Slicing functional programs by calculation

Program slicing is a well known family of techniques used to identify code fragments which depend on or are depended upon specific program entities. They are particularly useful in the areas of reverse engineering, program understanding, testing and software maintenance. Most slicing methods, usually targeting either the imperative or the object oriented paradigms, are based on some sort of graph structure representing program dependencies. Slicing techniques amount, therefore, to (sophisticated) graph transversal algorithms. This paper proposes a completely different approach to the slicing problem for functional programs. Instead of extracting program information to build an underlying dependencies’ structure, we resort to standard program calculation strategies, based on the so-called Bird- Meertens formalism. The slicing criterion is specified either as a projection or a hiding function which, once composed with the original program, leads to the identification of the intended slice. Going through a number of examples, the paper suggests this approach may be an interesting, even if not completely general alternative to slicing functional programs

A new frontier in biodiversity inventory: a proposal for estimators of phylogenetic and functional diversity

Copyright © 2014 The Authors. Methods in Ecology and Evolution © 2014 British Ecological Society.

Host-symbiont interactions in the deep-sea vent mussel Bathymodiolus azoricus : a molecular approach

Tese de Doutoramento, Ciências do Mar, especialidade de Biologia Marinha, 19 de Dezembro de 2015, Universidade dos Açores.

Neural-network approach to modeling liquid crystals in complex confinement

Finding the structure of a confined liquid crystal is a difficult task since both the density and order parameter profiles are nonuniform. Starting from a microscopic model and density-functional theory, one has to either (i) solve a nonlinear, integral Euler-Lagrange equation, or (ii) perform a direct multidimensional free energy minimization. The traditional implementations of both approaches are computationally expensive and plagued with convergence problems. Here, as an alternative, we introduce an unsupervised variant of the multilayer perceptron (MLP) artificial neural network for minimizing the free energy of a fluid of hard nonspherical particles confined between planar substrates of variable penetrability. We then test our algorithm by comparing its results for the structure (density-orientation profiles) and equilibrium free energy with those obtained by standard iterative solution of the Euler-Lagrange equations and with Monte Carlo simulation results. Very good agreement is found and the MLP method proves competitively fast, flexible, and refinable. Furthermore, it can be readily generalized to the richer experimental patterned-substrate geometries that are now experimentally realizable but very problematic to conventional theoretical treatments.

Viewpoints and goals: towards an integrated approach

Dissertação de Mestrado em Engenharia Informática

Neural-network approach to modeling liquid crystals in complex confinement

Finding the structure of a confined liquid crystal is a difficult task since both the density and order parameter profiles are nonuniform. Starting from a microscopic model and density-functional theory, one has to either (i) solve a nonlinear, integral Euler-Lagrange equation, or (ii) perform a direct multidimensional free energy minimization. The traditional implementations of both approaches are computationally expensive and plagued with convergence problems. Here, as an alternative, we introduce an unsupervised variant of the multilayer perceptron (MLP) artificial neural network for minimizing the free energy of a fluid of hard nonspherical particles confined between planar substrates of variable penetrability. We then test our algorithm by comparing its results for the structure (density-orientation profiles) and equilibrium free energy with those obtained by standard iterative solution of the Euler-Lagrange equations and with Monte Carlo simulation results. Very good agreement is found and the MLP method proves competitively fast, flexible, and refinable. Furthermore, it can be readily generalized to the richer experimental patterned-substrate geometries that are now experimentally realizable but very problematic to conventional theoretical treatments.

A new approach to assess defragmentation strategies in dynamically reconfigurable FPGAs

Fragmentation on dynamically reconfigurable FPGAs is a major obstacle to the efficient management of the logic space in reconfigurable systems. When resource allocation decisions have to be made at run-time a rearrangement may be necessary to release enough contiguous resources to implement incoming functions. The feasibility of run-time relocation depends on the processing time required to set up rearrangements. Moreover, the performance of the relocated functions should not be affected by this process or otherwise the whole system performance, and even its operation, may be at risk. Relocation should take into account not only specific functional issues, but also the FPGA architecture, since these two aspects are normally intertwined. A simple and fast method to assess performance degradation of a function during relocation and to speed up the defragmentation process, based on previous function labelling and on the application of the Euclidian distance concept, is proposed in this paper.

Evaluation of Opuntia spp. bioactive products as promising natural chemotherapeutical agents- an in vitro approach

Dissertation to obtain a Master Degree in Biotechnology

Insights into the clinical and functional significance of cardiac autonomic dysfunction in Chagas disease

INTRODUCTION: Exclusive or associated lesions in various structures of the autonomic nervous system occur in the chronic forms of Chagas disease. In the indeterminate form, the lesions are absent or mild, whereas in the exclusive or combined heart and digestive disease forms, they are often more pronounced. Depending on their severity these lesions can result mainly in cardiac parasympathetic dysfunction but also in sympathetic dysfunction of variable degrees. Despite the key autonomic effect on cardiovascular functioning, the pathophysiological and clinical significance of the cardiac autonomic dysfunction in Chagas disease remains unknown. METHODS: Review of data on the cardiac autonomic dysfunction in Chagas disease and their potential consequences, and considerations supporting the possible relationship between this disturbance and general or cardiovascular clinical and functional adverse outcomes. RESULTS: We hypothesise that possible consequences that cardiac dysautonomia might variably occasion or predispose in Chagas disease include: transient or sustained arrhythmias, sudden cardiac death, adverse overall and cardiovascular prognosis with enhanced morbidity and mortality, an inability of the cardiovascular system to adjust to functional demands and/or respond to internal or external stimuli by adjusting heart rate and other hemodynamic variables, and immunomodulatory and cognitive disturbances. CONCLUSIONS: Impaired cardiac autonomic modulation in Chagas disease might not be a mere epiphenomenon without significance. Indirect evidences point for a likely important role of this alteration as a primary predisposing or triggering cause or mediator favouring the development of subtle or evident secondary cardiovascular functional disturbances and clinical consequences, and influencing adverse outcomes.

Qualidade de vida na demência : estudo sobre a perceção de Qualidade de Vida em pessoas com demência, seus familiares e cuidadores profissionais em contexto de Internamento

RESUMO: Introdução: Ao fenómeno do envelhecimento está associado uma maior incidência de doenças crónicas e incapacitantes. Atualmente é consensual, a preocupação com a Qualidade de Vida (QdV) nesta faixa etária, acrescendo importância quando falamos em QdV em demência, dada a complexidade dos sintomas, morbilidades e co-morbilidades que se verificam nesta síndrome. Objetivo: O presente estudo tem como objetivo principal avaliar a perceção da QdV em pessoas com demência, seus familiares e cuidadores profissionais, de forma a identificar dimensões que mereçam uma maior atenção na definição de programas de intervenção em situação de institucionalização. Metodologia: Este estudo é de caráter descritivo transversal com componente qualitativa e quantitativa. A população compreende as pessoas com demência do Centro Psicogeriátrico Nª Sª de Fátima (CPNSF). A amostra foi constituída pelas residentes do CPNSF com diagnóstico de demência e classificação total de Mini Mental State Examination (MMSE) ≥ 10. As variáveis em análise foram: QdV, avaliada pela escala QOL-AD versão portuguesa, perfil sociodemográfico das pessoas com demência, familiares e cuidadores profissionais, por inquérito por questionário; Grau de defeito cognitivo, dependência funcional e sintomatologia depressiva das pessoas com demência, verificado por MMSE, índice de Barthel e Escala de Depressão Geriátrica (GDS-15). Foi ainda acedido ao entendimento pessoal sobre o construto de QdV, através de entrevista semiestruturada dirigida a todos os participantes. Resultados: Com base nos resultados obtidos foi possível determinar que as pessoas com demência, associam QdV a fatores como saúde física, humor/disposição, condições de vida, cognição, família, satisfação com a vida, dinheiro. Foram observadas relações negativas com sintomatologia depressiva e funcionalidade para as atividades instrumentais de vida diária. Os familiares associam positivamente QdV a bem-estar geral relacionado com as dimensões física, psicológica e relações sociais, e negativamente com o estado cognitivo e sintomatologia neuropsiquiátrica. Os cuidadores profissionais associam QdV das pessoas com demência a questões relacionadas com condições e satisfação com a vida, bem-estar físico, suporte emocional relações sociais e funcionalidade para as atividades instrumentais básicas de vida diária. Não foi possível correlacionar a QOL-AD com a dimensão funcionalidade por não existir nesta escala um item que inclua este conceito. Conclusão: Este estudo confirma que pessoas com demência, têm capacidade para aceder e avaliar aspetos da sua própria QdV, sendo que tendem a pontuar com valores mais elevados a sua QdV quando comparados com familiares e cuidadores profissionais.--------------- ABSTRACT:Background:: Aging is associated with higher incidence of chronic and debilitating illnesses. The study of quality of life in aging population has been an increasingly discussed topic. Quality of life in dementia is a particular challenging field given the complexity of symptoms, morbilities and co-morbilities that occur in this syndrome. Objective: This study aims to evaluate the perception of quality of life in elderly people with dementia and their families, in order to identify dimensions that should be prioritized in intervention programs aimed at increasing quality of life in persons with dementia living in institutions. Methodology: This study used a is cross-sectional descriptive mixed methods approach. The population comprises people with dementia in Psychogeriatric Center Nossa Senhora de Fátima (CPNSF). The sample consisted of the residents of CPNSF diagnosed with dementia and total score of Mini Mental State Examination (MMSE) ≥ 10. The variables analyzed were: quality of life, assessed by QOL-AD scale Portuguese version, socio-demographic profile of people with dementia, family members and professional caregivers, by questionnaire survey; Degree of cognitive impairment, functional dependence and depressive symptoms of people with dementia, using respectively MMSE, Barthel index and Geriatric Depression Scale (GDS-15). The personal understanding of the QoL construct was also assessed, through semi-structured interviews to all participants Results: The results supported that people with dementia, related quality of life to factors such as physical health, mood / disposition, living conditions, cognition, family, life satisfaction, and money. Negative relations were observed with depressive symptoms and functionality for the instrumental activities of daily living. The family members associate quality of life positively with overall well-being related to the physical, psychological and social relationships, and negatively with cognitive status and neuropsychiatric symptoms. Professional caregivers associate quality of life of people with dementia-related issues conditions and satisfaction with life, physical well-being, social relationships and emotional support functionality to the basic instrumental activities of daily living. It was not possible to correlate the QOL-AD with the size feature does not exist on this scale for an item that includes this concept. Conclusion: This study supports the idea that people with dementia are able to assess and evaluate aspects of their own quality of life, and tend to rate their quality of life higher than family and professional caregivers.

A relational algebra approach to ETL modeling

The MAP-i Doctoral Programme in Informatics, of the Universities of Minho, Aveiro and Porto

To be or not to be a pseudogene: a molecular epidemiological approach to the mclx genes and its impact in tuberculosis

Tuberculosis presents a myriad of symptoms, progression routes and propagation patterns not yet fully understood. Whereas for a long time research has focused solely on the patient immunity and overall susceptibility, it is nowadays widely accepted that the genetic diversity of its causative agent, Mycobacterium tuberculosis, plays a key role in this dynamic. This study focuses on a particular family of genes, the mclxs (Mycobacterium cyclase/LuxR-like genes), which codify for a particular and nearly mycobacterial-exclusive combination of protein domains. mclxs genes were found to be pseudogenized by frameshift-causing insertion(s)/deletion(s) in a considerable number of M. tuberculosis complex strains and clinical isolates. To discern the functional implications of the pseudogenization, we have analysed the pattern of frameshift-causing mutations in a group of M. tuberculosis isolates while taking into account their microbial-, patient- and disease-related traits. Our logistic regression-based analyses have revealed disparate effects associated with the transcriptional inactivation of two mclx genes. In fact, mclx2 (Rv1358) pseudogenization appears to be primarily driven by the microbial phylogenetic background, being mainly related to the Euro-American (EAm) lineage; on the other hand, mclx3 (Rv2488c) presents a higher tendency for pseudogenization among isolates from patients born on the Western Pacific area, and from isolates causing extra-pulmonary infections. These results contribute to the overall knowledge on the biology of M. tuberculosis infection, whereas at the same time launch the necessary basis for the functional assessment of these so far overlooked genes.

Are cognitive interventions for multiple sclerosis effective and feasible?

Purpose: Fifty percent of patients with Multiple Sclerosis (MS) are estimated to have cognitive impairments leading to considerable decline in productivity and quality of life. Cognitive intervention has been considered to complement pharmacological treatments. However, a lack of agreement concerning the efficacy of cognitive interventions in MS still exists. A systematic review and meta-analysis was conducted to assess the effects of cognitive interventions in MS. Methods: To overcome limitations of previous meta-analyses, several databases were searched only for Randomized Clinical Trials (RCTs) with low risk of bias. Results: Five studies (total of 139 participants) met our eligibility criteria. Although good completion and adherence rates were evident, we found no evidence of intervention effects on cognition or mood in post-intervention or follow-up assessments. Conclusions: This is the first meta-analysis assessing the effects of cognitive intervention in MS including only RCTs with comparable conditions. Research regarding efficacy, cost-effectiveness and feasibility is still in its infancy. Caution is advised when interpreting these results due to the small number of RCTs meeting the inclusion criteria. Considering the costs of disease, good completion and adherence rates of this approach, further research is warranted. Recommendations concerning improved research practices in the field are presented as well.

Cognitive rehabilitation in a visual variant of Alzheimer's disease

Alzheimer's disease (AD) is commonly associated with marked memory deficits; however, nonamnestic variants have been consistently described as well. Posterior cortical atrophy (PCA) is a progressive degenerative condition in which posterior regions of the brain are predominantly affected, therefore resulting in a pattern of distinctive and marked visuospatial symptoms, such as apraxia, alexia, and spatial neglect. Despite the growing number of studies on cognitive and neural bases of the visual variant of AD, intervention studies remain relatively sparse. Current pharmacological treatments offer modest efficacy. Also, there is a scarcity of complementary nonpharmacological interventions with only two previous studies of PCA. Here we describe a highly educated 57-year-old patient diagnosed with a visual variant of AD who participated in a cognitive intervention program (comprising reality orientation, cognitive stimulation, and cognitive training exercises). Neuropsychological assessment was performed across moments (baseline, postintervention, follow-up) and consisted mainly of verbal and visual memory. Baseline neuropsychological assessment showed deficits in perceptive and visual-constructive abilities, learning and memory, and temporal orientation. After neuropsychological rehabilitation, we observed small improvements in the patient's cognitive functioning, namely in verbal memory, attention, and psychomotor abilities. This study shows evidence of small beneficial effects of cognitive intervention in PCA and is the first report of this approach with a highly educated patient in a moderate stage of the disease. Controlled studies are needed to assess the potential efficacy of cognition-focused approaches in these patients, and, if relevant, to grant their availability as a complementary therapy to pharmacological treatment and visual aids.

Highly functional and biodegradable nanofibrous scaffolds combined with stem cells for bone and cartilage tissue engineering

Among the various possible embodiements of Advanced Therapies and in particular of Tissue Engineering the use of temporary scaffolds to regenerate tissue defects is one of the key issues. The scaffolds should be specifically designed to create environments that promote tissue development and not merely to support the maintenance of communities of cells. To achieve that goal, highly functional scaffolds may combine specific morphologies and surface chemistry with the local release of bioactive agents. Many biomaterials have been proposed to produce scaffolds aiming the regeneration of a wealth of human tissues. We have a particular interest in developing systems based in nanofibrous biodegradable polymers1,2. Those demanding applications require a combination of mechanical properties, processability, cell-friendly surfaces and tunable biodegradability that need to be tailored for the specific application envisioned. Those biomaterials are usually processed by different routes into devices with wide range of morphologies such as biodegradable fibers and meshes, films or particles and adaptable to different biomedical applications. In our approach, we combine the temporary scaffolds populated with therapeutically relevant communities of cells to generate a hybrid implant. For that we have explored different sources of adult and also embryonic stem cells. We are exploring the use of adult MSCs3, namely obtained from the bone marrow for the development autologous-based therapies. We also develop strategies based in extra-embryonic tissues, such as amniotic fluid (AF) and the perivascular region of the umbilical cord4 (Whartonâ s Jelly, WJ). Those tissues offer many advantages over both embryonic and other adult stem cell sourcess. These tissues are frequently discarded at parturition and its extracorporeal nature facilitates tissue donation by the patients. The comparatively large volume of tissue and ease of physical manipulation facilitates the isolation of larger numbers of stem cells. The fetal stem cells appear to have more pronounced immunomodulatory properties than adult MSCs. This allogeneic escape mechanism may be of therapeutic value, because the transplantation of readily available allogeneic human MSCs would be preferable as opposed to the required expansion stage (involving both time and logistic effort) of autologous cells. Topics to be covered: This talk will review our latest developments of nanostructured-based biomaterials and scaffolds in combination with stem cells for bone and cartilage tissue engineering.