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Diagnosis and management of bacterial infections in decompensated cirrhosis

World Journal of Hepatology 2013年第1期5卷 16-25页

作者： Maria Pleguezuelo Jose Manuel Benitez juan jurado Jose Luis Montero Manuel De la Mata Liver Research Unit Reina Sofia University HospitalAvda Menendez Pidal s/n14004 CordobaSpain

Bacterial infections are one of the most frequent complications in cirrhosis and result in high mortality rates.Patients with cirrhosis have altered and impaired immunity,which favours bacterial translocation.Episodes of infections are more frequent in patients with decompensated cirrhosis than those with compensated liver disease.The most common and life-threatening infection in cirrhosis is spontaneous bacterial peritonitis followed by urinary tract infections,pneumonia,endocarditis and skin and soft-tissue infections.Patients with decompensated cirrhosis have increased risk of developing sepsis,multiple organ failure and death.Risk factors associated with the development of infections are severe liver failure,variceal bleeding,low ascitic protein level and prior episodes of spontaneous bacterial peritonitis (SBP).The prognosis of these patients is closely related to a prompt and accurate diagnosis.An appropriate treatment decreases the mortality rates.Preventive strategies are the mainstay of the management of these patients.Empirical antibiotics should be started immediately following the diagnosis of SBP and the first-line antibiotic treatment is third-generation cephalosporins.However,the efficacy of currently recommended empirical antibiotic therapy is very low in nosocomial infections including SBP,compared to community-acquired episodes.This may be associated with the emergence of infections caused by Enterococcus faecium and extended-spectrum β-lactamaseproducing Enterobacteriaceae,which are resistant to the first line antimicrobial agents used for treatment.The emergence of resistant bacteria,underlines the need to restrict the use of prophylactic antibiotics to patients with the greatest risk of infections.Nosocomial infections should be treated with wide spectrum antibiotics.Further studies of early diagnosis,prevention and treatment are needed to improve the outcomes in patients with decompensated cirrhosis.

关键词： Cirrhosis Infections Spontaneous bacterial peritonitis Ascites Antibiotics

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A Note on Extreme Points in Dual Spaces

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Acta Mathematica Sinica,English Series 2013年第3期29卷 471-476页

作者： juan Francisco MENA-jurado juan Carlos NAVARRO-PASCUAL Departamento de Análisis Matemático Facultad de Ciencias Universidad de Granada Departamento de lgebra y Análisis Matemático Universidad de Almería

Given a normed space X it can be easily proven that every extreme point in Bx＊, the unit ball of X＊, is the restriction of an extreme point in Bx Our purpose is to study when the restrictions of extreme points in B... 详细信息

关键词： Extreme point Ll-predual M-ideal

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GenoDrawing:An Autoencoder Framework for Image Prediction from SNP Markers

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Plant Phenomics 2023年第4期5卷 816-824页

作者： Federico jurado-Ruiz David Rousseau juan A.Botía Maria José Aranzana Center for Research in Agricultural Genomics(CRAG) 08193 BarcelonaCerdanyolaSpain Universitéd'Angers LARISINRAe UMR IRHS49000 AngersFrance Department of Information and Communication Engineering University of Murcia30071 MurciaSpain IRTA(Institut de Recerca i Tecnologia Agroalimentàries) BarcelonaSpain

Advancements in genome sequencing have facilitated whole-genome characterization of numerous plant species,providing an abundance of genotypic data for genomic analysis.Genomic selection and neural networks(NNs),particularly deep learning,have been developed to predict complex traits from dense genotypic data.Autoencoders,an NN model to extract features from images in an unsupervised manner,has proven to be useful for plant phenotyping.This study introduces an autoencoder framework,GenoDrawing,for predicting and retrieving apple images from a low-depth single-nucleotide polymorphism(SNP)array,potentially useful in predicting traits that are difficult to define.GenoDrawing demonstrates proficiency in its task using a small dataset of shape-related SNPs.Results indicate that the use of SNPs associated with visual traits has substantial impact on the generated images,consistent with biological interpretation.While using substantial SNPs is crucial,incorporating additional,unrelated SNPs results in performance degradation for simple NN architectures that cannot easily identify the most important inputs.The proposed GenoDrawing method is a practical framework for exploring genomic prediction in fruit tree phenotyping,particularly beneficial for small to medium breeding companies to predict economically substantial heritable traits.Although GenoDrawing has limitations,it sets the groundwork for future research in image prediction from genomic markers.Future studies should focus on using stronger models for image reproduction,SNP information extraction,and dataset balance in terms of phenotypes for more precise outcomes.

关键词： Auto Drawing prediction

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Arabidopsis SWC4 Binds DNA and Recruits the SWR1 Complex to Modulate Histone H2A.Z Deposition at Key Regulatory Genes

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Molecular Plant 2018年第6期11卷 815-832页

作者： Angeles Gomez-Zambrano Pedro Crevillen Jose M. Franco-Zorrilla juan A. Lopez Jordi Moreno-Romero Pawel Roszak juan Santos-Gonzalez Silvia jurado Jesus Vazquez Claudia Kohler Roberto Solano Manuel Pineiro Jose A. Jarillo Centro de Biotecnologia y Genomica de Plantas Universidad Politecnica de Madrid (UPM) - Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA) Campus Montegancedo UPM Pozuelo de Alarcon 28223 Madrid Spain Plant Molecular Genetics Department and Genomics Unit Centro Nacional de Biotecnologia Consejo Superior de Investigaciones Cientfficas 28049 Madrid Spain Proteomics Unit Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC) 28029 Madrid Spain Department of Plant Biology Uppsala BioCenter Swedish University of Agricultural Sciences and Linnean Center for Plant Biology Uppsala 75652 Sweden Laboratory of Cardiovascular Proteomics Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC) 28029 Madrid Spain Instituto de Bioquimica Vegetal y Fotosintesis Consejo Superior de Investigaciones Cientfficas and Universidad de Sevilla 41092 Sevilla Spain Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB Campus UAB Bellaterra Barcelona Spain The Sainsbury Laboratory Cambridge CB2 1LR UK

Deposition of the H2A.Z histone variant by the SWR1 complex （SWRI-C） in regulatory regions of specific loci modulates transcription. Characterization of mutations in Arabidopsis thaliana homologs of yeast SWRI-C has revealed a role for H2A.Z exchange in a variety of developmental processes. Nevertheless, the exact composition of plant SWRI-C and how it is recruited to target genes remains to be established. Here we show that SWC4, the Arabidopsis homolog of yeast SANT domain protein Swc4/Eaf2, is a DNA-binding protein that interacts with SWR1-C subunits. We demonstrate that the swc4-1 knockout mutant is embryo- lethal, while SWC4 RNAi knockdown lines display pleiotropic phenotypic alterations in vegetative and repro- ductive traits, including acceleration of flowering time, indicating that SWC4 controls post-embryonic processes. Transcriptomic analyses and genome-wide profiling of H2A.Z indicate that SWC4 represses tran- scription of a number of genes, including the floral integrator FT and key transcription factors, mainly by modulating H2A.Z deposition. Interestingly, SWC4 silencing does not affect H2A.Z deposition at the FLC locus nor expression of this gene, a master regulator of flowering previously shown to be controlled by SWR1-C. Importantly, we find that SWC4 recognizes specific AT-rich DNA elements in the chromatin regions of target genes and that SWC4 silencing impairs SWRI-C binding at FT. Collectively, our data suggest that SWC4 regulates plant growth and development by aiding SWR1-C recruitment and modulating H2A.Z deposition.

关键词： Arabidopsis SWC4 chromatin SWR1 complex H2A.Z deposition flowering time

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Rare germline copy number variants in colorectal cancer predisposition characterized by exome sequencing analysis

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Journal of Genetics and Genomics 2018年第1期45卷 41-45页

作者： Sebastia Franch-Exposito Clara Esteban-jurado Pilar Garre Isabel Quintanilla Saray Duran-Sanchon Marcos Diaz-Gay Laia Bonjoch Miriam Cuatrecasas Esther Samper Jenifer Munoz Teresa Ocana Sabela Carballal Maria Lopez-Ceron Antoni Castells Maria Vila-Casadesus Sophia Derdak Steven Laurie Sergi Beltran Jaime carvajal Luis Bujanda Clara Ruiz-Ponte Jordi Camps Meritxell Gironella juan Jose Lozano Francesc Balaguer Joaquin Cubiella Trinidad Caldes Sergi Castellvi-Bel Gastroenterology Department Hospital Clinic de Barcelona August Pi i Sunyer Biomedical Research Institute CIBER of Hepatic and Digestive Diseases University of Barcelona Barcelona 08036 Spain Molecular Oncology Laboratory Hospital Clinico San Carlos Health Research Institute of the Hospital Clinico San Carlos Madrid 28040 Spain Department of Pathology Hospital Clinic de Barcelona Barcelona 08036 Spain EPICOLON consortium Bioinformatics Platform CIBER of Hepatic and Digestive Diseases Barcelona 08036 Spain National Center of Genomic Analysis Science Park of Barcelona Barcelona 08028 Spain Andalusian Developmental Biology Institute CSIC-Pablo de Olavide University-Andalusian Regional Government SeviUa 41013 Spain Gastroenterology Department Hospital Donostia-Biodonostia Institute CIBER of Hepatic and Digestive Diseases University of the Basque Country (UPV/EHU) San Sebastian 20080 Spain Galician Public Foundation of Genomic Medicine (FPGMX) CIBER of Rare Diseases Genomics Medicine Group Hospital Clinico Universitario University of Santiago de Compostela Santiago de Cornpostela 15706 Spain Castroenterology Department Complexo Hospitalario Universitario de Ourense Ourense Biomedical Research Institute Ourense 32005 Spain

Colorectal cancer （CRC） is one of the most common neoplasms and an important cause of mortality worldwide （http：//globocan. iarc.fr]）. Approximately 35% of the variation in CRC susceptibility is likely due to heritable factors （Lichtenstein et al., 2000}. Genetic variations in the human genome include single nucleotide variants （SNVs）, short insertions and deletions, and larger structural variants resulting in gain or loss of genomic DNA larger than 1 kb, such as copy number variants （CNVs）. Leaving aside the importance of CNVs in sporadic tumor development, these variants can also be present in the germline DNA of healthy individuals from the general population and be considered polymorphic.

关键词： WHOLE-EXOME GENE

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New genes emerging for colorectal cancer predisposition

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World Journal of Gastroenterology 2014年第8期20卷 1961-1971页

作者： Clara Esteban-jurado Pilar Garre Maria Vila juan José Lozano Anna Pristoupilova Sergi Beltrán Anna Abulí Jenifer Muoz Francesc Balaguer Teresa Ocaa Antoni Castells Josep M Piqué Angel Carracedo Clara Ruiz-Ponte Xavier Bessa Montserrat Andreu Luis Bujanda Trinidad Caldés Sergi Castellví-Bel Department of Gastroenterology Hospital ClínicCentro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas(CIBEREHD)Institut d’Investigacions Biomèdiques August Pi i Sunyer(IDIBAPS)University of Barcelona08036 BarcelonaCataloniaSpain Molecular Oncology Laboratory Hospital Clínico San CarlosInstituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC)28040 MadridSpain Bioinformatics platform Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD)08036 BarcelonaSpain Centre Nacional d’Anàlisi Genòmica (CNAG) Parc Científic de Barcelona08028 BarcelonaSpain Department of Gastroenterology Hospital del Mar-IMIM (Hospital del Mar Medical Research Centre)Pompeu Fabra University08003 BarcelonaSpain Galician Public Foundation of Genomic Medicine (FPGMX) Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)Genomics Medicine GroupHospital ClínicoSantiago de CompostelaUniversity of Santiago de Compostela15706 GaliciaSpain Center of Excellence in Genomic Medicine Research King Abdulaziz University21589 JeddahKingdom of Saudi Arabia Gastroenterology Department Hospital DonostiaNetworked Biomedical Research Centre for Hepatic and Digestive Diseases (CIBEREHD)Basque Country University20080 San SebastiánSpain

Colorectal cancer(CRC)is one of the most frequent neoplasms and an important cause of mortality in the developed world.This cancer is caused by both genetic and environmental factors although 35%of the variation in CRC susceptibility involves inherited genetic differences.Mendelian syndromes account for about5%of the total burden of CRC,with Lynch syndrome and familial adenomatous polyposis the most common forms.Excluding hereditary forms,there is an important fraction of CRC cases that present familial aggregation for the disease with an unknown germline genetic cause.CRC can be also considered as a complex disease taking into account the common diseasecommom variant hypothesis with a polygenic model of inheritance where the genetic components of common complex diseases correspond mostly to variants of low/moderate effect.So far,30 common,low-penetrance susceptibility variants have been identified for CRC.Recently,new sequencing technologies including exomeand whole-genome sequencing have permitted to add a new approach to facilitate the identification of new genes responsible for human disease predisposition.By using whole-genome sequencing,germline mutations in the POLE and POLD1 genes have been found to be responsible for a new form of CRC genetic predisposition called polymerase proofreading-associated polyposis.

关键词： Colorectal neoplasm,genetic predisposition to dise

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