bluuebunny/crossref_metadata_2025_split huggingface dataset:
GINS1/2/3/4&nbsp;Upregulation Predicts Poor Prognosis in Human Sarcoma
Authors: Wu Gen , Chen Ziyuan , Wu Tong , Zhou Jian , Tian Qunyan , Wu Ren , Dou Pengcheng , Jie Shuo , Wang Wanchun 
Published: January 2021

Abstract
Background: GINS family was reported to be highly expressed in many tumors. However, the association of GINS family with human sarcoma remained unknown. This study was undertaken to explore the expression and prognostic value of GINS family in human sarcoma.Methods: In terms of the expression levels of mRNA for GINS family members, a particular contrast in various cancers, especially human sarcoma, was conducted through ONCOMINE and GEPIA and CCLE databases. Kaplan-Meier Plotter was used to identify the prognostic value of GINS family in sarcoma.Results: We discovered that the mRNA expression levels of GINS1, GINS2, GINS3, and GINS4 were all higher in the majority of tumor tissues than in normal samples, of course, including sarcoma. Through the Cancer Cell Line Encyclopedia (CCLE), all the four members (GINS1, GINS2, GINS3, GINS4) expression were observed in high levels in sarcoma cell lines. In Gene Expression Profiling Analysis (GEPIA) and Kaplan-Meier Plotter, our results indicated that the poor overall survival (OS), disease-free survival (DFS) and relapse free survival (RFS) were tightly associated with the increased expression of GINS genes. Conclusion: The four GINS family members are all the prognostic biomarkers for the prognosis of human sarcoma.
Quality of Maternal and Newborn Health Care in Ethiopia: A Cross-Sectional Study
Authors: Biadgo Abera , Legesse Aynalem , Seifu Abiy , Singh Kavita , Mulissa Zewdie , Magge Hema , Kiflie Abiyou , Bitewulign Befikadu , Abate Mehiret , Alemu Haregeweyni 
Published: January 2021

Abstract
Background: Despite reports of universal access to and modest utilization of maternal and newborn health services in Ethiopia, mothers and newborns continue to die from preventable causes. Studies indicate this could be due to poor quality of care provided in health systems. Evidences show that high quality health care prevents more than half of all maternal deaths. In Ethiopia, there is limited knowledge surrounding the status of the quality of maternal and newborn health care in health facilities. This study aims to assess the quality of maternal and neonatal health care provision at the health facility level in four regions in Ethiopia.Methodology: This study employed a facility-based cross-sectional study design. It included 32 health facilities which were part of the facilities for prototyping maternal and neonatal health quality improvement interventions. Data was collected using a structured questionnaire, key informant interviews and record reviews. Data was entered in Microsoft Excel and exported to STATA for analysis. Descriptive analysis results are presented in texts, tables and graphs. Quality of maternal and neonatal health care was measured by input, process and outputs components. The components were developed by computing scores using standards used to measure the three components of the quality of maternal and neonatal health care.Result: The study was done in a total of 32 health facilities: 5 hospitals and 27 health centers in four regions. The study revealed that the average value of the quality of the maternal and neonatal health care input component among health facilities was 62%, while the quality of the process component was 43%. The quality of the maternal and neonatal health output component was 48%. According to the standard cut-off point for MNH quality of care, only 5 (15.6%), 3 (9.3%) and 3 (10.7%) of health facilities met the expected input, process and output maternal and neonatal health care quality standards, respectively.Conclusion: This study revealed that the majority of health facilities did not meet the national MNH quality of care standards. Focus should be directed towards improving the input, process and output standards of the maternal and neonatal health care quality, with the strongest focus on process improvement.
Prognostic Effect of lncRNA SNHG7 On Cancer Outcome: A Meta and Bioinformatic Analysis
Authors: zhang yunyuan , Tian Qingwu , Huang Shifeng , Wang Qing , Wu Hongmei , Dong Qian , chen xian 
Published: January 2021

Abstract
Background: New evidence from clinical and fundamental researches suggests that SNHG7 is involved in the occurrence and development of carcinomas. And the increase levels of SNHG7 are associated with poor prognosis in various kinds of tumors. However, the small sample size was the limitation for the prognostic value of SNHG7 in clinical application. The aim of the present meta-analysis was to conduct a qualitative analysis to explore the prognostic value of SNHG7 in various cancers. Methods: Articles related to the SNHG7 as a prognostic biomarker for cancer patients, were comprehensive searched in several electronic databases. The enrolled articles were qualified via the preferred reporting items for systematic reviews and meta-analysis of observational studies in epidemiology checklists. Additionally, an online database based on The Cancer Genome Atlas (TCGA) was further used to validate our results.Results: We analyzed 2418 cancer patients that met the specified criteria. The present research indicated that an elevated SNHG7 expression level was significantly associated with unfavorable overall survival (OS) (HR = 2.45, 95% CI: 2.12–2.85, p <0.001). Subgroup analysis showed that high expression levels of SNHG7 were also significantly associated with unfavorable OS in digestive system cancer (HR = 2.31, 95% CI: 1.90–2.80, p <0.001) and non-digestive system cancer (HR = 2.67, 95% CI: 2.12–3.37, p <0.001). Additionally, increased SNHG7 expression was found to be associated with tumor stage and progression (III/IV vs. I/II: HR = 1.76, 95% CI: 1.57–1.98, p <0.001). Furthermore, elevated SNHG7 expression significantly predicted lymph node metastasis (LNM) (HR = 1.98, 95% CI: 1.74–2.26, p <0.001) and distant metastasis (DM) (HR = 2.49, 95% CI: 1.88–3.30, p <0.001) respectively. No significant heterogeneity was observed among these studies. SNHG7 was significantly upregulated in four cancers and the elevated expression of SNHG7 predicted shorter OS in four malignancies and worse DFS in five malignancies based on the validation using the GEPIA cohort.Conclusions: The present analysis suggests that elevated SNHG7 is significantly associated with unfavorable OS, tumor progression, LNM and DM in various carcinomas, and may be used as a promising biomarker to guide therapy for cancer patients.
Identification and Evolution Analysis of the JAZ&nbsp;Gene Family in Maize
Authors: Han Yang , Luthe Dawn 
Published: January 2021

Abstract
Background: Jasmonates (JAs) are important for plants to coordinate growth, reproduction, and defense responses. In JA signaling, jasmonate ZIM-domain (JAZ) proteins serve as master regulators at the initial stage of herbivores attacks. Although discovered in many plant species, little in-depth characterization of JAZ gene expression has been reported in the agronomically important crop, maize (Zea mays L.). Results: In this study 16 JAZ genes from the maize genome were identified and classified. Phylogenetic analyses were performed from maize, rice, sorghum, Brachypodium, and Arabidopsis using deduced protein sequences, total six clades were proposed and conservation was observed in each group, such as similar gene exon/intron structures. Synteny analysis across four monocots indicated these JAZ gene families had a common ancestor, and duplication events in maize genome may drive the expansion of JAZ gene family, including genome-wide duplication (GWD), transposon, and/or tandem duplication. Strong purifying selection acted on all JAZ genes except those in group 4, which were under neutral selection. Further, we cloned three paralogous JAZ gene pairs from two maize inbreds differing in JA levels and insect resistance, and gene polymorphisms were observed between two inbreds.Conclusions: Here we analyzed the composition and evolution of JAZ genes in maize with three other monocot plants. Extensive phylogenetic and synteny analysis revealed the expansion and selection fate of maize JAZ. This is the first study comparing the difference between two inbreds, and we propose genotype-specific JAZ gene expression might be present in maize plants. Since genetic redundancy in JAZ gene family hampers our understanding of their role in response to specific elicitors, we hope this research could be pertinent to elucidating the defensive responses in plants.
Effects of L-Carnitine Supplementation on MicroRNA-217 Expression Level in Non-alcoholic Steatohepatitis Suffering Patients with Obesity: A Randomized Controlled Trial
Authors: Iravani Farzaneh , Roudi Fatemeh , Amiri-Moghadam Shirin , Asle-Mohajeri Mahsa , Salehi Maryam , Azimi-Nezhad Mohsen , Mojarrad Majid , Nematy Mohsen 
Published: January 2021

Abstract
BackgroundNonalcoholic steatohepatitis (NASH) is a severe subtype of Nonalcoholic fatty liver disease (NAFLD) and a progressive chronic liver disease which is associated with oxidative stress, inflammation, fibrosis, lipotoxicity, and altered mitochondrial metabolism. Silent Information Regulator 1 (SIRT1) gene is considered as a potential therapeutic target in NAFLD, microRNA-217 (MiRNA-217) inhibits expression of SIRT1 and this inhibition may play role in the pathogenesis of NASH. On the other hand, L-carnitine may have beneficial effects on NASH. Therefore, we investigated the effect of L-carnitine on the MiRNA-217 expression levels in obese NASH suffering patients.MethodsThis double-blind randomized controlled trial (RCT) was carried out in the nutrition clinic of Mashhad University of Medical Sciences (March 2013-June 2014). Seventy-one obese NASH suffering patients were enrolled and randomly assigned to receive L-carnitine (2000 mg/day) /placebo for 12 weeks. Micro RNA (MiR)-217 expression levels were assessed at the study baseline and at the end of study. The MiRNA-217 expression level were assessed in compare with 36 age, sex, and BMI matched NAFLD/NASH negative obese subjects, as control population.ResultsMiRNA-217 expression level was higher in NASH suffering group compared to NASH negative obese patients (P < 0.001). There was a significant difference in the expression level of MiRNA-217 between L-carnitine and placebo receiving groups after the study intervention (P = 0.001); while the expression levels had no significant difference between the two groups at the initiation of the study. L-carnitine supplementation reduced MiRNA-217 expression levels in participants who were assigned to the supplementation group; while MiRNA-217 expression levels in the placebo received NASH, positive obese patients didn’t change during the study.ConclusionMiRNA-217 expression level can be considered as a noninvasive practical biomarker for diagnosis, and treatment follow-up of NASH suffering patients. However, further studies are required to find out the exact relationships between MiRNA-217 expression and different stages of NAFLD.Trial registrationThis trial was registered on Iranian Clinical Trials Registry Platform IRCT201212052602N8 (https://en.irct.ir/trial/2379) on February 4, 2013.
COVID-19 Viral Load Not Associated with Disease Severity: Findings from A Retrospective Cohort Study
Authors: Abdulrahman Abdulkarim , Mallah Saad , AlQahtani Manaf 
Published: January 2021

Abstract
Background: Being able to use COVID-19 RT-PCR Ct values as simple markers of disease outcome or prognosis would allow for the easy and proactive identification and triaging of high-risk cases. This study’s objective was thus to assess whether a correlation exists between COVID-19 viral loads, as indicated by RT-PCR Ct values, and disease severity, as indicated by respiratory indices Results: A multi-centre cross-sectional retrospective study was conducted, using data obtained from Bahrain’s National COVID-19 Task force’s centralised database. The study period was from May 2, 2020 to July 31, 2020. A multivariable logistic regression was used to assess for a correlation. The covariates adjusted for included sex, age, presentation, and comorbidities. In our cohort, Ct value showed no statistical significance for an association with requirement for oxygenation on admission (Odds ratio 1.046; 95%CI 0.999 to 1.096, p=0.054). Conclusion: Viral load, as indicated by Ct values, did not seem to be associated with requirement for oxygenation on admission in our cohort. We postulate however that time since onset of symptom may have acted as an unaccounted-for confounder.
Deep Learning-Based Four-Region Lung Segmentation in Chest Radiography for COVID-19 Diagnosis
Authors: Kim Young-Gon , Kim Kyungsang , Wu Dufan , Ren Hui , Tak Won Young , Park Soo Young , Lee Yu Rim , Kang Min Kyu , Park Jung Gil , Kim Byung Seok , Chung Woo Jin , Kalra Mannudeep , Li Quanzheng 
Published: January 2021

Abstract
Imaging plays an important role in assessing severity of COVID-19 pneumonia. The recent COVID-19 researches indicate that in many cases, disease progress propagates from the bottom of the lungs to the top. However, semantic interpretation of chest radiography (CXR) findings do not provide a quantitative description of radiographic opacities, and the existing AI-assisted CXR image analysis frameworks do not quantify the severity regionally. To address this issue, we propose a deep learning-based four-region lung segmentation method to assist accurate quantification of COVID-19 pneumonia. Specifically, a segmentation model to separate left and right lung is firstly applied, and then a carina and left hilum detection network is used to separate the upper and lower lungs. To improve the segmentation performance of COVID-19 images, ensemble strategy with five models is exploited. For each region, we evaluated the clinical relevance of the proposed method compared with the Radiographic Assessment of the Quality of Lung Edema (RALE). The proposed ensemble strategy showed dice score of 0.900, which outperforms the conventional methods. Mean intensities of segmented four regions indicate positive correlation to the extent and density scores of pulmonary opacities based on the RALE framework. Therefore, the proposed method can accurately segment four-regions of the lungs and quantify regional pulmonary opacities of COVID-19 pneumonia patients.
Risk Factors for Pediatric Surgical Site Infection Following Neurosurgical Procedures for Hydrocephalus: A Retrospective Single-Center Cohort Study
Authors: Shibamura-Fujiogi Miho , Ormsby Jennifer , Breibart Mark , Warf Benjamin , Sandora Thomas , Priebe Gregory , Soriano Sulpicio , Yuki Koichi 
Published: January 2021

Abstract
Background Infection is a major complication following cerebral spinal fluid (CSF) diversion procedures for hydrocephalus. However, their pediatric risk factors for surgical site infection (SSI) are currently not well defined. Because SSI prevention bundle is increasingly introduced, the purpose of this study was to evaluate risk factors associated with SSIs following CSF diversion surgeries under SSI bundle at a single quaternary care pediatric hospital.Methods We performed a retrospective cohort study of patients undergoing CSF diversion procedures from 2017 to 2019. SSIs were identified prospectively through continuous surveillance. We performed univariate analyses to determine an association between SSIs and patient demographics, comorbidities and perioperative factors, with subsequent multivariate logistic regression analyses to identify independent risk factors for SSI.Results We identified a total of 561 CSF diversion procedures with an overall SSI rate of 3.6%. In univariate analyses, older age, number of previous shunt revisions and comorbid cardiac disease were significantly associated with SSI. In multivariate analyses, history of brain tumor (OR2.75, 95%CI 1.03-7.33, P=0.04) and cardiac comorbidities (OR9.47, 95%CI 2.15-41.73, P=0.003) were significantly associated with SSIs. When endoscopic third ventriculostomy was excluded, only cardiac disease was independently associated with SSI. Cardiac diseases associated with SSI included single ventricle disease with palliative repair and valvulopathy with underlying connective tissue diseases. Conclusion This study showed that comorbid conditions (cardiac disease, brain tumor) were more important than perioperative factors as risk factors for SSI in pediatric patients undergoing CSF diversion procedures. Further investigation is needed to define the mechanisms behind these associations.
Comparative Analysis of Cytokine mRNA&nbsp;Expressions in Human Tissues With Mycobacterium Tuberculosis Infection
Authors: Park Sung-Bae , Park Heechul , Choi Yoon-Sung , Park Ji Young , Lee Dongsup , Kim Jungho , Chang Hee-Kyung , Kim Sunghyun 
Published: January 2021

Abstract
Background: One of the widely used diagnostic methods for Mycobacterium tuberculosis (MTB) infection is the acid-fast bacilli staining of formalin-fixed paraffin-embedded (FFPE) tissues; however, this method cannot discriminate between MTB and nontuberculous mycobacteria (NTM) species. Moreover, confirming tuberculosis (TB) using FFPE tissue specimens may be difficult owing to their low bacterial load. In addition, interference in molecular diagnostic assays, including polymerase chain reaction (PCR), may occur owing to fragmentation and genomic DNA cross-linkage in FFPE tissues formed during formalin fixation or paraffin-embedding procedures. Therefore, we aimed to investigate whether an automated molecular diagnostic method based on PCR-reverse blot hybridization assay can discriminate between human MTB-positive and -negative FFPE tissues and to compare the relative mRNA expression levels of various host immune markers between MTB-infected and uninfected human tissues using quantitative reverse transcription (qRT) PCR. A total of 52 human FFPE tissue samples from various regions of the body, including the lungs, lymph nodes, tendons, colon, and appendix, were collected and used for the molecular identification of Mycobacterium species and analysis of cytokine mRNA expression. Results: IFN-γ, TNF-α, IP-10, CXCL9, CXCL11, and GM-CSF mRNA expression levels in MTB-infected tissues were significantly higher than those in uninfected samples. Additionally, the differences in the mRNA expression levels of IFN-γ, CXCL9, and GM-CSF between MTB-infected and uninfected tissues were statistically significant were statistically significant (p < 0.05). Correlation curve analysis indicated that the mRNA expression of IFN-γ was inversely proportional to that of IP-10 and that the mRNA expression levels of IFN-γ, TNF-α, CXCL9, CXCL11, GM-CSF, and TNFR were proportional and well-correlated. Furthermore, to establish marker profiles for detecting MTB infection, the statistically significant expression levels of three markers were combined. We confirmed that the combined profile of IFN-γ, CXCL9, and GM-CSF expression levels was statistically significant (P < 0.001). Conclusions: Although the mRNA expression patterns of host immune markers may vary according to MTB infection status, these patterns may be highly correlated and can be simultaneously used as an additional indicator for diagnosing TB in human tissue samples.
Multichannel optogenetics combined with laminar recordings for ultra-controlled neuronal interrogation
Authors: Eriksson David , Schneider Artur , Thirumalai Anupriya , Alyahyaey Mansour , Crompe Brice de la , Sharma Kirti , Ruther Patrick , Diester Ilka 
Published: January 2021

Abstract
Highlights: To combine large-scale recordings with optical perturbation we have developed a number of new techniques such as thin optical side-emitting fibers, a fiber matrix connector for thin fibers, an electro-optical commutator for multiple thin fibers, an active patch cord, a flexible fiber bundle ribbon cable, and a modular multi-optrode implantation holder.Summary: Simultaneous large-scale recordings and optogenetic interventions hold the promise to decipher the fast-paced and multifaceted dialogue between neurons that sustains brain function. Here we developed unprecedentedly thin, cell-sized Lambertian side-emitting optical fibers and combined them with silicon probes to achieve high quality recordings and ultrafast multichannel optogenetic inhibition in freely moving animals. Our new framework paves the way for large-scale photo tagging and controlled interrogation of rapid neuronal communication in any combination of brain areas.
CD8+ T Lymphocyte Co-expression Genes Correlates With Immune Microenvironment and Overall Survival in Breast Cancer
Authors: Jiang Jialing , Wang Yutao , Zhao Yi 
Published: January 2021

Abstract
Purpose: To identify CD8+ T lymphocyte related co-expressed genes that increase CD8+ T lymphocyte proportions in breast cancer, and to elucidate the underling mechanisms among relevant genes in the tumor microenvironment.Method: We obtained breast cancer expression matrix data, patient phenotype following information from TCGA–BRCA FPKM. Tumor purity, immune score, stromal score, and estimate score were calculated using the ‘estimate’ package in R. The CD8+ T lymphocyte proportions in each breast carcinoma sample were estimated using the CIBERSORT algorithm. The samples with P < 0.05 were considered to be significant and were taken into the weighted gene co-expression network analysis. Based on the CD8+ T lymphocyte proportion and tumor purity, we generated CD8+ T lymphocyte co-expression networks and selected the most CD8+ T lymphocyte related module as our interested co-expression modules. We constructed a Cox regression risk model based on CD8+ T cell-related factors and explored their correlations with microenvironmental indicators. Results: A breast carcinoma CD8+ T lymphocyte proportion co-expression yellow module was determined. Four CD8+ T lymphocyte proportion co-expressed genes (CD74, HLA-DMA, HCST and GIMAP4) were determined to increase the CD8+ T lymphocyte proportion levels in breast cancer patients. The yellow module was significantly enriched in the antigen presentation process, cellular response to interferon−gamma, and leukocyte proliferation. Subsequently, we generated risk scores based on CD74, HLA-DMA, HCST, and GIMAP4. The AUC of the CD8+ T lymphocyte related risk score was 0.66. The risk score showed significant prognostic ability in various subgroups. Expression levels of proteins encoded by CD74, HLA-DMA, HCST and GIMAP4 were lower in the breast carcinoma samples than in normal tissue, suggesting that expression differences both at the mRNA and the protein levels. Conclusion: These four CD8+ T lymphocyte proportion co-expression genes increase CD8+ T lymphocyte in breast cancer by an antigen presentation process. The mechanism might suggest new pathways to improve outcomes in patients who do not benefit from immune therapy.
Novel Mumps Virus Epitopes Reveal Robust Cytotoxic T Cell Responses After Natural Infection but Not After Vaccination
Authors: Kaaijk Patricia , Emmelot Maarten , Meiring Hugo , Els Cecile van , Wit Jelle de 
Published: January 2021

Abstract
Mumps is nowadays re-emerging despite vaccination. The contribution of T cell immunity to protection against mumps has not been clearly defined. Previously, we described a set of 41 peptides that were eluted from human leukocyte antigen (HLA) class I molecules of mumps virus (MuV)-infected cells. Here, we confirmed immunogenicity of five novel HLA-B*07:02- and HLA-A*01:01-restricted MuV T cell epitopes from this set of peptides. High frequencies of T cells against these five MuV epitopes could be detected ex vivo in all tested mumps patients. Moreover, these epitope-specific T cells derived from mumps patients displayed strong cytotoxic activity. In contrast, only marginal T cell responses against these novel MuV epitopes could be detected in recently vaccinated persons, corroborating earlier findings. Identifying which MuV epitopes are dominantly targeted in the mumps-specific CD8+ T- response is an important step towards better understanding in the discrepancies between natural infection or vaccination-induced cell-mediated immune protection