PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods

Background: With the decrease of DNA sequencing costs, sequence-based typing methods are rapidly becoming the gold standard for epidemiological surveillance. These methods provide reproducible and comparable results needed for a global scale bacterial population analysis, while retaining their usefulness for local epidemiological surveys. Online databases that collect the generated allelic profiles and associated epidemiological data are available but this wealth of data remains underused and are frequently poorly annotated since no user-friendly tool exists to analyze and explore it. Results: PHYLOViZ is platform independent Java software that allows the integrated analysis of sequence-based typing methods, including SNP data generated from whole genome sequence approaches, and associated epidemiological data. goeBURST and its Minimum Spanning Tree expansion are used for visualizing the possible evolutionary relationships between isolates. The results can be displayed as an annotated graph overlaying the query results of any other epidemiological data available. Conclusions: PHYLOViZ is a user-friendly software that allows the combined analysis of multiple data sources for microbial epidemiological and population studies. It is freely available at http://www.phyloviz.net.

Estudo sobre a influência da rotatividade de postos de trabalho na prevalência de sintomatologia músculo-esquelética auto-referida

Objectivo: O objectivo deste estudo foi avaliar a eficácia de um plano de rotatividade de postos de trabalho, específico, na prevalência de sintomatologia músculo-esquelética auto-referida, de operadoras de costura. Metodologia: Realizou-se um estudo quantitativo, observacional e analítico longitudinal, onde se avaliou o efeito de uma intervenção, em 25 operadoras que se voluntariaram para o estudo, de acordo com o interesse da empresa. Foram utilizados como instrumentos de avaliação o Risk Filter, o Questionário Nórdico Músculo-Esquelético e o Rapid Upper Limbs Assessment (RULA). O projecto englobou uma análise de factores de risco e classificação dos respectivos postos de trabalho de modo a estruturar uma (re)organização do trabalho (Plano de rotatividade de postos de trabalho). Resultados: A implementação do projecto reduziu significativamente (p<0,05) a sintomatologia músculo-esquelética auto-referida, sobretudo ao nível da cervical, tornozelos e pés, punhos e mãos, tendo sido estas últimas as áreas de maior prevalência referida. Verificou-se também uma diminuição da média da intensidade de dor reportada, pelas operadoras. Conclusões: O resultado deste estudo reforça a recomendação e implementação da variação do gesto (variação biomecânica da exposição), através da implementação de um plano de rotatividade de postos de trabalho, específico, tornando-se eficaz como intervenção preventiva e promotora de saúde, no que refere às lesões musculesqueléticas relacionadas com o trabalho.

Methods for automatic and assisted image annotation

Personal memories composed of digital pictures are very popular at the moment. To retrieve these media items annotation is required. During the last years, several approaches have been proposed in order to overcome the image annotation problem. This paper presents our proposals to address this problem. Automatic and semi-automatic learning methods for semantic concepts are presented. The automatic method is based on semantic concepts estimated using visual content, context metadata and audio information. The semi-automatic method is based on results provided by a computer game. The paper describes our proposals and presents their evaluations.

Typical load profiles in the smart grid context – a clustering methods comparison

The present research paper presents five different clustering methods to identify typical load profiles of medium voltage (MV) electricity consumers. These methods are intended to be used in a smart grid environment to extract useful knowledge about customer’s behaviour. The obtained knowledge can be used to support a decision tool, not only for utilities but also for consumers. Load profiles can be used by the utilities to identify the aspects that cause system load peaks and enable the development of specific contracts with their customers. The framework presented throughout the paper consists in several steps, namely the pre-processing data phase, clustering algorithms application and the evaluation of the quality of the partition, which is supported by cluster validity indices. The process ends with the analysis of the discovered knowledge. To validate the proposed framework, a case study with a real database of 208 MV consumers is used.

Technical and economic resources management in smart grids using heuristic optimization methods

Intensive use of Distributed Generation (DG) represents a change in the paradigm of power systems operation making small-scale energy generation and storage decision making relevant for the whole system. This paradigm led to the concept of smart grid for which an efficient management, both in technical and economic terms, should be assured. This paper presents a new approach to solve the economic dispatch in smart grids. The proposed methodology for resource management involves two stages. The first one considers fuzzy set theory to define the natural resources range forecast as well as the load forecast. The second stage uses heuristic optimization to determine the economic dispatch considering the generation forecast, storage management and demand response

Dor lombar em indivíduos da Escola Superior de Tecnologia da Saúde do Porto. Prevalência e incapacidade associada

OBJECTIVOS: Determinar a prevalência e incapacidade da dor lombar, nas últimas quatro semanas, na ESTSP. METODOLOGIA: 249 Indivíduos (alunos, docentes, administrativos e auxiliares), 37 do género masculino e 212 do género feminino, com média de idade 29.6 (±11.0) e 25.4 (±9.67) respectivamente. O estudo foi quantitativo observacional, analítico e transversal. RESULTADOS: A prevalência na ESTSP foi 50.2%, sendo superior no sexo feminino (51.9%), na classe [18-30] (51.1%) e nos administrativos 55.0%. A mediana da incapacidade foi 2.00 com intervalo [0.00;15.00]. CONCLUSÕES: A prevalência de dor lombar nos indivíduos da ESTSP foi 50%. Os valores de incapacidade revelaram incapacidade ligeira.

Electricity markets: transmission prices methods

In the context of electricity markets, transmission pricing is an important tool to achieve an efficient operation of the electricity system. The electricity market is influenced by several factors; however the transmission network management is one of the most important aspects, because the network is a natural monopoly. The transmission tariffs can help to regulate the market, for this reason transmission tariffs must follow strict criteria. This paper presents the following methods to tariff the use of transmission networks by electricity market players: Post-Stamp Method; MW-Mile Method Distribution Factors Methods; Tracing Methodology; Bialek’s Tracing Method and Locational Marginal Price. A nine bus transmission network is used to illustrate the application of the tariff methods.

Comparison between deterministic and meta-heuristic methods applied to ancillary services dispatch

This paper proposes two meta-heuristics (Genetic Algorithm and Evolutionary Particle Swarm Optimization) for solving a 15 bid-based case of Ancillary Services Dispatch in an Electricity Market. A Linear Programming approach is also included for comparison purposes. A test case based on the dispatch of Regulation Down, Regulation Up, Spinning Reserve and Non-Spinning Reserve services is used to demonstrate that the use of meta-heuristics is suitable for solving this kind of optimization problem. Faster execution times and lower computational resources requirements are the most relevant advantages of the used meta-heuristics when compared with the Linear Programming approach.

Ancillary services market clearing simulation: a comparison between deterministic and heuristic methods

Electricity market players operating in a liberalized environment requires access to an adequate decision support tool, allowing them to consider all the business opportunities and take strategic decisions. Ancillary services represent a good negotiation opportunity that must be considered by market players. For this, decision support tool must include ancillary market simulation. This paper proposes two different methods (Linear Programming and Genetic Algorithm approaches) for ancillary services dispatch. The methodologies are implemented in MASCEM, a multi-agent based electricity market simulator. A test case based on California Independent System Operator (CAISO) data concerning the dispatch of Regulation Down, Regulation Up, Spinning Reserve and Non-Spinning Reserve services is included in this paper.

Online versus postal questionnaires: a comparison between two data collection methods

Objectives : The purpose of this article is to find out differences between surveys using paper and online questionnaires. The author has deep knowledge in the case of questions concerning opinions in the development of survey based research, e.g. the limits of postal and online questionnaires. Methods : In the physician studies carried out in 1995 (doctors graduated in 1982-1991), 2000 (doctors graduated in 1982-1996), 2005 (doctors graduated in 1982-2001), 2011 (doctors graduated in 1977-2006) and 457 family doctors in 2000, were used paper and online questionnaires. The response rates were 64%, 68%, 64%, 49% and 73%, respectively. Results : The results of the physician studies showed that there were differences between methods. These differences were connected with using paper-based questionnaire and online questionnaire and response rate. The online-based survey gave a lower response rate than the postal survey. The major advantages of online survey were short response time; very low financial resource needs and data were directly loaded in the data analysis software, thus saved time and resources associated with the data entry process. Conclusions : The current article helps researchers with planning the study design and choosing of the right data collection method.

A comparison of two attenuation correction methods in 111In-Pentetriotide abdominal SPECT

Tomographic image can be degraded, partially by patient based attenuation. The aim of this paper is to quantitatively verify the effects of attenuation correction methods Chang and CT in 111In studies through the analysis of profiles from abdominal SPECT, correspondent to a uniform radionuclide uptake organ, the left kidney.

Derivative-free optimization and filter methods to solve nonlinear constrained problems

In real optimization problems, usually the analytical expression of the objective function is not known, nor its derivatives, or they are complex. In these cases it becomes essential to use optimization methods where the calculation of the derivatives, or the verification of their existence, is not necessary: the Direct Search Methods or Derivative-free Methods are one solution. When the problem has constraints, penalty functions are often used. Unfortunately the choice of the penalty parameters is, frequently, very difficult, because most strategies for choosing it are heuristics strategies. As an alternative to penalty function appeared the filter methods. A filter algorithm introduces a function that aggregates the constrained violations and constructs a biobjective problem. In this problem the step is accepted if it either reduces the objective function or the constrained violation. This implies that the filter methods are less parameter dependent than a penalty function. In this work, we present a new direct search method, based on simplex methods, for general constrained optimization that combines the features of the simplex method and filter methods. This method does not compute or approximate any derivatives, penalty constants or Lagrange multipliers. The basic idea of simplex filter algorithm is to construct an initial simplex and use the simplex to drive the search. We illustrate the behavior of our algorithm through some examples. The proposed methods were implemented in Java.

Reliability of nasal auscultation and their relation to middle ear condition – a clinical interest to pediatrics respiratory physiotherapy

Background: Acute respiratory infections are usual in children under three years old occurring in upper respiratory tract, having an impact on child and caregiver’s quality of life predisposing to otitis media or bronchiolitis. There are few valid and reliable measures to determine the child’s respiratory condition and to guide the physiotherapy intervention. Aim: To assess the intra and inter rater reliability of nasal auscultation, to analyze the relation between sounds’ classification and middle ear’s pressure and compliance as well as with the Clinical Severity Score. Methods: A cross-sectional observational study was composed by 125 nursery children aged up to three years old. Tympanometry, pulmonary and nasal auscultation and application of Clinical Severity Score were performed to each child. Nasal auscultation sounds’ were recorded and sent to 3 blinded experts, that classified, as “obstructed” and “unobstructed”, with a 48 hours interval, in order to analyze inter and intra rater reliability. Results: Nasal auscultation revealed a substantial inter and intra rater reliability (=0,749 and evaluator A - K= 0,691; evaluator B - K= 0,605 and evaluator C - K= 0,724, respectively). Both ears’ pressure was significantly lower in children with an "unobstructed" nasal sound when compared with an “obstructed” nasal sound (t=-3,599, p<0,001 in left ear; t=-2,258, p=0,026 in right ear). Compliance in both ears was significantly lower in children with an "obstructed" nasal sound when compared with “unobstructed” nasal sound (t=-2,728, p=0,007 in left ear; t=-3,830, p<0,001 in right ear). There was a statistically significant association between sounds’ classification and tympanograms types in both ear’s (=11,437, p=0,003 in left ear; =13,535, p=0,001 in right ear). There was a trend to children with an "unobstructed" nasal sound that had a lower clinical severity score when compared with “obstructed” children. Conclusion: It was observed a good intra and substantial inter reliability for nasal auscultation. Nasal auscultation sounds’ classification was related to middle ears’ pressure and compliance.

Efectividade de um programa de fisioterapia na radiculopatia cervical – estudo de caso

Introdução: Não existe um consenso quanto ao melhor tratamento para a radiculopatia cervical pois existe uma grande variedade de manifestações clínicas e opções terapêuticas, mas a sua selecção vai depender do caso particular do utente, sugerindo assim uma correcta avaliação do Fisioterapeuta. Objectivo: Este estudo pretende descrever e avaliar a efectividade de um programa de Fisioterapia num caso de radiculopatia cervical, na dor, funcionalidade e percepção da qualidade de vida. Participantes e Métodos: Estudo observacional descritivo tipo estudo de caso de um utente de 56 anos de idade, com radiculopatia cervical. Para a avaliação foram utilizados testes ortopédicos, a escala visual analógica e os questionários de incapacidade funcional da cervical e do membro superior bem como da percepção da qualidade de vida. Estes questionários foram aplicados em 3 momentos, antes da intervenção, no final e após 6 semanas e os restantes instrumentos foram utilizados em diversos momentos ao longo da intervenção. Esta foi efectuada duas vezes por semana, ao longo de 10 semanas recorrendo a técnicas de terapia manual, exercícios de controlo motor e educação do utente. Resultados: Verificou-se que a dor na cervical passou de 6,5 para 2/10 EVA e no cotovelo direito de 7,3 para 2/10. A resposta ao questionário de incapacidade funcional na cervical variou de 40% no primeiro momento para 11,1% no segundo, o da incapacidade funcional do membro superior variou de 63,6% para 33,5% e o questionário da percepção da qualidade de vida variou de 55,01 para 68,69. Seis semanas após a intervenção, todos estes resultados se mantinham praticamente inalterados. Conclusão: Este caso permitiu demonstrar o processo de raciocínio clínico efectuado ao longo de dez semanas de intervenção em que se utilizou uma abordagem centrada no utente, baseada na evidência científica e na experiência clínica anterior. Os resultados alcançados foram de encontro às expectativas iniciais e parecem evidenciar que, neste caso, o programa de fisioterapia teve efeitos positivos na dor, funcionalidade e percepção da qualidade de vida.