Structural stability of adenylate kinase from the sulfate-reducing bacteria Desulfovibrio gigas

Biophysical Chemistry 110 (2004) 83–92

Does 6-minutes walk test predict functional capacity in elderly people?

Portugal has an accentuated aging tendency, presenting an elderly population (individuals with more than 65 years old) of 19.2%. The average life expectancy is 79.2 years. Thus, it’s important to maintain autonomy and independency as long as possible. Functional ability concept rises from the need to evaluate the capacity to conduct daily activities in an independent way. It can be estimated with the 6-minute walk test (6MWT) and other validated test. This test is simple, reliable, valid and consists in a daily activity (walk). The goals of this study was to verify associations between functional capacity measured with two different instruments (6MWT and Composite Physical Function (CPF) scale) and between those results and characterization variables.

Impacto da síncope na qualidade de vida: validação duma escala de avaliação em doentes submetidos a teste de inclinação em mesa basculante

Introdução e objetivos: A síncope recorrente tem um impacto significativo na qualidade de vida. O desenvolvimento de escalas de medida de fácil aplicabilidade clínica para avaliar este impacto é fundamental. O objetivo do presente estudo é a validação preliminar da escala Impact of Syncope on Quality of Life, para a população portuguesa. Métodos: O instrumento foi submetido a um processo de tradução, validação, adequação cultural e cognitive debriefing. Participaram 39 doentes com história de síncopes recorrentes (>1 ano de evolução), submetidos a teste de inclinação em mesa basculante (teste de tilt), que constitui uma amostra de conveniência, com idade de 52,1±16,4 anos (21-83; 43,5% do sexo masculino), a maioria com uma situação profissional ativa (n=18) ou reformados (n=13). A versão portuguesa resultou numa versão semelhante unidimensional à original com 12 itens agregados num único somatório, tendo passado por validação estatística, com avaliação da fidelidade, validade e estabilidade no tempo. Resultados: Em relação à fidelidade, a consistência interna da escala é de 0,9. Avaliámos a validade convergente, tendo obtido resultados estatisticamente significativos (p<0,01). Avaliámos a validade divergente tendo obtido resultados estatisticamente significativos. Relativamente à estabilidade no tempo foi efetuado um teste-reteste do instrumento aos seis meses após o teste de inclinação com 22 doentes desta amostra não submetidos a intervenção clínica, que não mostrou alterações estatisticamente significativas da qualidade de vida. Conclusões: Os resultados obtidos indicam a pertinência da utilização deste instrumento em contexto português na avaliação da qualidade de vida de doentes com síncope recorrente.

Automatic learning for the classification of chemical reactions and in statistical thermodynamics

This Thesis describes the application of automatic learning methods for a) the classification of organic and metabolic reactions, and b) the mapping of Potential Energy Surfaces(PES). The classification of reactions was approached with two distinct methodologies: a representation of chemical reactions based on NMR data, and a representation of chemical reactions from the reaction equation based on the physico-chemical and topological features of chemical bonds. NMR-based classification of photochemical and enzymatic reactions. Photochemical and metabolic reactions were classified by Kohonen Self-Organizing Maps (Kohonen SOMs) and Random Forests (RFs) taking as input the difference between the 1H NMR spectra of the products and the reactants. The development of such a representation can be applied in automatic analysis of changes in the 1H NMR spectrum of a mixture and their interpretation in terms of the chemical reactions taking place. Examples of possible applications are the monitoring of reaction processes, evaluation of the stability of chemicals, or even the interpretation of metabonomic data. A Kohonen SOM trained with a data set of metabolic reactions catalysed by transferases was able to correctly classify 75% of an independent test set in terms of the EC number subclass. Random Forests improved the correct predictions to 79%. With photochemical reactions classified into 7 groups, an independent test set was classified with 86-93% accuracy. The data set of photochemical reactions was also used to simulate mixtures with two reactions occurring simultaneously. Kohonen SOMs and Feed-Forward Neural Networks (FFNNs) were trained to classify the reactions occurring in a mixture based on the 1H NMR spectra of the products and reactants. Kohonen SOMs allowed the correct assignment of 53-63% of the mixtures (in a test set). Counter-Propagation Neural Networks (CPNNs) gave origin to similar results. The use of supervised learning techniques allowed an improvement in the results. They were improved to 77% of correct assignments when an ensemble of ten FFNNs were used and to 80% when Random Forests were used. This study was performed with NMR data simulated from the molecular structure by the SPINUS program. In the design of one test set, simulated data was combined with experimental data. The results support the proposal of linking databases of chemical reactions to experimental or simulated NMR data for automatic classification of reactions and mixtures of reactions. Genome-scale classification of enzymatic reactions from their reaction equation. The MOLMAP descriptor relies on a Kohonen SOM that defines types of bonds on the basis of their physico-chemical and topological properties. The MOLMAP descriptor of a molecule represents the types of bonds available in that molecule. The MOLMAP descriptor of a reaction is defined as the difference between the MOLMAPs of the products and the reactants, and numerically encodes the pattern of bonds that are broken, changed, and made during a chemical reaction. The automatic perception of chemical similarities between metabolic reactions is required for a variety of applications ranging from the computer validation of classification systems, genome-scale reconstruction (or comparison) of metabolic pathways, to the classification of enzymatic mechanisms. Catalytic functions of proteins are generally described by the EC numbers that are simultaneously employed as identifiers of reactions, enzymes, and enzyme genes, thus linking metabolic and genomic information. Different methods should be available to automatically compare metabolic reactions and for the automatic assignment of EC numbers to reactions still not officially classified. In this study, the genome-scale data set of enzymatic reactions available in the KEGG database was encoded by the MOLMAP descriptors, and was submitted to Kohonen SOMs to compare the resulting map with the official EC number classification, to explore the possibility of predicting EC numbers from the reaction equation, and to assess the internal consistency of the EC classification at the class level. A general agreement with the EC classification was observed, i.e. a relationship between the similarity of MOLMAPs and the similarity of EC numbers. At the same time, MOLMAPs were able to discriminate between EC sub-subclasses. EC numbers could be assigned at the class, subclass, and sub-subclass levels with accuracies up to 92%, 80%, and 70% for independent test sets. The correspondence between chemical similarity of metabolic reactions and their MOLMAP descriptors was applied to the identification of a number of reactions mapped into the same neuron but belonging to different EC classes, which demonstrated the ability of the MOLMAP/SOM approach to verify the internal consistency of classifications in databases of metabolic reactions. RFs were also used to assign the four levels of the EC hierarchy from the reaction equation. EC numbers were correctly assigned in 95%, 90%, 85% and 86% of the cases (for independent test sets) at the class, subclass, sub-subclass and full EC number level,respectively. Experiments for the classification of reactions from the main reactants and products were performed with RFs - EC numbers were assigned at the class, subclass and sub-subclass level with accuracies of 78%, 74% and 63%, respectively. In the course of the experiments with metabolic reactions we suggested that the MOLMAP / SOM concept could be extended to the representation of other levels of metabolic information such as metabolic pathways. Following the MOLMAP idea, the pattern of neurons activated by the reactions of a metabolic pathway is a representation of the reactions involved in that pathway - a descriptor of the metabolic pathway. This reasoning enabled the comparison of different pathways, the automatic classification of pathways, and a classification of organisms based on their biochemical machinery. The three levels of classification (from bonds to metabolic pathways) allowed to map and perceive chemical similarities between metabolic pathways even for pathways of different types of metabolism and pathways that do not share similarities in terms of EC numbers. Mapping of PES by neural networks (NNs). In a first series of experiments, ensembles of Feed-Forward NNs (EnsFFNNs) and Associative Neural Networks (ASNNs) were trained to reproduce PES represented by the Lennard-Jones (LJ) analytical potential function. The accuracy of the method was assessed by comparing the results of molecular dynamics simulations (thermal, structural, and dynamic properties) obtained from the NNs-PES and from the LJ function. The results indicated that for LJ-type potentials, NNs can be trained to generate accurate PES to be used in molecular simulations. EnsFFNNs and ASNNs gave better results than single FFNNs. A remarkable ability of the NNs models to interpolate between distant curves and accurately reproduce potentials to be used in molecular simulations is shown. The purpose of the first study was to systematically analyse the accuracy of different NNs. Our main motivation, however, is reflected in the next study: the mapping of multidimensional PES by NNs to simulate, by Molecular Dynamics or Monte Carlo, the adsorption and self-assembly of solvated organic molecules on noble-metal electrodes. Indeed, for such complex and heterogeneous systems the development of suitable analytical functions that fit quantum mechanical interaction energies is a non-trivial or even impossible task. The data consisted of energy values, from Density Functional Theory (DFT) calculations, at different distances, for several molecular orientations and three electrode adsorption sites. The results indicate that NNs require a data set large enough to cover well the diversity of possible interaction sites, distances, and orientations. NNs trained with such data sets can perform equally well or even better than analytical functions. Therefore, they can be used in molecular simulations, particularly for the ethanol/Au (111) interface which is the case studied in the present Thesis. Once properly trained, the networks are able to produce, as output, any required number of energy points for accurate interpolations.

On the development of a test-bed application for the ART-WiSe architecture

The ART-WiSe (Architecture for Real-Time communications in Wireless Sensor Networks) framework aims at the design of new communication architectures and mechanisms for time-sensitive Wireless Sensor Networks (WSNs). We adopted a two-tiered architecture where an overlay Wireless Local Area Network (Tier 2) serves as a backbone for a WSN (Tier 1), relying on existing standard communication protocols and commercial-off-the-shell (COTS) technologies – IEEE 802.15.4/ZigBee for Tier 1 and IEEE 802.11 for Tier 2. In this line, a test-bed application is being developed for assessing, validating and demonstrating the ART-WiSe architecture. A pursuit-evasion application was chosen since it fulfils a number of requirements, namely it is feasible and appealing and imposes some stress to the architecture in terms of timeliness. To develop the testbed based on the previously referred technologies, an implementation of the IEEE 8021.5.4/ZigBee protocols is being carried out, since there is no open source available to the community. This paper highlights some relevant aspects of the ART-WiSe architecture, provides some intuition on the protocol stack implementation and presents a general view over the envisaged test-bed application.

Dynamic adaptation of stability periods for service level agreements

A QoS adaptation to dynamically changing system conditions that takes into consideration the user’s constraints on the stability of service provisioning is presented. The goal is to allow the system to make QoS adaptation decisions in response to fluctuations in task traffic flow, under the control of the user. We pay special attention to the case where monitoring the stability period and resource load variation of Service Level Agreements for different types of services is used to dynamically adapt future stability periods, according to a feedback control scheme. System’s adaptation behaviour can be configured according to a desired confidence level on future resource usage. The viability of the proposed approach is validated by preliminary experiments.

On a test-bed application for the ART-WiSe framework

This report describes the development of a Test-bed Application for the ART-WiSe Framework with the aim of providing a means of access, validate and demonstrate that architecture. The chosen application is a kind of pursuit-evasion game where a remote controlled robot, navigating through an area covered by wireless sensor network (WSN), is detected and continuously tracked by the WSN. Then a centralized control station takes the appropriate actions for a pursuit robot to chase and “capture” the intruder one. This kind of application imposes stringent timing requirements to the underlying communication infrastructure. It also involves interesting research problems in WSNs like tracking, localization, cooperation between nodes, energy concerns and mobility. Additionally, it can be easily ported into a real-world application. Surveillance or search and rescue operations are two examples where this kind of functionality can be applied. This is still a first approach on the test-bed application and this development effort will be continuously pushed forward until all the envisaged objectives for the Art-WiSe architecture become accomplished.

PV system modeling by five parameters and in Situ test

This paper focuses on a novel formalization for assessing the five parameter modeling of a photovoltaic cell. An optimization procedure is used as a feasibility problem to find the parameters tuned at the open circuit, maximum power, and short circuit points in order to assess the data needed for plotting the I-V curve. A comparison with experimental results is presented for two monocrystalline PV modules.

Shear modulus and strength of an acrylic adhesive by the notched plate shear method (Arcan) and the thick adherend shear test (TAST)

In this work, the shear modulus and strength of the acrylic adhesive 3M® DP 8005 was evaluated by two different methods: the Thick Adherend Shear Test (TAST) and the Notched Plate Shear Method (Arcan). However, TAST standards advise the use of a special extensometer attached to the specimen, which requires a very experienced technician. In the present study, the adhesive shear displacement for the TAST was measured using an optical technique, and also with a conventional inductive extensometer of 25 mm used for tensile tests. This allowed for an assessment of suitability of using a conventional extensometer to measure this parameter. Since the results obtained by the two techniques are identical, it can be concluded that using a conventional extensometer is a valid option to obtain the shear modulus for the particular adhesive used. In the Arcan tests, the adhesive shear displacement was only measured using the optical technique. This work also aimed the comparison of shear modulus and strength obtained by the TAST and Arcan test methods.

Validity and reliability of the Questionnaire for Compliance with Standard Precaution

ABSTRACT OBJECTIVE : To evaluate the validity and reliability of the Questionnaire for Compliance with Standard Precaution for nurses. METHODS : This methodological study was conducted with 121 nurses from health care facilities in Sao Paulo's countryside, who were represented by two high-complexity and by three average-complexity health care facilities. Internal consistency was calculated using Cronbach's alpha and stability was calculated by the intraclass correlation coefficient, through test-retest. Convergent, discriminant, and known-groups construct validity techniques were conducted. RESULTS : The questionnaire was found to be reliable (Cronbach's alpha: 0.80; intraclass correlation coefficient: (0.97) In regards to the convergent and discriminant construct validity, strong correlation was found between compliance to standard precautions, the perception of a safe environment, and the smaller perception of obstacles to follow such precautions (r = 0.614 and r = 0.537, respectively). The nurses who were trained on the standard precautions and worked on the health care facilities of higher complexity were shown to comply more (p = 0.028 and p = 0.006, respectively). CONCLUSIONS : The Brazilian version of the Questionnaire for Compliance with Standard Precaution was shown to be valid and reliable. Further investigation must be conducted with nurse samples that are more representative of the Brazilian reality. The use of the questionnaire may support the creation of educational measures considering the possible gaps that can be identified, focusing on the workers' health and on the patients' safety.

The effect of metal transfer stability (spattering) on fume generation, morphology and composition in short-circuit MAG welding

The main objective of this work was to evaluate the hypothesis that the greater transfer stability leads also to less volume of fumes. Using an Ar + 25%CO2 blend as shielding gas and maintaining constant the average current, wire feed speed and welding speed, bead-on-plate welds were carried out with plain carbon steel solid wire. The welding voltage was scanned to progressively vary the transfer stability. Using two conditions of low stability and one with high stability, fume generation was evaluated by means of the AWS F1.2:2006 standard. The influence of these conditions on fume morphology and composition was also verified. A condition with greater transfer stability does not generate less fume quantity, despite the fact that this condition produces fewer spatters. Other factors such as short-circuit current, arcing time, droplet diameters and arc length are the likely governing factors, but in an interrelated way. Metal transfer stability does not influence either the composition or the size/morphology of fume particulates. (c) 2014 Elsevier B.V. All rights reserved.

Using test infrastructures for (remote) online evaluation of the sensitivity to SEUs of FPGAs

This paper proposes an online mechanism that can evaluate the sensitivity of single event upsets (SEUs) of field programmable gate arrays (FPGAs). The online detection mechanism cyclically reads and compares the values form the external and internal configuration memories, taking into account the mask information. This remote detection method also signals any mismatch as a result of a SEU that affects both used and not-used FPGA parts, which maximizes the monitored area. By utilizing an external, Web-accessible controller that is connected to the test infrastructure, the possibility of running the same operation in a remote manner is enabled. Moreover, the need for a local memory to store the mask values is also eliminated.

Content validity and reliability of test of gross motor development in Chilean children

ABSTRACT OBJECTIVE To validate a Spanish version of the Test of Gross Motor Development (TGMD-2) for the Chilean population. METHODS Descriptive, transversal, non-experimental validity and reliability study. Four translators, three experts and 92 Chilean children, from five to 10 years, students from a primary school in Santiago, Chile, have participated. The Committee of Experts has carried out translation, back-translation and revision processes to determine the translinguistic equivalence and content validity of the test, using the content validity index in 2013. In addition, a pilot implementation was achieved to determine test reliability in Spanish, by using the intraclass correlation coefficient and Bland-Altman method. We evaluated whether the results presented significant differences by replacing the bat with a racket, using T-test. RESULTS We obtained a content validity index higher than 0.80 for language clarity and relevance of the TGMD-2 for children. There were significant differences in the object control subtest when comparing the results with bat and racket. The intraclass correlation coefficient for reliability inter-rater, intra-rater and test-retest reliability was greater than 0.80 in all cases. CONCLUSIONS The TGMD-2 has appropriate content validity to be applied in the Chilean population. The reliability of this test is within the appropriate parameters and its use could be recommended in this population after the establishment of normative data, setting a further precedent for the validation in other Latin American countries.

From design-for-test to design-for-debug-and-test: analysis of requirements and limitations for 1149.1

The increasing complexity of VLSI circuits and the reduced accessibility of modern packaging and mounting technologies restrict the usefulness of conventional in-circuit debugging tools, such as in-circuit emulators for microprocessors and microcontrollers. However, this same trend enables the development of more complex products, which in turn require more powerful debugging tools. These conflicting demands could be met if the standard scan test infrastructures now common in most complex components were able to match the debugging requirements of design verification and prototype validation. This paper analyses the main debug requirements in the design of microprocessor-based applications and the feasibility of their implementation using the mandatory, optional and additional operating modes of the standard IEEE 1149.1 test infrastructure.

Color and Luminescence stability of selected dental materials in vitro

To study luminescence, reflectance, and color stability of dental composites and ceramics. Materials and Methods: IPS e.max, IPS Classic, Gradia, and Sinfony materials were tested, both unpolished (as-cast) and polished specimens. Coffee, tea, red wine, and distilled water (control) were used as staining drinks. Disk-shaped specimens were soaked in the staining drinks for up to 5 days. Color was measured by a colorimeter. Fluorescence was recorded using a spectrofluorometer, in the front-face geometry. Time-resolved fluorescence spectra were recorded using a laser nanosecond spectrofluorometer. Results: The exposure of the examined dental materials to staining drinks caused changes in color of the composites and ceramics, with the polished specimens exhibiting significantly lower color changes as compared to unpolished specimens. Composites exhibited lower color stability as compared to ceramic materials. Water also caused perceptible color changes in most materials. The materials tested demonstrated significantly different initial luminescence intensities. Upon exposure to staining drinks, luminescence became weaker by up to 40%, dependent on the drink and the material. Time-resolved luminescence spectra exhibited some red shift of the emission band at longer times, with the lifetimes in the range of tens of nanoseconds. Conclusions: Unpolished specimens with a more developed surface have lower color stability. Specimens stored in water develop some changes in their visual appearance. The presently proposed methods are effective in evaluating the luminescence of dental materials. Luminescence needs to be tested in addition to color, as the two characteristics are uncorrelated. It is important to further improve the color and luminescence stability of dental materials.