bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of Several Carbapenems Resistant and Virulence Genes in Classical and Hyper-virulent Strains of Klebsiella pneumoniae Isolated from Hospitalized Neonates and Adults in Khartoum
Authors: Albasha Aalaa Mahgoub , Osman Esraa Hassan , Alhalim Saga Abd , Alshaib Elianz , Al-Hassan Leena , Altayb Hisham N 
Published: May 2020

Abstract
Background
Carbapenems resistant hypervirulent strains of Klebsiella pneumoniae are one of the most critical organisms that cause fatal nosocomial infections. This study aimed to detect and characterize K. pneumoniae virulence genes (mrkD, entB, rmpA, K2, kfu, and magA) and carbapenem resistant (blaNDM, blaIMP, blaOXA−48, and blaKPC) genes
Methods
Sixty K. pneumoniae strains were isolated from urine, blood, wound swab, and sputum samples, in two age groups: neonates and adults. String test was used to detect hypervirulent strains. Susceptibility testing for a wide range of antibiotics was performed on all isolates. DNA was extracted by the guanidine chloride method, then multiplex PCR was used for the detection of carbapenem-resistance and virulence genes.
Results
Seventy percent of the isolates were resistant to ceftazidime and 8% to imipenem, 35% were multi-drug resistant, and 7% extensively drug-resistant, all neonatal blood isolates (n = 15) were resistant to ceftazidime. entB was the most predominant virulence gene (93.3%), followed by mrkD (78.3%), kfu (60%), K2 (51.7%), magA (18.3%) and rmpA (5%). blaOXA−48 was the most predominant carbapenem-resistant gene (68.3%), followed by blaNDM (10%), blaKPC (8.3%), and blaIMP (3.3%). Eight hyper-virulent strains were positive for blaOXA−48 and two for blaNDM genes. The study concluded that there is a high rate of carbapenems resistant genes in hyper-virulent strains of K. pneumoniae isolated from hospitalized patients.
Conclusion
The study reported for the first time in Sudan presence of carbapenems resistant genes in hyper-virulent strains of K. pneumoniae isolated from hospitalized patients. Presence of MDR and XDR strains of K. pneumoniae in neonatal ward in some Sudanese hospitals.
Adsorption of Lead(II), Manganese(II), and Copper(II) onto biochar in landfill leachate: implication of non-linear regression analysis
Authors: Zand Ali Daryabeigi , Abyaneh Maryam Rabiee 
Published: May 2020

Abstract
The feasibility of using wood-derived biochar (BC) to remove Pb, Mn, and Cu from landfill leachate was investigated and modeled in this study. The effect of contact time, biochar dosage and particle size on adsorption of the heavy metals onto BC was examined. BC was used in two form i.e. pulverized (PWB) and crushed (CWB) to evaluate the effect of BC particle size on adsorption characteristics. Biochar was produced under the pyrolytic temperature of 740 °C. The kinetics of Pb, Mn, and Cu adsorption onto PWB and CWB were assessed using the pseudo second-order and Elovich models, where both applied models could well describe the adsorption kinetics. Equilibrium adsorption capacity of the heavy metals onto BC in leachate system was evaluated using the Langmuir, non-linearized Freundlich, linearized Freundlich, and Temkin isotherms and found to have the following order for PWB: Non-linearized Freundlich>Temkin>Langmuir>Linearized Freundlich. The Langmuir and linearized Freundlich models could not adequately represent adsorption of the heavy metals onto biochar, especially for CWB. Using the non-linearized Freundlich isotherm significantly reduced adsorption prediction error. The adsorption affinity of PWB for Pb, Mn, and Cu was greater than CWB in all treatments. Wood-derived biochar is suggested to be used for the removal of heavy metals from landfill leachate as an economical adsorbent.
Asthma Control According to the Community Pharmacists: Evidence and Potential Implications from an Italian Cross-Sectional Study
Authors: Caminati Marco , Cegolon Luca , Bacchini Marco , Segala Nadia , Dama Annarita , Bovo Chiara , Olivieri Bianca , Furci Fabiana , Senna Gianenrico 
Published: May 2020

Abstract
Background. Asthma control and monitoring still represents a challenge worldwide. Although the international guidelines suggest the interplay with primary care as an effective strategy, the community pharmacies’are rarely involved in asthma management.The present cross-sectional study aimed at providing a picture of the relationship between asthma severity and control according to the community pharmacies’ perspective of the health district of Verona (North-Eastern Italy).Methods. A call for participation was launched through the Pharmacists’ Association of Verona.Patients referring to the participating pharmacies with an anti-asthmatic drug medical prescription and an asthma exemption code were asked to completethe Asthma Control Testand a brief questionnaire collecting information on their age, sex, smoking status, aerobic physical exercise and usual asthma therapy, which also defined the severity level of asthma.A multinomial logistic regression model was fitted to investigate the risk of uncontrolled as well as poorly controlled vs. controlled asthma (base). Results were expressed as relative risk ratios (RRR) with 95% confidence interval (95%CI).Results.57 community pharmacies accepted to participate and 584 asthmatic patients (54% females; mean-age: 51 ± 19 years) were recruited. According to the ACT score 50.5% patients hada controlled asthma, 22.3% a poorly controlled and 27.2% uncontrolled. A variable proportion patients with uncontrolled asthma was observed at every level of severity, although more frequently in mild persistent form of disease. Most patients (92%) reported regular compliance with therapy. At multinomial regression analysis, patients under regular asthma treatment course (RRR=0.33; 95%CI: 0.15; 0.77) were less likely to have an ACT<16 compared to those not taking medications regularly.Conclusions.Overall, our findings highlighted an unsatisfactory asthma control from the pharmacists’ perspective, independently of the asthma severity level. The relevance of community pharmacies as a first line interface suggest their involvement inan effective asthma management plan, from disease control and treatment compliance assessment to referral of asthmatic patients to medical consultancies.
MiR-381 enhances the sensitivity of non-small cell lung cancer to radiotherapy by targeting ROCK2 to regulate NF-κB signaling pathway
Authors: Huang Jiuning , Zeng Jing , Zhang Shuping , Cai Jundong , Wang Wulong , Zhao Kaikai , Wang Xuelei , Pang Qingsong , Wang Ping 
Published: May 2020

Abstract
BackgroundWe investigated the effect of miR-381 on the sensitivity of non-small cell lung cancer (NSCLC) to radiotherapy, and examined its possible mechanism.MethodsNSCLC A549 cells and miR-381 overexpression and gene silencing cell lines were treated with radiotherapy. The cell proliferation was tested by CCK-8 assay and colony formation. Flow cytometry and TUNEL were used to detect the cell apoptosis. The expression of nuclear factor kappa B (NF-κB) signaling pathway related proteins were detected by western blot. NF-κB signaling pathway activator and inhibitor cell lines were further constructed and the above experiments were repeated. Double luciferase assay was used to verify the target of miR-381. Furthermore, a nude mouse xenograft model was constructed and treated with radiotherapy. The tumor volume and tumor weight were measured. The expression of PCNA protein in tumor tissues was observed by immunohistochemistry. The apoptosis related proteins in tumor tissues were detected by western blot.ResultsThe mRNA expression of miR-381 was increased after radiotherapy treatment. Radiotherapy treatment also can inhibit the proliferation and promote apoptosis of A549 cells. Compared with radiotherapy group, cell proliferation was significantly decreased and apoptosis was significantly increased in miR-381 overexpression group (p < 0.05). Moreover, ROCK2 is a target of miR-381, and overexpression of miR-381 can down-regulate the expression of ROCK2 protein. In nude mice, miR-381 mimic interference can reduce cell tumorigenicity and proliferation, and increase the apoptosis. However, the indicators above were contrary in miR-381 silencing group. Verification experiments further verify that NF-κB signaling pathway activator can reverse the role of miR-381.ConclusionMiR-381 overexpression could enhance the sensitivity of NSCLC to radiotherapy by targeting ROCK2 to inhibit NF-κB signaling pathway.
Recombinant tandem epitope vaccination provides cross protection against Actinobacillus pleuropneumoniae challenge in mice
Authors: Xiao Jiameng , Liu Jianfang , Bao Chuntong , Zhu Rining , Gu Jingmin , Sun Changjiang , Feng Xin , Du Chongtao , Han Wenyu , Li Yang , Lei Liancheng 
Published: May 2020

Abstract
Actinobacillus pleuropneumoniae (A. pleuropneumoniae/APP) is the pathogen that causes porcine contagious pleuropneumonia. Actinobacillus pleuropneumoniae is divided into 18 serovars, and the cross protection efficacy of epitopes is debatable, which has resulted in the slow development of a vaccine. Consequently, epitope-based vaccines conferring Actinobacillus pleuropneumoniae cross protection have rarely been reported. In this study, B cell epitopes in the head domain of trimeric autotransporter adhesin were predicted, and 6 epitopes were selected. Then, the predicted epitopes (Ba1, Bb5, C1, PH1 and PH2) were connected by linkers to construct a recombinant tandem antigen (rta) gene. The RTA protein encoded by the recombinant rta gene was expressed, and finally the ICR mice were immunized with the RTA protein with or without inactivated Actinobacillus pleuropneumoniae (serovars 1 and 5b) and challenged with Actinobacillus pleuropneumoniae to evaluate the protective effect of the epitope-based vaccine and combined vaccine.The mice in the RTA-immunized group and RTA plus inactivated Actinobacillus pleuropneumoniae vaccine group had a significant improvement in clinical symptoms and a higher level of antibody in the serum than those in the control group. The RTA immune group had a 40% survival rate after Actinobacillus pleuropneumoniae infection, whereas the combination of RTA and inactivated Actinobacillus pleuropneumoniae produced very strong cross immune protection in mice, at least 50% (RTA IB1+ C5) and at most 100% (RTA IB5 + C1), whereas no cross immunoprotection was found in the solo Actinobacillus pleuropneumoniae immune group. Overall, the combination of the RTA protein and inactivated bacteria significantly enhanced the cross protection effects. This implies that RTA protein in combination with a suitable inactivated Actinobacillus pleuropneumoniae strain could be a candidate vaccine for porcine contagious pleuropneumonia.
Dysbiosis of urine microbiota in obstructive urinary retention patients revealed by next-generation sequencing
Authors: Jiang Shan , Lu Saisai , Chen Xiaomin , Li Fengxia , Zhu Chengwei , Zheng Yuancai , Xu Shihao , Wang Xiaobing 
Published: May 2020

Abstract
Background
Urinary retention (UR) is a common urinary system disease can be caused by urinary tract obstruction with numerous reasons, however, the role of urine microbes in these disorders is still poorly understood. The aim of this study was to identify the urine microbial features of two common types of obstructive UR, caused by urinary stones or urinary tract tumors, with comparison to healthy controls.
Methods
Urine samples were collected from a cohort of 32 individuals with stone UR, 25 subjects with tumor UR and 25 healthy controls. The urine microbiome of all samples was analyzed using high-throughput 16S rRNA (16S ribosomal RNA) gene sequencing.
Results
We observed dramatically increased urine microbial richness and diversity in both obstructive UR groups compared to healthy controls. Despite different origins of UR, bacteria such as Pseudomonas, Acinetobacter and Sphingomonas were enriched, while Lactobacillus, Streptococcus, Gardnerella, Prevotella and Atopobium were decreased in both UR groups in comparison with healthy controls, exhibited an approximate urine microbial community and functional characteristics of two types of obstructive UR. Furthermore, disease classifiers were constructed using specific enriched genera in UR, which can distinguish stone UR or tumor UR patients from healthy controls with an accuracy of 92.29% and 97.96%, respectively.
Conclusion
We presented comprehensive microbial landscapes of two common types of obstructive urinary retention and demonstrated that urine microbial features of these patients are significantly different from that of healthy people. The urine microbial signatures would shed light on the pathogenesis of these types of urinary retention and might be used as potential classification tools in the future.
Immunological and clinicopathological characteristics of C1RL in 2143 glioma patients
Authors: Wang Junyou , Tong Luqing , Lin Gaojun , Wang Hui , Yang Xuejun 
Published: May 2020

Abstract
Glioma is a deadly and immunosuppressive brain tumor. Complement C1r Subcomponent Like (C1RL), as a prognostic biomarker in several kinds of tumors, has attracted increasing attention from oncologists. However, the role of C1RL in glioma remains unclear.
Through 2143 glioma patients from 5 public datasets, the relationships between C1RL expression and clinicopathological characteristics were analyzed. Furthermore, the C1RL associated genes were screened and GO analysis was conducted to investigate their biological process enrichment. In addition, tumor purity, leukocytes infiltration and overall survival were calculated based on C1RL expression.
We found that C1RL expression was upregulated in glioblastoma (GBM), especially mesenchymal GBM and primary GBM. Increased C1RL accompanied IDH1 wt both in lower grade glioma (LGG) and GBM. C1RL associated genes were mainly enriched in biological processes which are related to immune response. C1RL expression was also correlated with less tumor purity and more M2 macrophage infiltration. Higher C1RL expression predicted unfavorable survival for patients with glioma and therapeutic resistance in GBM.
Our results implied that C1RL is involved in immunological activities and is an independent unfavorable prognostic biomarker for patients with glioma. C1RL is a potential immunotherapeutic target for glioma in future clinical practice.
Development and Validation of a Deep Learning Model for Preoperative Screening of Myasthenia Gravis in Patients with Thymoma based on CT Images
Authors: Zhu Ying , Liu Zhen-guo , Yang Lei , Wang Kefeng , Wang Ming-Hui , Yang Xiao-yu , Wu Xi , Tian Xi , Zhang Rong-Guo , Ma Jie-chao , Yuan Yu-Jie , Ke zunfu 
Published: May 2020

Abstract
Objectives: Thymoma-associated myasthenia gravis (TAMG) is the most common paraneoplastic syndromeof thymoma. The screening of TAMG before thymoma resection is required to avoid severe perioperative complications, especiallyrespiratory failure. Herein, we developed a 3D DenseNet deep learning (DL) model based on preoperative computed tomography (CT) to detect TAMGin thymoma patients.Methods:A large cohort of 230 thymoma patientswere enrolled. 182 thymoma patients (81 with TAMG, 101 without TAMG) were used for training and model building. 48 cases from another hospital were used for external validation. A 3D-DenseNet-DL model and five machine learning models with radiomics features were performed to detectTAMG in thymoma patients. A comprehensive analysis by integrating 3D-DenseNet-DL model and general CT image features,named 3D-DenseNet-DL-based multi-model, was also performed to establish a more effective prediction model.Results: By elaborately comparing the prediction efficacy,the 3D-DenseNet-DL effectively identified TAMG patients, with a mean area under ROC curve (AUC), accuracy, sensitivity and specificity of 0.734, 0.724, 0.787 and 0.672, respectively. The effectiveness of the 3D-DenseNet-DL-based multi-model was further improved as evidenced bythe following metrics: AUC 0.766, accuracy 0.790, sensitivity 0.739 and specificity 0.801. External verification results confirmed the feasibility of this DL-based multi-model with metrics: AUC 0.730, accuracy 0.732, sensitivity 0.700 and specificity 0.690,respectively.Conclusions: Our 3D-DenseNet-DL model can effectively detect TAMG in patients with thymoma based on preoperative CT images. This model may serve as a non-invasive screening method or as a supplement to the conventional diagnostic criteria for identifyingTAMG.Key points:Thymoma-associated myasthenia gravis (TAMG) is a common paraneoplastic syndrome.3D-DenseNet-DL model can effectively detect TAMG based on preoperative CT images.This model may serve as a supplement for identifying TAMG.
Development of an immune-related gene pairs signature for predicting clinical outcome in lung adenocarcinoma
Authors: Wu Chunlei , Hu Quanteng , Ma Dehua 
Published: May 2020

Abstract
Background Lung adenocarcinoma (LUAD) is the main pathological subtype of Non-small cell lung cancer. The aim of this study was to establish an immune-related gene pairs (IRGPs) signature for predicting the prognosis of LUAD patients.Methods We downloaded the gene expression profile and immune-related gene set from TCGA and ImmPort database, respectively, to establish IRGPs. Then, IRGPs subjected to univariate Cox regression analysis, LASSO regression analysis and multivariable Cox regression analysis to screen and develop a IRGPs signature. The receiver operating characteristic curve (ROC) was applied for evaluating the predicting accuracy of this signature by calculating the area under ROC (AUC) and data from GEO was used to validate this signature.Results A IRGPs signature with 8 IRGPs was constructed. The AUC for 1- and 3-year overall survival in TCGA set was 0.867 and 0.870, respectively. Similar result was observed in the AUC of GEO set and Total set (GEO set [1-year: 0.819; 3-years: 0.803]; Total set [1-year: 0.845; 3-years: 0.801]). Survival analysis of three sets demonstrated high-risk LUAD patients exhibited poorer prognosis. The multivariable Cox regression indicated that risk score was independent prognostic factors.Conclusions We developed a novel IRGPs signature for predicting prognosis of LUAD.
Exploring the Efficacy of Using Hypertonic Saline for Nebulizing Treatment in Children with Bronchiolitis: a Meta-Analysis of Randomized Controlled Trials
Authors: Hsieh Chia-Wen , Su Hui-Chuan , Chen Kee-Hsin , Chen Chiehfeng 
Published: May 2020

Abstract
Introduction: Acute bronchiolitis is the most common lower respiratory infection in children. It is particularly prone to dyspnea among children under two years old. Inhaled hypertonic saline (HS) has recently been shown to be a favorable therapy, because of its facility to draw fluid from the submucosa and adventitial spaces, decreasing airway edema. The aim of this systematic review and meta-analysis was to evaluate the efficacy and safety of HS in the implementation of vapor treatment among children with bronchiolitis.Methods: A systematic literature search was conducted using Cochrane Library, PubMed, EMBASE and Airiti Library (Chinese Database) for randomized controlled trials from inception to July 2019. We calculated pooled risk ratios (RR), mean difference (MD) and 95% CI using RevMan 5.3 for meta-analysis.Results: In total, 4186 children from 32 publications were included. Compared to the control group, the HS group exhibited significantly reducing the level of severity of respiratory distress, included studies used the Clinical Severity Score (95% CI −1.15, −0.27, I² = 73%) and Respiratory Distress Assessment Instrument (95% CI −0.95, −0.26, I²= 0%) for evaluation respectively. Further, the HS group decreased the length of hospital stay 0.54 days (95% CI −0.86, −0.32, I²= 81%). Conclusion: We conclude that nebulized with 3% saline solution is effective in decreasing the length of hospital stay and the severity of symptoms as compared with 0.9% saline solution among children with acute bronchiolitis. Further rigor randomize controlled trails with large sample size are needed.
Association between serum markers of the humoral immune system and inflammation in the Swedish AMORIS study
Authors: santaolalla aida , Sollie Sam , Rislan Ali , Josephs Debra H. , Hammar Niklas , Walldius Goran , Jungner Ingmar , Karagiannis Sophia N. , Hemelrijck Mieke Van 
Published: May 2020

Abstract
Background: Although the onset of inflammatory cascades may profoundly influence the nature of antibody responses, the interplay between inflammatory and humoral immune markers remains unclear. Thus, we explored the reciprocity between the humoral immune system and inflammation and assessed how external socio-demographic factors influence these interactions.Methods: From the AMORIS cohort, 5,513 individuals were identified with baseline measurements of serum humoral immune (immunoglobulin G, A & M) and inflammation (CRP, albumin, haptoglobin, white blood cells, iron & total iron-binding capacity) markers measured on the same day. Correlation analysis, principal component analysis and hierarchical clustering were used to evaluate biomarkers correlation, variation and associations. Multivariate analysis of variance was used to assess associations between biomarkers and educational level, socio-economic status, sex and age.Results: Frequently used serum markers for inflammation, CRP, haptoglobin and white blood cells, correlated together. Markers of the humoral immune system, immunoglobulin A and G, also correlated together. Hierarchical clustering and principal component analysis confirmed the interaction between these main biological responses, showing an acute response component (CRP, Haptoglobin, WBC, IgM) and adaptive response component (Albumin, Iron, TIBC, IgA, IgG). A socioeconomic gradient associated with worse health outcomes was observed, specifically low educational level, older age and male sex were associated with serum levels that indicated infection and inflammation.Conclusions: These findings indicate that serum markers of the humoral immune system and inflammation closely interact in response to infection or inflammation. Correlation and clustering analysis presented two main immune response components: an acute and an adaptive response, comprising markers of both biological pathways. Future studies should shift from single internal marker assessment to multiple humoral and inflammation serum markers combined, when assessing risk of clinical outcomes such as cancer.
METTL3-mediated m6A methylation negatively modulates autophagy to support blastocyst development
Authors: Cao Zubing , Zhang Ling , Hong Renyun , Wang Yiqing , Qi Xin , Ning Wei , Gao Di , Xu Tengteng , Ma Yangyang , Yu Tong , Li Yunsheng , Knott Jason G , Sathanawongs Anucha , Zhang Yunhai 
Published: May 2020

Abstract
Background: N6-methyladenosine (m6A) catalyzed by METTL3 regulates the maternal-to-zygotic transition in zebrafish and mice. However, the role and mechanism of METTL3-mediated m6A methylation in blastocyst development remains unclear. Results: We found that reduced m6A levels triggered by METTL3 knockdown caused embryonic arrest during morula-blastocyst transition and developmental defects in trophectoderm cells. Intriguingly, overexpression of METTL3 in early embryos resulted in increased m6A levels and these embryos phenocopied METTL3 knockdown embryos. Mechanistically, METTL3 knockdown or overexpression resulted in a significant increase or decrease in expression of ATG5 and LC3 (an autophagy marker) in blastocysts, respectively. m6A modification of ATG5 mRNA mainly occurs at 3’UTR, and METTL3 knockdown enhanced ATG5 mRNA stability, suggesting that METTL3 negatively regulated autophagy in an m6A dependent manner. Furthermore, single-cell analysis revealed that METTL3 knockdown only increased expression of LC3 and ATG5 in trophectoderm cells, indicating preferential inhibitory effects of METTL3 on autophagy activity in the trophectoderm lineage. Importantly, autophagy restoration by 3MA (an autophagy inhibitor) treatment partially rescued developmental defects of METTL3 knockdown blastocysts. Conclusions: Our results demonstrate that METTL3-mediated m6A methylation negatively modulates autophagy to support blastocyst development.