bluuebunny/crossref_metadata_2025_split huggingface dataset:
lncRNA‐CIR regulates cell apoptosis of chondrocytes in osteoarthritis
Authors: Lu Zekai , Luo Min , Huang Yongpan 
Published: November 2018

AbstractBackground and ObjectivesOsteoarthritis (OA) is a complex chronic degenerative joint disease involving oxidative stress, inflammation, and apoptosis of chondrocytes. As decoys of micro RNAs, long non‐coding RNAs (lncRNAs) play important roles in various biological processes. This study was designed to investigate the interactions between lncRNA‐CIR, chondrocyte apoptosis, and the molecular mechanisms underlying OA.MethodsPrimary cultured chondrocytes were stressed using H2O2, IL‐1β, or TNF‐ɑ to simulate conditions found in OA. Quantitative real‐time PCR was performed to detect miR‐130a, lncRNA‐CIR, and Bim mRNA expression levels. Western blot analysis was used to detect Bim protein expression levels. Reactive oxygen species (ROS) levels were assayed by detecting the fluorescent signal of 2′,7′‐dichlorodihydrofluorescein diacetate (DCFH‐DA). Cell apoptosis was measured with combined staining of PI and DAPI. lncRNA‐CIR knockdown and miR‐130a over‐expression or inhibition were performed using small interfering RNAs, and miR‐130 mimics or inhibitors, respectively.ResultslncRNA‐CIR is significantly upregulated in OA patients, accompanied by downregulation of miR‐130a and upregulation of Bim. Bio‐informatics analysis predicted miR‐130a as a target of both lncRNA‐CIR and Bim. While lncRNA‐CIR knockdown significantly increased the expression of Bim, miR‐130a significantly suppressed Bim expression, with accompanying increases of ROS level, inflammatory mediator release, cell apoptosis, and relative luciferase activity.ConclusionsThe present findings demonstrated that the lncRNA‐CIR/miR‐130a/Bim axis is involved in oxidative stress‐related apoptosis of chondrocytes in OA.
Optimization of prostate cancer cell detection using multiplex tyramide signal amplification
Authors: Roy Sounak , Axelrod Haley D. , Valkenburg Kenneth C. , Amend Sarah , Pienta Kenneth J. 
Published: November 2018

AbstractApproximately 29 000 men die of prostate cancer (PCa) each year in the United States, and 90% to 100% of them are due to incurable bone metastasis. It is difficult to determine (1) when PCa disseminates in the natural history of the disease; (2) where cancer cell disseminates before becoming overt metastatic lesions; and (3) which tumors are aggressive and which are indolent. Tumor tissue and liquid (blood and bone marrow) biopsies provide important information to answer these questions, but significant limitations exist for immunostaining strategies that assess protein expression in these tissues. Classic immunohistochemistry (IHC) assays can typically assess expression of one or two proteins per tissue section. We have developed a novel immunofluorescence staining protocol to detect a panel of seven proteins on PCa tissue from primary tumor biopsies and metastatic lesion autopsy tissue, as well as cancer cells from liquid biopsies. We used a tyramide‐based system to amplify the true signal and optimized the protocol to reduce background signal, thereby boosting the signal‐to‐noise ratio. Any protein‐specific antibody in this protocol can be exchanged for a different validated antibody. This protocol therefore, represents a highly informative and flexible assay that can be used to provide important information about cancer tissue for the purpose of improving detection, diagnosis, and treatment.
Chronic obstructive pulmonary disease: A crosstalk on nucleotide compositional dynamics and codon usage patterns of the genes involved in disease
Authors: Nath Durbba , Deka Himangshu , Uddin Arif , Chakraborty Supriyo 
Published: November 2018

AbstractChronic obstructive pulmonary disease (COPD), a lung disease, affects a large number of people worldwide, leading to death. Here, we analyzed the compositional features and trends of codon usage of the genes influencing COPD to understand molecular biology, genetics, and evolutionary relationships of these genes as no work was reported yet. Coding sequences of COPD genes were found to be rich in guanine‐cytosine (GC) content. A high value (34‐60) of the effective number of codons of the genes indicated low codon usage bias (CUB). Correspondence analysis suggested that the COPD genes were distinct in their codon usage patterns. Relative synonymous codon usage values of codons differed between the more preferred codons and the less‐preferred ones. Correlation analysis between overall nucleotides and those at third codon position revealed that mutation pressure might influence the CUB of the genes. The high correlation between GC12 and GC3 signified that directional mutation pressure might have operated at all the three codon positions in COPD genes.
Diagnosing malignant pleural effusion using clinical and analytical parameters
Authors: Pan Yong , Bai Wenjing , Chen Jiangnan , Mao Yijian , Qian Xiaohong , Xu Ke , Tang Shaohua , Zhang Junwu , Chen Chong , Chen Jingyi , Hu Xingzhong 
Published: November 2018

BackgroundMalignant pleural effusion (MPE) is common and diagnosis is often problematic. A cancer ratio (serum lactate dehydrogenases: pleural adenosine deaminase ratio) has been proposed for diagnosing MPE. However, the usefulness of this “cancer ratio” and the clinical‐radiological criteria for diagnosing MPE has not been clearly determined to date. The aim of this study was to assess the performance of those parameters in the diagnosis of MPE.MethodsWe analyzed 240 patients including 120 with MPE and 120 with non‐MPE (93 tuberculous and 27 parapneumonic). Patients were divided into two groups: MPE and non‐MPE (eg, tuberculous and parapneumonic). We constructed two predictive models to assess the probability of MPE: (a) clinical‐radiological data only and (b) a combination of clinical‐radiological data, the cancer ratio, and the carcinoembryonic antigen (CEA). The performances of the predictive models were assessed using receiver operating characteristic (ROC) curves and by examining the calibration.ResultsThe area under the ROC curves for model 1 and model 2 were excellent, 0.936 and 0.998, respectively. The overall diagnostic accuracies for model 1 and model 2 were 87.5% and 98.8%, respectively.ConclusionThe results confirm that both models achieved a high diagnostic accuracy for MPE; however, model 2 was superior with the addition of its simplicity of use in daily practice. This model should be applied to determine which patients with a pleural effusion of unknown origin would not benefit from further invasive procedures.
A novel stopgain mutation c.G992A (p.W331X) in TACR3 gene was identified in nonobstructive azoospermia by targeted next‐generation sequencing
Authors: Geng Dongfeng , Yang Xiao , Wang Ruixue , Deng Shu , Li Leilei , Hu Xiaonan , Jiang Yuting , Liu Ruizhi 
Published: November 2018

BackgroundNonobstructive azoospermia (NOA) is one of the most severe forms of male infertility because of impaired spermatogenesis with the absence of spermatozoa in the ejaculate. The causes of this disease can be partly attributed to genetic factors. Some common structural variants and single nucleotide polymorphisms (SNPs) were reported to be associated with NOA. However, the underlying etiology and genetic mechanism(s) remain largely unclear. The aim of this study was to investigate the associated mutations of spermatogenic genes in Chinese infertile men with NOA.MethodsThe entire coding region of 25 genes associated with spermatogenesis was sequenced from 200 infertile men with NOA. Screening was carried out using the targeted exome sequencing to identify genetic variations and SNPs of the entire coding region of these genes.ResultsAfter the targeted exome sequencing data were filtered through several currently existing variation databases, a series of variations were found. In this paper, we report one novel stopgain variation c.G992A (p.W331X) in the exon 4 of TACR3 gene. The variant was heterozygous and categorized as pathogenic.ConclusionIn conclusion, our study revealed a novel stopgain mutation c.G992A (p.W331X) in TACR3 which expanded the mutation spectrum of TACR3 in Chinese NOA infertile men and advanced our understanding of the genetic susceptibility to NOA.
Analysis of estrogen and progesterone receptor gene polymorphisms in leiomyoma
Authors: Toprak Muhammed , Ates Omer , Ozsoy Asker Zeki , Bozkurt Nihan , Sezer Sondas Saime , Cakmak Bülent , Yılmaz Dogru Hatice , Delibas İlhan Bahri , Demirturk Fazlı 
Published: November 2018

BackgroundLeiomyoma, one of the most common benign tumors, causes morbidity during the reproductive years in women. The molecular pathogenesis of the disease is not clear. Leiomyomas are hormone‐sensitive tumors affecting around 20%‐25% of women. Gene polymorphism studies could be important and explaining in the evaluation of multifactorial diseases such as leiomyoma. Polymorphisms involving genes responsible for the synthesis and signalization of steroid hormones could be used as genetic markers for hormone‐related conditions. The purpose of this study was to analyze the effect of ERα‐351 XbaI A/G, ERα‐397 PvuII T/C, and progesterone receptor (PGR) PROGINS polymorphisms on the development of leiomyomas.Material and MethodsIn this study, 213 samples (103 leiomyoma patients and 110 healthy controls) participated. The ERα‐351 XbaI A/G and ERα‐397 PvuII T/C gene polymorphisms were analyzed using PCR‐RFLP method. PGR PROGINS polymorphism was analyzed by PCR method with specific primers.ResultsThe genotype distribution and allele frequency of the ERα‐351 XbaI A/G, ERα‐397 PvuII T/C, and PGR PROGINS polymorphisms were not statistically different between leiomyoma patient and control groups (p > 0.05).ConclusionThis study reflects that ERα and PGR PROGINS polymorphisms may not be one of the many genetic factors for leiomyoma susceptibility.
Correlation between hematological parameters and ancylostomiasis: A retrospective study
Authors: Hu Zuojian , Chen Huaping , Huang Li , Chen Siyuan , Huang Zhili , Qin Shanzi , Zhong Jianing , Qin Xue , Li Shan 
Published: November 2018

ObjectiveOur aim intended to determine the relationship between hematological parameters (neutrophil‐to‐lymphocyte ratio [NLR], platelet‐to‐lymphocyte ratio [PLR], and eosinophil‐to‐lymphocyte ratio [ELR]) and ancylostomiasis.MethodsThere were 140 patients with ancylostomiasis and 159 healthy controls enrolled in this study. All data were collected from electronic medical records of the First Affiliated Hospital of Guangxi Medical University.ResultsThe levels of NLR, PLR, and ELR in ancylostomiasis patients were significantly higher than those in the healthy controls (all P = 0.000). A receiver operating characteristic curve was generated to assess the diagnostic efficacy of these three hematological parameters. ELR (AUC = 0.850; sensitivity = 75.00%; specificity = 86.80%) showed the superior AUC than those of NLR (AUC = 0.718; sensitivity = 53.57%; specificity = 88.68%) and PLR (AUC = 0.806; sensitivity = 68.57%; specificity = 86.79%), respectively. A multivariate regression model using the two selected indices (RBC and ELR) was established with the model's sensitivity and specificity reached 82.86% and 96.23%, respectively. In the ancylostomiasis patient group, NLR (r = −0.452, P = 0.000) and PLR (r = −0.357, P = 0.000) were reversely associated with eosinophils.ConclusionThe pretreatment levels of the three hematological parameters (NLR, PLR, and ELR) may serve as valuable indicators for distinguishing patients with ancylostomiasis from healthy controls. NLR and PLR are negatively associated with the previous indicator, eosinophils.
Prospective evaluation of a screening algorithm for carbapenemase‐producing Enterobacteriaceae
Authors: Choquet Morgane , Guiheneuf Raphaël , Castelain Sandrine , Pluquet Emilie , Decroix Véronique 
Published: November 2018

AbstractBackgroundCarbapenemase‐producing Enterobacteriaceae (CPE) have become a major public health issue. The objective of the present study was to prospectively assess the analytical performance of a CPE detection algorithm based on phenotypic tests (the screening test) and MALDI‐ToF hydrolysis (the confirmatory test).MethodsOver a 6‐month period and based on a disk diffusion method, 74 carbapenem‐resistant strains were included in this study.ResultsOf the collected isolates, 54 turned out to be negative after phenotypic tests. Hence, 20 strains (including all of the CPEs) were checked with the confirmation test. Seven strains were positive. After molecular biology assessments in a reference center, three of the seven were found to be false positives. The algorithm had a negative predictive value and a sensitivity of 100%, a specificity of 77%, and a positive predictive value of 20%.ConclusionThe algorithm has a 24‐hour turnaround time and helps to avoid using expensive molecular biology tests; we consider that it can be used on a routine basis for screening clinical strains.
Prevalence and distribution of human papillomavirus genotypes among women with high‐grade squamous intraepithelial lesion and invasive cervical cancer in Ganzhou, China
Authors: Liao Linhong , Cheng Hui , Zeng Fansheng , Zhou Weijie , Ding Yanqing 
Published: November 2018

BackgroundHuman papillomavirus (HPV) infection can lead to the development of cervical cancer. This study assessed the genotype distribution of HPV of high‐grade squamous intraepithelial lesion (HSIL) and invasive cervical cancer (ICC) in Ganzhou population.MethodsA total of 935 females who got HPV testing from January 2016 to July 2018 in the maternal and child health hospital of Ganzhou were enrolled in the study, including 806 HSIL and 129 ICC. HPV detection and genotyping were tested by HPV Geno‐Array test kit.ResultsThe overall HPV‐positive rate was 74.0% in Ganzhou. Among the HSIL and ICC patients, the positive rates of HPV detection were 75.6% and 64.3%. Among the HSIL individuals, the most prevalent hr‐HPV genotype was HPV 16. And the 4 common subtypes in decreasing order were HPV 52, 58, 33, and 18. Of the ICC patients, the most frequently hr‐HPV subtype was HPV 16 followed by 18, 52, 58, and 59. Among the squamous cell carcinoma (SCC) patients, for hr‐HPV genotypes, HPV 16, 18, 52, 58, and 59 were five most common subtypes. In patients with adenocarcinoma (ADC), the most common hr‐HPV genotype was HPV 18, followed by HPV 16, 52, 56, 68, 73. And, we found U‐shaped and S‐shaped curves in the HPV distribution of different age groups.ConclusionThe prevalence and distribution of HPV genotypes in Ganzhou differed from other regions of China and Western countries. These results can serve as valuable reference for HPV vaccination programs for Ganzhou women.
Low serum adiponectin is a predictor of progressing to nonalcoholic fatty liver disease
Authors: Zhang Hongmei , Niu Yixin , Gu Hongxia , Lu Shuai , Zhang Weiwei , Li Xiaoyong , Yang Zhen , Qin Li , Su Qing 
Published: November 2018

BackgroundThe association between adiponectin and nonalcoholic fatty liver disease (NAFLD) has been studied before, but most of the studies are cross‐sectional and cannot prove a causal link.ObjectiveTo prospectively investigate the relationship between serum adiponectin levels and the incidence of NAFLD in 3 years.Subjects and methods.A total of 1325 subjects aged 40 to 70 from the Chongming District of Shanghai, China, were included. All of them did not have fatty liver according to the liver ultrasound examination at entry; alcohol abuse and hepatitis were also excluded. Serum adiponectin levels and other indices were measured at baseline. After 3 years of follow‐up, hepatic ultrasound examination was performed on each participant again to detect fatty liver.ResultsThe serum adiponectin levels at entry were significantly lower in subjects who developed NAFLD compared with those who did not develop NAFLD after 3 years (1.75 ± 0.89 ug/mL vs 2.37 ± 1.01 ug/mL, P < 0.001). After multiple adjustments, the highest odds ratios for NAFLD were in the second adiponectin quartile, the adjusted ORs were 1.89 (95% confidence interval [CI] 1.25 to 2.86) compared with those in the highest quartile. Multivariate logistic regression analysis showing variables at entry independently associated with NAFLD after 3 years was adiponectin (P < 0.01), sex (P < 0.01), BMI (P < 0.001), insulin (P < 0.001), HOMA‐IR (P < 0.01), GGT (P = 0.001), TG (P < 0.001), and WBC (P < 0.001).ConclusionsLower serum adiponectin level is a predictor of NAFLD among middle‐aged and elderly subjects.
Prediction of Abnormal Bone Density and Osteoporosis From Lumbar Spine MR Using Modified Dixon Quant in 257 Subjects With Quantitative Computed Tomography as Reference
Authors: Zhao Yinxia , Huang Mingqian , Ding Jie , Zhang Xintao , Spuhler Karl , Hu Shaoyong , LI Mianwen , Fan Wei , Chen Lin , Zhang Xiaodong , Li Shaolin , Zhou Quan , Huang Chuan 
Published: November 2018

BackgroundBone marrow fat increases when bone mass decreases, which could be attributed to the fact that adipogenesis competes with osteogenesis. Bone marrow fat has the potential to predict abnormal bone density and osteoporosis.PurposeTo investigate the predictive value of using vertebral bone marrow fat fraction(BMFF) obtained from modified Dixon(mDixon) Quant in the determination of abnormal bone density and osteoporosis.Study typeProspective.Population257 subjects (age: 20–79 years old; BMI: 16.6–32.9 kg/m2;181 females,76 males) without known spinal tumor, history of trauma, dysplasia, spinal surgery or hormone therapy.Field strength/sequence3.0T/mDixon.AssessmentBMFF was measured at the L1, L2 and L3 vertebral body on fat fraction maps of the lumbar spine. Bone mineral density (BMD) was obtained using quantitative computed tomography, which served as the reference standard.Statistical testsThe BMFF between the three groups (normal bone density, osteopenia and osteoporosis) was tested using one‐way analysis of variance in SPSS. The correlation and partial correlation of BMFF and BMD were analyzed before and after controlling for age, sex and BMI. Logistic regression analysis using independent training and validation data was conducted to evaluate the performance of predicting abnormal BMD or osteoporosis using BMFF.ResultsThere was a significant difference in vertebral BMFF between the three groups (P < 0.001). Moderate inverse correlation was found between vertebral BMFF and BMD after controlling age, sex and BMI (r = ‐0.529; P < 0.001). The mean area under the curve, sensitivity, specificity and negative predictive value (NPV) for predicting abnormal bone density were 0.940, 0.877, 0.896, and 0.890, respectively. The corresponding results for predicting subjects with osteoporosis were 0.896, 0.848, 0.853, and 0.969, respectively.Data conclusionmDixon Quant is a fast, simple, noninvasive and nonionizing method to access vertebral BMFF and has a high predictive power for identifying abnormal bone density and osteoporosis.Level of Evidence: 1Technical Efficacy: Stage 2J. Magn. Reson. Imaging 2019;49:390–399.
View‐Sharing Artifact Reduction With Retrospective Compressed Sensing Reconstruction in the Context of Contrast‐Enhanced Liver MRI for Hepatocellular Carcinoma (HCC) Screening
Authors: Shaikh Jamil , Stoddard Paul B. , Levine Evan G. , Roh Albert T. , Saranathan Manojkumar , Chang Stephanie T. , Muelly Michael C. , Hargreaves Brian A. , Vasanawala Shreyas S. , Loening Andreas M. 
Published: November 2018

BackgroundView‐sharing (VS) increases spatiotemporal resolution in dynamic contrast‐enhanced (DCE) MRI by sharing high‐frequency k‐space data across temporal phases. This temporal sharing results in respiratory motion within any phase to propagate artifacts across all shared phases. Compressed sensing (CS) eliminates the need for VS by recovering missing k‐space data from pseudorandom undersampling, reducing temporal blurring while maintaining spatial resolution.PurposeTo evaluate a CS reconstruction algorithm on undersampled DCE‐MRI data for image quality and hepatocellular carcinoma (HCC) detection.Study TypeRetrospective.SubjectsFifty consecutive patients undergoing MRI for HCC screening (29 males, 21 females, 52–72 years).Field Strength/Sequence3.0T MRI. Multiphase 3D‐SPGR T1‐weighted sequence undersampled in arterial phases with a complementary Poisson disc sampling pattern reconstructed with VS and CS algorithms.AssessmentVS and CS reconstructions evaluated by blinded assessments of image quality and anatomic delineation on Likert scales (1–4 and 1–5, respectively), and HCC detection by OPTN/UNOS criteria including a diagnostic confidence score (1–5). Blinded side‐by‐side reconstruction comparisons for lesion depiction and overall series preference (–3–3).Statistical AnalysisTwo‐tailed Wilcoxon signed rank tests for paired nonparametric analyses with Bonferroni‐Holm multiple‐comparison corrections. McNemar's test for differences in lesion detection frequency and transplantation eligibility.ResultsCS compared with VS demonstrated significantly improved contrast (mean 3.6 vs. 2.9, P < 0.0001) and less motion artifact (mean 3.6 vs. 3.2, P = 0.006). CS compared with VS demonstrated significantly improved delineations of liver margin (mean 4.5 vs. 3.8, P = 0.0002), portal veins (mean 4.5 vs. 3.7, P < 0.0001), and hepatic veins (mean 4.6 vs. 3.5, P < 0.0001), but significantly decreased delineation of hepatic arteries (mean 3.2 vs. 3.7, P = 0.004). No significant differences were seen in the other assessments.Data ConclusionApplying a CS reconstruction to data acquired for a VS reconstruction significantly reduces motion artifacts in a clinical DCE protocol for HCC screening.Level of Evidence: 3Technical Efficacy: Stage 2J. Magn. Reson. Imaging 2019;49:984–993.
General anesthesia / sedation requirement influences the way MRI brain scans are ordered in a tertiary pediatric hospital
Authors: Sum Min Yi , Low Kathy , Tang Phua Hwee 
Published: November 2018

BackgroundMRI guidelines have been created to help clinicians order scans appropriately. Some scans in children are carried out under general anesthesia (GA) / sedation.PurposeTo evaluate if the requirement for GA/sedation influences the way MRI brain scans are ordered.Study TypeRetrospective.PopulationChildren with MRI brain scans in 2015 to 2017.Field Strength3T, 1.5T.AssessmentInstitutional Review Board approval for waiver of consent was obtained. Clinical MRI brain reports for children were classified into whether they conformed to the American College of Radiology (ACR) 2013 guidelines by research assistants under supervision of a pediatric radiologist. Scans were sorted into those with normal brains or abnormality.Statistical TestThe statistical difference between groups was assessed using t‐test for continuous variables and chi‐square test for categorical variables with IBM SPSS 19.ResultsOf the total 1893 MRI scans, 431 were performed under GA and six under sedation. Of the 431 cases performed under GA/sedation, 383 (87.6%) were ordered according to guidelines. Of the 1456 cases that did not require GA/sedation, 710 (48.8%) conformed to guidelines. The percentage of scans ordered according to guidelines was 38.8% higher in those who had scans performed under GA/sedation (P < 0.001). MRI scans were normal in 635 (58.0%) out of the 1093 cases ordered according to guidelines and normal in 638 (79.8%) out of the 800 cases that did not follow guidelines. Scans not ordered according to guidelines had higher proportion of normal scans (21.8%) compared with those ordered according to guidelines (P < 0.001).Data ConclusionHigher adherence to imaging guidelines is seen in younger patients who were exposed to the risks of GA/sedation for the MRI. Scans not adhering to guidelines had a higher percentage of having no brain abnormality detected.Level of Evidence: 3Technical Efficacy: Stage 6J. Magn. Reson. Imaging 2019;49:e250–e255.