Biobank | Date: 2000-12-04
Computer software for scientific and commercial purposes, namely, analysis of biomolecules; evaluation of nucleic acid and protein sequences; chemical, clinical, medicinal and biological databases searches and analysis; analysis of physiological and genetic data, namely, hereditary phenotypes, genotypes, biological and genetic markers, nucleic acid or protein polymorphisms and mutations; analysis of chemical formulae; prediction of primary, secondary, and tertiary structure of biological and chemical molecules; prediction of activity and function of biological and chemical molecules; prediction of interaction between biological and chemical molecules; visualization of the structure, activity and interaction of biological and chemical molecules in two or three dimensions..
Tellier C.,University of Namur |
Desmet D.,University of Namur |
Petit L.,University of Leuven Medical School |
Finet L.,BIOBANK |
And 4 more authors.
Neoplasia (New York, N.Y.) | Year: 2015
Abnormal architecture of the tumor blood network, as well as heterogeneous erythrocyte flow, leads to temporal fluctuations in tissue oxygen tension exposing tumor and stromal cells to cycling hypoxia. Inflammation is another feature of tumor microenvironment and is considered as a new enabling characteristic of tumor progression. As cycling hypoxia is known to participate in tumor aggressiveness, the purpose of this study was to evaluate its role in tumor-promoting inflammation. Firstly, we assessed the impact of cycling hypoxia in vitro on endothelial inflammatory response induced by tumor necrosis factor α. Results showed that endothelial cells exposed to cycling hypoxia displayed an amplified proinflammatory phenotype, characterized by an increased expression of inflammatory cytokines, namely, interleukin (IL)-6 and IL-8; by an increased expression of adhesion molecules, in particular intercellular adhesion molecule-1 (ICAM-1); and consequently by an increase in THP-1 monocyte adhesion. This exacerbation of endothelial inflammatory phenotype occurs through nuclear factor-κB overactivation. Secondly, the role of cycling hypoxia was studied on overall tumor inflammation in vivo in tumor-bearing mice. Results showed that cycling hypoxia led to an enhanced inflammation in tumors as prostaglandin-endoperoxide synthase 2 (PTGS2), IL-6, CXCL1 (C-X-C motif ligand 1), and macrophage inflammatory protein 2 (murine IL-8 functional homologs) mRNA expression was increased and as a higher leukocyte infiltration was evidenced. Furthermore, cycling hypoxia-specific inflammatory phenotype, characterized by a simultaneous (baculoviral inhibitor of apoptosis repeat-containing 5)(low)/PTGS2(high)/ICAM-1(high)/IL-6(high)/IL-8(high) expression, is associated with a poor prognosis in human colon cancer. This new phenotype could thus be used in clinic to more precisely define prognosis for colon cancer patients. In conclusion, our findings evidenced for the first time the involvement of cycling hypoxia in tumor-promoting inflammation amplification. Copyright © 2014 Neoplasia Press, Inc. Published by Elsevier Inc. All rights reserved. Source
Mirghani H.,Gustave Roussy Cancer Campus |
Casiraghi O.,Gustave Roussy Cancer Campus |
Amen F.,Peterborough City Hospital |
He M.,Advanced Cell Diagnostics, Inc. |
And 11 more authors.
Modern Pathology | Year: 2015
Accurate screening of HPV-driven head and neck squamous cell carcinoma is a critical issue. Although there are commercial direct and indirect assays for HPV-related head and neck squamous cell carcinoma, none are ideal. Recently, a novel RNA in situ hybridization test (the RNAscope HPV-test) has been developed for the detection of high-risk HPV E6/E7 mRNA in formalin-fixed paraffin-embedded tissue. However, validation of this assay against the 'gold standard' (identification of high-risk HPV E6/E7 mRNA in fresh-frozen tissue by quantitative real-time (qRT)-PCR) has only been reported by one team. Formalin-fixed paraffin-embedded samples from 50 patients with tonsil or tongue base carcinoma were tested using the RNAscope HPV-test, p16 immunohistochemistry, and chromogenic in situ hybridization for high-risk HPV-DNA. The results were compared with those of qRT-PCR on matched fresh-frozen samples. Compared with the reference test, the sensitivity, specificity, positive, and negative predictive values of the RNAscope HPV-test and of p16 immunohistochemistry were 93%, 94%, 96%, 88% and 96%, 93%, 96%, and 93%, respectively. Five cases were discrepant between the RNAscope HPV-test and p16-immunohistochemisrty. The RNAscope HPV-test demonstrated excellent analytical performance against the 'gold standard' and is easier to interpret than chromogenic in situ hybridization. p16-immunohistochemistry also performed very well, however its main weakness is that it is an indirect marker of the presence of HPV. These data suggest that the RNAscope HPV-test is a promising test that could be developed as a clinical standard for the precise identification of HPV-driven oropharyngeal squamous cell carcinoma. © 2015 USCAP, Inc. Source
Suarez-Garcia I.,Infectious Diseases Unit |
Sobrino-Vegas P.,National Epidemiology Center |
Tejada A.,Ramon y Cajal Hospital |
Viciana P.,Virgen del Rocio Hospital |
And 28 more authors.
HIV Medicine | Year: 2014
Objectives: The aim of the study was to assess the adequacy of initial antiretroviral therapy (ART), in terms of its timing and the choice of regimens, according to the Spanish national treatment guidelines [Spanish AIDS Study Group-National Plan for AIDS (GeSIDA-PNS) Guidelines] for treatment-naïve HIV-infected patients. Methods: A prospective cohort study of HIV-positive ART-naïve subjects attending 27 centres in Spain from 2004 to 2010 was carried out. Regimens were classified as recommended, alternative or nonrecommended according to the guidelines. Delayed start of treatment was defined as starting treatment later than 12 months after the patient had fulfilled the treatment criteria. Multivariate logistic and Cox regression analyses were performed. Results: A total of 6225 ART-naïve patients were included in the study. Of 4516 patients who started treatment, 91.5% started with a recommended or alternative treatment. The use of a nonrecommended treatment was associated with a CD4 count>500 cells/μL [odds ratio (OR) 2.03; 95% confidence interval (CI) 1.14-3.59], hepatitis B (OR 2.23; 95% CI 1.50-3.33), treatment in a hospital with <500 beds, and starting treatment in the years 2004-2006. Fourteen per cent of the patients had a delayed initiation of treatment. Delayed initiation of treatment was more likely in injecting drug users, patients with hepatitis C, patients with higher CD4 counts and during the years 2004-2006, and it was less likely in patients with viral loads>5 log HIV-1 RNA copies/ml. The use of a nonrecommended regimen was significantly associated with mortality [hazard ratio (HR) 1.61; 95% CI 1.03-2.52; P=0.035] and lack of virological response. Conclusions: Compliance with the recommendations of Spanish national guidelines was high with respect to the timing and choice of initial ART. The use of nonrecommended regimens was associated with a lack of virological response and higher mortality. © 2013 British HIV Association. Source
Takahata M.,BIOBANK |
Fremont M.,VF Bioscience |
Desreumaux P.,University of Lille Nord de France |
Desreumaux P.,French Institute of Health and Medical Research |
And 6 more authors.
Journal of Functional Foods | Year: 2014
Infection of mice with Citrobacter rodentium serves as a model to study human intestinal infections. C. rodentium infection leads to increased production of inflammatory cytokines, immune cell infiltration and damage to the gut barrier. We used this model of colitis to evaluate the therapeutic properties of OM-X®, an extract prepared by fermentation of vegetables, seaweeds, fruits and mushrooms. Administration of OM-X® to C. rodentium-infected mice reduced damage to the intestinal epithelium, lowered inflammation scores, increased IL-10 expression and maintained FoxP3 gene expression. OM-X® also partially prevented bacterial translocation, increased expression of tight junction genes and increased proliferation of epithelial cells. PCR analysis of stool samples showed that OM-X® significantly reduced the populations of bacteria harboring buk gene (mostly Clostridium species). It is suggested that alterations of microbiota composition, following OM-X® consumption, contribute to protection against infection and epithelial damage, and lead to an increased expression of anti-inflammatory cytokines. © 2014 The Authors. Source