Development of computational tools for the integrated analysis of DNA microarray data with applications in cancer research

The MAP-i Doctoral Program of the Universities of Minho, Aveiro and Porto

Analysis of toxicity on Bacillus sphaericus from amazonian soils to Anopheles darlingi and Culex quinquefasciatus larvae

Bioassays under laboratory conditions aiming to determine the larvicidal activity of Bacillus sphaericus were carried out on Anopheles darlingi and Culex quinquefasciatus. In order to estimate the toxicity through median lethal concentration (LC50) and the relative potency of the strains to B. sphaericus standard strain 2362, probit analysis was performed utilizing the POLO-PC program. The findings of LC50 pointed out high effectiveness on strains IB15 (0.040 ppm), IB19 and S1116 (0.048 ppm), IB16 (0.052 ppm) and S265 (0.057 ppm). Strain IB15 presented nearly 50% more potency than strain 2362 in bioassays conducted on A. darlingi. It was observed that IB16 and S1116 strains were the most powerful against C. quinquefasciatus, showing to be about 300-400% stronger than 2362 strain. The results show that laboratory conditioned evaluation can be an important way to select promising bacteria with entomopathogenic action on biolarvicides production for use on mosquitoes breeding sites.

Analysis and selection of indicators for a sustainability assessment method for school buildings based on SBTool ‐ PT

Nowadays, the sustainability of buildings has an extreme importance. This concept goes towards the European aims of the Program Horizon 2020, which concerns about the reduction of the environmental impacts through such aspects as the energy efficiency and renewable technologies, among others. Sustainability is an extremely broad concept but, in this work, it is intended to include the concept of sustainability in buildings. Within the concept that aims the integration of environmental, social and economic levels towards the preservation of the planet and the integrity of the users, there are, currently, several types of tools of environmental certification that are applicable to the construction industry (LEED, BREEAM, DGNB, SBTool, among others). Within this context, it is highlighted the tool SBTool (Sustainable Building Tool) that is employed in several countries and can be subject to review in institutions of basic education, which are the base for the formation of the critical masses and for the development of a country. The main aim of this research is to select indicators that can be used in a methodology for sustainability assessment (SBTool) of school buildings in Portugal and in Brazil. In order to achieve it, it will also be analyzed other methodologies that already incorporate parameters directly related with the schools environment, such as BREEAM or LEED.

Longitudinal analysis of tumor marker CEA of breast cancer patients from Braga's hospital

Allied to an epidemiological study of population of the Senology Unit of Braga’s Hospital that have been diagnosed with malignant breast cancer, we describe the progression in time of repeated measurements of tumor marker Carcinoembryonic antigen (CEA). Our main purpose is to describe the progression of this tumor marker as a function of possible risk factors and, hence, to understand how these risk factors influences that progression. The response variable, values of CEA, was analyzed making use of longitudinal models, testing for different correlation structures. The same covariates used in a previous survival analysis were considered in the longitudinal model. The reference time used was time from diagnose until death from breast cancer. For diagnostic of the models fitted we have used empirical and theoretical variograms. To evaluate the fixed term of the longitudinal model we have tested for a changing point on the effect of time on the tumor marker progression. A longitudinal model was also fitted only to the subset of patients that died from breast cancer, using the reference time as time from date of death until blood test.

The use of canonical correlation analysis to assess the relationship between executive functioning and verbal memory in older adults

Executive functioning (EF), which is considered to govern complex cognition, and verbal memory (VM) are constructs assumed to be related. However, it is not known the magnitude of the association between EF and VM, and how sociodemographic and psychological factors may affect this relationship, including in normal aging. In this study, we assessed different EF and VM parameters, via a battery of neurocognitive/psychological tests, and performed a Canonical Correlation Analysis (CCA) to explore the connection between these constructs, in a sample of middle- aged and older healthy individuals without cognitive impairment (N = 563, 50+ years of age). The analysis revealed a positive and moderate association between EF and VM independently of gender, age, education, global cognitive performance level, and mood. These results confirm that EF presents a significant association with VM performance.

Blood Pressure Control in Hypertensive Patients in the "Hiperdia Program": A Territory-Based Study

Background:Systemic hypertension is highly prevalent and an important risk factor for cardiovascular events. Blood pressure control in hypertensive patients enrolled in the Hiperdia Program, a program of the Single Health System for the follow-up and monitoring of hypertensive patients, is still far below the desired level.Objective:To describe the epidemiological profile and to assess blood pressure control of patients enrolled in Hiperdia, in the city of Novo Hamburgo (State of Rio Grande do Sul, Brazil).Methods:Cross-sectional study with a stratified cluster random sample, including 383 adults enrolled in the Hiperdia Program of the 15 Basic Health Units of the city of Porto Alegre, conducted between 2010 and 2011. Controlled blood pressure was defined as ≤140 mmHg × 90 mmHg. The hypertensive patients were interviewed and their blood pressure was measured using a calibrated aneroid device. Prevalence ratios (PR) with 95% confidence interval, Wald's χ2 test, and simple and multiple Poisson regression were used in the statistical analysis.Results:The mean age was 63 ± 10 years, and most of the patients were females belonging to social class C, with a low level of education, a sedentary lifestyle, and family history positive for systemic hypertension. Diabetes mellitus (DM) was observed in 31%; adherence to the antihypertensive treatment in 54.3%; and 33.7% had their blood pressure controlled. DM was strongly associated with inadequate BP control, with only 15.7% of the diabetics showing BP considered as controlled.Conclusion:Even for hypertensive patients enrolled in the Hiperdia Program, BP control is not satisfactorily reached or sustained. Diabetic hypertensive patients show the most inappropriate BP control.

Blood Pressure and Hemodynamic Adaptations after a Training Program in Young Individuals with Down Syndrome

Background:Cardiovascular diseases affect people worldwide. Individuals with Down Syndrome (DS) have an up to sixteen-time greater risk of mortality from cardiovascular diseases.Objective:To evaluate the effects of aerobic and resistance exercises on blood pressure and hemodynamic variables of young individuals with DS.Methods:A total of 29 young individuals with DS participated in the study. They were divided into two groups: aerobic training (AT) (n = 14), and resistance training (TR) (n = 15). Their mean age was 15.7 ± 2.82 years. The training program lasted 12 weeks, and had a frequency of three times a week for AT and twice a week for RT. AT was performed in treadmill/ bicycle ergometer, at an intensity between 50%-70% of the HR reserve. RT comprised nine exercises with three sets of 12 repetition-maximum. Systolic blood pressure (SBP), diastolic blood pressure (DBP), mean blood pressure (MBP) and hemodynamic variables were assessed beat-to-beat using the Finometer device before/after the training program. Descriptive analysis, the Shapiro-Wilk test to check the normality of data, and the two-way ANOVA for repeated measures were used to compare pre- and post-training variables. The Pearson’s correlation coefficient was calculated to correlate hemodynamic variables. The SPSS version 18.0 was used with the significance level set at p < 0.05.Results:After twelve weeks of aerobic and/or resistance training, significant reductions in variables SBP, DBP and MBP were observed.Conclusion:This study suggests a chronic hypotensive effect of moderate aerobic and resistance exercises on young individuals with DS.

Analysis Treatment Guideline versus Clinical Practice Protocol in Patients Hospitalized due to Heart Failure

Background: Despite the availability of guidelines for treatment of heart failure (HF), only a few studies have assessed how hospitals adhere to the recommended therapies. Objectives: Compare the rates of adherence to the prescription of angiotensin-converting enzyme inhibitor or angiotensin II receptor blockers (ACEI/ARB) at hospital discharge, which is considered a quality indicator by the Joint Commission International, and to the prescription of beta-blockers at hospital discharge, which is recommended by national and international guidelines, in a hospital with a case management program to supervise the implementation of a clinical practice protocol (HCP) and another hospital that follows treatment guidelines (HCG). Methods: Prospective observational study that evaluated patients consecutively admitted to both hospitals due to decompensated HF between August 1st, 2006, and December 31st, 2008. We used as comparing parameters the prescription rates of beta-blockers and ACEI/ARB at hospital discharge and in-hospital mortality. Results: We analyzed 1,052 patients (30% female, mean age 70.6 ± 14.1 years), 381 (36%) of whom were seen at HCG and 781 (64%) at HCP. The prescription rates of beta-blockers at discharge at HCG and HCP were both 69% (p = 0.458), whereas those of ACEI/ARB were 83% and 86%, respectively (p = 0.162). In-hospital mortality rates were 16.5% at HCP and 27.8% at HCG (p < 0.001). Conclusion: There was no difference in prescription rates of beta-blocker and ACEI/ARB at hospital discharge between the institutions, but HCP had lower in-hospital mortality. This difference in mortality may be attributed to different clinical characteristics of the patients in both hospitals.

Caracteritació de models funcionals d'àmfores romanes mitjançant Finite Element Analysis

Projecte de recerca elaborat a partir d’una estada al Laboratory of Archaeometry del National Centre of Scientific Research “Demokritos” d’Atenes, Grècia, entre juny i setembre 2006. Aquest estudi s’emmarca dins d’un context més ampli d’estudi del canvi tecnològic que es documenta en la producció d’àmfores de tipologia romana durant els segles I aC i I dC en els territoris costaners de Catalunya. Una part d’aquest estudi contempla el càlcul de les propietats mecàniques d’aquestes àmfores i la seva avaluació en funció de la tipologia amforal, a partir de l’Anàlisi d’Elements Finits (AEF). L’AEF és una aproximació numèrica que té el seu origen en les ciències d’enginyeria i que ha estat emprada per estimar el comportament mecànic d’un model en termes, per exemple, de deformació i estrès. Així, un objecte, o millor dit el seu model, es dividit en sub-dominis anomenats elements finits, als quals se’ls atribueixen les propietats mecàniques del material en estudi. Aquests elements finits estan connectats formant una xarxa amb constriccions que pot ser definida. En el cas d’aplicar una força determinada a un model, el comportament de l’objecte pot ser estimat mitjançant el conjunt d’equacions lineals que defineixen el rendiment dels elements finits, proporcionant una bona aproximació per a la descripció de la deformació estructural. Així, aquesta simulació per ordinador suposa una important eina per entendre la funcionalitat de ceràmiques arqueològiques. Aquest procediment representa un model quantitatiu per predir el trencament de l’objecte ceràmic quan aquest és sotmès a diferents condicions de pressió. Aquest model ha estat aplicat a diferents tipologies amforals. Els resultats preliminars mostren diferències significatives entre la tipologia pre-romana i les tipologies romanes, així com entre els mateixos dissenys amforals romans, d’importants implicacions arqueològiques.

Aplicaciones Single Program Multiple Data (SPMD) en ambientes distribuidos

Un reto al ejecutar las aplicaciones en un cluster es lograr mejorar las prestaciones utilizando los recursos de manera eficiente, y este reto es mayor al utilizar un ambiente distribuido. Teniendo en cuenta este reto, se proponen un conjunto de reglas para realizar el cómputo en cada uno de los nodos, basado en el análisis de cómputo y comunicaciones de las aplicaciones, se analiza un esquema de mapping de celdas y un método para planificar el orden de ejecución, tomando en consideración la ejecución por prioridad, donde las celdas de fronteras tienen una mayor prioridad con respecto a las celdas internas. En la experimentación se muestra el solapamiento del computo interno con las comunicaciones de las celdas fronteras, obteniendo resultados donde el Speedup aumenta y los niveles de eficiencia se mantienen por encima de un 85%, finalmente se obtiene ganancias de los tiempos de ejecución, concluyendo que si se puede diseñar un esquemas de solapamiento que permita que la ejecución de las aplicaciones SPMD en un cluster se hagan de forma eficiente.

Mise en place d'un programme de prévention et de prise en charge du diabète en Suisse: le point de vue des patients et des professionnels de la santé [Implementation of a diabetes disease management program in Switzerland: patients' and healthcare professionals' point of view].

BACKGROUND: A reorganization of healthcare systems is required to meet the challenge of the increasing prevalence of chronic diseases, e.g. diabetes. In North-America and Europe, several countries have thus developed national or regional chronic disease management programs. In Switzerland, such initiatives have only emerged recently. In 2010, the canton of Vaud set up the "Diabetes Cantonal Program", within the framework of which we conducted a study designed to ascertain the opinions of both diabetic patients and healthcare professionals on the elements that could be integrated into this program, the barriers and facilitators to its development, and the incentives that could motivate these actors to participate. METHODS: We organized eight focus-groups: one with diabetic patients and one with healthcare professionals in the four sanitary areas of the canton of Vaud. The discussions were recorded, transcribed and submitted to a thematic content analysis. RESULTS: Patients and healthcare professionals were rather in favour of the implementation of a cantonal program, although patients were more cautious concerning its necessity. All participants envisioned a set of elements that could be integrated to this program. They also considered that the program could be developed more easily if it were adapted to patients' and professionals' needs and if it used existing structures and professionals. The difficulty to motivate both patients and professionals to participate was mentioned as a barrier to the development of this program however. Quality or financial incentives could therefore be created to overcome this potential problem. CONCLUSION: The identification of the elements to consider, barriers, facilitators and incentives to participate to a chronic disease management program, obtained by exploring the opinions of patients and healthcare professionals, should favour its further development and implementation.

Performance analysis and tuning in multicore environments

Performance analysis is the task of monitor the behavior of a program execution. The main goal is to find out the possible adjustments that might be done in order improve the performance. To be able to get that improvement it is necessary to find the different causes of overhead. Nowadays we are already in the multicore era, but there is a gap between the level of development of the two main divisions of multicore technology (hardware and software). When we talk about multicore we are also speaking of shared memory systems, on this master thesis we talk about the issues involved on the performance analysis and tuning of applications running specifically in a shared Memory system. We move one step ahead to take the performance analysis to another level by analyzing the applications structure and patterns. We also present some tools specifically addressed to the performance analysis of OpenMP multithread application. At the end we present the results of some experiments performed with a set of OpenMP scientific application.

Including the workload effect in the parallel program signature

Performance prediction and application behavior modeling have been the subject of exten- sive research that aim to estimate applications performance with an acceptable precision. A novel approach to predict the performance of parallel applications is based in the con- cept of Parallel Application Signatures that consists in extract an application most relevant parts (phases) and the number of times they repeat (weights). Executing these phases in a target machine and multiplying its exeuction time by its weight an estimation of the application total execution time can be made. One of the problems is that the performance of an application depends on the program workload. Every type of workload affects differently how an application performs in a given system and so affects the signature execution time. Since the workloads used in most scientific parallel applications have dimensions and data ranges well known and the behavior of these applications are mostly deterministic, a model of how the programs workload affect its performance can be obtained. We create a new methodology to model how a program’s workload affect the parallel application signature. Using regression analysis we are able to generalize each phase time execution and weight function to predict an application performance in a target system for any type of workload within predefined range. We validate our methodology using a synthetic program, benchmarks applications and well known real scientific applications.

Effect of a Road Safety Training Program on Drivers' Comparative Optimism

Reducing comparative optimism regarding risk perceptions in traffic accidents has been proven to be particularly difficult (Delhomme, 2000). This is unfortunate because comparative optimism is assumed to impede preventive action. The present study tested whether a road safety training course could reduce drivers' comparative optimism in high control situations. Results show that the training course efficiently reduced comparative optimism in high control, but not in low control situations. Mechanisms underlying this finding and implications for the design of road safety training courses are discussed.

Life history analysis of integrative and conjugative element activation in growing microcolonies of Pseudomonas.

Integrative and conjugative elements (ICE) are in some ways parasitic mobile DNA that propagate vertically through replication with the bacterial host chromosome but at low frequencies can excise and invade new recipient cells through conjugation and reintegration (horizontal propagation). The factors that contribute to successful horizontal propagation are not very well understood. Here, we study the influence of host cell life history on the initiation of transfer of a model ICE named ICEclc in bacteria of the genus Pseudomonas. We use time-lapse microscopy of growing and stationary-phase microcolonies of ICEclc bearing cells in combination with physiological staining and gene reporter analysis in stationary-phase suspended cells. We provide evidence that cell age and cell lineage are unlikely to play a role in the decision to initiate the ICEclc transfer program. In contrast, cells activating ICEclc show more often increased levels of reactive oxygen species and membrane damage than nonactivating cells, suggesting that some form of biochemical damage may make cells more prone to ICEclc induction. Finally, we find that ICEclc active cells appear spatially at random in a microcolony, which may have been a selective advantage for maximizing ICEclc horizontal transmission to new recipient species.