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.

Assessment of climate change statistical downscaling methods: Application and comparison of two statistical methods to a single site in Lisbon

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

Some reflections on acquisition, processing and analysis of statistical data in forest soils

Beyond the classical statistical approaches (determination of basic statistics, regression analysis, ANOVA, etc.) a new set of applications of different statistical techniques has increasingly gained relevance in the analysis, processing and interpretation of data concerning the characteristics of forest soils. This is possible to be seen in some of the recent publications in the context of Multivariate Statistics. These new methods require additional care that is not always included or refered in some approaches. In the particular case of geostatistical data applications it is necessary, besides to geo-reference all the data acquisition, to collect the samples in regular grids and in sufficient quantity so that the variograms can reflect the spatial distribution of soil properties in a representative manner. In the case of the great majority of Multivariate Statistics techniques (Principal Component Analysis, Correspondence Analysis, Cluster Analysis, etc.) despite the fact they do not require in most cases the assumption of normal distribution, they however need a proper and rigorous strategy for its utilization. In this work, some reflections about these methodologies and, in particular, about the main constraints that often occur during the information collecting process and about the various linking possibilities of these different techniques will be presented. At the end, illustrations of some particular cases of the applications of these statistical methods will also be presented.

Studies on the genetics of artemisinin resistance in malaria

A existência de estirpes de Plasmodium falciparum resistentes a multiplos fármacos é um dos problemas mais graves no controlo da malária. Novos fármacos, como a artemisinina (ART) e seus derivados são cada vez mais utilizados no tratamento da malaria e muito embora até ao momento não haja registos de fármaco-resistência estável à ART o seu surgimento seria desastroso devido á falta de alternativas. A investigação apresentada nesta tese descreve a selecção de resistência estável à ART e ao artesunato (ATN) utilizando um modelo roedor de malária, o parasita Plasmodium chabaudi chabaudi (Plasmodium chabaudi). Dois clones de Plasmodium chabaudi diferentes, AS-15CQ e AS-30CQ, foram inoculados em murganhos que por sua vez foram tratados na presença de concentrações sucessivamente crescentes de ATN e ART, sendo que no final do processo de seleção de resistência, os parasitas obtidos apresentavam uma resistência de 6 e 15 vezes superior ao ATN e à ART, respectivamente, em relação aos parasitas iniciais. Os clones obtidos foram nomeados respectivamente AS-ATN (obtido a partir de AS-15CQ por seleção com pressão de ATN) e AS-ART (obtido a partir de AS-30CQ por seleção com pressão de ART). A resistência obtida durante o processo de seleção é estável após clonagem, congelamento/descongelamento, passagem sanguínea na ausência de pressão de fármaco e transmissão natural através do mosquito vector. A sequência nucleotídica e o número de cópias dos genes previamente descritos na literatura como moduladores putativos de resistência à ART e seus derivados: mdr1, cg10, tctp e atp6; foi comparada entre parasitas resistentes e sensíveis, não tendo sido encontradas nenhumas alterações, quer na sequência quer no número de cópias destes genes. Posteriormente, numa tentativa de identificar os genes envolvidos na resistância à ART e ao ATN a técnica de Linkage Group Selection (LGS) foi utilizada. Para tal dois cruzamentos genéticos foram realizados. Estes cruzamentos foram realizados entre os clones fármaco-resistentes; AS-ART e AS-ATN e um clone geneticamente distinto dos anteriores e sensível aos fármacos em estudos, AJ. Após realização do LGS quatro loci genéticos; nos cromossomas de P. chabaudi 1, 2, 6 e 8 foram encontrados associados à resistência. Atendendo a que, a selecção no cromossoma 2 era a mais forte, este locus foi submetido a subsequentes análises genéticas, tendo sido encontradas duas mutações diferentes (V739F e V770F) num gene que codifica para um enzima de desubiquitinação (gene ubp-1).

Studies on the genetics of artemisinin resistance in malaria

A existência de estirpes de Plasmodium falciparum resistentes a multiplos fármacos é um dos problemas mais graves no controlo da malária. Novos fármacos, como a artemisinina (ART) e seus derivados são cada vez mais utilizados no tratamento da malaria e muito embora até ao momento não haja registos de fármaco-resistência estável à ART o seu surgimento seria desastroso devido á falta de alternativas. A investigação apresentada nesta tese descreve a selecção de resistência estável à ART e ao artesunato (ATN) utilizando um modelo roedor de malária, o parasita Plasmodium chabaudi chabaudi (Plasmodium chabaudi). Dois clones de Plasmodium chabaudi diferentes, AS-15CQ e AS-30CQ, foram inoculados em murganhos que por sua vez foram tratados na presença de concentrações sucessivamente crescentes de ATN e ART, sendo que no final do processo de seleção de resistência, os parasitas obtidos apresentavam uma resistência de 6 e 15 vezes superior ao ATN e à ART, respectivamente, em relação aos parasitas iniciais. Os clones obtidos foram nomeados respectivamente AS-ATN (obtido a partir de AS-15CQ por seleção com pressão de ATN) e AS-ART (obtido a partir de AS-30CQ por seleção com pressão de ART). A resistência obtida durante o processo de seleção é estável após clonagem, congelamento/descongelamento, passagem sanguínea na ausência de pressão de fármaco e transmissão natural através do mosquito vector. A sequência nucleotídica e o número de cópias dos genes previamente descritos na literatura como moduladores putativos de resistência à ART e seus derivados: mdr1, cg10, tctp e atp6; foi comparada entre parasitas resistentes e sensíveis, não tendo sido encontradas nenhumas alterações, quer na sequência quer no número de cópias destes genes. Posteriormente, numa tentativa de identificar os genes envolvidos na resistância à ART e ao ATN a técnica de Linkage Group Selection (LGS) foi utilizada. Para tal dois cruzamentos genéticos foram realizados. Estes cruzamentos foram realizados entre os clones fármaco-resistentes; AS-ART e AS-ATN e um clone geneticamente distinto dos anteriores e sensível aos fármacos em estudos, AJ. Após realização do LGS quatro loci genéticos; nos cromossomas de P. chabaudi 1, 2, 6 e 8 foram encontrados associados à resistência. Atendendo a que, a selecção no cromossoma 2 era a mais forte, este locus foi submetido a subsequentes análises genéticas, tendo sido encontradas duas mutações diferentes (V739F e V770F) num gene que codifica para um enzima de desubiquitinação (gene ubp-1).

Aborto recorrente das causas na mulher às consequências para o casal

RESUMO: O aborto recorrente (AR) é um evento extremamente traumático com grande impacto na vida dos casais. Apesar de avanços significativos verificados na investigação médica, cerca de 50% dos casos continua sem uma causa identificada. Alguns aspectos como a caracterização inadequada das doentes e das perdas gestacionais, assim como diferentes metodologias utilizadas no seu estudo, têm influenciado a prevalência de alguns dos factores causais e dificultado a compreensão do AR. Da mesma forma, pouco se sabe sobre as diferenças de género na vivência psicológica do aborto recorrente e das suas eventuais repercussões para o relacionamento do casal, centrando-se os poucos estudos existentes preferencialmente na mulher. Por esta razão, o objectivo desta tese foi a caracterização dos factores médicos associados ao AR e das consequências psicológicas desta entidade, contribuindo para promover estratégias clínicas baseadas na evidência específica. Na primeira parte desta tese (capítulos 1 e 2), após uma breve introdução geral e através de uma revisão da literatura, efectua-se uma reflexão sobre o tema, abordando a epidemiologia do aborto recorrente, os factores médicos e os aspectos psicológicos associados. Nos capítulos 3 e 4 descrevemos três estudos efectuados em mulheres portuguesas com aborto recorrente. O primeiro estudo teve por objectivo caracterizar os factores médicos e determinar o padrão da perda recorrente de gravidez, numa coorte de mulheres submetidas a um protocolo de diagnóstico definido. As participantes foram agrupadas de acordo com a paridade (AR primário ou secundário) e a idade gestacional das perdas (embrionárias ou fetais). As anomalias da cavidade uterina, a SAAF e as translocações equilibradas parentais foram os factores mais prevalentes. 15,6% das participantes eram obesas. Em 55,5% dos casos não foi identificado nenhum factor. A história obstétrica materna influenciou significativamente os resultados encontrados: os factores anatómicos e a SAAF foram mais prevalentes em nulíparas e as perdas inexplicadas foram mais frequentes em mulheres com AR secundário. Assim, os nossos dados reforçam os resultados de pesquisas anteriores sobre a importância da obesidade, da síndrome de anticorpos antifosfolípidos e das anomalias uterinas estruturais como factores associados ao AR e mostram que os a paridade é um moderador da importância desses factores. Capítulo 6 94 A ausência de resultados consensuais na literatura sobre a etiologia do AR condiciona a pesquisa sistemática de alguns factores, envolvendo exames dispendiosos, muitas vezes sem que exista evidência que suporte a sua associação com esta entidade. A trombofilia hereditária é uma das condições frequentemente investigadas nestas doentes. O nosso segundo estudo pretende contribuir para clarificar o papel de duas mutações (factor V Leiden e protrombina G20210A) na perda recorrente de gravidez e esclarecer a necessidade do seu rastreio nestas situações. Foi efectuada a pesquisa destes polimorfismos em 100 mulheres com AR inexplicado e num grupo de controlo de multíparas sem história de perdas de gravidez. Na nossa amostra não se verificou uma associação entre perdas embrionárias recorrentes e estas mutações. Nas mulheres com este tipo de perdas, a prevalência do FLV foi inclusive menor do que a verificada nos controlos. Pelo contrário, nas participantes com perdas fetais a prevalência destes polimorfismos foi muito superior à verificada nos controlos, sugerindo uma possível associação entre estas duas entidades. A pequena dimensão deste último subgrupo de mulheres, não nos permitiu contudo tirar conclusões. Uma investigação prospectiva multicêntrica é necessária antes de recomendar a pesquisa da trombofilia hereditária na investigação do AR. Procurámos incluir também nesta tese uma dimensão psicológica e contribuir assim para o conhecimento dos processos relacionais originados pelo AR. No terceiro estudo foram investigadas as diferenças de género na vivência do AR e o seu impacto no relacionamento e sexualidade do casal. Participaram neste estudo 30 casais sem filhos, com pelo menos 3 abortos espontâneos consecutivos. Cada membro do casal respondeu a um conjunto de questionários (Impact of Events Scale, Perinatal Grief Scale, Partnership Questionnaire e Intimate Relationship Scale). Os resultados mostram que as mulheres sofrem mais intensamente do que os homens com o AR, relacionando-se a intensidade do seu sofrimento com a qualidade do relacionamento conjugal. A sexualidade do casal é também afectada pelo stress e pelo sofrimento associados ao AR. Uma avaliação e acompanhamento deste tipo de problemas são imprescindíveis para ajudar estes casais a manterem a qualidade afectiva e sexual da sua relação. Finalmente, no capítulo 5 sumariámos as conclusões de toda a contribuição pessoal para a investigação sobre os factores associados e repercussões para o casal da perda recorrente de gravidez.-------------------ABSTRACT: Recurrent miscarriage (RM), a rare condition, has been described as a traumatic event for couples. Parental chromosomal anomalies, maternal thrombophilic disorders and structural uterine anomalies have been directly associated with RM. However, despite significant advances in medical research, the vast majority of cases remain unexplained. Aspects as the ethnic diversity of the population with different expression of genes, the inappropriate characterization of patients and of pregnancy losses, as well as different methodologies used in their study, have influenced the prevalence of etiological factors and have hampered the understanding of this problem. Similarly, little is known about gender differences in psychological experience of RM and its implications for the relationship of the couple. The first objective of this thesis is the characterization of the medical factors and of the psychological consequences related with RM, in the Portuguese population, helping to promote specific evidence-based clinical strategies. In the first part of this thesis, and after a brief general introduction (Chapter 1), a critical review of literature on the definition, the epidemiology and the dimensions involved, with a special emphasis on associated medical and psychological aspects of recurrent miscarriage, is presented (Chapter 2). In Chapters 3 and 4 we describe three studies carried out in Portuguese couples with RM. The first study aimed to investigate the etiological factors and the pattern of pregnancy loss in a cohort of women with RM. Subjects were divided in groups according to their parity (primary or secondary RM) and time of pregnancy loss (embryonic or fetal). Parental chromosome anomalies, uterine anomalies and antiphospholipid syndrome were the most prevalent medical factors. 15.6% of the women were obese. In the majority of cases (55.5%) no identifiable cause was detected. Parity influenced significantly our results. There was a higher prevalence of anatomic factors and antiphospholipid syndrome in primary RM. On the other hand, unexplained losses were more frequent in secondary RM. Except for the parental chromosomal abnormalities; the frequency of risk factors was similar among women with fetal or embryonic losses. Our data emphasizes the results of previous research on the importance of obesity, antiphospholipid syndrome and structural uterine abnormalities as known risk factors for RM, and shows that parity is an important moderator of the weight of those risk factors. Our second study aims to clarify the role of two mutations (factor V Leiden and prothrombin G20210A) and elucidate the need for their screening in Portuguese women with RM. FVL and PT G20210A analysis was carried out in 100 women with three or more consecutive miscarriages and a control group of 100 parous controls with no history of pregnancy losses. Secondary analysis was made regarding gestational age at miscarriage (embryonic and fetal loss). Overall the prevalence of FVL and PT G20210A was similar in RM women compared with controls. In the RM embryonic subgroup of women, FVL prevalence was inclusively lower than that of controls. Conversely in women with fetal losses both polymorphisms were much more frequent, although statistical significance was not reached due to the small size of this subgroup of patients. These data indicate that inherited maternal thrombophilia is not associated with RM prior to 10 weeks of gestation. Therefore, its screening is not indicated as an initial approach in Portuguese women with RM and a negative personal history of thromboembolic.96 Our second study aims to clarify the role of two mutations (factor V Leiden and prothrombin G20210A) and elucidate the need for their screening in Portuguese women with RM. FVL and PT G20210A analysis was carried out in 100 women with three or more consecutive miscarriages and a control group of 100 parous controls with no history of pregnancy losses. Secondary analysis was made regarding gestational age at miscarriage (embryonic and fetal loss). Overall the prevalence of FVL and PT G20210A was similar in RM women compared with controls. In the RM embryonic subgroup of women, FVL prevalence was inclusively lower than that of controls. Conversely in women with fetal losses both polymorphisms were much more frequent, although statistical significance was not reached due to the small size of this subgroup of patients. These data indicate that inherited maternal thrombophilia is not associated with RM prior to 10 weeks of gestation. Therefore, its screening is not indicated as an initial approach in Portuguese women with RM and a negative personal history of thromboembolic. In our third study, we investigate gender differences in RM experience and its impact on the couple's relationship and sexuality. Each member of 30 couples with RM answered a set of questionnaires, including the Impact of Events Scale (Horowitz et al., 1979), the Perinatal Grief Scale (Toedter et al., 1988), the Partnership Questionnaire (Hahlweg, 1979) and the Intimate Relationship Scale (Hetherington e Soeken, 1990). Results showed that men do grieve, but less intensely than women. Although the quality of the couple‟s relationship seemed not to be adversely affected by RM, both partners described sexual changes after those events. Grief was related to the quality of communication in the couple for women, and to the quality of sex life for men. An understanding of such issues is critical in helping these couples to maintain sexual and affective quality of their relationship. Finally, in Chapter 5, conclusions and clinical implications of all personal contribution to the investigation on associated factors and relational consequences of recurrent miscarriage are presented.

Study of the Reliability of Statistical Timing Analysis for Real-Time Systems

Presented at 23rd International Conference on Real-Time Networks and Systems (RTNS 2015). 4 to 6, Nov, 2015, Main Track. Lille, France.

Thermostability of heterophile antibodies from human sera infected with Schistosoma mansoni and geo-helminths: an immuno-metric statistical analysis

Antibody in human sera that induces lysis of sheep erythrocytes in hemolytic assay was investigated. The present study showed that the presence in serum of the thermostable cytolytic anti-sheep red blood cells antibodies is dependent on the Schistosoma mansoni infection, and this is more frequent in adults than in children. The thermostable characteristic of hemolysins in normal sera was not dependent on the presence of Ascaris lumbricoides, Trichuris trichiura or hookworm geo-helminths. Further, thermostable complement-activating heterophile antibodies were noticed in children in association with massive number of S. mansoni eggs. The results were obtained by using the z- and the chi-square tests. The z-test allows us to formulate a one-sided alternative, i.e., a tendency of one of the attributes. On the other hand, the chi-square test analyzes the independence between attributes by using a contingency table. Besides the obtained results being interesting in the field of schistosomiasis mansoni, they can provide a new insight into the use of statistics in medical science.

Induction of phagocytic activity and nitric-oxide production in natural populations of Trypanosoma Cruzi I and II from the state of Paraná, Brazil

Twelve strains of Trypanosoma cruzi isolated from wild reservoirs, triatomines, and chronic chagasic patients in the state of Paraná, southern Brazil, and classified as T. cruzi I and II, were used to test the correlation between genetic and biological diversity. The Phagocytic Index (PI) and nitric-oxide (NO) production in vitro were used as biological parameters. The PI of the T. cruzi I and II strains did not differ significantly, nor did the PI of the T. cruzi strains isolated from humans, triatomines, or wild reservoirs. There was a statistical difference in the inhibition of NO production between T. cruzi I and II and between parasites isolated from humans and the strains isolated from triatomines and wild reservoirs, but there was no correlation between genetics and biology when the strains were analyzed independently of the lineages or hosts from which the strains were isolated. There were significant correlations for Randomly Amplified Polymorphic Deoxyribonucleic acid (RAPD) and biological parameters for T. cruzi I and II, and for humans or wild reservoirs when the lineages or hosts were considered individually.

Exploraty Multivariate Statistical Methods Applied to Pharmaceutical Industry CRM Data

Dissertação apresentada como requisito parcial para obtenção do grau de Mestre em Estatística e Gestão de Informação

Factor V Leiden and Prothrombin G20210A in Portuguese Women with Recurrent Miscarriage: Is it Worthwhile to Investigate?

OBJECTIVE: To compare the prevalence of factor V Leiden (FVL) and prothrombin (PT) G20210A mutations in Portuguese women with unexplained recurrent miscarriage (RM) and a control group of parous women. MATERIALS AND METHODS: FVL and PT G20210A analysis were carried out in 100 women with three or more consecutive miscarriages and 100 controls with no history of pregnancy losses. Secondary analysis was made regarding gestational age at miscarriage (embryonic and fetal losses). RESULTS: Overall, the prevalence of FVL and PT G20210A was similar in women with RM (5 and 3%) compared with controls (5 and 1%) OR 1.36 (CI 95% 0.45-4.08). In RM embryonic subgroup, PT G20210A was observed in 1.3% of women and FVL prevalence (2.6%) was inclusively lesser than that of controls. Both polymorphisms were more prevalent in women with fetal losses than in controls, although statistical significance was not reached due to the small size of the >10 weeks' subgroup. CONCLUSION: These data indicate that neither FVL nor PT G20210A is associated with RM prior to 10 weeks of gestation. Therefore, its screening is not indicated as an initial approach in Portuguese women with embryonic RM and negative personal thromboembolic history.

Transplante hepático sequencial com preservação da veia cava inferior (técnica de "Duplo Piggyback") : uma técnica original

RESUMO:Desde a declaração de Bethesda em 1983, a transplantação hepática é considerada um processo válido e aceite na prática clínica para muitos doentes com doença hepática terminal, relativamente aos quais não houvesse outra alternativa terapêutica. Em 1991, por proposta de Holmgren, professor de genética, o cirurgião sueco Bo Ericzon realizou em Huntingdon (Estocolmo) o primeiro transplante hepático num doente PAF (Polineuropatia Amilloidótica Familiar), esperando que a substituição do fígado pudesse frenar a evolução da doença. Nesta doença hereditária autossómica dominante, o fígado, apesar de estrutural e funcionalmente normal, produz uma proteína anormal (TTR Met30) responsável pela doença. A partir de então, a transplantação hepática passou a ser a única terapêutica eficaz para estes doentes. Portugal é o país do mundo com mais doentes PAF, tendo sido o médico neurologista português Corino de Andrade quem, em 1951, identificou e descreveu este tipo particular de polineuropatia hereditária, também conhecida por doença de Andrade. Com o início da transplantação hepática programada em Setembro de 1992, o primeiro doente transplantado hepático em Portugal, no Hospital Curry Cabral, foi um doente PAF. Desde logo se percebeu que a competição nas listas de espera em Portugal, entre doentes hepáticos crónicos e doentes PAF viria a ser um problema clínico e ético difícil de compatibilizar. Em 1995, Linhares Furtado, em Coimbra, realizou o primeiro transplante dum fígado dum doente PAF num doente com doença hepática metastática, ficando este tipo de transplante conhecido como transplante sequencial ou “em dominó”. Fê-lo no pressuposto de que o fígado PAF, funcional e estruturalmente normal, apesar de produzir a proteína mutada causadora da doença neurológica, pudesse garantir ao receptor um período razoável de vida livre de sintomas, tal como acontece na história natural desta doença congénita, cujas manifestações clínicas apenas se observam na idade adulta. A técnica cirúrgica mais adequada para transplantar o doente PAF é a técnica de “piggyback”, na qual a hepatectomia é feita mantendo a veia cava do doente, podendo o transplante ser feito sem recorrer a bypass extracorporal. Antes de 2001, para fazerem o transplante sequencial, os diferentes centros alteraram a técnica de hepatectomia no doente PAF, ressecando a cava com o fígado conforme a técnica clássica, recorrendo ao bypass extracorporal. No nosso centro imaginámos e concebemos uma técnica original, com recurso a enxertos venosos, que permitisse ao doente PAF submeter-se à mesma técnica de hepatectomia no transplante, quer ele viesse a ser ou não dador. Essa técnica, por nós utilizada pela primeira vez a nível mundial em 2001, ficou conhecida por Transplante Sequencial em Duplo Piggyback. Este trabalho teve como objectivo procurar saber se a técnica por nós imaginada, concebida e utilizada era reprodutível, se não prejudicava o doente PAF dador e se oferecia ao receptor hepático as mesmas garantias do fígado de cadáver. A nossa série de transplantes realizados em doentes PAF é a maior a nível mundial, assim como o é o número de transplantes sequenciais de fígado. Recorrendo à nossa base de dados desde Setembro de 1992 até Novembro de 2008 procedeu-se à verificação das hipóteses anteriormente enunciadas. Com base na experiência por nós introduzida, a técnica foi reproduzida com êxito em vários centros internacionais de referência, que por si provaram a sua reprodutibilidade. Este sucesso encontra-se publicado por diversos grupos de transplantação hepática a nível mundial. Observámos na nossa série que a sobrevivência dos doentes PAF que foram dadores é ligeiramente superior àqueles que o não foram, embora sem atingir significância estatística. Contudo, quando se analisaram, apenas, estes doentes após a introdução do transplante sequencial no nosso centro, observa-se que existe uma melhor sobrevida nos doentes PAF dadores (sobrevida aos 5 anos de 87% versus 71%, p=0,047).Relativamente aos receptores observámos que existe um benefício a curto prazo em termos de morbi-mortalidade (menor hemorragia peri-operatória) e a longo prazo alguns grupos de doentes apresentaram diferenças de sobrevida, embora sem atingir significância estatística, facto este que pode estar relacionado com a dimensão das amostras parcelares analisadas. Estes grupos são os doentes com cirrose a vírus da hepatite C e os doentes com doença hepática maligna primitiva dentro dos critérios de Milão. Fora do âmbito deste trabalho ficou um aspecto relevante que é a recidiva da doença PAF nos receptores de fígado sequencial e o seu impacto no longo prazo. Em conclusão, o presente trabalho permite afirmar que a técnica por nós introduzida pela primeira vez a nível mundial é exequível e reprodutível e é segura para os doentes dadores de fígado PAF, que não vêem a sua técnica cirúrgica alterada pelo facto de o serem. Os receptores não são, por sua vez, prejudicados por receberem um fígado PAF, havendo mesmo benefícios no pós-operatório imediato e, eventualmente, alguns grupos específicos de doentes podem mesmo ser beneficiados.---------ABSTRACT: Ever since Bethesda statement in 1983, Liver Transplantation has been accepted as a clinical therapeutic procedure for many patients with advanced hepatic failure Holmgren, professor of genetics, suggested that one could expect that transplanting a new liver could lead to improve progressive neurological symptoms of Familial Amyloidotic Polyneuropathy (PAF). Bo Ericzon, the transplant surgeon at Huddinge Hospital in Stockholm, Sweden, did in 1991 the first Liver Transplant on a FAP patient. FAP is an inherited autosomal dominant neurologic disease in which the liver, otherwise structural an functionally normal, produces more than 90% of an abnormal protein (TTR Met30) whose deposits are responsible for symptoms. Liver Transplantation is currently the only efficient therapy available for FAP patients. Portugal is the country in the world where FAP is most prevalent. The Portuguese neurologist Corino de Andrade was the first to recognize in 1951 this particular form of inherited polyneuropathy, which is also known by the name of Andrade disease. Liver Transplantation started as a program in Portugal in September 1992. The first patient transplanted in Lisbon, Hospital Curry Cabral, was a FAP patient. From the beginning we did realize that competition among waiting lists of FAP and Hepatic patients would come to be a complex problem we had to deal with, on clinical and ethical grounds. There was one possible way-out. FAP livers could be of some utility themselves as liver grafts. Anatomically and functionally normal, except for the inherited abnormal trace, those livers could possibly be transplanted in selected hepatic patients. Nevertheless the FAP liver carried with it the ability to produce the mutant TTR protein. One could expect, considering the natural history of the disease that several decades would lapse before the recipient could suffer symptomatic neurologic disease, if at all. In Coimbra, Portugal, Linhares Furtado performed in 1995 the first transplant of a FAP liver to a patient with metastatic malignant disease, as a sequential or “domino” transplant. FAP Liver Transplant patients, because of some dysautonomic labiality and unexpected reactions when they are subjected to surgery, take special advantage when piggyback technique is used for hepatectomy. This technique leaves the vena cava of the patient undisturbed, so that return of blood to the heart is affected minimally, so that veno-venous extracorporeal bypass will not be necessary. The advantages of piggyback technique could not be afforded to FAP patients who became donors for sequential liver transplantation, before we did introduce our liver reconstruction technique in 2001. The hepatectomy took the vena cava together with the liver, which is the classical technique, and the use of extracorporeal veno-venous bypass was of necessity in most cases. The reconstruction technique we developed in our center and used for the first time in the world in 2001 consists in applying venous grafts to the supra-hepatic ostia of piggyback resected FAP livers so that the organ could be grafted to a hepatic patient whose liver was itself resected with preservation of the vena cava. This is the double piggyback sequential transplant of the liver. It is the objective of this thesis to evaluate the results of this technique that we did introduce, first of all that it is reliable and reproducible, secondly that the FAP donor is not subjected to any additional harm during the procedure, and finally that the recipient has the same prospects of a successful transplant as if the liver was collected from a cadaver donor. Our series of liver transplantation on FAP patients and sequential liver transplants represent both the largest experience in the world. To achieve the analysis of the questions mentioned above, we did refer to our data-base from September 1992 to November 2008. The reconstructive technique that we did introduce is feasible: it could be done with success in every case ion our series. It is also reproducible. It has been adopted by many international centers of reference that did mention it in their own publications. We do refer to our data-base in what concerns the safety for the FAP donor.Five years survival of FAP transplanted patients that have been donors (n=190) has been slightly superior to those who were not (n=77), with no statistical significance. However, if we consider five year survival of FAP transplanted patients after the beginning of sequential transplant program in our center, survival is better among those patients whose liver was used as a transplant (87% survival versus 71%, p=0.047). In what concerns recipients of FAP livers: Some short-term benefit of less perioperative morbi-mortality mainly less hemorrhage. In some groups of particular pathologies, there is a strong suggestion of better survival, however the scarcity of numbers make the differences not statistically significant. Patients with cirrhosis HVC (83% versus73%) and patients with primitive hepatic cancer within Milan criteria (survival of 70% versus 58%) are good examples. There is one relevant problem we left beyond discussion in the present work: this is the long-term impact of possible recurrence of FAP symptoms among recipients of sequential transplants. In Conclusion: The reconstruction technique that we did develop and introduce is consistently workable and reproducible. It is safe for FAP donors with the advantage that removal of vena cava can be avoided. Hepatic patients transplanted with those livers suffer no disadvantages and have the benefit of less hemorrhage. There is also a suggestion that survival could be better in cirrhosis HVC and primary liver cancer patients.

Influenza A(H1N1)pdm09 Resistance and Cross-Decreased Susceptibility to Oseltamivir and Zanamivir Antiviral Drugs

Neuraminidase inhibitors (NAIs) oseltamivir and zanamivir are currently the only effective antiviral drugs available worldwide for the management of influenza. The potential development of resistance is continually threatening their use, rationalizing and highlighting the need for a close and sustained evaluation of virus susceptibility. This study aimed to analyze and characterize the phenotypic and genotypic NAIs susceptibility profiles of A(H1N1)pdm09 viruses circulating in Portugal from 2009 to 2010/2011. A total of 144 cases of A(H1N1)pdm09 virus infection from community and hospitalized patients were studied, including three suspected cases of clinical resistance to oseltamivir. Oseltamivir resistance was confirmed for two of the suspected cases. Neuraminidase (NA) H275Y resistant marker was found in viruses from both cases but for one it was only present in 26.2% of virus population, raising questions about the minimal percentage of resistant virus that should be considered relevant. Cross-decreased susceptibility to oseltamivir and zanamivir (2-4 IC50 fold-change) was detected on viruses from two potentially linked community patients from 2009. Both viruses harbored the NA I223V mutation. NA Y155H mutation was found in 18 statistical non-outlier viruses from 2009, having no impact on virus susceptibility. The mutations at NA N369K and V241I may have contributed to the significantly higher baseline IC50 value obtained to oseltamivir for 2010/2011 viruses, compared to viruses from the pandemic period. These results may contribute to a better understanding of the relationship between phenotype and genotype, which is currently challenging, and to the global assessment of A(H1N1)pdm09 virus susceptibility profile and baseline level to NAIs.

Bronchial Asthma in Children: Clinical and Epidemiologic Approach in Different Portuguese Speaking Countries

BACKGROUND: Geographical differences in asthma prevalence are currently accepted, but evidence is sparse due to the lack of multicentre studies using the same protocol. OBJECTIVES: To compare the prevalence of asthma and atopy among schoolchildren from Portuguese speaking countries (ISAAC and Portuguese Study) and evaluate some environmental variables, such as house dust mite exposure. MATERIAL AND METHODS: Significant random samples of schoolchildren studied with standard validated methods--questionnaires, skin prick tests, methacholine bronchial challenge tests; dust bed sampling for analysis of mite antigens. RESULTS: In the ISAAC study, in the 13-14 year-old age group, statistical significant differences were found, with higher wheezing prevalence in Brazil than in Portugal (two-fold). In the Portuguese Study, atopy prevalence ranged between 6.0 and 11.9% in Sal and S. Vicente (Cape Verde), up to 48.6 and 54.1% in Macau and Madeira. Active asthma had the higher values in Madeira (14.6%), and the lower in Macau (1.3%). Cape Verde had intermediate asthma prevalence (10.6 and 7.0%). The bronchial challenge test was positive in 25, 66 and 70% of asthmatic children from Sal, S. Vicente and Madeira respectively. Significant HDM antigen concentrations (Der p1) were found in Cape Verde and Madeira. CONCLUSIONS: There are significant variations in asthma and atopy prevalence between these pediatric populations. The reasons remain under discussion, but genetics linked to race, seem to play a central role, modulated by environmental and lifestyle variables.