bluuebunny/crossref_metadata_2025_split huggingface dataset:
Construction and validation of a robust epigenetic gene-set based signature in ovarian cancer
Authors: Shen Wenbin , Jiang Wei , Ye Shuang , Sun Min , Yang Huijuan , Shan Boer 
Published: December 2020

Abstract
Background

Epigenetic factors play a critical role in tumor development and progression. The aim of this study was to construct and validate a robust epigenetic gene-set based signature for predicting prognosis of ovarian cancer (OC).
Methods

Public microarray data of OC patients from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases were identified and patients from TCGA dataset were randomized 3:1 into discovery and internal validation series. GSE14764 and GSE26712 from GEO database were combined as the external validation set. LASSO Cox regression model was performed in the discovery set to filter the most useful prognostic epigenetic factors.
Results

Based on LASSO Cox regression model, we built a 26 epigenetic factors based prognostic signature. In the discovery set, patients in high risk group showed significantly poorer overall survival than that patients in low risk group (HR: 2.11, 95% CI: 1.65–2.72, P < 0.001). The results were further validated in the internal validation set (HR: 1.69, 95% CI: 1.07–2.63, P = 0.020) and external validation set (HR 1.95, 95% CI 1.41–2.69; p < 0.001). Survival ROC at 5 year suggested that the epigenetic signature (AUC = 0.700) had better prognostic accuracy than any other clinicopathological factors in the entire cohort. In addition, survival decision curve analysis unveiled a considerable value of clinical utility of the epigenetic signature.
Conclusions

We successfully developed a robust epigenetic signature that can accurately predict prognosis in OC.
Antibody Response to a Live-Modified Virus Vaccine Against Bovine Viral Diarrhoea in Dairy Cattle in Field Trial
Authors: Klimowicz-Bodys Małgorzata Dorota , Ploneczka-Janeczko Katarzyna , Czopowicz Michał , Polak Mirosław P , Pruban Radosław , Rypula Krzysztof 
Published: December 2020

Abstract

Background: The objective of the study was to evaluate of the long-term antibody response of dairy cows to a single dose of a commercial modified-live virus (MLV) vaccine against bovine viral diarrhoea (Mucosiffa® CEVA Animal Health, Spain). The study was carried out in a dairy cattle herd counting 290 animals negative for BVDV. The vaccination was implemented in calves from the age of 2 months. Twelve adult lactating cows were randomly selected before study, and blood samples were collected right before the vaccination and then 12 times at 1-month intervals. The serum samples were screened using virus neutralization test (VNT) and ELISA. Results: Both tests showed that antibody titers increased significantly in all animals within the first month post vaccination, and continued to increase until the second (VNT) and third (ELISA) month post vaccination. Antibody titers remained high and stable until the end of the study. Moreover, cows did not show any adverse reactions or clinical symptoms of disease. Conclusion: The results of this study indicated that the administration of one dose MLV vaccine was able to stimulate long-lasting (12-months) and strong antibody response in all vaccinated cows.
Dose-Response Relationship Among Body Mass Index, Abdominal Adiposity and Atrial Fibrillation in Patients Undergoing Cardiac Surgery: A Meta-Analysis of 30 Prospective Studies
Authors: Liu Menglu , Mei Kaibo , Xie Lixia , Ma Jianyong , Yu Peng , Niu Siquan , Xu Ya , Zhao Yujie , liu xiao 
Published: December 2020

Abstract
Background: Whether being overweight increases the risk of postoperative atrial fibrillation (POAF) is unclear, and whether adiposity independently contributes to POAF has not been comprehensively studied. Thus, we conducted a meta-analysis to clarify the strength and shape of the exposure-effect relationship between adiposity and POAF.Methods: The PubMed, Cochrane Library, and EMBASE databases were searched for prospective studies (RCTs, cohort studies, and nest-case control studies) reporting data regarding the relationship between adiposity and the risk of POAF.Results: Thirty publications involving 139,302 patients were included. Analysis of categorical variables showed that obesity (RR: 1.39, P<0.001), but not being underweight (RR: 1.44, P=0.13) or being overweight (RR: 1.03, P=0.48), was associated with an increased risk of POAF. In the exposure-effect analysis, the summary RR for a 5-unit increment in body mass index (BMI) was 1.09 (P<0.001) for the risk of POAF. There was a significant linear relationship between BMI and POAF (Pnonlinearity=0.91); the curve was flat and began to rise steeply at a BMI of approximately 30. Notably, BMI levels below 30 (overweight) were not associated with a higher risk of POAF. In the subgroup analysis of surgery types, the pooled RR values for a BMI increase of 5 for coronary artery bypass graft and valve surgery were 1.21 (P<0.01) and 1.34 (P=0.25), respectively, suggesting that a potential difference in the association exists by surgery type. Additionally, waist obesity was associated with the risk of POAF (RR: 1.55, P<0.001).Conclusion: Based on the current evidence, our findings show that adiposity was independently associated with an increased risk of POAF, while being underweight or overweight might not significantly increase the POAF risk. The magnitude of the effect of obesity on AF in patients undergoing valve surgery might be small, and this finding needs to be further confirmed.
Demystifying Essential Containers and Places for Aedes Mosquito Control in Thailand
Authors: Sahavechaphan Naiyana , Chatrattikorn Asamaporn , Sadakorn Pongsakorn , Areechokechai Darin , Iamsirithaworn Sopon 
Published: December 2020

Abstract
Background: The strategy for prevention and control of Aedes-borne diseases relies on timely elimination of key breeding containers. There is thus a crucial need to identify key breeding containers to enhance vector control activities. The visual larval survey of wet containers has then been conducted as a routine mission of the Department of Disease Control (DDC). To facilitate this, DDC has deployed a mobile application, namely TanRabad SURVEY, since May 2016. As per an inspected place, TanRabad SURVEY supports the real-time collection of its larval survey data and processing of its larval indices and key breeding containers. Methods: Larval survey data from 2017 to 2019 were spatially and temporally collected by public health officials via TanRabad SURVEY. Several measurements were computed to identify the overall and regional key breeding containers and places; and the regional transmission potentiality of Aedes-borne diseases. The measurements for identifying essential containers were breeding potentiality, productivity, contribution and preference ratio. As for places, the larval productivity of places based on larval indices was employed. Such place productivity was also implemented for discovering the regional transmission potentiality of Aedes-borne diseases. Results: The overall essential breeding containers were water tank, unused containers, other used containers, old tyres, anti-ant bowls, drip tray of water dispensers, pet bowls and plant leaves. As for regional aspects, different regions had different essential breeding containers wherein their most common containers were unused containers, other used containers, old tyres and drip tray of water dispensers. All regions had similar experiences that villages and temples were the top two riskiest places, followed by schools, factories, hotels and hospitals. Additionally, all regions had high transmission potentiality of Aedes-borne disease as above 30 of all their places were moderate and high risk places. Conclusions: This study identified the overall and regional key breeding containers and places along with the regional transmission potentiality of Aedes-borne diseases. Beside this, the empirical evidence had shown that the breeding productivity of most containers and places in each type was gradually decreased from time to time. This was mainly because TanRabad SURVEY supported real-time risk communication to community participants and effective prevention and control program development.
Predicting Role of Dosimetric Parameters for Nonclassic Radiation-Induced Liver Disease After Helical Tomotherapy in Child-Pugh Class a Primary Liver Carcinoma Patients
Authors: Wang Boyan , Zhang Jianying , Zeng Zhaochong 
Published: December 2020

Abstract
PurposeThis study sought to analyze the predicting role of dosimetric parameters for nonclassic radiation-induced liver disease (RILD) after helical tomotherapy (HT) in Child-Pugh (CP) class A primary liver carcinoma (PLC) patients.Patients and methodsA total number of 71 CP class A PLC patients treated with HT from June 2011 to June 2015 were retrospectively reviewed. Clinical characteristics and dose-volume histogram (DVH) were recorded, and liver functions were followed up for 4 months after radiotherapy.ResultsIn all, 57 patients (80.3%) were male, and 14 (19.7%) were female, with a median age of 53 years. The mean gross tumor volume (GTV) was 226.8 cm3. A median dose of 55.0 Gy was delivered by HT with a median fraction size of 2.6 Gy. Twelve patients (16.9%) were diagnosed with nonclassic RILD. The mean dose to normal liver (MDTNL) and the percentage of total liver volume receiving more than 25 - 35 Gy irradiations (V25 - V35) were related to nonclassic RILD. MDTNL showed the highest AUC (0.705, p=0.026). The optimal cut-off value of MDTNL was 21.3 Gy with a sensitivity, specificity and accuracy of 83.3%, 62.7% and 67.6%, respectively. The tolerable volume percentages for DVH were less than: V25 of 42.3%, V30 of 33.9%, and V35 of 28.3%.Conclusion﻿This study suggests that MDTNL, V25, V30 and V35 are dosimetric predictors for nonclassic RILD in CP class A PLC patients. MDTNL < 21.3Gy, V25 < 42.3%, V30 < 33.9%, and V35 < 28.3% may be used to optimize HT planning.
Genetic Analysis of the Barley Variegation Mutant, Grandpa1.α
Authors: Yang Shengming , Overlander Megan , Fiedler Jason 
Published: December 2020

Abstract
Background Providing the photosynthesis factory for plants, chloroplasts are critical for crop biomass and economic yield. However, chloroplast development is a complicated process, coordinated by the cross-communication between the nucleus and plastids, and the underlying biogenesis mechanism has not been fully revealed. Variegation mutants have provided ideal models to identify genes or factors involved in chloroplast development. Well-developed chloroplasts are present in the green tissue areas, while the white areas contain undifferentiated plastids that are deficient in chlorophyll. Unlike albino plants, variegation mutants survive to maturity and enable investigation into the signaling pathways underlying chloroplast biogenesis. The allelic variegated mutants in barley, grandpa 1 (gpa1), have long been identified but have not been genetically characterized. Results We characterized and genetically analyzed the grandpa1.a (gpa1.a) mutant. The chloroplast ultrastructure was evaluated using transmission electron microscopy (TEM), and it was confirmed that chloroplast biogenesis was disrupted in the white sections of gpa1.a. To determine the precise position of Gpa1, a high-resolution genetic map was constructed. Segregating individuals were genotyped with the barley 50k iSelect SNP Array, and the linked SNPs were converted to PCR-based markers for genetic mapping. The Gpa1 gene was mapped to chromosome 2H within a gene cluster functionally related to photosynthesis or chloroplast differentiation. In the variegated gpa1.a mutant, we identified a large deletion in this gene cluster that eliminates a putative plastid terminal oxidase (PTOX).Conclusions Here we characterized and genetically mapped the gpa1.a mutation causing a variegation phenotype in barley. The PTOX-encoding gene in the delimited region is a promising candidate for Gpa1. Therefore, the present study provides a foundation for the cloning of Gpa1, which will elevate our understanding of the molecular mechanisms underlying chloroplast biogenesis, particularly in monocot plants.
Small RNA&nbsp;and Degradome Analyses Uncovering the Extensive Effects of miRNAs&nbsp;and Targets in Early Developing Grains of Common Wheat
Authors: Chen Qiaoyan , Xu Lina , Guan Yuanyuan , Buttar Zeeshan Ali , Li Gan , Zhang Guang , Li Chunxiao , Huang Jinyong , Liu Mingjiu , Wei Wenhui 
Published: December 2020

Abstract
Background: The development of grains is important for wheat production, and wheat (Triticum aestivum) is one of the staple food crops worldwide. MicroRNAs (miRNAs), as a kind of small regulatory RNAs, play important roles during plant growth and development. Although the development of plant grain/seed is widely researched, there is limited knowledge on miRNAs’s regulation of early developing wheat grains. Results: In the present study, miRNAs and their targets were explored in early developing grains of wheat cultivar “Bainong 4199” at 7DAP and 14 DAP using high-throughput small RNA and degradome sequencing. A total of 105 known and 79 novel miRNAs were identified, including 46 known and 32 novel miRNAs from 7 DAP library and 87 known and 78 novel miRNAs from 14 DAP library, respectively. Expression analysis of miRNAs revealed that 39 miRNAs including 19 known and 20 novel miRNAs were differentially expressed between 7 DAP and 14 DAP. In total, 266 targets for 40 known wheat miRNAs, 152 targets for 13 other known plant miRNAs and 258 targets for 25 novel miRNAs were predicted across small RNA and degradome analyses. For differentially expressed miRNAs, 23 targets were predicted to be cleaved by 7 miRNAs, including 3 known and 4 novel miRNAs. Majority of the miRNAs potentially regulated multiple targets, whereas some miRNAs only acted on a single target gene. Functional analyses showed that miRNAs and their targets widely participated in the regulations of early wheat grain development and metabolism. The expression patterns of the randomly selected miRNAs and targets were validated using quantitative real-time polymerase chain reaction, and showed consistent and reliable results. Conclusion: This study suggests that quite a few known and novel miRNAs and their targets play extensive roles during the early grain development of common wheat. Understanding of miRNA-mediated regulatory network involved in wheat grain development will help us to elucidate the molecular mechanisms underlying wheat grain development and carry out ingenious molecular improvements in wheat breeding.
Trend of Geographical Distribution of Stomach Cancer in Iran From 2004-2014
Authors: Moradian Farid , Fararouei Mohammad , Karami Maryam , Ghelichi-Ghojogh mousa , Gheibi Zahra , Nikeghbalian Zahra , Akbari Atieh , Akbari Mohammad-esmaeil 
Published: December 2020

Abstract
Background: Among different common types of cancer, Gastric cancer (GC) is a worldwide health priority in both developing and developed countries. The aim of this study was to map the distribution of incident cases of GC in Iran to provide a geographical presentation of the incidence of the disease.Methods: This study used the Iranian National Cancer Registry (INCR) data from 2004 to 2014. Excel was used to do the primary analysis including calculation of GC incidence for each province and also to provide a frequency table of the type and location of GC by the provinces. ArcGIS 10.5 (Redlands, CA, USA) mapping software was used to map the provincial age-standardized incidence rates by sex. The type and location of the GC cases were obtained from the NCR dataset.Results: According to the results of the present study, the patients were predominantly male 49,907 (70.0%). During the study period, the highest and lowest age-standardized incidence rates of GC in Iran in 2014 were reported from Ardebil (IR=30.19) and Ghom (IR=1.00) respectively. A significant difference was observed when the distribution of the location of GC tumors was compared between males and females (P<0.001).Conclusions: The results of the current study suggested a lower rate of GC incidence rate was reported in Iran when compared to the global figure in both females and males. The findings suggest involving different factors with different effects in GC among Iranian populations. Further studies are needed to better understand the epidemiology and etiology of the disease.
Prevalence of Depression and Associated Factors among Adults on Antiretroviral Therapy In Public Hospitals of Kembata Tembaro Zone, South Ethiopia
Authors: Girma Addisu , Tekleselasie Wondwosen , Yohannes Tadele 
Published: December 2020

Abstract
BackgroundCurrently, people living with Human Immunodeficiency Virus have longer life expectancies with the use of antiretroviral therapy. However; depression is the most common in these patients, which has markedly resulted to poor health outcomes due to reduced adherence to treatment and deterioration of medical outcomes, including treatment resistance, increase the demand for the utilization of medical resources and increase the morbidity and mortality. The aim of this study was to assess the prevalence and associated factors of depression among adult people living with HIV attending antiretroviral therapy clinic in public hospitals at KembataTembaro Zone, South Ethiopia,2020.MethodAn institution based cross sectional study was conducted in public Hospitals of KembataTembaro Zone from March 1/2020-April30/2020. Systematic random sampling technique was used to select the study participants. Data were collected using a pretested and structured questionnaire. Multivariable Logistic regression was performed to assess factors associated with depression using odds ratio at 95% confidence interval and P-value < 0.05.ResultsThe prevalence of depression was 44.3% (95% CI: 39.4% − 49.2 Being female (AOR = 2.03, 95% CI: 1.21,3.40), living alone (AOR = 3.09,95%CI :1.68,5.68), Having HIV related stigma (AOR = 2.85, 95% CI: 1.73, 4.71), poor social support (AOR = 2.55, 95% CI: 1.48, 4.78), CD4 count less than 350 cell/ul (AOR = 2.66, 95% CI: 1.48, 4.58) and Poor medication adherence (AOR = 2.19,95% CI: 1.32, 3.65) were factors significantly associated with depression.ConclusionThe prevalence of depression was high. Being female, living alone, having HIV related stigma, Poor social support, CD4 count less than 350 cell/ul and poor medication adherence were associated with depression. Depression should be included as part of the routine consultation of HIV patients to ensure early detection and treatment.
Accelerated Failure Time Model with Weighted Least-Squares Estimation: Application on Survival of HIV Positives
Authors: Mustefa Yesuf Abdela , Chen Ding-Geng 
Published: December 2020

Abstract
BackgroundSurvival analysis is the most appropriate method of analysis for time to event data. The classical accelerated failure time model is a more powerful and interpretable model than the Cox proportional hazards model provided that, model imposed distributional and homoscedasticity assumptions satisfied. However, most of the real data are heteroscedastic which violate the fundamental assumption and consequently, the statistical inference could be erroneous in accelerated failure time modeling. Weighted least squares estimation for accelerated failure time model is an efficient semi-parametric approach for time to event data without the homoscedasticity assumption, which is developed recently and not often utilized for real data analysis. Thus, the study was conducted to ascertain the predictive performance of weighted least squares estimation method over the classical methods.MethodsWe analyzed a sample of 203 real Antiretroviral Therapy dataset. We compared the results from clasical methods of estimation for accelerated failure time model with the results revealed from the weighted least squares estimation.ResultsWe found that the data are heteroscedastic. The weighted least squares estimation revealed more accurate, and efficient estimates of covariates effect. It also detected more significant covariates. Accordingly, survival of HIV positives varies with age, weight, functional status, CD4 percent, and clinical stages.ConclusionsThe weighted least squares estimation performed best in predicting the survival of HIV patients. Thus, we recommend future researchers should utilize weighted least squares estimation rather than the classical methods when the homoscedasticity assumption is violated.
Common Pathogens and Their Resistance to Antimicrobials in Community Acquired Pneumonia (CAP): A Single Center Study in Bangladesh
Authors: MA Kausar , M Nasir , S Paul , MH Rahman , A Kalam , FU Ahmed 
Published: December 2020

Abstract
Pneumonia is a worldwide, serious threat to health and an enormous socio-economic burden for health care system. Community-acquired pneumonia (CAP) is associated with a significant mortality and morbidity. Knowledge of predominant microbial patterns in CAP constitutes the basis for initial decisions about empirical antimicrobial treatment. The aim of this study was to identify the bacterial etiology of CAP in adult hospitalized patients and to see their antibiotic sensitivity pattern as well as to observe their clinical profile and short term outcome. It was a hospital based prospective observational study. A total of 87 hospitalized patients diagnosed with CAP were enrolled consecutively from the medicine ward of Chittagong Medical College Hospital (CMCH). Sputum for Gram staining, Z N staining, culture sensitivity, blood culture and sensitivity and PCR for Legionella pneumophila, Mycoplasma pneumoniae, Chlamydophila pneumonia and Streptococcus pneumonia were done. Patients were followed up for in-hospital outcome and 30-day mortality. The mean (±SD) age was 49.59±16.97 years and male female ratio was 1.56:1. Fever, chest pain and cough were the most common clinical features. Sputum culture, blood culture and PCR were positive in 60.9%, 1.1% and 4.6% of the samples respectively. Klebsiella pneumoniae was identified in the sputum culture of the majority of the patients (39.1%), followed by Pseudomonas aeruginosa (10.3%), Staphylococcus aureus and Escherichia coli (5.7%). The only one sample which was positive in blood culture and it was Staphylococcus aureus. Streptococcus pneumoniae was identified in all the 4 PCR positive cases. The highly sensitive drugs were meropenem, levofloxacin and amikacin. The mean (±SD) duration of hospital stay was 6.34±2.37. In hospital mortality and 30-day mortality was 6.9% and 16.1% respectively. Gram-negative bacteria pre-dominate in the bacteriologic profile of CAP using conventional sputum and blood culture. There is need for further conventional serologic tests for atypical and viral pathogens in all patients admitted with CAP.