A Factor Graph Approach to Automated GO Annotation

As volume of genomic data grows, computational methods become essential for providing a first glimpse onto gene annotations. Automated Gene Ontology (GO) annotation methods based on hierarchical ensemble classification techniques are particularly interesting when interpretability of annotation results is a main concern. In these methods, raw GO-term predictions computed by base binary classifiers are leveraged by checking the consistency of predefined GO relationships. Both formal leveraging strategies, with main focus on annotation precision, and heuristic alternatives, with main focus on scalability issues, have been described in literature. In this contribution, a factor graph approach to the hierarchical ensemble formulation of the automated GO annotation problem is presented. In this formal framework, a core factor graph is first built based on the GO structure and then enriched to take into account the noisy nature of GO-term predictions. Hence, starting from raw GO-term predictions, an iterative message passing algorithm between nodes of the factor graph is used to compute marginal probabilities of target GO-terms. Evaluations on Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster protein sequences from the GO Molecular Function domain showed significant improvements over competing approaches, even when protein sequences were naively characterized by their physicochemical and secondary structure properties or when loose noisy annotation datasets were considered. Based on these promising results and using Arabidopsis thaliana annotation data, we extend our approach to the identification of most promising molecular function annotations for a set of proteins of unknown function in Solanum lycopersicum.Fil: Spetale, Flavio Ezequiel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas. Universidad Nacional de Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas; ArgentinaFil: Krsticevic, Flavia Jorgelina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas. Universidad Nacional de Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas; ArgentinaFil: Roda, Fernando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas. Universidad Nacional de Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas; ArgentinaFil: Bulacio, Pilar Estela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas. Universidad Nacional de Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas; Argentin

Application of Neurochemical Markers for Assessing Health Effects after Developmental Methylmercury and PCB Coexposure

Cholinergic muscarinic receptors (MRs) and monoamine oxidase activity (MAO-B), expressed both in brain and blood cells, were investigated in animals and exposed subjects to assess (i) MeHg (0.5–1 mg/kg/day GD7-PD7) and/or PCB153 (20 mg/kg/day GD10–GD16) effects on cerebellar MAO-B and MRs, and lymphocyte MRs, in dams and offspring 21 days postpartum; (ii) MAO-B in platelets and MRs in lymphocytes of a Faroese 7-year-old children cohort, prenatally exposed to MeHg/PCBs. Animal Data. MAO-B was altered in male cerebellum by MeHg, PCB153, and their combination (35%, 45%, and 25% decrease, resp.). Cerebellar MRs were enhanced by MeHg alone in dams (87%) and male pups (27%). PCB153 alone and in mixture did not modify cerebellar MRs. Similarly to brain, lymphocyte MRs were enhanced in both dams and offspring by MeHg alone. All changes were caused by 1 MeHg mg/kg/day, the lower dose was ineffective. Human Data. Both biomarkers showed homogeneous distributions within the cohort (MRs, range 0.1–36.78 fmol/million cells; MAO-B, 0.95–14.95 nmol/mg protein/h). No correlation was found between the two biomarkers and neurotoxicant concentrations in blood (pre- and postnatally)

Determination of propofol by GC/MS and fast GC/MS-TOF in two cases of poisoning

Two cases of suspected acute and lethal intoxication caused by propofol were delivered by the judicial authority to the Department of Sciences for Health Promotion and Mother-Child Care in Palermo, Sicily. In the first case a female nurse was found in a hotel room, where she lived with her mother; four 10 mg/mL vials and two 20 mg/mL vials of propofol were found near the decedent along with syringes and needles. In the second case a male nurse was found in the operating room of a hospital, along with a used syringe. In both cases a preliminary systematic and toxicological analysis indicated the presence of propofol in the blood and urine. As a result, a method for the quantitative determination of propofol in biological fluids was optimized and validated using a liquid-liquid extraction protocol followed by GC/MS and fast GC/MS-TOF. In the first case, the concentration of propofol in blood was determined to be 8.1 \u3bcg/mL while the concentration of propofol in the second case was calculated at 1.2 \u3bcg/mL. Additionally, the tissue distribution of propofol was determined for both cases. Brain and liver concentrations of propofol were, respectively, 31.1 and 52.2 \u3bcg/g in Case 1 and 4.7 and 49.1 \u3bcg/g in Case 2. Data emerging from the autopsy findings, histopathological exams as well as the toxicological results aided in establishing that the deaths were due to poisoning, however, the manner of death in each were different: homicide in Case 1 and suicide in Case 2

Relativistic simulations of rotational core collapse : II. Collapse dynamics and gravitational radiation

We have performed hydrodynamic simulations of relativistic rotational supernova core collapse in axisymmetry and have computed the gravitational radiation emitted by such an event. The Einstein equations are formulated using the conformally flat metric approximation, and the corresponding hydrodynamic equations are written as a first-order flux-conservative hyperbolic system. Details of the methodology and of the numerical code have been given in an accompanying paper. We have simulated the evolution of 26 models in both Newtonian and relativistic gravity. The initial configurations are di erentially rotating relativistic 4=3-polytropes in equilibrium which have a central density of 10^10 g cm^−3. Collapse is initiated by decreasing the adiabatic index to some prescribed fixed value. The equation of state consists of a polytropic and a thermal part for a more realistic treatment of shock waves. Any microphysics like electron capture and neutrino transport is neglected. Our simulations show that the three di erent types of rotational supernova core collapse and gravitational waveforms identified in previous Newtonian simulations (regular collapse, multiple bounce collapse, and rapid collapse) are also present in relativistic gravity. However, rotational core collapse with multiple bounces is only possible in a much narrower parameter range in relativistic gravity. The relativistic models cover almost the same range of gravitational wave amplitudes (4x10^−21 <= h^TT 3x10^−20 for a source at a distance of 10 kpc) and frequencies (60 Hz <= ν <= 1000 Hz) as the corresponding Newtonian ones. Averaged over all models, the total energy radiated in the form of gravitational waves is 8.2 10^−8 Moc^2 in the relativistic case, and 3.6 10^−8 Moc^2 in the Newtonian case. For all collapse models that are of the same type in both Newtonian and relativistic gravity, the gravitational wave signal is of lower amplitude. If the collapse type changes, either weaker or stronger signals are found in the relativistic case. For a given model, relativistic gravity can cause a large increase of the characteristic signal frequency of up to a factor of five, which may have important consequences for the signal detection. Our study implies that the prospects for detection of gravitational wave signals from axisymmetric supernova rotational core collapse do not improve when taking into account relativistic gravity. The gravitational wave signals obtained in our study are within the sensitivity range of the first generation laser interferometer detectors if the source is located within the Local Group. An online catalogue containing the gravitational wave signal amplitudes and spectra of all our models is available at the URL http://www.mpa-garching.mpg.de/Hydro/hydro.html.Font Roda, Jose Antonio, [email protected]

Determination of daptomycin in human plasma and breast milk by UPLC/MS-MS

During the lactation, the choice of a proper antibiotic is crucial since the drug can cross into breast milk causing toxicity to the infant. Therefore, an extraction protocol and LC/MS-MS method for the determination of daptomycin in human milk and plasma were developed, validated and applied to a case of a breastfeeding mother affected by a purulent acute soft skin infection treated with daptomycin. Because of daptomycin high protein binding and its high molecular weight, the optimisation of the extraction protocol and analytical conditions were deeply investigated, and several parameters were taken into account: in particular the type of extraction, internal standard, the type of organic modifier, pH of the aqueous solution, and gradient. The use of a protein precipitation protocol coupled to a C8-reverse phase LC-MS/MS allows for a reliable quantification of daptomycin in both plasma (in the range of 19\u2013199 \u3bcg/mL) and breast milk (in the range of 0.12\u20130.32 \u3bcg/mL). The determination of milk/plasma (M/P) ratio, which ranged from 0.002 to 0.006, allowed to assess that daptomycin, effective for the mother, was contemporarily safe for the breastfed newborn

A device to characterize optical fibres

ATLAS is a general purpose experiment approved for the LHC collider at CERN. An important component of the detector is the central hadronic calorimeter; for its construction more than 600,000 Wave Length Shifting (WLS) fibres (corresponding to a total length of 1,120 Km) have been used. We have built and put into operation a dedicated instrument for the measurement of light yield and attenuation length over groups of 20 fibres at a time. The overall accuracy achieved in the measurement of light yield (attenuation length) is 1.5% (3%). We also report the results obtained using this method in the quality control of a large sample of fibres.Comment: 17 pages 20 figeres submitted to NIM journa