bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antimicrobials in Chicken Commercial Feeds in Vietnam: A Three-Year Longitudinal Study Before A Nationwide Ban of Growth Promoters
Authors: Carrique-Mas Juan , Cuong Nguyen Van , Kiet Bach Tuan , Hien Bo Ve , Truong Bao Dinh , Phu Doan Hoang , Thwaites Guy , Choisy Marc 
Published: May 2020

Abstract
Background Antimicrobial growth promoters (AGPs) are included in commercial animal feed rations in many low- and middle-income countries. We measured antimicrobial use (AMU) in commercial feed products consumed by 338 small-scale chicken flocks in the Mekong Delta of Vietnam, before a nation-wide ban on AGPs which is to be phased in over the coming three years. We reviewed the labels of commercial feeds and calculated amounts of antimicrobial active ingredients (AAIs) given to flocks, highlighting those that did not comply with Government regulations.Results Thirty five of 99 different antimicrobial-containing feed products (35.3%) included at least one AAI. Eight different AAIs (avilamycin, bacitracin, chlortetracycline, colistin, enramycin, flavomycin, oxytetracycline, virginamycin) belonging to 5 classes were identified. Brooding feeds contained antimicrobials the most (51.2%), followed by grower (34.6%) and finisher feeds (12.5%). The average amount of AAIs given to flocks per kg of chicken at consumption time was 84.8 (SEM ± 9.3 mg). Quantitatively, chlortetracycline was consumed most (42.2 mg/kg SEM ± 0.34; 50.0% of total use), followed by enramycin (18.4 mg SEM ± 0.03, 21.8%) and bacitracin (16.4 mg SEM ± 0.20, 19.4%). Antimicrobials in commercial feeds were more commonly given to flocks in the earlier part of the production cycle. A total of 10 (9.3%) products were not compliant with existing Vietnamese regulation (06/2016/TT-BNNPTNT) either because they included a non-authorised AAI (4), had AAIs over the permitted limits (4), or both (2).Conclusions and recommendation We found a discrepancy between current legislation and the types and quantities of AGPs found in chicken feeds; this may be a challenge in coming years when the full ban is implemented, and would require that the authorities step up monitoring efforts. Results from this study should encourage discussion about policies on AGPs in low- and middle-income countries.
Radiogenomic analysis of cervical lymph node metastasis in papillary thyroid carcinoma: A preliminary study
Authors: Tong Yuyang , Sun Peixuan , Huang Yunxia , Zhou Jin , Yong Juanjuan , Guo Yi , Yu Jinhua , Wang Yuanyuan , Zhou Shichong , Chang Cai 
Published: May 2020

Abstract
Background

Papillary thyroid carcinoma (PTC) is characterized by frequent metastasis to cervical lymph nodes (CLNs), and the presence of lymph node metastasis at diagnosis has a significant impact on the surgical approach. Therefore, we established a radiomic signature to predict the CLN status of PTC patients using preoperative thyroid ultrasound and investigated the association between the radiomic features and underlying molecular characteristics of PTC tumours.
Methods

A radiogenomic map linking radiomics features to gene modules was constructed, and immunohistochemistry was performed to validate key associations. In all, 180 patients were enrolled in this prospective study, and 47 radiomic features, including tumour size, shape, position, margin, echo pattern and calcification, were extracted. Total protein extracted from 49 tumour samples was analysed with LC/MS and iTRAQ technology. Gene modules acquired by clustering were chosen for their diagnostic significance. A radiogenomic map linking radiomic features to gene modules was constructed with the Spearman correlation matrix. Immunohistochemistry was performed to validate key associations between radiomic features and gene modules.
Results

The diagnostic performance of radiomics signature was better than that of the ultrasound-based method in predicting CLN status. Weighted gene co-expression network analysis generated 16 gene modules, and a radiogenomic map with nine significant correlations between radiomics features and gene modules was created. For example, the feature ‘minimum calcification area’ was significantly associated with module MEblue, which represents cell-cell adhesion and glycolysis. Immunohistochemistry showed that LAMC1 and THBS1 expression was associated with several radiomics features.
Conclusions

The radiomic signature proposed here has the potential to noninvasively predict the CLN status in PTC patients. Merging imaging phenotypes with genomic data could allow the noninvasive identification of the molecular properties of PTC tumours, which would support clinical decision making with personalized management.
Trail registration:

This prospective study was approved by the ethics committee of the Fudan University Shanghai Cancer Centre (1809191-1-NSFC) in July 2018.
Identifying emerging trends in rheumatoid arthritis research: A scientometric analysis
Authors: Li Xiang , Chen Gong , Seery Samuel , Zhao Zhehui , Zhang Haijing , Peng Ying , Wu Lianqiu 
Published: May 2020

Abstract
Background Rheumatoid arthritis (RA) is a systemic autoimmune disease, characterized as chronic and progressive with acute inflammatory attacks. RA is highly prevalent across all societies and over the past two decades there has been substantial effort to improve diagnostics and therapeutics.Methods We searched for pertinent studies using CiteSpace and created maps to understand the intellectual structure of RA research. Pertinent studies over the past two decades were retrieved from Web of Science. Scientometric analysis in this study includes time distribution, cluster analysis, time-zones and time-lines of keywords, as well as burst detection.Results Our analysis has revealed a steady upward trend in publications from 2010 until 2018 which perhaps reflects growing global concern and investment. While the etiology of RA appears unknown, there is a plethora of studies into pathological mechanisms, diagnostics and drug development through one of the phases of basic and clinical research. RA pathogenesis has been shown to involve immune cells, including T cells, B cells, macrophages and synoviocytes which have a key role in invasive synovium and joint inflammation. X-rays and blood testing can support differential diagnostics, and there are a number of treatments available which are selected depending upon RA staging.Conclusions TNF-α, apoptosis, pathogenesis, and NF-κB are the most frequently used terms across this specialism in 2020. These terms represent the new theoretical understanding and necessitates further research because they may guide patient selection and more individualised RA care.
Physical Function and Clinical Outcomes in Hemodialysis Patients: The China Dialysis Outcomes and Practice Pattern Study
Authors: Niu Qingyu , Zhao Xinju , Gan Liangying , Liang Xinling , Ni Zhaohui , Chen Xiaonong , Chen Yuqing , Hou Fan Fan , Zuo Li 
Published: May 2020

Abstract
Background: Hemodialysis (HD) patients usually have impaired physical function compared with general population. Self-reported physical function is a simple method to implement in daily dialysis care. This study aimed to examine the association of self-reported physical function with clinical outcomes of HD patients.Methods: Dialysis Outcomes and Practice Patterns Study (DOPPS) is a prospective cohort study. Data on 1427 HD patients in China DOPPS5 were analyzed. Self-reported physical function was characterized by 2 items of ‘moderate activities limited level’ and ’climbing stairs limited level’. Demographic data, comorbidities, hospitalization and death records were collected from patients’ records. Associations between physical function and outcomes were analyzed using COX regression models. The generalized linear mixed models were used to examine correlates of physical function limited level.Results: Compared to ‘limited a lot’ in moderate activities, ‘limited a little’ and ‘not limited at all’ groups were associated with lower all-cause mortality after adjusted for covariates (HR: 0.652, 95% CI: 0.435-0.977 and HR: 0.472, 95% CI: 0.241-0.927, respectively). And not limited in moderate activities was associated with lower risk of hospitalization compared with ‘limited a lot’ group after adjusted for covariates (HR: 0.747, 95% CI: 0.570-0.978). Meanwhile, compared to ‘limited a lot’ in climbing stairs, ‘limited a little’ and ‘not limited at all’ groups were associated with lower all-cause mortality (HR: 0.574, 95% CI: 0.380-0.865 and HR: 0.472, 95% CI: 0.293-0.762, respectively) but not hospitalization after fully adjusted. Factors including old age, female gender, longer dialysis vintage, catheter use, low serum albumin and combining with diabetes, coronary artery disease and cerebrovascular disease were related to higher limited levels of physical function (P < 0.05).Conclusion: Higher limited levels in self-reported physical function were associated with higher risk of all-cause mortality and hospitalization in HD patients.
Knocking out Analysis of the CpxP gene using Crispr/Cas9 in Escherichia coli MG1655
Authors: he xiaoliang , Ren Yuwen , Meng Wanli , Yu Xinran , Zhou Xiaohui 
Published: May 2020

Abstract
Based on the analysis of CpxP genes among Escherichia coli strains, CpxP gene-targeting short guide RNA (sgRNA) was designed and inserted into the pGL3-MGP-RNA. The donor sequences (MG-HR) for homologous repair were designed and cloned by PCR. MG-HR and pGL3-MGP-RNA were transformed into E. coli MG1655 (pCas9). The CpxP gene expression cassette was amplified by PCR and subcloned into pBBR1MCS-2. Then the pBBR-CpxP was independently transformed into E. coli MG1655. The results of motility experiment suggest that CpxP gene had a significant effect on the movement ability of E. coli strain. The CpxP protein had a significant inhibition of bacterial activity. The lastest 81 CpxP proteins sequences were selected and analyzed by multi-sequence alignment and molecular cluster. The CpxP proteins were roughly divided into three categories. Our results suggest that the CpxP protein was involved in bacterial motility, infection and pathogenicity.
Infrequent home-cooked meal consumption is related to the inadequacy of dietary fibre and minerals intake among Japanese adults aged 18-64 years: analysis from the 2015 National Health and Nutrition Survey
Authors: Matsumoto Mai , Saito Aki , Okada Chika , Okada Emiko , Takimoto Hidemi 
Published: May 2020

Abstract
Background: Consumption of home-cooked meals may lead to better nutritional intake. Few studies have examined the effect of frequency of home-cooked meal consumption on inadequacy of nutritional intake based on nutritional standards. We therefore aimed to examine the association between the frequency of home-cooked meal consumption and nutrient intake inadequacy among Japanese adults.Methods: This study was a secondary analysis of the 2015 National Health and Nutrition survey in Japan, involving 921 men and 1300 women aged 18–64 years, a cross-sectional survey. The frequency of home-cooked meal consumption was determined using two questions enquiring about the frequency of eating out and take-away meals. Data on dietary intake were collected using a one-day semi-weighed household dietary record. The inadequacy of each nutrient intake was assessed by comparing estimated average requirement (EAR) level for 14 nutrients and the range of the dietary goal (DG) for seven nutrients according to the 2015 version of the Dietary Reference Intake for Japanese. Participants were stratified into three groups based on the frequency of consuming home-cooked meals. Group differences in EAR and DG were assessed using the covariate and logistic regression analysis, respectively.Results: Among men and women, the proportion of participants who consumed home-cooked meals almost every day and meals prepared out of home at least once a day were 34.9% and 46.8%, and 14.7% and 6.3%, respectively. A higher frequency of consumption of home-cooked meals was associated with higher intake and adequacy of dietary fiber and minerals (iron, calcium, potassium etc.), and with higher intake of vegetables and lower intake of oils.Conclusions: Low frequency of home-cooked meal consumption was associated with insufficient intake of dietary fiber and multiple mineral intakes among Japanese adults. Dietary fiber and mineral intake may need to the focus of interventions aimed at improving nutrient intake in individuals who predominantly eat food prepared away from home.
Downregulation of miR-342-3p/miR-342-5p in type 1 diabetes mellitus and vascular health; Case controlled study in peripheral blood mononuclear cells and plasma, CD45dimCD34+CD133+ cells, inflammatory markers, CXCR1/2 and PANEX2 mRNA combined with Ingenuity Pathway Analysis
Authors: Ray Sabina L , Coulson David J , Yeoh Megan LY , Bakhashab Sherin , Tamara Alice , Latief Jevi S , Weaver Jolanta U 
Published: May 2020

Abstract
BACKGROUND Cardiovascular disease (CVD), the leading causes of death worldwide, correlates with inflammation and shortens life span in type 1 diabetes (T1DM). In animals, miR-342 were shown to be anti-inflammatory in CVD. We hypothesise: proangiogenic miR-342-3p/-5p are downregulated in T1DM whereas inflammatory cytokines are upregulated.METHODS We studied plasma/peripheral blood mononuclear cells (PBMCs) in 29 T1DM and 20 controls (HC). Vascular health was measured by Fibronectin Adhesion Assay (FAA), CD45 dim CD34 + 133 + cells (flow cytometry) and Tissue inhibitor of metalloproteases (TIMP-1). Inflammatory markers IL-7, IL-8, TNFα and VEGF-C were assayed by Mesoscale assay, mRNA for chemokine receptor CXCR1/2, PANX2 and miR 342-3p/5p by qRT-PCR. Analysis: Unpaired Student t test, Pearson correlation and Ingenuity Pathway Analysis (IPA) to predict miR-342-3p/-5p targets.RESULTS In T1DM, pro-inflammatory cytokines IL-8 and TNF-α, IL-7 and growth factor VEGF-C were increased versus HCs; p=0.008, p=0.003, p=0.041 and p=0.013 respectively. MiR-342-3p/-5p were downregulated in PBMCs in T1DM versus HC; p=0.01, but not in plasma. PANX2, CXCR1 and CXCR2 mRNA were increased in PBMCs in T1DM versus HCs; p=0.004, p=0.017 and p<0.001 respectively. MiR-342-3p correlated negatively with TIMP-1, IL-6, IL-8, TNF-α, HbA 1c ; p=0.006, p=0.031, p=0.029, p=0.038, p=0.001, p=0.031 whilst miR-342-5p with TIMP-1, IL-6, IL-8, HbA 1c , p=0.005, p=0.034, p=0.029, p=0.001, p=0.042 respectively. There was positive correlation between miR-342-3p and FAA, CXCR1, CXCR2; p=0.006, p=0.019, p=0.001 and between miR-342 - 5p and FAA, CXCR2; p=0.038, p=0.036 respectively. IPA predicted miR-342-3p/-5p to be anti-inflammatory through the indirect regulation of mitogen-activated protein 3 kinase 1, inhibitor of nuclear factor kappa B kinase regulatory subunit Gamma, Surfactant protein A1 and PANX2 as well as predicting IL-8, TNF-α, IL-7 and glucose to activate the inflammatory response. ROC curve analyses showed: miR-342-3p/-5p to be a biomarker for T1DM: p=0.01, p =0.006 respectively (2) significant downregulation of miR-342-3p/-5p has occured at HbA 1c > 46.45 mmol/mol, p=0.006, p =0.005 respectively.CONCLUSION Our findings validated animal studies. Downregulation of miR-342-3p/-5p by hyperglycaemia and increase in cytokines confirmed inflammation in T1DM. MiR-342-3p/5p correlated with indices of vascular health and defined early CVD at HbA1c of 46.5 mmol/mol cut off point. MiR-342-3p/-5p based either intervention or monitoring may prove to be beneficial in CVD in T1DM.
Ocular Manifestation of Elizabethkingia Meningoseptica
Authors: LEUNG KAI CHING PETER , KO TAK CHUEN SIMON 
Published: May 2020

Abstract
Background: Elizabethkingia is a Gram-negative, obligate aerobic, oxidase positive bacillus that is known to cause a variety of nosocomial infections and has emerged as an important pathogen because of multiple anti-microbial resistance. We present the largest case series of Elizabethkingia ophthalmic infections, with specific emphasis on its clinical spectrum, risk factors, treatment and outcome.Method: Microbiological specimens growing Elizabethkingia were reviewed retrospectively at a regional tertiary hospital from 2005-2019. Clinical manifestation, risk factors, treatment including types of antibiotics, treatment duration and clinical outcome were documented. Results: Ten cases of culture positive Elizabethkingia ophthalmic infection were identified, which all cultured E. meningoseptica. Four cases keratitis, three cases of conjunctivitis, two cases of blepharitis and one case blepharitis-conjunctivitis were observed. Four cases were found to be associated with contact lens use and were found to colonize E. meningoseptica. One case of blepharitis was associated with and ocular prosthesis (scleral shell) an eviscerated eye. Fluoroquinolone and chloramphenicol were most commonly used topical antibiotics for treatment. The mean treatment duration for all infections was averaged at 6.5 weeks. Conclusion: E. meningoseptica is found to be the predominant species that has caused infection at the ocular surface. Contact lens use and ocular prosthesis appears to be a risk factor for infection due to ocular surface barrier disruption and bacteria colonization. Combination of fluroquinolone and chloramphenicol is a safe and effective treatment against Elizabethkingia ocular infections. Further studies are required to determine the susceptibility of commonly used topical anti-microbial agents to Elizabethkingia species.
Differentiating novel coronavirus pneumonia from general pneumonia based on machine learning
Authors: Liu Chenglong , Wang Xiaoyang , Liu Chenbin , Sun Qingfeng , Peng Wenxian 
Published: May 2020

Abstract
Background
Chest CT screening as supplementary means is crucial in diagnosing novel coronavirus pneumonia (COVID-19) with high sensitivity and popularity. Machine learning was adept in discovering intricate structures from CT images and achieved expert-level performance in medical image analysis.
Methods
To develop and validate an integrated machine learning framework on chest CT images for differentiating COVID-19 from common pneumonia (CP). Seventy-three confirmed COVID-19 cases were consecutively enrolled together with twenty-seven confirmed common pneumonia patients from Ruian People’s Hospital, from January 2020 to March 2020. Statistical textual features of COVID-19 and CP images were extracted. After feature selection, the reserved features were applied to the ensemble of bagged tree (EBT) and four other machine learning classifiers with 10-fold cross-validation.
Results
The classification accuracy, precision, sensitivity, specificity and F1 score of our proposed method are 91.66%, 97.91%, 85.26%, 98.15% and 91.15% respectively. The AUC of its receiver operating characteristic is 0.98.
Conclusions
The experimental results indicate that the EBT algorithm with statistical textural features on chest CT for differentiating COVID-19 from common pneumonia achieved high transferability, efficiency, specificity, and impressive accuracy.
Etiological characteristic and risk factors of ESBL-Urinary Tract Infections: A nomogram had been built and Urologist should act in time
Authors: Wei Yi , Yu Chengjun , Zhao Tianxing , Lin Tao , He Dawei , Wu Sheng-de , Wei Guanghui 
Published: May 2020

Abstract
Background: The presence of urinary tract infection (UTI) due to Extended-Spectrum Beta-Lactamase (ESBL)-producing bacteria is reported increased. Aim to study the most frequent uropathogens and the antibiotic susceptibility patterns of them in children and identify whether urodynamic change, underlying neurologic disorders and undernourishment were independent risk factors for ESBL positive UTI which is unclear. Methods: We retrospectively reviewed microbial etiologies and antimicrobial resistance among patients experiencing UTI events in the urology ward of Chongqing Medical University Afflicated Chlidren's Hospital from January 1994 and December 2019. All strains were cultured and identified by the Clinical Microbiology Laboratory. Results: A total of 854 patients with UTI over a 26-years period were evaluated and Escherichia coli was the most common pathogen. During the study period, the proportion of UTI cases attributed to Enterococci increased significantly. Susceptibilities to carbapenems and amikacin decreased significantly, indicating increased antibiotic resistance of pathogens associated with UTI. Interestingly, the susceptibilities to piperacillin/tazobactam have increased. 72.64% were caused by ESBL bacteria and ESBL-producing bacteria increased significantly. ESBL (+) and ESBL (-) UTI were compared and there were no significant differences in the clinical presentation between gender, side of the lesion and urodynamic results. Significant potential risk factors of ESBL-UTI were presence of congenital urological abnormalities, vesicoureteral reflux, neurologic disorder, age <12months, fever and previous use of antibiotics in the last 3 months. On logistic regression analysis, underlying neurologic disorder (OR =8, CI 1.845-34.695) and history of previous antibiotics administration in the last 3 months (OR =4.764, CI 3.114-7.289) were identified as an independent significant risk factor for ESBL- UTI. The nomogram generated was well calibrated for all predictions of ESBL+ probability, and the accuracy of the model nomogram measured by Harrell’s C statistic (C-index) was 0.741. Conclusions: The current situation of multiple bacterial antibiotic resistance has become a worrisome issue in UTI, and urologist should act timely. Our data will greatly assist physicians recognizing the risk factors of ESBL-UTI and optimising antibiotic use.
Human development, social vulnerability and COVID-19 in Brazil: A study of the social determinants of health
Authors: de Souza Carlos Dornels Freire , Machado Michael Ferreira , Carmo Rodrigo Feliciano do 
Published: May 2020

Abstract
Background: COVID-19 was confirmed in Brazil in February 2020. Since then, the disease has spread throughout the country, reaching the poorest areas. This study analyzes the relationship between COVID-19 and the population’s living conditions. We aimed to identify social determinants related to the incidence, mortality, and case fatality rate of COVID-19 in Brazil, in 2020.Methods: This is an ecological study evaluating the relationship between incidence, mortality, and case fatality rates and 49 social indicators of human development and social vulnerability. For the analysis, bivariate spatial correlation and multivariate and spatial regression models (spatial lag model and spatial error models) were used, considering a 95% confidence interval and a significance level of 5%.Results: A total of 44.8% of municipalities registered confirmed cases of COVID-19 and 14.7% had deaths. We observed that 56.2% of municipalities with confirmed cases had very low human development (incidence: 59.00/100,000; mortality: 36.75/million), and 52.8% had very high vulnerability (incidence: 41.68/100,000; mortality: 27.46/million). The regression model showed 17 indicators associated with transmission of COVID-19 in Brazil.Conclusions: Although COVID-19 first arrived in the most developed and least vulnerable municipalities in Brazil, it has already reached locations that are farther from large urban centers, whose populations are exposed to a context of intense social vulnerability. Based on these findings, it is necessary to adopt measures that take local social aspects into account in order to contain the pandemic.