bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeted Exome Sequencing Identified a Novel USH2A Mutation in a Chinese Usher Syndrome Family
Authors: Xing Dongjun , Zhou Huaiyu , Yu Rongguo , Wang Linni , Hu Liying , Li Zhiqing , Li Xiaorong 
Published: March 2020

Abstract
Background To identify the gene mutation in a Chinese family with Usher syndrome type 2 and describe the clinical features. Methods A 23-year-old man complain of 10-year nyctalopia and a 3-year decline in visual acuity in both eyes accompanied by congenital dysaudia. To clarify the diagnosis, the clinical symptoms of the patient were observed and analysed in combination with comprehensive ophthalmologic examinations as well as genetic analysis(Targeted exome sequencing, TES). Results Typical clinical presentation of Usher syndrome on fundus features was found, which included a wax yellow-like disc, bone-spicule formations, and retinal vessel stenosis. Optical coherence tomography(OCT) and optical coherence tomography angiography (OCTA) showed loss of the ellipsoid zone and a reduction in paracaval vessel density in both eyes. Genetic analysis identified the presence of novel homozygote of c.8483_8486del (p.S2828fs) in USH2A, a gene responsible for Usher syndrome type 2 (OMIM:276901). This novel mutation in USH2A led to premature translation termination, resulting in the deletion of 19 fibronectin type 3 domains(FN3), which plays an important role in protein binding. Based on the clinical manifestations and genetic result, the patient was diagnosed with Usher syndrome type 2. Conclusions We found a novel mutation of c.8483_8486del in USH2A gene through TES techniques for 381 inherited retinal disease (IRD) related genes. The results of this study broaden the spectrum of mutations in Usher syndrome type 2 and suggest that the combination of TES molecular diagnosis and clinical information can help USH patients obtain a better diagnoses.
Universal risk assessment upon hospital admission for screening of carriage with multidrug-resistant microorganisms (MDRO) in a Dutch tertiary care centre (2016 – 2019)
Authors: Hout Denise van , Bruijning-Verhagen Patricia , Blok Hetty , Troelstra Annet , Bonten Marc 
Published: March 2020

Abstract
Background In Dutch hospitals a 6-point questionnaire is mandatory for risk-assessment to identify carriers of multidrug-resistant organisms (MDRO) at the time of hospitalization. Presence of one or more risk factors is followed by microbiological culturing and pre-emptive isolation. We evaluated the test characteristics of this screening tool in identifying new MDRO carriers. MethodsA cross-sectional study using routinely collected healthcare data was performed in a Dutch tertiary hospital between 1 January 2015 and 1 August 2019 including all admissions with an MDRO risk assessment performed on the day of admission. MDRO risk-assessment included: (1) known MDRO carriage, (2) previous hospitalization in another Dutch hospital during a known outbreak, (3) previous hospitalization in a foreign hospital, (4) living in an asylum centre, (5) professional exposure to livestock farming and (6) household membership of a methicillin-resistant Staphylococcus aureus (MRSA) carrier. Sensitivity of the risk assessment was estimated by comparing observed prevalence of newly detected MDRO carriage to expected prevalence of carriage in the Dutch population upon hospital admission. Results 144,051 hospital admissions of 84,485 unique patients were included. In total, 4,480 (3.1%) admissions had a positive MDRO risk-assessment (i.e. ≥1 risk factors present). In 1,516 (34%) admissions microbiological screening was performed, of which 341 (23%) yielded MDRO. 81 patients were categorized as new MDRO carriers, as identified through MDRO risk-assessment, reflecting 0.06% (95% CI: 0.04%–0.07%) of all admissions and 1.8% (95% CI: 1.4%–2.2%) of those with positive risk assessment. MDRO included ESBL-producing and/or multidrug-resistant Enterobacterales (n=52, 64%), MRSA (n=26, 32%), carbapenem-resistant Enterobacterales (CRE) (n=2, 3%) and VRE (n=1, 1%). The numbers of “MDRO risk-assessments needed to perform” and individual “MDRO risk-assessment questions needed to ask” to detect one new MDRO carrier upon admission were 1,778 and 10,420, respectively. Estimated sensitivities of the risk-assessment for detecting MDRO carriage were <1%, for ESBL-E and VRE, <2% for CRE and 18% for MRSA. Conclusions The number of risk-assessments needed to perform to detect one new MDRO carrier upon hospital admission was high, and the vast majority of carriers most likely remained undetected. The current MDRO risk assessment upon admission strategy needs thorough reconsideration.
Prognostic model based on the Geriatric Nutritional Risk Index and sarcopenia in patients with diffuse large B-cell lymphoma
Authors: Go Se-Il , Kim Hoon-Gu , Kang Myoung Hee , Park Sungwoo , Lee Gyeong-Won 
Published: March 2020

Abstract
Background Systemic inflammation and cachexia are associated with adverse clinical outcomes in diffuse large B-cell lymphoma (DLBCL). The Geriatric Nutritional Risk Index (GNRI) is one of the main parameters used to assess these conditions, but its efficacy in DLBCL is inconclusive. Methods We retrospectively reviewed 228 DLBCL patients who were treated with R-CHOP immunochemotherapy (rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone). The patients were stratified according to GNRI score (> 98, 92 to 98, 82 to < 92, and < 82) as defined in previous studies. Additionally, the extent of sarcopenia was categorized as sarcopenia-both, sarcopenia-L3/PM alone, and non-sarcopenia-both according to skeletal muscle index. Results Survival curves plotted against a combination of GNRI and sarcopenia scores revealed two clear groups as follows: high cachexia risk (HCR) group (GNRI < 82, sarcopenia-both, or GNRI 82-92 with sarcopenia-L3/PM alone) and low cachexia risk (LCR) group (others). The HCR group had a lower complete response rate (46.5% vs. 86.6%) and higher frequency of treatment-related mortality (19.7% vs. 3.8%) and early treatment discontinuation (43.7% vs. 8.3%) compared with the LCR group. The median progression-free survival (PFS) (not reached vs. 10.3 months, p < 0.001) and overall survival (OS) (not reached vs. 12.9 months, p < 0.001) were much shorter in the HCR group than in the LCR group. On multivariable analyses, the HCR group was shown to be an independent negative prognostic factor for PFS and OS after adjusting the National Comprehensive Cancer Network-International Prognostic Index (NCCN-IPI). Conclusions A combined model of GNRI and sarcopenia may provide prognostic information independently of the NCCN-IPI in DLBCL.
Identification of a four-gene panel predicting overall survival for lung adenocarcinoma
Authors: Chunyu Li , Qizhong Long , Danni Zhang , Jun Li , Xianming Zhang 
Published: March 2020

Abstract
Object Lung cancer is the most frequently diagnosed carcinoma and the leading cause of cancer-related mortality. Although molecular targeted therapy and immunotherapy have made great progress, the overall survival (OS) is still poor due to a lack of accurate and available prognostic biomarkers. Therefore, in this study we aimed to establish a multiple-gene panel predicting OS for lung adenocarcinoma. Methods We obtained the mRNA expression and clinical data of lung adenocarcinoma (LUAD) from TCGA database for further integrated bioinformatic analysis. Lasso regression and Cox regression were performed to establish a prognosis model based on a multi-gene panel. Nomogram was built based on the model. The receiver operating characteristic (ROC) curve and the Kaplan–Meier curve were used to assess the predicted capacity of the model. The prognosis value of the multi-gene panel was further validated using a dataset from GEO. Gene set enrichment analysis (GSEA) was performed to explore potential biological mechanisms of a novel prognostic gene signature. Results A four-gene panel (including DKK1, GNG7, LDHA, MELTF) was established as a prognostic indicator for OS of LUAD. The ROC curve revealed good predicted performance in both test cohort (AUC = 0.740) and validation cohort (AUC = 0.752). Each patient was calculated a risk score according to the model based on the four-gene panel. The results showed that the risk score was an independent prognostic factor, and the high-risk group had a worse OS compared with the low-risk group. The nomogram based on this model shows better prediction performance. GNG7 was decreased in LUAD and its mRNA expression was negatively correlated with the DNA methylation level. GSEA demonstrated the main enrichment pathways of GNG7 were cell cycle, RNA degradation, DNA replication, et al. Conclusion Our study proposed a novel four-gene panel to predict the OS of LUAD, which may contribute to predicting prognosis accurately and making the clinical decisions of individual therapy for LUAD patients. GNG7 might act a crucial role in genesis and progression of LUAD.
Feasibility of Multi-Parametric Magnetic Resonance Imaging Combined with Machine Learning in the Assessment of Necrosis of Osteosarcoma after Neoadjuvant Chemotherapy: A Preliminary Study
Authors: Huang Bingsheng , Wang Jifei , Sun Meili , Chen Xin , Xu Danyang , Li Zi-Ping , Ma Jinting , Feng Shi-Ting , Gao Zhenhua 
Published: March 2020

Abstract
Background Response evaluation of neoadjuvant chemotherapy (NACT) in patients with osteosarcoma is significant for the termination of ineffective treatment, the development of postoperative chemotherapy regimens, and the prediction of prognosis. However, histological response and tumour necrosis rate can currently be evaluated only in resected specimens after NACT. A preoperatively accurate, noninvasive, and reproducible method of response assessment to NACT is required. In this study, the value of multi-parametric magnetic resonance imaging (MRI) combined with machine learning for assessment of tumour necrosis after NACT for osteosarcoma was investigated. Methods Twelve patients with primary osteosarcoma of limbs underwent NACT and received MRI examination before surgery. Postoperative tumour specimens were made corresponding to the transverse image of MRI. One hundred and two tissue samples were obtained and pathologically divided into tumour survival areas (non-cartilaginous and cartilaginous tumour viable areas) and tumour-nonviable areas (non-cartilaginous tumour necrosis areas, post-necrotic tumour collagen areas, and tumour necrotic cystic/haemorrhagic and secondary aneurismal bone cyst areas). The MRI parameters, including standardised apparent diffusion coefficient (ADC) values, signal intensity values of T2-weighted imaging (T2WI) and subtract-enhanced T1-weighted imaging (ST1WI) were used to train machine learning models based on the random forest algorithm. Three classification tasks of distinguishing tumour survival, non-cartilaginous tumour survival, and cartilaginous tumour survival from tumour nonviable were evaluated by five-fold cross-validation. Results For distinguishing non-cartilaginous tumour survival from tumour nonviable, the classifier constructed with ADC achieved an AUC of 0.93, while the classifier with multi-parametric MRI improved to 0.97 ( P =0.0933). For distinguishing tumour survival from tumour nonviable, the classifier with ADC achieved an AUC of 0.83, while the classifier with multi-parametric MRI improved to 0.90 ( P <0.05). For distinguishing cartilaginous tumour survival from tumour nonviable, the classifier with ADC achieved an AUC of 0.61, while the classifier with multi-parametric MRI parameters improved to 0.81( P <0.05). Conclusions The combination of multi-parametric MRI and machine learning significantly improved the discriminating ability of viable cartilaginous tumour components, which can provide an objective and accurate basis for NACT response evaluation in osteosarcoma.
Reactive breastfeeding support at an Australian Breastfeeding Association drop-in service
Authors: Burns Elaine , Duursma Louise , Triandafilidis Zoi 
Published: March 2020

Abstract
Background In Australia, during the early establishment phase of breastfeeding, women can access telephone peer support counselling provided by the Australian Breastfeeding Association (ABA) however options for face-to-face peer support are limited. The known factors which improve ongoing and exclusive breastfeeding include face-to-face support, peer and/or professional support, and trained personnel. This study aimed to examine women’s experiences of accessing one breastfeeding drop-in peer support service provided by trained peer support volunteer counsellors from the ABA.Methods Women who accessed the service were invited to participate in an anonymous online survey which collected both quantitative and qualitative data. Participants were asked about their experiences of breastfeeding support, as well as their experiences of the drop-in service. In total, 53 women completed the online survey, and subsequent analysis generated descriptive statistics and qualitative themes.Findings Responses to the survey revealed that women attended the drop-in lounge with infants ranging in age from less than 1 week through to 12 months of age. Most women reported attending with infants aged 0-8 weeks of age 72% (n37). The predominant presenting problems identified were sore/damaged nipples, difficulties with infant latching to the breast, or concerns about using nipple shields. Analysis of the open text qualitative responses revealed one overarching theme ‘Support to continue breastfeeding’ and four subthemes: ‘feeling listened to and not judged’; ‘emotional support and confidence building’; ‘the importance of face-to-face, practical support'; and ‘the need for ongoing, free access’.Discussion In this study many women were seeking support for ongoing breastfeeding difficulties. Some were referred to health professional’s for investigation of restricted tongue movement. Health professionals who had limited breastfeeding knowledge and skills were identified as most unhelpful in providing support with ongoing breastfeeding difficulties. Women valued having access to trained peer counsellors, who had the capacity to provide non-judgemental, face-to-face support; who could sit through a feed; in a space that was ‘safe’; and who could enhance a woman’s confidence with breastfeeding over the course of her full breastfeeding journey.Conclusion Women described the importance of access to a reactive drop-in service which was dedicated to breastfeeding support and which was available in response to need.
Determinants of Mother to Child Transmission of HIV In Public Hospitals of West Shewa Zone, Oromiya Region: mixed method study.
Authors: Banja Fufa Hunduma , Gebrehanna Ewnat 
Published: March 2020

Abstract
Background: Mother-to-child transmission of HIV (MTCT) is when Human Immune deficiency Virus (HIV) of positive mother passes the virus to her baby. Without intervention transmission rate of HIV ranges from 15% to 45%, which can be reduced to below 5% with effective intervention. In Ethiopia, final mother-to-child transmission rate was 15% in 2016 which is much higher than target of the country to reduce transmission to lower than 5% by 2020. Aim of the study is to identify determinants of transmission of HIV from mother to child in West Shoa zone of Oromiya Region which has total population more than 2.1 million.Methods: Mixed methods: unmatched case-control study among children tested HIV positive and negatives at the end of PMTC follow up; N=96(24 cases, 72 controls) and one-on-one questioner for mothers of positive infant conducted during June to August 2019; focusing on PCR done during the last two years (June 2017 to July 2019), in public hospitals. Variables of interest were collected using structured and semi-structured questioner and data abstraction forms from mothers of exposed infants, medical records of mothers and children.Result: Majority among cases(70.8%) were not included in to option B+ program. Home delivery increases 6 times chance of HIV, AOR = 6.0; CI (1.5–29.2), none inclusion in to option B+ increase 18 chance of HIV transmission, AOR = 18.0; CI (5.0–68.1). Partner noninvolvement to HIV care increases chance of transmission by 7.3 times, AOR=7.3; CI(1.1–37.4). Mother-to- mother support program decrease chance of transmission by 86.5% with AOR = 0.13; CI (0.11–0.39). Poor ANC knowledge and practices among rural residents and unstable marriage in urban residents contributed to unaware MTCT of HIV.Conclusion: ART clinics should focus on and strengthen mother-to-mother support program, should create space for partner involvement to HIV care and provide training for Health Extension Workers(HEW). Health education and awareness creation should be implemented by HEW to improve ANC practice, reduce home delivery and increase voluntary counseling and testing among residents.
Genome-wide analysis of the WRKY gene family in the cucumber genome and transcriptome‑wide identification of WRKY transcription factors that respond to biotic and abiotic stresses
Authors: Chen Chunhua , Chen Xueqian , Han Jing , Lu Wenli , Ren Zhonghai 
Published: March 2020

Abstract
Background: Cucumber ( Cucumis sativus L.) is an economically important vegetable crop species. However, it is susceptible to various abiotic and biotic stresses. WRKY transcription factors play important roles in plant growth and development, particularly in the plant response to biotic and abiotic stresses. However, little is known about the expression pattern of WRKY genes under different stresses in cucumber. Results: In the present study, an analysis of the new assembly of the cucumber genome (v3.0) allowed the identification of 61 cucumber WRKY genes. Phylogenetic and synteny analyses were performed using related species to investigate the evolution of the cucumber WRKY genes. The 61 CsWRKYs were classified into three main groups, within which the gene structure and motif compositions were conserved. Tissue expression profiles of the WRKY genes demonstrated that 24 CsWRKY genes showed constitutive expression (FPKM > 1 in all samples), and some WRKY genes showed organ-specific expression, suggesting that these WRKYs might be important for plant growth and organ development in cucumber. Importantly, analysis of the CsWRKY gene expression patterns revealed that 7 CsWRKY genes strongly responded to both salt and heat stresses, 12 genes were observed to be expressed in response to infection from downy mildew and powdery mildew, and three CsWRKY genes simultaneously responded to all treatments analysed. Some CsWRKY genes were observed to be induced/repressed at different times after abiotic or biotic stress treatment, demonstrating that cucumber WRKY genes might play different roles during different stress responses and that their expression patterns vary in response to stresses. Conclusions: Sixty-one WRKY genes were identified in cucumber, and insight into their classification, evolution, and expression patterns was gained in this study. Responses to different abiotic and biotic stresses in cucumber were also investigated. Our results provide a better understanding of the function of Cs WRKY genes in improving abiotic and biotic stress resistance in cucumber.
Perioperative Hypoalbuminemia is a Risk Factor for Wound Complications Following Posterior Lumbar Interbody Fusion
Authors: He Zhongyuan , Zhou Kai , Zhong Weiyang , Tang Ke , Quan Zhengxue , Liu Shaoyu , Su Bao 
Published: March 2020

Abstract
Abstract
Background: Although serum albumin levels are increasingly used as an indicator of nutritional status in the clinic, the relationship between perioperative hypoalbuminemia and wound complications after posterior lumbar interbody fusion in the treatment of lumbar degenerative disease remains ambiguous. The aim of this study was to evaluate perioperative serum albumin in relation to postoperative wound complications after posterior lumbar interbody fusion in the treatment of single-segment lumbar degenerative disease.
Methods: We reviewed patients who underwent single-segment posterior lumbar interbody fusion surgery from December 2014 to April 2017 in the Department of Orthopedics at the First Affiliated Hospital of Chongqing Medical University. Perioperative (preoperative and early postoperative) serum albumin levels were assessed in all patients and were used to quantify nutritional status. We divided the patients into a surgical wound dehiscence ( SWD ) group and a normal wound healing group, and into an surgical site infection(SSI)group and a non-SSI group. To evaluate the relationship between perioperative serum albumin level and postoperative wound complications, we conducted univariate and multiple logistic regression analyses.
Results: A total of 554 patients were enrolled in the study.The univariate and multiple logistic regression analysis of these differences showed that preoperative serum albumin <3.5 g/dl and postoperative serum albumin:<3.0 g/dl were significantly related to SWD (P<0.05). There were also significant differences between the surgical site infection (SSI) groups in terms of preoperative serum albumin <3.5 g/dl(P=0.001), postoperative serum albumin <3.5 g/dl (P<0.023) and <3.0 g/dl(P<0.001).Additionally, the increased hospitalization costs and length of hospitalization were statistically significant for patients with perioperative hypoproteinemia.
Conclusions: For patients who underwent single-segment posterior lumbar interbody fusion surgery, we need to pay more attention to steroid use,perioperative hypoalbuminemia, which are more likely to be associated with increased wound complications, hospitalization costs and length of hospitalization after surgery. Adequate assessment and management of these risk factors will help reduce wound complications and hospital stays for surgical patients and will save medical costs.
Keywords: hypoalbuminemia,malnutrition,risk factors,single-segment lumbar fusion,postoperative incision complications,retrospective studies.
Profiles of autophagy-related genes in esophageal adenocarcinoma
Authors: Zhu Lei , Dong Lin , Yang Fugui , Li Qinchuan 
Published: March 2020

Abstract
Background: Several studies have demonstrated autophagy was involved in the process of esophageal adenocarcinoma (EAC). The aim of this study was to explore autophagy-related genes (ARGs) correlated with overall survival (OS) in EAC patients. Methods: Expressions of ARGs in EAC and normal samples were downloaded from TCGA database. GO and KEGG enrichment analyses were used to investigate the ARGs bioinformatics functions. Univariate and multivariate cox regressions were performed to identify prognostic ARGs and the independent risk factors. ROC curve was established to evaluate the feasibility to predict the prognosis. Finally, the correlations between ARGs and clinical features were further explored. Results: Thirty significantly different ARGs were selected from EAC and normal tissues. Functional enrichments showed these ARGs were mainly related apoptosis. Multivariate cox regression analyses demonstrated eight ARGs were significantly associated with OS. Among these eight genes, BECN1 (HR=0.321, P=0.046), DAPK1 (HR=0.636, P=0.025) and CAPN1 (HR=0.395, P=0.004) played protective roles in survival. Gender (HR=0.225, P=0.032), stage (HR=5.841, P=0.008) and risk score (HR=1.131, P＜0.001) were independent prognostic risk factors. ROC curves showed better efficacy to predict survival using the risk score. Additionally, we found BECN1, DAPK1, VAMP7 and SIRT1 genes were correlated significantly with survival status, gender, primary tumor and tumor stage (all P ＜0.05). Conclusion: Our findings suggested that autophagy was involved in the process of EAC. Several ARGs probably could serve as diagnostic and prognostic biomarkers and may help facilitate therapeutic targets in EAC patients.