This was determined by two individual raters, who also reached a consensus. Coefficients for indicators for the first method, per project. Detailed issue-tracing data for each project: what occurred and when. Time logs for each project. Fire Drill in source-code data: <strong>Four</strong> technical reports that document the developed method of how to translate a description into a detectable pattern, and to use the pattern to detect the presence and to score it (similar to the rating). Also includes a report for how activities were assigned to individual commits. Source code density data (metrics) for each commit in each of the nine projects as a separate dataset. Code: a snapshot of the repository that holds all code, models, notebooks, and pre-computed results, for utmost reproducibility (the code is written in R).
description: The repository for the source code based method is at: https://github.com/MrShoenel/anti-pattern-models
DOI: 10.5281/zenodo.4734053
title: Detection of the Fire Drill anti-pattern: 15 real-world projects with ground truth, issue-tracking data, source code density, models and code

description: This package contains artifacts for <strong>15</strong> real-world software projects. The data is supposed to aid the detection of the presence of the Fire Drill anti-pattern. We include original data, ground truth, code (experimental setups and models), and notebooks. The data supports two distinct methods of detecting the AP: a) through issue-tracking data, and b) through the underlying source code. This version of the dataset corresponds to <strong>v8</strong> of the technical report and the GitHub repository. The package includes the following: Original data: For each project, its <strong>original</strong> artifacts (e.g., wikis, meeting minutes, mentor's notes, etc.) Evaluation of raters' notes by the assessor Fire Drill in issue-tracking data: <strong>Ground truth</strong> for whether and how strong each project exhibits the Fire Drill AP, on a scale from [0,10]. This was determined by two individual raters, who also reached a consensus. Coefficients for indicators for the first method, per project. Detailed issue-tracing data for each project: what occurred and when. Time logs for each project. Fire Drill in source-code data: <strong>Four</strong> technical reports that document the developed method of how to translate a description into a detectable pattern, and to use the pattern to detect the presence and to score it (similar to the rating). Also includes a report for how activities were assigned to individual commits. Source code density data (metrics) for each commit in each of the nine projects as a separate dataset. Code: a snapshot of the repository that holds all code, models, notebooks, and pre-computed results, for utmost reproducibility (the code is written in R).
description: The repository for the source code based method is at: https://github.com/MrShoenel/anti-pattern-models
DOI: 10.5281/zenodo.7584238
title: Data supplement to 'Astrochronology for the Miocene Climatic Optimum at Ocean Drilling Program Site 959 in the eastern Equatorial Atlantic'

description: Data supplement to "Astrochronology for the Miocene Climatic Optimum at Ocean Drilling Program Site 959 in the eastern Equatorial Atlantic". <strong>Table </strong><strong>T1</strong>: Depth conversion to rmbsf. <strong>Table T2</strong>: List of all Early to Middle Miocene calcareous nannofossil and diatom bioevents at ODP Site 959. <strong>Table T3</strong>: Diagnostic diatoms range chart <strong>Table T4</strong>: Diagnostic calcareous nannofossils range chart <strong>Table T5</strong>: Magnetic susceptibility data <strong>Table T6</strong>: Bulk carbonate δ<sup>1</sup><sup>8</sup>O and δ<sup>13</sup>C data <strong>Table T7</strong>: Wt% CaCO<sub>3 </sub>data <strong>Table T8</strong>: DeCrack mean greyscale, redness, greenness and blueness data
DOI: 10.5281/zenodo.7584237
title: Data supplement to 'Astrochronology for the Miocene Climatic Optimum at Ocean Drilling Program Site 959 in the eastern Equatorial Atlantic'

description: Data supplement to "Astrochronology for the Miocene Climatic Optimum at Ocean Drilling Program Site 959 in the eastern Equatorial Atlantic". <strong>Table </strong><strong>T1</strong>: Depth conversion to rmbsf. <strong>Table T2</strong>: List of all Early to Middle Miocene calcareous nannofossil and diatom bioevents at ODP Site 959. <strong>Table T3</strong>: Diagnostic diatoms range chart <strong>Table T4</strong>: Diagnostic calcareous nannofossils range chart <strong>Table T5</strong>: Magnetic susceptibility data <strong>Table T6</strong>: Bulk carbonate δ<sup>1</sup><sup>8</sup>O and δ<sup>13</sup>C data <strong>Table T7</strong>: Wt% CaCO<sub>3 </sub>data <strong>Table T8</strong>: DeCrack mean greyscale, redness, greenness and blueness data
DOI: 10.23708/gvncql
title: Microplastic concentrations in riverine environments of Can Tho, Southern Vietnam, under CounterMEASUREII project (2021-2022)

description: Microplastic (300-5000µm) concentrations were measured in Eau River and two canals, Cai Khe and Cai rang of Can Tho, Southern Vietnam, under CounterMEASUREII project (2021-2022). Microplastic were sampled using a 80µm mesh size net from a local boat. The samples were extracted in the laboratory using enzymatic digestion, NaCl density separation and were filtrated on GF-A filter. Then microplastic were observed on stereomicroscope and length, area, color were measured for fragments, line and circle. Concentrations are given in total microplastic per m3, fragment per m3 and fibers per m3. The sampling dates are January 2022 under the CounterMEASUREII project.
DOI: 10.5281/zenodo.7584226
title: Raster representing the probability of the upper forest-cover in the near future in the Romanian Carpathians (selected mountain units)

description: The dataset represents the estimated probability for the upper forest-cover across 11 selected mountain units in the Romanian Carpathians, merged into a single map to show the regional differences induced by several biophysical and anthropogenic factors.
DOI: 10.5281/zenodo.7584225
title: Raster representing the probability of the upper forest-cover in the near future in the Romanian Carpathians (selected mountain units)

description: The dataset represents the estimated probability for the upper forest-cover across 11 selected mountain units in the Romanian Carpathians, merged into a single map to show the regional differences induced by several biophysical and anthropogenic factors.
DOI: 10.5281/zenodo.7534175
title: Datasets for training and for testing ligand-based reverse screening to predict drug targets.

description: Bioactivity data were obtained from the ChEMBL (version 25) and the Reaxys<sup>®</sup> (version 03.2019) databases for training/screening and testing target prediction of small molecule drug by reverse screening. A short extract of the raw ChEMBL data for training is given in <strong>Supplementary Table 1 </strong>(Supp_Table_1.xlsx) to show three lines corresponding to an active, an inactive and an ‘gray area’ datapoints, respectively. Processed data are deposited here. The screening set file contains (CHEMBL-screeningset.csv), for each active compound, the standardized SMILES, the ChEMBLID, the number of experimental target(s) and their UniProt identifier(s). The test set file (Reaxys-testset-with300-SMILES.csv) contains, for each 364201 active compound, the ReaxysID, the number of experimental target(s) and the UniProt identifier(s). For Reaxys users, the chemical structure can be obtained through bulk request on the website. Access to www.reaxys.com and to Reaxys data can be obtained by contacting Elsevier directly. The first 300 entries display the standardized SMILES so that every reader can reproduce the results obtained by the reverse screening exercise. Further datasets can be obtained at www.swisstargetprediction.ch/download.php
DOI: 10.5281/zenodo.7534174
title: Datasets for training and for testing ligand-based reverse screening to predict drug targets.

description: Bioactivity data were obtained from the ChEMBL (version 25) and the Reaxys<sup>®</sup> (version 03.2019) databases for training/screening and testing target prediction of small molecule drug by reverse screening. A short extract of the raw ChEMBL data for training is given in <strong>Supplementary Table 1 </strong>(Supp_Table_1.xlsx) to show three lines corresponding to an active, an inactive and an ‘gray area’ datapoints, respectively. Processed data are deposited here. The screening set file contains (CHEMBL-screeningset.csv), for each active compound, the standardized SMILES, the ChEMBLID, the number of experimental target(s) and their UniProt identifier(s). The test set file (Reaxys-testset-with300-SMILES.csv) contains, for each 364201 active compound, the ReaxysID, the number of experimental target(s) and the UniProt identifier(s). For Reaxys users, the chemical structure can be obtained through bulk request on the website. Access to www.reaxys.com and to Reaxys data can be obtained by contacting Elsevier directly. The first 300 entries display the standardized SMILES so that every reader can reproduce the results obtained by the reverse screening exercise. Further datasets can be obtained at www.swisstargetprediction.ch/download.php
DOI: 10.5281/zenodo.7584149
title: Viral Agents and Systemic Levels of Inflammatory Cytokines in Vulnerable and Stable Atherosclerotic Carotid Plaques

description: Mazzaccaro D, Dolci M, Perego F, Delbue S, Giannetta M, Cardani R, Valentina Renna L, Costa E, Corsi-Romanelli MM, Galli C, Pariani E, Nano G, Clemente C, Basilico N. Viral Agents and Systemic Levels of Inflammatory Cytokines in Vulnerable and Stable Atherosclerotic Carotid Plaques. Ann Vasc Surg. 2022 May;82:325-333. doi: 10.1016/j.avsg.2021.10.070. Epub 2021 Dec 11. PMID: 34902464. Abstract <strong>Background: </strong>To investigate the presence of genetic material of viral agents and the serum level of inflammatory cytokines in patients submitted to carotid endarterectomy having vulnerable versus stable atherosclerotic plaques. <strong>Methods: </strong>Data of patients consecutively submitted to carotid endarterectomy for a significant stenosis from July 2019 to December 2019 were prospectively collected. The genetic material of Epstein-Barr (EBV), CitoMegalo (CMV), Herpes Simplex (HSV), Varicella-Zoster (VZV) and Influenza (IV) Viruses was searched in the patient's plaques, both in the "mid" of the plaque and in an adjacent lateral portion of no-plaque area. The serum levels of TNF-α, IL-1β, IL-6, IL10 and CCL5 were determined. The obtained results were then correlated to the histologic vulnerability of the removed carotid plaque. P values &lt; 0.05 were considered statistically significant. <strong>Results: </strong>Data of 50 patients were analyzed. A vulnerable plaque was found in 31 patients (62%). The genome of CMV, HSV, VZV and IV was not found in any of the vascular samples, while the EBV genome was found in the "mid" of 2 vulnerable plaques, but not in their respective control area. Eighty-two percent of patients who did not receive anti-IV vaccination (23/28) had vulnerable carotid plaque, compared with 36% of vaccinated patients (8/22, P = 0.001). Serum levels of TNF-α and IL-6 were higher in patients with a vulnerable plaque compared to patients with a stable plaque (73.6 ± 238.2 vs. 3.9 ± 13.1 pg/ml, P= 0.01, and 45.9 ± 103.6 vs. 10.1 ± 25.3 pg/ml, P= 0.01, respectively), independent of comorbidities, viral exposure or flu vaccination. <strong>Conclusions: </strong>The EBV genome was found in the "core" of 2 vulnerable carotid plaques, but not in their respective adjacent control. Influenza vaccination was associated with a lower incidence of carotid plaque vulnerability. Serum levels of TNF-α and IL-6 were higher in patients with a vulnerable plaque compared to patients with a stable plaque.