cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19802296.v1
title: Additional file 10 of Bulk and single-cell transcriptome profiling reveal necroptosis-based molecular classification, tumor microenvironment infiltration characterization, and prognosis prediction in colorectal cancer

description: Additional file 10. Supplementary Table S1. The description of patients with bulk RNA expression data, including clinical characteristics and consensus clusters.
DOI: 10.6084/m9.figshare.19802311
title: Additional file 14 of Bulk and single-cell transcriptome profiling reveal necroptosis-based molecular classification, tumor microenvironment infiltration characterization, and prognosis prediction in colorectal cancer

description: Additional file 14. Supplementary Table S5. NRG_score of TCGA and meta_GEO cohort.
DOI: 10.6084/m9.figshare.19802311.v1
title: Additional file 14 of Bulk and single-cell transcriptome profiling reveal necroptosis-based molecular classification, tumor microenvironment infiltration characterization, and prognosis prediction in colorectal cancer

description: Additional file 14. Supplementary Table S5. NRG_score of TCGA and meta_GEO cohort.
DOI: 10.6084/m9.figshare.19802300
title: Additional file 1 of Insights into AIM-InDel diversities in Yunnan Miao and Hani ethnic groups of China for forensic and population genetic purposes

description: Additional file 1: Supplementary Table 1. List of reference populations and their abbreviations, sample sizes and locations. Supplementary Table 2. r2 values, x2 and their p-values for pairwise loci in the linkage disequilibrium analyses (Yunnan Hani group). Supplementary Table 3. r2 values, x2 and their p-values for pairwise loci in the linkage disequilibrium analyses (Yunnan Miao group). Supplementary Table 4. Forensic parameters of 39 AIM-InDel loci as well as their p values for Hardy-Weinberg equilibrium tests in Yunnan Miao ethnic group of China (n = 203). Supplementary Table 5. Forensic parameters of 39 AIM-InDel loci as well as their p values for Hardy-Weinberg equilibrium tests in Yunnan Hani ethnic group of China (n = 203). Supplementary Table 6. The FST values between the studied groups and reference populations. Supplementary Table 7. Allele frequency differential (δ) of 38 AIM-InDel loci in pairwise intercontinental populations.
DOI: 10.6084/m9.figshare.19802300.v1
title: Additional file 1 of Insights into AIM-InDel diversities in Yunnan Miao and Hani ethnic groups of China for forensic and population genetic purposes

description: Additional file 1: Supplementary Table 1. List of reference populations and their abbreviations, sample sizes and locations. Supplementary Table 2. r2 values, x2 and their p-values for pairwise loci in the linkage disequilibrium analyses (Yunnan Hani group). Supplementary Table 3. r2 values, x2 and their p-values for pairwise loci in the linkage disequilibrium analyses (Yunnan Miao group). Supplementary Table 4. Forensic parameters of 39 AIM-InDel loci as well as their p values for Hardy-Weinberg equilibrium tests in Yunnan Miao ethnic group of China (n = 203). Supplementary Table 5. Forensic parameters of 39 AIM-InDel loci as well as their p values for Hardy-Weinberg equilibrium tests in Yunnan Hani ethnic group of China (n = 203). Supplementary Table 6. The FST values between the studied groups and reference populations. Supplementary Table 7. Allele frequency differential (δ) of 38 AIM-InDel loci in pairwise intercontinental populations.
DOI: 10.6084/m9.figshare.11937996
title: Additional file 1 of Genome-wide analysis reveals molecular convergence underlying domestication in 7 bird and mammals

description: Additional file 1. Supplementary Tables
DOI: 10.6084/m9.figshare.11937996.v1
title: Additional file 1 of Genome-wide analysis reveals molecular convergence underlying domestication in 7 bird and mammals

description: Additional file 1. Supplementary Tables
DOI: 10.6084/m9.figshare.14035169
title: Two-dimensional shear wave elastography for screening varices in Asian patients with primary biliary cholangitis

description: <b>Objectives</b>: The presence of varices affects the survival of patients with primary biliary cholangitis (PBC). The aim of this study is to assess the criteria based on liver stiffness (LS) measured by two-dimensional shear wave elastography (2D-SWE) and platelet count (PLT), and recently published noninvasive models for triaging PBC patients. <b>Methods</b>: 231 patients with PBC who underwent EGD and 2D-SWE examination were enrolled. Areas under the receiver-operating characteristic curve (AUROC) were used to assess the performance of 2D-SWE for predicting all-size varices and high-risk varices. All-size varices and high-risk varices miss rate &lt; 10% and &lt;5%, respectively, were acceptable for screening varices. <b>Results</b>: The AUROCs of LS for predicting all-size varices and high-risk varices were 0.87 (95%CI: 0.82–0.91) and 0.84 (95%CI: 0.74–0.86), respectively. LS &lt;25 kPa and PLT &gt;110 × 10<sup>9</sup>/L spared 46.3% EGD screening, with 3.7% high-risk varices miss rate and 8.4% all-size varices miss rate. One hundred and sixteen (50.2%) patients met the Newcastle varices in PBC score (cutoff, 0.5), with 4.3% high-risk varices miss rate and 11.2% all-size varices miss rate. <b>Conclusion</b>: The criteria based on LS and PLT are useful for triaging PBC patients. LS &lt;25 kPa and PLT &gt;110 × 10<sup>9</sup>/L could be the optimal criteria for screening varices.
DOI: 10.6084/m9.figshare.12986581
title: Additional file 3 of Multi-omics profiling highlights lipid metabolism alterations in pigs fed low-dose antibiotics

description: Additional file 3: Table S1. Phenotypic (productive) data of all the DLY piglet samples. Table S2. Summary of metabolic parameters in serum samples. Table S3. Differential lipids between the antibiotic and control group. Table S4. Pathway analysis results of these differential lipids by MetaboAnalyst 4.0. Table S5. Data summary of liver transcriptome. Table S6. DEG information by transcriptome data processing. Table S7. KEGG enrichment analysis of DEGs. Table S8. Liver methylome data processing. Table S9. DMRs on different chromosomes based on LHC-BS data processing. Table S10. Primer used in quantitative RT-PCR.
DOI: 10.6084/m9.figshare.12986581.v1
title: Additional file 3 of Multi-omics profiling highlights lipid metabolism alterations in pigs fed low-dose antibiotics

description: Additional file 3: Table S1. Phenotypic (productive) data of all the DLY piglet samples. Table S2. Summary of metabolic parameters in serum samples. Table S3. Differential lipids between the antibiotic and control group. Table S4. Pathway analysis results of these differential lipids by MetaboAnalyst 4.0. Table S5. Data summary of liver transcriptome. Table S6. DEG information by transcriptome data processing. Table S7. KEGG enrichment analysis of DEGs. Table S8. Liver methylome data processing. Table S9. DMRs on different chromosomes based on LHC-BS data processing. Table S10. Primer used in quantitative RT-PCR.
DOI: 10.6084/m9.figshare.14035169.v1
title: Two-dimensional shear wave elastography for screening varices in Asian patients with primary biliary cholangitis

description: <b>Objectives</b>: The presence of varices affects the survival of patients with primary biliary cholangitis (PBC). The aim of this study is to assess the criteria based on liver stiffness (LS) measured by two-dimensional shear wave elastography (2D-SWE) and platelet count (PLT), and recently published noninvasive models for triaging PBC patients. <b>Methods</b>: 231 patients with PBC who underwent EGD and 2D-SWE examination were enrolled. Areas under the receiver-operating characteristic curve (AUROC) were used to assess the performance of 2D-SWE for predicting all-size varices and high-risk varices. All-size varices and high-risk varices miss rate &lt; 10% and &lt;5%, respectively, were acceptable for screening varices. <b>Results</b>: The AUROCs of LS for predicting all-size varices and high-risk varices were 0.87 (95%CI: 0.82–0.91) and 0.84 (95%CI: 0.74–0.86), respectively. LS &lt;25 kPa and PLT &gt;110 × 10<sup>9</sup>/L spared 46.3% EGD screening, with 3.7% high-risk varices miss rate and 8.4% all-size varices miss rate. One hundred and sixteen (50.2%) patients met the Newcastle varices in PBC score (cutoff, 0.5), with 4.3% high-risk varices miss rate and 11.2% all-size varices miss rate. <b>Conclusion</b>: The criteria based on LS and PLT are useful for triaging PBC patients. LS &lt;25 kPa and PLT &gt;110 × 10<sup>9</sup>/L could be the optimal criteria for screening varices.
DOI: 10.6084/m9.figshare.19802357
title: Additional file 1 of Predictors of long-term mortality after intertrochanteric fractures surgery: a 3-year retrospective study

description: Additional file 1:
DOI: 10.6084/m9.figshare.19802357.v1
title: Additional file 1 of Predictors of long-term mortality after intertrochanteric fractures surgery: a 3-year retrospective study

description: Additional file 1:
DOI: 10.6084/m9.figshare.6695222
title: MOESM2 of Genome-scale metabolic model analysis indicates low energy production efficiency in marine ammonia-oxidizing archaea

description: Additional file 2. Model NmrFL413 in SBMLÂ format.
DOI: 10.6084/m9.figshare.23996738
title: A pharmacovigilance study of adverse event profiles and haemorrhagic safety of bevacizumab based on the FAERS database

description: Bevacizumab is used for the treatment of advanced malignant tumors; it acts by inhibiting angiogenesis. This study aimed to examine adverse events (AEs) of bevacizumab, especially hemorrhage, using the Food and Drug Administration Adverse Event Reporting System (FAERS) database. The reporting odds ratio (ROR) and proportional reporting ratio (PRR) were used to analyze the AEs of bevacizumab using FAERS registration data from January 2004 to September 2022. Clinical information regarding hemorrhagic signals was further analyzed. The number of bevacizumab-associated AE reports was 96,477. Our study found that 892 significant preferred terms (PTs) were spread throughout 25 organ systems. The system organ classes (SOCs) focus on general disorders, administration site conditions, blood and lymphatic system disorders, injury, poisoning, and procedural complications. A total of 2,847 bevacizumab-related hemorrhage cases were reported, and 37 hemorrhagic signals were identified. Hemorrhagic signals were focused on SOC levels in vascular, gastrointestinal, and nervous system disorders. Colorectal, lung, and breast cancers are the three most common malignancies associated with BV-induced hemorrhage. The AE report from the present study confirms the majority of label information for bevacizumab, while also identifying new AEs. In addition, this was a large descriptive study of bevacizumab-induced hemorrhage.
DOI: 10.6084/m9.figshare.23996738.v1
title: A pharmacovigilance study of adverse event profiles and haemorrhagic safety of bevacizumab based on the FAERS database

description: Bevacizumab is used for the treatment of advanced malignant tumors; it acts by inhibiting angiogenesis. This study aimed to examine adverse events (AEs) of bevacizumab, especially hemorrhage, using the Food and Drug Administration Adverse Event Reporting System (FAERS) database. The reporting odds ratio (ROR) and proportional reporting ratio (PRR) were used to analyze the AEs of bevacizumab using FAERS registration data from January 2004 to September 2022. Clinical information regarding hemorrhagic signals was further analyzed. The number of bevacizumab-associated AE reports was 96,477. Our study found that 892 significant preferred terms (PTs) were spread throughout 25 organ systems. The system organ classes (SOCs) focus on general disorders, administration site conditions, blood and lymphatic system disorders, injury, poisoning, and procedural complications. A total of 2,847 bevacizumab-related hemorrhage cases were reported, and 37 hemorrhagic signals were identified. Hemorrhagic signals were focused on SOC levels in vascular, gastrointestinal, and nervous system disorders. Colorectal, lung, and breast cancers are the three most common malignancies associated with BV-induced hemorrhage. The AE report from the present study confirms the majority of label information for bevacizumab, while also identifying new AEs. In addition, this was a large descriptive study of bevacizumab-induced hemorrhage.
DOI: 10.6084/m9.figshare.25268392
title: A table showing contig gene annotation information for the complete genome of <i>Acidovorax temperans</i> strain (GenBank accession number GCA_028596105.1).

description: A heavy metal and xenobiotic-tolerant strain of <i>Acidovorax temperans</i> strain LMJ, was isolated from a contaminated Tris-Acetate-Phosphate medium plate of a green micro-alga, <i>Chlamydomonas reinhardtii strain </i>Chlamydomonas Library Project LMJ.SG0182. The complete genome of this bacterium was sequenced using PacBio continuous long read technology on a Sequel II machine at the Georgia Genomics and Bioinformatics core located at the University of Georgia (Athens, GA, USA). The complete genome consisted of three contigs. The complete genome has been submitted to the GenBank (GenBank accession number GCA_028596105.1). This table summarizes the gene annotation information of the GenBank-submitted three contigs:Contig1/Chromosome (CP117193.1)Contig2/plasmid EP1 (CP117194.1)Contig 3/plasmid JG1 (CP117195.1)The table contains the following information:<br>Total # of genesTotal # of protein-coding genesTotal # of complete rRNA-coding genesTotal # of tRNA-coding genesTotal # of genes coding for non-coding RNAsTotal # of pseudogenes<br><br><br>
DOI: 10.6084/m9.figshare.25268392.v2
title: A table showing contig gene annotation information for the complete genome of <i>Acidovorax temperans</i> strain (GenBank accession number GCA_028596105.1).

description: A heavy metal and xenobiotic-tolerant strain of <i>Acidovorax temperans</i> strain LMJ, was isolated from a contaminated Tris-Acetate-Phosphate medium plate of a green micro-alga, <i>Chlamydomonas reinhardtii strain </i>Chlamydomonas Library Project LMJ.SG0182. The complete genome of this bacterium was sequenced using PacBio continuous long read technology on a Sequel II machine at the Georgia Genomics and Bioinformatics core located at the University of Georgia (Athens, GA, USA). The complete genome consisted of three contigs. The complete genome has been submitted to the GenBank (GenBank accession number GCA_028596105.1). This table summarizes the gene annotation information of the GenBank-submitted three contigs:Contig1/Chromosome (CP117193.1)Contig2/plasmid EP1 (CP117194.1)Contig 3/plasmid JG1 (CP117195.1)The table contains the following information:<br>Total # of genesTotal # of protein-coding genesTotal # of complete rRNA-coding genesTotal # of tRNA-coding genesTotal # of genes coding for non-coding RNAsTotal # of pseudogenes<br><br><br>
DOI: 10.6084/m9.figshare.25268392.v1
title: A table showing contig gene annotation information for the complete genome of Acidovorax temperans strain (GenBank accession number GCA_028596105.1).

description: A heavy metal and xenobiotic-tolerant strain of <i>Acidovorax temperans</i> strain LMJ, was isolated from a contaminated Tris-Acetate-Phosphate medium plate of a green micro-alga, <i>Chlamydomonas reinhardtii</i>. The complete genome of this bacterium was sequenced using PacBio continuous long read technology on a Sequel II machine at the Georgia Genomics and Bioinformatics core located at the University of Georgia (Athens, GA, USA). The complete genome (three contigs) has been submitted to the GenBank (GenBank accession number GCA_028596105.1). This table summarizes the gene annotation information of the three contigs:Contig1/Chromosome (CP117193.1)Contig2/plasmid EP1 (CP117194.1)Contig 3/plasmid JG1 (CP117195.1)The table contains the following information:<br>Total # of genesTotal # of protein-coding genesTotal # of complete rRNA-coding genesTotal # of tRNA-coding genesTotal # of genes coding for non-coding RNAsTotal # of pseudogenes<br><br><br>
DOI: 10.6084/m9.figshare.6695252
title: Additional file 3: of DeepCRISPR: optimized CRISPR guide RNA design by deep learning

description: Comparison of sgRNA on-target efficacy predictions in an independent dataset with Spearman correlation. (XLSX 48 kb)
DOI: 10.6084/m9.figshare.6695222.v1
title: MOESM2 of Genome-scale metabolic model analysis indicates low energy production efficiency in marine ammonia-oxidizing archaea

description: Additional file 2. Model NmrFL413 in SBMLÂ format.
DOI: 10.6084/m9.figshare.6695252.v1
title: Additional file 3: of DeepCRISPR: optimized CRISPR guide RNA design by deep learning

description: Comparison of sgRNA on-target efficacy predictions in an independent dataset with Spearman correlation. (XLSX 48 kb)
DOI: 10.6084/m9.figshare.12986728
title: Additional file 5 of Identification of lipid biomarker from serum in patients with chronic obstructive pulmonary disease

description: Additional file 5.
DOI: 10.6084/m9.figshare.12986728.v1
title: Additional file 5 of Identification of lipid biomarker from serum in patients with chronic obstructive pulmonary disease

description: Additional file 5.
DOI: 10.5281/zenodo.10666940
title: Chapter 3 Results - All sections

description: Companion dataset of the Thesis titled "Alternative splicing programs in tumor development and progression". This collection corresponds to all sections in Chapter 3 Results. The prefix in every file indicates the corresponding section.
DOI: 10.5517/ccdc.csd.cc22hr5j
title: CCDC 1921757: Experimental Crystal Structure Determination

description: Related Article: K.M.Turdybekov, Zh.B.Satpaeva, O.F.Nurkenov|2022|CSD Communication|||
description: Related Article: Oralgazy A. Nurkenov, Serik D. Fazylov, Zhanarkul B. Satpaeva, Tulegen M. Seilkhanov, Dastan M. Turdybekov, Anel Zh. Mendibayeva, Saule B. Akhmetova, Zarina T. Shulgau, Larisa E. Alkhimova, Ivan V. Kulakov|2023|Chem. Data Collect.|48|101089|doi:10.1016/j.cdc.2023.101089
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc22hr6k
title: CCDC 1921758: Experimental Crystal Structure Determination

description: Related Article: K.M.Turdybekov, Zh.B.Satpaeva, O.A.Nurkenov|2022|CSD Communication|||
description: Related Article: Oralgazy A. Nurkenov, Serik D. Fazylov, Zhanarkul B. Satpaeva, Tulegen M. Seilkhanov, Dastan M. Turdybekov, Anel Zh. Mendibayeva, Saule B. Akhmetova, Zarina T. Shulgau, Larisa E. Alkhimova, Ivan V. Kulakov|2023|Chem. Data Collect.|48|101089|doi:10.1016/j.cdc.2023.101089
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2c7mnx
title: CCDC 2182079: Experimental Crystal Structure Determination

description: Related Article: Benjamin Théron, Valentin Vaillant-Coindard, Cédric Balan, Yoann Rousselin, Jérôme Bayardon, Raluca Malacea-Kabbara, Pierre Le Gendre|2023|Dalton Trans.|52|7854|doi:10.1039/D3DT01216F
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.34740/kaggle/dsv/7680729
title: Forex Exchange Rates Since 2004 (Updated Daily)
DOI: 10.5281/zenodo.10666939
title: Chapter 3 Results - All sections

description: Companion dataset of the Thesis titled "Alternative splicing programs in tumor development and progression". This collection corresponds to all sections in Chapter 3 Results. The prefix in every file indicates the corresponding section.
DOI: 10.34945/f51c7b
title: Example AMPA Receptor and Housekeeping Protein Expression Data from Male Long-Evans Rats for the Purpose of Demonstrating the blotRig Western Blot Tool

description: STUDY PURPOSE: The purpose of this study is to demonstrate best practices in analyzing western blot data. This study uses example western blot data from a spared peripheral nerve + spinal cord injury model to illustrate how technical replications and counterbalancing of experimental groups across western blot gels can improve rigor and reproducibility. The data are organized to be used easily in the blotRig tool, which we developed to aid in western blot experimental design and analysis. DATA COLLECTED: The data collected are from 29 male Long-Evans rats that were grouped prior to western blot analysis into one of two groups, and spinal cord tissue was prepared for western blot analysis. Each sample was run on three technical replicate western blot gels, and densitometry values for the target protein (GluA2 AMPA receptor subunit) and beta actin loading controls were collected and analyzed. DATA USAGE NOTES:
DOI: 10.6084/m9.figshare.21842435
title: ICF-linking and psychometric properties of upper extremity mobility outcome measures in spinal cord injury – a scoping review

description: The purpose of this study was to explore the outcome measures used in upper extremity rehabilitation and research in spinal cord injury and to investigate their psychometry. Scoping review. PubMed, the Cochrane library, PEDro, Medline (Ovid). The search process and study selection was carried out as follows: Firstly, a systematic search was carried out for articles on upper extremity rehabilitation after SCI. Performance or observational outcome measures which were designed for a clinical setting were collected from selected studies. Secondly, eligible outcome measures were linked to the ICF. The ICF-linked outcome measures were further screened for inclusion according to how comprehensively they covered ICF categories. Finally, a search of the selected outcome measures was performed to investigate their psychometry. A total of four outcome measures and nine psychometric studies were selected for the scoping review; six studies addressed GRASSP, one addressed AuSpinal, one addressed SHFT and one addressed TRI-HFT. Of the 13 COSMIN measurement properties, studies of GRASSP covered seven, AuSpinal covered five and both SHFT and TRI-HFT covered three properties. The psychometric properties of GRASSP were most extensively studied showing eligible reliability and validity. Although there are still some measurement properties to be explored, GRASSP can be recommended for use in the evaluation of upper extremity mobility in the SCI rehabilitation and research. More research is needed on the psychometrics of other outcome measures in people with spinal cord injuries before the outcome measures can be unconditionally recommended.