bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of biomarkers and pathways associated with immune infiltration and prognosis in melanoma patients
Authors: Huang Biao , Han Wei , Sheng Zu-Feng , Shen Guo-Liang 
Published: March 2020

Abstract
Background Skin cutaneous melanoma (SKCM) is one of the most malignancy and aggressive cancers, causing about 72% of deaths in skin carcinoma. Although extensive study has explored the mechanism of recurrence and metastasis, the tumorigenesis of melanoma remains unclear. Exploring the tumorigenesis mechanism may help to identify prognostic biomarkers that could serve to guide cancer therapy . Methods We identified differentially expressed genes (DEGs) between patients with primary melanoma and normal skin in three data sets including GSE46517, GSE15605, GSE114445. Functional annotation including KEGG pathway and gene ontology (GO) enrichment analysis was performed by DAVID. Subsequently, protein ‐ protein interaction network of DEGs was developed and the most significant module was constructed as hub genes for further study. ClueGO was used to investigate significant pathways in hub genes. The Kaplan–Meier method was performed to assess prognostic genes. ROC curves were used to describe diagnosis value of hub genes. Then, genes expression and clinical characteristics were validated by TCGA profiles. In addition, we explored the correlation between prognostic genes and immune cell infiltration. Results A total of 308 DEGs and 12 hub genes were identified. GO enrichment results demonstrated a correlation between DEGs and the immune response, inflammatory response and transcriptional control. Hallmark pathways of hub genes including interleukin-10 signaling, chemokine receptors bind chemokine signaling ， peptide ligand-binding receptors. Survival analysis and ROC curves suggested that CCL4, CCL5, NMU, CXCL9, CXCL10, CXCL13 were independent prognostic factors (except GAL). Furthermore, prognostic genes were highly expressed in tumor tissue and related to pathological stages and Breslow depth. In addition, the expressions of CCL4, CCL5, CXCL9, CXCL10, CXCL13 were positively correlated with six immune cell infiltration (B-cell, CD8+ T cells, CD4+ T cells, macrophages, Neutrophils, Dendritic cells) and 28 types of TILs such as activated CD8 T cells, regulatory T cells, natural killer T cells while NMU and GAL were negatively correlated with it. Conclusion In summary, this study identified significant hub genes and pathways closely associated with immune infiltrations and prognosis in SKCM patients, which might help us evaluate underlying carcinogenesis progress from skin to melanoma.
WITHDRAWN: A Double Blind Randomized Clinical Trail: Comparing Lactobacillus plantarum 299v with Placebo in treating irritable bowel syndrome patients
Authors: haq Moeen-ul- , Ullah Fazl , Hassan Muhammad Kamran , Babar Ahmad Nawaz , Ullah Anwar 
Published: March 2020

Abstract
Irritable bowel syndrome (IBS) is a gastrointestinal disease of intestinal mobility. IBS present with variable clinical symptoms making the treatment difficult. IBS is quiet prevalent around the globe with different frequency. Differences in frequency and gender is due to diet habit. It is less frequent where diary product and vegetable are frequently consumed as compared to those who consumed meat. Lactobacillus plantarum 299v (L. plantarum 299v) is the most widely studied strain in the IBS patients. It is resistant to the actions of intestinal acids and bile, colonizes the human colonic mucosa and is non-pathogenic in nature. The efficacy of Lactobacillus plantarum 299v L is different in different study. The present study was designed to find the efficacy of Lactobacillus plantarum 299v in comparison to placebo in randomized control trial.
Effects of perioperative enhanced recovery after surgery pathway management versus traditional management on the clinical outcomes of laparoscopic-assisted radical resection of distal gastric cancer: study protocol for a randomized controlled trial
Authors: Tian Yulong , Cao Shougen , Li Leping , He Qingsi , Xia Lijian , Jiang Lixin , Ding Yinlu , Wang Xinjian , Wang Hao , Mao Weizheng , Hui Xizeng , Shi Yiran , Zhang Huanhu , Chu Xianqun , Zhou Yanbing , Kehlet Henrik 
Published: March 2020

Abstract
Background: The incidence of gastric cancer in East Asia is much higher than the international average. Therefore, improving the prognosis of patients and establishing effective clinical pathways are important topics for the prevention and treatment of gastric cancer. At present, the enhanced recovery after surgery (ERAS) pathway is widely used in the field of gastric surgery. Many randomized controlled trial (RCT) studies have proven that the ERAS regimen can improve the short-term clinical outcomes of gastric cancer patients. However, a prospective study on the effect of the ERAS pathway on the prognosis of gastric cancer patients has not yet been reported. This trial aims to confirm whether the ERAS pathway can improve the disease-free survival (DFS) and overall survival (OS) of patients undergoing laparoscopic-assisted radical resection for distal gastric cancer. Methods/design: This study is a prospective, multicentre, randomized controlled trial. This experiment will include randomly divided groups, the experimental group and the control group, according to a 1:1 ratio. The perioperative period of the experimental group will be managed according to the ERAS pathway, and that of the control group will be managed according to the traditional management mode. An estimated 400 patients will be enrolled. The main endpoint for comparison is the 3-year OS and DFS between the two groups. Discussion: The results of this RCT should clarify whether the ERAS pathway is superior to traditional treatment on inflammatory indexes, short-term clinical outcome and survival for laparoscopic-assisted radical resection of distal gastric cancer. It is hoped that our data will provide evidence that the ERAS pathway improves survival in patients with gastric cancer.
Existence of Hepatitis B Virus Surface Protein Mutations and Other Variants: Demand for Hepatitis B Infection Control in Cambodia
Authors: Ko Ko , Takahashi Kazuaki , Nagashima Shintaro , Yamamoto Chikako , Vichit Ork , Sugiyama Aya , Akita Tomoyuki , Ohisa Masayuki , Chuon Channarena , Hoss Shafiqul Md , Mao Bunsoth , Tanaka Junko 
Published: March 2020

Abstract
Aims : This study aimed to detect Hepatitis B virus (HBV) genome sequences and their variants as of nationwide scale using dried blood spot (DBS) samples and to provide up-to-date reference data for infection control and surveillance in Cambodia.
Method: Among 2,518 children age 5-7 years and their 2,023 mothers participated in 2017 Cambodia nationwide sero-survey on hepatitis B surface antigen (HBsAg) prevalence using multistage random sampling strategy, 95 mothers and 13 children positive to HBsAg were included in this study. HBV DNA was extracted from DBS, then performed polymerase chain reaction. HBV genotypes and potential variants were examined by partial and full length genomic analysis.
Results : HBsAg positive rate was 4.7% (95/2023) in mothers and 0.52% (13/2518) in their children. Genotype C (80.49%) was abundantly found throughout the whole Cambodia whilst genotype B (19.51%) was exclusively found in regions bordering Vietnam. S gene mutants of HBV were found in 24.29% of mothers and 16.67% of children with HBV DNA positive sera. Full-length genome analysis revealed the homology of 99.62-100% in each mother-child pair. Genotype B was clarified to recombinant genotype B4/C2 and B2/C2. Double (48.39%) and combination mutation (32.26%) were observed in core promoter region of HBV C1 strains.
Conclusion : This study showed the capable of DBS for large-scale molecular epidemiological study of HBV in resource limited countries. Full-genome sequences yield the better understanding of sub-genotypes, their variants and the degree of homology between strains isolated from mother-child pairs calls for effective strategies on prevention, control and surveillance of mother-to-child HBV transmission in Cambodia.
Identifying contexts and mechanisms in multiple behavior change interventions affecting smoking cessation success: A rapid realist review
Authors: Minian Nadia , Corrin Tricia , Lingam Mathangee , deRuiter Wayne K , Rodak Terri , Taylor Valerie H. , Manson Heather , Dragonetti Rosa , Zawertailo Laurie , Melamed Osnat C. , Hahn Margaret , Selby Peter 
Published: March 2020

Abstract
Background: Smoking continues to be a leading cause of preventable chronic disease-related morbidity and mortality, excess healthcare expenditure, and lost work productivity. Tobacco users are disproportionately more likely to be engaging in other modifiable risk behaviours such as excess alcohol consumption, physical inactivity, and poor diet. While hundreds of interventions addressing the clustering of smoking and other modifiable risk behaviours have been conducted worldwide, there is insufficient information available about the context and mechanisms in these interventions that promote successful smoking cessation. The aim of this rapid realist review was to identify possible contexts and mechanisms used in multiple health behaviour change interventions (targeting tobacco and two or more additional risk behaviours) that are associated with improving smoking cessation outcome.Methods: This realist review method incorporated the following steps: (1) clarifying the scope, (2) searching for relevant evidence, (3) relevance confirmation, data extraction, and quality assessment, (4) data analysis and synthesis.Results: Of the 20,423 articles screened, 138 articles were included in this realist review. Following Michie et al.’s behavior change model (the COM-B model), capability, opportunity, and motivation were used to identify the mechanisms of behaviour change. Universally, increasing opportunities (i.e. factors that lie outside the individual that prompt the behaviour or make it possible) for participants to engage in healthy behaviours was associated with smoking cessation success. However, increasing participant’s capability or motivation to make a behaviour change was only successful within certain contexts. Conclusion: In order to address multiple health behaviours and assist individuals in quitting smoking, public health promotion interventions need to shift away from ‘individualistic epidemiology’ and invest resources into modifying factors that are external from the individual (i.e. creating a supportive environment).Study registration: PROSPERO registration number: CRD42017064430
Clinical Characteristics of Patients with 2019 Coronavirus disease in a non-Wuhan area of Hubei Province, China: a retrospective study
Authors: Zhao Xin-Ying , Xu Xuan-Xuan , Yin Hai-Sen , Hu Qin-Ming , Xiong Tao , Tang Yuan-Yan , Yang Ai-Ying , Yu Bao-Ping , Huang Zhi-Ping 
Published: March 2020

Abstract
Background: Since December, 2019, the 2019 Coronavirus disease (COVID-19) from Wuhan, China, has caused worldwide outbreak with more than 200,000 people infected and thousands of deaths. The clinical characteristics of COVID-19 patients in non-Wuhan areas of Hubei province have not been described.

Methods: We retrospectively analyzed the clinical characteristics and treatment progress of 91 patients diagnosed with COVID-19 in Jingzhou Central Hospital.

Results: Of the 91 patients diagnosed with COVID-19, 30 (33.0%) cases were severe and two (2.2%) patients died. The severe patients tended to be older (50.5 vs 42.0, P=0.049), and have more chronic disease (40% vs 14.75%, P=0.009), compared to mild group. Only 73.6% of the patients were quantitative polymerase chain reaction (qPCR) positive on their first tests, while typical chest computed tomographic (CT) images were obtained for each patient. The most common complaints were cough (75, 82.4%), fever (59, 64.8%), fatigue (35, 38.5%), and diarrhea (14, 15.4%). Non-respiratory injur y was identified by elevated levels of aspartate aminotransferase (18, 19.8%), creatinine (5, 5.5%) and creatine kinase (14, 15.4%) in laboratory tests. In sum, 28 (30.8%) cases suffered non-respiratory injury, including 50% of the critically ill patients and 21.3% of the mild patients.

Conclusions: Overall, the mortality rate of patients in Jingzhou is lower than that of Wuhan. Importantly, we discovered liver, kidney, digestive tract and heart injury in COVID-19 cases besides respiratory problems. Combining Chest CT images with qPCR of throat swab samples would improve the accuracy of COVID-19 diagnose.
Woman in The Vulnerability and Disaster Risk of Merapi Eruption in Indonesia
Authors: Hastuti Hastuti , Widodo Edi , Giyarsih Sri Rum , Wicaksono Pramaditya 
Published: March 2020

Abstract
This study was aimed to depict the characteristics of women's vulnerability, as well as to study and analyze their efforts to reduce the disaster risk of Merapi eruption in the South Merapi Slope, Sleman Regency, Yogyakarta Special Territory. The data collection was conducted through interviews on the demographic characteristics of the women, with qualitative data consisting of the social and economic condition in the area under study, including the women’s demographic characteristics, vulnerability, and risk. The qualitative data were used to complement the quantitative data obtained in the first data collection stage. Thus, the research data analysis was based on the quantitative and qualitative data. The results showed that women were vulnerable in terms of their financial security, particularly due to their lack of bank saving, protection in the place of business, land, and residence. Their social vulnerability was shown by how most of the women and elderly people in the households of the area under study required protection when disaster occurred. The vulnerability in organizations was due to the lack of organizations to care for the women. Most women also experienced environmental vulnerability.
A multiobjective DEA model to assess the eco-efficiency of major cereal crops production within the carbon and nitrogen footprint in China
Authors: chen zhongdu , xu chunchun , ji long , fang fuping 
Published: March 2020

Abstract
Agricultural production systems are facing the challenges of increasing food production while reducing environmental cost, particularly in China. Understanding the eco-efficiency of the staple food crop production contributes to sustainable agriculture. In this study, the eco-efficiency of rice, wheat and maize production within the carbon (C) footprints (CF) and nitrogen (N) footprint (NF) at a province scale based on 555 farm survey data from China was measured in which a combination of life cycle assessment (LCA) and data envelopment analysis (DEA) was used. The results showed that the CF for the rice, wheat and maize was 0.87±0.32, 0.30± 0.11, and 0.24 ± 0.06 kg CO 2 -eq kg −1 year −1 at yield-scale, respectively. In addition, the NF was 17.11±7.73, 14.26±5.73, and 6.83±1.83 gN-eq kg −1 year −1 at yield-scale for the rice, wheat and maize, respectively. Synthetic N fertilizer applications and CH 4 emissions dominated the CF of crop production, while NH 3 volatilization was the main contributors to the NF in the grain crop production process. Based on DEA-based sustainability performance assessment results, the eco-efficiency of major cereal crops production were all found to be inefficient (eco-efficiency <1). An increase in yields had only limited effects on improvement in eco-efficiency of rice, wheat and corn production because the yield increase potential rates were very small (0.1~3.4%), and there were no significant differences in increase potentials of yields between provinces. From a perspective of environmental impact reduction potential rates, GWP (22.7~25.1%) was more important for the environmental mitigation target than Nr (10.9~17.9%) in rice production, but the opposite scenario appears in wheat and corn production. Improving crop management practices by reducing N fertilizer use and adopting water-saving irrigation technology could be strategic options to mitigate climate change and eutrophication and improve the eco-efficiency of the staple food crop production in Chinese agriculture.
Arabidopsis V-ATPase d2 subunit plays a role in plant responses to oxidative stress
Authors: Feng Shuang , Peng Yun , Liu Enhui , Ma Hongping , Qiao Kun , Zhou Aimin , Liu Shenkui , Bu Yuanyuan 
Published: March 2020

Abstract

Background: Vacuolar-type H + -ATPase (V-ATPase) is a multisubunit proton pump located on the endomembranes, which plays an important role in plant growth. The Arabidopsis V-ATPase d subunit consists of two isoforms, AtVHA-d1 and AtVHA-d2. Results: In this study, the function of the AtVHA-d2 gene was investigated. Histochemical analysis revealed that the AtVHA-d1 and AtVHA-d2 genes were generally and highly overlapping expressed in multiple tissues at different developmental stages of Arabidopsis. Subcellular localization showed that AtVHA-d2 was mainly localized to the vacuole. The AtVHA-d2 expression was significantly induced by oxidative stress. Furthermore, the phenotypic analysis showed that the atvha-d2 mutant was sensitive to oxidative stress. The non-invasive micro-test measurement demonstrated that the net H + influx in the atvha-d2 roots was weaker than that of the wild type under normal conditions. However, oxidative stress resulted in the H + efflux in atvha-d2 roots, which was significantly different from the wild type. RNA-seq combined with qPCR analysis showed that the expression of several members of the plasma membrane H + -ATPase gene ( AtAHA ) family in atvha-d2 were significant different from wild type under normal and oxidative stress. Conclusion: Overall, our results indicate that AtVHA-d2 plays a role in Arabidopsis in response to oxidative stress by affecting H + flux and AtAHA gene expression.
Early life Exposure to Triclosan Impacted Thyroid Follicular Structure and Decreased Thyroid Hormone Levels in Zebrafish
Authors: Tang Ning , Fan Pianpian , Yu Xiaogang , Wang Xu , Wang Weiye , Ouyang Fengxiu 
Published: March 2020

Abstract
Background: Triclosan (TCS) is an antimicrobial chemical widely used in personal care products. Most of TCS is discharged into aquatic ecosystem after usage. While TCS has potential thyroid-disrupting effect, it is unknown whether early exposure to TCS affects thyroid grand and thyroid hormone levels. We used zebrafish model to examine this topic.Methods: The fertilized zebrafish eggs were exposed to TCS. We inspected hatching and mortality of larvae. The total triiodothyronine (TT3), total thyroxine (TT4), free triiodothyronine (FT3), and free thyroxine (FT4) levels were measured at 7, 14 and 120 days post fertilization (dpf). Thyroid histopathological analysis was conducted at 120 dpf of zebrafish.Results: The hatching rate of embryos decreased from 95.8% in control group to 18.3% in TCS highest exposure in 3 days. In 900 ng/mL TCS exposure all larvae died within one day. With increasing concentration of TCS exposure, TT3 and FT3 level decreased after 14 days. FT4 decreased, and the height and nuclear area of thyroid follicular cell increased with TCS exposure after 120 days.Conclusions: High TCS exposure decreased the hatching rate of zebrafish embryos, and also decreased thyroid hormone levels owing to structural change of thyroid follicles. Our study raised the concern that TCS exposure in early life may profoundly affect neurodevelopment.
Income differences in screening, incidence, postoperative complications, and mortality of thyroid cancer in South Korea: a national population-based time trend study
Authors: Kang Hee-Yeon , Kim Ikhan , Kim Yeon-Yong , Bahk Jinwook , Khang Young-Ho 
Published: March 2020

Abstract
Introduction: The incidence of thyroid cancer (TC) has increased rapidly over the past few decades in Korea. This study investigated whether the TC epidemic has been driven by overdiagnosis.Methods: We calculated the TC screening rate from mid-2008 through mid-2014, and the incidence, postoperative complications, and mortality rates of TC between 2006 and 2015, using data from the Korea Community Health Survey, the National Health Insurance Database, and the cause-of-death data of Statistics Korea. Trends in age-standardized rates of all indicators were examined, along with income gaps therein. Analyses were conducted for lung cancer and stroke as negative control outcomes.Results: The incidence rate of TC increased from 46.6 per 100,000 to 115.0 per 100,000 between 2006 and 2012, and then decreased to 63.5 per 100,000 in 2015. Despite these remarkable changes in incidence, mortality did not fluctuate during the same period. High income was associated with high rates of screening, incidence, and postoperative complications, while low income showed an association with a high mortality rate. Analyses using negative control outcomes showed that high income was associated with low rates of both incidence and mortality, which contrasted with the patterns of TC. The recent decreases in TC incidence and postoperative complications, which reflect societal concerns about the overdiagnosis of TC, were more pronounced in high-income individuals than in low-income individuals. sConclusions: The time trends in income gaps in screening, incidence, postoperative complications, and mortality of TC, as well as negative control outcomes, provided corroborating evidence of TC overdiagnosis in Korea.
Zebrafish xenograft model of human lung cancer for studying the function of LINC00152 in cell proliferation and invasion
Authors: Shen Wenyi , Pu Juan , Sun Jing , Tan Bing , Wang Wei , Wang Lili , Cheng Jianmeng , Zuo Yangsong 
Published: March 2020

Abstract
Background: Numerous studies show that long non-coding RNAs take important roles in human cancer progression. Although zebrafish xenograft become a novel in vivo model for human cancer research recently, whether it can be used for studying the function of lncRNAs remains unknown.Methods: In vitro studies validated the roles of LINC00152 in the proliferation and invasion of lung cancer cells. In vivo studies by using zebrafish xenograft also confirmed these roles of LINC00152. In vivo confocal imaging was also used to evaluate the function of LINC00152 in cell proliferation and migration more accurately. Pharmacology experiments were further performed to study the potential tumor treatment of LINC00152 downregulation combined with EGFR inhibitor in cultured cells and zebrafish xenograft.Results: Silencing of LINC00152 suppressed cell proliferation and invasion in SPCA1 and A549 lung cancer cell lines in vitro . In zebrafish xenograft model, knockdown of LINC00152 reduced the proliferation and migration of lung cancer cells by two imaging methods at different magnification. Moreover, knocking-down LINC00152 enhanced the inhibition effect of afatinib for lung cancer progression in cultured cells and zebrafish xenograft model.Conclusion: Our study reveals the oncogenic roles and potential tumor treatment target of LINC00152 in lung cancer cells by zebrafish xenograft models, suggesting that this model could be used for the functional and application study of human lncRNA in tumor biology.* Wenyi Shen and Juan Pu contributed equally to this work.