bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of D-TACE combined with endovascular brachytherapy for HCC with MPVTT
Authors: Wu Zhiyuan , Gong Ju , Huang Wei , Wang Qingbing , Wang Ziyin , Liu Qin , Liu Jingjing , Gu Junwei , Ding Xiaoyi , Wang Zhongmin 
Published: August 2020

Abstract
BackgroundThe goal of this study was to compare the clinical results of conventional transcatheter arterial chemoembolization (C-TACE) and doxorubicin-eluting bead transcatheter arterial chemoembolization (D-TACE) combined with endovascular stent implantation with an iodine-125 seed strand in hepatocellular carcinoma (HCC) patients with main portal vein tumor thrombus (MPVTT).MethodsThis study was a prospective controlled study with follow-up dates spanning from Mar 2015 to Feb 2020. Patients with both HCC and MPVTT were randomly divided into two groups. Portal vein stents with iodine-125 seed strands were implanted first; then, C-TACE or D-TACE was administered to all patients. Objective response rates were assessed. The time to disease progression and survival rate were compared between the two groups.ResultsA total of 26 patients were enrolled, with 13 in each group. During follow-up, the portal stent patency times were 112.3 ± 98.2 days in the C-TACE group and 101.7 ± 90.4 days in the D-TACE group. The time to disease progression was 42 days in the C-TACE group and 120 days in the D-TACE group (p = 0.03). The overall survival time from the first intervention procedure was 216 days in the C-TACE group and 239 days in the D-TACE group (p = 0.047). The D-TACE group was superior to the C-TACE group in terms of progression-free survival (PFS) and overall survival (OS) times.ConclusionEndovascular implantation of a stent with an iodine-125 seed strand combined with TACE is safe and effective in HCC patients with MPVTT. Compared to C-TACE, D-TACE achieves more benefits regarding PFS and OS.Trial registrationThis study was a cohort study, no health-related interventions to evaluate the effects on health outcomes. This study wasn’t a clinical trial.
Variation of HLA-DPB1 Gene in Hepatitis B Infection
Authors: Ou Guo-Jin , Liu Xiao , Xu Haixia , Ji Xin , Liu Xiaojuan , Wang Jue 
Published: August 2020

Abstract
Background: Hepatitis B virus (HBV) affects approximately 68 million people in China. 10-15% of adult infected with HBV will develop to chronic HBV, liver cirrhosis (LC), liver failure and hepatocellular carcinoma (HCC). The human leukocyte antigen HLA-DPB1 gene polymorphism and expression were identified to be associated with HBV susceptible and spontaneous clearance. We evaluated the role of HLA-DPB1 gene polymorphism in HBV infection.Methods: In this study, HLA-DPB1, rs9277535 polymorphisms were investigated in 259 HBV infection patients (CHB) and 442 healthy controls (HC) by using a sequence based typing. The mRNA of HLA-DPB1 were measured by real-time polymerase chain reaction (RT-PCR). Results: The results shown that DPB1 gene, rs9277535 were all associated with HBV infection in the Sichuan Han population. Rs9277535A, DPB1*04:02 play a protected role in HBV infection, Rs9277535G, DPB1*05:01 prone to susceptible to HBV infection. rs9277535GG have significantly higher HLA-DPB1 mRNA expression in HBV group compared that in HC group. DPB1*05:01 and DPB1*21:01 have a significantly lower HLA-DPB1 mRNA expression in HBV infection group compared than HC group. The meta-analysis revealed that HLA-DPB1*02:01, DPB1*02:02, DPB1*04:01 and DPB1*04:02 protected against HBV infection, while DPB1*05:01, DPB1*09:01, and DPB1*13:01 were risk factors for HBV infection susceptibility. DPB1*02:01 and DPB1*04:01 were prone to HBV spontaneous clearance, while DPB1*05:01 and DPB1*13:01 were associated with chronic HBV infection.Conclusions: DPB1 alleles and rs9277535 have a major effect on the risk of HBV infection, HBV infection associated with lower HLA-DPB1 expression. DPB1 alleles have important role in HBV susceptible and spontaneous clearance.
Per1 has the capacity to serve as a diagnostic biomarker for cholangiocarcinoma patient
Authors: Wang Ning , Li Yanni , Zheng Yanfang , Chen Huoming , Wen Xiaolong , Li Zhaoxia 
Published: August 2020

Abstract
Background

Period 1 (Per1) had been reported to be involved in the tumorigenesis and progression of human cancers. However, the clinical significance of Per1 in cholangiocarcinoma (CCA) was unclear. The purpose of this study was to explore the diagnostic value of serum Per1 in CCA patients.
Methods

Serum levels of Per1 in CCA patients and healthy individuals were detected by quantitative real-time polymerase chain reaction (qRT-PCR). Chi-square test was used to evaluate the relationship between Per1 expression and clinical characteristics of patients. The diagnostic value of Per1 in CCA was estimated by establishing a receiver operating characteristic (ROC) curve.
Results

Serum Per1 level was significantly down-regulated in CCA patients compared to that in healthy controls (P < 0.001). Moreover, the decreased expression of Per1 was closely associated with poor histological differentiation (P = 0.040), advanced TNM stage (P = 0.035) and positive lymph node metastasis (P = 0.007). ROC curve indicated that the area under the curve (AUC) was 0.863 with a sensitivity of 88.1% and a specificity of 72.1%, revealing the high diagnostic value of serum Per1 in CCA.
Conclusions

Per1 is down-regulated in CCA and negatively correlated with tumor progression. Serum Per1 may be a potential biomarker for early screening of CCA.
SOX9 stands for a bio-marker for prostate cancer detection
Authors: Zi Hao , Tao Wen-Lin , Gao Lei , Yu Zhao-Hua , Bai Xiao-Dong , Li Xiao-Dong 
Published: August 2020

Abstract
Background

Prostate cancer is one of common cancers around the world, and in our country the incidence and mortality of PCa are both increasing. More and more reports have revealed that SOX9 is involved in various human cancers. In this study, we aimed to explore the relationship between SOX9 expression and diagnostic value of PCa patients.
Methods

In this study, quantitative real-time PCR (qRT-PCR) was performed to determine the expression of SOX9 of the 131 PCa patients and 74 healthy volunteers. And receiver operating characteristic (ROC) curve was used to determine the diagnostic value of SOX9 for PCa patients.
Results

The results of qRT-PCR showed that the expression of serum SOX9 in PCa patients was higher than that in healthy controls (P < 0.05). And the expression of SOX9 was significantly associated with PSA (P = 0.001), differentiation (P = 0.000), and lymph node metastasis (P = 0.000). Besides, the area under the ROC curve (AUC) was 0.966 with the sensitivity of 93.2% and specificity of 87.8% respectively. The optimal cutoff value of SOX9 was 2.34.
Conclusions

Our results found that SOX9 is a novel oncogene for PCa, and may be a novel and effective biomarker for the diagnosis of patients with PCa.
Comprehensive Analysis of Non Redundant Protein Database
Authors: Bagheri Hamid , Dyer Robert , Severin Andrew , Rajan Hridesh 
Published: August 2020

Abstract
Background: Scientists around the world use NCBI’s non-redundant (NR) database to identify the taxonomic origin and functional annotation of their favorite protein sequences using BLAST. Unfortunately, due to the exponential growth of this database, many scientists do not have a good understanding of the contents of the NR database. There is a need for tools to explore the contents of large biological datasets, such as NR, to better understand the assumptions and limitations of the data they contain. Results: Protein sequence data, protein functional annotation, and taxonomic assignment from NCBI’s NR database were placed into a BoaG database, a domain-specific language and shared data science infrastructure for genomics, along with a CD-HIT clustering of all these protein sequences at different sequence similarity levels. We show that BoaG can efficiently perform queries on this large dataset to determine the average length of protein sequences and identify the most common taxonomic assignments and functional annotations. Using the clustering information, we also show that the non-redundant (NR) database has a considerable amount of annotation redundancy at the 95% similarity level. Conclusions: We implemented BoaG and provided a web-based interface to BoaG’s infrastructure that will help researchers to explore the dataset further. Researchers can submit queries and download the results or share them with others. Availability and implementation: The web-interface of the BoaG infrastructure can be accessed here: http://boa.cs.iastate.edu/boag. Please use user = boag and password = boag to login. Source code and other documentation are also provided as a GitHub repository: https://github.com/boalang/NR_Dataset.
Breastfeeding Practice Among Teenage Mothers And The Nutritional Status Of Their 0-6 Month Old Infants
Authors: Sholichah Farohatus , Muis S. Fatimah , Margawati Ani 
Published: August 2020

Abstract
Background: The percentage of early marriage in Indonesia is the second highest in ASEAN after Kamboja. The purpose of this study is to analyze breastfeeding practise among teenage mothers and the nutritional status of their 0-6 months infants. Methods: The study was conducted on 16 teenage mothers. The qualitative method with in-depth interview and observation were used to obtain breastfeeding data. Quantitative method was used for obtaining data of infants’ food intake (recall 2x24 hours) and anthropometry. Content analysis was used for the qualitative data, while the descriptive analysis was used for the quantitative data. Results: The majority (87.5%) provided non-exclusive breastfeeding and 12.5% stopped breastfeeding. The majority (93.75%) during one month of study was exposed to infectious disease (fever, cough, runny nose, diarrhea). Conclusions: All infants stayed well nourished, but the score of nutritional status decreased (62.5%).
A nonsense mutation of bone morphogenetic protein-15 (BMP15) causes both infertility and increased litter size in pigs.
Authors: Flossmann Gabriele , Wurmser Christine , Pausch Hubert , Tenghe Amabel , Dodenhoff Jörg , Dahinten Günther , Götz Kay-Uwe , Russ Ingolf , Fries Ruedi 
Published: August 2020

Abstract
Background: Atypical external genitalia are often a sign of reproductive organ pathologies and infertility with both environmental or genetic causes, including karyotypic abnormalities. Genome-wide association studies (GWAS) provide a means for identifying chromosomal regions harboring deleterious DNA-variants causing such phenotypes. We performed a GWAS to unravel the causes of incidental cases of atypically small vulvae in German Landrace gilts.Results: A case-control GWAS involving Illumina porcine SNP60 BeadChip-called genotypes of 17 gilts with atypically small vulvae and 1,818 control animals (fertile German Landrace sows) identified a significantly associated region on the X-chromosome (P = 8.81 × 10− 43). Inspection of whole-genome sequencing data in the critical area allowed us to pinpoint a likely causal variant in the form of a nonsense mutation of bone morphogenetic protein-15 (Sscrofa11.1_X:g.44618787C > T, BMP15:p.R212X). The mutant allele occurs at a frequency of 6.2% in the German Landrace breeding population. Homozygous gilts exhibit underdeveloped, most likely not functional ovaries and are not fertile. Male carriers do not seem to manifest defects. Heterozygous sows produce 0.41 ± 0.02 (P = 4.5 × 10− 83) piglets more than wildtype animals. However, the mutant allele’s positive effect on litter size accompanies a negative impact on lean meat growth.Conclusion: Our results provide an example for the power of GWAS in identifying the genetic causes of a fuzzy phenotype and add to the list of natural deleterious BMP15 mutations that affect fertility in a dosage-dependent manner, the first time in a poly-ovulatory species. We advise eradicating the mutant allele from the German Landrace breeding population since the adverse effects on the lean meat growth outweigh the larger litter size in heterozygous sows.
Serum interleukin-6 is an indicator for severity in 901 patients with SARS-CoV-2 infection: A cohort study
Authors: Zhang Jing , Hao Yiqun , Ou Wuling , Ming Fei , Liang Gai , Qian Yu , Cai Qian , Dong Shuang , Hu Sheng , Wang Weida , Wei Shaozhong 
Published: August 2020

Abstract
Background
Interleukin-6 (IL-6) was proposed to be associated with the severity of coronavirus disease 2019 (COVID-19). The present study aimed to explore the kinetics of IL-6 levels, validate this association in COVID-19 patients, and report preliminary data on the efficacy of IL-6 receptor blockade.
Methods
We conducted a retrospective single-institutional study of 901 consecutive confirmed cases. Serum IL-6 concentrations were tested on admission and/or during hospital stay. Tocilizumab was given to 16 patients with elevated IL-6 concentration.
Results
366 patients were defined as common cases, 411 patients as severe, and 124 patients as critical according to the Chinese guideline on diagnosis and treatment of COVID-19. The median concentration of IL-6 was < 1.5 pg/ml (IQR < 1.50–2.15), 1.85 pg/ml (IQR < 1.50–5.21), and 21.55 pg/ml (IQR 6.47–94.66) for the common, severe, and critical groups respectively (P༜0.001). The follow-up kinetics revealed serum IL-6 remained high in critical patients even when cured. An IL-6 concentration higher than 37.65 pg/ml was predictive of in-hospital death (AUC 0.97 [95%CI 0.95–0.99], P < 0.001) with a sensitivity of 91.7% and a specificity of 95.7%. In the 16 patients who received tocilizumab, IL-6 concentrations were significantly increased after administration, and survival outcome was not significantly different from that of propensity-score matched counterparts (n = 53, P = 0.12).
Conclusion
Serum IL-6 should be included in diagnostic work-up to stratify disease severity, but the benefit of tocilizumab needs further confirmation.
Trial registration:
retrospectively registered.
Comparative analysis of patients with upper urinary tract urothelial carcinoma in black-foot disease endemic and non-endemic area
Authors: Chang Che-Wei , Ou Chien-Hui , Yu Chih-Chin , Lo Chi-Wen , Tsai Chung-You , Cheng Pai-Yu , Chen Yung-Tai , Huang Hsu-Che , Wu Chia-Chang , Wu Wen-Jeng , Li Ching-Chia , Li Wei-Ming , Ke Hung-Lung , Lee Hsiang-Ying 
Published: August 2020

Abstract
Objective

High incidence of upper urinary tract urothelial carcinoma has been reported in South- Western area of Taiwan, where arsenic water contamination was considered to be the main cause. However, there is no definite proof to show the correlation between the arsenic water contamination and upper urinary tract urothelial carcinoma. To investigate the clinical and epidemiological features of the patients with upper urinary tract urothelial carcinoma between arsenic water endemic and non-endemic areas, we analyzed patients in terms of characteristics, stratified overall survival, disease-free survival and cancer-specific survival

Method

The records of a total 1194 patients diagnosed with upper urinary tract urothelial carcinoma were retrospectively reviewed. Clinical data and current medical status were collected from medical records. Statistical analyses were performed to determine the clinical variables and stratified survival curves between endemic and non-endemic groups.

Results

Female predominance was revealed in both endemic and non-endemic groups (Male:Female=1:1.2- 1.4). No statistical differences were found in histological types, staging and tumor size among two groups. Nonetheless, patients with characteristics of aging and having end stage renal disease outnumbered in non-endemic group while higher prevalence of previous bladder tumor and more ureteral tumor were found in endemic group. Adjusted stratified cumulative survival curves suggested poorer prognosis fashion in endemic patients, especially in disease free survival of early stage disease.

Conclusions

Higher mortality rate with more previous bladder cancer history and ureteral tumor were seen in patients with upper urinary tract urothelial carcinoma residing in arsenic water contamination area. This may attribute to the long-term carcinogenesis effect of arsenic underground water.
Male Breast Cancer with Ureteral Metastasis: A Case Report
Authors: Yanbo Chen , Jiannan Wu , Tingting Hu , Juanjuan Wang , Fengxi Su 
Published: August 2020

Abstract
Background: Breast cancer is rare in men and there is no report of male breast cancer (MBC) with ureteral metastasis. In this study, we report the first case of MBC with ureteral metastasis. Case presentation: A 60-year-old man was diagnosed with triple negative breast cancer (TNBC) with lymph nodes metastasis. After surgery, chemotherapy and radiotherapy he was diagnosed with ureter metastasis because of hematuria. This patient took a Precitype gene test (immune index and PAM50) after several lines of treatment and the result indicated that this was a Luminal A subtype case, which was quite different from his immunohistochemical staining. We adjusted his therapeutic regimen according to the genetic test but there was no obvious efficacy and he passed away five months later. Conclusions: MBC patients with urinary symptoms should be considered for the possibility of metastasis although urinary metastasis in breast cancer is rare. We still need more research and evidence of treatment recommendations for MBC.
Development and validation of an immune gene-set based prognostic signature for soft tissue sarcoma
Authors: Shen Rui , Meng Xiangying , Li Jianyi , Yu Tengbo , Xu Kuishuai 
Published: August 2020

Abstract
Background
Sarcomas is a group of heterogeneous malignant tumors originated from mesenchymal tissue and different types of sarcomas have disparate outcomes. The present study aims to identify the prognostic value of immune-related genes (IRGs) in sarcoma and establish a prognostic signature based on IRGs.
Methods
We collected the expression profile and clinical information of 255 soft tissue sarcoma samples from The Cancer Genome Atlas (TCGA) database and 2498 IRGs from the ImmPort database. The LASSO algorithm and Cox regression analysis were used to identify the best candidate genes and construct a signature. The prognostic ability of the signature was evaluated by ROC curves and Kaplan-Meier survival curves and validated in an independent cohort. Besides, a nomogram based on the IRGs and independent prognostic clinical variables was developed.
Results
A total of 19 IRGs were incorporated into the signature. In the training cohort, the AUC values of signature at 1-, 2-, and 3-years were 0.938, 0.937 and 0.935, respectively. The Kaplan-Meier survival curve indicated that high-risk patients were significantly worse prognosis(P < 0.001). In the validation cohort, the AUC values of signature at 1-, 2-, and 3-years were 0.730, 0.717 and 0.647, respectively. The Kaplan-Meier survival curve also showed significant distinct survival outcome between two risk groups. Furthermore, a nomogram based on the signature and four prognostic variables showed great accuracy in whole sarcoma patients and subgroup analyses. More importantly, the results of the TF regulatory network and immune infiltration analysis revealed the potential molecular mechanism of IRGs.
Conclusions
In general, we identified and validated an IRG-based signature, which can be used as an independent prognostic signature in evaluating the prognosis of sarcoma patients and provide potential novel immunotherapy targets.
PVT1 Assumes Signifying Capacity in Cervical Cancer Diagnosis.
Authors: Cao Shuangqing , Zheng Lei 
Published: August 2020

Abstract
Background: Cervical cancer (CC) is the second most prevalent malignancy among women, which severely threatens patients’ health. The study was conducted to determine the diagnostic role of plasmacytoma variant translocation 1 (PVT1) in CC to improve patients outcomes.Methods: The qRT-PCR was used to determine the expression level of PVT1 mRNA in CC samples and healthy controls. Chi-square test was used to determine the clinical effects of patients’ features on PVT1 expression. The receiver operating characteristics (ROC) curve with the area under the curve (AUC) was used as a tool for assessing the diagnostic role of PVT1 expression in CC.Results: The PVT1 mRNA level was significantly higher in CC samples than healthy controls (P<0.0001). Large tumor size (P=0.006), positive uterus infiltration (P=0.031) and advanced FIGO stages (P=0.011) were contributed to the elevated expression of PVT1 level. However, there was no close relationship between PVT1 expression and other clinical parameters, including age (P=0.205), family history (P=0.073), positive HPV infection (P=0.155 and histological type (P=0.159). The ROC curve showed the optimal cutoff point for PVT1 was 2.325, providing the sensitivity and specificity of 85.84% and 72.15%, respectively. Moreover, the AUC was 0.856, suggesting PVT1 level could be regarded as a diagnostic biomarker in CC (P<0.0001, 95%CI= 0.803-0.909).Conclusion: In summary, the level of PVT1 mRNA was significantly increased in CC samples and the up-regulation of PVT1 could distinguish CC patients from healthy controls.
Sjogren's syndrome in clinical trials of traditional Chinese medicine: protocol for the development of a core outcome set
Authors: Liu Ming , Gao Ya , Yuan Yuan , Shi Shuzhen , Yang Kelu , Shi Jiyuan , Wu Jiarui , Tian Jinhui , Zhang Junhua 
Published: August 2020

Abstract
Background: Sjogren's syndrome (SS) is a chronic autoimmune rheumatic disease, and the incidence of 0.03% to 0.3%. There are an increasing number of randomised controlled trials of traditional Chinese medicine (TCM) for SS. However, there are generally some problems in clinical trials: lack of reporting primary or long term outcomes, and the heterogeneous in different clinical trials’ outcome. Our study aims to determine the priority outcomes and standard TCM syndromes for all stakeholders, and reach agreement on the COS and syndromes to be measured and reported in all future TCM trials in patients with SS.Methods: A phase-wise refinement approach will be used, consisting of three phases, yet complementary, sub-work phases, whereby each phase will inform the next coming phases. The following are the three phases: (Ⅰ-a) Identifying of a long initial list of outcomes through: (1) systematic literature review; (2) semi-structured qualitative interviews. (Ⅰ-b) Identifying an initial list of TCM syndromes through: (1) systematic literature review; (2) referencing ancient Chinese medical books; (3) retrospective studies of medical records. (Ⅱ) Prioritization of outcomes using Delphi survey with different stakeholders, such as health professionals and patients. (Ⅲ) Through consensus meetings with patients and professionals to agree on the final COS and TCM syndromes.Results: We summarized the actions of COS into three points: direct action, indirect action, final action. Our study is very necessary.Conclusion: After the final COSs is completed, we will publish this research in a journal to promote communication.Trial registration number: Core Outcome Measures in Effectiveness Trials Initiative (COMET) number: 1429.