Detecting and sorting targeting peptides wtih neural networks and support vector machines

This paper presents a composite multi-layer classifier system for predicting the subcellular localization of proteins based on their amino acid sequence. The work is an extension of our previous predictor PProwler v1.1 which is itself built upon the series of predictors SignalP and TargetP. In this study we outline experiments conducted to improve the classifier design. The major improvement came from using Support Vector machines as a "smart gate" sorting the outputs of several different targeting peptide detection networks. Our final model (PProwler v1.2) gives MCC values of 0.873 for non-plant and 0.849 for plant proteins. The model improves upon the accuracy of our previous subcellular localization predictor (PProwler v1.1) by 2% for plant data (which represents 7.5% improvement upon TargetP).

Genes for the majority of group A streptococcal virulence factors and extracellular surface proteins do not confer an increased propensity to cause invasive disease

Background. The factors behind the reemergence of severe, invasive group A streptococcal (GAS) diseases are unclear, but it could be caused by altered genetic endowment in these organisms. However, data from previous studies assessing the association between single genetic factors and invasive disease are often conflicting, suggesting that other, as-yet unidentified factors are necessary for the development of this class of disease. Methods. In this study, we used a targeted GAS virulence microarray containing 226 GAS genes to determine the virulence gene repertoires of 68 GAS isolates (42 associated with invasive disease and 28 associated with noninvasive disease) collected in a defined geographic location during a contiguous time period. We then employed 3 advanced machine learning methods (genetic algorithm neural network, support vector machines, and classification trees) to identify genes with an increased association with invasive disease. Results. Virulence gene profiles of individual GAS isolates varied extensively among these geographically and temporally related strains. Using genetic algorithm neural network analysis, we identified 3 genes with a marginal overrepresentation in invasive disease isolates. Significantly, 2 of these genes, ssa and mf4, encoded superantigens but were only present in a restricted set of GAS M-types. The third gene, spa, was found in variable distributions in all M-types in the study. Conclusions. Our comprehensive analysis of GAS virulence profiles provides strong evidence for the incongruent relationships among any of the 226 genes represented on the array and the overall propensity of GAS to cause invasive disease, underscoring the pathogenic complexity of these diseases, as well as the importance of multiple bacteria and/ or host factors.

A real options based method for power system planning

A deregulated electricity market is characterized with uncertainties, with both long and short terms. As one of the major long term planning issues, the transmission expansion planning (TEP) is aiming at implementing reliable and secure network support to the market participants. The TEP covers two major issues: technical assessment and financial evaluations. Traditionally, the net present value (NPV) method is the most accepted for financial evaluations, it is simple to conduct and easy to understand. Nevertheless, TEP in a deregulated market needs a more dynamic approach to incorporate a project's management flexibility, or the managerial ability to adapt in response to unpredictable market developments. The real options approach (ROA) is introduced here, which has clear advantage on counting the future course of actions that investors may take, with understandable results in monetary terms. In the case study, a Nordic test system has been testified and several scenarios are given for network expansion planning. Both the technical assessment and financial evaluation have been conducted in the case study.

Telemedical support for Iraq

The Swinfen Charitable Trust (SCT) provided two kinds of telemedical support to Iraq during 2004. Starting in January 2004, the Al-Yarmouk Teaching Hospital in Baghdad was able to refer cases into the well established global e-health network that the SCT has operated for the last five years. (In the first quarter of 2004, the SCT dealt with a total of 57 referrals from 15 hospitals in eight countries.) Two cases were referred from Baghdad in March 2004, both gynaecological, which were dealt with by consultants from the UK and Australia. The SCT administrators visited Basrah during April 2004 and met Iraqi doctors at the Shaibah Hospital as part of the international initiatives to improve health care there. Following this visit, the SCT network expanded to include another four hospitals in Iraq (Table 1). In addition, the SCT provided an electronic health records (EHR) system to support the rebuilding of maternity services, which has been led by the British Royal Colleges. The maternity records system is a Web-based EHR system, running on a secure server, which allows integrated access from antenatal clinics, from hospitals and from postnatal clinics in Iraq. Patients can view their own notes, thus promoting ownership of medical information, and doctors can view the notes of their own patients, from any Internet-connected PC. No special software is required by the user.

Relations between social support, appraisal and coping and both positive and negative outcomes for children of a parent with multiple sclerosis and comparisons with children of healthy parents

Objective: To examine adjustment in children of a parent with multiple sclerosis within a stress and coping framework and compare them with those who have 'healthy' parents. Subjects: A total of 193 participants between 10 and 25 years completed questionnaires; 48 youngsters who had a parent with multiple sclerosis and 145 youngsters who reported that they did not have a parent with an illness or disability. Method: A questionnaire survey methodology was used. Variable sets included caregiving context (e.g. additional parental illness, family responsibilities, parental functional impairment, choice in helping), social support (network size, satisfaction), stress appraisal, coping (problem solving, seeking support, acceptance, wishful thinking, denial), and positive (life satisfaction, positive affect, benefits) and negative (distress, health) adjustment outcomes. Results: Caregiving context variables significantly correlated with poorer adjustment in children of a parent with multiple sclerosis included additional parental illness, higher family responsibilities, parental functional impairment and unpredictability of the parent's multiple sclerosis, and less choice in helping. As predicted, better adjustment in children of a parent with multiple sclerosis was related to higher levels of social support, lower stress appraisals, greater reliance on approach coping strategies (problem solving, seeking support and acceptance) and less reliance on avoidant coping (wishful thinking and denial). Compared with children of 'healthy' parents, children of a parent with multiple sclerosis reported greater family responsibilities, less reliance on problem solving and seeking social support coping, higher somatization and lower life satisfaction and positive affect. Conclusions: Findings delineate the key impacts of young caregiving and support a stress and coping model of adjustment in children of a parent with multiple sclerosis.

An FPGA network architecture for accelerating 3DES - CBC

This paper presents a DES/3DES core that will support cipher block chaining (CBC) and also has a built in keygen that together take up about 10% of the resources in a Xilinx Virtex II 1000-4. The core will achieve up to 200Mbit/s of encryption or decryption. Also presented is a network architecture that will allow these CBC capable 3DES cores to perform their processing in parallel.