bluuebunny/crossref_metadata_2025_split huggingface dataset:
Primary Renal Pelvis Squamous Cell Carcinoma: A Case Report
Authors: Xiao Wei , Cai Hongjia , Wang Xiaomin , Zhang Neng 
Published: November 2020

Abstract
Background: Primary renal pelvic squamous cell carcinoma (SCC) is exceedingly rare neoplasm and poor prognosis. We reported a patient who underwent surgery for radical nephrectomy.Methods and results: The patient was a 72-year old man, who visited doctors with complaints of dull aching in right flank region and occasional gross hematuria. Abdominal contrast-enhanced magnetic resonance imaging (MRI) revealed a neoplasm and hydronephrosis in the right kidney. The preoperative diagnosis of malignant tumor in right kidney was made by urologist, and open radical nephrostomy was performed. The resected tumor was shown histologically to be squamous cell carcinoma of right renal pelvis.Conclusions: Renal SCC is a rare tumor usually presented in advanced stage with poor prognosis. Early diagnosis and surgical treatment are beneficial for patients’ survival. Most patients are associated with risk factors of Renal SCC such as renal calculi and infection, but patient with no risk factors shouldn’t be ignored. We encountered a rare case with no risk factors.
High Level Plasmid-Mediated Quinolone Resistance in Clinical Infections at a Tertiary Healthcare Institution in South-West Nigeria
Authors: Ojewuyi Abiodun Ronke , Odetoyin Babatunde , Aboderin Aaron Oladipo 
Published: November 2020

Abstract
Background Plasmid-mediated quinolone resistance (PMQR) has become a growing clinical concern worldwide. Recent reports from Nigeria revealed that qunolone resistant clinical isolates have become commomplace. However, few reports regarding the prevalence of PMQR are available. Hence, this study aimed to determine the prevalence of PMQR genes in qunolone resistant clinical isolates from a tertiary care hospital in Nigeria. Methods This was a cross-sectional hospital based study involving 390 non-repetitive Gram negative bacilli from diverse clinical infections. The isolates were characterized by the MicrobactTM identification kit and their susceptibility patterns determined by the Kirby-Bauer disc diffusion technique. All quinolone resistant isolates were investigated for the carriage of PMQR genes by multiplex polymerase chain reaction (PCR). Data analysis was with appropriate descriptive and inferential statistics.Results The isolates were distributed as Escherichia coli (n=121; 31.0%), Klebsiella species (n= 112;28.7%), Pseudomonas aeruginosa (n=59;15.1%), Proteus species (n=43;11.0%), Salmonella species (n=6;1.3%) and others. They were commonly resistant to nalidixic (62.6%), co-amoxiclav (57.7%); norfloxacin (52.3%), ofloxacin(52.1%) and ciprofloxacin(51.0%), but were least resistant to imipenem; (n=36; 9.2%). Out of 244 isolates that were resistant to at least one quinolone, 180 (73.8%) harboured one or more PMQR gene with a high prevalence of efflux-mediating determinants (qepA, 22.5%; oqxAB, 21.1%), and the aminoglycoside acetyltransferase (aac(6’)-Ib-cr, 19.7%). Proportionately low level of target-protecting determinants; qnrB, 13.2%; qnrS, 8.7%; qnrA, 5.9%; qnrD, 4.5% and qnrC, 4.2% were found in these isolates.Conclusion There is high level quinolone resistance and wide distribution of PMQR genes in clinical isolates in Nigeria with a preponderance of Efflux-mediating determinants and the aminoglycoside acetyltransferase. This emphasizes the need for regular resistance surveillance and antimicrobial stewardship to guide the appropriate and judicious use of antibiotics.
Compliance of daily iron supplementation during pregnancy affecting the hemoglobin level in second trimester and at term
Authors: S Romthira - , Thinkhamrop Jadsada , Chaiyarach Sukanya - , Kreetiyutanont Sukanya - 
Published: November 2020

Abstract
Objectives: To determine the compliance rate of iron supplementation during pregnancy and the hemoglobin concentration in second trimester and at term.Methods: The study conducted among term pregnant women admission to the hospital for delivery who had non-anemic status at the initial visit for antenatal care, received daily iron supplementation before 20 weeks of gestation. They were interviewed to obtain the personal data, daily taking the supplemented tablet and side-effects. The compliance rate categorized as >80%, >50-80%, 25-50%, and < 25% according to the women’s response that they took daily tablet of 6-7, 3-5, 2, and 0-1 days/week, respectively. The type of supplementation and laboratory results of hemoglobin level were retrieved from their medical records.Results: Almost 90% of 350 participants had the compliance rate of >80%. The common side-effects were nausea and constipation. The side-effect rates were 10.5%, 12.1%, 66.7% in >80%, >50-80%, <25% compliance groups, respectively. In second trimester and term pregnancy revealed some anemic women. While hemoglobin concentrations above 13 gm/dl, which defined as high concentrated hemoglobin, revealed 12% during second trimester, and up to 30% at term in high compliance group.Conclusions: There was high compliance rate of iron supplementation with the high hemoglobin level markedly found in high compliance group.
Urinary microRNA Biomarkers for Detecting the Presence of Esophageal Cancer
Authors: Okuda Yusuke , Shimura Takaya , Iwasaki Hiroyasu , Fukusada Shigeki , Nishigaki Ruriko , Kitagawa Mika , Katano Takahito , Okamoto Yasuyuki , Yamada Tamaki , Horike Shin-ichi , Kataoka Hiromi 
Published: November 2020

Abstract
Background: Esophageal cancer (EC) including esophageal squamous cell carcinoma (ESCC) and adenocarcinoma (EAC) generally exhibits poor prognosis; hence, a noninvasive biomarker enabling early detection is necessary. Thus, this study aimed to establish novel urinary miRNA biomarkers for diagnosing EC.Methods: Out of 343 patients (299 healthy controls [HCs] and 44 ESCCs), 150 HCs and 43 patients with ESCC, which were both age- and sex-matched, were analyzed and randomly divided into two groups: 9 patients (6 HCs and 3 ESCCs) in the discovery cohort for microarray analysis and 184 patients (144 HCs and 40 ESCCs) in the training/test cohort with cross-validation for qRT-PCR analysis. Using 152 urine samples (144 HCs and 8 EACs), we validated the urinary miRNA biomarkers for EAC diagnosis.Results: Eight miRNAs were selected as biomarker candidates in the discovery cohort. In the training/test cohort, five of the eight miRNAs (miR-1273f, miR-619-5p, miR-150-3p, miR-4327, and miR-3135b) in the ESCC group had significantly higher urinary levels than those in the HC group. Consistently, these five urinary miRNAs were significantly different between HC and ESCC in both training and test sets. Especially, urinary miR-1273f and miR-619-5p showed excellent values of area under the curve (AUC) ≥ 0.80 for diagnosing stage I ESCC. Consistent with the ESCC group, the EAC group had significantly higher urinary levels of these five miRNAs than the HC group, and it also exhibited AUC values of approximately 0.80.Conclusion: The present study established novel urinary miRNA biomarkers that can early detect ESCC and EAC.
Human Cost of Tyranny in Kurdistan Region of Iraq
Authors: Ameen Jamal 
Published: November 2020

Abstract
Background The 2003 liberation/invasion of Iraq and the resulting casualties from civilians and armed forces attracted researchers publishing in high prestigious journals but little mentioned about the events that led to the armed intervention. This paper is assessing the human cost of successive Iraqi governments tyrannical rule in Kurdistan Region of Iraq over three decades.Method The two most recent and reliable census datasets of 1947 and 1957 were used to estimate fertility and survival rates by age group under normal circumstances. These were used in the classical Leslie Matrix to predict 2007 Kurdistan Region of Iraq population. Results were contrasted with estimates for the same year that were obtained by the World Food Programme as part of their Food Security Analysis for Iraq to arrive at estimates that would indicate the scale of the loss in human capital from Saddam’s tyranny that was imposed on the region. Findings Kurdistan Region has lost around 1,911,479 of which 1,043,549 were male and 867,930 female of different age groups. These include direct victims of the past genocide actions of successive Iraqi governments as well as those who thought refuge beyond the boundaries of Kurdistan Region during the past decades. Interpretation Saddam’s actions were directed to all indigenous inhabitants irrespective of gender and age. As such, any possible offspring, had life continued as normal, is counted as human loss. Impacts of changes in demography, socio-political and the environment of Saddam’s tyrannical rule are worth further investigation.Funding None
Integrative transcriptomic, proteomic, and machine learning approach to identifying feature genes of atrial fibrillation
Authors: Liu Yaozhong , Bai Fan , Tang Zhenwei , Liu Na , Liu Qiming 
Published: November 2020

Abstract
Background: Atrial fibrillation (AF) is the most common arrhythmia with poorly understood mechanisms. We aimed to investigate the biological mechanism of AF and to discover feature genes by analyzing multi-omics data and by applying a machine learning approach. Methods: At the transcriptomic level, four microarray datasets (GSE41177, GSE79768, GSE115574, GSE14975) were downloaded from the Gene Expression Omnibus database, which included 130 available atrial samples from AF and sinus rhythm (SR) group. Microarray meta-analysis was adopted to identified differentially expressed genes (DEGs). At the proteomic level, a qualitative and quantitative analysis of proteomics in the left atrial appendage of 18 patients (9 with AF and 9 with SR) was conducted. The machine learning correlation-based feature selection (CSF) method was introduced to selected feature genes of AF using the training set of 130 samples involved in the microarray meta-analysis. The Naive Bayes (NB) based classifier constructed using training set was evaluated on an independent validation test set GSE2240. Results: 863 DEGs with a FDR<0.05 and 482 differentially expressed proteins (DEPs) with a FDR<0.1 and fold change >1.2 were obtained from the transcriptomic and proteomic study, respectively. The DEGs and DEPs were then analyzed together which identified 30 biomarkers with consistent trends. Further, 10 feature, including 8 upregulated genes (CD44, CHGB, FHL2, GGT5, IGFBP2, NRAP, SEPTIN6, YWHAQ) and 2 downregulated genes (TNNT1, TRDN) were selected from the 30 biomarkers through machine learning CFS method using training set. The NB based classifier constructed using the training set accurately and reliably classify AF from SR samples in the validation test set with a precision of 87.5% and AUC of 0.995.Conclusion: Taken together, our present work might provide novel insights into the molecular mechanism and provide some promising diagnostic and therapeutic targets of AF.
Generation of restriction endonucleases barcode map to trace SARS-CoV-2 origin and evolution.
Authors: Colombo Federico , Corsiero Elisa , Lewis Myles J. , Pitzalis Costantino 
Published: November 2020

Abstract
Since the first report of SARS-CoV-2 in China in 2019, there has been a huge debate about the origin. In this work, using a different method we aimed to strengthen the observation that no evidence of genetic manipulation has been found by i) detecting classical restriction site (RS) sequence in human SARS-CoV-2 genomes and ii) comparing them with other recombinant SARS-CoV-like virus created for experimental purposes. Finally, we propose a novel approach consisting in the generation of a restriction endonucleases site map of SARS-CoV-2 and other related coronavirus genomes to be used as a fingerprint to trace the virus evolution.
Systemic Lupus Erythematosus triggered by SARS-CoV-2 Infection: A Systematic Review Based on a Case Report
Authors: Gracia-Ramos Abraham Edgar , Saavedra-Salinas Miguel Angel 
Published: November 2020

Abstract
Systemic lupus erythematosus (SLE) is an autoimmune and multisystemic chronic inflammatory disease that can affect various organs, including skin, joints, kidneys, lungs and the nervous system. Infectious agents have long been implicated in the pathogenesis of SLE. The new viral infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has shown that, in genetically predisposed patients, could trigger the presentation or exacerbation of autoimmune disease. We herein report a case of a 45-year-old man who presented respiratory symptoms, bilateral pleural effusion, ascites, splenomegaly, severe thrombocytopenia and renal failure with proteinuria and hematuria. SARS-CoV-2 PCR confirmed the COVID-19 diagnosis. We diagnosed the patient with SLE based on the clinical manifestations and positive immunological markers (2019 European League Against Rheumatism/American College of Rheumatology score of 18). Glucocorticoid pulses were administered to the patient with improvement in renal function. However, thrombocytopenia was also refractory to IV immunoglobulin and rituximab, so the patient underwent splenectomy. Through a systematic search of the medical literature, we retrieved 2 cases with SLE new onset and 5 cases with previous SLE diagnosis that shown activity of disease due SARS-CoV-2 infection. We herein present a systemic review of these cases and discuss the clinical manifestations that could help to the diagnosis of this clinical condition.
Quantification of Arterial, Venous, and Cerebrospinal Fluid Flow Dynamics by Magnetic Resonance Imaging Under Simulated Micro-Gravity Conditions
Authors: Zahid Arslan , Martin Bryn , Collins Stephanie , Oshinski John N. , Ethier Christopher Ross 
Published: November 2020

Abstract
Background: Astronauts undergoing long-duration spaceflight are exposed to numerous health risks, including Spaceflight-Associated Neuro-Ocular Syndrome (SANS), a spectrum of ophthalmic changes that can result in permanent loss of visual acuity. The etiology of SANS is not well understood but is thought to involve changes in cerebrovascular flow dynamics in response to microgravity. There is a paucity of knowledge in this area; in particular, cerebrospinal fluid (CSF) flow dynamics have not been well characterized under microgravity conditions. Our study was designed to determine the effect of simulated microgravity (head-down tilt [HDT]) on cerebrovascular flow dynamics. We hypothesized that microgravity conditions simulated by HDT would result in increased intracranial pressure (ICP) reflected by increases in CSF pulsatile flow.Methods: In a prospective cohort study, we measured flow in major cerebral arteries, veins, and CSF spaces in fifteen healthy volunteers using phase contrast magnetic resonance (PCMR) before and during 15° HDT.Results: We found a decrease in all CSF flow variables [systolic peak flow (p=0.009), and peak-to-peak pulse amplitude (p=0.001)]. Cerebral arterial average flow (p=0.04), systolic peak flow (p=0.04), and peak-to-peak pulse amplitude (p=0.02) all also significantly decreased. We additionally found a decrease in average cerebral arterial flow (p=0.040). Finally, a significant increase in cerebral venous cross-sectional area with HDT (p=0.005) was also observed.Conclusions: These results collectively demonstrate that acute application of 15° HDT caused a reduction in CSF flow variables (systolic peak flow and peak-to-peak pulse amplitude) which, when coupled with a decrease in average cerebral arterial flow, systolic peak flow, and peak-to-peak pulse amplitude, is consistent with a decrease in cardiac-related pulsatile CSF flow. These results suggest that decreases in cerebral arterial inflow were the principal drivers of decreases in CSF pulsatile flow.
Novel mutation in the TGFBI gene in a Moroccan family with atypical corneal dystrophy: a case report
Authors: BENBOUCHTA Yahya , JAOUAD Imane CHERKAOUI , TAZI Habiba , ELORCH Hamza , OUHENACH Mouna , ZRHIDRI Abdelali , SADKI Khalid , SEFIANI Abdelaziz , LYAHYAI Jaber , BERRAHO Amina 
Published: November 2020

Abstract
Background: Corneal dystrophies (CDs) are a heterogeneous group of bilateral, genetically determined, non-inflammatory bilateral corneal diseases which are usually limited to the cornea. CD is characterized by a large variability in the age of onset, evolution and visual impact and the accumulation of insoluble deposits at different depths of the cornea. Clinical symptoms revealed bilaterally multiple superficial, epithelial, and stromal anterior granular opacities, in different stages of severity among three patients of this family. 99 genes are involved in CDs.The aim of this study is to identify pathogenic variant caused atypical corneal dystrophy in a large Moroccan family and to describe the clinical phenotype with their severe different stages of evolution.Case presentation: In this study, we report a large Moroccan family with CD. Whole Exome Sequencing (WES) was performed in the three affected members who shared a phenotype of a corneal dystrophy in different stages of severity. The variant validation and familial segregation were done by Sanger sequencing in affected sister and mothers and in two unaffected brothers. Whole exome sequencing showed a novel heterozygous mutation (c.1772C>A; p.Ser591Tyr) in TGFBI gene. Clinical examinations demonstrated bilaterally multiple superficial, epithelial and stromal anterior granular opacities; in different stages of severity among three patients of this family. Conclusions: This report presents a novel mutation in TGFBI gene, found in three family members affected with different phenotypic aspects. This mutation is associated with Thiel-Behnke corneal dystrophy and therefore, it could be considered as a novel phenotype genotype correlation, which will help in genetic counseling for this family
Modeling Count Data for Healthcare Utilization: an Empirical Study of Outpatient Visits Among Vietnamese Older People
Authors: Le Dung Duc , Leon-Gonzalez Roberto , Matola Joseph Upile 
Published: November 2020

Abstract
Background Vietnam is undergoing a fast aging process that poses potential critical issues for older people and central among those is demand for healthcare utilization. However, healthcare utilization, here measured as count data, creates challenges for modeling because such data typically has distributions that are skewed with a large mass at zero. This study compares empirical econometric strategies for the modeling of healthcare utilization (measured as the number of outpatient visits in the last 12 months), and identifies the determinants of healthcare utilization among Vietnamese older people based on the best-fitting model identified. Methods Using the Vietnam Household Living Standard Survey in 2006 (N=2426), nine econometric regression models for count data were examined to identify the best-fitting one. We used model selection criteria; statistical tests; and goodness-of-fit for in-sample model selection. In addition, we conducted 10-fold cross-validation checks to examine reliability of in-sample model selection. Finally, we utilized marginal effects to identify the factors associated with the number of outpatient visits among Vietnamese older people based on the best-fitting model identified. Results We found strong evidence in favor of hurdle negative binomial model 2 (HNB2) for both in-sample selection and 10-fold cross-validation checks. The marginal effect results of the HNB2 showed that ethnicity, region, household size, health insurance, smoking status, non-communicable diseases, and disability were significantly associated with the number of outpatient visits. The predicted probabilities for each count event showed the distinct trends of healthcare utilization among specific groups: at low count events, women and people in the younger age group used more healthcare utilization than did men and their counterparts in older age groups, but a reversed trend was found at higher count events. Conclusions Data come in all shapes and sizes, this study highlights the importance of model specification checks and model selection criteria to avoid potential biased estimates as a result of model misspecifications. This study’s findings lay the groundwork for future research on the modeling of healthcare utilization in developing countries and those findings could be used to forecast on healthcare demand and making provisions for healthcare costs.
Ion channel profiling of the Lymnaea stagnalis ganglia via transcriptome analysis
Authors: Dong Nan , Bandura Julia , Zhang Zhaolei , Wang Yan , Labadie Karine , Noel Benjamin , Davison Angus , Koene Joris M , Sun Hong-Shuo , Coutellec Marie-Agnes , Feng Zhong-Ping 
Published: November 2020

Abstract
Background. The pond snail Lymnaea stagnalis (L. stagnalis) has been widely used as a model organism in neurobiology, ecotoxicology, and parasitology due to the relative simplicity of its central nervous system (CNS). However, its usefulness is restricted by a limited availability of transcriptome data. While sequence information for the L. stagnalis CNS transcripts has been obtained from EST library and a de novo RNA-seq assembly, the quality of these assemblies is limited by a combination of low coverage of EST libraries, the fragmented nature of de novo assemblies, and lack of reference genome. Results. In this study, taking advantage of the recent availability of a preliminary L. stagnalis genome, we generated an RNA-seq library from the adult L. stagnalis CNS, using a combination of genome-guided and de novo assembly programs to identify 17,832 protein-coding L. stagnalis transcripts. We combined our library with existing resources to produce a transcript set with greater sequence length, completeness, and diversity than previously available ones. Using our assembly and functional domain analysis, we profiled L. stagnalis CNS transcripts encoding ion channels and ionotropic receptors, which are key proteins for CNS function, and compared their sequences to other vertebrate and invertebrate model organisms. Interestingly, L. stagnalis transcripts encoding numerous putative Ca2+ channels showed the most sequence similarity to those of Mus musculus, Danio rerio, Xenopus tropicalis, Drosophila melanogaster, and Caenorhabditis elegans, suggesting that many calcium channel-related signaling pathways may be evolutionarily conserved. Conclusions. Our study provides the most thorough characterization to date of the L. stagnalis transcriptome and provides insights into differences between vertebrates and invertebrates in CNS transcript diversity, according to function and protein class. Furthermore, this study provides a complete characterization of the ion channels of Lymnaea stagnalis, opening new avenues for future research on fundamental neurobiological processes in this model system.