cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9783434.v1
title: Additional file 2 of A novel evolutionary model for constructing gene coexpression networks with comprehensive features

description: R code for running evolutionary model 1. This R code is for running evolutionary model 1 when the number of new genes in each step is known. (R 11 kb)
DOI: 10.6084/m9.figshare.9783443
title: Additional file 3 of A novel evolutionary model for constructing gene coexpression networks with comprehensive features

description: The network 0 formed by genes from branch 0. This file is support for running evolutionary models 1 and 2. (CSV 15,567 kb)
DOI: 10.6084/m9.figshare.9783443.v1
title: Additional file 3 of A novel evolutionary model for constructing gene coexpression networks with comprehensive features

description: The network 0 formed by genes from branch 0. This file is support for running evolutionary models 1 and 2. (CSV 15,567 kb)
DOI: 10.6084/m9.figshare.12926093.v1
title: Additional file 7 of An RTM-GWAS procedure reveals the QTL alleles and candidate genes for three yield-related traits in upland cotton

description: Additional file 7: Table S6. Gene names expressed mainly in fibers or ovules of upland cotton by two RNA-seq data.
DOI: 10.6084/m9.figshare.12924131.v1
title: Additional file 1 of Developmental stage-specific A-to-I editing pattern in the postnatal pineal gland of pigs (Sus scrofa)

description: Additional file 1 Summary of the identified A-to-I editing sites in the Sus scrofa pineal gland.
DOI: 10.6084/m9.figshare.8207504
title: MOESM3 of LncRNA H19 regulates PI3Kâ Akt signal pathway by functioning as a ceRNA and predicts poor prognosis in colorectal cancer: integrative analysis of dysregulated ncRNA-associated ceRNA network

description: Additional file 3. GO terms of differentially expressed mRNAs in the ceRNA network.
DOI: 10.6084/m9.figshare.9783452
title: Additional file 4 of A novel evolutionary model for constructing gene coexpression networks with comprehensive features

description: The coreness of genes in the network 0. This file is support for running evolutionary models 1 and 2. (CSV 127 kb)
DOI: 10.6084/m9.figshare.9783452.v1
title: Additional file 4 of A novel evolutionary model for constructing gene coexpression networks with comprehensive features

description: The coreness of genes in the network 0. This file is support for running evolutionary models 1 and 2. (CSV 127 kb)
DOI: 10.6084/m9.figshare.9783458
title: Additional file 5 of A novel evolutionary model for constructing gene coexpression networks with comprehensive features

description: The network 1 formed by genes from branch 0 and branch 1. This file is support for running evolutionary models 1 and 2. (CSV 17,312 kb)
DOI: 10.6084/m9.figshare.9783458.v1
title: Additional file 5 of A novel evolutionary model for constructing gene coexpression networks with comprehensive features

description: The network 1 formed by genes from branch 0 and branch 1. This file is support for running evolutionary models 1 and 2. (CSV 17,312 kb)
DOI: 10.6084/m9.figshare.17120423.v1
title: Additional file 5 of Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data

description: Additional file 5. Cell-cell crosstalk networks.
DOI: 10.6084/m9.figshare.9783461
title: Additional file 6 of A novel evolutionary model for constructing gene coexpression networks with comprehensive features

description: R code for running evolutionary model 2. This R code is for running evolutionary model 2 when the length of evolutionary time in each step is known. (R 12 kb)
DOI: 10.6084/m9.figshare.9783461.v1
title: Additional file 6 of A novel evolutionary model for constructing gene coexpression networks with comprehensive features

description: R code for running evolutionary model 2. This R code is for running evolutionary model 2 when the length of evolutionary time in each step is known. (R 12 kb)
DOI: 10.6084/m9.figshare.13450553.v1
title: Long non-coding RNA XIST promotes the progression of esophageal squamous cell carcinoma through sponging miR-129-5p and upregulating CCND1 expression

description: Long non-coding RNA (lncRNA) X inactive specific transcript (XIST) has been identified as an oncogenic lncRNA in a series of human cancers, including esophageal squamous cell carcinoma (ESCC). In this study, we aimed to further explore the underlying mechanism of XIST on ESCC progression. qRT-PCR assay was used to determine the levels of XIST and miR-129-5p. Western blot analysis was performed to assess cyclin D1 (CCND1) expression. Bioinformatic analysis was performed using starBase v2.0 software. Dual-luciferase reporter and RNA immunoprecipitation assays were employed to confirm the interaction between XIST and miR-129-5p or miR-129-5p and CCND1. Cell cycle progression and apoptosis were measured by flow cytometric analysis, and cell migration and invasion were detected by transwell assay. Mouse studies were used to observe the effect of XIST silencing on tumor growth <i>in vivo</i>. Our results indicated that XIST was upregulated and miR-129-5p was downregulated in ESCC. XIST silencing or miR-129-5p overexpression repressed cell cycle progression, proliferation, migration, invasion, and promoted the apoptosis in ESCC cells. Moreover, XIST directly interacted with miR-129-5p and repressed miR-129-5p expression. MiR-129-5p mediated the regulatory effect of XIST on ESCC cell progression <i>in vitro</i>, and XIST promoted CCND1 expression by sponging miR-129-5p. Additionally, XIST silencing inhibited tumor growth <i>in vivo</i>. Our findings suggested that XIST silencing repressed the progression of ESCC at least partly through regulating the miR-129-5p/CCND1 axis. Targeting XIST might be a potential therapeutic strategy for ESCC treatment.
DOI: 10.6084/m9.figshare.9783467
title: Additional file 7 of A novel evolutionary model for constructing gene coexpression networks with comprehensive features

description: The time intervals between each branch. This file is support for running evolutionary model 2. (CSV 1 kb)
DOI: 10.6084/m9.figshare.9783467.v1
title: Additional file 7 of A novel evolutionary model for constructing gene coexpression networks with comprehensive features

description: The time intervals between each branch. This file is support for running evolutionary model 2. (CSV 1 kb)
DOI: 10.6084/m9.figshare.9783473
title: Additional file 8 of A novel evolutionary model for constructing gene coexpression networks with comprehensive features

description: Table S2. This table contains the original human RNA-seq data for 14341 different genes in 71 tissues. Element NA in this table means there is no expression value for this gene in the corresponding tissue. This table is downloaded from reference [28] ( http://longlab.uchicago.edu/?q=SD_GB ). (XLSX 5582 kb)
DOI: 10.6084/m9.figshare.9783473.v1
title: Additional file 8 of A novel evolutionary model for constructing gene coexpression networks with comprehensive features

description: Table S2. This table contains the original human RNA-seq data for 14341 different genes in 71 tissues. Element NA in this table means there is no expression value for this gene in the corresponding tissue. This table is downloaded from reference [28] ( http://longlab.uchicago.edu/?q=SD_GB ). (XLSX 5582 kb)
DOI: 10.6084/m9.figshare.19220658
title: Uranium data from Palougou section, North China

description: Uranium data series of the Palougou section, North China
DOI: 10.6084/m9.figshare.9783479
title: Additional file 9 of A novel evolutionary model for constructing gene coexpression networks with comprehensive features

description: Table S3. This table contains the selected human RNA-seq data for 8237 different genes in 26 different tissues. (CSV 1085 kb)
DOI: 10.6084/m9.figshare.9783479.v1
title: Additional file 9 of A novel evolutionary model for constructing gene coexpression networks with comprehensive features

description: Table S3. This table contains the selected human RNA-seq data for 8237 different genes in 26 different tissues. (CSV 1085 kb)
DOI: 10.6084/m9.figshare.13093882
title: Additional file 2 of A systematic review and meta-analysis of Liuzijue in stable patients with chronic obstructive pulmonary disease

description: Additional file 2: Table S2 Adverse Events.
DOI: 10.6084/m9.figshare.12402410
title: Fish consumption and risk of non-Hodgkin lymphoma: A meta-analysis of observational studies

description: <b>Objectives:</b> Whether a relationship between fish consumption and non-Hodgkin lymphoma (NHL) risk exists is an open issue. We carried out a meta-analysis to explore this association according to the published observational studies. <b>Methods:</b> We performed a search of databases in MEDLINE and EMBASE to identify relevant studies. We derived meta-analytic estimates using random-effects models, and assessed between-study heterogeneity using the Cochran's <i>Q</i> and <i>I</i><sup>2</sup> statistics. <b>Results:</b> We identified a total of seven case–control and two prospective cohort studies, including 7696 subjects with NHL. The summary relative risks (SRRs) estimated for NHL were 0.80 (95% confidence intervals (CIs): 0.68–0.94) for those in the highest fish consumption category compared with those in the lowest consumption category. There was evidence of significant heterogeneity across studies (<i>Q</i> = 26.72, <i>P</i><sub>heterogeneity</sub> = 0.002, <i>I</i><sup>2</sup> = 66.3%). Stratified analysis by study design indicated that a significant risk association between fish consumption and NHL was observed in case–control studies, but not in cohort studies. Based on the dose–response meta-analysis, the SRRs of NHL were 0.85 (95% CIs: 0.71–1.01) for three servings increased per week of fish consumed with evidence of significant heterogeneity (<i>P</i><sub>heterogeneity</sub> = 0.007, <i>I</i><sup>2</sup> = 63.9%). <b>Conclusions:</b> Findings from our meta-analysis indicate that consumption of fish may be not related to NHL risk.
DOI: 10.6084/m9.figshare.12926388.v1
title: Additional file 1 of Circular RNA CDR1as disrupts the p53/MDM2 complex to inhibit Gliomagenesis

description: Additional file 1 Table S1. Multivariate Cox regression analysis of prognosis in glioma. *p &lt; 0.05; **p &lt; 0.01. Table S2. The list of qPCR primers. Table S3. The list of siRNA sequence.
DOI: 10.6084/m9.figshare.7686371.v1
title: MOESM3 of Peripheral T cell receptor beta immune repertoire is promptly reconstituted after acute myocardial infarction

description: Additional file 3: Table S2. The distribution of V and J gene segments in each sample.
DOI: 10.6084/m9.figshare.8207714.v1
title: Additional file 2: of miR156f integrates panicle architecture through genetic modulation of branch number and pedicel length pathways

description: Primer sequences used in this study. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.9783539
title: Additional file 2: of Physiological and metabolomics analyses of young and old leaves from wild and cultivated soybean seedlings under low-nitrogen conditions

description: The contributions of ions among young and old leaves of W and C seedlings to the first principal component (PC1) and the second principal component (PC2). C, cultivar soybean; W, wild soybean; CK, control treatment; LN, low-nitrogen stress (XLSX 12 kb)
DOI: 10.5281/zenodo.10679095
title: The grammatically annotated corpus of the pericopes of the Old Lithuanian Postil of Jonas Bretkūnas

description: This grammatically annoted corpus aims at facilitating linguistic research on Old Lithuanian based on the Postil of Jonas Bretkūnas from the year 1591. In addition to the two subcorpora "pericopes" and "homilies" of the version 1.0, the current version 2.0includes also "passion harmony", "pericope (prophet)" and "prayer". In this new version, the tokens occurring in biblical citations can be specifically searched for. The search results also show the corresponding passage in the BrP pericopes.For full description see the BrP_2.0._documentation.md included in the files.

The pericopes were annotated using SIL Toolbox and converted to be used in the search-tool ANNIS using the conversion tool PEPPER.

Three formats are provided in this release: 1. the Toolbox files, 2. the transitional Excel files and 3. a zipped folder to be imported into ANNIS.

Created in the project B02, Emergence and change of registers: The case of Lithuanian and Latvian of the CRC 1412 "Register" (funded by the Deutsche Forschungsgemeinschaft: DFG, German Research Foundation: 416591334).
DOI: 10.5281/zenodo.7890989
title: The grammatically annotated corpus of the pericopes of the Old Lithuanian Postil of Jonas Bretkūnas

description: This grammatically annoted corpus aims at facilitating linguistic research on Old Lithuanian based on the Postil of Jonas Bretkūnas from the year 1591. In addition to the two subcorpora "pericopes" and "homilies" of the version 1.0, the current version 2.0includes also "passion harmony", "pericope (prophet)" and "prayer". In this new version, the tokens occurring in biblical citations can be specifically searched for. The search results also show the corresponding passage in the BrP pericopes.For full description see the BrP_2.0._documentation.md included in the files.

The pericopes were annotated using SIL Toolbox and converted to be used in the search-tool ANNIS using the conversion tool PEPPER.

Three formats are provided in this release: 1. the Toolbox files, 2. the transitional Excel files and 3. a zipped folder to be imported into ANNIS.

Created in the project B02, Emergence and change of registers: The case of Lithuanian and Latvian of the CRC 1412 "Register" (funded by the Deutsche Forschungsgemeinschaft: DFG, German Research Foundation: 416591334).
DOI: 10.5281/zenodo.7890990
title: The grammatically annotated corpus of the pericopes of the Old Lithuanian Postil of Jonas Bretkūnas

description: This grammatically annoted corpus aims at facilitating linguistic research on Old Lithuanian based on the Postil of Jonas Bretkūnas from the year 1591. The corpus is divided into two subcorpora, "pericopes" and "homilies" to make register related research easier. The pericopes were annotated using SIL Toolbox and converted to be used in the search-tool ANNIS using the conversion tool PEPPER. Three formats are provided in this release: 1. the Toolbox files, 2. the transitional Excel files and 3. a zipped folder to be imported into ANNIS. Created in the project B02, <em>Emergence and change of registers: The case of Lithuanian and Latvian</em> of the CRC 1412 "Register" (funded by the Deutsche Forschungsgemeinschaft: DFG, German Research Foundation: 416591334).
description: {"references": ["Hock, W., Fecht, R., Feulner, A. H., Hill, E., Wodtko, D. S. (2019). Altlitauisches etymologisches W\u00f6rterbuch (ALEW) Version 1.1. Humboldt-Universit\u00e4t zu Berlin. Leicht bearbeitete und verbesserte Fassung des Altlitauischen etymologischen W\u00f6rterbuchs (ALEW), erschienen 2015 bei Baar, Hamburg. (https://alew.hu-berlin.de/)", "Aleknavi\u010dien\u0117, Ona (2005). Jono Bretk\u016bno \"Postil\u0117\" : studija, faksimil\u0117 ir kompaktin\u0117 plok\u0161tel\u0117, Vilnius: Lietuvi\u0173 kalbos institutas.", "Kurschat, Alexander (1968\u20131973). Litauisch-Deutsches W\u00f6rterbuch. Thesaurus Linguae Lituanicae. Vandenhoeck & Ruprecht .", "Krause, Thomas (2019). ANNIS: A graph-based query system for deeply annotated text corpora. PhD thesis. Humboldt-Universit\u00e4t zu Berlin, Mathematisch-Naturwissenschaftliche Fakult\u00e4t. doi: 10.18452/19659."]}
DOI: 10.6084/m9.figshare.9783539.v1
title: Additional file 2: of Physiological and metabolomics analyses of young and old leaves from wild and cultivated soybean seedlings under low-nitrogen conditions

description: The contributions of ions among young and old leaves of W and C seedlings to the first principal component (PC1) and the second principal component (PC2). C, cultivar soybean; W, wild soybean; CK, control treatment; LN, low-nitrogen stress (XLSX 12 kb)
DOI: 10.6084/m9.figshare.9783557
title: Additional file 4: of Physiological and metabolomics analyses of young and old leaves from wild and cultivated soybean seedlings under low-nitrogen conditions

description: The contributions of metabolites among young leaves of W and C seedlings to the first principal component (PC1) and the second principal component (PC2). C, cultivar soybean; W, wild soybean; CK, control treatment; LN, low-nitrogen stress (XLSX 14 kb)
DOI: 10.6084/m9.figshare.9783557.v1
title: Additional file 4: of Physiological and metabolomics analyses of young and old leaves from wild and cultivated soybean seedlings under low-nitrogen conditions

description: The contributions of metabolites among young leaves of W and C seedlings to the first principal component (PC1) and the second principal component (PC2). C, cultivar soybean; W, wild soybean; CK, control treatment; LN, low-nitrogen stress (XLSX 14 kb)
DOI: 10.6084/m9.figshare.9783560
title: Additional file 5: of Physiological and metabolomics analyses of young and old leaves from wild and cultivated soybean seedlings under low-nitrogen conditions

description: The contributions of metabolites among old leaves of W and C seedlings to the first principal component (PC1) and the second principal component (PC2). C, cultivar soybean; W, wild soybean; CK, control treatment; LN, low-nitrogen stress (XLSX 15 kb)
DOI: 10.6084/m9.figshare.9783560.v1
title: Additional file 5: of Physiological and metabolomics analyses of young and old leaves from wild and cultivated soybean seedlings under low-nitrogen conditions

description: The contributions of metabolites among old leaves of W and C seedlings to the first principal component (PC1) and the second principal component (PC2). C, cultivar soybean; W, wild soybean; CK, control treatment; LN, low-nitrogen stress (XLSX 15 kb)
DOI: 10.6084/m9.figshare.12926388
title: Additional file 1 of Circular RNA CDR1as disrupts the p53/MDM2 complex to inhibit Gliomagenesis

description: Additional file 1 Table S1. Multivariate Cox regression analysis of prognosis in glioma. *p &lt; 0.05; **p &lt; 0.01. Table S2. The list of qPCR primers. Table S3. The list of siRNA sequence.
DOI: 10.6084/m9.figshare.12402710.v1
title: Excel file with blood cell types and telomeres from Telomere length varies substantially between blood cell types in a reptile

description: Telomeres are repeat sequences of non-coding DNA-protein molecules that cap or intersperse metazoan chromosomes. Interest in telomeres has increased exponentially in recent years, to now include their ongoing dynamics and evolution within natural populations where individuals vary in telomere attributes. Phylogenetic analyses show profound differences in telomere length across non-model taxa. However, telomeres may also differ in length within individuals and between tissues. The latter becomes a potential source of error when researchers use different tissues for extracting DNA for telomere analysis and scientific inference. A commonly used tissue type for assessing telomere length is blood, a tissue that itself varies in terms of nuclear content among taxa, in particular to what degree their thrombocytes and red blood cells (RBCs) contain nuclei or not. Specifically, when RBCs lack nuclei, leucocytes become the main source of telomeric DNA. RBCs and leucocytes differ in lifespan and how long they have been exposed to ‘senescence' and erosion effects. We report on a study in which cells in whole blood from individual Australian painted dragon lizards (<i>Ctenophorus pictus</i>) were identified using flow cytometry and their telomere length simultaneously measured. Lymphocyte telomeres were on average 270% longer than RBC telomeres, and in azurophils (a reptilian monocyte), telomeres were greater than 388% longer than those in RBCs. If this variation in telomere length among different blood cell types is a widespread phenomenon, and DNA for comparative telomere analyses are sourced from whole blood, evolutionary inference of telomere traits among taxa may be seriously complicated by the blood cell type comprising the main source of DNA.
DOI: 10.6084/m9.figshare.9783596
title: Additional file 1: of Analysis of widely targeted metabolites of the euhalophyte Suaeda salsa under saline conditions provides new insights into salt tolerance and nutritional value in halophytic species

description: Table S1. All detected metabolites in the leaves of S. salsa treated with different concentrations of NaCl. (XLSX 109 kb)
DOI: 10.6084/m9.figshare.9783596.v1
title: Additional file 1: of Analysis of widely targeted metabolites of the euhalophyte Suaeda salsa under saline conditions provides new insights into salt tolerance and nutritional value in halophytic species

description: Table S1. All detected metabolites in the leaves of S. salsa treated with different concentrations of NaCl. (XLSX 109 kb)
DOI: 10.6084/m9.figshare.9783599
title: Additional file 2: of Analysis of widely targeted metabolites of the euhalophyte Suaeda salsa under saline conditions provides new insights into salt tolerance and nutritional value in halophytic species

description: Table S2. All differential metabolites in the leaves of S. salsa treated with different concentrations of NaCl. (XLSX 68 kb)
DOI: 10.6084/m9.figshare.9783599.v1
title: Additional file 2: of Analysis of widely targeted metabolites of the euhalophyte Suaeda salsa under saline conditions provides new insights into salt tolerance and nutritional value in halophytic species

description: Table S2. All differential metabolites in the leaves of S. salsa treated with different concentrations of NaCl. (XLSX 68 kb)
DOI: 10.6084/m9.figshare.9783605
title: Additional file 3: of Analysis of widely targeted metabolites of the euhalophyte Suaeda salsa under saline conditions provides new insights into salt tolerance and nutritional value in halophytic species

description: Table S3. Differential metabolites in the leaves of S. salsa at salinity, when compared to controls. (XLSX 30 kb)
DOI: 10.6084/m9.figshare.9783605.v1
title: Additional file 3: of Analysis of widely targeted metabolites of the euhalophyte Suaeda salsa under saline conditions provides new insights into salt tolerance and nutritional value in halophytic species

description: Table S3. Differential metabolites in the leaves of S. salsa at salinity, when compared to controls. (XLSX 30 kb)
DOI: 10.6084/m9.figshare.9783614
title: Additional file 4: of Analysis of widely targeted metabolites of the euhalophyte Suaeda salsa under saline conditions provides new insights into salt tolerance and nutritional value in halophytic species

description: Table S4. Differentially significant metabolite annotations classified by KEGG pathways. (XLSX 44 kb)
DOI: 10.6084/m9.figshare.9783614.v1
title: Additional file 4: of Analysis of widely targeted metabolites of the euhalophyte Suaeda salsa under saline conditions provides new insights into salt tolerance and nutritional value in halophytic species

description: Table S4. Differentially significant metabolite annotations classified by KEGG pathways. (XLSX 44 kb)
DOI: 10.6084/m9.figshare.12926538
title: Additional file 2 of Bayesian copy number detection and association in large-scale studies

description: Additional file 2 Supplemental Tables for Bayesian copy number detection and association in large-scale studies.
DOI: 10.6084/m9.figshare.21314225
title: Additional file 1 of The long non-coding RNA lncMYOZ2 mediates an AHCY/MYOZ2 axis to promote adipogenic differentiation in porcine preadipocytes

description: Additional file 1.
DOI: 10.6084/m9.figshare.21842250
title: Pleistocene accelerated exhumation within the Sumatran fault: Implications for late Cenozoic evolution of Sumatra (Indonesia)

description: Calculation of long-term exhumation rates
Figures S1 to S3
Tables S1 to S2