bluuebunny/crossref_metadata_2025_split huggingface dataset:
Could remnant-like particle cholesterol become a risk factor in diabetic menopausal women with coronary artery disease? A cross-sectional study of single academic center in China
Authors: Feng Xunxun , Guo Qianyun , Zhou Shu , Sun Tienan , Liu Yuyang , Zhou Zhiming , Zhou Yujie 
Published: February 2020

Abstract
Background and aims It has been confirmed that remnant-like particle cholesterol (RLP-C) mediates the progression of coronary artery disease (CAD). Currently there is limited information on RLP-C in menopausal women. With the special status of diabetes mellitus (DM) combined with the special body changes of the menopausal women, the RLP-C is particularly important when studying the changes that occurred in response to CAD and its associated risk factors. This study discussed whether RLP-C could be an independent risk factor for menopausal women with CAD and DM. Methods The cohort consisted of 4753 menopausal women who had undergone coronary angiography. Subjects were separated into CAD and non-CAD groups, and univariate and multivariate logistic regression analysis of CAD risk factors were performed. All patients with a history of DM were divided into DM subgroups. Then, the univariate and multivariate logistic regression analysis of the risk factors of CAD and the comparison among age groups in the DM subgroup were performed. After age stratification of the DM group, the Kruskal-Wallis test was used to analyze the differences of various lipid indexes among age groups. Results The multivariate logistic regression showed that RLP-C was an independent risk factor for CAD in menopausal women (OR 1.232, 95%CI 1.070-1.419). In the DM subgroup, it was also found that RLP-C was an independent risk factor for CAD (OR 1.366, 95%CI 1.043-1.791). Kruskal-Wallis test analysis found that RLP-C had no significant difference among three groups (P>0.05). Conclusions RLP-C was proved to be an independent risk factor for menopausal women with CAD and DM.
Multi-omics analysis reveals the influence of genetic and environmental risk factors on developing gut microbiota in infants at risk of celiac disease
Authors: Leonard Maureen M , Karathia Hiren , Pujolassos Meritxell , Troisi Jacopo , Valitutti Francesco , Subramanian Poorani , Camhi Stephanie , Kenyon Victoria , Colucci Angelo , Serena Gloria , Cucchiara Salvatore , Montuori Monica , Malamisura Basilio , Francavilla Ruggiero , Elli Luca , Fanelli Brian , Colwell Rita , Hasan Nur , Zomorrodi Ali R , Fasano Alessio , Team CDGEMM Study 
Published: February 2020

Abstract
Background : Celiac disease (CD) is an autoimmune digestive disorder that occurs in genetically susceptible individuals in response to ingesting gluten, a protein found in wheat, rye, and barley. Research shows that genetic predisposition and exposure to gluten are necessary but not sufficient to trigger the development of CD. This suggests that exposure to other environmental stimuli early in life, e.g., cesarean section delivery, exposure to antibiotics or formula feeding, may also play a key role in CD pathogenesis through yet unknown mechanisms. Here, we use multi-omics analysis to investigate how genetic and early environmental risk factors alter the development of the gut microbiota in infants at risk of CD. Results : Toward this end, we took advantage of a large-scale prospective birth cohort study of infants with a first-degree relative with CD. We then performed rigorous multivariate association, cross-sectional and longitudinal analyses using metagenomic and metabolomic data collected at birth, three months and six months of age to explore the impact of genetic predisposition and environmental risk factors on the gut microbiota composition, function and metabolome prior to the introduction of trigger (gluten). These analyses revealed several microbial species, functional pathways and metabolites that are associated with each genetic and environmental risk factor or that are differentially abundant between environmentally exposed and non-exposed infants or between time points. Among our significant findings, we found that cesarean section delivery is associated with a decreased abundance of Bacteroides vulgatus and Bacteroides dorei and of folate biosynthesis pathway, and with an increased abundance of hydroxyphenylacetic acid, alterations that are implicated in immune system dysfunction and inflammatory conditions. Additionally, longitudinal analysis revealed that, in infants not exposed to any environmental risk factor, the abundances of Bacteroides uniforms and of metabolite 3-3-hydroxyphenylproprionic acid increase over time, while those for lipoic acid and methane metabolism pathways decrease, patterns that are linked to beneficial immunomodulatory and anti-inflammatory effects. Conclusions : Overall, our study provides unprecedented insights into major taxonomic and functional shifts in the developing gut microbiota of infants at risk of CD ultimately linking genetic and environmental risk factors to detrimental immunomodulatory and inflammatory effects. Keywords: Microbiota; Celiac disease; Multi-omics analysis, gut microbiome
Prediction and analysis of Metagenomic operons via MetaRon: a Pipeline for Prediction of Metagenomic OpeRons
Authors: Zaidi Syed Shujaat Ali , Kayani Masood Ur Rehman , Zhang Xuegong , Shamsi Imran Haider 
Published: February 2020

Abstract
Background: Efficient regulation of bacterial genes against the environmental stimulus results in unique operonic organizations. Lack of complete reference and functional information makes metagenomic operon prediction challenging and therefore opens new perspectives on the interpretation of the host-microbe interactions. Methods: Here we present MetaRon (pipeline for the prediction of Metagenomic operons), an open-source pipeline explicitly designed for the metagenomic shotgun sequencing data. It recreates the operonic structure without functional information. MetaRon identifies closely packed co-directional gene clusters with a promoter upstream and downstream of the first and last gene, respectively. Promoter prediction marks the transcriptional unit boundary (TUB) of closely packed co-directional gene clusters.Results: Escherichia coli (E. coli) K-12 MG1655 presents a gold standard for operon prediction. Therefore, MetaRon was initially implemented on two simulated illumina datasets: (1) E. coli MG1655 genome (2) a mixture of E. coli MG1655, Mycobacterium tuberculosis H37Rv and Bacillus subtilis str. 168 genomes. Operons were predicted in the single genome and mixture of genomes with a sensitivity of 97.8% and 93.7%, respectively. In the next phase, operons predicted from E. coli c20 draft genome isolated from chicken gut metagenome achieved a sensitivity of 94.1%. Lastly, the application of MetaRon on 145 paired-end gut metagenome samples identified 1,232,407 unique operons. Conclusion: MetaRon removes two notable limitations of existing methods: (1) dependency on functional information, and (2) liberates the users from enormous metagenomic data management. Current study showed the idea of using operons as subset to represent the whole-metagenome in terms of secondary metabolites and demonstrated its effectiveness in explaining the occurrence of a disease condition. This will significantly reduce the hefty whole-metagenome data to a small more precise data set. Furthermore, metabolic pathways from the operonic sequences were identified in association with the occurrence of type 2 diabetes (T2D). Presumably, this is the first organized effort to predict metagenomic operons and perform a detailed analysis in association with a disease, in this case T2D. The application of MetaRon to metagenome data at diverse scale will be beneficial to understand the gene regulation and therapeutic metagenomics.
Discriminatory ability and prognostic evaluation of presepsin for sepsis-related acute respiratory distress syndrome
Authors: Zhao Jiangnan , Tan Yan , Wang Li , Shi Yi 
Published: February 2020

Abstract
Background Sepsis-related acute respiratory distress syndrome (ARDS) has worse clinical outcomes than non-sepsis-related ARDS. Early identification of sepsis-related or non-sepsis-related ARDS is challenging. Presepsin is known to be elevated in sepsis, but little is known about its discriminatory ability and prognostic evaluation in patients with sepsis-related ARDS.Methods This study was a multicenter prospective cohort study of 225 consecutive patients, enrolled based on the Berlin criteria for ARDS between September 2017 and August 2019. The patients were stratified into two groups: sepsis-related ARDS and non-sepsis-related ARDS. Plasma presepsin and serum procalcitonin (PCT) were measured, and the Sequential Organ Failure Assessment (SOFA) and Acute Physiology and Chronic Health Evaluation II (APACHE II) scores were calculated to evaluate disease severity.Results Patients with sepsis-related ARDS had higher presepsin levels at admission than patients with non-sepsis-related ARDS (P<0.001). The area under the receiver operating characteristic (ROC) curve of presepsin (0.81) was significantly greater than that of PCT (0.62) in diagnosing sepsis-related ARDS (P=0.001). Among patients with sepsis-related ARDS, presepsin levels were significantly higher in non-survivors than in survivors (P<0.001). Presepsin was found to be an independent predictor of in-hospital mortality in sepsis-related ARDS. Based on ROC analysis, the addition of presepsin improved discrimination based on SOFA or APACHE II scores from 0.77 to 0.87 or 0.73 to 0.85 (all P<0.05), respectively. The levels of plasma presepsin were positively correlated with disease severity, as determined by the SOFA score in the sepsis-related ARDS group (P<0.001).Conclusions Presepsin is a valuable biomarker for early stratification of sepsis-related ARDS. Higher plasma presepsin levels are associated with increased mortality in sepsis-related ARDS.
Expression and function of&nbsp;an HAC1-regulated multi-copy xylanase&nbsp;gene in Saccharomyces cerevisiae
Authors: Zhang Sitong , Bao Changjie , Li Jiping , Chen Huan , Sun Yang , Wang Gang , Chen Guang 
Published: February 2020

Abstract
To investigate the effects of transcription factor HAC1, which is involved in the unfolded protein response pathway, on the expression of xynB in Saccharomyces cerevisiae , we used overlap extension polymerase chain reaction (PCR), rDNA integration, and droplet digital PCR technology to generate a S . cerevisiae strain (S8) containing eight copies of the xylanase gene, allowing high-yield secretory expression of xylanase. HAC1 was then overexpressed in the S8 strain, and the GeXP system was used to study the effects of HAC1 overexpression on the expression of genes associated with protein folding in the endoplasmic reticulum (ER). Results confirmed the constitutive secretory expression of the multiple copies of the xylanase gene in S . cerevisiae following rDNA-based integration of the expression cassette. Specifically, recombinant S . cerevisiae strain S8, containing eight copies of the xylanase gene, showed maximum xylanase expression, with a yield of 325 U/mL. However, overexpression of HAC1 further improved xylanase production by strain S8, resulting in a yield of 381 U/mL. These results confirmed that overexpression of HAC1 improves the expression of genes associated with protein folding in the ER, enhancing the protein folding and assembly functions of the ER and increasing xylanase expression.
Microglial and neuronal cell pyroptosis induced by oxygen-glucose deprivation/reoxygenation aggravates cell injury via activation of the caspase-1/GSDMD signaling pathway
Authors: Dong Zhaofei , Peng Qingxia , Pan Kuang , Lin Weijye , Wang Yidong 
Published: February 2020

Abstract
Background Pyroptosis is a new type of programmed cell death, which induces a strong pro-inflammatory reaction. However, the mechanism of pyroptosis after brain ischemia/reperfusion (I/R) and the interaction between different neural cells are still unclear. This study comprehensively explored the mechanisms and interactions of microglial and neuronal pyroptosis in the simulated I/R environment in vitro. Methods The BV2 and HT22 cells were treated by oxygen-glucose deprivation/reoxygenation (OGD/R). The pyroptotic cells were detected by dye uptake method. The expression levels of pyroptotic-related proteins were determined by western blotting, immunofluorescence and enzyme linked immunosorbent assay. The cell viability was assessed using MTT assay Kit. AC-YVAD-CMK, necrosulfonamide and the siRNA of Gasdermin D (GSDMD) were used to observe the inhibited effect on caspase-1 and GSDMD, respectively. A transwell co-culture model was applied to observe pyroptosis and interactions between BV2 and HT22 cell after OGD/R. Results Both BV2 and HT22 cells underwent pyroptosis after OGD/R, and the pyroptosis occurred at earlier time point in HT22 than that of BV2. Caspase-11 and Gasdermin E (GSDME) expression in BV2 and HT22 cells did not change significantly after OGD/R. Inhibition of caspase-1 or GSDMD activity, or down-regulation of GSDMD expression, alleviated pyroptosis in both BV2 and HT22 cells after OGD/R. Transwell studies further showed that OGD/R-treated HT22 or BV2 cells aggravated pyroptosis of adjacent non-OGD/R-treated cells, which could be relieved by inhibition of caspase-1 or GSDMD. Conclusions OGD/R induces pyroptosis of microglia and neuronal cells and aggravates cell injury via activation of caspase-1/GSDMD signaling pathway. Our findings suggest that caspase-1 and GSDMD may be therapeutic targets after cerebral I/R. Necrosulfonamide, a chemical inhibitor of GSDMD, may be a potential drug to prevent cerebral I/R-induced brain injury.
Oncological resection, myasthenia gravis and staging as prognostic factors in thymic tumors: A Chilean case series
Authors: Salas Patricio , Solovera Maria Eliana , Bannura Felipe , Muñoz-Medel Matias , Cordova-Delgado Miguel , Sanchez Cesar , Ibañez Carolina , Garrido Marcelo , Koch Erica , Acevedo Francisco , Mondaca Sebastian , Nervi Bruno , Madrid Jorge , Peña Jose , Pinto Mauricio P. , Valbuena José , Galindo Hector 
Published: February 2020

Abstract
Background: Thymic epithelial tumors are rare and highly heterogeneous. Reports from the United States suggest an overall incidence of 0.15 per 100,000/year. In contrast, the incidence of these tumors in Latin America is largely unknown and reports are scarce, somewhat limited to case reports.Methods: Herein, we report a series of 38 thymic tumors from a single institution, retrospectively incorporated into this study. Patient characteristics and outcomes including age, sex, stage, paraneoplastic syndromes, treatment regimens and the date of decease were obtained from medical records.Results: Most cases in our series were females and young age (<50 years-old) and early stage by Masaoka-Koga or the Moran staging systems. Also, a 34% of patients had myasthenia gravis (MG). Next, we analyzed overall survival (OS) rates in our series and found that the quality of surgery (R0, R1 or R2), MG status, and staging (Masaoka-Koga or Moran) were prognostic factors. Finally, we compared our data to larger thymic tumor series.Conclusions: Overall, our study confirms complete surgical resection as the standard, most effective treatment for thymic epithelial tumors. Also, the Masaoka-Koga staging system remains as a reliable prognostic factor but also the Moran staging system should be considered for thymomas.
Clinical aspects and detection of Zika virus RNA in several tissues of experimentally infected BALB/c mice
Authors: Bandeira Derick Mendes , Caldas Gabriela Cardoso , Jácome Fernanda Cunha , Rasinhas Arthur da Costa , Almeida Ana Luisa Teixeira de , Tourinho Renata Santos , Amorim Juliana Fernandes da Silva , Trindade Gisela Freitas , Barth Ortrud Monika , Barreto-Vieira Debora Ferreira 
Published: February 2020

Abstract
The aim of the present study was to infect BALB/c mice with ZIKV to evaluate clinical signs and to quantify the viral load in different tissues at three different kinetic points. For this purpose, fifteen mice were inoculated with a 100µl of a viral solution and five other mice were used as negative controls. After euthanasia, nine different tissues were collected and macerated for RNA extraction and quantification. The infections were not lethal. Some of them, however, showed great agitation, hair bristling and itchy skin. Viral RNA was detected in one heart sample, eight samples of spleen and two of skeletal muscle. Seven out of eleven positive samples were from mice euthanized on the third day after infection. Only spleen yielded positive results at a later time of infection. These results contribute to a better understanding of clinical signs and replication dynamics of Zika virus in different organs of BALB/c mice, which are still scarce data in the scientific literature.
Evaluation Of The Morphometric Covariation Between Palatal And Craniofacial Skeletal Morphology In Class III Malocclusion Growing Subjects
Authors: Paoloni Valeria , Gastaldi Giorgio , Franchi Lorenzo , De Razza Francesca Chiara , Cozza Paola 
Published: February 2020

Abstract
Background: To study the covariation between palatal and craniofacial skeletal morphology in Class III growing patients through geometric morphometric analysis (GMM).Methods: In this retrospective study, 54 Class III subjects (24F,30M;7.6±0.8yy) were enrolled following these inclusion criteria: European ancestry, Class III skeletal and dental relationship, early mixed dentition, prepubertal skeletal maturation, familiarity for Class III malocclusion, no pseudo Class III malocclusion. Each patient provided upper digital cast and cephalogram before starting the therapy. Landmarks and semilandmarks were digitized (239 on the casts;121 on the lateral radiographs) and GMM was used. Procrustes analysis and principal component analysis (PCA) were applied to show the principal components of palatal and craniofacial skeletal shape variation. Two-block partial least squares analysis (PLS) was used to assess pattern of covariation between palatal and craniofacial morphology.Results: Regarding palatal shape variation, PC with largest variance (PC1) described morphological changes in the three space dimensions, while, concerning the craniofacial complex components, PC1 revealed morphological differences along the vertical plane. A significant covariation was found between palatal and craniofacial shape. PLS1 accounted for more than 61,7% of the whole covariation, correlating the craniofacial divergence to palatal height and width.Conclusions: In Class III subjects increments of angle divergence are related to a narrow and high palate.
Survival curve identifies critical period for postoperative mortality in cardiac patients undergoing emergency general surgery
Authors: Martines Diego , Nii Fernanda , Medeiros Kayo , Carvalho Barbara , Pipek Leonardo , Mesquita Gustavo , Iuamoto Leandro , Oliveira Gustavo , Bianco Antonio Carlos , Meyer Alberto 
Published: February 2020

Abstract
Introduction: The number of non-cardiac major surgeries carried out has significantly increased in recent years to around 200 million procedures carried out annually. Approximately 30% of patients submitted to non-cardiac surgery present some form of cardiovascular comorbidity. In emergency situations, with less surgery planning time and greater clinical severity, the risks become even more significant. The aim of this study is to determine the incidence and clinical outcomes in patients with cardiovascular disease submitted to non-cardiac surgical procedures in a single cardiovascular referral center. Methods: This is a prospective cohort study of patients with cardiovascular disease submitted to non-cardiovascular surgery. All procedures were carried out by the same surgeon, between January 2006 and January 2018. Results: 240 patients included were elderly, 154 were male (64%), 8 patients presented two diagnoses. Of the resulting 248 procedures carried out, 230 were emergency (92.8%). From the data obtained it was possible to estimate the day from which the occurrence of mortality is less probable in the postoperative phase. Conclusion: Our research evaluated the epidemiological profile of the surgeries and we were able to estimate the survival and delimit the period of greatest risk of mortality in these patients. The high rate of acute mesenteric ischemia was notable, a serious and frequently fatal condition.
Multifunctional Nanobubbles Carrying Indocyanine Green and Paclitaxel for Molecular Imaging and Treatment of Prostate Cancer
Authors: Lan Minmin , Zhu Lianhua , Wang Yixuan , Shen Dajia , Fang Kejing , Liu Yu , Peng Yanli , Qiao Bin , Guo Yanli 
Published: February 2020

Abstract
Background: Combining ultrasound imaging with photoacoustic imaging provides tissue imaging with high contrast and high resolution, thereby enabling rapid and direct measurement and tracking of tumor growth and metastasis. At the same time, ultrasound targeted nanobubble destruction (UTND) provides an effective way to drug accumulation; effectively increasing the content of the drug in the tumor area and reducing potential side effects, thereby contributing effectively to the treatment of the tumors.Result: In this study, we prepared multifunctional nanobubbles (NBs) carrying indocyanine green (ICG) and paclitaxel (PTX) (ICG-PTX NBs), and study their application in ultrasound imaging of prostate cancer as well as their therapeutic effect on prostate cancer when combined with ultrasound targeted nanobubble destruction (UTND). ICG-PTX NBs were prepared by mechanical oscillation method. Their particle size and Zeta potential of ICG-PTX NBs were 469.5±32.87 nm and -21.70±1.222 mV, respectively. The encapsulation efficiency and drug loading efficiency of ICG were 68% and 6.2%, respectively. In vitro imaging experiments showed that ICG-PTX NBs were highly amenable to multimodal imaging including ultrasound, photoacoustic and fluorescence imaging, and the imaging effect is positively correlated with their concentration. The imaging effect of tumor xenografts also indicated that ICG-PTX NBs were of good use for multimodal imaging. In experiments testing the growth of PC-3 cells in vitro and tumor xenografts in vivo, the ICG-PTX NBs+US group showed more significant inhibition of cell proliferation and promotion of cell apoptosis compared to the other groups (P < 0.05). Blood biochemical analysis of the six groups showed that the levels of aspartate aminotransferase (AST), phenylalanine aminotransferase (ALT), serum creatinine (CRE) and blood urea nitrogen (BUN) in the ICG-PTX NBs group and the ICG-PTX NBs+US group were significantly lower than those in the PTX group (P < 0.05). Moreover, H&E staining of tissue sections from vital organ showed no obvious abnormalities in the ICG-PTX NBs group and the ICG-PTX NBs+US group.Conclusions: ICG-PTX NBs can be used as a non-invasive, pro-apoptotic contrast agent for both diagnosis and treatment that can achieve enhanced imaging, effective inhibition and killing of prostate cancer under the guidance of multimodal imaging including ultrasound, fluorescence and photoacoustic imaging.