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.

Body image in Brazil: recent advances in the state of knowledge and methodological issues

OBJECTIVE To analyze Brazilian literature on body image and the theoretical and methodological advances that have been made. METHODS A detailed review was undertaken of the Brazilian literature on body image, selecting published articles, dissertations and theses from the SciELO, SCOPUS, LILACS and PubMed databases and the CAPES thesis database. Google Scholar was also used. There was no start date for the search, which used the following search terms: “body image” AND “Brazil” AND “scale(s)”; “body image” AND “Brazil” AND “questionnaire(s)”; “body image” AND “Brazil” AND “instrument(s)”; “body image” limited to Brazil and “body image”. RESULTS The majority of measures available were intended to be used in college students, with half of them evaluating satisfaction/dissatisfaction with the body. Females and adolescents of both sexes were the most studied population. There has been a significant increase in the number of available instruments. Nevertheless, numerous published studies have used non-validated instruments, with much confusion in the use of the appropriate terms (e.g., perception, dissatisfaction, distortion). CONCLUSIONS Much more is needed to understand body image within the Brazilian population, especially in terms of evaluating different age groups and diversifying the components/dimensions assessed. However, interest in this theme is increasing, and important steps have been taken in a short space of time.

Non-adherence to telemedicine interventions for drug users: systematic review

OBJECTIVE To estimate rates of non-adherence to telemedicine strategies aimed at treating drug addiction. METHODS A systematic review was conducted of randomized controlled trials investigating different telemedicine treatment methods for drug addiction. The following databases were consulted between May 18, 2012 and June 21, 2012: PubMed, PsycINFO, SciELO, Wiley (The Cochrane Library), Embase, Clinical trials and Google Scholar. The Grading of Recommendations Assessment, Development and Evaluation was used to evaluate the quality of the studies. The criteria evaluated were: appropriate sequence of data generation, allocation concealment, blinding, description of losses and exclusions and analysis by intention to treat. There were 274 studies selected, of which 20 were analyzed. RESULTS Non-adherence rates varied between 15.0% and 70.0%. The interventions evaluated were of at least three months duration and, although they all used telemedicine as support, treatment methods differed. Regarding the quality of the studies, the values also varied from very poor to high quality. High quality studies showed better adherence rates, as did those using more than one technique of intervention and a limited treatment time. Mono-user studies showed better adherence rates than poly-user studies. CONCLUSIONS Rates of non-adherence to treatment involving telemedicine on the part of users of psycho-active substances differed considerably, depending on the country, the intervention method, follow-up time and substances used. Using more than one technique of intervention, short duration of treatment and the type of substance used by patients appear to facilitate adherence.

Phytotherapy in primary health care

OBJECTIVE To characterize the integration of phytotherapy in primary health care in Brazil. METHODS Journal articles and theses and dissertations were searched for in the following databases: SciELO, Lilacs, PubMed, Scopus, Web of Science and Theses Portal Capes, between January 1988 and March 2013. We analyzed 53 original studies on actions, programs, acceptance and use of phytotherapy and medicinal plants in the Brazilian Unified Health System. Bibliometric data, characteristics of the actions/programs, places and subjects involved and type and focus of the selected studies were analyzed. RESULTS Between 2003 and 2013, there was an increase in publications in different areas of knowledge, compared with the 1990-2002 period. The objectives and actions of programs involving the integration of phytotherapy into primary health care varied: including other treatment options, reduce costs, reviving traditional knowledge, preserving biodiversity, promoting social development and stimulating inter-sectorial actions. CONCLUSIONS Over the past 25 years, there was a small increase in scientific production on actions/programs developed in primary care. Including phytotherapy in primary care services encourages interaction between health care users and professionals. It also contributes to the socialization of scientific research and the development of a critical vision about the use of phytotherapy and plant medicine, not only on the part of professionals but also of the population.

Self-reported diabetes in older people: comparison of prevalences and control measures

OBJECTIVE The objective of this study was to analyze the prevalence of diabetes in older people and the adopted control measures.METHODS Data regarding older diabetic individuals who participated in the Health Surveys conducted in the Municipality of Sao Paulo, SP, ISA-Capital, in 2003 and 2008, which were cross-sectional studies, were analyzed. Prevalences and confidence intervals were compared between 2003 and 2008, according to sociodemographic variables. The combination of the databases was performed when the confidence intervals overlapped. The Chi-square (level of significance of 5%) and the Pearson’s Chi-square (Rao-Scott) tests were performed. The variables without overlap between the confidence intervals were not tested.RESULTS The age of the older adults was 60-69 years. The majority were women, Caucasian, with an income of between > 0.5 and 2.5 times the minimum salary and low levels of schooling. The prevalence of diabetes was 17.6% (95%CI 14.9;20.6) in 2003 and 20.1% (95%CI 17.3;23.1) in 2008, which indicates a growth over this period (p at the limit of significance). The most prevalent measure adopted by the older adults to control diabetes was hypoglycemic agents, followed by diet. Physical activity was not frequent, despite the significant differences observed between 2003 and 2008 results. The use of public health services to control diabetes was significantly higher in older individuals with lower income and lower levels of education.CONCLUSIONS Diabetes is a complex and challenging disease for patients and the health systems. Measures that encourage health promotion practices are necessary because they presented a smaller proportion than the use of hypoglycemic agents. Public health policies should be implemented, and aimed mainly at older individuals with low income and schooling levels. These changes are essential to improve the health condition of older diabetic patients.

Efficient middleware for database replication

Dissertação de Mestrado em Engenharia Informática

Dpws middleware to support agent-based manufacturing control and simulation

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do grau de Mestre em Engenharia Electrotécnica e de Computadores

Factors associated to breastfeeding in the first hour of life: systematic review

OBJECTIVE To identify independent risk factors for non-breastfeeding within the first hour of life.METHODS A systematic review of Medline, LILACS, Scopus, and Web of Science electronic databases, till August 30, 2013, was performed without restrictions on language or date of publishing. Studies that used regression models and provided adjusted measures of association were included. Studies in which the regression model was not specified or those based on specific populations regarding age or the presence of morbidities were excluded.RESULTS The search resulted in 155 articles, from which 18 met the inclusion criteria. These were conducted in Asia (9), Africa (5), and South America (4), between 1999 and 2013. The prevalence of breastfeeding within the first hour of life ranged from 11.4%, in a province of Saudi Arabia, to 83.3% in Sri Lanka. Cesarean delivery was the most consistent risk factor for non-breastfeeding within the first hour of life. “Low family income”, “maternal age less than 25 years”, “low maternal education”, “no prenatal visit”, “home delivery”, “no prenatal guidance on breastfeeding” and “preterm birth” were reported as risk factors in at least two studies.CONCLUSIONS Besides the hospital routines, indicators for low socioeconomic status and poor access to health services were also identified as independent risk factors for non-breastfeeding within the first hour of life. Policies to promote breastfeeding, appropriate to each context, should aim to reduce inequalities in health.

Intervenção da fisioterapia na esclerose múltipla: uma revisão da literatura

Mestrado em Fisioterapia

Cyclosporine versus tacrolimus: cost-effectiveness analysis for renal transplantation in Brazil

OBJECTIVE To analyze the cost-effectiveness of treatment regimens with cyclosporine or tacrolimus, five years after renal transplantation.METHODS This cost-effectiveness analysis was based on historical cohort data obtained between 2000 and 2004 and involved 2,022 patients treated with cyclosporine or tacrolimus, matched 1:1 for gender, age, and type and year of transplantation. Graft survival and the direct costs of medical care obtained from the National Health System (SUS) databases were used as outcome results.RESULTS Most of the patients were women, with a mean age of 36.6 years. The most frequent diagnosis of chronic renal failure was glomerulonephritis/nephritis (27.7%). In five years, the tacrolimus group had an average life expectancy gain of 3.96 years at an annual cost of R$78,360.57 compared with the cyclosporine group with a gain of 4.05 years and an annual cost of R$61,350.44.CONCLUSIONS After matching, the study indicated better survival of patients treated with regimens using tacrolimus. However, regimens containing cyclosporine were more cost-effective.

An internet remote laboratory to teach industrial automation

This paper presents the new internet remote laboratory (IRL), constructed at Mechanical Engineering Department (MED), Instituto Superior de Engenharia de Lisboa (ISEL), to teach Industrial Automation, namely electropneumatic cycles. The aim of this work was the development and implementation of a remote laboratory that was simple and effective from the user point of view, allowing access to all its functionalities through a web browser without having to install any other program and giving access to all the features that the students can find at the physical laboratory. With this goal in mind, it has been implemented a simple architecture with the new programmable logic controller (PLC) SIEMENS S7-1200, and with the aid of several free programs, programming technologies such as JavaScript, PHP and databases, it was possible to have a remote laboratory, with a simple interface, to teach industrial automation students.

Readability of medicinal package leaflets: a systematic review

OBJECTIVE To review studies on the readability of package leaflets of medicinal products for human use.METHODS We conducted a systematic literature review between 2008 and 2013 using the keywords “Readability and Package Leaflet” and “Readability and Package Insert” in the academic search engine Biblioteca do Conhecimento Online,comprising different bibliographic resources/databases. The preferred reporting items for systematic reviews and meta-analyses criteria were applied to prepare the draft of the report. Quantitative and qualitative original studies were included. Opinion or review studies not written in English, Portuguese, Italian, French, or Spanish were excluded.RESULTS We identified 202 studies, of which 180 were excluded and 22 were enrolled [two enrolling healthcare professionals, 10 enrolling other type of participants (including patients), three focused on adverse reactions, and 7 descriptive studies]. The package leaflets presented various readability problems, such as complex and difficult to understand texts, small font size, or few illustrations. The main methods to assess the readability of the package leaflet were usability tests or legibility formulae. Limitations with these methods included reduced number of participants; lack of readability formulas specifically validated for specific languages (e.g., Portuguese); and absence of an assessment on patients literacy, health knowledge, cognitive skills, levels of satisfaction, and opinions.CONCLUSIONS Overall, the package leaflets presented various readability problems. In this review, some methodological limitations were identified, including the participation of a limited number of patients and healthcare professionals, the absence of prior assessments of participant literacy, humor or sense of satisfaction, or the predominance of studies not based on role-plays about the use of medicines. These limitations should be avoided in future studies and be considered when interpreting the results.

Fetal deaths in Brazil: a systematic review

OBJECTIVE To review the frequency of and factors associated with fetal death in the Brazilian scientific literature.METHODS A systematic review of Brazilian studies on fetal deaths published between 2003 and 2013 was conducted. In total, 27 studies were analyzed; of these, 4 studies addressed the quality of data, 12 were descriptive studies, and 11 studies evaluated the factors associated with fetal death. The databases searched were PubMed and Lilacs, and data extraction and synthesis were independently performed by two or more examiners.RESULTS The level of completeness of fetal death certificates was deficient, both in the completion of variables, particularly sociodemographic variables, and in defining the underlying causes of death. Fetal deaths have decreased in Brazil; however, inequalities persist. Analysis of the causes of death indicated maternal morbidities that could be prevented and treated. The main factors associated with fetal deaths were absent or inadequate prenatal care, low education level, maternal morbidity, and adverse reproductive history.CONCLUSIONS Prenatal care should prioritize women that are most vulnerable (considering their social environment or their reproductive history and morbidities) with the aim of decreasing the fetal mortality rate in Brazil. Adequate completion of death certificates and investment in the committees that investigate fetal and infant deaths are necessary.

Prevalence of self-medication in the adult population of Brazil: a systematic review

OBJECTIVE To evaluate the prevalence of self-medication in Brazil’s adult population.METHODS Systematic review of cross-sectional population-based studies. The following databases were used: Medline, Embase, Scopus, ISI, CINAHL, Cochrane Library, CRD, Lilacs, SciELO, the Banco de teses brasileiras(Brazilian theses database) (Capes) and files from the Portal Domínio Público (Brazilian Public Domain). In addition, the reference lists from relevant studies were examined to identify potentially eligible articles. There were no applied restrictions in terms of the publication date, language or publication status. Data related to publication, population, methods and prevalence of self-medication were extracted by three independent researchers. Methodological quality was assessed following eight criteria related to sampling, measurement and presentation of results. The prevalences were measured from participants who used at least one medication during the recall period of the studies.RESULTS The literature screening identified 2,778 records, from which 12 were included for analysis. Most studies were conducted in the Southeastern region of Brazil, after 2000 and with a 15-day recall period. Only five studies achieved high methodological quality, of which one study had a 7-day recall period, in which the prevalence of self-medication was 22.9% (95%CI 14.6;33.9). The prevalence of self-medication in three studies of high methodological quality with a 15-day recall period was 35.0% (95%CI 29.0;40.0, I2 = 83.9%) in the adult Brazilian population.CONCLUSIONS Despite differences in the methodologies of the included studies, the results of this systematic review indicate that a significant proportion of the adult Brazilian population self-medicates. It is suggested that future research projects that assess self-medication in Brazil standardize their methods.

Gender in the allocation of organs in kidney transplants: meta-analysis

OBJECTIVE To analyze whether gender influence survival results of kidney transplant grafts and patients.METHODS Systematic review with meta-analysis of cohort studies available on Medline (PubMed), LILACS, CENTRAL, and Embase databases, including manual searching and in the grey literature. The selection of studies and the collection of data were conducted twice by independent reviewers, and disagreements were settled by a third reviewer. Graft and patient survival rates were evaluated as effectiveness measurements. Meta-analysis was conducted with the Review Manager® 5.2 software, through the application of a random effects model. Recipient, donor, and donor-recipient gender comparisons were evaluated.RESULTS : Twenty-nine studies involving 765,753 patients were included. Regarding graft survival, those from male donors were observed to have longer survival rates as compared to the ones from female donors, only regarding a 10-year follow-up period. Comparison between recipient genders was not found to have significant differences on any evaluated follow-up periods. In the evaluation between donor-recipient genders, male donor-male recipient transplants were favored in a statistically significant way. No statistically significant differences were observed in regards to patient survival for gender comparisons in all follow-up periods evaluated.CONCLUSIONS The quantitative analysis of the studies suggests that donor or recipient genders, when evaluated isolatedly, do not influence patient or graft survival rates. However, the combination between donor-recipient genders may be a determining factor for graft survival.