FunFOLDQA: a quality assessment tool for protein-ligand binding site residue predictions

The estimation of prediction quality is important because without quality measures, it is difficult to determine the usefulness of a prediction. Currently, methods for ligand binding site residue predictions are assessed in the function prediction category of the biennial Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiment, utilizing the Matthews Correlation Coefficient (MCC) and Binding-site Distance Test (BDT) metrics. However, the assessment of ligand binding site predictions using such metrics requires the availability of solved structures with bound ligands. Thus, we have developed a ligand binding site quality assessment tool, FunFOLDQA, which utilizes protein feature analysis to predict ligand binding site quality prior to the experimental solution of the protein structures and their ligand interactions. The FunFOLDQA feature scores were combined using: simple linear combinations, multiple linear regression and a neural network. The neural network produced significantly better results for correlations to both the MCC and BDT scores, according to Kendall’s τ, Spearman’s ρ and Pearson’s r correlation coefficients, when tested on both the CASP8 and CASP9 datasets. The neural network also produced the largest Area Under the Curve score (AUC) when Receiver Operator Characteristic (ROC) analysis was undertaken for the CASP8 dataset. Furthermore, the FunFOLDQA algorithm incorporating the neural network, is shown to add value to FunFOLD, when both methods are employed in combination. This results in a statistically significant improvement over all of the best server methods, the FunFOLD method (6.43%), and one of the top manual groups (FN293) tested on the CASP8 dataset. The FunFOLDQA method was also found to be competitive with the top server methods when tested on the CASP9 dataset. To the best of our knowledge, FunFOLDQA is the first attempt to develop a method that can be used to assess ligand binding site prediction quality, in the absence of experimental data.

Use of the mini nutritional assessment tool in elderly people from long-term institutions of southeast of Brazil

Background: the Mini Nutritional Assessment (MNA) is a multidimensional method of nutritional evaluation that allows the diagnosis of malnutrition and risk of malnutrition in elderly people, it is important to mention that this method has not been well studied in Brazil. Objective: to verify the use of the MNA in elderly people that has been living in long term institutions for elderly people. Design: transversal study. Participants: 89 people (>= 60 years), being 64.0% men. The average of age for both genders was 73.7 +/- 9.1 years old, being 72.8 +/- 8.9 years old for men, and 75.3 +/- 9.3 years old for women. Setting: long-term institutions for elderly people located in the Southeast of Brazil. Methods: it was calculated the sensibility, specificity, and positive and negative predictive values. It was data to set up a ROC curve to verify the accuracy of the MNA. The variable used as a ""standard"" for the nutritional diagnosis of the elderly people was the corrected arm muscle area because it is able to provide information or an estimative of the muscle reserve of a person being considered a good indicator of malnutrition in elderly people. Results: the sensibility was 84.0%, the specificity was 36.0%, the positive predictive value was 77.0%, and the negative predictive value was 47.0%; the area of the ROC curve was 0.71 (71.0%). Conclusion: the MNA method has showed accuracy, and sensibility when dealing with the diagnosis of malnutrition and risk of malnutrition in institutionalized elderly groups of the Southeastern region of Brazil, however, it presented a low specificity.

Tradução, adaptação cultural e propriedades psicométricas da versão brasileira do Short-Form of the Mobility Assessment Tool (MAT-sf)

Objectives: to translate and assess the psychometric properties of the Brazilian short-form of the Mobility Assessment Tool (MAT-sf) in Brazilians community elderly. Methds: the 12 items MAT-sf went through the process of translation and back translation into Portuguese of the Brazil, considering the semantic and cultural adaptation. In a sample of 150 aged 65-74 years living in the community, the instrument's psychometric properties were evaluated by analysis of convergent and construct validity and test-retest reliability. The main outcomes measures used for validation included in the battery of tests of physical ability, self-repor measures of functional limitations, health, depression, cognitive and sex. The test-retest reliability of the instrument was assessed using the intra-class correlation coefficient (ICC), 40 subjects were reassessed after an interval of 14 days of assessment. Results: the concurrent validity for the MAT-sf was evidenced by significant correlations with SPPB (r = 0,53), number of functional limitations (r = -0,62) and depressive symptoms (r = -0,45). The construct validity of the instrument was measured by gradual and significant increase of the MAT-sf scores with high levels of physical performance and with positive self-reported health, also found that MAT-sf scores were statistically differents according to sex. The variation in MAT-sf scores (R2 = 0,41) was explained by SPPB, number of limitations for activities of daily life and depressive symptoms. High values for test-retest reliability was evidencend by ICC = 0,94, 95% CI = 0,90 0,97. Conclusions: the Brazilian version of the short-form of the Mobility Assessment Tool has values of validity and reliability to ensure its use in elderly populations living in communities

Defining a fish bio-assessment tool to monitoring the biological condition of a cascade reservoirs system in tropical area

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Modelagem do transporte de sedimentos na alta Bacia do Córrego Cachoeirinha (Rio Claro, SP) através do software Soil and Water Assessment Tool (SWAT)

This study aimed to simulate and evaluate the sediment transport in Upper Basin Stream Cachoeirinha in Rio Claro, SP, and compare the results with previous studies performed in the same basin. The modeling software used in this study was Soil and Water Assessment Tool (SWAT), which is a very comprehensive tool that discusses many physical processes. In this work, the hydrosedimentological processes were treated, aiming to understand the sediment production and transport. The Basin Stream Cachoeirinha has an area with predominantly agricultural use, especially sugar cane. The database for inclusion in software was constructed from the following elements: climatic, topographical, soil type and use and land cover of the area, also including the parameters of Modified Universal Soil Loss Equation (MUSLE). The analysis was conducted for a period of 16 years (1994-2010), which is the range of data available from CEAPLA. The results were analyzed in terms of annual runoff and sediment yield. The average sediment delivery in the simulation was 0.94 t/ha/year, while the maximum annual contribution was 7.28 t/ha/year

Avaliação da erosão hídrica e transporte de sedimentos através do modelo hidrossedimentológico SWAT (Soil and Water Assessment Tool)

Pós-graduação em Geociências e Meio Ambiente - IGCE

Randomized trial of a computerized coronary heart disease risk assessment tool in HIV-infected patients receiving combination antiretroviral therapy

Exposure to combination antiretroviral therapy (cART) can lead to important metabolic changes and increased risk of coronary heart disease (CHD). Computerized clinical decision support systems have been advocated to improve the management of patients at risk for CHD but it is unclear whether such systems reduce patients' risk for CHD.

Proposal on How To Conduct a Biopharmaceutical Process Failure Mode and Effect Analysis (FMEA) as a Risk Assessment Tool

With the publication of the quality guideline ICH Q9 "Quality Risk Management" by the International Conference on Harmonization, risk management has already become a standard requirement during the life cycle of a pharmaceutical product. Failure mode and effect analysis (FMEA) is a powerful risk analysis tool that has been used for decades in mechanical and electrical industries. However, the adaptation of the FMEA methodology to biopharmaceutical processes brings about some difficulties. The proposal presented here is intended to serve as a brief but nevertheless comprehensive and detailed guideline on how to conduct a biopharmaceutical process FMEA. It includes a detailed 1-to-10-scale FMEA rating table for occurrence, severity, and detectability of failures that has been especially designed for typical biopharmaceutical processes. The application for such a biopharmaceutical process FMEA is widespread. It can be useful whenever a biopharmaceutical manufacturing process is developed or scaled-up, or when it is transferred to a different manufacturing site. It may also be conducted during substantial optimization of an existing process or the development of a second-generation process. According to their resulting risk ratings, process parameters can be ranked for importance and important variables for process development, characterization, or validation can be identified. LAY ABSTRACT: Health authorities around the world ask pharmaceutical companies to manage risk during development and manufacturing of pharmaceuticals. The so-called failure mode and effect analysis (FMEA) is an established risk analysis tool that has been used for decades in mechanical and electrical industries. However, the adaptation of the FMEA methodology to pharmaceutical processes that use modern biotechnology (biopharmaceutical processes) brings about some difficulties, because those biopharmaceutical processes differ from processes in mechanical and electrical industries. The proposal presented here explains how a biopharmaceutical process FMEA can be conducted. It includes a detailed 1-to-10-scale FMEA rating table for occurrence, severity, and detectability of failures that has been especially designed for typical biopharmaceutical processes. With the help of this guideline, different details of the manufacturing process can be ranked according to their potential risks, and this can help pharmaceutical companies to identify aspects with high potential risks and to react accordingly to improve the safety of medicines.

Spike-triggered reaction-time EEG as a possible assessment tool for driving ability

The impact of interictal epileptic activity (IEA) on driving is a rarely investigated issue. We analyzed the impact of IEA on reaction time in a pilot study. Reactions to simple visual stimuli (light flash) in the Flash test or complex visual stimuli (obstacle on a road) in a modified car driving computer game, the Steer Clear, were measured during IEA bursts and unremarkable electroencephalography (EEG) periods. Individual epilepsy patients showed slower reaction times (RTs) during generalized IEA compared to RTs during unremarkable EEG periods. RT differences were approximately 300 ms (p < 0.001) in the Flash test and approximately 200 ms (p < 0.001) in the Steer Clear. Prior work suggested that RT differences >100 ms may become clinically relevant. This occurred in 40% of patients in the Flash test and in up to 50% in the Steer Clear. When RT were pooled, mean RT differences were 157 ms in the Flash test (p < 0.0001) and 116 ms in the Steer Clear (p < 0.0001). Generalized IEA of short duration seems to impair brain function, that is, the ability to react. The reaction-time EEG could be used routinely to assess driving ability.

Effect of standardized training on the reliability of the Cochrane risk of bias assessment tool: a study protocol

BACKGROUND The Cochrane risk of bias (RoB) tool has been widely embraced by the systematic review community, but several studies have reported that its reliability is low. We aim to investigate whether training of raters, including objective and standardized instructions on how to assess risk of bias, can improve the reliability of this tool. We describe the methods that will be used in this investigation and present an intensive standardized training package for risk of bias assessment that could be used by contributors to the Cochrane Collaboration and other reviewers. METHODS/DESIGN This is a pilot study. We will first perform a systematic literature review to identify randomized clinical trials (RCTs) that will be used for risk of bias assessment. Using the identified RCTs, we will then do a randomized experiment, where raters will be allocated to two different training schemes: minimal training and intensive standardized training. We will calculate the chance-corrected weighted Kappa with 95% confidence intervals to quantify within- and between-group Kappa agreement for each of the domains of the risk of bias tool. To calculate between-group Kappa agreement, we will use risk of bias assessments from pairs of raters after resolution of disagreements. Between-group Kappa agreement will quantify the agreement between the risk of bias assessment of raters in the training groups and the risk of bias assessment of experienced raters. To compare agreement of raters under different training conditions, we will calculate differences between Kappa values with 95% confidence intervals. DISCUSSION This study will investigate whether the reliability of the risk of bias tool can be improved by training raters using standardized instructions for risk of bias assessment. One group of inexperienced raters will receive intensive training on risk of bias assessment and the other will receive minimal training. By including a control group with minimal training, we will attempt to mimic what many review authors commonly have to do, that is-conduct risk of bias assessment in RCTs without much formal training or standardized instructions. If our results indicate that an intense standardized training does improve the reliability of the RoB tool, our study is likely to help improve the quality of risk of bias assessments, which is a central component of evidence synthesis.