BIT: Biosignal Igniter Toolkit

The study of biosignals has had a transforming role in multiple aspects of our society, which go well beyond the health sciences domains to which they were traditionally associated with. While biomedical engineering is a classical discipline where the topic is amply covered, today biosignals are a matter of interest for students, researchers and hobbyists in areas including computer science, informatics, electrical engineering, among others. Regardless of the context, the use of biosignals in experimental activities and practical projects is heavily bounded by the cost, and limited access to adequate support materials. In this paper we present an accessible, albeit versatile toolkit, composed of low-cost hardware and software, which was created to reinforce the engagement of different people in the field of biosignals. The hardware consists of a modular wireless biosignal acquisition system that can be used to support classroom activities, interface with other devices, or perform rapid prototyping of end-user applications. The software comprehends a set of programming APIs, a biosignal processing toolbox, and a framework for real time data acquisition and postprocessing. (C) 2014 Elsevier Ireland Ltd. All rights reserved.

Surgical correction of scoliosis: Numerical analysis and optimization of the procedure

A previously developed model is used to numerically simulate real clinical cases of the surgical correction of scoliosis. This model consists of one-dimensional finite elements with spatial deformation in which (i) the column is represented by its axis; (ii) the vertebrae are assumed to be rigid; and (iii) the deformability of the column is concentrated in springs that connect the successive rigid elements. The metallic rods used for the surgical correction are modeled by beam elements with linear elastic behavior. To obtain the forces at the connections between the metallic rods and the vertebrae geometrically, non-linear finite element analyses are performed. The tightening sequence determines the magnitude of the forces applied to the patient column, and it is desirable to keep those forces as small as possible. In this study, a Genetic Algorithm optimization is applied to this model in order to determine the sequence that minimizes the corrective forces applied during the surgery. This amounts to find the optimal permutation of integers 1, ... , n, n being the number of vertebrae involved. As such, we are faced with a combinatorial optimization problem isomorph to the Traveling Salesman Problem. The fitness evaluation requires one computing intensive Finite Element Analysis per candidate solution and, thus, a parallel implementation of the Genetic Algorithm is developed.

Fluorescence Microscopy Imaging Denoising with Log-Euclidean Priors and Photobleaching Compensation

Fluorescent protein microscopy imaging is nowadays one of the most important tools in biomedical research. However, the resulting images present a low signal to noise ratio and a time intensity decay due to the photobleaching effect. This phenomenon is a consequence of the decreasing on the radiation emission efficiency of the tagging protein. This occurs because the fluorophore permanently loses its ability to fluoresce, due to photochemical reactions induced by the incident light. The Poisson multiplicative noise that corrupts these images, in addition with its quality degradation due to photobleaching, make long time biological observation processes very difficult. In this paper a denoising algorithm for Poisson data, where the photobleaching effect is explicitly taken into account, is described. The algorithm is designed in a Bayesian framework where the data fidelity term models the Poisson noise generation process as well as the exponential intensity decay caused by the photobleaching. The prior term is conceived with Gibbs priors and log-Euclidean potential functions, suitable to cope with the positivity constrained nature of the parameters to be estimated. Monte Carlo tests with synthetic data are presented to characterize the performance of the algorithm. One example with real data is included to illustrate its application.

Active and passive behaviors of soft tissues: Pelvic floor muscles

: A new active-contraction visco-elastic numerical model of the pelvic floor (skeletal) muscle is presented. Our model includes all elements that represent the muscle constitutive behavior, contraction and relaxation. In contrast with the previous models, the activation function can be null. The complete equations are shown and exactly linearized. Small verification and validation tests are performed and the pelvis is modeled using the data from the intra-abdominal pressure tests

Die Surface Designer System

This paper defines Die Surface Designer (DSD) System for fast draw die in the product development feasibility phase on surfaces coming from styling. We propose a CAD integration, for better support the design process in industry, particularly on the development of new products in automotive sector. The DSD system intends to reduce the lead time by providing and integrating flexible and efficient capabilities for testing early concepts from surface analysis points of view in automotive product development.

Risco e incerteza no pensamento biomédico: notas teóricas sobre o advento da quantificação e da prova experimental na medicina moderna

A biomedicina é um domínio do saber no qual a proliferação do conceito de risco se tem evidenciado de forma expressiva, o que revela uma preocupação em proceder ao controlo sistemático dos problemas através de um modelo de racionalização instrumental. Tal procedimento é elucidativo do investimento que é feito na interpretação das incertezas como riscos. Consequentemente, a dimensão estatística que lhe está associada é cada vez mais um dos principais traços do seu perfil científico. Biomedicine is a field where the concept of risk has shown an impressive increase in its importance. This fact demonstrates a concern with a systematic problem control through an instrumental rationalizing model, expressing eloquently the investment being made in interpreting uncertainty as risk and the consequent statistical dimension as an ever-more quintessential feature of its scientific profile.

Tuning Iris Recognition for Noisy Images

The use of iris recognition for human authentication has been spreading in the past years. Daugman has proposed a method for iris recognition, composed by four stages: segmentation, normalization, feature extraction, and matching. In this paper we propose some modifications and extensions to Daugman's method to cope with noisy images. These modifications are proposed after a study of images of CASIA and UBIRIS databases. The major modification is on the computationally demanding segmentation stage, for which we propose a faster and equally accurate template matching approach. The extensions on the algorithm address the important issue of pre-processing that depends on the image database, being mandatory when we have a non infra-red camera, like a typical WebCam. For this scenario, we propose methods for reflection removal and pupil enhancement and isolation. The tests, carried out by our C# application on grayscale CASIA and UBIRIS images show that the template matching segmentation method is more accurate and faster than the previous one, for noisy images. The proposed algorithms are found to be efficient and necessary when we deal with non infra-red images and non uniform illumination.

MDAI: Model based Design in Automobile Industry

It is proposed a new approach based on a methodology, assisted by a tool, to create new products in the automobile industry based on previous defined processes and experiences inspired on a set of best practices or principles: it is based on high-level models or specifications; it is component-based architecture centric; it is based on generative programming techniques. This approach follows in essence the MDA (Model Driven Architecture) philosophy with some specific characteristics. We propose a repository that keeps related information, such as models, applications, design information, generated artifacts and even information concerning the development process itself (e.g., generation steps, tests and integration milestones). Generically, this methodology receives the users' requirements to a new product (e.g., functional, non-functional, product specification) as its main inputs and produces a set of artifacts (e.g., design parts, process validation output) as its main output, that will be integrated in the engineer design tool (e.g. CAD system) facilitating the work.

A checkpointing-enabled and resource-aware Java Virtual Machine for efficient and robust e-Science applications in grid environments

Object-oriented programming languages presently are the dominant paradigm of application development (e. g., Java,. NET). Lately, increasingly more Java applications have long (or very long) execution times and manipulate large amounts of data/information, gaining relevance in fields related with e-Science (with Grid and Cloud computing). Significant examples include Chemistry, Computational Biology and Bio-informatics, with many available Java-based APIs (e. g., Neobio). Often, when the execution of such an application is terminated abruptly because of a failure (regardless of the cause being a hardware of software fault, lack of available resources, etc.), all of its work already performed is simply lost, and when the application is later re-initiated, it has to restart all its work from scratch, wasting resources and time, while also being prone to another failure and may delay its completion with no deadline guarantees. Our proposed solution to address these issues is through incorporating mechanisms for checkpointing and migration in a JVM. These make applications more robust and flexible by being able to move to other nodes, without any intervention from the programmer. This article provides a solution to Java applications with long execution times, by extending a JVM (Jikes research virtual machine) with such mechanisms. Copyright (C) 2011 John Wiley & Sons, Ltd.

A Service Integration Platform for Collaborative Networks

Integrated manufacturing constitutes a complex system made of heterogeneous information and control subsystems. Those subsystems are not designed to the cooperation. Typically each subsystem automates specific processes, and establishes closed application domains, therefore it is very difficult to integrate it with other subsystems in order to respond to the needed process dynamics. Furthermore, to cope with ever growing marketcompetition and demands, it is necessary for manufacturing/enterprise systems to increase their responsiveness based on up-to-date knowledge and in-time data gathered from the diverse information and control systems. These have created new challenges for manufacturing sector, and even bigger challenges for collaborative manufacturing. The growing complexity of the information and communication technologies when coping with innovative business services based on collaborative contributions from multiple stakeholders, requires novel and multidisciplinary approaches. Service orientation is a strategic approach to deal with such complexity, and various stakeholders' information systems. Services or more precisely the autonomous computational agents implementing the services, provide an architectural pattern able to cope with the needs of integrated and distributed collaborative solutions. This paper proposes a service-oriented framework, aiming to support a virtual organizations breeding environment that is the basis for establishing short or long term goal-oriented virtual organizations. The notion of integrated business services, where customers receive some value developed through the contribution from a network of companies is a key element.

Chromatographic behaviour of monoclonal antibodies against wild-type amidase from Pseudomonasaeruginosa on immobilized metal chelates

The aim of this work was to devise a one-step purification procedure for monoclonal antibodies (MAbs) of IgG class by immobilized metal affinity chromatography (IMAC). Therefore, several stationary phases were prepared containing immobilized metal chelates in order to study the chromatographic behaviour of MAbs against wild-type amidase from Pseudomonas aeruginosa. Such MAbs adsorbed to Cu(II), Ni(II), Zn(II) and Co(II)-IDA agarose columns. The increase in ligand concentration and the use of longer spacer arms and higher pH values resulted in higher adsorption of MAbs into immobilized metal chelates. The dynamic binding capacity and the maximum binding capacity were 1.33 +/- 0.015 and 3.214 +/- 0.021 mg IgG/mL of sedimented commercial matrix, respectively. A K(D) of 4.53 x 10(-7) M was obtained from batch isotherm measurements. The combination of tailor-made stationary phases of IMAC and the correct selection of adsorption conditions permitted a one-step purification procedure to be devised for MAbs of IgG class. Culture supernatants containing MAbs were purified by IMAC on commercial-Zn(II) and EPI-30-IDA-Zn(II) Sepharose 6B columns and by affinity chromatography on Protein A-Sepharose CL-4B. This MAb preparation revealed on SDS-PAGE two protein bands with M(r) of 50 and 22 kDa corresponding to the heavy and light chains, respectively. Copyright (C) 2011 John Wiley & Sons, Ltd.

Finite element studies of the mechanical behaviour of the diaphragm in normal and pathological cases

The diaphragm is a muscular membrane separating the abdominal and thoracic cavities, and its motion is directly linked to respiration. In this study, using data from a 59-year-old female cadaver obtained from the Visible Human Project, the diaphragm is reconstructed and, from the corresponding solid object, a shell finite element mesh is generated and used in several analyses performed with the ABAQUS 6.7 software. These analyses consider the direction of the muscle fibres and the incompressibility of the tissue. The constitutive model for the isotropic strain energy as well as the passive and active strain energy stored in the fibres is adapted from Humphrey's model for cardiac muscles. Furthermore, numerical results for the diaphragmatic floor under pressure and active contraction in normal and pathological cases are presented.

IOPT Petri Net State Space Generation Algorithm with Maximal-Step Execution Semantics

This paper presents an algorithm to efficiently generate the state-space of systems specified using the IOPT Petri-net modeling formalism. IOPT nets are a non-autonomous Petri-net class, based on Place-Transition nets with an extended set of features designed to allow the rapid prototyping and synthesis of system controllers through an existing hardware-software co-design framework. To obtain coherent and deterministic operation, IOPT nets use a maximal-step execution semantics where, in a single execution step, all enabled transitions will fire simultaneously. This fact increases the resulting state-space complexity and can cause an arc "explosion" effect. Real-world applications, with several million states, will reach a higher order of magnitude number of arcs, leading to the need for high performance state-space generator algorithms. The proposed algorithm applies a compilation approach to read a PNML file containing one IOPT model and automatically generate an optimized C program to calculate the corresponding state-space.

Neonatal anthropometry: a tool to evaluate the nutritional status and predict early and late risks

Neonatal anthropometry is an inexpensive, noninvasive and convenient tool for bedside evaluation, especially in sick and fragile neonates. Anthropometry can be used in neonates as a tool for several purposes: diagnosis of foetal malnutrition and prediction of early postnatal complications; postnatal assessment of growth, body composition and nutritional status; prediction of long-term complications including metabolic syndrome; assessment of dysmorphology; and estimation of body surface. However, in this age group anthropometry has been notorious for its inaccuracy and the main concern is to make validated indices available. Direct measurements, such as body weight, length and body circumferences are the most commonly used measurements for nutritional assessment in clinical practice and in field studies. Body weight is the most reliable anthropometric measurement and therefore is often used alone in the assessment of the nutritional status, despite not reflecting body composition. Derived indices from direct measurements have been proposed to improve the accuracy of anthropometry. Equations based on body weight and length, mid-arm circumference/head circumference ratio, and upper-arm cross-sectional areas are among the most used derived indices to assess nutritional status and body proportionality, even though these indices require further validation for the estimation of body composition in neonates.

Avaliação e controlo da dor em pediatria: uma década

Introdução – A negligência no controlo da dor é um problema amplamente reconhecido em Portugal. Desde 2001 têm sido realizadas inúmeras iniciativas para melhorar a prática de cuidados nesta área. Desenvolveram-se ações de sensibilização e formação dos profissionais de saúde, publicaram-se orientações técnicas e guias de boas práticas e realizaram-se os primeiros estudos para se fazer um diagnóstico da situação. Objetivos – O objetivo deste trabalho foi o de caracterizar os cuidados prestados na avaliação e no controlo da dor nas crianças até aos 18 anos internadas em serviços hospitalares em Portugal e analisar a evolução feita nos cuidados entre os anos de 2002 e 2012. Metodologia – Estudo descritivo, transversal, de consulta retrospetiva seriada de registos intermitentes efetuados no processo clínico em relação a um período de 24 horas. O recrutamento da amostra foi aleatório e incluiu todos os processos clínicos de crianças até aos 18 anos internados em serviços de quatro hospitais Portugueses entre agosto e dezembro de 2011. Resultados – A prevalência de dor reduziu de forma significativa entre 2002 e 2012. As crianças livres de dor subiram de 37% para 75%. O registo da avaliação da intensidade da dor e a colheita de informação sobre a história de dor passou a ser uma prática comum na maioria dos casos (53% e 64%, respetivamente), embora ainda direcionada para o modelo de cuidados biomédico. A prevalência das intervenções farmacológicas não se alterou (43% versus 42%), mas a implementação de estratégias não-farmacológicas baixou significativamente (72% versus 15%). Conclusões – As ações de sensibilização/formação realizadas no âmbito das políticas implementadas nestes últimos dez anos na área da avaliação e controlo da dor pediátrica geraram evidentes ganhos na qualidade de cuidados prestados, pelo que o investimento na formação deve continuar. No entanto, deve ser dada prioridade à formação para a aplicação de estratégias de intervenção não-farmacológicas e ao desenvolvimento de mais investigação que suporte as práticas.