bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA methylation of individual repetitive elements in hepatitis C virus infection-induced hepatocellular carcinoma
Authors: Zheng Yinan , Hlady Ryan A. , Joyce Brian T. , Robertson Keith D. , He Chunyan , Nannini Drew R. , Kibbe Warren A. , Achenbach Chad J. , Murphy Robert L. , Roberts Lewis R. , Hou Lifang 
Published: October 2019

Abstract

Background
The two most common repetitive elements (REs) in humans, long interspersed nuclear element-1 (LINE-1) and Alu element (Alu), have been linked to various cancers. Hepatitis C virus (HCV) may cause hepatocellular carcinoma (HCC) by suppressing host defenses, through DNA methylation that controls the mobilization of REs. We aimed to investigate the role of RE methylation in HCV-induced HCC (HCV-HCC).

Results
We studied methylation of over 30,000 locus-specific REs across the genome in HCC, cirrhotic, and healthy liver tissues obtained by surgical resection. Relative to normal liver tissue, we observed the largest number of differentially methylated REs in HCV-HCC followed by alcohol-induced HCC (EtOH-HCC). After excluding EtOH-HCC-associated RE methylation (FDR < 0.001) and those unable to be validated in The Cancer Genome Atlas (TCGA), we identified 13 hypomethylated REs (11 LINE-1 and 2 Alu) and 2 hypermethylated REs (1 LINE-1 and 1 Alu) in HCV-HCC (FDR < 0.001). A majority of these REs were located in non-coding regions, preferentially enriched with chromatin repressive marks H3K27me3, and positively associated with gene expression (median correlation r = 0.32 across REs). We further constructed an HCV-HCC RE methylation score that distinguished HCV-HCC (lowest score), HCV-cirrhosis, and normal liver (highest score) in a dose-responsive manner (p for trend < 0.001). HCV-cirrhosis had a lower score than EtOH-cirrhosis (p = 0.038) and HCV-HCC had a lower score than EtOH-HCC in TCGA (p = 0.024).

Conclusions
Our findings indicate that HCV infection is associated with loss of DNA methylation in specific REs, which could implicate molecular mechanisms in liver cancer development. If our findings are validated in larger sample sizes, methylation of these REs may be useful as an early detection biomarker for HCV-HCC and/or a target for prevention of HCC in HCV-positive individuals.
Dynamic derangement in amino acid profile during and after a stroke-like episode in adult-onset mitochondrial disease: a case report
Authors: Fukuda Mai , Nagao Yoshiro 
Published: October 2019

Abstract

Background
Maternally inherited diabetes and deafness, and mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes are examples of mitochondrial diseases that are relatively common in the adult population. Mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes are assumed to be associated with decreases in arginine and citrulline. Biomarkers, such as growth differentiation factor-15, were developed to assist in the diagnosis of mitochondrial diseases.

Case presentation
A 55-year-old Japanese man, an insulin user, presented after a loss of consciousness. A laboratory test showed diabetic ketoacidosis. He and his mother had severe hearing difficulty. Bilateral lesions on magnetic resonance imaging, the presence of seizure, and an elevated ratio of lactate to pyruvate, altogether suggested a diagnosis of mitochondrial disease. Mitochondrial DNA in our patient’s peripheral blood was positive with a 3243A>G mutation, which is the most frequent cause of maternally inherited diabetes and deafness, and mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes. As a result, maternally inherited diabetes and deafness/mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes was diagnosed. We measured growth differentiation factor-15 and multiple amino acids in his blood, longitudinally during and after the stroke-like episode. Growth differentiation factor-15 was increased to an immeasurably high level on the day of the stroke-like episode. Although his diabetes improved with an increased dose of insulin, the growth differentiation factor-15 level gradually increased, suggesting that his mitochondrial insufficiency did not improve. Multiple amino acid species, including arginine, citrulline, and taurine, showed a decreased level on the day of the episode and a sharp increase the next day. In contrast, the level of aspartic acid increased to an extremely high level on the day of the episode, and decreased gradually thereafter.

Conclusions
Growth differentiation factor-15 can be used not only for the diagnosis of mitochondrial disease, but as an indicator of its acute exacerbation. A stroke-like episode of mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes reflects a drastic derangement of multiple amino acids. The involvement of aspartic acid in the episodes should be explored in future studies.
Multi-compositional MRI evaluation of repair cartilage in knee osteoarthritis with treatment of allogeneic human adipose-derived mesenchymal progenitor cells
Authors: Zhao Xinxin , Ruan Jingjing , Tang Hui , Li Jia , Shi Yingxuan , Li Meng , Li Suke , Xu Cuili , Lu Qing , Dai Chengxiang 
Published: October 2019

Abstract

Background
We used multimodal compositional magnetic resonance imaging (MRI) techniques, combined with clinical outcomes, to differentiate the alternations of composition in repair cartilage with allogeneic human adipose-derived mesenchymal progenitor cells (haMPCs) in knee osteoarthritis (KOA) patients.

Methods
Eighteen patients participated a phase I/IIa clinical trial. All patients were divided randomly into three groups with intra-articular injections of haMPCs: the low-dose (1.0 × 107 cells), mid-dose (2.0 × 107), and high-dose (5.0 × 107) groups with six patients each. Compositional MRI examinations and clinical evaluations were performed at different time points.

Results
Significant differences were observed in quantitative T1rho, T2, T2star, R2star, and ADC measurements in patients of three dose groups, suggesting a possible compositional changes of cartilage with the treatment of allogeneic haMPCs. Also significant reduction in WOMAC and SF-36 scores showed the symptoms might be alleviated to some extent with this new treatment. As regards sensibilities of multi-parametric mappings to detect compositional or structural changes of cartilage, T1rho mapping was most sensitive to differentiate difference between three dose groups.

Conclusions
These results showed that multi-compositional MRI sequences might be an effective tool to evaluate the promotion of the repair of cartilage with allogeneic haMPCs by providing information of compositional alterations of cartilage.

Trial registration
Clinicaltrials, NCT02641860. Registered 3 December 2015.
The dynamic properties of solutions for a nonlinear shallow water equation
Authors: Su Yeqin , Lai Shaoyong , Ming Sen 
Published: October 2019

Abstract
The local well-posedness for the Cauchy problem of a nonlinear shallow water equation is established. The wave-breaking mechanisms, global existence, and infinite propagation speed of solutions to the equation are derived under certain assumptions. In addition, the effects of coefficients λ, β, a, b, and index k in the equation are illustrated.
Infection control management and surveillance of carbapenem-resistant Gram-negative bacteria in hematopoietic stem cell recipients
Authors: Baier Claas , Beck Maleen , Panagiota Viktoria , Lueck Catherina , Kharazipour Daniel , Hintze Sophie Charlotte , Bollin Robin , Ebadi Ella , Ziesing Stefan , Eder Matthias , Bange Franz-Christoph , Beutel Gernot 
Published: October 2019

Abstract
Hematopoietic stem cell transplantation (HSCT) is a curative treatment option for selected diseases of the hematopoietic system. In the context of HSCT, bloodstream infections caused by Gram-negative bacteria (GNB) significantly contribute to morbidity and mortality. Antibiotic treatment of bloodstream infections with carbapenem-resistant (CR) GNB presents a particular challenge. As a part of our infection control management, the admission of a patient who was known to be colonized with a CR Acinetobacter baumannii triggered an active weekly screening of all patients to determine the prevalence and potential transmission of CR GNB and CR Acinetobacter baumannii in particular. Over a 3 month period a total of 71 patients were regularly screened for colonization with CR GNB. Including the index patient, a total of three patients showed CR GNB colonization representing a prevalence of 4.2%. Nosocomial transmission of CR Acinetobacter baumannii or other CR GNB was not observed. However, the index patient developed a subsequent bloodstream infection with the CR Acinetobacter baumannii, therefore empiric antibiotic therapy based on the known resistance profile was initiated. A weekly prevalence screening for CR GNB might be an effective monitoring tool for potential transmission, may enhance existing infection control management concepts and may support the decision making for empiric antibiotic therapy.
Linezolid use in German acute care hospitals: results from two consecutive national point prevalence surveys
Authors: Kramer Tobias Siegfried , Schwab Frank , Behnke Michael , Hansen Sonja , Gastmeier Petra , Aghdassi Seven Johannes Sam 
Published: October 2019

AbstractBackgroundLinezolid belongs to a reserve group of antibiotics. In recent years, reports on linezolid resistance in gram-positive cocci have become more frequent. Overuse of linezolid is a relevant factor for resistance development. The objective of this study was to describe current prescription practices of linezolid in German hospitals and identify targets for antimicrobial stewardship interventions.MethodsWe analyzed all linezolid prescriptions from the datasets of the consecutive national point prevalence surveys performed in German hospitals in 2011 and 2016. In both surveys, data on healthcare-associated infections and antimicrobial use were collected following the methodology of the European Centre for Disease Prevention and Control.ResultsOverall, the percentage of linezolid among all documented antimicrobials increased significantly from 2011 to 2016 (p < 0.01). In 2011, 0.3% (119 of 41,539) patients received linezolid, in 2016 this proportion was significantly higher (0.4%; 255 of 64,412 patients; p < 0.01). In 2016, intensive care units (ICUs) were the wards most frequently prescribing linezolid. The largest proportion of patients receiving linezolid were non-ICU patients. Roughly 38% of linezolid prescriptions were for treatment of skin/soft tissue and respiratory tract infections. In 2016, linezolid was administered parenterally in 70% (n = 179) of cases. Multivariable analysis showed that the ward specialty ICU posed an independent risk factor, while Northern and Southwestern regions in Germany were independent protective factors for a high rate of linezolid prescriptions.ConclusionsIn conclusion, we detected potentials for improving linezolid prescription practices in German hospitals. Given the emergence of linezolid resistance, optimization of linezolid use must be a target of future antimicrobial stewardship activities.
Patterns of self-medication with antibiotics in Maputo City: a qualitative study
Authors: Torres Neusa F. , Solomon Vernon P. , Middleton Lyn E. 
Published: October 2019

Abstract

Background
Mozambique classifies but does not yet enforce antibiotics as prescription-only-medicine (POM) allowing the public access to a variety of antibiotics that otherwise are provided on prescription. This contributes to the growing practice of self-medication with antibiotics (SMA) which systematically exposes individuals to the risk of developing antibiotic resistance, antibiotic side effects and increases the health service costs and morbidity. This study aimed at describing the patterns of SMA among Maputo city pharmacy customers.

Methods
A qualitative study conducted between October 2018 and March 2019 was developed with thirty-two pharmacy customers and seventeen pharmacists. Using convenience sampling, customers were recruited after buying antibiotics without prescription from nine private pharmacies. Of the thirty-two participants, twenty participated in in-depth interviews and twelve in two focus groups discussions (FGD) with six participants each. Purposive sampling and a snowball technique were used to recruit pharmacists. The transcripts were coded and analyzed using latent content analysis. Nvivo 11 was used to store and retrieve the data. The COREQ (Tong, 2007) checklist for interviews and FGD was performed.

Results
Customers admitted practices of SMA, pharmacists admitted dispensing a variety of antibiotics without prescription. Non-prescribed antibiotics (NPA) were obtained through five different patterns including; using the generic name, describing the physical appearance and using empty package, describing symptoms or health problem to pharmacists, using old prescriptions and sharing antibiotics with family, friends, and neighbors.

Conclusion
Different patterns of SMA are contributing to the indiscriminate use of antibiotics among customers. The NPA utilization is perceived as an expression of self-care where participants experience self-perceived symptoms and indulge in self-treatment as a method of caring for themselves. Moreover, antibiotics are mostly used to treat diseases that do not necessarily need antibiotics. Strong and effective public health education and promotion initiatives should be implemented to discourage inappropriate utilization of antibiotics and SMA practices.
Selection and dissemination of antimicrobial resistance in Agri-food production
Authors: Cheng Guyue , Ning Jianan , Ahmed Saeed , Huang Junhong , Ullah Rizwan , An Boyu , Hao Haihong , Dai Menghong , Huang Lingli , Wang Xu , Yuan Zonghui 
Published: October 2019

Abstract
Public unrest about the use of antimicrobial agents in farming practice is the leading cause of increasing and the emergences of Multi-drug Resistant Bacteria that have placed pressure on the agri-food industry to act. The usage of antimicrobials in food and agriculture have direct or indirect effects on the development of Antimicrobial resistance (AMR) by bacteria associated with animals and plants which may enter the food chain through consumption of meat, fish, vegetables or some other food sources. In addition to antimicrobials, recent reports have shown that AMR is associated with tolerance to heavy metals existing naturally or used in agri-food production. Besides, biocides including disinfectants, antiseptics and preservatives which are widely used in farms and slaughter houses may also contribute in the development of AMR. Though the direct transmission of AMR from food-animals and related environment to human is still vague and debatable, the risk should not be neglected. Therefore, combined global efforts are necessary for the proper use of antimicrobials, heavy metals and biocides in agri-food production to control the development of AMR. These collective measures will preserve the effectiveness of existing antimicrobials for future generations.
From fiction to science: clinical potentials and regulatory considerations of gene editing
Authors: Schacker Maria , Seimetz Diane 
Published: October 2019

AbstractGene editing technologies such as CRISPR/Cas9 have emerged as an attractive tool not only for scientific research but also for the development of medicinal products. Their ability to induce precise double strand breaks into DNA enables targeted modifications of the genome including selective knockout of genes, correction of mutations or precise insertion of new genetic material into specific loci. Gene editing‐based therapies hold a great potential for the treatment of numerous diseases and the first products are already being tested in clinical trials. The treatment indications include oncological malignancies, HIV, diseases of the hematopoietic system and metabolic disorders. This article reviews ongoing preclinical and clinical studies and discusses how gene editing technologies are altering the gene therapy landscape. In addition, it focusses on the regulatory challenges associated with such therapies and how they can be tackled during the drug development process.
Validation of the Recent Life Changes Questionnaire (RLCQ) for stress measurement among adults residing in urban communities in Pakistan
Authors: Artani Azmina , Kamal Ayeesha K. , Azam Syed Iqbal , Artani Moiz , Bhamani Shireen Shehzad , Saif Mehreen , Khan Fariha Afzal , Alam Nazir 
Published: October 2019

Abstract

Background
Recent Life Changes Questionnaire (RLCQ) developed by Richard Rahe has enabled quantification of stress by analyzing life events. The overall aim of the study was to create a reliable version of the Rahe’s RLCQ for measuring stress in individuals living in developing countries and assess its validity. This paper discusses criterion validation of the adapted RLCQ in urban communities in Pakistan.

Methods
This is a criterion validation study. Four urban communities of Karachi, Pakistan were selected for the study in which households were randomly chosen. Two data collectors were assigned to administer the adapted RLCQ to eligible participants after obtaining written informed consent. Following this interaction, two psychologists interviewed the same participants with a diagnostic gold standard of Mini International Neuropsychiatric Interview (MINI) which is utilized in usual practice within Pakistan to confirm the presence of stress related mental disorders such as Depression, Anxiety, Dysthymia, Suicide, Phobia, OCD, Panic Disorder, PTSD, Drug abuse and dependence, Alcohol abuse and dependence, Eating Disorders and Antisocial Personality Disorder to validate the accuracy of the adapted RLCQ. We generated the ROC curves for the adapted RLCQ with suggested cut-offs, and analyzed the sensitivity and specificity of the adapted RLCQ.

Results
The area under the receiver operating characteristic curve (ROC) of common mental disorders such as depression and anxiety was 0.64, where sensitivity was 66%, specificity was 56% and the corresponding cut off from the adapted RLCQ was 750. Individuals scoring ≥750 were classified as high stress and vice versa. In contrast, the area under the ROC curve for serious mental disorder and adverse outcomes such as suicide, bipolar and dysthymia was 0.75, where sensitivity was 72% and specificity was 60% at the cut off of 800 on the adapted RLCQ. Individuals scoring ≥800 were classified as high stress and vice versa. The rate of agreement between the two psychologists was 94.32% (Kappa = 0.84).

Conclusion
The adapted and validated RLCQ characterizes common mental disorders such as depression and anxiety with moderate accuracy and severe mental disorders such as suicide, bipolar and dysthymia with high accuracy.

Trial registration
Clinicaltrials.gov NCT02356263. Registered January 28, 2015. (Observational Study Only).
Radiogenomic analysis of vascular endothelial growth factor in patients with diffuse gliomas
Authors: Sun Zhiyan , Li Yiming , Wang Yinyan , Fan Xing , Xu Kaibin , Wang Kai , Li Shaowu , Zhang Zhong , Jiang Tao , Liu Xing 
Published: October 2019

Abstract

Objective
To predict vascular endothelial growth factor (VEGF) expression in patients with diffuse gliomas using radiomic analysis.

Materials and methods
Preoperative magnetic resonance images were retrospectively obtained from 239 patients with diffuse gliomas (World Health Organization grades II–IV). The patients were randomly assigned to a training group (n = 160) or a validation group (n = 79) at a 2:1 ratio. For each patient, a total of 431 radiomic features were extracted. The minimum redundancy maximum relevance (mRMR) algorithm was used for feature selection. A machine-learning model for predicting VEGF status was then developed using the selected features and a support vector machine classifier. The predictive performance of the model was evaluated in both groups using receiver operating characteristic curve analysis, and correlations between selected features were assessed.

Results
Nine radiomic features were selected to generate a VEGF-associated radiomic signature of diffuse gliomas based on the mRMR algorithm. This radiomic signature consisted of two first-order statistics or related wavelet features (Entropy and Minimum) and seven textural features or related wavelet features (including Cluster Tendency and Long Run Low Gray Level Emphasis). The predictive efficiencies measured by the area under the curve were 74.1% in the training group and 70.2% in the validation group. The overall correlations between the 9 radiomic features were low in both groups.

Conclusions
Radiomic analysis facilitated efficient prediction of VEGF status in diffuse gliomas, suggesting that using tumor-derived radiomic features for predicting genomic information is feasible.
Determinants of modern contraceptive use among postpartum women in two health facilities in urban Ghana: a cross-sectional study
Authors: Coomson Jonathan Ian , Manu Abubakar 
Published: October 2019

Abstract

Background
Postpartum contraception is important for spacing and limiting childbirth. Although the use of modern contraception has been shown to reduce maternal and child morbidities and mortalities, postpartum women have one of the highest unmet needs for family planning. Inter-birth intervals less than 24 months have adverse effects on both the mother and the child, yet very limited empirical evidence exist on contraceptive use among postpartum women in Ghana. This study sought to determine the prevalence and determinants of modern contraceptive use among postpartum women in the Tema Metropolis, Ghana.

Methods
A facility-based cross-sectional survey was conducted among 320 postpartum women with babies aged between three and 15 months. Participants were recruited from child welfare clinics in two government health facilities in the Tema metropolitan area using a simple random sampling technique. Data were analyzed using STATA version 15. Chi-square and multiple logistic regressions techniques were used to examine associations between postpartum contraceptive use and key independent variables. Statistical significance was set at p = 0.05. Adjusted odds ratios and their 95% confidence intervals were used to assess the strength of association.

Results
The prevalence rate of modern contraceptive use among postpartum women was 26.3%. Postpartum contraceptive use was significantly associated with past contraceptive use [AOR = 7.7 (95%CI: 3.4–17.5)]; return of menses [AOR = 4.3 (95%CI: 1.7–11.3)]; resumption of sexual activity [AOR = 4.7 (95%CI: 1.4–15.4)]; discussion of family planning with male partner [AOR = 3.1 (95%CI: 1.03–9.2)]; male partners’ approval of modern contraception [AOR = 18.1 (95%CI: 6.3–51.6)]; family planning counselling received during antenatal care [AOR = 3.5 (95%CI: 1.3–9.9)] and knowledge of at least one modern methods of contraception available at the health facility [AOR = 4.7 (95%CI: 1.9–11.5)].

Conclusions
Postpartum contraceptive uptake is low among women in the Tema area. Factors that influence modern contraceptive uptake among postpartum women include past modern contraceptive use, resumption of sexual activity and menstruation, male partner involvement in contraception, family planning counselling during antenatal care and knowledge of the modern methods of contraception available at the health facility. Strengthening family planning education and counselling during antenatal care and using a multi-prong strategy to engage men as partners in family planning will improve postpartum contraceptive uptake.