cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10093703.v1
title: Genetic admixture history and forensic characteristics of Turkic-speaking Kyrgyz population via 23 autosomal STRs

description: Kyrgyz people, a Turkic-speaking ethnic group native to Central Asia, are considered as one mixed population from different historical tribes through the processes of conquest, intermarriage, assimilation and migration. The aim of this study was to infer the forensic statistical parameters and genetic structure of Chinese Kyrgyz and explore the patterns of their genetic relationships with adjacent and worldwide reference populations. We genotyped 25 forensic-related markers (amelogenin, Y-indel of rs2032678 and 23 Autosomal Short Tandem Repeats, A-STRs) in 491 Chinese Kyrgyzs. Allele frequency and forensic parameters were calculated using the STRAF software. Pairwise genetic distances were estimated using Phylip and subsequently dissected via principal component analysis, multidimensional scaling plots and phylogenetic relationship reconstruction. Investigations of allele frequency and forensic parameters indicated that all studied A-STRs are informative in the Chinese Kyrgyz population and can be used as a powerful tool in forensic individual identification and parentage testing. Results from genetic relationship analyses demonstrated that Akto Kyrgyz people harbour a genetically close relationship with Turkic-speaking Uyghur and Kazakh. Genetic structure analysis based on the raw genotype data among Eurasian populations further suggested that genetic ancestries and population substructures in Asia are largely associated with language and geography.
DOI: 10.6084/m9.figshare.14286455
title: Sarcopenia predicts prognosis of patients with renal cell carcinoma: A systematic review and meta-analysis

description: ABSTRACT Sarcopenia, a concept reflecting the loss of skeletal muscle mass, was reported to be associated with the prognosis of several tumors. However, the prognostic value of sarcopenia in patients with renal cancer remains unclear. We carried out this metaanalysis and systematic review to evaluate the prognostic value of sarcopenia in patients with renal cell carcinomas. We comprehensively searched PubMed, Embase, and Cochrane Library from inception to December 2018. Hazard ratio (HR) and 95% confidence interval (CI) were pooled together. A total of 5 studies consisting of 771 patients were enrolled in this quantitative analysis, 347 (45.0%) of which had sarcopenia. Patients with sarcopenia had a worse OS compared with those without sarcopenia (HR=1.76; 95%CI, 1.35-2.31; P &lt;0.001). In the subgroup of patients with localized and advanced/metastatic diseases, sarcopenia was also associated with poor OS (HR=1.48, P=0.039; HR=2.14, P &lt;0.001; respectively). With a limited sample size, we did not observe difference of PFS between two groups (HR=1.56, 95% CI, 0.69-3.50, P=0.282). In the present meta-analysis, we observed that patients with sarcopenia had a worse OS compared with those without sarcopenia in RCC. Larger, preferably prospective studies, are needed to confirm and update our findings.
DOI: 10.6084/m9.figshare.20055218
title: In-situ observation of storm-induced wave-supported fluid mud occurrence in the subaqueous Yellow River delta

description:  These Datasets are used in a manuscript submitted to JGR-Oceans (# 2021JC018190RR ).
DOI: 10.24403/jp.1320048
title: 100 Jahre Thüringische Botanische Gesellschaft / Friedrich Karl Meyer
DOI: 10.6084/m9.figshare.14286465
title: Novel semirigid ureterorenoscope with irrigation and vacuum suction system: introduction and initial experience for management of upper urinary calculi

description: ABSTRACT Objective: This study aims to design a novel semirigid ureterorenoscope with irrigation and vacuum suction system and a modified ureteral access sheath (UAS) named Sotn ureterorenoscope® (Sotn=ShuoTong Medical Company) to overcome the deficiencies of the current procedure and to improve the efficiency and safety of using Sotn ureterorenoscope® for treatment of upper urinary calculi. Materials and Methods: Fifty-eight patients, comprising 31 males and 27 females, were evaluated. The medical records of 58 patients with upper urinary calculi treated with Sotn ureterorenoscope® from March 2015 to June 2017 were retrospectively reviewed at the Second Affiliate Hospital of Guangzhou University of Chinese Medicine in China. The primary outcome was stone-free rate (SFR) assessed by computed tomography on the 1st day and one month after treatment. The secondary outcome was postoperative complication rate. Results: The mean and SD of operative duration was 48.5 (10.4) min, and the mean and SD of stone size was 15.6 (5.6) mm. The primary overall SFR was 89.7% (52/58) and 100% at 1 month follow-up. Complication, which was Clavien I (minor fever managed by antipyretic therapy), was detected in 1.7% (1/58) of the patients. Conclusions: Sotn ureterorenoscope® is technically feasible, efficacious and safe for treatment of upper urinary calculi because of its advantages of high SFR and low complication rates.
DOI: 10.24403/jp.1320049
title: Die Verbreitung der Gattung Pinguicula L. in Südamerika — ein Beispiel für Beziehungen zwischen holarktischer und andischer Flora? / S. Jost Casper
DOI: 10.6084/m9.figshare.24249655
title: An updated database of virus circular RNAs provides new insights into the biogenesis mechanism of the molecule

description: Virus circular RNAs (circRNA) have been reported to be extensively expressed and play important roles in viral infections. Previously we build the first database of virus circRNAs named VirusCircBase which has been widely used in the field. This study significantly improved the database on both the data quantity and database functionality: the number of virus circRNAs, virus species, host organisms was increased from 46440, 23, 9 to 60859, 43, 22, respectively, and 1902 full-length virus circRNAs were newly added; new functions were added such as visualization of the expression level of virus circRNAs and visualization of virus circRNAs in the Genome Browser. Analysis of the expression of virus circRNAs showed that they had low expression levels in most cells or tissues and showed strong expression heterogeneity. Analysis of the splicing of virus circRNAs showed that they used a much higher proportion of non-canonical back-splicing signals compared to those in animals and plants, and mainly used the A5SS (alternative 5’ splice site) in alternative-splicing. Most virus circRNAs have no more than two isoforms. Finally, human genes associated with the virus circRNA production were investigated and more than 1000 human genes exhibited moderate correlations with the expression of virus circRNAs. Most of them showed negative correlations including 42 genes encoding RNA-binding proteins. They were significantly enriched in biological processes related to cell cycle and RNA processing. Overall, the study provides a valuable resource for further studies of virus circRNAs and also provides new insights into the biogenesis mechanisms of virus circRNAs.
DOI: 10.6084/m9.figshare.24249655.v1
title: An updated database of virus circular RNAs provides new insights into the biogenesis mechanism of the molecule

description: Virus circular RNAs (circRNA) have been reported to be extensively expressed and play important roles in viral infections. Previously we build the first database of virus circRNAs named VirusCircBase which has been widely used in the field. This study significantly improved the database on both the data quantity and database functionality: the number of virus circRNAs, virus species, host organisms was increased from 46440, 23, 9 to 60859, 43, 22, respectively, and 1902 full-length virus circRNAs were newly added; new functions were added such as visualization of the expression level of virus circRNAs and visualization of virus circRNAs in the Genome Browser. Analysis of the expression of virus circRNAs showed that they had low expression levels in most cells or tissues and showed strong expression heterogeneity. Analysis of the splicing of virus circRNAs showed that they used a much higher proportion of non-canonical back-splicing signals compared to those in animals and plants, and mainly used the A5SS (alternative 5’ splice site) in alternative-splicing. Most virus circRNAs have no more than two isoforms. Finally, human genes associated with the virus circRNA production were investigated and more than 1000 human genes exhibited moderate correlations with the expression of virus circRNAs. Most of them showed negative correlations including 42 genes encoding RNA-binding proteins. They were significantly enriched in biological processes related to cell cycle and RNA processing. Overall, the study provides a valuable resource for further studies of virus circRNAs and also provides new insights into the biogenesis mechanisms of virus circRNAs.
DOI: 10.6084/m9.figshare.21102161
title: Additional file 1 of Hcp2a of APEC affects mRNA splicing and protein quality control in DF-1 cells

description: Additional file 1: Supplementary Table S1. The differentially expressed proteins comparing the experimental group and control group.
DOI: 10.6084/m9.figshare.21102161.v1
title: Additional file 1 of Hcp2a of APEC affects mRNA splicing and protein quality control in DF-1 cells

description: Additional file 1: Supplementary Table S1. The differentially expressed proteins comparing the experimental group and control group.
DOI: 10.6084/m9.figshare.21102164.v1
title: Additional file 2 of Hcp2a of APEC affects mRNA splicing and protein quality control in DF-1 cells

description: Additional file 2: Supplementary Table S2. GO and GO enrichment analysis of the DEPs.
DOI: 10.6084/m9.figshare.21102164
title: Additional file 2 of Hcp2a of APEC affects mRNA splicing and protein quality control in DF-1 cells

description: Additional file 2: Supplementary Table S2. GO and GO enrichment analysis of the DEPs.
DOI: 10.6084/m9.figshare.21102167
title: Additional file 3 of Hcp2a of APEC affects mRNA splicing and protein quality control in DF-1 cells

description: Additional file 3: Supplementary Table S3. KO categorization and KEGG enrichment analysis of the DEPs.
DOI: 10.6084/m9.figshare.21102167.v1
title: Additional file 3 of Hcp2a of APEC affects mRNA splicing and protein quality control in DF-1 cells

description: Additional file 3: Supplementary Table S3. KO categorization and KEGG enrichment analysis of the DEPs.
DOI: 10.24403/jp.1320050
title: Bemerkungen zum binnenländischen Vorkommen des Salzschwadens (Puccinellia distans [JACQ.] PARL.) / Wolfgang Heinrich
DOI: 10.24403/jp.1320053
title: Die Brandpilze Thüringens — Nachtrag I / Gerald Hirsch
DOI: 10.6084/m9.figshare.14286456.v1
title: Diagnosis accuracy of PCA3 level in patients with prostate cancer: a systematic review with meta-analysis

description: ABSTRACT Background: The diagnostic value and suitability of prostate cancer antigen 3 (PCA3) for the detection of prostate cancer (PCa) have been inconsistent in previous studies. Thus, the aim of the present meta-analysis was performed to systematically evaluate the diagnostic value of PCA3 for PCa. Materials and Methods: A meta-analysis was performed to search relevant studies using online databases EMBASE, PubMed and Web of Science published until February 1st, 2019. Ultimately, 65 studies met the inclusion criteria for this meta-analysis with 8.139 cases and 14.116 controls. The sensitivity, specificity, positive likelihood ratios (LR+), negative likelihood ratios (LR−), and other measures of PCA3 were pooled and determined to evaluate the diagnostic rate of PCa by the random-effect model. Results: With PCA3, the pooled overall diagnostic sensitivity, specificity, LR+, LR−, and 95% confidence intervals (CIs) for predicting significant PCa were 0.68 (0.64-0.72), 0.72 (0.68-0.75), 2.41 (2.16-2.69), 0.44 (0.40-0.49), respectively. Besides, the summary diagnostic odds ratio (DOR) and 95% CIs for PCA3 was 5.44 (4.53-6.53). In addition, the area under summary receiver operating characteristic (sROC) curves and 95% CIs was 0.76 (0.72-0.79). The major design deficiencies of included studies were differential verification bias, and a lack of clear inclusion and exclusion criteria. Conclusions: The results of this meta-analysis suggested that PCA3 was a non-invasive method with the acceptable sensitivity and specificity in the diagnosis of PCa, to distinguish between patients and healthy individuals. To validate the potential applicability of PCA3 in the diagnosis of PCa, more rigorous studies were needed to confirm these conclusions.
DOI: 10.6084/m9.figshare.14286465.v1
title: Novel semirigid ureterorenoscope with irrigation and vacuum suction system: introduction and initial experience for management of upper urinary calculi

description: ABSTRACT Objective: This study aims to design a novel semirigid ureterorenoscope with irrigation and vacuum suction system and a modified ureteral access sheath (UAS) named Sotn ureterorenoscope® (Sotn=ShuoTong Medical Company) to overcome the deficiencies of the current procedure and to improve the efficiency and safety of using Sotn ureterorenoscope® for treatment of upper urinary calculi. Materials and Methods: Fifty-eight patients, comprising 31 males and 27 females, were evaluated. The medical records of 58 patients with upper urinary calculi treated with Sotn ureterorenoscope® from March 2015 to June 2017 were retrospectively reviewed at the Second Affiliate Hospital of Guangzhou University of Chinese Medicine in China. The primary outcome was stone-free rate (SFR) assessed by computed tomography on the 1st day and one month after treatment. The secondary outcome was postoperative complication rate. Results: The mean and SD of operative duration was 48.5 (10.4) min, and the mean and SD of stone size was 15.6 (5.6) mm. The primary overall SFR was 89.7% (52/58) and 100% at 1 month follow-up. Complication, which was Clavien I (minor fever managed by antipyretic therapy), was detected in 1.7% (1/58) of the patients. Conclusions: Sotn ureterorenoscope® is technically feasible, efficacious and safe for treatment of upper urinary calculi because of its advantages of high SFR and low complication rates.
DOI: 10.6084/m9.figshare.7470737.v1
title: Additional file 4: of Characterization of Mycobacterium tuberculosis strains in Beijing, China: drug susceptibility phenotypes and Beijing genotype family transmission

description: Detailed information about genotyping patterns and DST results isolated from 1189â M.tb strains in Beijing. (XLSX 123 kb)
DOI: 10.6084/m9.figshare.7470782
title: Additional file 4: of Evaluating the profound effect of gut microbiome on host appetite in pigs

description: Table S2. The OTUs significantly associated with the ADFI by the two-part model (FDRâ &lt;â 0.05). (XLS 44 kb)
DOI: 10.6084/m9.figshare.14286462
title: Comparison and trend of perioperative outcomes between robot-assisted radical prostatectomy and open radical prostatectomy: nationwide inpatient sample 2009-2014

description: ABSTRACT Purpose: To make a further evaluation of perioperative outcomes between the robot-assisted radical prostatectomy (RARP) and open radical prostatectomy (ORP), we conducted a comparison and trend analysis by using the Nationwide Inpatient Sample (NIS) from 2009 to 2014. Materials and Methods: Adult prostate cancer patients with radical prostatectomy were abstracted from the NIS. RARP and ORP were identified according to the International Classification of Diseases, 9th Revision, Clinical Modification procedure codes. The perioperative outcomes included blood transfusion, intraoperative and postoperative complications, prolonged length of stay (pLOS), and in-hospital mortality. Propensity score matching method and multivariable logistic regression model were performed to adjust for the pre-defined covariates. The annual percent change (APC) was used to detect the change trend of rates for outcomes. Results: A total of 77.054 patients were included in our study. According to the results of propensity score matching analyses, RARP outperformed ORP in blood transfusion (1.96% vs. 9.40%), intraoperative complication (0.73% vs. 1.25%), overall postoperative complications (8.87% vs. 11.97%), and pLOS (13.39% vs. 36.70%). We also found that there was a significant decreasing tendency of incidence in blood transfusion (APC=-9.81), intraoperative complication (APC=-12.84), and miscellaneous surgical complications (APC=-14.09) for the RARP group. The results of multivariable analyses were almost consistent with those of propensity score matching analyses. Conclusions: The RARP approach has lower incidence rates of perioperative complications than the ORP approach, and there is a potential decreasing tendency of complication incidence rates for the RARP.
DOI: 10.6084/m9.figshare.7470773.v1
title: Additional file 3: of Evaluating the profound effect of gut microbiome on host appetite in pigs

description: Table S1. The significant differences of ADFI values between pigs in different pens detected by pairwise comparison. (XLS 30 kb)
DOI: 10.6084/m9.figshare.7470782.v1
title: Additional file 4: of Evaluating the profound effect of gut microbiome on host appetite in pigs

description: Table S2. The OTUs significantly associated with the ADFI by the two-part model (FDRâ &lt;â 0.05). (XLS 44 kb)
DOI: 10.6084/m9.figshare.14286462.v1
title: Comparison and trend of perioperative outcomes between robot-assisted radical prostatectomy and open radical prostatectomy: nationwide inpatient sample 2009-2014

description: ABSTRACT Purpose: To make a further evaluation of perioperative outcomes between the robot-assisted radical prostatectomy (RARP) and open radical prostatectomy (ORP), we conducted a comparison and trend analysis by using the Nationwide Inpatient Sample (NIS) from 2009 to 2014. Materials and Methods: Adult prostate cancer patients with radical prostatectomy were abstracted from the NIS. RARP and ORP were identified according to the International Classification of Diseases, 9th Revision, Clinical Modification procedure codes. The perioperative outcomes included blood transfusion, intraoperative and postoperative complications, prolonged length of stay (pLOS), and in-hospital mortality. Propensity score matching method and multivariable logistic regression model were performed to adjust for the pre-defined covariates. The annual percent change (APC) was used to detect the change trend of rates for outcomes. Results: A total of 77.054 patients were included in our study. According to the results of propensity score matching analyses, RARP outperformed ORP in blood transfusion (1.96% vs. 9.40%), intraoperative complication (0.73% vs. 1.25%), overall postoperative complications (8.87% vs. 11.97%), and pLOS (13.39% vs. 36.70%). We also found that there was a significant decreasing tendency of incidence in blood transfusion (APC=-9.81), intraoperative complication (APC=-12.84), and miscellaneous surgical complications (APC=-14.09) for the RARP group. The results of multivariable analyses were almost consistent with those of propensity score matching analyses. Conclusions: The RARP approach has lower incidence rates of perioperative complications than the ORP approach, and there is a potential decreasing tendency of complication incidence rates for the RARP.
DOI: 10.6084/m9.figshare.7470791
title: Additional file 6: of Evaluating the profound effect of gut microbiome on host appetite in pigs

description: Table S3. Five OTUs out of the 34 ADFI-associated OTUs whose relative abundances were significantly influenced by pens. (XLS 33 kb)
DOI: 10.6084/m9.figshare.7470767.v1
title: MOESM2 of Variability among autumn migration patterns of Mongolian Common Shelducks (Tadorna tadorna)

description: Additional file 2: Table S1. Detailed migration timing and site location of tracked Common Shelducks.
DOI: 10.5281/zenodo.10648681
title: Data Anonymization of Indonesia Citizen Data Using K-Anonymity, L-Diversity, and T-Closeness
DOI: 10.5281/zenodo.10648682
title: Data Anonymization of Indonesia Citizen Data Using K-Anonymity, L-Diversity, and T-Closeness
DOI: 10.6084/m9.figshare.7470800
title: Additional file 7: of Evaluating the profound effect of gut microbiome on host appetite in pigs

description: Table S4. The correlation between the relative abundance of KOs and the ADFI by MaAsLin. (XLS 65 kb)
DOI: 10.6084/m9.figshare.14286572
title: Adjunctive medical expulsive therapy with tamsulosin for repeated extracorporeal shock wave lithotripsy: a systematic review and meta-analysis

description: ABSTRACT Purpose: To evaluate the efficacy of adjunctive medical expulsive therapy (MET) with tamsulosin for the promotion of stone fragments clearance for repeated extracorporeal shock wave lithotripsy (ESWL). Materials and Methods: This meta-analysis was conducted by systematic search for randomized controlled trial (RCT) studies in PubMed/Medline, Scopus, Cochrane Library, Web of Science databases in January 2020, which compared tamsulosin with either placebo or non-placebo control for repeated ESWL. The primary endpoint was stone-free rate (SFR), the second endpoints were stone clearance time and complications. The quality assessment of included studies was performed by using the Cochrane System and Jadad score. Results: 7 RCTs were included in this meta-analysis. Tamsulosin provided higher SFR (for stones larger than 1cm, OR: 5.56, p=0.0003), except for patients with stones less than 1cm. For patients with renal stones (OR: 2.97, p=0.0005) or upper ureteral stones (OR: 3.10, p=0.004), tamsulosin can also provide a higher SFR. In addition, tamsulosin provided a shorter stone clearance time (WMD: −9.40, p=0.03) and lower pain intensity (WMD=-17.01, p &lt;0.0001) and incidences of steinstrasse (OR: 0.37, p=0.0002). Conclusion: Adjunctive MET with tamsulosin is effective in patients with specific stone size or location that received repeated ESWL. However, no well-designed RCT that used computed tomography for the detection and assessment of residual stone fragments was found. More studies with high quality and the comparison between tamsulosin and secondary ESWL are needed in the future.
DOI: 10.15156/bio/sh1858684.08fu
title: SH1858684.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.