bluuebunny/crossref_metadata_2025_split huggingface dataset:
Machine Learning and Integrative Analysis Reveals Stemness Index-associated Signature in Acute Myeloid Leukemia
Authors: Xu Qiang , Zhou Hao , Cao Dedong , Fang Bin , Yan Siqi , Li Ziping , Hu Yu , Guo Tao 
Published: October 2020

Abstract
Background: The rapidly growing research in leukemia has provided unequivocal proof that cancer stem cells exist in acute myeloid leukemia. However, the mechanisms of the growth and self-renewal of acute myeloid leukemia stem cells (LSCs), which play an important role in the development of AML, were still elusive. Methods: We first used a trained stemness index model based on a recently described machine learning method one-class logistic regression (OCLR) to score AML samples. We then obtained the mRNA expression based-index (mRNAsi), DNA methylation based-index (mDNAsi), and epigenetic regulation based-index (EREG-mRNAsi). With the acquired three stemness indices, we investigated the relationship between the stemness index and the tumor immune microenvironment/somatic mutation, clinical characteristics of AML patients. Furthermore, a weighted gene co-expression network analysis (WGCNA) and protein-protein interaction (PPI) network were performed to obtain key genes associated with the stemness index. Bedsides, GO and KEGG enrichment analysis was performed to explore the biological functions. Finally, we validated the key genes by applying it to the Oncomine and GEO datasets.Result: The results suggested that EREG-mRNAsi might accurately predict overall survival (OS) in AML patients from TCGA, while the mRNAsi and mDNAsi was not significantly statistically associated with the OS. Furthermore, the mRNAsi was significantly correlated with the clinical characteristics of the FAB category, age, gender, immune score, WT1, and CEBPA mutation. Additionally, the EREG-mRNAsi was significantly associated with the cytogenetics risk category, TP53 mutation. The mDNAsi was significantly associated with the FAB-category, NPM1, IDH1, IDH2, and DNMT3A mutation. Several key genes related to the stemness index of AML were indicated to be possible and promising therapeutic targets for inhibiting LSCs in AML.Conclusions: Our research based on machine learning and WGCNA analysis revealed a set of key genes contributed to the stemness index of AML. These genes may become therapeutic targets to inhibit the LSCs of AML in the future.
Identification of Prognostic Genes Associated with Expression Differentiation During Metabolism Process in Hepatocellular Carcinoma (HCC)
Authors: Yang Xin , Cao Chuang-jie , Dou Cheng-Yun , Tang Hai-Bo , Liu Qiong , Zou Juan , Li Yu-kun , Zeng Tian , Xie Xia 
Published: October 2020

Abstract
Background: Metabolic disorders have attracted more and more attention from scientists in the research of various tumors, especially in hepatocellular carcinoma (HCC). The purpose of this study is to assess the prognostic significance of metabolism in HCC.Methods: The expression profile of metabolism-related gene (MRGs) were extracted from the cancer genome atlas (TCGA) database of 349 HCC-surviving patients. Subsequently, A series of biomedical computational algorithms were used to identify seven-MRGs signature as a prognostic model. GSEA analysis indicated the function and pathway enrichment of these MRGs. Then, drug sensitivity analysis found the hub gene, which tested by IHC staining.Results: 420 differential MRGs and 116 differential transcription factor (TFs) expression were extracted from HCC patients based on TCGA database. Metabolic disturbance might be involved in the development of HCC by GO and KEGG enrichment analyses. LASSO regression analysis constructed seven-MRGs signature (DHDH, ENO1, G6PD, LPCAT1, PDE6D, PIGU and PPAT), which were used to predict the prognosis of HCC patients. Further GSEA analysis found the function and pathway enrichment of these seven MRGs. Then, drug sensitivity analysis indicated G6PD might play a key role in the prognosis of HCC by chemoresistance. Finally, we used IHC staining to demonstrate the relationship of G6PD expression and clinical parameter in HCC patients.Conclusion: This study provides a potential clue for predicting the prognosis of HCC patients and further studies on HCC metabolism.
Investigation of ancestral alleles in the Bovinae subfamily
Authors: Naji Maulana M , Utsunomiya Yuri T , Solkner Johann , Rosen Benjamin D. , Meszaros Gabor 
Published: October 2020

Abstract
Background: In evolutionary theory, divergence and speciation can arise from long periods of reproductive isolation, genetic mutation, selection and environmental adaptation. After divergence, alleles can either persist in their initial state (ancestral allele - AA), co-exist or be replaced by a mutated state (derived alleles -DA). In this study, we aligned whole genome sequences of individuals from the Bovinae subfamily to the cattle reference genome (ARS.UCD-1.2) for defining ancestral alleles necessary for selection signatures study.Results: Accommodating independent divergent of each lineage from the initial ancestral state, AA were defined based on fixed alleles on at least two groups of yak, bison and gayal-gaur-banteng resulting in ~32.4 million variants. Using non-overlapping scanning windows of 10 Kb, we counted the AA observed within taurine and zebu cattle. We focused on the extreme points, regions with top 0. 1% (high count) and regions without any occurrence of AA (null count). High count regions preserved gene functions from ancestral states that are still beneficial in the current condition, while null counts regions were linked to mutated ones. For both cattle, high count regions were associated with basal lipid metabolism, essential for survival of various environmental pressures. Mutated regions were associated to productive traits in taurine, i.e. higher metabolism, cell development and behaviors and in immune response domain for zebu.Conclusions: Our findings suggest that retaining and losing AA in some regions are varied and made it species-specific with possibility of overlapping as it depends on the selective pressure they had to experience.
Community-Driven Citizen Science Approach to Explore Cardiovascular Disease Risk Perception, and Develop Prevention Advocacy Strategies in Sub-Saharan Africa: A Programme Protocol
Authors: Okop Kufre , Murphy Kathy , Lambert Estelle Victoria , Kedir Kiya , Getachew Hailemichael , Howe Rawleigh , Berchmans Jean , Ntawuyirushintege Selemani , Bavuma Charlotte , Rulisa Stephen , Kasenda Stephen , Chipeta Effie , Bunn Christopher , Crampin Amelia C. , King Abby C. , Chapotera Gertrude , Banchoff Ann , Winter Sandra J. , Levitt Naomi S 
Published: October 2020

Abstract
Background: In sub-Saharan Africa (SSA), which experiences a disproportionately high cardiovascular disease (CVD) burden, population-based screening and prevention measures are hampered by low levels of knowledge about CVD and associated risk factors, and inaccurate perceptions of severity of risk. Methods: This protocol describes the planned processes for implementing community-driven participatory research, using a citizen science method to explore CVD risk perceptions and to develop community-specific advocacy and prevention strategies in rural and urban SSA settings. Research teams in four selected African countries will engage with and train community members living in rural and urban communities as citizen scientists to facilitate conceptualization, co-designing of research, data gathering, and co-creation of knowledge that can lead to a shared agenda to support collaborative participation in community-engaged science. The emphasis is on robust community engagement, using mobile technology to support data gathering, participatory learning, and co-creation of knowledge and disease prevention advocacy. Discussion: Contextual processes applied and lessons learned in specific settings will support redefining or disassembling boundaries in participatory science to foster effective implementation of sustainable prevention intervention programmes in Low- and Middle-income countries.
Composition and Risk Assessment of Perioperative Patient Safety Incidents Reported by Anesthesiologists from 2009 to 2019, a single-center retrospective cohort study
Authors: Zhang Xue , Ma Shuang , Sun Xueqin , Zhang Yuelun , Chen Weiyun , Chang Qing , Pan Hui , Zhang Xiuhua , Shen Le , Huang Yuguang 
Published: October 2020

Abstract
Background: Patient safety incident reporting has been an important means of improving patient safety and enhancing organizational quality control. Reports of anesthesia-related incidents are of great value for analysis to improve perioperative patient safety. However, the utilization of incident data is far from sufficient, especially in developing countries such as China.Methods: All patient safety incidents reported by anesthesiologists in a Chinese academic hospital between September 2009 and August 2019 were collected from the incident reporting system. We reviewed the freeform text reports, supplemented them with information from the patient medical record system. Composition analysis and risk assessment were performed.Results: In total, 847 patient safety incidents were voluntarily reported by anesthesiologists during the study period among 452,974 anesthetic procedures, with a reported incidence of 0.17%, much less than the incidence reported by some developed countries. Patients with worse ASA physical status were more vulnerable to suffering from PSIs. The most common type of incident was related to the airway (N=208, 27%), followed by cardio-cerebrovascular (N=99, 13%) and pharmacological incidents (N=79, 10%). Those preventable incidents with extreme or high risk were found out through risk assessment, to provide reference for the department to implement more standard operation procedures.Conclusions: This study describes characteristics of 847 patient safety incidents voluntarily reported by anesthesiologists within eleven years in a Chinese academic hospital. Airway incidents constitute the majority of incidents reported by anesthesiologists. Under-reporting is severe in China, and the importance of summarizing and utilizing anesthesia incident data should be scrutinized.
Which One of the Human Immune Genes are more Involved in Against HTLV-1 Infection?
Authors: Keikha Masoud , Ali-Hassanzadeh Mohammad , Bagheri Ramin , Karbalaei Mohsen 
Published: October 2020

Abstract
Background: Human T-lymphotropic virus type 1 (HTLV-1) is a main member of type C retrovirus. This virus was first isolated from cutaneous T-cell lymphoma cases. Among all infected individuals, only 5% of cases progress to acute form, and 4% of them to chronic form. Nevertheless, about 90% of patients remain asymptomatic. Adult T cell leukaemia/lymphoma (ATLL) and HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) are accounted as acute and chronic forms of disease respectively.Methods: The gene expression profile of CD4+ T cells in four groups, healthy donors, asymptomatic HTLV-1 carriers (ACs), HAM/TSP (HTLV-1-associated myelopathy/tropical spastic paraparesis), and ATLL (Adult T-cell leukemia/lymphoma) based on GPL9686 platform was evaluated. Results: According to Gene enrichment analysis, it was determined that hub genes in present study are able effect on various pathways such as apoptosis, proliferation and T cell activation, Ras signaling pathway, integrin signaling pathway, P53 signaling pathway, CCKR, TLR, FGF, DNA Damage, MAPK signaling, integrated cancer, Caspase, NF-κB, BCL-2 family, survival complex, breast cancer, Pancreatic cancer.Conclusions: Overall, based on scientific results in the present study, it seems the immune system via stimulation of biological processes such as cell survival, proliferation, CTLs exhaustion, and apoptosis concomitant, caused immortalization of HTLV-1 infected CD4+ T cells.
A hSCARB2-transgenic mouse model for Coxsackievirus A16 pathogenesis
Authors: Chen Yanli , Li Heng , Yang Jinxi , Zheng Huiwen , Guo Lei , Li Weiyu , Yang Zening , Song Jie , Liu Longding 
Published: October 2020

Abstract
Background: Coxsackievirus A16 (CA16) is one of the neurotropic pathogen that has been associated with severe neurological forms of hand, foot, and mouth disease (HFMD), but its pathogenesis is not yet clear. The limited species tropism of CA16 make the establishment of a suitable animal model that can recapitulate the neurological pathology observed in human HFMD more difficult. Because the human scavenger receptor class B, member 2 (hSCARB2) is a cellular receptor for CA16, we used transgenic mice bearing human SCARB2 and nasally infected them with CA16 to study the pathogenicity of the virus.Methods: Coxsackievirus A16 was administered by intranasal instillation to groups of hSCARB2 transgenic mice and clinical signs were observed. Sampled at different time-points to document and characterize the mode of viral dissemination, pathological change and immune response of CA16 infection. Results: Weight loss and virus replication in lung and brain were observed in hSCARB2 mice infected with CA16, indicating that these animals could model the neural infection process. Viral antigens were observed in the alveolar epithelia and brainstem cells. The typical histopathology was interstitial pneumonia with infiltration of significant lymphocytes into the alveolar interstitial in lung and diffuse punctate hemorrhages in the capillaries of the brainstem. In addition, we detected the expression levels of inflammatory cytokines and detected high levels of interleukin IL-1β, IL-6, IL-18, and IFN-γ in nasal mucosa, lungs and brain tissues. Conclusions: The hSCARB2-transgenic mice can be productively infected with CA16 via respiratory route and exhibited a clear tropism to lung and brain tissues, which can serve as a model to investigate the pathogenesis of CA16 associated respiratory and neurological disease.
A Contribution to the Phylogeny and Taxonomy of Phlebiopsis (Polyporales, Basidiomycota)
Authors: Zhao Ya-Nan , Nakasone Karen K. , Chen Che-Chi , Liu Shi-Liang , Cao Yi-Feng , He Shuang-Hui 
Published: October 2020

Abstract
An in-depth study of the phylogeny and taxonomy of the corticioid genus Phlebiopsis (Phanerochaetaceae) was conducted. Phylogenetic analyses of the ITS1-5.8S-ITS2 and nrLSU sequences demonstrated that Phlebiopsis is a strongly supported clade that is distinct from its sister clade that includes Phaeophlebiopsis, Hapalopilus and Rhizochaete. Two genera, Australohydnum and Hjortstamia, are reduced to synonyms under Phlebiopsis because generic type species A. griseofuscescens and H. friesii, respectively, are embedded in the Phlebiopsis clade. Twenty-four lineages are resolved in the ITS phylogenetic tree of Phlebiopsis, including six new taxa from Sri Lanka and China — P. albescens, P. brunnea, P. cylindrospora, P. magnicystidiata, P. membranacea and P. sinensis. Five new combinations are proposed — Phaeophlebiopsis mussooriensis, Phlebiopsis bambusicola, P. dregeana, P. griseofuscescens and P. novae-granatae. Phlebiopsis crassa is a morphological species complex with three distinct lineages. Phlebiopsis lamprocystidiata is determined to be a later synonym of P. darjeelingensis. The new taxa are described, illustrated, and compared and contrasted to morphologically similar species. An emended description of Phlebiopsis is provided along with an identification key to 27 accepted species.
Illnesses Associated With Increased Length of Stay for Individuals Experiencing Homelessness: A Retrospective Cohort Study of Emergency Department Visits and Hospitalizations.
Authors: Ghosh Sumantra Monty , Sikdar Khokan , Koleade Adetola , Farris Peter , Ross Jordan , Tanguay Robert , Lang Eddy S. , Messier Geoffrey , Tang Karen 
Published: October 2020

Abstract
Background: Individuals experiencing homelessness (IEH) tend to have increased length of stay (LOS) in acute care settings, which negatively impacts health care costs and resource utilization. It is unclear however, what specific factors account for this increased LOS. This study attempts to define which diagnoses most impact LOS for IEH and if there are differences based on their demographics. Methods: A retrospective cohort study was conducted looking at ICD-10 diagnosis codes and LOS for patients identified as IEH seen in Emergency Departments (ED) and also for those admitted to. Data were stratified based on diagnosis, gender and age. Statistical analysis was conducted to determine which ICD-10 diagnoses were significantly associated with increased ED and inpatient LOS for IEH compared to housed individuals.Results: Homelessness admissions were associated with increased LOS regardless of gender or age group. The absolute mean difference of LOS between IEH and housed individuals was 1.62 hours [95% CI 1.49 – 1.75] in the ED and 3.02 days [95% CI 2.42-3.62] for inpatients. Males age 18-24 years spent on average 7.12 more days in hospital, and females aged 25-34 spent 7.32 more days in hospital compared to their housed counterparts. Thirty-one diagnoses were associated with increased LOS in EDs for IEH compared to their housed counterparts; maternity concerns and coronary artery disease were associated with significantly increased inpatient LOS. Conclusion: Homelessness significantly increases the LOS of individuals within both ED and inpatient settings. We have identified numerous diagnoses that are associated with increased LOS in IE; these inform the prioritization and development of targeted interventions to improve the health of IEH.
Evaluation of Serum Immunoglobulin (IgG, IgM, IgA) in Oral Cancer Patients – A Case Control Study
Authors: M. Tarsariya Vivek , Raval Nilesh , Mehta Dhaval , Asrani Mukesh , Asrani Vijay , Barot Kaushik 
Published: October 2020

Abstract
Background: Very few studies have been done to evaluate level of serum immunoglobulins (IgG,IgM,IgA) in patients with Oral cancer as tumour markers.Aims and Objectives: To estimate the serum immunoglobulins level (IgG, IgM, IgA) in oral cancer patients and its comparison with control groups and weather these values can be used to predict severity of disease or not.Materials and Methods: 30 patients with different clinical stages oral cancer and 30 healthy controls were selected at random and subjected for analysis of serum IgG, IgA, IgM. Statistical methods employed were the mean, standard deviation and t-test.Results: Significant elevated levels of all the immunoglobulins in oral cancer patients observed when compared with the control group and levels were increasing with clinical stages. (p<0.05).Conclusions: All these immunoglobulins are indicative of tumour burden or transformation of malignancy in higher stage and might be employed as prognostic indicators in oral cancer.
Identification and integrated analysis of neuropathic pain-related circular RNA signature
Authors: Wang Kun , Zhou Zhimin , Bao Junping , Liu Dong , Hu Yuanbin , Wu Xiaotao 
Published: October 2020

Abstract
Background: More and more evidences show that non-coding RNAs are involved in neuropathic pain, however, there are few reports on the regulatory mechanism of competitive endogenous RNA (ceRNA) in neuropathic pain. The purpose of this study is to explore the possible molecular mechanisms of neuropathic pain. Methods: We collected neuropathic pain-related microarray datasets providing expression profile of circular RNAs (circRNAs) and mRNAs from the Gene Expression Omnibus (GEO) and then performed bioinformatics analysis on them. Results: The present study has identified that up-regulated circRNAs primarily regulate the activity of focal adhesion-associated biological processes and down-regulated primarily regulate the activity of metabolic-associated biological processes by means of ceRNAs. Conclusions: Our data suggest that circRNAs may be candidates for pathogenesis in neuropathic pain and may be considered as promising therapeutic targets in the future.
Uterine prolapse and associated factors among reproductive age women in Dawro zone, southwest Ethiopia: a community based cross sectional study
Authors: Badacho Abebe Sorsa , Lelu Mengistu Auro , Gelan Zegeye 
Published: October 2020

Abstract
Background: Uterine Prolapse is an important but one of the most neglected public health problems causing maternal morbidity and mortality among women of reproductive age in developing countries including Ethiopia. However, yet few data are available with respect to uterine prolapse. The objective of this study was to assess the prevalence of, and factors associated with uterine prolapse among women of reproductive age.Methods: A community based cross-sectional study was conducted in Loma Woreda, Dawro southwest Ethiopia, from November to December 2019. A total of 422 randomly selected women of reproductive age were participated in the study. Data were collected by face-to-face interview with pre-structured questionnaire and clinical diagnoses were carried out. Epi data 3.2.1 and SPSS version 24 were used for data entry, processing and analysis. Binary Logistic regression was used to find out the association between dependent and independent variables. Variables with P-value less than 0.25 in bivariate logistic regression were further examined using multivariate logistic regression to investigate an association between dependent variable and independent variables. Results: The mean age of the respondents was 35.4 years (±7.994 SD). This study identified that the prevalence of symptomatic and anatomical uterine prolapse was 6.6 %(28) and 5.9%(25) respectively. The prevalence of anatomical prolapse was used as a reference when determining the associated factors. Age at first marriage (AOR: 0.25, 95%CI (0.07, 0.89), place of delivery (AOR: 3.33, 95%CI (1.21, 9.13), birth attendant assisted delivery (AOR 0.21; 95%CI (0.06, 0.71) and history of abortion (AOR: 2.94, 95%CI (1.08, 7.97) were found to have significantly and independently associated with prevalence of uterine prolapse. Conclusion: Uterine prolapse is common among women of reproductive age group age at first marriage, place of delivery, birth attendant assisted delivery, and history of abortion were found to be independent predictors of prevalence of uterine prolapse.
Effectiveness of Adjunctive Corticosteroid Therapy in Patients with Severe COVID-19: A Retrospective Cohort Study
Authors: Xiong Bin , Qin Yuan-Yuan , He Li-Min , Du Hu , Zhan Zhu , Zhou Yi-Hong , Chen Yao-Kai , Zhang An 
Published: October 2020

Abstract
Objective: To investigate the effectiveness of adjunctive corticosteroid therapy in patients with severe COVID-19.Methods: We conducted a retrospective analysis of the difference in several outcomes between patients with severe COVID-19 who received corticosteroid therapy (the corticosteroid group) and patients with severe COVID-19 who did not receive corticosteroid therapy (the non-corticosteroid group).Results: Seventy-five patients were included in this study. Of these, 47 patients were in the corticosteroid group and 28 patients were in the non-corticosteroid group. There were no differences between the two groups in the total length of hospital stay (LOS), the length of ICU stay, high-flow oxygen days, non-invasive ventilator days, invasive ventilation days, and mortality rate. Total lesion volume ratio, consolidation volume ratio and GGO volume ratio in the corticosteroid group decreased significantly on day 14, while those in the non-corticosteroid group did not show a significant decrease.Conclusions: Our results show that adjunctive corticosteroid use did not significantly improve clinical outcomes in severe COVID-19 patients, but might promote the absorption of pulmonary lesions. Larger multicenter randomized controlled studies may be needed to confirm this.