bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of Multidrug-resistant Extended-spectrum Beta-lactamase-producing Enterobacteria from Community Infections in the city of Reynosa, Tamaulipas Mexico
Authors: Cruz-González Eduardo , Ramírez-Moreno Esther , Ortega-Balleza Jessica , Heredia-Mireles Itzel , Ramirez-Puente Imelda , Cruz-Pulido Wendy , Rivera Gildardo , Bocanegra-García Virgilio 
Published: December 2020

Abstract
Production of extended spectrum beta-lactamases (ESBL) is one of the main problems related to antimicrobial resistance worldwide, with the CTX-M, TEM and SHV types standing out as the most prevalent. These enzymes are usually related to plasmids which facilitates their horizontal genetic transmission. In the northeast region of Tamaulipas their clinical prevalence is unknown. Therefore, the aim of this work was to define the molecular epidemiology of ESBL-producing Enterobacteriaceae in clinical strains collected in Reynosa Tamaulipas, Mexico. A selection of 123 Enterobacteriaceae strains from different clinical patients were collected from August 2018 to December 2019. These strains were phenotypically identified by double disk synergy tests (DDST) and subsequently subjected to polymerase chain reaction for the detection and amplification of the blaTEM, blaSHV, blaCTX−M−1, blaCTX−M−2, blaCTX−M−9 and blaCTX−M−8/25 genes. Lastly, antimicrobial resistance profiles were determined by plate diffusion method and their capacity to transfer this sort of resistance by conjugation was assessed. Our results showed a prevalence of 48.78% (60/123) of ESBL-producing enterobacteria, with the blaTEM and blaCTX−M−1 genes most commonly detected in 76.67% (46/60) and 58.33% (35/60), respectively. Additionally, a 68.33% (41/60) of these ESBL-producing Enterobacteriaceae were multidrug-resistant, while 51.67% (31/60) were able to transfer some genes related to ESBL production, being blaCTX−M−1 the most common. This is the first study in the region that evaluates ESBL production in clinical Enterobacteriaceae strains, as well as the content of genes related to this phenotype and the ability to transfer this type of antimicrobial resistance.
Convergence of Heteromodal Lexical Retrieval in the Lateral Prefrontal Cortex
Authors: Aabedi Alexander , Kakaizada Sofia , Young Jacob , Kaur Jasleen , Wiese Olivia , Valdivia Claudia , Krishna Saritha , Weyer-Jamora Christina , Berger Mitchel , Weissman Daniel , Brang David , Hervey-Jumper Shawn 
Published: December 2020

Abstract
Lexical retrieval requires selecting and retrieving the most appropriate word from the lexicon to express a desired concept. Few studies have probed lexical retrieval with tasks other than picture naming, and when non-picture naming lexical retrieval tasks have been applied, both convergent and divergent results emerged. The presence of a single construct for auditory and visual processes of lexical retrieval would influence cognitive rehabilitation strategies for patients with aphasia. In this study, we perform support vector regression lesion-symptom mapping using a brain tumor model to test the hypothesis that brain regions specifically involved in lexical retrieval from visual and auditory stimuli represent overlapping neural systems. We find that principal components analysis of language tasks revealed multicollinearity between picture naming, auditory naming, and a validated measure of word finding, implying the existence of redundant cognitive constructs. Nonparametric, multivariate lesion-symptom mapping across participants was used to model accuracies on each of the four language tasks. Lesions within overlapping clusters of 8,333 voxels and 21,512 voxels in the left lateral prefrontal cortex (PFC) were predictive of impaired picture naming and auditory naming, respectively. These data indicate a convergence of heteromodal lexical retrieval within the PFC.
Modelling and Estimating the Transmissibility of COVID-19: Transmission Dynamics in Shaanxi Province of China as a Case Study
Authors: Zhang Xu-Sheng , Liu Wei , Xiong Huan , Chen Zhengji 
Published: December 2020

Abstract
To control and contain the outbreaks of emerging infectious diseases such as COVID-19, it is important to know how easy and fast they transmit among people. To explore the essential information of the novel infectious agents, people always confront an inverse problem: using (partially) observed numbers of infected people by time and region to dig up the underlying characteristics of unknown infectious agents. Epidemics armed with advanced statistical inference and mathematical theory has been developed to help reconstruct transmission dynamics processes and to estimate key features of infectious diseases. In this study we use COVID-19 outbreak in Shaanxi province as an example to illustrate how the infectious disease dynamics method can be used to help build the transmission process and to estimate the transmissibility of COVID-19. Three transmission dynamics models were proposed for this. By separating continuous importation from local transmission and treating imported cases as the source rather than results of local transmission, the basic reproduction number of COVID-19 in Shaanxi province was estimated in the range from 0.46 to 0.61, well below the critical value of 1.0. This indicates that COVID-19 cannot self-sustain in Shaanxi province and reflects the timely and strong control measures taken in Shaanxi province.
Gender Differences in Healthcare-Seeking Behaviors in China’s Ageing Population: An Empirical Study of Shanghai
Authors: Liu Luxue , Wang Chunlan , Yang Shangguang , Lo Kevin , Yang Xi 
Published: December 2020

Abstract
Background: Given the growing healthcare demands of the elderly, an improved understanding of the factors influencing their healthcare-seeking behaviors is necessary to enhance the effectiveness of the current healthcare system. This study empirically investigates the factors influencing the elderly population’s healthcare-seeking behaviors in Shanghai, China, from a gender differences perspective.Methods: We combine both quantitative and qualitative analyses by constructing a binary logistic regression model and identifying the relevant influential factors based on the following types of dimensions: individual, family, and cultural.Results: The results indicate that gender differences exist in the elderly population with common diseases but not in those with severe diseases, and that the female elderly are more likely to choose non-tertiary hospitals than males. In addition, age, marital status, employment status, income, health conditions, medical insurance, family support, and social capital are found to be critical influencing factors.Conclusions: The findings provide a better understanding of the elderly population’s healthcare demands and can be used to promote healthcare equality.
Influence of Tumor Mutational Burden on Immune-infiltrating Cells in Stomach Adenocarcinoma
Authors: Zhao Zongxian , Li Shilong , Li Shuliang , Yang Huaxiang , Wang Daohan , Fu Weihua 
Published: December 2020

Abstract
Background: Gastric cancer (GC) is one of the most common and fatal cancers worldwide. Tumor mutational burden (TMB) is described as a novel powerful signature to predict response to immunotherapy in gastric cancer. Nevertheless, tumor-infiltrating immune cells (TIICs) in different TMB GC remains unknown.Results: (1) The most common missense were single nucleotide polymorphisms and C>T. Furthermore, titin (TTN), tumor protein p53 (TP53), and mucin 16 (MUC16) had a higher rate of mutations in STAD. (2) TMB-high and -low groups were not associated with survival, T stage, M stage, and grade of patients with stomach adenocarcinoma (STAD) (Psurvival=0.086, PT=0.331, PM=0.804, Pgrade=0.695). However, TMB groupings were related with N stage and sex (PN=0.003, Psex=0.003). (3) There were intricate differences in immune infiltration cells (eg, T cells, monocytes, and mast cells) between the TMB-high and TMB-low groups. (4) A total of 458 genes were identified as DEGs; Dynein cytoplasmic 1 intermediate chain 1(DYNC1I1), matrix metalloproteinase 13 (MMP13) and zinc finger and BTB domain containing 16 (ZBTB16) were correlated with overall survival (OS). (5) DEGs were mainly involved in the regulation of the extracellular matrix-receptor interaction, and the Wnt and PI3K-AKT signaling pathways.Conclusion: The present study provides a comprehensive and systematic analysis of TMB and its clinical significance, and reveals the complicated differences of 22 TIICs between TMB-high and TMB-low groups in STAD.
Assessment and Documentation of Indigenous and Introduced Soil and Water Conservation Measures in Some Parts of Southern Ethiopia
Authors: Kanito Dawit , Bekele Tsegaye , Dawit Tesfaye , T/yohannes Seyfu 
Published: December 2020

Abstract
BackgroundIn Ethiopia, soil and water conservation activities were started after the famines of 1973 and 1985. Following this, different conservation measures were implemented by the government, non-government organizations, and the community to facilitate the optimum level of production from a given area of land while keeping soil loss below a critical value. This study was conducted at Wolaita, Hadiya, Kambata Tambaro, and Dawro Zones of Southern Ethiopia. It was designed to identify indigenous and introduced soil and water conservation practices, measure and describe identified practices, and document the identified practice for further reference. ResultsThe result revealed that three types of soil and water conservation practices namely biological, physical, and agronomical were implementing in the study areas. The result from the technical evaluation showed that soil bund and fanya juu has channel depth and embankment height lower than the recommended dimension. The result also indicated that less attention was given to indigenous soil and water conservation practices. Besides, the sustainability gap in constructed conservation practices was widely perceived.ConclusionsFarmers in the study area are well acquainted with soil erosion, its cause, and consequent reduction in land productivity. They confirm that implementing SWC measures are insurance to sustain and boost soil fertility and land productivity. In southern Ethiopia government and peoples were invested much more time, money, knowledge, and manpower to construct SWC measures. But, year by year structures get damage and yet seem not substantial to achieve the sector of sustainable agriculture. Besides, the study revealed that identified practices such as traditional cutoff drain, fanya juu, soil bund, stone-faced soil bund, fanya juu, brushwood, and gabion check-dams have technical, social, and institutional difficulties. The major gap observed with indigenous conservation practices is, it had been taken less attention by different stakeholders including GOs, NGOs, and research institutes. As a result, their respective dimension was not modified, effective measures were not up-scaled and circulated to other areas having similar agroecology and farming system. Thus, apparently, traditional conservation measures are aggravating soil erosion and their construction did not consider the downstream effect on dwelling community, water bodies, and aquatic lives.
Calciprotein particles are a sensitive marker predicting vascular calcification in patients with chronic kidney disease
Authors: Moriya Hidekazu , Mochida Yasuhiro , Ishioka Kunihiro , Oka Machiko , Maesato Kyoko , Hidaka Sumi , Ohtake Takayasu , Miura Yutaka , Kuro-o Makoto , Kobayashi Shuzo 
Published: December 2020

Abstract
Background: In chronic kidney disease (CKD) patients, vascular calcification occurs in the early stage of CKD, before the titer of existing CKD mineral bone disorder (CKD-MBD)-related markers exceed the threshold. Calciprotein particles (CPPs) are crystals in which excessive phosphorus and calcium in the blood form colloidal particles and are associated with vascular calcification. However, it is unknown whether CPPs are a more sensitive marker for detecting calcification than others.
Methods: In a prospective cohort study of 58 patients with CKD we examined CKD-MBD markers, including CPPs. Vascular arterial calcification score (ACS) of the lower extremities was measured with the Agatston score. One year later, the markers and ACS were reevaluated, and the relationship between the degree of progression of vascular calcification and CKD-MBD markers was evaluated.
Results: The CPP titer was significantly correlated with that of serum phosphate and corrected calcium. However, the CPP titer showed no correlation with eGFR or ACS in the lower extremities. After one year, the basic titers of serum creatinine, eGFR, FGF-23, intact-PHT, 1.25-dihydroxyvitamin D3 and CPP were not significantly correlated with ACS changes in the lower extremities. There was a significant correlation between the rate of change in ACS and that in CPP (r = 0.292, p = 0.0258). CPP was an independent risk factor for the progression of calcification in the lower extremities in a multivariate analysis (p = 0.0144).
Conclusions: CPP is a more sensitive marker of arterial calcification than other CKD-MBD markers in patients with CKD.
Key words: Calciprotein particle, Chronic kidney disease, Vascular calcification
Genome Mining Reveals Secondary Metabolites of Antarctic Bacterium Streptomyces Albidoflavus ANT_B131 Related to Antimicrobial and Antiproliferative Activities
Authors: França Paula de , Costa Jonas , Fill Taícia , Lancelotti Marcelo , Ruiz Ana , Fantinatti-Garboggini Fabiana 
Published: December 2020

Abstract
The antimicrobial resistance requires the urgent mining of new antimicrobials. Actinobacteria, specially Streptomyces genus, are responsible for production of numerous clinical antibiotics and anticancer agents. The use of genome mining can reveal the genetic potential of a strain to produce natural products, however the potential may not be express under laboratory conditions. In the present study, the Antarctic bacterium was taxonomically affiliated as Streptomyces albidoflavus, ANT_B131. The crude extracts showed antimicrobial activity against fungi, Gram-positive and Gram-negative bacteria and antiproliferative activity against five human tumor cell lines. Whole genome sequencing reveals a 6.96 Mb genome size and the genome mining showed 24 BGCs, representing 13.3% of the genome. The use of three culture media and extraction methods reveal the expression and recovery of 20% of the BGCs. The natural products identified were surugamide A, surugamide D, desferrioxamine B + Al, desferrioxamine E, and ectoine. This study reveals the potential of S. albidoflavus ANT_B131 as a natural product producer. Yet, the diversity of culture media and extraction methods could enhance the BGCs expression and recovery of natural products, and could be a new strategy to intensify the BGC expression of natural products.
Development of a Deep-learning Pipeline to Recognize and Characterize Macrophages in Colo-rectal Liver Metastasis
Authors: Cancian Pierandrea , Cortese Nina , Donadon Matteo , Maio Marco Di , Soldani Cristiana , Marchesi Federica , Savevski Victor , Santambrogio Marco Domenico , Cerina Luca , Torzilli Guido , Mantovani Alberto , Terracciano Luigi , Roncalli Massimo , Tommaso Luca Di 
Published: December 2020

Abstract

Quantitative analysis of tumor microenvironment (TME) provides prognostic and predictive information in several human cancers but, with few exceptions, it is not performed in the daily clinical practice being time-consuming. We recently showed that the morphology of tumor associated macrophages (TAM) correlates with outcome in patients with colo-rectal liver metastases (CLM). However, as for other TME components, recognizing and characterizing hundreds of TAM in a single histopathological slide is unfeasible. To fasten this process, we explored a deep-learning based solution. We tested three convolutional neural networks (CNN), Unet, SegNet and DeepLab-v3, and compared their results according to IoU (intersection over union), a metric describing the similarity between what CNN predicts as TAM and the ground truth and SBD (symmetric best dice), which indicates the ability of CNN to separate different TAMs. Unet and SegNet showed intrinsic limitations in discriminating single TAMs (highest SBD 61.34 ± 2.21), whereas DeepLab-v3 accurately recognized TAM from the background [IoU (89.13 ± 3.85)] and separated different TAM [SBD (79.00 ± 3.72)]. This deep-learning pipeline to recognize TAMs in digital slides, will allow the characterization of TAM-related metrics in the daily clinical practice, allowing the implementation of prognostic tools
Demodex Folliculorum and Bacterial Co-Infection in Patients With Blepharitis
Authors: Kosik-Bogacka Danuta Izabela , Pyzia Joanna , Galant Katarzyna , Czepita Maciej , Kot Karolina , Łanocha-Arendarczyk Natalia , Czepita Damian 
Published: December 2020

Abstract
Background Demodex mites are obligate ectoparasites found in the pilosebaceous follicle and sebaceous gland of many mammals. The aim of the study was to examine prevalence of bacterial infection in Demodex folliculorum infected patients with blepharitis. Methods The study included patients with a diagnosis of blepharitis with D. folliculorum (n=128) and healthy volunteers (n=103). Patients were questioned about their age, sex, social habits, and literacy status and per capita income. The examination consisted of examining the vision of the patient with and without ocular correction, tonus in both eyes and a careful examination of the anterior segment of both eyes. The bacterial culture of the conjunctival sac was obtained by inoculating the samples on Columbia agar with 5% sheep blood and identified based on morphological characteristics and stained by the Gram method. Species identification was performed by coagulase test or VITEK Compact. ResultsPhysiological flora was found in 8.7% participants from uninfected and all infected with D. folliculorum patients. We isolated Staphylococcus aureus, Acinetobacter baumannii, Streptococcus pneumoniae, Klebsiella oxytoca, and Bacillus spp. in the conjunctival sac only in patients infected with D. folliculorum. In patients with D. folliculorum infection mean intraocular pressure and visual acuity were lower than in uninfected participants. ConclusionsPatients infected with D. folliculorum should also undergo microbiological examination of conjunctival swabs. The treatment of each patient should be individualized, adapted to the clinical condition, and in cases of bacterial co-infection.
Identification of the Signature Associated With m6A RNA Methylation Regulators and m6A-related Genes and Construction of the Risk Score for Prognostication in Early-stage Lung Adenocarcinoma
Authors: Guo Bingzhou , Zhang Hongliang , Wang Jinliang , Wu Rilige , Zhang Junyan , Zhang Qiqin , Xu Lu , shen Ming , Zhang Zhibo , Gu Fangyan , Zeng Weiliang , yin Chengliang 
Published: December 2020

Abstract
Background: N6-methyladenosine (m6A) RNA modification play critical roles in tumorigenesis because it can change gene expression and even the function in multiple levels including the regulation of degradation, subcellular localization, splicing and local conformation changes of RNA transcripts. In this study, we aim to conduct comprehensive investigation on m6A RNA methylation regulators and m6A-related genes and their association with prognosis in early-stage Lung adenocarcinoma (LUAD). Methods: The relevant datasets which were used to analyze 21 m6A RNA methylation regulators and 887 m6A-related genes in m6Avar were downloaded from Gene Expression Omnibus database (GEO) and The Cancer Genome Atlas (TCGA) databases. Univariate cox regression analysis, random survival forest analysis, Kaplan-Meier anylysis, STRING and multivariate cox analysis were carried out on the datasets, and a risk prognostic model based on five feature genes was constructed.Results: Respectively, we treated GSE31210 (n=226) as training set, GSE50081 (n=128) and TCGA data (n=461) as test set. By performing univariable cox regression and random survival forest algorithm in the training group, five prognosis-related genes including DENND1A, KBTBD6, KIF4A, BMPER, and YTHDC2 were screened out, which could divide LUAD patients into low-risk group and high-risk group (log rank P < 0.001). The predictive efficacy of these genes was confirmed in the test group GSE50081 (log rank P < 0.01) and TCGA datasets (log rank P < 0.001). Cox analysis showed that this five-gene signature was an independent risk factor in LUAD. Further, genes in the signature were also external validated using online database. YTHDC2 played vital role of readers in m6A methylation.Conclusion: The findings of this study suggested that associated with m6A-related genes and m6A RNA methylation regulators, five-gene signature was reliable prognostic indicator for LUAD patients, indicating a clinical application prospect to serve as a potential therapeutic target.
Vasohibin 2 Promotes Lymphangiogenesis of Lung Squamous Cell Carcinoma Through Snail-dependent VEGF-D Signaling Pathway
Authors: Liu Pengpeng , Zhang Rui , Han Lei , Zhang Xiao , Ye Yingnan , Yu Wenwen , Ren Xiubao , Zhang Weijia , Yu Jinpu 
Published: December 2020

Abstract
The authors have requested that this preprint be removed from Research Square.
Sustained of mir-499-5p delivery from injection alters the muscle metabolomic profiles in broiler chicken
Authors: Li Zhixiong , Lin Yaqiu , Yuan Mao , Jiang Xiaosong , Yang Chaowu , Yu Chunlin , Chen Ling 
Published: December 2020

Abstract
Background

Myogenic miRNAs (myomiRs) which dramatically increased during myogenesis have been shown to play critical roles in many aspects of muscle function. As a myomiR, miR-499-5p, has been identified to be highly expressed in cardiac and skeletal muscle. The study focused on the effects of miR-499-5p on muscle metabolism in broiler chicken.
Methods

In the current study, we assigned 16 broiler chicks to control group and treatment group and then monitored the effects using metabolomics. Chicks were fed basal diets without or with miR-499-5p delivery. Muscle samples were collected and analyzed by ultra-high-performance liquid chromatography–tandem mass spectrometry (UHPLC-MS/MS).
Results

Our findings revealed that miR-499-5p injection altered the concentrations of a variety of metabolites in the muscle. Thereinto, a total of 46 metabolites were identified at higher (P < 0.05) concentrations and 30 metabolites were identified at lower (P < 0.05) concentrations in the treatment group as compared with the control group. These metabolites were primarily involved with the regulation of lipid and carbohydrate metabolism. Further metabolic pathway analysis revealed that fructose and mannose metabolism, galactose metabolism, inositol phosphate metabolism and terpenoid backbone biosynthesis were the most important and critical pathway which may partially interpret the effects of miR-499-5p.
Conclusions

To our knowledge, this research is the first report of metabolic signatures and related metabolic pathways in the skeletal muscle for miR-499-5p injection and provide new insight into the effect of miRNA on growth performance.