cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14317628.v1
title: Examination of Ureaplasma urealyticum and Mycoplasma hominis in 4082 Chinese patients

description: The objective of this study was to analyze the infection rate and drug resistance of Ureaplasma urealyticum (UU) and Mycoplasma hominis (MH) in the genitourinary tract of Chinese patients. From December 2018 to June 2019, vaginal secretion or urinary secretion of outpatients in our hospital were selected for culture and drug sensitivity analysis of Ureaplasma urealyticum and Mycoplasma hominis. In 4082 Chinese samples, 1567 Mycoplasma were detected, a detection rate of 38.39%, among which 1366 cases were UU single positive, accounting for 33.47%, 15 cases were MH single positive, accounting for 0.36%, 186 cases were UU and MH mixed positive, accounting for 4.56%. The most affected age groups were 21-30 years and 31-40 years, accounting for 19.09 and 15.05%, respectively. The results of drug sensitivity showed that doxycycline, minocycline, josamycin, clarithromycin, and roxithromycin were more sensitive to mycoplasma infection. The distribution of Ureaplasma urealyticum and Mycoplasma hominis in the human genitourinary system and their sensitivity to antibiotics is different for sex and age groups.
DOI: 10.6084/m9.figshare.14317635.v1
title: Down-regulation of HCP5 inhibits cell proliferation, migration, and invasion through regulating EPHA7 by competitively binding miR-101 in osteosarcoma

description: Patients with osteosarcoma (OS) usually have poor overall survival because of frequent metastasis. Long non-coding RNAs (lncRNAs) have been reported to be associated with tumorigenesis and metastasis. In this study, we investigated the expression and roles of lncRNA human histocompatibility leukocyte antigen (HLA) complex P5 (HCP5) in OS, aiming to provide a novel molecular mechanism for OS. HCP5 was up-regulated both in OS tissues and cell lines and high expression of HCP5 was associated to low survival in OS patients. Down-regulation of HCP5 inhibited cell proliferation, migration, and invasion, suggesting its carcinogenic role in OS. miR-101 was targeted by HCP5 and its expression was decreased in OS. The inhibitor of miR-101 reversed the impact of HCP5 down-regulation on cell proliferation, apoptosis, and metastasis in OS. Ephrin receptor 7 (EPHA7) was proved to be a target of miR-101 and had ability to recover the effects of miR-101 inhibitor in OS. In conclusion, lncRNA HCP5 knockdown suppressed cell proliferation, migration, and invasion, and induced apoptosis through depleting the expression of EPHA7 by binding to miR-101, providing a potential therapeutic strategy of HCP5 in OS.
DOI: 10.6084/m9.figshare.14317664.v1
title: MicroRNA-302b mitigates renal fibrosis via inhibiting TGF-β/Smad pathway activation

description: Renal fibrosis is one of the most significant pathological changes after ureteral obstruction. Transforming growth factor-β (TGF-β) signaling pathway plays essential roles in kidney fibrosis regulation. The aims of the present study were to investigate effects of microRNA-302b (miR-302b) on renal fibrosis, and interaction between miR-302b and TGF-β signaling pathway in murine unilateral ureteral obstruction (UUO) model. Microarray dataset GSE42716 was downloaded by retrieving Gene Expression Omnibus database. In accordance with bioinformatics analysis results, miR-302b was significantly down-regulated in UUO mouse kidney tissue and TGF-β1-treated HK-2 cells. Masson's trichrome staining showed that miR-302b mimics decreased renal fibrosis induced by UUO. The increased mRNA expression of collagen I and α-smooth muscle actin (α-SMA) and decreased expression of E-cadherin were reversed by miR-302b mimics. In addition, miR-302b up-regulation also inhibited TGF-β1-induced epithelial mesenchymal transition (EMT) of HK-2 cells by restoring E-cadherin expression and decreasing α-SMA expression. miR-302b mimics suppressed both luciferase activity and protein expression of TGF-βR2. However, miR-302b inhibitor increased TGF-βR2 luciferase activity and protein expression. Meanwhile, miR-302b mimics inhibited TGF-βR2 mRNA expression and decreased Smad2 and Smad3 phosphorylation in vivo and in vitro. Furthermore, over-expression of TGF-βR2 restored the miR-302b-induced decrease of collagen I and α-SMA expression. In conclusion, this study demonstrated that miR-302b attenuated renal fibrosis by targeting TGF-βR2 to suppress TGF-β/Smad signaling activation. Our findings showed that elevating renal miR-302b levels may be a novel therapeutic strategy for preventing renal fibrosis.
DOI: 10.6084/m9.figshare.6453899.v1
title: Detection of cardioembolic stroke with B-type natriuretic peptide or N-terminal pro-BNP: a comparative diagnostic meta-analysis

description: <b>Background</b>: B-type natriuretic peptides (BNPs) have shown promise in detecting cardioembolic stroke. However, there has been little investigation comparing the diagnostic efficacy of BNP and its cleavage by-product N-terminal peptide (NT-proBNP) in cardioembolic stroke patients. Therefore, the aim of this meta-analysis will be to comparatively assess the diagnostic efficacy of BNP versus NT-proBNP in distinguishing cardioembolic stroke from non-cardioembolic stroke in adult ischemic stroke patients. <b>Methods</b>: We conducted a literature search of several databases for prospective studies assessing the use of BNP or NT-proBNP to detect cardioembolic stroke in adult acute ischemic stroke patients. Only clinical studies reporting the diagnostic performance of BNP or NT-proBNP in predicting cardioembolic stroke in adult ischemic stroke patients were included. Diagnostic performance outcomes were summarized using forest plots and summary receiver operating characteristic (SROC) curves. <b>Results</b>: Ten BNP prospective cohort studies and six NT-proBNP prospective cohort studies were finally included in the meta-analysis. BNP showed a summary sensitivity of 0.65 (95% confidence interval (CI): 0.63-0.68), a summary specificity of 0.85 (95% CI: 0.83-0.87), and an area under the SROC curve of 0.8718 (standard error (SE): 0.0248). NT-proBNP showed a summary sensitivity of 0.55 (95% CI: 0.52–0.59), a summary specificity of 0.93 (95% CI: 0.91–0.94), and an AUC of 0.8746 (SE: 0.0280). <b>Discussion</b>: BNP and NT-proBNP display closely equivalent overall diagnostic accuracies in distinguishing cardioembolic stroke from non-cardioembolic stroke in adult ischemic stroke patients, with BNP showing a superior sensitivity and NT-proBNP showing a superior specificity.
DOI: 10.6084/m9.figshare.21129975
title: Additional file 4 of RETSAT associates with DDX39B to promote fork restarting and resistance to gemcitabine based chemotherapy in pancreatic ductal adenocarcinoma

description: Additional file 4.
DOI: 10.6084/m9.figshare.21129973.v1
title: Additional file 2 of RETSAT associates with DDX39B to promote fork restarting and resistance to gemcitabine based chemotherapy in pancreatic ductal adenocarcinoma

description: Additional file 2.
DOI: 10.34740/kaggle/ds/4433310
title: Jgggghbccff
DOI: 10.6084/m9.figshare.16935599.v1
title: Additional file 2 of Genome-wide identification and characteristic analysis of the downstream melatonin metabolism gene GhM2H in Gossypium hirsutum L.

description: Additional file 2: Calculation of non-synonymous (Ka) to synonymous (Ks) substitution.
DOI: 10.6084/m9.figshare.16945657
title: Raw data for Fig. 2

description: Raw data for Fig. 2
DOI: 10.6084/m9.figshare.14317679
title: WeChat-based education and rehabilitation program in unprotected left main coronary artery disease patients after coronary artery bypass grafting: an effective approach in reducing anxiety, depression, loss to follow-up, and improving quality of life

description: This study aimed to investigate the effect of WeChat-based education and rehabilitation program (WERP) on anxiety, depression, health-related quality of life (HRQoL), major adverse cardiac/cerebrovascular events (MACCE)-free survival, and loss to follow-up rate in unprotected left main coronary artery disease (ULMCAD) patients after coronary artery bypass grafting (CABG). In this randomized controlled study, 140 ULMCAD patients who underwent CABG were randomly assigned to WERP group (n=70) or control care (CC) group (n=70). During the 12-month intervention period, anxiety and depression (using hospital anxiety and depression scale (HADS)) and HRQoL (using 12-Item Short-Form Health Survey (SF-12)) were assessed longitudinally. During the total 36-month follow-up period (12-month intervention and 24-month non-intervention periods), MACCE and loss to follow-up were recorded. During the intervention period, HADS-anxiety score at month 9 (M9) (P=0.047) and month 12 (M12) (P=0.034), anxiety rate at M12 (P=0.028), and HADS-D score at M12 (P=0.048) were all reduced in WERP group compared with CC group. As for HRQoL, SF-12 physical component summary score at M9 (P=0.020) and M12 (P=0.010) and SF-12 mental component summary score at M9 (P=0.040) and M12 (P=0.028) were all increased in WERP group compared with CC group. During the total follow-up period, WERP group displayed a trend of longer MACCE-free survival than that in CC group but without statistical significance (P=0.195). Additionally, loss to follow-up rate was attenuated in WERP group compared with CC group (P=0.033). WERP serves as an effective approach in optimizing mental health care and promoting life quality in ULMCAD patients after CABG.
DOI: 10.6084/m9.figshare.16945675
title: Raw Data for Fig. 3

description: Raw data for Fig. 3
DOI: 10.6084/m9.figshare.16945684
title: Raw Data for Fig. 6

description: Raw data for Fig. 6
DOI: 10.6084/m9.figshare.22182019
title: Evaluation of duration of antibiotic therapy across hospitals in Scotland including the impact of COVID-19 pandemic: a segmented interrupted time series analysis

description: Little is known about the duration of antibiotic use in hospital settings. We evaluated the duration of hospital antibiotic therapy for four commonly prescribed antibiotics (amoxicillin, co-amoxiclav, doxycycline, and flucloxacillin) including the assessment of COVID-19 impact. A repeated, cross-sectional study using the Hospital Electronic Prescribing and Medicines Administration system (January/2019-March/2022). Monthly median duration of therapy/duration categories was calculated, stratified by routes of administration, age, and sex. The impact of COVID-19 was assessed using segmented time-series analysis. There were significant variations in the median duration of therapy across routes of administration (P &lt; 0.05), with the highest value among those antibiotic courses composed of both oral and IV antibiotics (‘Both’ group). Significantly higher proportions of prescriptions within the ‘Both’ group had a duration of &gt;7 days compared to oral or IV. The duration of therapy differed significantly by age. Some small statistically significant changes in the level/trends of duration of therapy were observed in the post-COVID-19 period. No evidence for prolonged duration of therapy were observed, even during COVID-19 pandemic. The duration of IV therapy was relatively short, suggesting timely clinical review and consideration of IV to oral switch. Longer duration of therapy was observed among older patients.
DOI: 10.6084/m9.figshare.14318159
title: Nigella sativa ameliorates oxidative stress induced adverse effects in rodent modeling studies: Indices of serum chemistry and hematology

description: Abstract In this era, various traditional medicinal herbs were researched for their toxicological and safety aspects. The present study focused on using Nigella sativa fixed (NSFO) and essential oil (NSEO) to mitigate the adverse consequences of oxidative stress. For the purpose, oxidative stress was induced in Sprague Dawley rats using potassium bromate injection. The effect of NSFO and NSEO on indices of serum chemistry and hematology were studied. The results indicated that potassium bromate imparted drastic changes in serum chemistry and hematology e.g. it increased the blood cholesterol and blood glucose along with decreasing the insulin secretion. Oxidative stress also influenced the hematological attributes negatively but experimental diets were slightly successful in normalizing the values. The experimental diets especially essential oil that contains significant quantities of thymoquinone modulated the adverse consequences of oxidative stress with special reference to hematology and serological attributes. In the nutshell, NSFO and NSEO hold potential to mitigate the oxidative stress, and improved various serological and hematological attributes.
DOI: 10.6084/m9.figshare.8032811.v1
title: Additional file 2 of LightCpG: a multi-view CpG sites detection on single-cell whole genome sequence data

description: The size of the HepG2 dataset. (XLSX 10.8 kb)
DOI: 10.6084/m9.figshare.20085520
title: Rank-Based Greedy Model Averaging for High-Dimensional Survival Data

description: Model averaging is an effective way to enhance prediction accuracy. However, most previous works focus on low-dimensional settings with completely observed responses. To attain an accurate prediction for the risk effect of survival data with high-dimensional predictors, we propose a novel method: rank-based greedy (RG) model averaging. Specifically, adopting the transformation model with splitting predictors as working models, we doubly use the smooth concordance index function to derive the candidate predictions and optimal model weights. The final prediction is achieved by weighted averaging all the candidates. Our approach is flexible, computationally efficient, and robust against model misspecification, as it neither requires the correctness of a joint model nor involves the estimation of the transformation function. We further adopt the greedy algorithm for high dimensions. Theoretically, we derive an asymptotic error bound for the optimal weights under some mild conditions. In addition, the summation of weights assigned to the correct candidate submodels is proven to approach one in probability when there are correct models included among the candidate submodels. Extensive numerical studies are carried out using both simulated and real datasets to show the proposed approach’s robust performance compared to the existing regularization approaches. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.8032838.v1
title: Additional file 6 of LightCpG: a multi-view CpG sites detection on single-cell whole genome sequence data

description: The performance of different features using the HCCs dataset. (XLSX 21.3 kb)
DOI: 10.6084/m9.figshare.8032844.v1
title: Additional file 7 of LightCpG: a multi-view CpG sites detection on single-cell whole genome sequence data

description: The results of different methods using the HCCs dataset. (XLSX 35.8 kb)
DOI: 10.6084/m9.figshare.8032850.v1
title: Additional file 8 of LightCpG: a multi-view CpG sites detection on single-cell whole genome sequence data

description: The results of different methods using the HepG2 dataset. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.14317679.v1
title: WeChat-based education and rehabilitation program in unprotected left main coronary artery disease patients after coronary artery bypass grafting: an effective approach in reducing anxiety, depression, loss to follow-up, and improving quality of life

description: This study aimed to investigate the effect of WeChat-based education and rehabilitation program (WERP) on anxiety, depression, health-related quality of life (HRQoL), major adverse cardiac/cerebrovascular events (MACCE)-free survival, and loss to follow-up rate in unprotected left main coronary artery disease (ULMCAD) patients after coronary artery bypass grafting (CABG). In this randomized controlled study, 140 ULMCAD patients who underwent CABG were randomly assigned to WERP group (n=70) or control care (CC) group (n=70). During the 12-month intervention period, anxiety and depression (using hospital anxiety and depression scale (HADS)) and HRQoL (using 12-Item Short-Form Health Survey (SF-12)) were assessed longitudinally. During the total 36-month follow-up period (12-month intervention and 24-month non-intervention periods), MACCE and loss to follow-up were recorded. During the intervention period, HADS-anxiety score at month 9 (M9) (P=0.047) and month 12 (M12) (P=0.034), anxiety rate at M12 (P=0.028), and HADS-D score at M12 (P=0.048) were all reduced in WERP group compared with CC group. As for HRQoL, SF-12 physical component summary score at M9 (P=0.020) and M12 (P=0.010) and SF-12 mental component summary score at M9 (P=0.040) and M12 (P=0.028) were all increased in WERP group compared with CC group. During the total follow-up period, WERP group displayed a trend of longer MACCE-free survival than that in CC group but without statistical significance (P=0.195). Additionally, loss to follow-up rate was attenuated in WERP group compared with CC group (P=0.033). WERP serves as an effective approach in optimizing mental health care and promoting life quality in ULMCAD patients after CABG.
DOI: 10.6084/m9.figshare.14317682.v1
title: Neuroprotective effects of zonisamide on cerebral ischemia injury via inhibition of neuronal apoptosis

description: It is known that neuronal apoptosis contributes to pathology of cerebral ischemia injury. Zonisamide (ZNS) has shown anti-apoptosis effects in recent studies. The present study investigated whether the anti-apoptotic effect can account for the neuroprotective action of ZNS on cerebral ischemia. Neuronal cells were maintained under oxygen-glucose deprivation conditions to simulate cerebral ischemia and treated with ZNS simultaneously. The apoptosis of the cells and expression of apoptosis-related proteins were investigated by flow cytometry and western blot analysis, respectively. A cerebral ischemia mouse model was created via middle cerebral artery occlusion, and the mice were treated with ZNS. Neurological deficit scores and infarct volumes of the cerebral ischemia mice were measured. The apoptosis status of the neuronal cells was evaluated by TUNEL staining. In vitro, the ZNS treatment inhibited both the apoptosis of the neuronal cells and apoptosis-related protein expression (caspase-3, caspase-8, and calpain-1) induced by the oxygen-glucose deprivation. The anti-apoptosis effect of ZNS could occur through the blocking of reactive oxygen species. Moreover, ZNS treatment significantly ameliorated neurological deficits and reduced infarct volumes in the cerebral ischemia mice model. In this study, ZNS exerted neuroprotective effects by inhibition of apoptosis in neuronal cells in cerebral ischemia. Therefore, ZNS might be a promising therapy for cerebral ischemia.
DOI: 10.6084/m9.figshare.14317688
title: Knockdown of lncRNA H19 suppresses endometriosis in vivo

description: The long noncoding RNA (lncRNA) H19 is involved in the pathogenesis of endometriosis by modulating the proliferation and invasion of ectopic endometrial cells in vitro, but related in vivo studies are rare. This study aimed to investigate the role of lncRNA H19 in a nude mouse model of endometriosis. Ectopic endometrial stromal cells (ecESCs) were isolated from ectopic endometrium of patients with endometriosis and infected with lentiviruses expressing short hairpin RNA (shRNA) negative control (LV-NC-shRNA) or lncRNA-H19 shRNA (LV-H19-shRNA). The ecESCs infected with LV-NC-shRNA and LV-H19-shRNA were subcutaneously implanted into forty 6- to 8-week-old female nude mice. The size and weight of the endometriotic implants were measured at 1, 2, 3, and 4 weeks after implantation and compared, and lncRNA H19 levels in endometriotic implants were evaluated using real-time polymerase chain reaction (RT-PCR). All nude mice survived the experimental period, and no significant differences in body weight were observed between the experimental group and the control group. All nude mice developed histologically confirmed subcutaneous endometriotic lesions with glandular structures and stroma after 1 week of implantation. The subcutaneous lesions in the LV-NC-shRNA group after 1, 2, 3, and 4 weeks of implantation were larger than those in the LV-H19-shRNA group, and lncRNA H19 levels in subcutaneous lesions in the LV-NC-shRNA group were significantly higher than those in the LV-H19-shRNA group. Knockdown of lncRNA H19 suppresses endometriosis in vivo. Further study is required to explore the underlying mechanism in the future.
DOI: 10.6084/m9.figshare.8032919
title: Additional file 6: of Identification of genomic regions associated with multi-silique trait in Brassica napus

description: Table S5. GO enrichment in cellular components (CC) category of the genes. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.16415533.v1
title: A pan-cancer analysis revealed the role of the SLC16 family in cancer

description: Cancer is one of the serious diseases that endanger human health and bring a heavy burden to world economic development. Although the current targeted therapy and immunotherapy have achieved initial results, the emergence of drug resistance shows that the existing research is far from enough. In recent years, the tumor microenvironment has been found to be an important condition for tumor development and has profound research value. The SLC16 family is a group of monocarboxylic acid transporters involved in cancer metabolism and the formation of the tumor microenvironment. However, there have been no generalized cancer studies in the SLC16 family. In this study, we conducted a pan-cancer analysis of the SLC16 family. The results showed that multiple members of the SLC16 family could be used as prognostic indicators for many tumors, and were associated with immune invasion and tumor stem cells. Therefore, the SLC16 family has extensive exploration value in the future.
DOI: 10.6084/m9.figshare.11703033
title: Mass spectrometry proteomics reveals a function for mammalian CALCOCO1 in MTOR-regulated selective autophagy

description: Macroautophagy/autophagy is suppressed by MTOR (mechanistic target of rapamycin kinase) and is an anticancer target under active investigation. Yet, MTOR-regulated autophagy remains incompletely mapped. We used proteomic profiling to identify proteins in the MTOR-autophagy axis. Wild-type (WT) mouse cell lines and cell lines lacking individual autophagy genes (<i>Atg5</i> or <i>Ulk1/Ulk2</i>) were treated with an MTOR inhibitor to induce autophagy and cultured in media with either glucose or galactose. Mass spectrometry proteome profiling revealed an elevation of known autophagy proteins and candidates for new autophagy components, including CALCOCO1 (calcium binding and coiled-coil domain protein 1). We show that CALCOCO1 physically interacts with MAP1LC3C, a key protein in the machinery of autophagy. Genetic deletion of <i>CALCOCO1</i> disrupted autophagy of the endoplasmic reticulum (reticulophagy). Together, these results reveal a role for CALCOCO1 in MTOR-regulated selective autophagy. More generally, the resource generated by this work provides a foundation for establishing links between the MTOR-autophagy axis and proteins not previously linked to this pathway. <b>Abbreviations:</b> ATG: autophagy-related; CALCOCO1: calcium binding and coiled-coil domain protein 1; CALCOCO2/NDP52: calcium binding and coiled-coil domain protein 2; CLIR: MAP1LC3C-interacting region; CQ: chloroquine; KO: knockout; LIR: MAP1LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MEF: mouse embryonic fibroblast; MLN: MLN0128 ATP-competitive MTOR kinase inhibitor; MTOR: mechanistic target of rapamycin kinase; reticulophagy: selective autophagy of the endoplasmic reticulum; TAX1BP1/CALCOCO3: TAX1 binding protein 1; ULK: unc 51-like autophagy activating kinase; WT: wild-type.
DOI: 10.6084/m9.figshare.6978191.v1
title: Additional file 7: of Aberrantly expressed messengerÂ RNAs and long noncoding RNAs in degenerative nucleus pulposus cells co-cultured with adipose-derived mesenchymal stem cells

description: Full list of differentially expressed mRNAs and lncRNAs. (XLSX 1394 kb)