bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic Characterization of A Multidrug-resistant Citrobacter freundii Strain ZT01-0079 Co-Producing blaNDM-1&nbsp;and&nbsp;blaSHV-12&nbsp;using MiSeq and MinION
Authors: Zhang Tingyan , Lin Yanfeng , Li Zhonghong , Liu Xiong , Li Jinhui , Li Lizhong , Wang Kaiying , Liu Zhongdong , Lu Lanfen , Li Peng , Wang Hongyan 
Published: October 2020

Abstract
Background: The emergence of multi-drug resistant Citrobacter freundii poses daunting challenges to the treatment of clinical infections. The purpose of this study was to characterize the genome of a C. freundii strain with an IncX3 plasmid encoding both the blaNDM-1 and blaSHV-12 genes.Methods: Strain ZT01-0079 was isolated from a clinical urine sample. The Vitek2 system was used for identification and antimicrobial susceptibility testing. The presence of blaNDM-1 was detected by PCR and sequencing. Conjugation experiments and Southern blotting were performed to determine the transferability of the blaNDM-1- carrying plasmid. Nanopore and Illumina sequencing were performed to better understand the genomic characteristics of the strain.Results: Strain ZT01-0079 was identified as C. freundii, and the coexistence of blaNDM-1 and multiple drug resistance genes was confirmed. Electrophoresis and Southern blotting showed that blaNDM-1 was located on a ~53kb IncX3 plasmid. The NDM-1-encoding plasmid was successfully transferred at a frequency of 1.68×10−3. Both blaNDM-1 and blaSHV-12 were located on the self-transferable IncX3 plasmid.Conclusion: The rapid spread of the IncX3 plasmid highlights the importance of continuous monitoring of the prevalence of NDM-1-encoding Enterobacteriaceae. Mutations of existing carbapenem resistance genes will bring formidable challenges to clinical treatment.
Dyslipidemia in Type 2 Diabetes Mellitus With Poor Glycemic Control: Prevalence, Associated Factors, and Relationship Between HbA1c and Lipid Profile.
Authors: liu lin , Xu Huiwen , Qiu Shuang , Yuan Xiaodan , Zhu Pinting , Zou Yan 
Published: October 2020

Abstract
BackgroundCcompared with HbA1c<7% ,T2DM patients with HbA1c≥7% had significantly higher levels of lipid profile, however, it is unknown whether there was a linear and significant increase levels of lipid profile associated with HbA1c value of ≥7%. This study identified the lipid profile across a full range of poor glycemic control and the association between lipid profiles with different specific HbA1c cutoffs.MethodsA total of 1183 type 2 diabetes patients with poor glycemic control (HbA1c>7%) selected through convenience sampling in three hospitals of Jiangsu province were surveyed. Dyslipidemia was defined according to criteria of the Third Report of the National Cholesterol Education Program Adult Treatment Panel III (NCEP ATP III). ResultsThe prevalence of dyslipidemia was 55.2 % overall. Of 1183 subjects, 13.0% had high TC, 33.1% had low HDL-C, 9.9% had high LDL-C, and 28.4% had high TG concentrations. There was an increase in frequency of dyslipidemia in patients with different cutoff values of HbA1c (P<0.05).The prevalence of high TC was closely related with different cutoff values of HbA1c (adjusted OR =1.77, 2.56 3.82, respectively). Patients with HbA1c values 9%≤HbA1c<11% and HbA1c≥13% had significantly higher prevalence of dyslipidemia compared with the patients who had 7≤HbA1c<9%.ConclusionDiabetic patients with 9%≤HbA1c<11% and HbA1c≥13% tend to have moderate and severe dyslipidemia respectively and suggest the importance of glycemic control in normalizing dyslipidemia.
Integrative Analysis of Multi-omics Data Improves Model Predictions: An Application to Lung Cancer
Authors: Ponzi Erica , Thoresen Magne , Nøst Therese Haugdahl , Møllersen Kajsa 
Published: October 2020

Abstract
Background: Cancer genomic studies often include data collected from several omics platforms. Each omics data source contributes to the understanding of the underlying biological process via source speciﬁc (”individual”) patterns of variability. At the same time, statistical associations and potential interactions among the diﬀerent data sources can reveal signals from common biological processes that might not be identiﬁed by single source analyses. These common patterns of variability are referred to as ”shared” or ”joint”. To capture both contributions of variance, integrative dimension reduction techniques are needed. Integrated PCA is a model based generalization of principal components analysis that separates shared and source speciﬁc variance by iteratively estimating covariance structures from a matrix normal distribution. Angle based JIVE is a matrix factorization method that decomposes joint and individual variation by permutation of row subspaces. We apply these techniques to identify joint and individual contributions of DNA methylation, miRNA and mRNA expression collected from blood samples in a lung cancer case control study nested within the Norwegian Woman and Cancer (NOWAC) cohort study.Results: In this work, we show how an integrative analysis that preserves both components of variation is more appropriate than analyses considering uniquely individual or joint components. Our results show how both joint and individual components contribute to a better quality of model predictions, and facilitate the interpretation of the underlying biological processes.Conclusions: When compared to a non integrative analysis of the three omics sources, integrative models that simultaneously include joint and individual components result in better prediction of cancer status and metastatic cancer at diagnosis.
Putative Digenic GJBI2/MYO7A Inheritance of Hearing Loss Detected in a Patient with 48, XXYY Klinefelter Syndrome
Authors: Qin Tian-tian , Zhang Qin , Hu Wen-mu , Janjua Muhammad Usman , Long Qin , Jin Ping 
Published: October 2020

Abstract
Background: 48, XXYY Klinefelter syndrome is a rare sex chromosome abnormality. Nonsyndromic hearing loss (NSHL) is the most frequent hereditary type of hearing impairment. There has been no report of NSHL combined with 48XXYY. The purpose of this study was to explore the underlying genetic cause in a three-generation family affected by NSHL. The proband had concomitant NSHL and 48, XXYY syndrome. The whole-exome sequencing was performed in the proband. The candidate pathogenic variants identified by whole-exome sequencing were then confirmed by Sanger sequencing and segregation analysis.Results: The proband was identified to be compound heterozygous for c.109G>A (p.V37I) variant in the GJB2 gene and additional heterozygous for the c.1039C>A (p.L347I) variants in the MYO7A gene. His mother had normal hearing and did not have any form of variant. His father and uncle, both had NSHL, were digenic compound heterozygote for the GJB2 p.V37I and MYO7A p.L347I variants, thus suggesting a possible GJB2/MYO7A digenic inheritance of NSHL in this family consist with the clinical phenotype.Conclusions: Our findings reported a putative GJB2/MYO7A digenic inheritance form of hearing loss, which expands the mutation spectrum of NSHL. This is also the first report of concomitant NSHL and 48, XXYY syndrome.
Proteomic Analysis of Grain Protein in the Winter Wheat Jimai44 and Jimai229 Based on Strong Gluten Characteristics
Authors: Mao FengXin , Han Ran , Han Ran , Cheng Dungong , Cheng Dungong , Li Haosheng , Li Haosheng , Liu Jianjun , Liu Jianjun , Cao Xinyou , Cao Xinyou , Song Jianmin , Song Jianmin , Liu Cheng , Liu Cheng , Guo Jun , Guo Jun , Li Faji , Li Faji , Zhai Shengnan , Zhai Shengnan , Zi Yan , Zi Yan , Wang Xiaolu , Wang Xiaolu , Zhao Zhendong , Zhao Zhendong , Liu Aifeng 
Published: October 2020

Abstract
Background：To determine the grain proteome of the strong gluten wheat, TMT technology was used to analyze proteomic differences between the winter wheat varieties Jimai 44 and the strong gluten Jimai 229. Results：Comparisons were also made with the winter wheat Jimai 22 as a control. It was found that there were 120 differentially expressed proteins between Jimai 44 and Jimai 22, while 173 between Jimai 229 and Jimai 22. Among these, 27 proteins were up-regulated and 23 down-regulated in jimai 44 and in jimai 229. Conclusions：GO analysis and KEGG pathway analysis showed that the differentially expressed proteins were mainly enriched in cell functions relating to nutrient reservoir activity, metabolic processes, protein processing in endoplasmic reticulum, phenylpropane biosynthesis and nitrogen metabolism. Amongst the screened proteins, many differences were related to storage proteins. This study provides an important basis for further exploring the key factors of quality improvement and genetic variation of gluten protein expression.
The Impact of COVID-19 on Sexual and Reproductive Health: A Systematic Review Protocol
Authors: Alizadeh Shiva , Ozgoli Giti 
Published: October 2020

Abstract
Background: COVID-19 affects the sexual health and fertility directly (by eliminating the distance between individuals and saliva exchange and also affecting the reproductive system) or indirectly (refusing the sexual intercourse and reducing fertility) and has consequences for couples and society. The present review study will be conducted to investigate the consequences of COVID-19 on sexual and reproductive health.Methods: The study will investigate the articles published from the onset of the disease in the world until July 30, 2020. To this end, all articles will be extracted and those with the inclusion criteria will be selected by searching on valid scientific databases, including PubMed, Scopus, Web of Science, ProQuest, SID, and Magiran and using keywords relating to the research purpose. Systematic review articles, letters to the editor-in-chief, abstracts, and clinical trials will be deleted. Articles will be separately evaluated by two researchers. The STROBE checklist will be used to check the quality of the articles.Discussion: The research results will be sent to journals for reviewing systematic articles and will be presented in PROSPERO. Also, this protocol is registered in PROSPERO with number CRD42020212621.The present systematic review will examine the effects of COVID-19 on sexual and reproductive health in women and men. The research results will be a guide for health planners to help reduce fertility and sexual problems during this period of COVID-19 by providing necessary programs in this regard.Systematic review registration: PROSPERO CRD42020212621
The Effects of Resistant Starch Consumption in Adult Patients with Chronic Kidney Disease: A Systematic Review Protocol
Authors: Kingra Kulwant , Mollard Rebecca , Curtis Sarah , Shamloo Maryam , Askin Nicole , Tangri Navdeep , MacKay Dylan 
Published: October 2020

Abstract
Background: Dietary modifications represent an important intervention to reduce the risk of chronic disease. Appropriate dietary changes can be simple to implement and are usually suggested as first line recommendations for many types of chronic disease management including diseases like hypertension and diabetes. Resistant starch is a non-digestible carbohydrate which passes through untouched to the colon where it becomes a digestible substrate for beneficial colonic bacteria. The normal gut flora becomes damaged in patients with chronic kidney disease with an additional buildup of uremic toxins and resulting intra-renal inflammation. Resistant starch supplementation has been studied for its effects on reducing harmful metabolite buildup through a restoration of normal gut flora. The following systematic review aims to compile the evidence of resistant starch use in adult patients with chronic kidney disease to answer whether or not the dietary intervention can reduce the progression of renal disease. Methods: We will perform a literature search with a knowledge synthesis librarian including the following databases: MEDLINE, Cochrane Central, Embase, CINAHL, and Web of Science. Collected data will be extracted and organized in MS Excel 2019. The extraction of the data will include study details, study population details, intervention details, and outcome details.Discussion: Results from this systematic review may help to determine a simple and effective method for prolonging the need for renal replacement therapy through resistant starch supplementation. Lack of evidence may highlight the need for additional trials or new interventions. PROSPERO ID: Currently being assessed, ID: 203138.
The Effects of Lithium on Inflammation Profiles and Nf-κB Nuclear Translocation in Raw 264.7 Macrophages Exposed to Rift Valley Fever Virus
Authors: Makola Raymond Tshepiso , Kgaladi Joe , More Garland Kgosi , Vuren Petrus Jansen van , Paweska Janusz Tadeusz , Matsebatlela Thabe Moses 
Published: October 2020

Abstract
IntroductionRift Valley fever virus is a mosquito-transmitted zoonotic viral infection that results in Rift Valley fever disease. RVFV and other viruses have developed mechanism to circumvent the immune recognition in an attempt to advance their viral progeny. The RVFV S segment encodes a non-structural protein (NSs) known to be the main virulence factor that aid in immune suppression and viral replication. Thus, this study is aimed at investigating the inflammatory effects of lithium using macrophages as innate immune model.MethodsThe supernatant from RVFV-infected Raw 264.7 cells and treated with lithium, was examined with Elisa assay kit to measure production levels of the cytokines and chemokines. The H2DCF-DA and DAF-2 DA oxidant florigenic assays were used to determine the levels of ROS and RNS by measuring the fluorescence intensity shown by the cells post RVFV-infection and lithium treatment. While on the other hand Western blotting assay was used to measure expression levels of the inflammatory proteins and immunocytochemistry measured the cellular location of the NF-κB.ResultsLithium have shown to stimulate production of IFN-γ 3 hrs pi and reached its peak 12 hrs later. Moreover, the secondary pro-inflammatory cytokine and chemokine, IL-6, and RANTES were elevated at 12 hrs pi. Lithium was shown to stimulate expression of the primary pro-inflammatory molecule, TNF-α as early as 3 hrs pi. In addition to TNF-α expression, the regulatory cytokine, IL-10, was stimulated by lithium and reached its peak 12 hrs pi. The RVFV-infected cells treated with lithium have shown lowered ROS and RNS production as opposed to lithium-free RVFV-infected control cells. The regulatory properties of lithium were further supported by the protein expression assay that showed low expression of the iNOS while stimulating heme oxygenase (HO) and IκB. Lithium was shown to reverse NF-κB nuclear translocation in RVFV-infected Raw 264.7 cells as shown by the Immunocytochemistry assay. Moreover, lithium lowered the presence of nuclear NF-κB in RVFV-infected cells as opposed to untreated RVFV-infected cells and 5 mg/ml LPS controls as shown by the protein expression assay.ConclusionThis study demonstrates that lithium inhibits NF-kB nuclear translocation and modulate inflammation profiles in RVFV-infected Raw 264.7 cells.
VoSE: An algorithm to Separate and Enhance Voices from Mixed Signals using Gradient Boosting
Authors: Gupta Monica , Singh R K , Sinha Sachin 
Published: October 2020

Abstract
Voice Separation and Enhancement (VoSE) algorithm aims at designing a predictive model to solve the problem of speech enhancement and separation from a mixed signal. VoSE can be used for any language, with or without a large Datasets. VoSE can be utilized by any voice response system like, Siri, Alexa, Google Assistant which as of now work on single voice command. The pre-processing of the voice is done using a Trimming Negative and Nonzero voice filter (TNNVF), designed by the authors. TNNVF is independent of language, it works on any voice signal. The segmentation of a voice is generally carried out on frequency domain or time domain. Independently they are known to have ripple or rising effect. To rule out the ripple effect, data is filtered in the time-frequency domain. Voice print of the entire sound files is created for the training and testing purpose. 80% of the voice prints are used to train the network and 20% are kept for testing. The training set contains over 48,000 voice prints. LightGBM with TensorFlow helps in generating unique voice prints in a short time. To enhance the retrieved voice signals, Enhance Predictive Voice(EPV) function is designed. The tests are conducted on English and Indian languages. The proposed work is compared with K-means, Decision Stump, Naïve Bayes, and LSTM.
Bacterial and fungal co-infections, antimicrobial treatment and clinical outcome in COVID-19 patients in an acute Irish hospital
Authors: Omar Amro Ahmed , Williams Shianna Malika Cudeshia , Finn Jack Patrick , Eltayeb Siddig Omer , Dornikova Gabriela 
Published: October 2020

Abstract
Background Serious bacterial infections may be missed when all attention focuses on COVID-19. It is therefore important to consider bacterial infection when assessing the febrile patient.Aims The aim of the study was to look at the bacterial and fungal co-infections, antimicrobial treatment and clinical outcome in COVID-19 patients in an acute Irish hospital.Methods A retrospective study of all laboratory confirmed COVID-19 cases admitted to a secondary care university hospital was performed, and clinical, radiology and laboratory data was extracted and analysed.Results 42 patients met eligibility criteria for the study inclusion. Male/female ratio was 22/20 (52.4%/47.6%), median age of the patients was 64 years and the median duration of hospital stay was 11 day. In-hospital mortality rate was 3 (7.1%). Four laboratory confirmed co-infections were identified in 3 (7.1%) patients. All 3 patients were discharged home. Out of 42 patients, 12 (28.6%) patients received specific antiviral treatment. 34 (85.0%) patients were prescribed antimicrobials with antibacterial effect and 3 (7.5%) antimicrobials with antifungal effect.Conclusions We found a low frequency of bacterial and fungal co-infections in confirmed COVID-19 cases. Further prospective data are needed to be collected in relation to the co-infections in COVID-19.
COVID-19 and Insurance market returns in emerging and developed markets: A comparative study based on Wavelet methods
Authors: Fareed Zeeshan , Iqbal Najaf 
Published: October 2020

Abstract
This study investigates the co-movement nexus between COVID-19 and insurance industry returns for emerging and developed markets using a wavelet-based framework. Analysis on the daily observations from 22nd January 2020 to 14th September 2020 reveals that insurance returns (INS) responded strongly and negatively, right after the onset of the global COVID-19 outbreak, but asymmetrically later. Additionally, the devastation brought to INS is comparatively more severe but short-lived for emerging markets. The wavelet-based Granger causality and correlation confirm the robustness of our results. These findings are important for policymakers and investors in the insurance industry in the aftermath of COVID-19.
Performance evaluation of anoxic–oxic–anoxic processes in illuminated biofilm reactor (AOA-IBR) treating septic tank effluent
Authors: Kamngam Sittikorn , Koottatep Thammarat , Surinkul Nawatch , Chaiwong Chawalit , Polprasert Chongrak 
Published: October 2020

Abstract
This study was conducted to evaluate the treatment performance of the anoxic–oxic–anoxic processes in illuminated biofilm reactor (AOA-IBR) in removing organics and nitrogen contained in septic tank effluent. The 27 L of the AOA-IBR was illuminated with red light-emitting diode (LED) lamps (peak wavelength of 635 nm, intensity of 100 μmol/(m2s)). Three types of biofilm media, namely ball ring®, plastic sheets and zeolite beads, were placed in the anoxic, oxic and anoxic zones, respectively, of the reactor to support the growth of microalgal–bacterial biofilm. The AOA-IBR was continuously fed with septic tank effluent and operated at hydraulic retention times (HRTs) of 24, 48 and 72 h. The experimental results found the increases in chemical oxygen demand (COD), total nitrogen (TN) and ammonia nitrogen (NH4-N) removal efficiencies with increasing HRTs in which the HRT of 72 h resulted in 78.6, 72.8 and 90.6% removals of COD, TN and NH4-N, respectively. The effluent quality of the AOA-IBR could meet the ISO 30500 effluent standards for Non-Sewered Sanitation Systems. The predominant microalgal biofilm species was observed to be Oscillatoria sp., while Proteobacteria was the predominant bacterial phylum found in the biofilm growing in the reactor. The above results suggested the applicability of the AOA-IBR in improving septic tank treatment performance which should result in better water pollution control.
Effects of weir geometry on scour development in the downstream of Piano Key Weirs
Authors: Yazdi Alireza Mosalman , Hoseini S. Abbas , Nazari Sohrab , Amanian Nosratollah 
Published: October 2020

Abstract
Scouring in the downstream of all weirs, including Piano Key Weirs (PKWs), can have major safety implications. Since the research on downstream scouring of PKWs is very limited, and the weir geometry is also known to have an impact on downstream scouring, this study investigated scouring in the downstream of PKWs with rectangular and trapezoidal geometries and two different heights. The scour hole measurements showed that in both rectangular and trapezoidal models, scour hole parameters increased both with the increase in discharge rate and the increase in weir height. Under similar discharge conditions, the scour depth downstream from the rectangular model was greater than that downstream from the trapezoidal model. The dimensionless maximum scour depth, the distance of maximum scour depth from the weir toe, and the scour hole length for the trapezoidal PKW were, on average, 6, 13, and 11% lower than the corresponding ones for the rectangular PKW, respectively. However, these differences decreased with the increase in falling height. For both weir geometries, the maximum scour depth was aligned with the outlet keys. In addition, the maximum scour depth under the outlet keys was 13% greater than the one under the inlet keys.
A LIGA ACADÊMICA DE DIREITO CONSTITUCIONAL DO NORTE DE MINAS GERAIS
Authors: Ribeiro da Silva Wellem 
Published: October 2020

Repensar o ensino e a educação no Brasil de modo geral é imperativo visto que o paradigma no Brasil ainda é de um ensino com bases tradicionais. No ensino jurídico isso não é diferente, mostrando-se frequentemente formalista e com aprendizagem compartimentada pautada na acumulação de informações. A Extensão Universitária vive um momento de reconhecimento crescente como um verdadeiro pilar de formação intelectual na academia. Nesse contexto, o presente artigo pretende abordar e criticizar conceitos e aspectos formativos da atividade extensionista para um curso de Direito, mostrando a experiência exitosa da primeira liga acadêmica de Direito Constitucional na região extrema do Norte de Minas Gerais, fundada em uma instituição privada que é a mais próxima para uma grande população porém também cercada de desafios de acesso como o transporte e rodovias, além de limitações de tempo e finanças dos estudantes. Defende-se no texto a possibilidade de um outro olhar para o ensino aprendizagem pautado no discente como autor principal do processo.