bluuebunny/crossref_metadata_2025_split huggingface dataset:
Methylation of WT1, CA10 in peripheral blood leukocyte is associated with breast cancer risk: a case-control study
Authors: Ge Anqi , Gao Song , Liu Yupeng , Zhang Hui , Wang Xuan , Zhang Lei , Pang Da , Zhao Yashuang 
Published: July 2020

Abstract
Background: Studies have shown that abnormal changes of specific-gene DNA methylation in leukocytes may be associated with an elevated risk of cancer. However, associations between the methylation of the zinc-related genes, WT1 and CA10, and breast cancer risk remain unknown. Methods: The methylation of WT1 and CA10 was analyzed by methylation-sensitive high-resolution-melting (MS-HRM) in a case-control study with female subjects (N=959). Logistic regression was used to analyze the associations, and propensity score (PS) method was used to adjust confounders. Results: The results showed that WT1 hypermethylation was associated with an increased risk of breast cancer, with an odds ratio (OR) of 3.07 [95% confidence interval (CI): 1.67-5.64, P<0.01]. Subgroup analyses showed that WT1 hypermethylation was specifically associated with an elevated risk of luminal A subtype (OR=2.62, 95% CI: 1.11-6.20, P=0.03) and luminal B subtype (OR=3.23, 95% CI: 1.34-7.80, P=0.01). CA10 hypermethylation was associated with an increased risk of luminal B subtype (OR=1.80, 95% CI: 1.09-2.98, P=0.02). Conclusion: The results of the present study suggest that the hypermethylation of WT1 methylation in leukocytes is significantly associated with an increased risk of breast cancer. The hypermethylation of WT1 is associated with an increased risk of luminal subtypes of breast cancer, and the hypermethylation of CA10 is associated with an increased risk of luminal B subtype of breast cancer.
Circular DNA intermediates in the generation of large human segmental duplications.
Authors: Chicote Javier Ugarte , López-Sánchez Marcos , Marquès-Bonet Tomàs , Callizo José , Pérez-Jurado Luis Alberto , Garcia-España Antonio 
Published: July 2020

Abstract
Background: Duplications of large genomic segments provide genetic diversity in genome evolution. Despite their importance, how these duplications are generated remains uncertain, particularly for distant duplicated genomic segments. Results: Here we provide evidence of the participation of circular DNA intermediates in the single generation of some large human segmental duplications. A specific reversion of sequence order from A-B/C-D to B-A/D-C between duplicated segments and the presence of only microhomologies and short indels at the evolutionary breakpoints suggest a circularization of the donor ancestral locus and an accidental replicative interaction with the acceptor locus. Conclusions: This novel mechanism of random genomic mutation could explain several distant genomic duplications including some of the ones that took place during recent human evolution.
Cancer Patient Management Strategy in a Cancer Center of Zhejiang, China During the COVID-19 Pandemic
Authors: Xu Song-xiao , Cheng Xiang-dong , Pan Zhi-wen , Song Qian , Wang Yi-hong , Xiong Juan , Chen Yong-yi , Fan Fan , Zhu Jing , Wu Wan-ying , Deng Xue-ying , Yu Yan-pin , Xu Xiao-hong , Chen Wen-hu , Zhu Tao , Yu Yang , Liu Kai-zhong , Shao Guo-liang , Chen Ming , Yu En-yan 
Published: July 2020

Abstract
Background: Due to the increased risk of viral infection and the severe shortage of medical resources during the pandemic of COVID-19, most hospitals in the epidemic areas significantly reduced non-emergency admissions and services, if not closed. As a result, it has been difficult to treat cancer patients on time, which adversely affects their prognosis. To address this problem, cancer centers must develop a strategic plan to manage both inpatients and outpatients during the pandemic, provide them with the necessary treatment, and at the same time prevent the spread of the virus among patients, visitors and medical staff. Methods: Based upon the epidemic situation in Zhejiang Province, China, the number of running non-emergency medical wards in the Zhejiang Cancer Hospital was gradually increased in a controlled manner. All staff of the hospital received COVID-19 preventive training and was provided with three different levels of protection according to the risks of their services. Only patients without a known history of SARS-CoV-2 contact were eligible to schedule an appointment. Body temperature was measured on all patients upon their arrival at the hospital. Chest CT image, blood cell counting and travel/contact history were investigated in patients with fever. Respiratory tract samples, such as sputum and throat swabs, from all patients, including those clinically suspected of SARS-CoV-2 infection, were collected for nucleic acid detection of SARS-CoV-2 before treatment.Results: A total of 3697 inpatients and 416 outpatients seeking cancer treatment were enrolled from February 1 to April 3, 2020, in compliance with the hospital’s infection-control interventions. The clinicopathological parameters of the patients were summarized herein. 4237 samples from 4101 patients produced negative RNA testing results. Four clinically suspected patients all presented negative RNA test results and were excluded from the SARS-CoV-2 infection through follow-up retesting and monitoring. Seven patients with only N-gene positive results were retested, followed by CT scan and SARS-CoV-2 contact history investigation. All of them were finally diagnosed as non-infected patients. There was one outpatient who was confirmed positive by virus RNA test and then followed up. She might be an asymptomatic laboratory-confirmed case. During the study period, there was no SARS-CoV-2 infection among staff, patients and escorts of patients in the Zhejiang Cancer Hospital.Conclusion: This study suggested our infection-control interventions, including viral nucleic acid test, could be used as a reliable method to screen cancer patients in the area with moderate COVID-19 prevalence. Cancer may not be a high-risk factor of SARS-CoV-2 infection.
Peer supervision experiences of drug sellers in a rural district in East-Central Uganda: a qualitative study
Authors: Bagonza Arthur , Wamani Henry , Peterson Stefan , Mårtensson Andreas , Mutto Milton , Musoke David , Kitutu Freddy Eric , Mukanga David , Gibson Linda , Awor Phyllis 
Published: July 2020

Abstract
Background

Support supervision improves performance outcomes among health workers. However, the national professional guidelines for new licenses and renewal for class C drug shops in Uganda prescribe self-supervision of licensed private drug sellers. As such, inappropriate treatment of malaria, pneumonia and diarrhoea among children under five years of age continues unabated. This study assessed experiences of drug sellers and peer supervisors at the end of a peer supervision intervention in Luuka district in East Central Uganda.

Methods

Eight in-depth interviews (IDIs) were held with peer supervisors while five focus group discussions (FGDs) were conducted among registered drug sellers at the end of the peer supervision intervention. The study assessed experiences and challenges of peer supervisors and drug sellers regarding peer supervision. Transcripts were imported into Atlas ti 7 qualitative data management software (ATLAS.ti GmbH, Berlin) where they were analysed using qualitative thematic content analysis.

Results

Initially, peer supervisors were disliked and regarded as another extension of drug inspectors by drug sellers. However, with time a good relationship was established between drug sellers and peer supervisors leading to regular, predictable and supportive peer supervision. This increased confidence of drug sellers in using respiratory timers and rapid diagnostic tests in diagnosing pneumonia symptoms and uncomplicated malaria respectively among children under five years. There was also an improvement in completing the sick child register which was used for self-assessment by drug sellers. The drug shop association was mentioned as a place where peer supervision should be anchored since it was a one-stop center for sharing experiences and continuous professional development. Drug sellers proposed including community health workers in monthly drug shop association meetings so that they may also gain from the associated benefits. Untimely completion of the sick child registers by drug sellers and lack of adequate resources were the main peer supervision challenges mentioned.

Conclusion

Drug sellers benefitted from peer supervision by developing a good relationship with peer supervisors. This relationship guaranteed reliable and predictable supervision ultimately leading to improved treatment practices. There is need to explore the bare minimum resources needed for peer supervision.
Outpatient vs. Inpatient Hip Arthroplasty: A Matched Case-Control Study on 90-Day Complication Rate and 2-Year Patient Reported Outcomes
Authors: Rosinsky Philip J. , Chen Sarah L. , Yelton Mitchell J. , Lall Ajay C. , Maldonado David R. , Shapira Jacob , Meghpara Mitchell B , Domb Benjamin G 
Published: July 2020

Abstract
Background: The transition to outpatient-based surgery is a major development occurring in recent years in the field of total hip arthroplasty (THA). The effect of this transition on patient reported outcomes (PROs) is still not well established. The purpose of the current study was to compare patients undergoing inpatient THA (iTHA) to patients undergoing outpatient THA (oTHA) regarding (1) perioperative variables including: surgical time, blood loss, and length of stay (2) 90-day complication rates and unplanned emergency room or office visits (3) 2-year PROs including: modified Harris hip score (mHHS), Harris hip score (HHS), forgotten joint score (FJS), pain, and satisfaction, as well as quality of live measures. Methods: The XXX registry was analyzed for patients undergoing THA between July 2014 and April 2016. The first 100 patients undergoing oTHA were selected and matched to 100 patients undergoing iTHA via propensity matching based on the following variables: age, sex, body mass index (BMI), Charlson comorbidity index (CCI), and smoking status. The primary outcomes were PROs at two years post-operatively. The secondary outcomes were perioperative surgical variables, 90-day complication rates, and unplanned emergency and clinic visits. Results: After exclusions, 91 patients remained in each group and were compared. The oTHA group showed improved 2-year PROs with regard to mHHS (91.5 vs. 86.2; P=0.02), HHS (92.3 vs. 87.4; P=0.02), and pain (1.0 vs. 1.5; P=0.04). The oTHA group had an average length of stay of 6.8 hours compared to 43.2 hours for the iTHA group (P<0.001). There were no significant differences between the groups regarding readmissions, emergency room visits, and unplanned clinic visits. Complications and revision rates were similar in both groups. Conclusion: In appropriately selected, younger patients, oTHA can achieve improved postoperative 2-year PROs compared to iTHA. We found no differences regarding postoperative short-term complications or two-year revision rates, and no differences in unplanned office visits or readmissions.
Increasing Fat Deposition via Upregulates the Transcription of Peroxisome Proliferator-Activated Receptor Gamma (PPARγ) in Native Crossbred Chicken
Authors: Tunim Supanon , Phasuk Yupin , Aggrey Samuel E. , Duangjinda Monchai 
Published: July 2020

Abstract
Background: Crossbreeding using exotic breeds is usually employed to improve the growth characteristics of indigenous chickens. This mating not only provides growth but affect adversely to fat deposition as well. We studied the growth, abdominal, subcutaneous and intramuscular fat and mRNA expression of peroxisome proliferator-activated receptor (PPAR) α and PPARγ in adipose and muscle tissues of four chicken breeds [Chee breed (CH) (100% Thai native chicken), Kaimook e-san1 (KM1; 50% CH background), Kaimook e-san2 (KM2; 25% CH background), and broiler (BR)]. This study was aim to study role of PPARs on fat deposition in native crossbred chicken.Results: The BR chickens had higher abdominal fat than other breeds (P<0.05) and the KM2 had an abdominal fat percentage higher than KM1 and CH respectively (P<0.05). The intramuscular fat (IMF) of BR was greater than KM1 and CH (P<0.05). In adipose tissue, PPARα transcription expression was different among the chicken breeds. However, there were breed differences in PPARγ gene expression. Study of abdominal fat PPARγ gene expression showed the BR breed, KM1, and KM2 breed significantly greater (P<0.05) than CH. In 8 to 12 weeks of age, the result shows that the PPARγ expression of the CH breed is less than (P<0.05) KM2. The result of PPARs expression in muscle tissue was similar result in adipose tissue.Conclusion: Crossbreeding improved the growth of the Thai native breed, there was also a corresponding increase in carcass fatness. However, there appears to be a relationship between PPARγ expression and fat deposition traits. therefore, PPARγ activity plays a key role in lipid accumulation by up-regulation.
Cytokine Profile During Occult Hepatitis B Virus Infection In Chronic Hepatitis C Patients
Authors: Ribeiro Camilla Rodrigues de Almeida , de Almeida Nathalia Alves Araújo , Martinelli Katrini Guidolini , Pires Marcia Amendola , Mello Carlos Eduardo Brandao , De Paula Vanessa Salete , Barros José J. 
Published: July 2020

Abstract
Background: The hepatitis B virus (HBV) is one of the leading causes of acute, chronic and occult hepatitis (OBI) representing a serious public health threat. Cytokines are known to be important chemical mediators that regulate the differentiation, proliferation and function of immune cells. Accumulating evidence indicate that the inadequate immune responses are responsible for HBV persistency. The aim of this study were to investigate the cytokines IFN-γ, TNF, IL-2, IL-4, IL-6, IL-10 and IL-17A in patients with OBI and verify if there is an association between the levels of these cytokines with the determination of clinical courses during HBV occult infection. Methods: 114 patients with chronic hepatitis C were investigated through serological and molecular tests, the OBI coinfected patients were subjected to the test for cytokines using the commercial human CBA kit and the results were compared with healthy controls with no history of liver diseases. Results: Among 114 HCV patients investigated, 11 individuals had occult hepatitis B. The levels of cytokines were heterogeneous between the groups, most of the cytokines showed higher levels of production detection among OBI individuals when compared to the control group. We found a high level of IL-17A in the control group and high levels of TNF, IL-10, IL-6, IL-4 and IL-2 in OBI patients. Conclusion: These cytokines could be involved in the persistence of HBV DNA in hepatocytes triggers a constant immune response, inducing continuous liver inflammation, which can accelerate liver damage and favor the development of liver cirrhosis in other chronic liver diseases.
Comparison of mixed model based approaches for correcting for population substructure with application to extreme phenotype sampling.
Authors: Onifade Maryam Yetunde , Roy-Gagnon Marie-Hélène , Parent Marie-Élise , Burkett Kelly M 
Published: July 2020

Abstract
BackgoundMixed models are used to correct for confounding due to population stratification and hidden relatedness in genome-wide association studies. This class of models includes linear mixed models and generalized linear mixed models. Existing mixed model approaches to correct for population substructure have been previously investigated with both continuous and case/control response variables. However, they have not been investigated in the context of extreme phenotype sampling (EPS), where genetic covariates are only collected on samples having extreme response variable values.MethodsIn this work, we compare the performance of existing binary trait mixed model approaches (GMMAT, LEAP and CARAT) on EPS data. Since linear mixed models are commonly used even with binary traits, we also evaluate the performance of a popular linear mixed model implementation (GEMMA). We use simulation to estimate the type 1 error of all approaches under confounding due to population stratification. We also apply all methods to a real dataset from a Québec, Canada, case-control study that is known to have population substructure.ResultsOur simulation results show that for a common candidate variant, both LEAP and GMMAT control the type 1 error rate. We observe similar type 1 error control with the analysis on the Québec dataset. However, for rare variants the false positive rate remains inflated even after correction with mixed model approaches.ConclusionsThe methods compared in this study do not perform equally well. Therefore, when data are from an EPS study, care should be taken to ensure that the models underlying the methodology are suitable to the sampling strategy and to the minor allele frequency of the candidate SNPs.
Regeneration of a Full-thickness Defect of Rotator Cuff Tendon with Freshly Thawed Umbilical Cord-Derived Mesenchymal Stem Cells in a Rat Model
Authors: Yea Ji-Hye , Park Jin-Kyung , Kim InJa , Sym Gayoung , Bae Tae Soo , Jo Chris Hyunchul 
Published: July 2020

Abstract
The authors have withdrawn this preprint due to erroneous posting.
Mitigative efficacy of the clinical dosage administration of granulocyte colony-stimulating factor and romiplostim in mice with severe acute radiation syndrome
Authors: Yamaguchi Masaru , Suzuki Marino , Funaba Moeri , Chiba Akane , Kashiwakura Ikuo 
Published: July 2020

Abstract
Background: It has been reported that the high-dosage administration of domestically approved pharmaceutical drugs, especially granulocyte colony-stimulating factor (G-CSF) and romiplostim (RP), is a rapid and appropriate medical treatment for preventing severe acute radiation syndrome (ARS) of victims exposed to lethal total-body irradiation (TBI). However, it remains unclear whether or not the clinical dosage administration of these drugs can ameliorate TBI-induced ARS and related high mortality in order to find various drug treatment options and less toxic optimum protocol depending on the situation surrounding the radiological accidents.Methods: We assessed the clinical dosage administration in combination with G-CSF and RP as intraperitoneal injection in C57BL/6J mice exposed to more than 7-Gy lethal dose of X-ray TBI for the survival study evaluated by the log-rank test. Bone marrow and splenic cells were collected on the 21st day, when 1 week have passed from last administration, to detect the level of cell apoptosis, intracellular reactive oxygen species (ROS), and nuclear factor erythroid 2-related factor 2 (Nrf2)-related anti-oxidative gene expressions, and enzyme-linked immune sorbent assay using sera was performed for cell senescence and inflammation status analyzed with one-way ANOVA and Tukey-Kramer or Bonferroni/Dunn multiple comparison tests.Results: The combined once-daily administration of 10 μg/kg G-CSF for 4 times and 10 μg/kg RP once a week for 3 times improve the 30-day survival rate of lethal TBI mice compared with untreated TBI mice, accompanied by a gradual increase in the body weight and hematopoietic cell numbers. The radio-mitigative effect is probably attributed to the scavenging of ROS and the reduction in cell apoptosis. These changes were associated with the upregulation of Nrf2 and its downstream anti-oxidative targets in TBI mice. Furthermore, this combination modulated TBI-induced cell senescence and inflammation markers. Conclusions: This study suggested that the clinical dosage administration in combination with G-CSF and RP may also have radio-mitigative effects on mice exposed to lethal TBI and may be a potent therapeutic agent for mitigating radiation-induced severe ARS.
Students’ Perspectives of Factors Related to Delayed Completion of Online RN-BSN Programs
Authors: Iheduru-Anderson Kechinyere 
Published: July 2020

Abstract
Background

There are multiple educational programs for individuals to become registered nurses (RNs), and the transition from an associate degree or diploma to a Bachelor of Science (BSN) degree is vital to healthcare. This study examined the factors contributing to delayed completion or withdrawal from online nursing programs from students’ perspectives.

Method

Thematic content analyses were conducted on qualitative data obtained from semi-structured interviews ( N = 26).

Results

Complex factors contributed to delayed completion of online RN to BSN programs, including student-, institutional-, and faculty-related factors.

Conclusion

This study validated and extends previous studies without delineating students in fully online programs from hybrid and face-to-face programs. Students, faculties, and institutions all have a role to play in facilitating on-time program completion. Recognizing and mitigating the barriers that delay on-time program completion is required to foster nurses to obtain a BSN degree.
gCAnno: A Graph-based Single Cell Type Annotation Method
Authors: Yang Xiaofei , Gao Shenghan , Wang Tingjie , Yang Boyu , Dang Ningxin , Ye Kai 
Published: July 2020

Abstract
Background
Current single cell analysis methods annotate cell types at cluster-level rather than ideally at single cell level. Multiple exchangeable clustering methods and many tunable parameters have a substantial impact on the clustering outcome, often leading to incorrect cluster-level annotation or multiple runs of subsequent clustering steps. To address these limitations, methods based on well-annotated reference atlas has been proposed. However, these methods are currently not robust enough to handle datasets with different noise levels or from different platforms.
Results
Here, we present gCAnno, a graph-based Cell type Annotation method. First, gCAnno constructs cell type-gene bipartite graph and adopts graph embedding to obtain cell type specific genes. Then, a naïve Bayes classifier is built for annotation. We compared the performance of gCAnno to other state-of-art methods on multiple single cell datasets, either with various noise levels or from different platforms. The results showed that gCAnno outperforms other state-of-art methods with higher accuracy and robustness.
Conclusions
gCAnno is a robust and accurate cell type annotation tool for single cell RNA analysis. The source code of gCAnno is publicly available at https://github.com/xjtu-omics/gCAnno.