Developing an individualized survival prediction model for rectal cancer

This work presents a survivability prediction model for rectal cancer patients developed through machine learning techniques. The model was based on the most complete worldwide cancer dataset known, the SEER dataset. After preprocessing, the training data consisted of 12,818 records of rectal cancer patients. Six features were extracted from a feature selection process, finding the most relevant characteristics which affect the survivability of rectal cancer. The model constructed with six features was compared with another one with 18 features indicated by a physician. The results show that the performance of the six-feature model is close to that of the model using 18 features, which indicates that the first may be a good compromise between usability and performance.FCT - Fuel Cell Technologies Program (SFRH/BD/85291/2012)info:eu-repo/semantics/publishedVersio

An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance

BACKGROUND: Motif finding algorithms have developed in their ability to use computationally efficient methods to detect patterns in biological sequences. However the posterior classification of the output still suffers from some limitations, which makes it difficult to assess the biological significance of the motifs found. Previous work has highlighted the existence of positional bias of motifs in the DNA sequences, which might indicate not only that the pattern is important, but also provide hints of the positions where these patterns occur preferentially.RESULTS: We propose to integrate position uniformity tests and over-representation tests to improve the accuracy of the classification of motifs. Using artificial data, we have compared three different statistical tests (Chi-Square, Kolmogorov-Smirnov and a Chi-Square bootstrap) to assess whether a given motif occurs uniformly in the promoter region of a gene. Using the test that performed better in this dataset, we proceeded to study the positional distribution of several well known cis-regulatory elements, in the promoter sequences of different organisms (S. cerevisiae, H. sapiens, D. melanogaster, E. coli and several Dicotyledons plants). The results show that position conservation is relevant for the transcriptional machinery.CONCLUSION: We conclude that many biologically relevant motifs appear heterogeneously distributed in the promoter region of genes, and therefore, that non-uniformity is a good indicator of biological relevance and can be used to complement over-representation tests commonly used. In this article we present the results obtained for the S. cerevisiae data sets.publishersversionpublishe

Developmental arrest in Drosophila melanogaster caused by mitochondrial DNA replication defects cannot be rescued by the alternative oxidase

The xenotopic expression of the alternative oxidase AOX from the tunicate Ciona intestinalis in diverse models of human disease partially alleviates the phenotypic effects of mitochondrial respiratory chain defects. AOX is a non-proton pumping, mitochondrial inner membrane-bound, single-subunit enzyme that can bypass electron transport through the cytochrome segment, providing an additional site for ubiquinone reoxidation and oxygen reduction upon respiratory chain overload. We set out to investigate whether AOX expression in Drosophila could counteract the effects of mitochondrial DNA (mtDNA) replication defects caused by disturbances in the mtDNA helicase or DNA polymerase gamma. We observed that the developmental arrest imposed by either the expression of mutant forms of these enzymes or their knockdown was not rescued by AOX. Considering also the inability of AOX to ameliorate the phenotype of tko(25t), a fly mutant with mitochondrial translation deficiency, we infer that this alternative enzyme may not be applicable to cases of mitochondrial gene expression defects. Finding the limitations of AOX applicability will help establish the parameters for the future putative use of this enzyme in gene therapies for human mitochondrial diseases.Peer reviewe

A mobile and evolving tool to predict colorectal cancer survivability

In this work, a tool for the survivability prediction of patients with colon or rectal cancer, up to five years after diagnosis and treatment, is presented. Indeed, an accurate survivability prediction is a difficult task for health care professionals and of high concern to patients, so that they can make the most of the rest of their lives. The distinguishing features of the tool include a balance between the number of necessary inputs and prediction performance, being mobile-friendly, and featuring an online learning component that enables the automatic evolution of the prediction models upon the addition of new cases.This work has been supported by FCT - Fundacao para a Ciencia e Tecnologia within the Project Scope UID/CEC/00319/2013. The work of Tiago Oliveira is supported by a FCT grant with the reference SFRH/BD/85291/2012.info:eu-repo/semantics/publishedVersio

Expression of Ciona intestinalis AOX causes male reproductive defects in Drosophila melanogaster

Background: Mitochondrial alternative respiratory-chain enzymes are phylogenetically widespread, and buffer stresses affecting oxidative phosphorylation in species that possess them. However, they have been lost in the evolutionary lineages leading to vertebrates and arthropods, raising the question as to what survival or reproductive disadvantages they confer. Recent interest in using them in therapy lends a biomedical dimension to this question. Methods: Here, we examined the impact of the expression of Ciona intestinalis alternative oxidase, AOX, on the reproductive success of Drosophila melanogaster males. Sperm-competition assays were performed between flies carrying three copies of a ubiquitously expressed AOX construct, driven by the a-tubulin promoter, and wild-type males of the same genetic background. Results: In sperm-competition assays, AOX conferred a substantial disadvantage, associated with decreased production of mature sperm. Sperm differentiation appeared to proceed until the last stages, but was spatially deranged, with spermatozoids retained in the testis instead of being released to the seminal vesicle. High AOX expression was detected in the outermost cell-layer of the testis sheath, which we hypothesize may disrupt a signal required for sperm maturation. Conclusions: AOX expression in Drosophila thus has effects that are deleterious to male reproductive function. Our results imply that AOX therapy must be developed with caution.Peer reviewe

Expression of Ciona intestinalis AOX causes male reproductive defects in Drosophila melanogaster

Background: Mitochondrial alternative respiratory-chain enzymes are phylogenetically widespread, and buffer stresses affecting oxidative phosphorylation in species that possess them. However, they have been lost in the evolutionary lineages leading to vertebrates and arthropods, raising the question as to what survival or reproductive disadvantages they confer. Recent interest in using them in therapy lends a biomedical dimension to this question. Methods: Here, we examined the impact of the expression of Ciona intestinalis alternative oxidase, AOX, on the reproductive success of Drosophila melanogaster males. Sperm-competition assays were performed between flies carrying three copies of a ubiquitously expressed AOX construct, driven by the a-tubulin promoter, and wild-type males of the same genetic background. Results: In sperm-competition assays, AOX conferred a substantial disadvantage, associated with decreased production of mature sperm. Sperm differentiation appeared to proceed until the last stages, but was spatially deranged, with spermatozoids retained in the testis instead of being released to the seminal vesicle. High AOX expression was detected in the outermost cell-layer of the testis sheath, which we hypothesize may disrupt a signal required for sperm maturation. Conclusions: AOX expression in Drosophila thus has effects that are deleterious to male reproductive function. Our results imply that AOX therapy must be developed with caution.Peer reviewe

Avaliação da qualidade ecológica de rios portugueses baseado nas comunidades de macroinvertebrados bentónicos

Com o desenvolvimento dum Programa Nacional de Monitorização de Sistemas Aquáticos, a Autoridade Florestal Nacional (AFN) pretendeu, baseado no Projecto AQUARIPORT, obter uma informação base de suporte ao ordenamento dos recursos piscícolas de Portugal e ainda contribuir para a avaliação da qualidade ecológica de rios tendo em conta os princípios emanados pela Directiva Quadro da Água (DQA). Neste âmbito, desde 2004 até 2009 foram monitorizadas as comunidades de peixes e de macroinvertebrados numa rede de amostragem apreciável (600) distribuídas pelos diferentes sistemas lóticos das bacias hidrográficas de Portugal. De forma complementar foram também utilizadas variáveis abióticas relacionadas com a qualidade da água, a hidromorfologia e a zona ripária dos sistemas aquáticos. Com base nas famílias de macroinvertebrados foram determinadas diferentes métricas, como a diversidade Shannon-Wiener (H’), EPT, IBMWP, e aplicado Índice Português de Invertebrados (IPtIN e IPtIS) recentemente desenvolvido pela DQA. Os impactos resultantes da poluição, regularização, corte da vegetação ribeirinha, entre outros, estão na base da detecção duma menor qualidade ecológica dos rios do litoral e sul de Portugal. Por sua vez, os parâmetros hidromorfológicos e ambientais que influenciam significativamente a composição das comunidades de macroinvertebrados foram a condutividade, profundidade e largura média do curso de água, presença de hidrófitos, urbanização nas áreas circundantes e as características do substrato e da mata rípícol

Rapid granulation and stable performance of a microalgal-bacterial granular sludge system treating saline wastewater

info:eu-repo/semantics/publishedVersio

Bacteriocin production of the probiotic Lactobacillus acidophilus KS400

In the last years, the use of probiotics, including Lactobacillus species, has received much attention to prevent and treat vaginal disorders. These species have been described as having the ability to colonize the epithelial surface and produce antimicrobial metabolites that are able to control the remaining vaginal microflora. This study aimed to identify and characterize, for the first time, a bacteriocin natively produced by Lactobacillus acidophilus KS400 (probiotic strain from Gynoflor®-Medinova AG, Switzerland) and its antimicrobial activity against relevant urogenital pathogens. After organic acids and hydrogen peroxide neutralization in the fermented Lactobacillus acidophilus KS400 culture medium, bacteriocin activity was tested against the indicator microorganism Lactobacillus delbrueckii ATCC9649. The fermentation of Lactobacillus acidophilus KS400 for bacteriocin production was carried out in batch mode, and its antimicrobial activity, optical density and pH were monitored. After production and extraction, the bacteriocin molecular weight was estimated by electrophoresis and tested against vaginal pathogenic microorganisms. As described for other bacteriocins, batch fermentation profiles indicated that bacteriocin production occurs during the exponential growth phase of the lactobacilli, and declines during their stationary growth phase. The molecular weight of the bacteriocin is approximately 7.5 kDa. The bacteriocin containing protein extract was shown to inhibit the growth of Gardnerella vaginalis, Streptococcus agalactiae, Pseudomonas aeruginosa and the indicator strain Lactobacillus delbrueckii ATCC9649. We conclude that L. acidophilus KS400 produces bacteriocin with antimicrobial activity against relevant urogenital pathogens.Project POCI-01-0145-FEDER-007491; Medinovainfo:eu-repo/semantics/publishedVersio

Avaliação da qualidade ecológica de rios portugueses (Projecto AQUARIPORT): síntese dos resultados referentes à análise das comunidades de macroinvertebrados bentónicos

O projecto AQUARIPORT serve de base ao Programa Nacional de Monitorização de sistemas aquáticos e tem como objectivos (1) a recolha de informação base de suporte ao ordenamento dos recursos piscícolas nacionais; (2) o desenvolvimento e a implementação de índices bióticos, baseados na ictiofauna e nos macroinvertebrados bentónicos, que permitam a avaliação da qualidade ecológica de rios no enquadramento nos princípios da Directiva Quadro da Água. Neste âmbito, avalia-se, com base nas comunidades de macroinvertebrados, a integridade ecológica de 107 pontos localizados nas bacias hidrográficas dos rios Douro, Minho, Lima, Mondego, Vouga, Tejo, Sado, Mira e Guadiana das Ribeiras do Oeste e do Algarve. Complementarmente às amostragens de macroinvertebrados também se avalia a condição ambiental de cada ponto amostrado (e.g., estrutura da zona ripícola, substrato do leito, largura do rio, perturbações antropogénicas, condutividade, temperatura, oxigénio dissolvido). Com base nas famílias de macroinvertebrados presentes foram determinados para cada ponto os valores do índice biótico IBMWP. Verificou-se que em 62,3% dos pontos amostrados predominam grupos mais intolerantes à degradação ambiental o que indica que estes locais possuem boa qualidade ambiental (Classes I e II). 24,6% apresentam degradação moderada (Classe III). A qualidade ambiental dos restantes 13,1% encontra-se muito a fortemente degradada, uma vez que os grupos tolerantes ou muito tolerantes à degradação ambiental são dominantes (Classes IV e V). Os parâmetros morfológicos e ambientais que influenciam significativamente a composição das comunidades de macroinvertebrados, são a condutividade, profundidade e largura média do curso de água, presença de hidrófitos, intensidade da urbanização nas áreas circundantes, características do substrato e da mata rípícola