cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14405372.v1
title: Supplementary Material for: Swimming Exercise Ameliorates Hypertension-Induced Kidney Dysfunction via Alleviating Renal Interstitial Fibrosis and Apoptosis

description: <b><i>Background:</i></b> Hypertensive nephropathy is one of the major causes of ESRD. Exercise has been considered a nonpathological therapy for hypertension and its complications, yet mechanisms remain unclear. We sought to investigate whether periodic swimming could ameliorate hypertension-induced kidney dysfunction and its underlying mechanisms. <b><i>Methods:</i></b> Four-week male spontaneously hypertensive rats (SHRs) were randomly divided into the hypertension group (SHR, <i>n</i> = 8) and exercise group (SE, <i>n</i> = 8, 60 min swimming/day, 6 days per week, for 8 weeks). Wistar-Kyoto rats (WKY, <i>n</i> = 8) were served as a sedentary normotensive group. Bodyweight and blood pressure (BP) were recorded weekly. After 8-week sedentary or swimming exercise, lipids profile, BUN, and Cr were measured. The renal interstitial fibrosis was examined by the histopathological analysis using Masson’s trichrome staining and hematoxylin and eosin staining. The kidney cell apoptosis was tested by TUNEL staining. The expressions of critical proteins responsible for the TGF-β1/Smad signaling of fibrosis, that is, TGF-β1, Smad2/3, and Smad7, as well as apoptosis related proteins, Bax and Bcl-2 in kidney cortex tissues were measured. <b><i>Results:</i></b> The 8-week swimming exercise reduced BP and bodyweight, lowered concentrations of BUN, and serum Cr, compared with SHR. Exercise remarkably inhibited hypertension-induced tubular degeneration, cellular cluster, and tubular cell swelling as well as glomerular degeneration in the kidney cortical tissues, attenuated renal interstitial fibrosis, and renal cell apoptosis. Moreover, expressions of TGF-β1, Smad2/3, and Bax were higher in the SHR than the WKY, which were significantly suppressed by the exercise. In contrast, hypertension-reduced expressions of Smad7 and Bcl-2 were enhanced by the swimming exercise. Strong correlations were found between kidney function indices, blood lipids, and key protein expressions. <b><i>Conclusion:</i></b> Our results demonstrate beneficial effects of the periodic swimming on ameliorating hypertension-induced kidney dysfunction highlighting the potential of swimming exercise as a nonpathological therapy for early prevention of hypertension-caused kidney diseases.
DOI: 10.5519/qd.3uxxbqm0
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (0 records)
DOI: 10.6084/m9.figshare.14405987
title: Supplementary Material for: Current Status and Quality of Machine Learning-Based Radiomics Studies for Glioma Grading: A Systematic Review

description: <b><i>Introduction:</i></b> Radiomics now has significant momentum in the era of precision medicine. Glioma is one of the pathologies that has been extensively evaluated by radiomics. However, this technique has not been incorporated into clinical practice. In this systematic review, we selected and reviewed the published studies about glioma grading by radiomics to evaluate this technique’s feasibility and its challenges. <b><i>Material and Methods:</i></b> Using seven different search strings, we considered all published English manuscripts from 2015 to September 2020 in PubMed, Embase, and Scopus databases. After implementing the exclusion and inclusion criteria, the final papers were selected for the methodological quality assessment based on our in-house Modified Radiomics Standard Scoring (RQS) containing 43 items (minimum score of 0, maximum score of 44). Finally, we offered our opinion about the challenges and weaknesses of the selected papers. <b><i>Results:</i></b> By our search, 1,177 manuscripts were found (485 in PubMed, 343 in Embase, and 349 in Scopus). After the implementation of inclusion and exclusion criteria, 18 papers remained for the final analysis by RQS. The total RQS score ranged from 26 (59% of maximum possible score) to 43 (97% of maximum possible score) with a mean of 33.5 (76% of maximum possible score). <b><i>Conclusion:</i></b> The current studies are promising but very heterogeneous in design with high variation in the radiomics software, the number of extracted features, the number of selected features, and machine learning models. All of the studies were retrospective in design; many are based on small datasets and/or suffer from class imbalance and lack of external validation data­sets.
DOI: 10.34740/kaggle/ds/1268595
title: Computer Science Articles & Journals, 2019
DOI: 10.6084/m9.figshare.14405846
title: Supplementary Material for: Differential DNA Methylation of the <b><i>IMMP2L</i></b> Gene in Families with Maternally Inherited 7q31.1 Microdeletions is Associated with Intellectual Disability and Developmental Delay

description: Most copy number variations (CNVs) in the human genome display incomplete penetrance with unknown underlying mechanisms. One such mechanism may be epigenetic modification, particularly DNA methylation. The <i>IMMP2L</i> gene is located in a critical region for autism susceptibility on chromosome 7q (AUTS1). The level of DNA methylation was assessed by bisulfite sequencing of 87 CpG sites in the <i>IMMP2L</i> gene in 3 families with maternally inherited 7q31.1 microdeletions affecting the <i>IMMP2L</i> gene alone. Bisulfite sequencing revealed comparable levels of DNA methylation in the probands, healthy siblings without microdeletions, and their fathers. In contrast, a reduced DNA methylation index and increased <i>IMMP2L</i> expression were observed in lymphocytes from the healthy mothers compared with the probands. A number of genes were upregulated in the healthy mothers compared to controls and downregulated in probands compared to mothers. These genes were enriched in components of the ribosome and electron transport chain, as well as oxidative phosphorylation and various degenerative conditions. Differential expression in probands and mothers with <i>IMMP2L</i> deletions relative to controls may be due to compensatory processes in healthy mothers with <i>IMMP2L</i> deletions and disturbances of these processes in probands with intellectual disability. The results suggest a possible partial compensation for <i>IMMP2L</i> gene haploinsufficiency in healthy mothers with the 7q31.1 microdeletion by reducing the DNA methylation level. Differential DNA methylation of intragenic CpG sites may affect the phenotypic manifestation of CNVs and explain the incomplete penetrance of chromosomal microdeletions.
DOI: 10.5523/bris.28n44fl84kgbp2o12ugep52ark
title: Gore et al (2021) - C2 OES data

description: Spatially and wavelength resolved imaging measurements of emission from electronically excited C2 radicals in microwave activated C/H plasmas, with associated modelling demonstrating the role of chemiluminescent bimolecular reactions in this oft observed emission
DOI: 10.5281/zenodo.4506829
title: Alteration of gut microbiota with a broad-spectrum antibiotic does not impair maternal care in the European earwig

description: Dataset, R script and detailed bioinformatic pipelines used in the publication "Alteration of gut microbiota with a broad-spectrum antibiotic does not impair maternal care in the European earwig"
description: This research has been supported by a research grant from the French Ministry of Research (to S.V.M.) and a research grant from the ANR (project MicroSoc to J.M.)
DOI: 10.5281/zenodo.4072980
title: Alteration of gut microbiota with a broad-spectrum antibiotic does not impair maternal care in the European earwig

description: Dataset, R script and detailed bioinformatic pipelines used in the publication "Alteration of gut microbiota with a broad-spectrum antibiotic does not impair maternal care in the European earwig"
description: This research has been supported by a research grant from the French Ministry of Research (to S.V.M.) and a research grant from the ANR (project MicroSoc to J.M.)
DOI: 10.5281/zenodo.4682824
title: MALDI-TOF mass spectra data included in Hu et al. 2021

description: MALDI-TOF mass spectra data of isolates obtained from an enrichment
DOI: 10.5281/zenodo.4682823
title: MALDI-TOF mass spectra data included in Hu et al. 2021

description: MALDI-TOF mass spectra data of isolates obtained from an enrichment
DOI: 10.5281/zenodo.4682860
title: DNA Metabarcoding Enables High-Throughput Detection of Spotted Wing Drosophila (Drosophila suzukii) within Unsorted Trap Catches

description: Data to support the paper: DNA Metabarcoding Enables High-Throughput Detection of Spotted Wing Drosophila (Drosophila suzukii) within Unsorted Trap Catches
DOI: 10.17632/pxngkh7krj.1
title: DSQSS: Discrete Space Quantum Systems Solver

description: The Discrete Space Quantum Systems Solver (DSQSS) is a program package for solving quantum many-body problems defined on lattices. The DSQSS is based on the quantum Monte Carlo method in Feynman’s path integral representation and covers a broad range of problems using flexible input files that define arbitrary unit cells in arbitrary dimensions and arbitrary matrix elements representing the interactions among an arbitrary number of degrees of freedom. Finite temperature calculations of quantum spin and the Bose–Hubbard models can be performed by specifying parameters such as the number of dimensions, the lattice size, coupling constants, and temperature. The present paper details the use of DSQSS and presents a number of applications thereof.
DOI: 10.17632/xjtfcjwj7h.1
title: GOAS

description: This data set includes the test instances used in the paper titled"A Matheuristic for the Generalized Order Acceptance and Scheduling Problem" (Tarhan and Oğuz).
DOI: 10.17632/djpw9rpv5b.1
title: GITR: An accelerated global scale particle tracking code for wall material erosion and redistribution in fusion relevant plasma-material interactions

description: The global impurity transport code (GITR - pronounced “guitar”) has been developed as a high-performance Monte Carlo particle (neutral atom and ion) tracking code to simulate the erosion, ionization, migration, and redistribution of plasma-facing components in magnetically confined fusion devices. The trace impurity assumption allows for a highly parallel computational model that enables increased scaling in the number of particles simulated as well as the domain size and geometric fidelity. Novel custom algorithms that query the 3D surface geometry has alleviated the need for traditional meshing needs. Presented here is the physics model, numerical schemes, algorithmic implementation, and example simulations.
DOI: 10.17632/7yvc8mmnyv.1
title: GROMACS implementation of free energy calculations with non-pairwise Variationally derived Intermediates

description: Gradients in free energies are the driving forces of physical and biochemical systems. To predict free energy differences with high accuracy, Molecular Dynamics (MD) and other methods based on atomistic Hamiltonians conduct sampling simulations in intermediate thermodynamic states that bridge the configuration space densities between two states of interest (’alchemical transformations’). For uncorrelated sampling, the recent Variationally derived Intermediates (VI) method yields optimal accuracy. The form of the VI intermediates differs fundamentally from conventional ones in that they are non-pairwise, i.e., the total force on a particle in an intermediate states cannot be split into additive contributions from the surrounding particles. In this work, we describe the implementation of VI into the widely used GROMACS MD software package (2020, version 1). Furthermore, a variant of VI is developed that avoids numerical instabilities for vanishing particles. The implementation allows the use of previous non-pairwise potential forms in the literature, which have so far not been available in GROMACS. Example cases on the calculation of solvation free energies, and accuracy assessments thereof, are provided.
DOI: 10.17632/p66rmf7nw2.1
title: Superplastic deformation mechanical behavior and constitutive modelling of a near-α titanium alloy TNW700 sheet

description: True stress-true strain data used in Figure 4 and corresponding engineering stress- engineering strain data which are not provided in the manuscript.
DOI: 10.17632/77pgthjfs3.1
title: Raw data-Development of a protein scaffold for arginine sensing generated through the dissection of the arginine-binding protein from thermotoga maritima

description: research data of the work
DOI: 10.17632/8yj7cp3vw7.1
title: Raw data-KCTD15 protein expression in peripheral blood and acute myeloid Leukemia

description: research data of the work
DOI: 10.17632/gtbc75gdpw.1
title: Raw data-A Rare Case of Sigmoid Colon Carcinoma in Incarcerated Inguinal Hernia

description: research data of the work
DOI: 10.5522/04/14400947
title: Priority effects and the macroevolutionary dynamics of biodiversity: Raw output of the simulation models

description: All RData files for the realisations of the IS, SC and RS models under different conditions (e.g. parameters and modelling decisions). Each individual file contains one single simulation run, which contents are further detailed in the 'run_model/1_call_script.R' of the code archive. Analyses of, for instance, phylogenetic imbalance, speciation rates, and other temporal and spatial patterns can be repeated using these files. Note that for plotting purposes only, the simulations are not require as output of the analyses has been included in the 'code' archive. Further specifics on the simulations included can be found in the readme.txt file within and the Appendix of the manuscript.<br><br>Reijenga B.R, Murrell D. M, Pigot A. L. (Accepted) Priority effects and the macroevolutionary dynamics of biodiversity, Ecology Letters<br>
DOI: 10.17632/959kpw5hzf.1
title: Raw data-Prognostic significance of PET/CT in patients with chronic lymphocytic leukemia (CLL) treated with frontline chemoimmunotherapy

description: research data of the work - 2
DOI: 10.5522/04/14400947.v1
title: Priority effects and the macroevolutionary dynamics of biodiversity: Raw output of the simulation models

description: All RData files for the realisations of the IS, SC and RS models under different conditions (e.g. parameters and modelling decisions). Each individual file contains one single simulation run, which contents are further detailed in the 'run_model/1_call_script.R' of the code archive. Analyses of, for instance, phylogenetic imbalance, speciation rates, and other temporal and spatial patterns can be repeated using these files. Note that for plotting purposes only, the simulations are not require as output of the analyses has been included in the 'code' archive. Further specifics on the simulations included can be found in the readme.txt file within and the Appendix of the manuscript.<br><br>Reijenga B.R, Murrell D. M, Pigot A. L. (Accepted) Priority effects and the macroevolutionary dynamics of biodiversity, Ecology Letters<br>
DOI: 10.17632/skk6ngjjwp.1
title: Replication Package for “The political economy of protection in GVCs: Evidence from Chinese micro data”, By Rodney D. Ludema, Anna Maria Mayda, Zhi Yu and Miaojie Yu.

description: Replication Package for “The political economy of protection in GVCs: Evidence from Chinese micro data”, By Rodney D. Ludema, Anna Maria Mayda, Zhi Yu and Miaojie Yu.
DOI: 10.17632/gdcmgkcf88.1
title: BMI and PTSD among HCWs

description: The survey was carried out among 58 front-line HCWs from two emergency hospitals in Ekaterinburg, Russia. The mean age of the sample was 44.05 ± 12.5 years. PTSD was assessed using the PTSD Symptom Scale-Self-Report (PSS-SR); subjective distress was assessed using the Impact of Event Scale-Revised (IES-R).
DOI: 10.5522/04/14364845
title: All Preprocessed Datasets for Gurnani and Silver, 2021

description: Population imaging of cerebellar Golgi cells in Crus I/II and lobule IV/V (vermis) of awake, head-fixed mice.
DOI: 10.5522/04/14364845.v1
title: All Preprocessed Datasets for Gurnani and Silver, 2021

description: Population imaging of cerebellar Golgi cells in Crus I/II and lobule IV/V (vermis) of awake, head-fixed mice.
DOI: 10.7483/opendata.atlas.53pm.j6ps
title: Simulated low-level channel readout for Z-&gt;ee+jets decays in the ATLAS detector
DOI: 10.17632/6r388827fz.2
title: DIRAC Site Director: Analysis and Performance Evaluation

description: To take advantage of the computing power offered by grid and opportunistic resources, developers of the DIRAC Workload Management System have adopted the Pilot-Job paradigm and deliver tools to deploy Pilot-Jobs on available resources. In this work, we study the DIRAC Site Director, the mechanism designed to supply grid resources with Pilot-Jobs, making use of the so-called grid push model that prevents to fully exploit the grid resources. Data focus on the analysis of the capabilities and limitations of the DIRAC Site Director in the LHCb production environment. Data mainly include CSV and JSON files related to the jobs and pilot-jobs submitted and processed, as well as a Jupyter Notebook to present plots based on data. Data show the evolution of the Site Directors through time highlighting the benefits of the different updates that seem to increase the number of pilot-jobs submitted as well as the number of jobs processed.
DOI: 10.6084/m9.figshare.12548093
title: Supplemental data

description: This repository contains Excel files of all the measurements made for this study with a Word document to describe them.
DOI: 10.6084/m9.figshare.12548093.v2
title: Supplemental data

description: This repository contains Excel files of all the measurements made for this study with a Word document to describe them.
DOI: 10.5281/zenodo.4679174
title: Arca - Evaluation

description: Dataset of Arca evaluation.
DOI: 10.5517/ccdc.csd.cc23fmnv
title: CCDC 1949517: Experimental Crystal Structure Determination

description: Related Article: Huafeng Li, Peipei He, Rong Wan, Yan Zou, Xue Zhao, Pengtao Ma, Jingyang Niu, Jingping Wang|2020|Dalton Trans.|49|2895|doi:10.1039/C9DT04616J
DOI: 10.5517/ccdc.csd.cc23fr4g
title: CCDC 1949625: Experimental Crystal Structure Determination

description: Related Article: Huafeng Li, Peipei He, Rong Wan, Yan Zou, Xue Zhao, Pengtao Ma, Jingyang Niu, Jingping Wang|2020|Dalton Trans.|49|2895|doi:10.1039/C9DT04616J
DOI: 10.5517/ccdc.csd.cc26w1jp
title: CCDC 2051782: Experimental Crystal Structure Determination

description: Related Article: Esmeralda Bukuroshi, Siena Wong, Thanmayee Mudigonda, Kyle Nova, Antoine Dumont, Devon Holst, Zheng-Hong Lu, Timothy P. Bender|2021|MSDE|6|308|doi:10.1039/D0ME00175A
DOI: 10.5517/ccdc.csd.cc26w1kq
title: CCDC 2051783: Experimental Crystal Structure Determination

description: Related Article: Esmeralda Bukuroshi, Siena Wong, Thanmayee Mudigonda, Kyle Nova, Antoine Dumont, Devon Holst, Zheng-Hong Lu, Timothy P. Bender|2021|MSDE|6|308|doi:10.1039/D0ME00175A
DOI: 10.5517/ccdc.csd.cc26w1lr
title: CCDC 2051784: Experimental Crystal Structure Determination

description: Related Article: Esmeralda Bukuroshi, Siena Wong, Thanmayee Mudigonda, Kyle Nova, Antoine Dumont, Devon Holst, Zheng-Hong Lu, Timothy P. Bender|2021|MSDE|6|308|doi:10.1039/D0ME00175A
DOI: 10.5517/ccdc.csd.cc26w1ms
title: CCDC 2051785: Experimental Crystal Structure Determination

description: Related Article: Esmeralda Bukuroshi, Siena Wong, Thanmayee Mudigonda, Kyle Nova, Antoine Dumont, Devon Holst, Zheng-Hong Lu, Timothy P. Bender|2021|MSDE|6|308|doi:10.1039/D0ME00175A
DOI: 10.5281/zenodo.4655844
title: Dataset related to article "Virtual biopsy using MRI radiomics for prediction of BRAF status in melanoma brain metastasis"

description: Clinical database of patients undergoing Virtual biopsy using MRI radiomics for prediction of BRAF status in melanoma brain metastasis
DOI: 10.5281/zenodo.4655843
title: Dataset related to article "Virtual biopsy using MRI radiomics for prediction of BRAF status in melanoma brain metastasis"

description: Clinical database of patients undergoing Virtual biopsy using MRI radiomics for prediction of BRAF status in melanoma brain metastasis
DOI: 10.5281/zenodo.4473715
title: High resolution global industrial and smallholder oil palm map for 2019

description: The dataset contains 634 100x100 km tiles, covering areas where oil palm plantations were detected. The file '<em>grid.shp</em>' contains the grid that covers the potential distribution of oil palm. The file '<em>grid_withOP.shp</em>' shows the 100x100 grid squares with presence of oil palm plantations. The classified images (‘<em>oil_palm_map</em>’ folder, in geotiff format) are the output of the convolutional neural network based on Sentinel-1 and Sentinel-2 half-year composites. The images have a spatial resolution of 10 meters and contain three classes: [1] Industrial closed-canopy oil palm plantations, [2] Smallholder closed-canopy oil palm plantations, and [3] other land covers/uses that are not closed canopy oil palm. The file ‘<em>Validation_points_GlobalOilPalmLayer_2019.shp</em>’ includes the 13,495 points that were used to validate the product. Each point includes the attribute ‘Class’, which is the labelled class assigned by visual interpretation, and the attribute ‘predClass, which reflects the predicted class by the convolutional neural network. The ‘Class’ and ‘predClass’ values are the same as the raster files: [1] Industrial closed-canopy oil palm plantations, [2] Smallholder closed-canopy oil palm plantations, and [3] other land covers/uses that are not closed canopy oil palm. See article for additional information: Descals, Adrià, et al. "High-resolution global map of smallholder and industrial closed-canopy oil palm plantations." <em>Earth System Science Data</em> 13.3 (2021): 1211-1231. Changelog v1: - The analysis was extended to Sri Lanka, South India, and countries in Eastern Africa where oil palm can potentially grow. - The validation dataset only includes the points drawn by simple random sampling and stratified random sampling in the grid cells where the IUCN industrial layer detected oil palm. - The 'Class' and 'predClass' values in the validation dataset were reclassified with the same values as the raster images: [1] Industrial plantations, [2] Smallholder plantations, and [3] Other land covers/uses.