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- Pathogens-in-foods: a database of occurrence of microbial hazerds in foods commercialised in EuropePublication . Deusdado, Sérgio; Cadavez, Vasco; Rodrigues, Vânia; Kooh, Pauline; Moez, Sanna; Gonzales-Barron, Ursula; Rodrigues, VâniaThe objective of this study was to build a database of the occurrence (both prevalence and counts) of the most important biological hazards in foods commercialised in Europe. For this, systematic literature searches were first conducted for every pathogen; namely, Salmonella, Campylobacter, Shigatoxin-producing Escherichia co//, Listería monocytogenes, Yersinia enterocolitica, Bacillus cereus, Clostridium perfringens, Staphylococcus aureus, Toxoplasma gondií, norovirus, Hepatitis A vírus, Hepatitis E virus, Cryptosporidium ana Giardia duodenalis; and after screening for relevance and methodological quality assessment, data were carefully extracted from the primary studies into a harmonised arrangement consisting of primary study characteristics, food characteristics ana stage within the food chain, microbiological methods, prevalence results, enumeration results and potential for bias. Based on the microbiological survey results extracted from 977 primary studies, the database Pathogens-ln-Foods hás been constructed to facilitate data access and retrieval according to hazard, food class, country or any other relevant variable, with the ability to execute simple statistical calculations.
- Solanum lycopersicum - Fusarium oxysporum Fo47 interaction study using ml classifiers in transcriptomic dataPublication . Rodrigues, Vânia; Deusdado, Sérgio; Rodrigues, VâniaFusarium oxysporum Fo47 is a pervasive endophyte that can colonize plant roots, initiating an interaction that can provide phytosanitary defenses. The response triggered by this non-pathogenic fungus is not well understood. To elucidate the Solanum lycopersicum - Fusarium oxysporum Fo47 interaction, machine learning methods were used to identify the informative genes (IGs) using publicly available transcriptomic data. The assembled dataset revealed 244 significantly differentially expressed genes (DEGs). The experimental work with machine learning classifiers achieved significant identification of these DEGs. Multilayer Perceptron (MLP) classifiers and Kernel Logistic Regression metalearners (meta-KLR) parameterization was optimized, achieving MLP-b and meta-KLR-b near optimal performance. Afterwards, these classifiers were used as attribute evaluators identifying two sets (A,B) of highest-rated genes, 393 (set A) by MLP-b and 317 (set B) by meta-KLR-b. Regarding the percent of significantly differentially expressed genes found by the classifiers compared to the total 244 DEGs, the set A presented 92.2%, while the set B presented 84.8%. Considering B⊂A, the IGs identified by MLP-b (set A) were used in the subsequent analysis. Among this 393 IGs, 379 were identified as Solanum lycopersicum genes, 1 as Escherichia coli protein (Hygromycin-B 4-O-kinase), 1 as Saccharomyces cerevisiae protein (galactose-responsive transcription factor GAL4) and 12 were unidentified. Then, a functional enrichment analysis of the Solanum lycopersicum IGs showed 283 biological processes and 20 biological pathways involved in the Solanum lycopersicum - Fo47 interaction.
- Hierarquização dos factores de risco associados à salmonelose por meta-análise de estudos caso-controloPublication . Rodrigues, Vânia; Cadavez, Vasco; Gonzales-Barron, Ursula; Kooh, Pauline; Sanaa, Moez; Rodrigues, VâniaOs estudos caso-controlo são uma metodologia de investigação em epidemiologia que permitem analisar, de forma retrospectiva, a exposição a factores de risco das doenças entéricas. O objectivo deste trabalho foi sintetizar a associação entre as infecções esporádicas por Salmonella spp. e os factores de risco, através da combinação dos resultados de estudos casocontrolo. Para uniformizar as categorias de exposição, desenvolvemos uma classificação dos eventuais factores de risco, com as seguintes categorias: viagem, especificidades do hospedeiro, transmissão de pessoa a pessoa, contacto com animais, contaminação pelo ambiente e consumo de alimentos. A pesquisa da literatura relevante foi realizada através dos portais da Science Direct, Pubmed, Scielo, 151 Web of Science e Scopus. Em cada estudo caso-controlo, foi recolhida a medida de associação oddsratio (ORs) da doença com a exposição. Os estudos seleccionados foram classificados quanto ao seu potencial de enviesamento, resultante de deficiências do desenho experimental, da selecção da população e dos métodos utilizados na análise dos dados. Foram também extraídas outras características consideradas importantes, tais como: a população, o desenho experimental, a análise estatística dos dados e o(s) factor(es) de risco. Posteriormente, os ORs globais, para cada factor de risco e das rotas de transmissão, foram estimados por modelos de meta-análise com o software R, e hierarquizados.
- Deterministic Classifiers Accuracy Optimization for Cancer Microarray DataPublication . Rodrigues, Vânia; Deusdado, Sérgio; Rodrigues, VâniaThe objective of this study was to improve classification accuracy in cancer microarray gene expression data using a collection of machine learning algorithms available in WEKA. State of the art deterministic classification methods, such as: Kernel Logistic Regression, Support Vector Machine, Stochastic Gradient Descent and Logistic Model Trees were applied on publicly available cancer microarray datasets aiming to discover regularities that provide insights to help characterization and diagnosis correctness on each cancer typology. The implemented models, relying on 10-fold cross-validation, parameterized to enhance accuracy, reached accuracy above 90%. Moreover, although the variety of methodologies, no significant statistic differences were registered between them, at significance level 0.05, confirming that all the selected methods are effective for this type of analysis.
- Automatic tracking of red blood cells in micro channels using OpenCVPublication . Rodrigues, Vânia; Rodrigues, Pedro João; Pereira, Ana I.; Lima, Rui A.; Rodrigues, VâniaThe present study aims to develop an automatic method able to track red blood cells (RBCs) trajectories flowing through a microchannel using the Open Source Computer Vision (OpenCV). The developed method is based on optical flux calculation assisted by the maximization of the template-matching product. The experimental results show a good functional performance of this method.
- Food source atribution of human campylobacteriosis by meta-analysis of case-control studiesPublication . Rodrigues, Vânia; Cadavez, Vasco; Kooh, Pauline; Moez, Sanna; Gonzales-Barron, Ursula; Rodrigues, VâniaA case-control study is a powerful approach among epidemiologists to investigate the causal effect of exposure and enteric illness. To combine the associations between sporadic campylobacteriosis and the different food pathways of exposure, the results from relevant case-control studies were extracted and their odds-ratio (OR) measures were meta-analysed within food category partitions by population type, extracting the variability due to both primary studies and model types. In the mixed population, the most important determinants of disease turned out to be: consumption of raw milk (pooted OR=2. 64), poultry (OR=1. 78), raw milk's cheese (OR=1. 72), BBQ meats (OR=1. 67), fast-food composite (OR=1. 59) and raw seafood (OR=1. 50). On the other hand, consumption of raw-egg containing products (OR=4. 85), raw milk (OR=3. 05), pork (OR=2. 34), minced beef (OR=2.27), processed meats (OR=2.18), any composite food eaten out (OR=2.16) and poultry meat (OR=2.08) were found to bear the highest risk of campylobacteriosis in the children population.
- Liquid phase stability via global optimizationPublication . Rodrigues, Vânia; Pereira, Ana I.; Ferreira, Olga; Pinho, Simão; Rodrigues, VâniaIn this work, the Penalty Stretched Simulated Annealing Method and the Multilocal Branch and Bound method were applied to identify the stationary points of the tangent plane distance function defined for the Gibbs energy. The classic excess Gibbs energy Non Random Two Liquid model was used for these studies in several multicomponent mixtures, for which specific numerical difficulties were shown. The preliminary results obtained by applying the methodology developed in this work were satisfactory.
- Meta-análise do contato com animais como rota de transmissão de toxoplasmose esporádicaPublication . Rodrigues, Vânia; Cadavez, Vasco; Kooh, Pauline; Sanaa, Moez; Gonzales-Barron, Ursula; Rodrigues, VâniaA toxoplasmose é uma infeção causada pelo parasita Toxoplasma gondii, cuja transmissão ocorre por ingestão de alimentos contaminados, contato com animais (zoonose) e de mãe para filho (congénita). O objetivo deste estudo foi sintetizar a associação entre a infeção esporádica por T. gondii e o contato com animais, através da combinação dos resultados de estudos de caso-controlo relevantes, usando a meta-análise para produzir uma estimativa mais precisa da associação global entre o fator de risco e a doença.
- Meta-análise do contato com animais e do consumo de carne como fontes de salmonelose esporádicaPublication . Gonçalves-Tenório, Andiara; Cadavez, Vasco; Rodrigues, Vânia; Kooh, Pauline; Sanaa, Moez; Gonzales-Barron, Ursula; Rodrigues, VâniaAs doenças gastrointestinais representam um importante problema de saúde pública em todo mundo, desta forma a identificação da origem de transmissão é de grande importância para a avaliação e atribuição de risco. Os estudos epidemiológicos de casocontrolo são usados para identificar os fatores de risco associados à transmissão das doenças. A salmonelose, doença causada por vários serotipos de Salmonella spp., pode ser transmitida ao homem de diversas formas. De uma forma geral, os casos esporádicos de salmonelose não partilham o mesmo fator de risco ou rota de contaminação, de modo que os estudos que medem a relação de probabilidades (“odds ratio”, OR) de qualquer fonte de transmissão podem ocultar os riscos reais tornando-os mais difíceis de detetar (Fullerton et al., 2012). Por exemplo, o frango assado é uma importante fonte de contaminação por Salmonella spp., todavia a maioria das porções de frango não estão contaminadas, de modo que a probabilidade de uma pessoa adquirir salmonelose pelo consumo de frango assado é apenas um pouco superior à das pessoas que não consomem frango assado (controlo).
- Microbiological safety of goat milk and cheese: evidences from a meta-analysisPublication . Cadavez, Vasco; Rodrigues, Vânia; Gonzales-Barron, Ursula; Rodrigues, VâniaThis chapter synthesizes published information concerning the incidence of zoonotic pathogenic microorganisms – Listeria monocytogenes, Staphylococcus aureus and shigatoxin-producing Escherichia coli – in raw goat milk and cheese. Meta-analytical data were extracted from primary studies undertaken in Brazil, China, Czech Republic, Germany, Iran, Italy, Malaysia, Mexico, Norway, Portugal, Spain, Sweden, Switzerland, Turkey and USA. In both raw goat milk (overall incidence 42.6%; 95% CI: 23.0-64.8%) and cheese (overall incidence 26.4%; 95% CI: 10.8-51.6%), S. aureus was found to be the most frequent contaminant bacterium, which suggests that control measures during milk handling are still to be reinforced. In addition, the high frequency of detection of generic E. coli in raw goat milk cheese (overall incidence 11.9%; 95% CI: 3.8- 31.6%) is another indicator of hygiene deficiencies during production. Moreover, E. coli strains with virulence genes have been very frequently detected in raw goat milk (overall incidence 10.5%; 95% CI: 5.3–19.6%). L. monocytogenes, a pathogen that mainly affects the susceptible population, presented a high incidence in both raw goat milk (overall incidence 3.4%; 95% CI: 2.2-5.1%) and goat milk cheese (overall incidence 8.5%; 95% CI: 4.9-14.6%). In conclusion, the present meta-analysis confirms that raw goat milk and cheese are important vehicles of transmission of food-borne diseases. Further research work towards improving the current microbiological quality of these products, particularly in traditional production units, is essential.