cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17296370.v1
title: Supplementary Material for: Exercise-Based Cardiac Rehabilitation Associates with Lower Major Adverse Cardiovascular Events in People with Stroke

description: <b><i>Background:</i></b> The risk of major adverse cardiovascular events is substantially increased following a stroke. Although exercise-based cardiac rehabilitation has been shown to improve prognosis following cardiac events, it is not part of routine care for people following a stroke. We therefore investigated the association between cardiac rehabilitation and major adverse cardiovascular events for people with stroke. <b><i>Methods:</i></b> This retrospective analysis was conducted on June 20, 2021, using anonymized data within TriNetX, a global federated health research network with access to electronic medical records from participating healthcare organizations, predominantly in the USA. All participants were aged ≥18 years with cerebrovascular disease and at least 2 years of follow-up. People with stroke and an electronic medical record of exercise-based cardiac rehabilitation were 1:1 propensity score matched to people with stroke but without cardiac rehabilitation using participant characteristics, comorbidities, cardiovascular procedures, and cardiovascular medications. <b><i>Results:</i></b> Of 836,923 people with stroke and 2-year follow-up, 2,909 met the inclusion for the exercise-based cardiac rehabilitation cohort. Following propensity score matching (<i>n</i> = 5,818), exercise-based cardiac rehabilitation associated with 53% lower odds of all-cause mortality (odds ratio 0.47, 95% confidence interval: 0.40–0.56), 12% lower odds of recurrent stroke (0.88, 0.79–0.98), and 36% lower odds of rehospitalization (0.64, 0.58–0.71), compared to controls. No significant association between cardiac rehabilitation and incident atrial fibrillation was observed. <b><i>Conclusion:</i></b> Exercise-based cardiac rehabilitation prescribed for people following a stroke associated with significantly lower odds of major adverse cardiovascular events at 2 years, compared to usual care.
DOI: 10.6084/m9.figshare.12173394.v1
title: Data for "Oikos doi: 10.1111/oik.07006"

description: Raw data for "Yue, K., Jarvie, S., Senior, A. M., Van Meerbeek, K., Peng, Y., Ni, X., Wu, F. and Svenning, J.-C. 2020. Changes in plant diversity and its relationship with productivity in response to nitrogen addition, warming, and increased rainfall. – Oikos doi: 10.1111/oik.07006", please contact Kai for only use of the data.
DOI: 10.6084/m9.figshare.13676518.v1
title: Novakomyces olei sp. nov., the First Member of a Novel Taphrinomycotina Lineage

description: Annotation data, alignements and an Excel table in which the missing and present genes of <i>Novakomyces olei</i> sp. nov., are listed.
DOI: 10.6084/m9.figshare.26936224.v2
title: GTDR simulation data

description: These data sets are simulation data for the review process of the manuscript, entitled 'Geographical and Temporal Density Regression'
DOI: 10.6084/m9.figshare.5715103.v2
title: gpu-cuda-spinodal-9pt

description: Solution to the CHiMaD Phase Field benchmark problem on spinodal decomposition using CUDA, with a 9-point discrete Laplacian stencil
DOI: 10.6084/m9.figshare.28633553.v1
title: Pharos database, version 3.19 (MySQL)

description: This is the MySQL data dump that Pharos uses to show data on https://pharos.nih.gov/.It is a modified version of the TCRD database (https://github.com/unmtransinfo/TCRD)
DOI: 10.6084/m9.figshare.28728989.v1
title: Data

description: Impact of GenAI on children's education
DOI: 10.6084/m9.figshare.11999991.v1
title: Supplementary Material for: Effectiveness of the Air Purification Strategies for the Treatment of Allergic Asthma: A Meta-Analysis

description: We updated the meta-analysis published by McDonald et al. [Chest 2002;122;1535–1542] by reviewing the effectiveness of air purification for the treatment of home-related allergic asthma (dust mite, dog, cat, and cockroach). We analysed the trials included by McDonald et al. as well as studies published since 2000. Data on asthma symptoms scores (ASS), medication use, forced expiratory volume in 1 s as a percentage of the predicted value (FEV<sub>1</sub> %pred), histamine provocative concentration causing a 20% reduction in FEV<sub>1</sub> (PC<sub>20</sub>), Asthma Quality of Life Questionnaire (AQLQ) scores, and fractional exhaled nitric oxide (FeNO) levels were extracted. The effectiveness was examined using metafor (registered in Prospero CRD42019127227). Ten trials including a total of 482 patients (baseline characteristics: mean FEV<sub>1</sub> %pred 83.2%, <i>I</i><sup>2</sup> = 96.7%; mean PC<sub>20</sub> 4.93 mg/mL, <i>I</i><sup>2</sup> = 44.0%; mean AQLQ 4.67 [max. 7], <i>I</i><sup>2</sup> = 93.7%; mean FeNO 36.5 ppb, <i>I</i><sup>2</sup> = 0%) were included. We assessed the mean differences in the AQLQ scores as +0.36 (95% CI 0.10 to 0.62, <i>p</i> = 0.01, <i>n</i> = 302, <i>I</i><sup>2</sup> = 0%) and the FeNO levels as –6.67 ppb (95% CI –10.56 to –2.77, <i>p</i> = 0.0008, <i>n</i> = 304, <i>I</i><sup>2</sup> = 0%). The standardised mean differences in all other health outcomes were not significant (ASS –0.68, <i>p</i> = 0.20; medication use: –0.01, <i>p</i> = 0.94; FEV<sub>1</sub> %pred –0.11, <i>p</i> = 0.34; PC<sub>20</sub> +0.24, <i>p</i> = 0.53). We found statistically significant mean differences in the AQLQ scores and FeNO levels in patients with predominantly mild to moderate asthma at baseline. A large trial reported great improvement in the subgroup of patients receiving Global Initiative for Asthma step 4 therapy. We recommend that future studies on air purification focus on patients with severe and poorly controlled allergic asthma.
DOI: 10.6084/m9.figshare.14213885.v2
title: Common decision-making models

description: The common ethical decision-making models
DOI: 10.6084/m9.figshare.20115467.v1
title: Data for "Eighty million years of rapid evolution of the primate Y chromosomes"

description: This folder contains data for "Eighty million years of rapid evolution of the primate Y chromosome" gene_set.zip contains gene annotation (GFF, CDS, PEP, POS.ADD) for the 30 species used in this study XY_location.zip contains the genomic coordinates for PAR, nonPARX and nonPARY (BED format). Species names are in the 4th column. gametolog_alignment.tar.gz contains gametolog alignment (PHY format) used to calculate pairwise dN/dS. S5.tree.zip contains alignment (FASTA format) and constructed phylogeny (NWK format) for each S5 gametologs. Conserved_Segments.100K.inferCARs contains conserved blocks of the X chromosome across species (inferCARs format) XY_SV.zip contains the sequences used in Y reconstruction analysis (FASTA format), and the recontruction results under 30 Kb resolution (30K/) and 50 Kb resolution (50K/) NLGN4XY.sort.prank.best.fas contains alignment of NLGN4X/Y of each primate trait_selection_analysis.zip contains sequence alignment (FASTA format) of each Y-linked genes used for dN/dS calculation in trait selection analysis. <br> <br> <br>
DOI: 10.6084/m9.figshare.27193464.v1
title: <b>MangroveDB: A comprehensive online database for mangroves based on multi-omics data</b>

description: Mangroves are dominant flora of intertidal zones along tropical and subtropical coastline around the world that offer important ecological and economic value. Recently, the genomes of mangroves have been decoded, and massive omics data were generated and deposited in the public databases. Reanalysis of multi-omics data can provide new biological insights excluded in the original studies. However, the requirements for computational resource and lack of bioinformatics skill for experimental researchers limit the effective use of the original data. To fill this gap, we uniformly processed 942 transcriptome data, 386 whole-genome sequencing data, and provided 13 reference genomes and 40 reference transcriptomes for 53 mangroves. Finally, we built an interactive web-based database platform MangroveDB (https://github.com/Jasonxu0109/MangroveDB), which was designed to provide comprehensive gene expression datasets to facilitate their exploration and equipped with several online analysis tools, including principal components analysis, differential gene expression analysis, tissue-specific gene expression analysis, GO and KEGG enrichment analysis. MangroveDB not only provides query functions about genes annotation, but also supports some useful visualization functions for analysis results, such as volcano plot, heatmap, dotplot, PCA plot, bubble plot, population structure <i>etc</i>. In conclusion, MangroveDB is a valuable resource for the mangroves research community to efficiently use the massive public omics datasets.
DOI: 10.6084/m9.figshare.28816622.v1
title: TE info Padilla-Garcia et al

description: This table gathers all the information of TE insertions detected in Padilla-Garcia et al. (MBE)
DOI: 10.6084/m9.figshare.1545544.v4
title: Heart rate of long distance runners collected one day before and during three days after a 100 km run

description: The data presents changes in the circulatory system of long distance runners before and just after extreme physical effort. In order to achieve that a group of voluntaries from the Sport Centre of the University of Physical Education and Sport in Gdansk had joined the research programme. They were obligated to take part in regular measurements of their heart rate just after the effort, as well as 24 and 48 hours after.The long distance run covered 100 km on a 3375 m loop with the total altitude difference not greater than 2 m. The run started at 07:20+01 in the morning and lasted for approximately 10 hours. The weather conditions during the run as follows: air temperature 4--5 degrees C, relative air humidity 86% with no wind. The heart rate of all voluntaries measured before the run was around 64--72/min, while just after the run was around 141--158/min.The heart rate of the runners was measured continuously from 12 minutes and thanks to that 450 sample long time series were collected. All heart rate signals were recorded based on the time intervals between successive R-waves of electrocardiographic signals.<br>The data is ordered according to the participants, i.e. each file 1.csv to 13.csv represents a single participant and his measurements gathered during the study. The column "day" indicates the day of the examination. The 1st day of examination took place on 2012-11-16 (one day preceding the extreme physical effort), the 2nd on 2012-11-17 (right after the effort), the 3rd on 2012-11-18 (one day following the effort), and the 4th on 2012-11-19 (two days following the effort). The column "timestamp" indicates the precise time of the examination (hh:mm:ss.sss), whereas the column "HR" contains the heart rate measurements in 1/min.
DOI: 10.6084/m9.figshare.26360977.v1
title: Supplementary Material for: Predicting Acute Exacerbation Phenotype in Chronic Obstructive Pulmonary Disease Patients using VGG-16 Deep Learning

description: Introduction：Exacerbations of chronic obstructive pulmonary disease (COPD) have a significant impact on hospitalizations, morbidity, and mortality of patients. This study aimed to develop a model for predicting acute exacerbation in COPD patient (AECOPD) based on deep learning (DL) features. 
Methods: We performed a retrospective study on 219 patients with COPD who underwent inspiratory and expiratory HRCT scans. By recording the acute respiratory events of the previous year, these patients were further divided into Non-AECOPD group and AECOPD group according to the presence of acute exacerbation events. 69 Quantitative CT (QCT) parameters of emphysema and airway were calculated by NeuLungCARE software and 2000 DL features were extracted by VGG-16 method. The Logistic regression method was employed to identify AECOPD patients and 29 patients of external validation cohort were used to access the robustness of the results. 
Results: The Model 3-B achieved an AUC of 0.933, and 0.865 in the testing cohort and external validation cohort respectively. Model 3-I obtained AUC of 0.895 in the testing cohort and AUC of 0.774 in the external validation cohort. Model 7-B combined clinical characteristics, QCT parameters, and DL features achieved the best performance with an AUC of 0.979 in the testing cohort and demonstrating robust predictability with an AUC of 0.932 in the external validation cohort. Likewise, Model 7-I achieving an AUC of 0.938, and 0.872 in the testing cohort and external validation cohort respectively. 
Conclusions: DL features extracted from HRCT scans can effectively predict acute exacerbation phenotype in COPD patients.
DOI: 10.6084/m9.figshare.8003945.v1
title: Pancrustacean evolution illuminated by taxon-rich genomic-scale data sets with an expanded remipede sampling

description: Amino acid matrices, Orthogroups and Phylogenetic Trees<br><br>We provide the concatenated alignments in fasta format of Matrix A and B (untrimmed and trimmed) with a nexus file with the gene partitions. We also provide in fasta format those orthogroups predicted by OMA standalone software that were present at least in 50% of the considered transcriptomes. Gene trees are included in nexus format.<br>
DOI: 10.6084/m9.figshare.8851853.v1
title: Supplementary Material for: Amino Acid Loss during Continuous Venovenous Hemofiltration in Critically Ill Patients

description: <b><i>Background/Objectives:</i></b> During continuous venovenous hemofiltration (CVVH), there is unwanted loss of amino acids (AA) in the ultrafiltrate (UF). Solutes may also be removed by adsorption to the filter membrane. The aim was to quantify the total loss of AA via the CVVH circuit using a high-flux polysulfone membrane and to differentiate between the loss by ultrafiltration and adsorption. <b><i>Methods:</i></b> Prospective observational study in ten critically ill patients, receiving predilution CVVH with a new filter, blood flow 180 mL/min, and predilution flow 2,400 mL/h. Arterial blood, postfilter blood, and UF samples were taken at baseline, and 1, 8, and 24-h after CVVH initiation, to determine AA concentrations and hematocrit. Mass transfer calculations were used to determine AA loss in the filter and by UF, and the difference between these 2. <b><i>Results:</i></b> The median AA loss in the filter was 10.4 g/day, the median AA loss by UF was 13.4 g/day, and the median difference was –2.9 g/day (IQR –5.9 to –1.4 g/day). For the individual AA, the difference ranged from –1 g/day to +0.4 g/day, suggesting that some AA were consumed or adsorbed and others were generated. AA losses did not significantly change over the 24-h study period. <b><i>Conclusion:</i></b> During CVVH with a modern polysulfone membrane, the estimated AA loss was 13.4 g/day, which corresponds to a loss of about 11.2 g of protein per day. Adsorption did not play a major role. However, individual AA behaved differently, suggesting complex interactions and processes at the filter membrane or peripheral AA production.
DOI: 10.6084/m9.figshare.19145072.v1
title: Supplementary Material for: The Efficacy of Early Additional Hemoperfusion Therapy for Severe COVID-19 Patients: A Prospective Cohort Study

description: <b><i>Introduction:</i></b> Currently, the effect of hemoperfusion on outcome in severe COVID-19 patients is still unknown. Therefore, we aimed to investigate the effects of early HA-330 hemoperfusion in severe COVID-19 patients. <b><i>Methods:</i></b> We conducted a single center, prospective cohort study on patients who were diagnosed with severe COVID-19 patients and admitted to ICU. Patients in hemoperfusion group (defined as patients who were treated with hemoperfusion therapy at least 3 sessions in combination with standard therapy) were compared with the control group (defined as patients who received standard treatment alone or received less than 3 sessions of hemoperfusion therapy). The primary outcome was daily sequential organ failure assessment (SOFA) scores. Secondary outcomes were all-cause mortality at 28 days, mechanical ventilator-free day, daily C-reactive protein (CRP), oxygenation (defined by PaO<sub>2</sub>/FiO<sub>2</sub> ratio), and severity score of lung infiltration on the chest X-ray (CXR RALE score). All outcomes were adjusted by regression analysis to reduce the confounders due to some difference in baseline characteristics. <b><i>Results:</i></b> A total number of 29 severe and critical COVID-19 confirmed patients were enrolled. Fifteen patients were defined as hemoperfusion group and 14 were control group. The median of CRP and SOFA score at the baseline (the day after severe pneumonia diagnosis or before hemoperfusion) in hemoperfusion and control groups were comparable, 96.79 mg/L and 87.3 mg/L, <i>p</i> = 0.53, 3.53 ± 0.99 versus 4.3 ± 1.89, <i>p</i> = 0.15, respectively. Clinical improvement associated with decreased SOFA score and improvement of CXR RALE score were found in hemoperfusion group compared to control group (<i>p</i> = 0.008 and <i>p</i> = 0.005, respectively). The 28-day mortality rate was significantly lower in hemoperfusion group compared to control group (6.67% vs. 85.71%, <i>p</i> &lt; 0.001) and the adjusted hazard ratio of death was 0.017 (95% confidence interval = 0.008–0.351, <i>p</i> = 0.008). <b><i>Conclusions:</i></b> The addition of early HA-330 hemoperfusion to standard therapy improved severity of organ failure and might reduce the mortality rate. However, the results were affected by the baseline confounders and limited sample size.
DOI: 10.6084/m9.figshare.26048572.v1
title: Supplementary Material for: Real-Time Cardiac Abnormality Monitoring and Nursing for Patient using Electrocardiographic Signals

description: Introduction
Cardiovascular disease care is a critical clinical application that necessitates real-time monitoring models. Previous models required the use of multi-lead signals and could not be customized as needed. Traditional methods relied on manually designed supervised algorithms, based on empirical experience, to identify waveform abnormalities and classify diseases, and were incapable of monitoring and alerting abnormalities in individual waveforms.
Methods
This research reconstructed the vector model for arbitrary leads using the phase space time delay method, enabling the model to arbitrarily combine signals as needed while possessing adaptive denoising capabilities. After employing automatically constructed machine learning algorithms and designing for rapid convergence, the model can identify abnormalities in individual waveforms and classify diseases, as well as detect and alert on abnormal waveforms.
Result
Effective noise elimination was achieved, obtaining a higher degree of loss function fitting. Afterwards, the detail differences of the electrocardiogram signal were amplified using a single-lead three-dimensional model. A cropping algorithm was used to remove waveforms severely interfered by external factors. Then, automatic neural network recognition was used. The automatic network generation model was designed effectively for different data types. The accuracy of patient identification is 98.2%, and the accuracy for healthy patients is 99.2%.
Conclusion
The elastic wavelet neural network can automatically denoise. Through the three-dimensional model, the detailed changes of electrocardiogram signals of different diseases can be observed. The cropping algorithm effectively identified the interfered and destroyed waveforms. The automatic neural network is capable of carrying out disease type classification and patient identity classification.
DOI: 10.6084/m9.figshare.6844496.v1
title: Supplementary Material for: Human Cervical Epithelial Cells Release Antiviral Factors and Inhibit HIV Replication in Macrophages

description: The female reproductive tract is a major site of HIV sexual transmission. We here examined whether human cervical epithelial cells (HCEs) can be immunologically activated and produce antiviral factors against HIV. We demonstrated that HCEs (End1/E6E7 cells) possess the functional toll-like receptor (TLR)3 signaling system, which could be activated by Poly I:C and induce multiple cellular HIV restriction factors. The treatment of primary human macrophages with supernatant (SN) from TLR3-activated End1/E6E7 cell cultures resulted in HIV inhibition. This SN-mediated HIV inhibition was mainly through the induction of interferons (IFN)-β and IFN-λs, as the antibodies to IFN-β or IFN-λs receptor could effectively block the SN-mediated anti-HIV effect. Further studies showed that the incubation of macrophages with SN from the activated cervical epithelial cell cultures induced the expression of a number of IFN-stimulated genes (ISGs), including IFN-stimulated gene (ISG15), ISG56, 2′, 5′-oligoadenylate synthetase 1 (OAS 1), OAS 2, Myxovirus Resistance A (MxA), MxB, and Guanylate-binding protein 5 (GBP5). In addition, TLR3-activated cells produced the CC chemokines [regulated on activation, normal T cell expressed and secreted (RANTES), Human macrophage inflammatory protein 1 alpha (MIP-1α), MIP-1β] the ligands of HIV entry co-receptor CCR5. These observations support further studies on HCEs as potentially crucial and alternative targets for immunological intervention to control and prevent HIV sexual transmission.
DOI: 10.6084/m9.figshare.692034.v1
title: IsoCleft Finder Dataset version 1.6 (ICFDB v. 1.6)

description: Non-redundant dataset of 7339 entries representing unique Pfam/PDB-ligand (hetero group code) combinations with known levels of cognate ligand similarity. Each entry includes a ligand and a set of interacting residues in PDB format.
DOI: 10.6084/m9.figshare.13516382.v1
title: All data for Mast cell activation ameliorates

description: datasets
DOI: 10.6084/m9.figshare.7670756.v2
title: Extensive loss of cell cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts

description: Cell cycle checkpoints and DNA repair processes protect organisms from potentially lethal mutational damage. Compared to other budding yeasts in the subphylum Saccharomycotina, we noticed that a lineage in the genus Hanseniaspora exhibited very high evolutionary rates, low GC content, small genome sizes, and lower gene numbers. To better understand Hanseniaspora evolution, we analyzed 25 genomes, including 11 newly sequenced, representing 18 / 21 known species in the genus. Our phylogenomic analyses identify two Hanseniaspora lineages, a faster-evolving lineage (FEL), which began diversifying ~87 million years ago (mya), and a slower-evolving lineage (SEL), which began diversifying ~54 mya. Remarkably, both lineages lost genes associated with the cell cycle and genome integrity, but these losses were greater in the FEL. For example, all species lost the cell cycle regulator WHI5, and the FEL lost components of the spindle checkpoint pathway (e.g., MAD1, MAD2) and DNA damage checkpoint pathway (e.g., MEC3, RAD9). Similarly, both lineages lost genes involved in DNA repair pathways, including the DNA glycosylase gene MAG1, which is part of the base excision repair pathway, and the DNA photolyase gene PHR1, which is involved in pyrimidine dimer repair. Strikingly, the FEL lost 33 additional genes, including polymerases (i.e., POL4 and POL32) and telomere-associated genes (e.g., RIF1, RFA3, CDC13, PBP2). Echoing these losses, molecular evolutionary analyses reveal that, compared to the SEL, the FEL stem lineage underwent a burst of accelerated evolution, which resulted in greater mutational loads, homopolymer instabilities, and higher fractions of mutations associated with the common endogenously damaged base, 8-oxoguanine. We conclude that Hanseniaspora is an ancient lineage that has diversified and thrived, despite lacking many otherwise highly conserved cell cycle and genome integrity genes and pathways, and may represent a novel system for studying cellular life without them.