Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data

Motivation: DNA assembly programs classically perform an all-against-all comparison of reads to identify overlaps, followed by a multiple sequence alignment and generation of a consensus sequence. If the aim is to assemble a particular segment, instead of a whole genome or transcriptome, a target-specific assembly is a more sensible approach. GenSeed is a Perl program that implements a seed-driven recursive assembly consisting of cycles comprising a similarity search, read selection and assembly. The iterative process results in a progressive extension of the original seed sequence. GenSeed was tested and validated on many applications, including the reconstruction of nuclear genes or segments, full-length transcripts, and extrachromosomal genomes. The robustness of the method was confirmed through the use of a variety of DNA and protein seeds, including short sequences derived from SAGE and proteome projects.

Formal validation of automated policy refinement in the management of network security systems

Policy hierarchies and automated policy refinement are powerful approaches to simplify administration of security services in complex network environments. A crucial issue for the practical use of these approaches is to ensure the validity of the policy hierarchy, i.e. since the policy sets for the lower levels are automatically derived from the abstract policies (defined by the modeller), we must be sure that the derived policies uphold the high-level ones. This paper builds upon previous work on Model-based Management, particularly on the Diagram of Abstract Subsystems approach, and goes further to propose a formal validation approach for the policy hierarchies yielded by the automated policy refinement process. We establish general validation conditions for a multi-layered policy model, i.e. necessary and sufficient conditions that a policy hierarchy must satisfy so that the lower-level policy sets are valid refinements of the higher-level policies according to the criteria of consistency and completeness. Relying upon the validation conditions and upon axioms about the model representativeness, two theorems are proved to ensure compliance between the resulting system behaviour and the abstract policies that are modelled.

European resarch school on large scale solar thermal - SHINE

The Solar HeatIntegration NEtwork (SHINE) is a European research school in which 13 PhDstudents in solar thermal technologies are funded by the EU Marie-Curie program.It has five PhD course modules as well as workshops and seminars dedicated to PhDstudents both within the project as well as outside of it. The SHINE researchactivities focus on large solar heating systems and new applications: ondistrict heating, industrial processes and new storage systems. The scope ofthis paper is on systems for district heating for which there are five PhDstudents, three at universities and two at companies. The PhD students allstarted during the early part of 2014 and their initial work has concentratedon literature studies and on setting up models and data collection to be usedfor validation purposes. The PhD students will complete their studies in2017-18.

Automatic spiral analysis for objective assessment of motor symptoms in Parkinson's disease

Objective: To develop a method for objective quantification of PD motor symptoms related to Off episodes and peak dose dyskinesias, using spiral data gathered by using a touch screen telemetry device. The aim was to objectively characterize predominant motor phenotypes (bradykinesia and dyskinesia), to help in automating the process of visual interpretation of movement anomalies in spirals as rated by movement disorder specialists. Background: A retrospective analysis was conducted on recordings from 65 patients with advanced idiopathic PD from nine different clinics in Sweden, recruited from January 2006 until August 2010. In addition to the patient group, 10 healthy elderly subjects were recruited. Upper limb movement data were collected using a touch screen telemetry device from home environments of the subjects. Measurements with the device were performed four times per day during week-long test periods. On each test occasion, the subjects were asked to trace pre-drawn Archimedean spirals, using the dominant hand. The pre-drawn spiral was shown on the screen of the device. The spiral test was repeated three times per test occasion and they were instructed to complete it within 10 seconds. The device had a sampling rate of 10Hz and measured both position and time-stamps (in milliseconds) of the pen tip. Methods: Four independent raters (FB, DH, AJ and DN) used a web interface that animated the spiral drawings and allowed them to observe different kinematic features during the drawing process and to rate task performance. Initially, a number of kinematic features were assessed including ‘impairment’, ‘speed’, ‘irregularity’ and ‘hesitation’ followed by marking the predominant motor phenotype on a 3-category scale: tremor, bradykinesia and/or choreatic dyskinesia. There were only 2 test occasions for which all the four raters either classified them as tremor or could not identify the motor phenotype. Therefore, the two main motor phenotype categories were bradykinesia and dyskinesia. ‘Impairment’ was rated on a scale from 0 (no impairment) to 10 (extremely severe) whereas ‘speed’, ‘irregularity’ and ‘hesitation’ were rated on a scale from 0 (normal) to 4 (extremely severe). The proposed data-driven method consisted of the following steps. Initially, 28 spatiotemporal features were extracted from the time series signals before being presented to a Multilayer Perceptron (MLP) classifier. The features were based on different kinematic quantities of spirals including radius, angle, speed and velocity with the aim of measuring the severity of involuntary symptoms and discriminate between PD-specific (bradykinesia) and/or treatment-induced symptoms (dyskinesia). A Principal Component Analysis was applied on the features to reduce their dimensions where 4 relevant principal components (PCs) were retained and used as inputs to the MLP classifier. Finally, the MLP classifier mapped these components to the corresponding visually assessed motor phenotype scores for automating the process of scoring the bradykinesia and dyskinesia in PD patients whilst they draw spirals using the touch screen device. For motor phenotype (bradykinesia vs. dyskinesia) classification, the stratified 10-fold cross validation technique was employed. Results: There were good agreements between the four raters when rating the individual kinematic features with intra-class correlation coefficient (ICC) of 0.88 for ‘impairment’, 0.74 for ‘speed’, 0.70 for ‘irregularity’, and moderate agreements when rating ‘hesitation’ with an ICC of 0.49. When assessing the two main motor phenotype categories (bradykinesia or dyskinesia) in animated spirals the agreements between the four raters ranged from fair to moderate. There were good correlations between mean ratings of the four raters on individual kinematic features and computed scores. The MLP classifier classified the motor phenotype that is bradykinesia or dyskinesia with an accuracy of 85% in relation to visual classifications of the four movement disorder specialists. The test-retest reliability of the four PCs across the three spiral test trials was good with Cronbach’s Alpha coefficients of 0.80, 0.82, 0.54 and 0.49, respectively. These results indicate that the computed scores are stable and consistent over time. Significant differences were found between the two groups (patients and healthy elderly subjects) in all the PCs, except for the PC3. Conclusions: The proposed method automatically assessed the severity of unwanted symptoms and could reasonably well discriminate between PD-specific and/or treatment-induced motor symptoms, in relation to visual assessments of movement disorder specialists. The objective assessments could provide a time-effect summary score that could be useful for improving decision-making during symptom evaluation of individualized treatment when the goal is to maximize functional On time for patients while minimizing their Off episodes and troublesome dyskinesias.

Large-scale metabolomic profiling identifies novel biomarkers for incident coronary heart disease

Analyses of circulating metabolites in large prospective epidemiological studies could lead to improved prediction and better biological understanding of coronary heart disease (CHD). We performed a mass spectrometry-based non-targeted metabolomics study for association with incident CHD events in 1,028 individuals (131 events; 10 y. median follow-up) with validation in 1,670 individuals (282 events; 3.9 y. median follow-up). Four metabolites were replicated and independent of main cardiovascular risk factors [lysophosphatidylcholine 18∶1 (hazard ratio [HR] per standard deviation [SD] increment = 0.77, P-value<0.001), lysophosphatidylcholine 18∶2 (HR = 0.81, P-value<0.001), monoglyceride 18∶2 (MG 18∶2; HR = 1.18, P-value = 0.011) and sphingomyelin 28∶1 (HR = 0.85, P-value = 0.015)]. Together they contributed to moderate improvements in discrimination and re-classification in addition to traditional risk factors (C-statistic: 0.76 vs. 0.75; NRI: 9.2%). MG 18∶2 was associated with CHD independently of triglycerides. Lysophosphatidylcholines were negatively associated with body mass index, C-reactive protein and with less evidence of subclinical cardiovascular disease in additional 970 participants; a reverse pattern was observed for MG 18∶2. MG 18∶2 showed an enrichment (P-value = 0.002) of significant associations with CHD-associated SNPs (P-value = 1.2×10-7 for association with rs964184 in the ZNF259/APOA5 region) and a weak, but positive causal effect (odds ratio = 1.05 per SD increment in MG 18∶2, P-value = 0.05) on CHD, as suggested by Mendelian randomization analysis. In conclusion, we identified four lipid-related metabolites with evidence for clinical utility, as well as a causal role in CHD development.

Design and validation of a sheet metal shearing experimental procedure

Throughout the industrial processes of sheet metal manufacturing and refining, shear cutting is widely used for its speed and cost advantages over competing cutting methods. Industrial shears may include some force measurement possibilities, but the force is most likely influenced by friction losses between shear tool and the point of measurement, and are in general not showing the actual force applied to the sheet. Well defined shears and accurate measurements of force and shear tool position are important for understanding the influence of shear parameters. Accurate experimental data are also necessary for calibration of numerical shear models. Here, a dedicated laboratory set-up with well defined geometry and movement in the shear, and high measurability in terms of force and geometry is designed, built and verified. Parameters important to the shear process are studied with perturbation analysis techniques and requirements on input parameter accuracy are formulated to meet experimental output demands. Input parameters in shearing are mostly geometric parameters, but also material properties and contact conditions. Based on the accuracy requirements, a symmetric experiment with internal balancing of forces is constructed to avoid guides and corresponding friction losses. Finally, the experimental procedure is validated through shearing of a medium grade steel. With the obtained experimental set-up performance, force changes as result of changes in studied input parameters are distinguishable down to a level of 1%.

Health system context and implementation of evidence-based practices-development and validation of the Context Assessment for Community Health (COACH) tool for low- and middle-income settings

Background: The gap between what is known and what is practiced results in health service users not benefitting from advances in healthcare, and in unnecessary costs. A supportive context is considered a key element for successful implementation of evidence-based practices (EBP). There were no tools available for the systematic mapping of aspects of organizational context influencing the implementation of EBPs in low- and middle-income countries (LMICs). Thus, this project aimed to develop and psychometrically validate a tool for this purpose. Methods: The development of the Context Assessment for Community Health (COACH) tool was premised on the context dimension in the Promoting Action on Research Implementation in Health Services framework, and is a derivative product of the Alberta Context Tool. Its development was undertaken in Bangladesh, Vietnam, Uganda, South Africa and Nicaragua in six phases: (1) defining dimensions and draft tool development, (2) content validity amongst in-country expert panels, (3) content validity amongst international experts, (4) response process validity, (5) translation and (6) evaluation of psychometric properties amongst 690 health workers in the five countries. Results: The tool was validated for use amongst physicians, nurse/midwives and community health workers. The six phases of development resulted in a good fit between the theoretical dimensions of the COACH tool and its psychometric properties. The tool has 49 items measuring eight aspects of context: Resources, Community engagement, Commitment to work, Informal payment, Leadership, Work culture, Monitoring services for action and Sources of knowledge. Conclusions: Aspects of organizational context that were identified as influencing the implementation of EBPs in high-income settings were also found to be relevant in LMICs. However, there were additional aspects of context of relevance in LMICs specifically Resources, Community engagement, Commitment to work and Informal payment. Use of the COACH tool will allow for systematic description of the local healthcare context prior implementing healthcare interventions to allow for tailoring implementation strategies or as part of the evaluation of implementing healthcare interventions and thus allow for deeper insights into the process of implementing EBPs in LMICs.

A JML-Based strategy for incorporating formal specifications into the software development process

This thesis presents a JML-based strategy that incorporates formal specifications into the software development process of object-oriented programs. The strategy evolves functional requirements into a “semi-formal” requirements form, and then expressing them as JML formal specifications. The strategy is implemented as a formal-specification pseudo-phase that runs in parallel with the other phase of software development. What makes our strategy different from other software development strategies used in literature is the particular use of JML specifications we make all along the way from requirements to validation-and-verification.

Tradução, adaptação e validação da versão brasileira do questionário utian quality of life (uqol) para avaliação da qualidade de vida no climatério

The present study had as objective translates, to do equivalence and validation of the Utian Quality of Life (UQOL) for the Brazilian population through methods internationally accepted, in which the original questionnaire was translated for the Portuguese by three teachers and the consensual version was translated back for English by two American teachers (back translation). A multidisciplinary committee evaluated all versions and the final version in Portuguese was applied to climacteric women for the process of adaptation. Validation of the instrument was performed by measuring the reliability and validity properties. Construct validity was examined through the comparison between UQOL and the general measuring scale of quality of life Short Form-36 (SF-36). The final version of translation process was easily recognized by the target population, that didn't tell understanding problems. The results obtained for the reliability intra and interobserver showed significant agreement in all of the subjects. The construct validity was obtained through correlations statistically significant among the domains occupational, health and emotional of UQOL with the SF-36 domains. For the exploratory factorial analysis, it was verified that three factors explain 60% of the total variance of the data, the present study allowed concluding that UQOL was appropriately translated and adapted for applicability in Brazil, presenting high reliability and validity. In that way, the executed project provided the involvement of different areas as gynecology, psychology and physiotherapy (interdisciplinary). Thus, this instrument can be included and used in Brazilian studies to assessment the quality of life during the climacteric years

Fatores de decisão da adoção do gás natural na geração de energia elétrica em pequena escala em postos de combustíveis: um estudo de anális de decusão usando o processo de hierarquia analítica AHP

A modeling of criterias and alternatives is through and applied a questionnaire based on method AHP to proprietors of gas stations. The considered alternatives had been the maintenance of the current state with electric energy of the deliverer and the generation in small scale based on the natural gas. The used criteria had been Cost of the Investment, Final Cost of the Energy, Operational cost, Ambient Benefits, Risk and Variation of Costs. The study it was carried through in the city of Natal, RN in ranks that make use of the natural as for resale, where the generation alternative on the basis of the available gas is present. The main results evidence in a dimension the viability of use of method AHP with questionnaire by means of validation of the judgments with analysis of variance beyond proper the normal mechanisms of analysis of consistency to the method. The main results of the analysis help to show that in this in case that the profile of models of criteria and judgments of the actors is similar, with the final evidence of that it has a dominance of the maintenance of the energy of the deliverer. The main criterion to influence this decision was the risk

Simulação computacional da interação fluido-estrutura em bombas de cavidades progressivas

The pumping through progressing cavities system has been more and more employed in the petroleum industry. This occurs because of its capacity of elevation of highly viscous oils or fluids with great concentration of sand or other solid particles. A Progressing Cavity Pump (PCP) consists, basically, of a rotor - a metallic device similar to an eccentric screw, and a stator - a steel tube internally covered by a double helix, which may be rigid or deformable/elastomeric. In general, it is submitted to a combination of well pressure with the pressure generated by the pumping process itself. In elastomeric PCPs, this combined effort compresses the stator and generates, or enlarges, the clearance existing between the rotor and the stator, thus reducing the closing effect between their cavities. Such opening of the sealing region produces what is known as fluid slip or slippage, reducing the efficiency of the PCP pumping system. Therefore, this research aims to develop a transient three-dimensional computational model that, based on single-lobe PCP kinematics, is able to simulate the fluid-structure interaction that occurs in the interior of metallic and elastomeric PCPs. The main goal is to evaluate the dynamic characteristics of PCP s efficiency based on detailed and instantaneous information of velocity, pressure and deformation fields in their interior. To reach these goals (development and use of the model), it was also necessary the development of a methodology for generation of dynamic, mobile and deformable, computational meshes representing fluid and structural regions of a PCP. This additional intermediary step has been characterized as the biggest challenge for the elaboration and running of the computational model due to the complex kinematic and critical geometry of this type of pump (different helix angles between rotor and stator as well as large length scale aspect ratios). The processes of dynamic generation of meshes and of simultaneous evaluation of the deformations suffered by the elastomer are fulfilled through subroutines written in Fortan 90 language that dynamically interact with the CFX/ANSYS fluid dynamic software. Since a structural elastic linear model is employed to evaluate elastomer deformations, it is not necessary to use any CAE package for structural analysis. However, an initial proposal for dynamic simulation using hyperelastic models through ANSYS software is also presented in this research. Validation of the results produced with the present methodology (mesh generation, flow simulation in metallic PCPs and simulation of fluid-structure interaction in elastomeric PCPs) is obtained through comparison with experimental results reported by the literature. It is expected that the development and application of such a computational model may provide better details of the dynamics of the flow within metallic and elastomeric PCPs, so that better control systems may be implemented in the artificial elevation area by PCP

Pyrolysis and auto-gasification of black liquor in presence of ZnO: An integrated process for Zn/ZnO nanostructure production and bioenergy generation

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Discoloration process modeling by neural network

The photo-oxidation of acid orange 52 dye was performed in the presence of H2O2, utilizing UV light, aiming the discoloration process modeling and the process variable influence characterization. The discoloration process was modeled by the use of feedforward neural network. Each sample was characterized by five independent variables (dye concentration, pH, hydrogen peroxide volume, temperature and time of operation) and a dependent variable (absorbance). The neural model has also provided, through Garson Partition coefficients and the Pertubation method, the independent variable influence order determination. The results indicated that the time of operation was the predominant variable and reaction mean temperature was the lesser influent variable. The neural model obtained presented coefficients of correlation on the order 0.98, for sets of trainability, validation and testing, indicating the power of prediction of the model and its character of generalization. (c) 2007 Elsevier B.V. All rights reserved.

Construct validity of a figure rating scale for Brazilian adolescents

Background: Figure rating scales were developed as a tool to determine body dissatisfaction in women, men, and children. However, it lacks in the literature the validation of the scale for body silhouettes previously adapted. We aimed to obtain evidence for construct validity of a figure rating scale for Brazilian adolescents.Methods: The study was carried out with adolescent students attending three public schools in an urban region of the municipality of Florianopolis in the State of Santa Catarina (SC). The sample comprised 232 10-19-year-old students, 106 of whom are boys and 126 girls, from the 5th series (i.e. year) of Primary School to the 3rd year of Secondary School. Data-gathering involved the application of an instrument containing 8 body figure drawings representing a range of children's and adolescents' body shapes, ranging from very slim (contour 1) to obese (contour 8). Weights and heights were also collected, and body mass index (BMI) was calculated later. BMI was analyzed as a continuous variable, using z-scores, and as a dichotomous categorical variable, representing a diagnosis of nutritional status (normal and overweight including obesity).Results: Results showed that both males and females with larger BMI z-scores chose larger body contours. Girls with higher BMI z-scores also show higher values of body image dissatisfaction.Conclusion: We provided the first evidence of validity for a figure rating scale for Brazilian adolescents.

A new short and simple health-related quality of life measurement for paediatric rheumatic diseases: initial validation in juvenile idiopathic arthritis

Objective. To develop and validate a new short and simple measure of health-related quality of life (HRQL) in children with juvenile idiopathic arthritis (JIA).Methods. The Paediatric Rheumatology Quality of Life Scale (PRQL) is a 10-item questionnaire that explores HRQL in two domains: physical health (PhH) and psychosocial health (PsH). Validation of the parent proxy report and child self-report versions of the instrument was accomplished by evaluating 472 JIA patients and similar to 800 healthy children. Validation analyses included assessment of feasibility, face and content validity; construct and discriminative ability; internal structure and consistency; test-retest reliability; responsiveness to clinical change; and minimal clinically important difference.Results. The PRQL was found to be feasible and to possess both face and content validity. The PRQL score correlated in the predicted range with most of the other JIA outcome measures, thereby demonstrating good construct validity, and discriminated well between different levels of disease severity. Assessment of internal structure (factor analysis) revealed that the PhH and PsH subscales identify two unambiguously separated domains. The internal consistency (Cronbach's alpha) was 0.86. The intraclass correlation coefficient for test-retest reliability was 0.91. The PRQL revealed fair responsiveness, with a standardized response mean of 0.67 in improved patients. Overall, the PRQL appeared to be more able to capture physical HRQL than psychosocial HRQL.Conclusion. The PRQL was found to possess good measurement properties and is, therefore, a valid instrument for the assessment of HRQL in children with JIA. This tool is primarily proposed for use in standard clinical care.