1,721,052 research outputs found
Visita Massachusetts Institute of Technology (MIT)
No full textOptimization and ontology for computational and system biolog
OREMPdb: a semantic dictionary of computational pathway models
No full textFrom Eighth Annual Meeting of the Italian Society of Bioinformatics (BITS)
Pisa, Italy. 20-22 June 2011Background The information coming from biomedical ontologies and computational pathway models is expanding continuously: research communities keep this process up and their advances are generally shared by means of dedicated resources published on the web. In fact, such models are shared to provide the characterization of molecular processes, while biomedical ontologies detail a semantic context to the majority of those pathways. Recent advances in both fields pave the way for a scalable information integration based on aggregate knowledge repositories, but the lack of overall standard formats impedes this progress. Indeed, having different objectives and different abstraction levels, most of these resources "speak" different languages. Semantic web technologies are here explored as a means to address some of these problems. Methods Employing an extensible collection of interpreters, we developed OREMP (Ontology Reasoning Engine for Molecular Pathways), a system that abstracts the information from different resources and combines them together into a coherent ontology. Continuing this effort we present OREMPdb; once different pathways are fed into OREMP, species are linked to the external ontologies referred and to reactions in which they participate. Exploiting these links, the system builds species-sets, which encapsulate species that operate together. Composing all of the reactions together, the system computes all of the reaction paths from-and-to all of the species-sets. Results OREMP has been applied to the curated branch of BioModels (2011/04/15 release) which overall contains 326 models, 9244 reactions, and 5636 species. OREMPdb is the semantic dictionary created as a result, which is made of 7360 species-sets. For each one of these sets, OREMPdb links the original pathway and the link to the original paper where this information first appeared.Università degli studi della Calabria (PhD student fellowship)Singapore-MIT Alliance for Research and Technology (Program in Computational and Systems Biology)Università di Catani
Novel method for automated analysis of retinal images. results in subjects with hypertensive retinopathy and CADASIL
Full text linkMorphological analysis of the retinal vessels by fundoscopy provides noninvasive means for detecting and staging systemic microvascular damage. However, full exploitation of fundoscopy in clinical settings is limited by paucity of quantitative, objective information obtainable through the observer-driven evaluations currently employed in routine practice. Here, we report on the development of a semiautomated, computer-based method to assess retinal vessel morphology. The method allows simultaneous and operator-independent quantitative assessment of arteriole-to-venule ratio, tortuosity index, and mean fractal dimension. The method was implemented in two conditions known for being associated with retinal vessel changes: hypertensive retinopathy and Cerebral Autosomal Dominant Arteriopathy with Subcortical Infarcts and Leukoencephalopathy (CADASIL). The results showed that our approach is effective in detecting and quantifying the retinal vessel abnormalities. Arteriole-to-venule ratio, tortuosity index, and mean fractal dimension were altered in the subjects with hypertensive retinopathy or CADASIL with respect to age- and gender-matched controls. The interrater reliability was excellent for all the three indices (intraclass correlation coefficient ≥ 85%). The method represents simple and highly reproducible means for discriminating pathological conditions characterized by morphological changes of retinal vessels. The advantages of our method include simultaneous and operator-independent assessment of different parameters and improved reliability of the measurements
Varianti genotipiche del virus di Epstein Barr e loro usi come possibili predittori di rischio, biomarcatori e target terapeutici nella sclerosi multipla
No full textLa presente invenzione si riferisce ad un acido nucleico codificante per una variante dell’antigene nucleare 2 di Epstein Barr (EBNA2) per uso come biomarcatore per predire il rischio per lo sviluppo e/o la diagnosi e/o la prognosi della sclerosi multipla, e ad un metodo in vitro per predire il rischio per lo sviluppo e/o la diagnosi e/o la prognosi della sclerosi multipla in un soggetto, comprendente il rilevamento della presenza di detto acido nucleico
Analysis and Optimization of C3 Photosynthetic Carbon Metabolism
No full textWe have studied the C3 photosynthetic carbon metabolism centering our investigation on the following four design principles. (1) Optimization of the photosynthetic rate by modifying the partitioning of resources between the different enzymes of the C3 photosynthetic carbon metabolism using a constant amount of protein-nitrogen. (2) Identify sensitive and less sensitive enzymes of the studied model. (3) Maximize photosynthetic productivity rate through the choice of robust enzyme concentrations using a new precise definition of robustness. (4) Modeling photosynthetic carbon metabolism as a multi-objective problem of two competing biological selection pressures: light-saturated photosynthetic rate versus total protein-nitrogen requirement. Using the designed single-objective optimization algorithms, PAO and A-CMA-ES, we have obtained an increase in photosynthetic productivity of the 135% from 15.486 μmol m-2s-1 to 36.382 μmol m-2s-1, and improving the previous best-found photosynthetic productivity value (27.261 μmol m -2s-1, 76% of enhancement). Optimized enzyme concentrations express a maximal local robustness (100%) and a high global robustness (97.2%), satisfactory properties for a possible "in vitro" manufacturing of the optimized pathway. Morris sensitivity analysis shows that 11 enzymes over 23 are high sensitive enzymes, i.e., the most influential enzymes of the carbon metabolism model. Finally, we have obtained the tradeoff between the maximization of the leaf CO2 uptake rate and the minimization of the total protein-nitrogen concentration. This trade-off search has been carried out for the three ciconcentrations referring to the estimate of CO2 concentration in the atmosphere characteristic of 25 million years ago, nowadays and in 2100 a.C. Remarkably, the three Pareto frontiers identify the highest photosynthetic productivity rates together with the fewest protein-nitrogen usage. © 2010 IEEE
OREMP: Ontology Reasoning Engine for Molecular Pathways
Full text linkThe information about molecular processes is shared continuously in the form of runnable pathway collections, and biomedical ontologies provide a semantic context to the majority of those pathways. Recent advances in both fields pave the way for a scalable information integration based on aggregate knowledge repositories, but the lack of overall standard formats impedes this progress. Here we propose a strategy that integrates these resources by means of extended ontologies built on top of a common meta-format. Information sharing, integration and discovery are the primary features provided by the system; additionally, two current field applications of the system are reported
Identification of Sensitive Enzymes in the Photosynthetic Carbon Metabolism
No full textUnderstanding and optimizing the CO2 fixation process would allow human beings to address better current energy and biotechnology issues. We focused on modeling the C3 photosynthetic Carbon metabolism pathway with the aim of identifying the minimal set of enzymes whose biotechnological alteration could allow a functional re-engineering of the pathway. To achieve this result we merged in a single powerful pipe-line Sensitivity Analysis (SA), Single- (SO) and Multi-Objective Optimization (MO), and Robustness Analysis (RA). By using our recently developed multipurpose optimization algorithms (PAO and PMO2) here we extend our work exploring a large combinatorial solution space and most importantly, here we present an important reduction of the problem search space. From the initial number of 23 enzymes we have identified 11 enzymes whose targeting in the C3 photosynthetic Carbon metabolism would provide about 90% of the overall functional optimization. Both in terms of maximal CO2 Uptake and minimal Nitrogen consumption, these 11 sensitive enzymes are confirmed to play a key role. Finally we present a RA to confirm our findings. © 2012 Springer Science+Business Media, LLC
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
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