cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20677009
title: Synthesis and SARS-CoV-2 3CL Protease Inhibitory Effects of Oxazolidinone Derivatives

description: The 3-chymotrypsin-like protease (3CLpro) is an attractive target for the development of anti-SARS (severe acute respiratory syndrome) drugs. In this work, a series of oxazolidinone derivatives 3a-3v were synthesized and their inhibitory activities against SARS coronavirus 2 (SARS-CoV-2) 3CLpro were evaluated by the fluorescence resonance energy transfer (FRET)-based enzymatic assay. Among synthesized compounds, 3g displayed the best inhibitory activity, with a half maximal inhibitory concentration (IC50) value of 14.47 μM. Also, docking studies implied that compound 3g was fitted into the active pocket of 3CLpro, forming a hydrogen bond with Glu166.
DOI: 10.6084/m9.figshare.23905560
title: Files for manuscript 'Why am I overwhelmed by bright lights? The behavioural mechanisms of post-stroke visual hypersensitivity'

description: Dataset for manuscript 'Why am I overwhelmed by bright lights? The behavioural mechanisms of post-stroke visual hypersensitivity'
DOI: 10.6084/m9.figshare.17006963.v1
title: Additional file 4 of Whole-transcriptome sequencing reveals a vernalization-related ceRNA regulatory network in chinese cabbage (Brassica campestris L. ssp. pekinensis)

description: Table S4. List of GO terms for differentially expressed (DE) mRNAs, lncRNAs, circRNAs, and miRNAs.
DOI: 10.6084/m9.figshare.5472661
title: Identification of novel PPARα/γ dual agonists by virtual screening, ADMET prediction and molecular dynamics simulations

description: PPARα and PPARγ have been the most widely studied Peroxisome proliferator-activated receptor (PPAR) subtypes due to their important roles in regulating glucose, lipids, and cholesterol metabolism. By combining the lowering serum triglyceride levels benefit of PPARα agonists (such as fibrates) with the glycemic advantages of the PPARγ agonists (such as TZD), the dual PPAR agonists approach can both improve the metabolic effects and minimize the side effects caused by either agent alone, and hence, has become a promising strategy for designing effective drugs against type-2 diabetes. In this study, by means of virtual screening, ADMET prediction and molecular dynamics (MD) simulations techniques, one compound-ASN15761007 with high binding score, low toxicity were gained. It was observed by MD simulations that ASN15761007 not only possessed the same function as AZ242 did in activating PPARα and BRL did in activating PPARγ, but also had more favorable conformation for binding to the two receptors. Our results provided an approach to rapidly produce novel PPARα/γ dual agonists which might be a potential lead compound to develop against insulin resistance and hyperlipidemia.
DOI: 10.6084/m9.figshare.21201338
title: Supplementary data 2: effect sizes from Combined effects of warming and drought on plant biomass depend on plant woodiness and community type: a meta-analysis

description: Calculated effect sizes based on the data extracted from the different studies in our database. The file is divided in warming*drought studies and warming*flooding studies.
DOI: 10.6084/m9.figshare.20677009.v1
title: Synthesis and SARS-CoV-2 3CL Protease Inhibitory Effects of Oxazolidinone Derivatives

description: The 3-chymotrypsin-like protease (3CLpro) is an attractive target for the development of anti-SARS (severe acute respiratory syndrome) drugs. In this work, a series of oxazolidinone derivatives 3a-3v were synthesized and their inhibitory activities against SARS coronavirus 2 (SARS-CoV-2) 3CLpro were evaluated by the fluorescence resonance energy transfer (FRET)-based enzymatic assay. Among synthesized compounds, 3g displayed the best inhibitory activity, with a half maximal inhibitory concentration (IC50) value of 14.47 μM. Also, docking studies implied that compound 3g was fitted into the active pocket of 3CLpro, forming a hydrogen bond with Glu166.
DOI: 10.6084/m9.figshare.21201341.v1
title: Supplementary data 1: database with extracted data from Combined effects of warming and drought on plant biomass depend on plant woodiness and community type: a meta-analysis

description: This file shows raw data extracted from the different studies in our database. Individual rows are used as independent data points.
DOI: 10.6084/m9.figshare.5472661.v1
title: Identification of novel PPARα/γ dual agonists by virtual screening, ADMET prediction and molecular dynamics simulations

description: PPARα and PPARγ have been the most widely studied Peroxisome proliferator-activated receptor (PPAR) subtypes due to their important roles in regulating glucose, lipids, and cholesterol metabolism. By combining the lowering serum triglyceride levels benefit of PPARα agonists (such as fibrates) with the glycemic advantages of the PPARγ agonists (such as TZD), the dual PPAR agonists approach can both improve the metabolic effects and minimize the side effects caused by either agent alone, and hence, has become a promising strategy for designing effective drugs against type-2 diabetes. In this study, by means of virtual screening, ADMET prediction and molecular dynamics (MD) simulations techniques, one compound-ASN15761007 with high binding score, low toxicity were gained. It was observed by MD simulations that ASN15761007 not only possessed the same function as AZ242 did in activating PPARα and BRL did in activating PPARγ, but also had more favorable conformation for binding to the two receptors. Our results provided an approach to rapidly produce novel PPARα/γ dual agonists which might be a potential lead compound to develop against insulin resistance and hyperlipidemia.
DOI: 10.6084/m9.figshare.13348082
title: Methylomic Signatures of High Grade Serous Ovarian Cancer

description: High-grade serous ovarian cancer (HGSOC) harbours aberrant epigenetic features, including DNA methylation. In this study we delineate pathways and networks altered by DNA methylation and associated with HGSOC initiation and progression to a platinum-resistant state. By including tumours from patients who had been treated with the hypomethylating agent (HMA) guadecitabine, we also addressed the role of HMAs in treatment of HGSOC. Tumours from patients with primary (platinum-naïve) HGSOC (n = 20) were compared to patients with recurrent platinum-resistant HGSOC and enrolled in a recently completed clinical trial (NCT01696032). Human ovarian surface epithelial cells (HOSE; n = 5 samples) served as normal controls. Genome-wide methylation profiles were determined. DNA methyltransferase (DNMT) expression levels were examined by immunohistochemistry and correlated with clinical outcomes. Cancer-related and tumorigenesis networks were enriched among differentially methylated genes (DMGs) in primary OC vs. HOSE. When comparing platinum-resistant and primary tumours, 452 CpG island (CGI)-containing gene promoters acquired DNA methylation; of those loci, decreased (P &lt; 0.01) methylation after HMA treatment was observed in 42% (n = 189 CGI). Stem cell pluripotency and cytokine networks were enriched in recurrent platinum-resistant OC tumours, while drug metabolism and transport-related networks were downregulated in tumours from HMA-treated patients compared to HOSE. Lower DNMT1 and 3B protein levels in pre-treatment tumours were associated with improved progression-free survival. The findings provide important insight into the DNA methylation landscape of HGSOC tumorigenesis, platinum resistance and epigenetic resensitization. Epigenetic reprogramming plays an important role in HGSOC aetiology and contributes to clinical outcomes.
DOI: 10.6084/m9.figshare.7045574.v1
title: Captopril alleviates hypertension-induced renal damage, inflammation, and NF-κB activation

description: Hypertensive renal damage generally occurs during the middle and late stages of hypertension, which is typically characterized by proteinuria and renal inflammation. Captopril, an angiotensin-converting enzyme (ACE) inhibitor, has been widely used for therapy of arterial hypertension and cardiovascular diseases. However, the protective effects of captopril on hypertension-induced organ damage remain elusive. The present study was designed to explore the renoprotective action of captopril in spontaneously hypertensive rats (SHR). The 6-week-old male SHR and age-matched Wistar-Kyoto rats were randomized into long-term captopril-treated (34 mg/kg) and vehicle-treated groups. The results showed that in SHR there was obvious renal injury characterized by the increased levels of urine albumin, total protein, serum creatinine, blood urea nitrogen, renal inflammation manifested by the increased mRNA and protein expression of inflammatory factors including tumor necrosis factor-α, interleukin (IL)-1β, IL-6, and inducible nitric oxide synthase, and enhanced nuclear factor-κB (NF-κB) activation. Captopril treatment could lower blood pressure, improve renal injury, and suppress renal inflammation and NF-κB activation in SHR rats. In conclusion, captopril ameliorates renal injury and inflammation in SHR possibly via inactivation of NF-κB signaling.
DOI: 10.6084/m9.figshare.12806068
title: Additional file 4 of Proteomic analysis revealed common, unique and systemic signatures in gender-dependent hepatocarcinogenesis

description: Additional file 4: Figure S4. The presentation of images of original membrane for Western blot.
DOI: 10.6084/m9.figshare.17007152.v1
title: Additional file 2 of Comparative genomic analysis of the tricarboxylic acid cycle members in four Solanaceae vegetable crops and expression pattern analysis in Solanum tuberosum

description: Detailed list of orthologous gene clusters and singletons between Solanum tuberosum, Solanum lycopersicum, Solanum melongena, Capsicum annuum, and Arabidopsis thaliana.
DOI: 10.6084/m9.figshare.17007078
title: Additional file 3 of The legume-specific transcription factor E1 controls leaf morphology in soybean

description: Additional file 3: Data S1. List of genes with significant expression changes. (XLS 6546 kb)
DOI: 10.6084/m9.figshare.7569977
title: Additional file 1: of Duplication and expression of horizontally transferred polygalacturonase genes is associated with host range expansion of mirid bugs

description: Table S1. Primers used in this study. Table S2. Summary of the sequence assembly after Illumina sequencing. As = Adelphocoris suturalis, Af = A. fasciaticollis, Al = A. lineolatus, Nt = Nesidiocoris tenuis. Table S3. Identification of polygalacturonase genes in Adelphocoris suturalis. Table S4. Identification of polygalacturonase genes in Adelphocoris fasciaticollis. Table S5. Identification of polygalacturonase genes in Adelphocoris lineolatus. Table S6. Identification of polygalacturonase genes in Nesidiocoris tenuis. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.7569977.v1
title: Additional file 1: of Duplication and expression of horizontally transferred polygalacturonase genes is associated with host range expansion of mirid bugs

description: Table S1. Primers used in this study. Table S2. Summary of the sequence assembly after Illumina sequencing. As = Adelphocoris suturalis, Af = A. fasciaticollis, Al = A. lineolatus, Nt = Nesidiocoris tenuis. Table S3. Identification of polygalacturonase genes in Adelphocoris suturalis. Table S4. Identification of polygalacturonase genes in Adelphocoris fasciaticollis. Table S5. Identification of polygalacturonase genes in Adelphocoris lineolatus. Table S6. Identification of polygalacturonase genes in Nesidiocoris tenuis. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.8105318.v1
title: Additional file 6: of Gene expression profiling analysis to investigate the role of remote ischemic postconditioning in ischemia-reperfusion injury in rats

description: Table S4. The differently expressed genes identified by IRIâ +â RPostC vs. control comparison. (XLSX 3221 kb)
DOI: 10.6084/m9.figshare.8094308
title: Supplementary Material from <i>In silico</i> simulation of a clinical trial with anti-CTLA-4 and anti-PD-L1 immunotherapies in metastatic breast cancer using a systems pharmacology model.

description: Model SBML code
DOI: 10.6084/m9.figshare.14385586.v1
title: Additional file 1 of Role of tumor mutation burden-related signatures in the prognosis and immune microenvironment of pancreatic ductal adenocarcinoma

description: Additional file 1: Figure S1. GO analysis and GSEA of the TRGs. (A) GO analysis showed the function of TRGs. (B) GSEA showed differentially enriched pathways of TRGs using the GO gene-sets. Figure S2. Mutational landscape of the TMB_high and TMB_low groups. Figure S3. Lasso regression identifies 16 TRGs for model construction. (A) The curve shows that the partial likelihood deviance changed along with the lambda value. The lambda value is determined when the partial likelihood deviance is at its minimum value. (B) When the lambda value is determined, the corresponding coefficient of each gene can be determined. Figure S4. Validation of the constructed model using the same coefficients and cutoff values. (A) PDAC patients were divided into high- and low-risk groups based on their scores calculated by the model. (B) The survival time and status of PDAC patients varied with increasing risk scores. (C) Patients with low lasso risk scores had prolonged OS. (D) Patients with high lasso risk scores featured increased cumulative hazards. (E) ROC curve to assess the accuracy of the model. Figure S5. The differential expression of four genes in the prognostic model based on bulk sequencing and qPCR validation. Target genes from left to right were GBP1, HIST1H1C, MMP28 and PPP1R15A, respectively. Cell-lines from top to bottom were capan-1, panc-1, Mia-paca-2 and SW1990. Figure S6. Correlation analysis between ANKRD55 expression and immune checkpoints (A) DNA transmethylases (B) and DNA repair-related proteins (C). Table S1. Primer sequencing of the genes that need to be validate by PCR. Table S2. A summary of survival-associated TRGs in PDAC. Table S3. Genes used in the construction of prognosis model. Table S4. Characterization of validation cohorts. Table S5. The association between CD8 + T cells infiltration and TMB score.
DOI: 10.6084/m9.figshare.8094308.v2
title: Supplementary Material from <i>In silico</i> simulation of a clinical trial with anti-CTLA-4 and anti-PD-L1 immunotherapies in metastatic breast cancer using a systems pharmacology model.

description: Model SBML code
DOI: 10.6084/m9.figshare.17007149
title: Additional file 1 of Comparative genomic analysis of the tricarboxylic acid cycle members in four Solanaceae vegetable crops and expression pattern analysis in Solanum tuberosum

description: The TCA cycle proteins in four Solanaceous crops.
DOI: 10.6084/m9.figshare.17007149.v1
title: Additional file 1 of Comparative genomic analysis of the tricarboxylic acid cycle members in four Solanaceae vegetable crops and expression pattern analysis in Solanum tuberosum

description: The TCA cycle proteins in four Solanaceous crops.
DOI: 10.6084/m9.figshare.17007155.v1
title: Additional file 3 of Comparative genomic analysis of the tricarboxylic acid cycle members in four Solanaceae vegetable crops and expression pattern analysis in Solanum tuberosum

description: Detailed list of paralogous gene pairs in Solanum tuberosum, Solanum lycopersicum, Solanum melongena, Capsicum annuum, and Arabidopsis thaliana.
DOI: 10.6084/m9.figshare.22774387.v1
title: Additional file 2 of Modeling group heteroscedasticity in single-cell RNA-seq pseudo-bulk data

description: Additional file 2: Table S1. Summary of filtering steps applied to each dataset.
DOI: 10.6084/m9.figshare.7569995
title: Additional file 3: of Duplication and expression of horizontally transferred polygalacturonase genes is associated with host range expansion of mirid bugs

description: The coding sequence of PGs identified in this study. (ZIP 71 kb)
DOI: 10.6084/m9.figshare.14910096.v1
title: Metadata record for the article: Genetic Epidemiology of BRCA1- and BRCA2-associated Cancer Across Latin America

description: <b>Summary</b><br>

This
metadata record provides details of the data supporting the claims of the
related article: “Genetic Epidemiology of BRCA1- and
BRCA2-associated Cancer Across Latin America”.

The
related study reports the results of employing a sequential genetic testing
strategy to detect BRCA

pathogenic
variants (PVs) in a large sample of Latin Americans meeting referral criteria,
using a combination of Sequenom MassARRAY technology, Ion Torrent semiconductor
sequencing, and

PCR-based
methodologies for copy number variants (CNVs).

 

Type of data:
pathogenic BRCA variants and VUS; clinical data

Subject of
data: <i>Homo sapiens</i>

Population
characteristics: Patients seen for genetic cancer risk assessment (GCRA) through
Clinical Cancer Genomics Community Research Network (CCGCRN) at 13,46 sites in
Latin America between December 2012 and August 2017 were prospectively enrolled
after informed consent on an IRB-approved protocol and offered genetic testing.
Six Latin American cancer centres were included: 1) Instituto Nacional de
Cancerlogía (INCan) in Mexico City, Mexico; 2) Instituto Jalisciense de
Cancerologia, in Guadalajara, Mexico; 3) Instituto des Enfermedades Neoplásicas
(INEN) in Lima, Peru; 4) Clínica del Country, Oncology Center, in Bogota,
Colombia; 5) The University of Puerto Rico and MD Anderson Cancer Center in San
Juan, Puerto Rico; 6) Hospital de Clínicas de Porto Alegre in Porto Alegre,
Brazil. Patients met the National
Comprehensive Cancer Network (NCCN) guidelines for genetic/familial high-risk
assessment: breast and ovarian. Demographic characteristics, clinical variables
and four-generation pedigrees focused on family cancer history were obtained.
When more than one person was enrolled and tested in a family, the first person
tested was selected for inclusion in study.

Trial
registration number: NCT04185935

 

<b>Data
access</b>

The pathogenic BRCA variants and VUS
data are included as separate tabs in ‘Supplemental tables 2 and 3.xlsx’, which
is available via the online version of the related article as well as in Excel
format as part of this data record. Unique variants have been deposited in <i>ClinVar </i>under accessions https://identifiers.org/clinvar.submission:SCV001739435
to <br>
https://identifiers.org/clinvar.submission:SCV001739444. The minimum dataset

necessary to interpret, replicate
and/or build upon the methods of the related article will be made available
upon request to the corresponding author.

 

<b>Corresponding author(s) for this study</b>

Jeffrey
N. Weitzel, M.D., 578 Acacia Street, Sierra Madre, CA 91024, USA. jnweitzel57@gmail.com
Phone: (626) 233-9713<br>
<br>
<b></b>

<b>Study
approval </b>

The
overall protocol was approved by the IRB at City of Hope (#96144) data
coordinating center, and approved separately, as a Federated consortium at each
participating center.
DOI: 10.6084/m9.figshare.23292018.v1
title: Additional file 2 of m6A-mediated upregulation of LINC01003 regulates cell migration by targeting the CAV1/FAK signaling pathway in glioma

description: Additional file 2: Table S2. Top 20 KEGG enrichment pathways in the downregulated mRNAs.
DOI: 10.6084/m9.figshare.24347102.v1
title: Efficient Model-free Subsampling Method for Massive Data

description: Subsampling plays a crucial role in tackling problems associated with the storage and statistical learning of massive datasets. However, most existing subsampling methods are model-based, which means their performances can drop significantly when the underlying model is misspecified. Such an issue calls for model-free subsampling methods that are robust under diverse model specifications. Recently, several model-free subsampling methods are developed. However, the computing time of these methods grows explosively with the sample size, making them impractical for handling massive data. In this paper, an efficient model-free subsampling method is proposed, which segments the original data into some regular data blocks and obtains subsamples from each data block by the data-driven subsampling method. Compared with existing model-free subsampling methods, the proposed method has a significant speed advantage and performs more robustly for datasets with complex underlying distributions. As demonstrated in simulation experiments, the proposed method is an order of magnitude faster than other commonly used model-free subsampling methods when the sample size of the original dataset reaches the order of 10<sup>7</sup>. Moreover, simulation experiments and case studies show that the proposed method is more robust than other model-free subsampling methods under diverse model specifications and subsample sizes.
DOI: 10.6084/m9.figshare.12288485.v1
title: Acute kidney injury after nephron sparing surgery and microwave ablation: focus on incidence, survival impact and prediction

description: To compare acute kidney injury (AKI) incidence between nephron sparing surgery (NSS) and microwave ablation (MWA) for T1a RCC patients, reveal the effect of AKI on survival prognosis, construct AKI nomogram and use Law of Total Probability for survival probability (SP) prediction. Patients were studied retrospectively after NSS (<i>n</i> = 1267) or MWA (<i>n</i> = 210) from January 1, 2011 to June 30, 2017. Using one to one Propensity Score Matching (PSM), 158 pairs of patients were identified for the cohort study. AKI incidence, risk factors and impact on survival outcomes were analyzed using Chi-square test, logistic and cox regression analysis. AKI risk and SP were predicted by nomogram and Law of Total Probability. The performance of the nomogram was assessed with respect to its discrimination, calibration, and clinical usefulness. AKI occurred more commonly in NSS (27.85%) cohort, when compared to MWA (17.72%) cohort (<i>p</i> = 0.032), but treatment modality was not independently predictive of AKI occurrence (odds ratio [OR]: 0.598; 95% confidence interval [CI]: 0.282–1.265; <i>p</i> = 0.178). The 5-yr overall survival (OS) was lower in AKI patients (73.5%) compared with non-AKI patients (94.8%; <i>p</i> &lt; 0.001). AKI was an independent risk factor for all-cause mortality in RCC patients (hazard ratio [HR]: 2.820; 95% confidence interval [CI]: 1.110–7.165; <i>p</i> = 0.029). Predictors for both NSS- and MWA-related AKI included tumor diameter, baseline eGFR and CCI score. RENAL score and tumor blood supply can predict AKI after NSS and MWA, respectively. The AKI normograms demonstrated good discrimination, with AUCs &gt;0.86, excellent calibration and net benefits at the decision curve analysis with probabilities ≥5%. SP predicted by Law of Total Probability was comparable to actual OS. AKI was an early indicator for poor overall survival in RCC patients. It can be predicted by several oncological parameters. Nomogram and Law of Total Probability can accurately predict AKI risk and SP.
DOI: 10.6084/m9.figshare.17007078.v1
title: Additional file 3 of The legume-specific transcription factor E1 controls leaf morphology in soybean

description: Additional file 3: Data S1. List of genes with significant expression changes. (XLS 6546 kb)
DOI: 10.4121/61f283ae-c30c-42d1-9a7c-89b454e013b3
title: Data underlying the publication: Robust Multi-Modal Density Estimation

description: This dataset contains three folders related to the samples used for validating the approach proposed in "ROME: Robust Multi-Modal Density Estimation". The folder "Fitted Distributions" contains the distributions obtained by using both ROME and other methods which we compare to in the publication. "Log Likelihoods" contains the likelihood values for the samples that make up the previously mentioned distributions. Lastly, "Results" contain the metric values which provide the basis for the final data analysis and results reported in the publication.<br>This data is to be used in conjunction to the code available at https://github.com/anna-meszaros/ROME/tree/main , and contains the results obtained using this code.
DOI: 10.34740/kaggle/dsv/7624329
title: COVID Vaccination in World (updated daily)