cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14386641
title: T-tube or no T-tube for biliary tract reconstruction in orthotopic liver transplantation: an updated systematic review and meta-analysis

description: <b>Objectives</b>: Biliary tract reconstruction with or without T-tube is commonly used in orthotopic liver transplantation (OLT). However, the efficacy and safety of T-tube usage remain controversial. This meta-analysis was conducted to assess the latest evidence of clinical outcomes. <b>Methods</b>: Embase, Cochrane Library, PubMed, and Web of Science were systematically searched from inception to 20 January 2021 for eligible studies. The analyses were performed using Review Manager and Stata. <b>Results</b>: A total of 24 trials involving 3320 participants were included in the meta-analysis. Compared with the no T-tube group, there was a higher incidence of overall biliary complications (OR:1.54; 95%CI, 1.06–2.24; <i>P </i>= 0.02), bile leaks (OR:2.34; 95%CI,1.57–3.48; <i>P </i>&lt; 0.0001), cholangitis (OR:2.78; 95%CI,1.19–6.51; <i>P </i>= 0.002), and longer cold ischemia time (MD:22.27; 95%CI,0.80–43.74; <i>P </i>= 0.04) in the T-tube group. Furthermore, the no T-tube group had significantly higher odds of biliary strictures than the T-tube group (OR:0.60; 95%CI, 0.47–0.78; <i>P </i>= 0.0001). <b>Conclusion</b>: T-tube is still not routinely recommended, but is a good choice for OLT patients at high risk of biliary strictures. Notably, the higher rate of biliary complications in the T-tube group did not translate into an increase in endoscopic or re-operative interventions.
DOI: 10.6084/m9.figshare.17000985
title: CRISPR-dependent endogenous gene regulation is required for virulence in piscine <i>Streptococcus agalactiae</i>

description: The clustered regularly interspaced palindromic repeats (CRISPR)-Cas (CRISPR-associated) system is a prokaryotic defence against invading mobile genetic elements, such as bacteriophages or exogenous plasmids. Beyond this, this system has been shown to play an important role in controlling the virulence of some bacterial pathogens. <i>Streptococcus agalactiae</i> strain GD201008-001, a causative agent of septicemia and meningitis in tilapia, contains a single type II CRISPR-Cas system with Cas9 as a signature protein. In this study, we found that the deletion of CRISPR significantly reduced adhesion, invasion, cytotoxicity and haemolysis, and caused severely attenuated virulence in the piscine <i>S. agalactiae</i> strain. RNA-Seq identified 236 endogenous genes regulated by CRISPR, with 159 genes upregulated and 77 genes downregulated. The resulting change in gene transcription by CRISPR was much more pronounced than that by <i>cas9</i> in this bacterium, indicating CRISPR-mediated endogenous gene regulation was mostly independently of <i>cas9</i>. Subsequent studies showed that CovR/S two-component system was transcriptionally upregulated due to CRISPR deletion, which repressed the expression of the <i>cylE</i> gene coding for a cytolytic toxin, and thus decreased the activity of β-haemolysin/cytolysin. However, upregulation of CovR/S was not the contributor to the attenuation phenotype of ΔCRISPR. Further, we demonstrated that CRISPR is capable of repressing the expression of Toll-like receptor 2 (TLR2)-activating lipoprotein Sag0671 and thus dampens the innate immune response. This study revealed that the CRISPR system of <i>S. agalactiae</i> exhibited extraordinary potential capability in the regulation of endogenous transcripts, which contributes to bacterial innate immune evasion and virulence.
DOI: 10.6084/m9.figshare.8088206.v1
title: Superovulation alters global DNA methylation in early mouse embryo development

description: Assisted reproductive technologies are known to alter the developmental environment of gametes and early embryos during the most dynamic period of establishing the epigenome. This may result in the introduction of errors during active DNA methylation reprogramming. Controlled ovarian hyperstimulation, or superovulation, is a ubiquitously used intervention which has been demonstrated to alter the methylation of certain imprinted genes. The objective of this study was to investigate whether ovarian hyperstimulation results in genome-wide DNA methylation changes in mouse early embryos. Ovarian hyperstimulation was induced by treating mice with either low doses (5 IU) or high doses (10 IU) of PMSG and hCG. Natural mating (NM) control mice received no treatment. Zygotes and 8-cell embryos were collected from each group and DNA methylomes were generated by whole-genome bisulfite sequencing. In the NM group, mean CpG methylation levels slightly decreased from zygote to 8-cell stage, whereas a large decrease in mean CpG methylation level was observed in both superovulated groups. A separate analysis of the mean CpG methylation levels within each developmental stage confirmed that significant genome-wide erasure of CpG methylation from the zygote to 8-cell stage only occurred in the superovulation groups. Our results suggest that superovulation alters the genome-wide DNA methylation erasure process in mouse early pre-implantation embryos. It is not clear whether these changes are transient or persistent. Further studies are ongoing to investigate the impact of ovarian hyperstimulation on DNA methylation re-establishment in later stages of embryo development.
DOI: 10.6084/m9.figshare.14903874.v1
title: Additional file 1 of Trends in breastfeeding practices and mothers’ experience in the French NutriNet-Santé cohort

description: Additional file 1. Mothers’ perceptions on (A) breastfeeding cessation and (B) support to breastfeeding cessation. Self-reported mothers’ perceptions about factors known to have an impact on (A) breastfeeding cessation (B) support to breastfeeding cessation, but that were not felt by mothers to have played a role. Results are percentages of answers. Mothers had choice to answer from totally agree to totally disagree for each item (see legend); a not applicable answer was possible if the item was not adapted to the mother’s life.
DOI: 10.6084/m9.figshare.24872973
title: Limited future carbon sink in China as forests become mature

description: This dataset includes calibrated PFT maps, LUC and wood harvest forcing data used in the simulations, as well as the source data for the figures in the main text. Due to the difference in future afforestation scenarios, forcing datasets are divided into two periods, one for historical period and the other for future period. There is no change in the PFT maps after 2061. Historical LUC data includes two parts (net change fraction and land turnover fraction) and the year 1701 represents the change during 1700-1701, while future period only provide net change information. We provided wood harvest data used in the historical S<sub>2</sub> and S<sub>3 </sub>(S<sub>age</sub>) simulations, and in the future S<sub>0</sub>, S<sub>1</sub>, S<sub>2</sub> and S<sub>3</sub> simulations.<br>
DOI: 10.6084/m9.figshare.24872992
title: Additional file 1 of Diagnostic value of a CT-based radiomics nomogram for discrimination of benign and early stage malignant ovarian tumors

description: Additional file 1.  Radiomics features extracted from ROI
DOI: 10.6084/m9.figshare.24872992.v1
title: Additional file 1 of Diagnostic value of a CT-based radiomics nomogram for discrimination of benign and early stage malignant ovarian tumors

description: Additional file 1.  Radiomics features extracted from ROI
DOI: 10.6084/m9.figshare.24598638
title: Data for "Intraspecific variability of leaf form and function across habitat types"

description: Files in the folder:1 - dbReady.csvIt contains:standName: species binomial according to the World Flora Online (https://www.worldfloraonline.org/).EUNIS_1L: habitat classification according to the first level of EUNIS habitat classification (Chytrý et al., 2020, Applied Vegetation Science, 23, 648-675).LMA: log10-transformed leaf dry mass per unit leaf area (original unit: g m-2).LA: log10-transformed individual projected leaf area (original unit: mm2).2 - dbReady_reorderedThis dataset is needed to reproduce the phylogenetic analysis.It contains:standName: species binomial according to the World Flora Online (https://www.worldfloraonline.org/).<i>Note that species order follows the order in the phylogenetic tree (</i><i>Phylo_dbReady.tree</i><i>)</i>LMA: log10-transformed leaf dry mass per unit leaf area (original unit: g m-2).LA: log10-transformed individual projected leaf area (original unit: mm2).3 - Phylo_dbReady.treeThe phylogenetic tree for the species list in dbReady.csv. <br>
DOI: 10.6084/m9.figshare.24598638.v1
title: Data for "Intraspecific variability of leaf form and function across habitat types"

description: Data to reproduce the main results in "Intraspecific variability of leaf form and function across habitat types".
DOI: 10.6084/m9.figshare.25213607
title: Phyloseq object

description: The uploaded Phyloseq object includes a taxonomy table and metadata, which are essential components for microbiome data analysis:<b>Taxonomy Table (</b><code><strong>tax_table</strong></code><b>)</b>: This matrix contains the taxonomic classification of each observed feature (e.g., OTUs) across various taxonomic ranks such as kingdom, phylum, class, order, family, genus, and species.<b>Sample Data (</b><code><strong>sample_data</strong></code><b>)</b>: This data frame holds metadata for each sample in the study, which may include information like environmental conditions, patient demographics, or experimental treatments.
DOI: 10.6084/m9.figshare.24873082
title: Additional file 1 of A Bayesian approach to pilot-pivotal trials for bioequivalence assessment

description: Additional file 1.
DOI: 10.6084/m9.figshare.24873082.v1
title: Additional file 1 of A Bayesian approach to pilot-pivotal trials for bioequivalence assessment

description: Additional file 1.
DOI: 10.6084/m9.figshare.7564025
title: Additional file 5: of Molecular mapping of the Cf-10 gene by combining SNP/InDel-index and linkage analysis in tomato (Solanum lycopersicum)

description: Table S1. The primer information of KASP markers. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7564043.v1
title: Additional file 8: of Molecular mapping of the Cf-10 gene by combining SNP/InDel-index and linkage analysis in tomato (Solanum lycopersicum)

description: Table S4. The qRT-PCR reaction system. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.22776017
title: Datasets for paper titled" Divergence in cell cycle progression is associated with shifted phenology in a multivoltine moth: the European corn borer, Ostrinia nubilalis" submitted to Journal of Experimental Biology

description: These datasets contain cell cycle phase proportions and transcript abundance data for two strains of European corn borer (<em>Ostrinia nubilalis</em>) with different diapause timing. The study aimed to investigate potential differences in cell cycle progression between the two strains across diapause and nondiapause development. The cell cycle phases analyzed were G0/G1, S, and G2/M. Transcript abundance data focused on cell cycle associated genes between the two strains across diapause and nondiapause development.
DOI: 10.6084/m9.figshare.14379603
title: Additional file 1 of Single cell RNA sequencing identifies IGFBP5 and QKI as ciliated epithelial cell genes associated with severe COPD

description: Additional file 1: Table S1. Transcriptomic markers per cell type (top 100 genes per cluster).
DOI: 10.6084/m9.figshare.7563998.v1
title: Additional file 1: of Molecular mapping of the Cf-10 gene by combining SNP/InDel-index and linkage analysis in tomato (Solanum lycopersicum)

description: Table S5. The KASP genotyping results. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.7563998
title: Additional file 1: of Molecular mapping of the Cf-10 gene by combining SNP/InDel-index and linkage analysis in tomato (Solanum lycopersicum)

description: Table S5. The KASP genotyping results. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.7564013.v1
title: Additional file 3: of Molecular mapping of the Cf-10 gene by combining SNP/InDel-index and linkage analysis in tomato (Solanum lycopersicum)

description: Table S6. The sub-cellular location prediction of Cf-10. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.14379615
title: Additional file 5 of Single cell RNA sequencing identifies IGFBP5 and QKI as ciliated epithelial cell genes associated with severe COPD

description: Additional file 5: Table S5. Genes present in the GSEA core enrichment with the 127 emphysema gene signature.
DOI: 10.6084/m9.figshare.7564025.v1
title: Additional file 5: of Molecular mapping of the Cf-10 gene by combining SNP/InDel-index and linkage analysis in tomato (Solanum lycopersicum)

description: Table S1. The primer information of KASP markers. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7564034.v1
title: Additional file 7: of Molecular mapping of the Cf-10 gene by combining SNP/InDel-index and linkage analysis in tomato (Solanum lycopersicum)

description: Table S3. The primer information of EFÎą1 and candidate gene. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8088206
title: Superovulation alters global DNA methylation in early mouse embryo development

description: Assisted reproductive technologies are known to alter the developmental environment of gametes and early embryos during the most dynamic period of establishing the epigenome. This may result in the introduction of errors during active DNA methylation reprogramming. Controlled ovarian hyperstimulation, or superovulation, is a ubiquitously used intervention which has been demonstrated to alter the methylation of certain imprinted genes. The objective of this study was to investigate whether ovarian hyperstimulation results in genome-wide DNA methylation changes in mouse early embryos. Ovarian hyperstimulation was induced by treating mice with either low doses (5 IU) or high doses (10 IU) of PMSG and hCG. Natural mating (NM) control mice received no treatment. Zygotes and 8-cell embryos were collected from each group and DNA methylomes were generated by whole-genome bisulfite sequencing. In the NM group, mean CpG methylation levels slightly decreased from zygote to 8-cell stage, whereas a large decrease in mean CpG methylation level was observed in both superovulated groups. A separate analysis of the mean CpG methylation levels within each developmental stage confirmed that significant genome-wide erasure of CpG methylation from the zygote to 8-cell stage only occurred in the superovulation groups. Our results suggest that superovulation alters the genome-wide DNA methylation erasure process in mouse early pre-implantation embryos. It is not clear whether these changes are transient or persistent. Further studies are ongoing to investigate the impact of ovarian hyperstimulation on DNA methylation re-establishment in later stages of embryo development.
DOI: 10.6084/m9.figshare.14379612.v1
title: Additional file 4 of Single cell RNA sequencing identifies IGFBP5 and QKI as ciliated epithelial cell genes associated with severe COPD

description: Additional file 4: Table S4. Biological process gene ontology enrichment in genes downregulated in each cluster in COPD.
DOI: 10.6084/m9.figshare.14379618.v1
title: Additional file 6 of Single cell RNA sequencing identifies IGFBP5 and QKI as ciliated epithelial cell genes associated with severe COPD

description: Additional file 6: Table S6. Genes from the 127 gene signature differentially expressed by cell type.
DOI: 10.6084/m9.figshare.7564034
title: Additional file 7: of Molecular mapping of the Cf-10 gene by combining SNP/InDel-index and linkage analysis in tomato (Solanum lycopersicum)

description: Table S3. The primer information of EFÎą1 and candidate gene. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7564106
title: Additional file 12: of Systematic evaluation of C. elegans lincRNAs with CRISPR knockout mutants

description: Table S6. Primers used in this study. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.7564043
title: Additional file 8: of Molecular mapping of the Cf-10 gene by combining SNP/InDel-index and linkage analysis in tomato (Solanum lycopersicum)

description: Table S4. The qRT-PCR reaction system. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7564106.v1
title: Additional file 12: of Systematic evaluation of C. elegans lincRNAs with CRISPR knockout mutants

description: Table S6. Primers used in this study. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.7564112
title: Additional file 1: of Systematic evaluation of C. elegans lincRNAs with CRISPR knockout mutants

description: Table S1. Expression profiles of lincRNAs. (XLSX 68 kb)
DOI: 10.6084/m9.figshare.7039802
title: Three new synonyms of <i>Macromitrium microstomum</i> (Hook. & Grev.) Schwägr. (Bryophyta, Orthotrichaceae), with comments on its morphological variations

description: <i>Macromitrium filicaule</i> Müll.Hal., <i>M. pacificum</i> var. <i>brevisetum</i> Thér. and <i>M. subnitidum</i> Müll.Hal are placed in synonymy with <i>Macromitrium microstomum</i> (Hook. & Grev.) Schwägr. The morphological variations of <i>M. microstomum</i> branch leaves, perichaetial leaves and capsules are illustrated by digital images.
DOI: 10.6084/m9.figshare.14379654
title: Additional file 5 of FISH landmarks reflecting meiotic recombination and structural alterations of chromosomes in wheat (Triticum aestivum L.)

description: Additional file 5: Table S1. Oligonucleotide probes used for ND-FISH assays in this study.
DOI: 10.6084/m9.figshare.7039877
title: RETRACTED ARTICLE: miR-135 promotes proliferation and stemness of oesophageal squamous cell carcinoma by targeting RERG

description: We, the Editors and Publisher of the journal <i>Artificial Cells, Nanomedicine, and Biotechnology</i>, have retracted the following article: Yan Zhang, Shuang Ren, Fengfeng Yuan, Kaishang Zhang, Yingying Fan, Shaozhong Zheng, Zhen Gao, Jia Zhao, Teng Mu, Song Zhao, AnQuan Shang, Xiangnan Li and Ying Jie. (2018). miR-135 promotes proliferation and stemness of oesophageal squamous cell carcinoma by targeting RERG. Artificial Cells, Nanomedicine, and Biotechnology. 46:S2, S1210–S1219, DOI: 10.1080/21691401.2018.1483379 Since publication, the authors noticed errors in their data calculation. As this error directly impacts the reported results and conclusions the authors alerted the issue to the Editor and Publisher and all have agreed to retract the article to ensure correction of the scholarly record. We have been informed in our decision-making by our policy on publishing ethics and integrity and the COPE guidelines on retractions. The retracted article will remain online to maintain the scholarly record, but it will be digitally watermarked on each page as ‘Retracted’.
DOI: 10.6084/m9.figshare.7039877.v3
title: RETRACTED ARTICLE: miR-135 promotes proliferation and stemness of oesophageal squamous cell carcinoma by targeting RERG

description: We, the Editors and Publisher of the journal <i>Artificial Cells, Nanomedicine, and Biotechnology</i>, have retracted the following article: Yan Zhang, Shuang Ren, Fengfeng Yuan, Kaishang Zhang, Yingying Fan, Shaozhong Zheng, Zhen Gao, Jia Zhao, Teng Mu, Song Zhao, AnQuan Shang, Xiangnan Li and Ying Jie. (2018). miR-135 promotes proliferation and stemness of oesophageal squamous cell carcinoma by targeting RERG. Artificial Cells, Nanomedicine, and Biotechnology. 46:S2, S1210–S1219, DOI: 10.1080/21691401.2018.1483379 Since publication, the authors noticed errors in their data calculation. As this error directly impacts the reported results and conclusions the authors alerted the issue to the Editor and Publisher and all have agreed to retract the article to ensure correction of the scholarly record. We have been informed in our decision-making by our policy on publishing ethics and integrity and the COPE guidelines on retractions. The retracted article will remain online to maintain the scholarly record, but it will be digitally watermarked on each page as ‘Retracted’.
DOI: 10.6084/m9.figshare.7564136.v1
title: Additional file 3: of Systematic evaluation of C. elegans lincRNAs with CRISPR knockout mutants

description: Table S2. List of worm strains. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.14387700
title: The first-line cluster headache medication verapamil alters the circadian period and elicits sex-specific sleep changes in mice

description: Verapamil is the first-line preventive medication for cluster headache, an excruciating disorder with strong circadian features. Whereas second- and third-line preventives include known circadian modulators, such as melatonin, corticosteroids, and lithium, the circadian effects of verapamil are poorly understood. Here, we characterize the circadian features of verapamil using both in vitro and in vivo models. In <i>Per2::LucSV</i> reporter fibroblasts, treatment with verapamil (0.03–10 µM) showed a dose-dependent period shortening of the reporter rhythm which reached a nadir at 1 µM, and altered core clock gene expression at 10 µM. Mouse wheel-running activity with verapamil (1 mg/mL added to the drinking water) also resulted in significant period shortening and activity reduction in both male and female free-running wild-type C57BL6/J mice. The temporal patterns of activity reduction, however, differ between the two sexes. Importantly, piezo sleep recording revealed sexual dimorphism in the effects of verapamil on sleep timing and bout duration, with more pronounced adverse effects in female mice. We also found altered circadian clock gene expression in the cerebellum, hypothalamus, and trigeminal ganglion of verapamil-treated mice. Verapamil did not affect reporter rhythms in ex vivo suprachiasmatic nucleus (SCN) slices from <i>Per2:Luc</i> reporter mice, perhaps due to the exceptionally tight coupling in the SCN. Thus, verapamil affects both peripheral (trigeminal ganglion) and central (hypothalamus and cerebellum) nervous system structures involved in cluster headache pathophysiology, possibly with network effects instead of isolated SCN effects. These studies suggest that verapamil is a circadian modulator in laboratory models at both molecular and behavioral levels, and sex is an important biological variable for cluster headache medications. These observations highlight the circadian system as a potential convergent target for cluster headache medications with different primary mechanisms of action.
DOI: 10.6084/m9.figshare.14903963.v1
title: Additional file 2 of DNA double-strand break repair gene mutation and the risk of papillary thyroid microcarcinoma: a case–control study

description: Additional file 2. Data of Clinicopathological characteristics of Papillary Thyroid Microcarcinoma.
DOI: 10.6084/m9.figshare.22776362
title: Data files from " Modulation of deep neural circuits with sonogenetics"

description:  Data files from " Modulation of deep neural circuits with sonogenetics  " Xian et al 2023
DOI: 10.6084/m9.figshare.22776389
title: Shenzhen Institute of Advanced Technology Lower Limb Motion Dataset (SIAT-LLMD)

description: This study presents a novel lower limb motion dataset (SIAT-LLMD), comprising sEMG, kinematic, and kinetic data with corresponding labels acquired from 40 healthy humans during 16 limb movements.
DOI: 10.6084/m9.figshare.14903960
title: Additional file 1 of DNA double-strand break repair gene mutation and the risk of papillary thyroid microcarcinoma: a case–control study

description: Additional file 1. Data of Clinicopathological characteristics of Benign Thyroid Nodules.