Towards a logic-based method to infer provenance-aware molecular networks

International audienceProviding techniques to automatically infer molecular networks is particularly important to understand complex relationships between biological objects. We present a logic-based method to infer such networks and show how it allows inferring signalling networks from the design of a knowledge base. Provenance of inferred data has been carefully collected, allowing quality evaluation. More precisely, our method (i) takes into account various kinds of biological experiments and their origin; (ii) mimics the scientist's reasoning within a first-order logic setting; (iii) specifies precisely the kind of interaction between the molecules; (iv) provides the user with the provenance of each interaction; (v) automatically builds and draws the inferred network

Comparative Performance Analysis of State-of-the-Art Classification Algorithms Applied to Lung Tissue Categorization

In this paper, we compare five common classifier families in their ability to categorize six lung tissue patterns in high-resolution computed tomography (HRCT) images of patients affected with interstitial lung diseases (ILD) and with healthy tissue. The evaluated classifiers are naive Bayes, k-nearest neighbor, J48 decision trees, multilayer perceptron, and support vector machines (SVM). The dataset used contains 843 regions of interest (ROI) of healthy and five pathologic lung tissue patterns identified by two radiologists at the University Hospitals of Geneva. Correlation of the feature space composed of 39 texture attributes is studied. A grid search for optimal parameters is carried out for each classifier family. Two complementary metrics are used to characterize the performances of classification. These are based on McNemar's statistical tests and global accuracy. SVM reached best values for each metric and allowed a mean correct prediction rate of 88.3% with high class-specific precision on testing sets of 423 ROI

The prodrome of autism: early behavioral and biological signs, regression, peri- and post-natal development and genetics

Autism is one of the most heritable neurodevelopmental conditions and has an early onset, with symptoms being required to be present in the first 3 years of life in order to meet criteria for the ‘core’ disorder in the classification systems. As such, the focus on identifying a prodrome over the past 20 years has been on pre-clinical signs or indicators that will be present very early in life, certainly in infancy. A number of novel lines of investigation have been used to this end, including retrospective coding of home videos, prospective population screening and ‘high risk’ sibling studies; as well as the investigation of pre- and peri-natal, brain developmental and other biological factors. Whilst no single prodromal sign is expected to be present in all cases, a picture is emerging of indicative prodromal signs in infancy and initial studies are being undertaken to attempt to ameliorate the early presentation and even ‘prevent’ emergence of the full syndrome

Malignant catatonia due to anti-NMDA-receptor encephalitis in a 17-year-old girl: case report

Anti-NMDA-Receptor encephalitis is a severe form of encephalitis that was recently identified in the context of acute neuropsychiatric presentation. Here, we describe the case of a 17-year-old girl referred for an acute mania with psychotic features and a clinical picture deteriorated to a catatonic state. Positive diagnosis of anti-NMDA-receptor encephalitis suggested specific treatment. She improved after plasma exchange and immunosuppressive therapy. Post-cognitive sequelae (memory impairment) disappeared within 2-year follow-up and intensive cognitive rehabilitation

Towards a logic-based method to infer provenance-aware molecular networks

International audienceProviding techniques to automatically infer molecular networks is particularly important to understand complex relationships between biological objects. We present a logic-based method to infer such networks and show how it allows inferring signalling networks from the design of a knowledge base. Provenance of inferred data has been carefully collected, allowing quality evaluation. More precisely, our method (i) takes into account various kinds of biological experiments and their origin; (ii) mimics the scientist's reasoning within a first-order logic setting; (iii) specifies precisely the kind of interaction between the molecules; (iv) provides the user with the provenance of each interaction; (v) automatically builds and draws the inferred network

Screening for Staphylococcal Superantigen Genes Shows No Correlation with the Presence or the Severity of Chronic Rhinosinusitis and Nasal Polyposis

BACKGROUND: Staphylococcus aureus secretes numerous exotoxins which may exhibit superantigenic properties. Whereas the virulence of several of them is well documented, their exact biological effects are not fully understood. Exotoxins may influence the immune and inflammatory state of various organs, including the sinonasal mucosa: their possible involvement in chronic rhinosinusitis has been suggested and is one of the main trends in current research. The aim of this study was to investigate whether the presence of any of the 22 currently known staphylococcal exotoxin genes could be correlated with chronic rhinosinusitis. METHODOLOGY/PRINCIPAL FINDINGS: We conducted a prospective, multi-centred European study, analysing 93 Staphylococcus aureus positive swabs taken from the middle meatus of patients suffering from chronic rhinosinusitis, with or without nasal polyposis, and controls. Strains were systematically tested for the presence of the 22 currently known exotoxin genes and genotyped according to their agr groups. No direct correlation was observed between chronic rhinosinusitis, with or without nasal polyposis, and either agr groups or the presence of the most studied exotoxins genes (egc, sea, seb, pvl, exfoliatins or tsst-1). However, genes for enterotoxins P and Q were frequently observed in nasal polyposis for the first time, but absent in the control group. The number of exotoxin genes detected was not statistically different among the 3 patient groups. CONCLUSIONS/SIGNIFICANCE: Unlike many previous studies have been suggesting, we did not find any evident correlation between staphylococcal exotoxin genes and the presence or severity of chronic rhinosinusitis with or without nasal polyposis

Burn wounds infected with Pseudomonas aeruginosa triggers weight loss in rats

BACKGROUND: Despite dramatic improvements in the management of burns, infection still remains a serious risk for the burn patient. The aim of this study was to shed light on the impact of acute burn injury with or without infection on cytokine profiles. METHODS: Sprague-Dawley rats (n = 21) were randomized into three groups: 1) burn only 2) burn and infection or 3) sham burn. Weight was monitored and blood was collected for cytokine ELISA, LPS quantification, and peripheral blood analysis. Animals were sacrificed either after 6 or 12 days. RESULTS: Infected animals showed substantial weight loss until day 6 post-burn as compared to burn alone. Endotoxin and TNF-α levels were elevated early in the infected burn group within 48 hours post-burn. In contrast, significant up-regulation of the anti-inflammatory cytokine IL-10 occurred later in the clinical course and was associated with the recovery from weight loss. CONCLUSION: Our results suggest that in the presence of infection, you get a SIRS response possibly due to transient endotoxemia that is only seen in the infection group. In contrast, both burn and infection get a late IL-10 (CARS) response, which is then associated with a return to normal weight in the infection group

Education as a Predictor of Chronic Periodontitis: A Systematic Review with Meta-Analysis Population-Based Studies

The impact of socioeconomic inequalities on health is well-documented. Despite the links of periodontal disease with cardiovascular diseases, adverse pregnancy outcomes and diabetes, no meta-analysis of socioeconomic variations in periodontal disease exists. This meta-analytic review was conducted to determine the extent to which education attainment influences risk of periodontitis in adults aged 35+ years in the general population.The authors searched studies published until November 2010 using EMBASE and MEDLINE databases. References listed were then scrutinised, our own files were checked, and, finally, we contacted experts in the field. The authors included only general population-based studies conducted in adults aged 35 years and more. All articles were blind reviewed by two investigators. In the case of disagreement, a third investigator arbitrated. Using PRISMA statement, two reviewers independently extracted papers of interest.Relative to the higher education group, people with low education attainment experience a greater risk of periodontitis (OR: 1.86 [1.66–2.10]; p<0.00001). The association was partially attenuated after adjustment for covariates (OR: 1.55 [1.30–1.86]; p<0.00001). Sensitivity analyses showed that methods used to assess periodontitis, definition of cases, study country and categorization of education are largely responsible for the heterogeneity between studies. No significant bias of publication was shown using both the Egger (p = 0.16) and rank correlation tests (p = 0.35).In the studies reviewed, low educational attainment was associated with an increased risk of periodontitis. Although this evidence should be cautiously interpreted due to methodological problems in selected studies, efforts to eliminate educational inequalities in periodontitis should focus on early life interventions