Quantificação da difusão na ressonância magnética da mama: ADC e Kurtosis

Mestrado em Radiações Aplicadas às Tecnologias da Saúde. Área de especialização: Ressonância Magnética

PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods

Background: With the decrease of DNA sequencing costs, sequence-based typing methods are rapidly becoming the gold standard for epidemiological surveillance. These methods provide reproducible and comparable results needed for a global scale bacterial population analysis, while retaining their usefulness for local epidemiological surveys. Online databases that collect the generated allelic profiles and associated epidemiological data are available but this wealth of data remains underused and are frequently poorly annotated since no user-friendly tool exists to analyze and explore it. Results: PHYLOViZ is platform independent Java software that allows the integrated analysis of sequence-based typing methods, including SNP data generated from whole genome sequence approaches, and associated epidemiological data. goeBURST and its Minimum Spanning Tree expansion are used for visualizing the possible evolutionary relationships between isolates. The results can be displayed as an annotated graph overlaying the query results of any other epidemiological data available. Conclusions: PHYLOViZ is a user-friendly software that allows the combined analysis of multiple data sources for microbial epidemiological and population studies. It is freely available at http://www.phyloviz.net.

Quantificação por imagem ponderada em difusão (DWI) das lesões tumorais da mama

Introdução – A técnica de Difusão por Ressonância Magnética (RM), ao avaliar o movimento das moléculas de água nos tecidos, permite inferir sobre a arquitetura dos mesmos, em particular relativamente à celularidade, volume celular e permeabilidade das membranas. O Coeficiente de Difusão Aparente (ADC) é um parâmetro quantificável da imagem ponderada em difusão (DWI). A sua análise poderá fornecer informação clínica adicional sobre estas lesões, sobretudo em relação à sua caracterização histológica. Objetivos – Caracterizar e diferenciar tipos e alguns subtipos de lesões mamárias através da análise do ADC. Metodologia – 20 Mulheres com 23 lesões mamárias foram submetidas a RM mamária: 3 lesões benignas (3 Fibroadenomas-FA) e 20 malignas (16 Carcinomas Ductais Invasivos-CDI, 2 Carcinomas Ductais In Situ-CDIS e 2 Carcinomas Invasivos Lobulares-CLI). Num equipamento 1.5T aplicou-se uma sequência de Difusão (b=0,50,250,500,750,1000 s/mm2). Obteve-se o ADC através do ajuste exponencial da intensidade de sinal das lesões em função do valor de b, fazendo-se corresponder os valores de ADC à respetiva caracterização histológica e posterior comparação com a literatura. Resultados e Discussão – As lesões malignas apresentaram ADCs significativamente (p=0,014) inferiores [(0,94±0,22)x10-3 mm2/s] aos das benignas [(1,43±0,25)x10-3 mm2/s]. A justificação pode residir no aumento da celularidade e consequente restrição da Difusão que se observa nas lesões malignas. Os CDI apresentaram ADCs baixos [(0,88±0,17)x10-3 mm2/s], enquanto que os CDIS apresentaram ADCs mais elevados [(1,33±0,29)x10-3 mm2/s]. Estes resultados estão de acordo com o facto dos CDIS estarem limitados aos ductos mamários, mantendo-se menos alterada a estrutura do tecido adjacente e resultando numa menor restrição à difusão que nos CDI. Verificaram-se diferenças significativas entre FA e CDI (p=0,010) e entre CDI e CDIS (p=0,049). Conclusões – O ADC possibilita a diferenciação entre lesões mamárias benignas e malignas, bem como entre alguns tipos histológicos. O desenvolvimento deste conceito pode representar um avanço no papel da RM na avaliação destas neoplasias. ABSTRACT - Introduction – The Magnetic Resonance (MR) diffusion technique measures the movement of water molecules in tissues. Therefore, it provides useful information about tissue architecture, specially regarding tissue cellularity, cell volume and membrane permeability. The quantification of diffusion weighted imaging (DWI) data is done by measuring the so-called. Apparent Diffusion Coefficient (ADC). This parameter provides additional clinical information about breast lesions, and potentially allows for in-vivo histological characterization. Purpose – To characterize and differentiate breast lesions through ADC analysis. Methodology – The study comprised 20 women, with 23 breast lesions: 3 benign lesions - 3 Fibroadenomas (FA); and 20 malignant - 16 Invasive Ductal Carcinomas (CDI), 2 Ductal Carcinomas In Situ (CDIS), 2 Invasive Lobular Carcinoma (CLI). On a 1.5T equipment a diffusion-weighted sequence with 6 b-values (b=0,50,250,500,750,1000 s/mm2) was used to examine the patients. ADC was obtained by fitting an exponential to data of lesion signal intensity vs. b values. A correspondence of ADC values to histological lesion characterization was done and finally, the results were comparison with the literature. Results and Discussion – Malignant lesions showed inferior ADCs significantly (p=0.014) lower ((0.94±0.22)x10-3 mm2/s) than the benign lesions ((1.43±0.25)x10-3 mm2/s). This may be associated to increasead cellularity in malignant lesions, which result in higher tissue restriction to diffusion. CDI showed low ADC values ((0.88±0.17)x10-3 mm2/s), while the CDIS showed higher ADCs ((1.33±0.29)x10-3 mm2/s). These results agree with the fact that CDIS are limited to mammary ducts, maintaining a less altered neighboring tissue structure, which results in a lower restriction to diffusion than observed in CDI. Significant differences between FA and CDI (p=0.010) and between CDI and CDIS (p=0.049) were observed. Conclusion – The ADC parameter is able to differentiate between malignant and benign breast lesions, as well as between some histological types.

Soleus activity in post-stroke subjects: movement sequence from standing to sitting

O documento em anexo encontra-se na versão post-print (versão corrigida pelo editor).

Phase diagrams of binary mixtures of patchy colloids with distinct numbers and types of patches: Theempty fluid regime

We investigate the effect of distinct bonding energies on the onset of criticality of low functionality fluid mixtures. We focus on mixtures ofparticles with two and three patches as this includes the mixture where "empty" fluids were originally reported. In addition to the number of patches, thespecies differ in the type of patches or bonding sites. For simplicity, we consider that the patches on each species are identical: one species has threepatches of type A and the other has two patches of type B. We have found a rich phase behavior with closed miscibility gaps, liquid-liquid demixing, and negative azeotropes. Liquid-liquid demixing was found to pre-empt the "empty" fluid regime, of these mixtures, when the AB bonds are weaker than the AA or BB bonds. By contrast, mixtures in this class exhibit "empty" fluid behavior when the AB bonds are stronger than at least one of the other two. Mixtureswith bonding energies epsilon(BB) = epsilon(AB) and epsilon(AA) < epsilon(BB), were found to exhibit an unusual negative azeotrope. (C) 2011 American Institute of Physics. [doi:10.1063/1.3561396]

Resistance to β-lactams in bacteria isolated from different types of Portuguese cheese

The purpose of this study was to investigate the presence of beta-lactam-resistant bacteria in six different types of Portuguese cheese. The numbers of ampicillin resistant (AMP(r)) bacteria varied from 4.7 x 10(2) to 1.5 x 10(7) CFU/g. Within 172 randomly selected beta-lactam-resistant bacteria, 44 resistant phenotypes were found and 31.4% were multidrug resistant. The majority (85%) of the isolates identified belonged to the Enterobacteriaceae family. The presence of the bla(TEM) gene was detected in 80.9% of the tested isolates. The results suggest that without thermal processing of the milk and good hygienic practices, cheese may act as a vehicle of transfer of beta-lactam-resistant bacteria to the gastrointestinal tract of consumers.

Side information creation for efficient Wyner-Ziv video coding: Classifying and reviewing

Video coding technologies have played a major role in the explosion of large market digital video applications and services. In this context, the very popular MPEG-x and H-26x video coding standards adopted a predictive coding paradigm, where complex encoders exploit the data redundancy and irrelevancy to 'control' much simpler decoders. This codec paradigm fits well applications and services such as digital television and video storage where the decoder complexity is critical, but does not match well the requirements of emerging applications such as visual sensor networks where the encoder complexity is more critical. The Slepian Wolf and Wyner-Ziv theorems brought the possibility to develop the so-called Wyner-Ziv video codecs, following a different coding paradigm where it is the task of the decoder, and not anymore of the encoder, to (fully or partly) exploit the video redundancy. Theoretically, Wyner-Ziv video coding does not incur in any compression performance penalty regarding the more traditional predictive coding paradigm (at least for certain conditions). In the context of Wyner-Ziv video codecs, the so-called side information, which is a decoder estimate of the original frame to code, plays a critical role in the overall compression performance. For this reason, much research effort has been invested in the past decade to develop increasingly more efficient side information creation methods. This paper has the main objective to review and evaluate the available side information methods after proposing a classification taxonomy to guide this review, allowing to achieve more solid conclusions and better identify the next relevant research challenges. After classifying the side information creation methods into four classes, notably guess, try, hint and learn, the review of the most important techniques in each class and the evaluation of some of them leads to the important conclusion that the side information creation methods provide better rate-distortion (RD) performance depending on the amount of temporal correlation in each video sequence. It became also clear that the best available Wyner-Ziv video coding solutions are almost systematically based on the learn approach. The best solutions are already able to systematically outperform the H.264/AVC Intra, and also the H.264/AVC zero-motion standard solutions for specific types of content. (C) 2013 Elsevier B.V. All rights reserved.

A hybrid MLS technique for room impulse response estimation

The measurement of room impulse response (RIR) when there are high background noise levels frequently means one must deal with very low signal-to-noise ratios (SNR). if such is the case, the measurement might yield unreliable results, even when synchronous averaging techniques are used. Furthermore, if there are non-linearities in the apparatus or system time variances, the final SNR can be severely degraded. The test signals used in RIR measurement are often disturbed by non-stationary ambient noise components. A novel approach based on the energy analysis of ambient noise - both in the time and in frequency - was considered. A modified maximum length sequence (MLS) measurement technique. referred to herein as the hybrid MLS technique, was developed for use in room acoustics. The technique consists of reducing the noise energy of the captured sequences before applying the averaging technique in order to improve the overall SNRs and frequency response accuracy. Experiments were conducted under real conditions with different types of underlying ambient noises. Results are shown and discussed. Advantages and disadvantages of the hybrid MLS technique over standard MLS technique are evaluated and discussed. Our findings show that the new technique leads to a significant increase in the overall SNR. (C) 2008 Elsevier Ltd. All rights reserved.

Differential expression of the eukaryotic release factor 3 (eRF3/GSPT1) according to gastric cancer histological types

Background: There are now several lines of evidence to suggest that protein synthesis and translation factors are involved in the regulation of cell proliferation and cancer development. Aims: To investigate gene expression patterns of eukaryotic releasing factor 3 (eRF3) in gastric cancer. Methods: RNA was prepared from 25 gastric tumour biopsies and adjacent non-neoplastic mucosa. Real time TaqMan reverse transcription polymerase chain reaction (RT-PCR) was performed to measure the relative gene expression levels. DNA was isolated from tumour and normal tissues and gene dosage was determined by a quantitative real time PCR using SYBR Green dye. Results: Different histological types of gastric tumours were analysed and nine of the 25 tumours revealed eRF3/GSPT1 overexpression; moreover, eight of the 12 intestinal type carcinomas analysed overexpressed the gene, whereas eRF3/GSPT1 was overexpressed in only one of the 10 diffuse type carcinomas (Kruskal-Wallis Test; p , 0.05). No correlation was found between ploidy and transcript expression levels of eRF3/GSPT1. Overexpression of eRF3/GSPT1 was not associated with increased translation rates because the upregulation of eRF3/GSPT1 did not correlate with increased eRF1 levels. Conclusions: Overexpression of eRF3/GSPT1 in intestinal type gastric tumours may lead to an increase in the translation efficiency of specific oncogenic transcripts. Alternatively, eRF3/GSPT1 may be involved in tumorigenesis as a result of its non-translational roles, namely (dis)regulating the cell cycle, apoptosis, or transcription.

The complete sequence of a 9000 bp fragment of the right arm of Saccharomyces cerevisiae chromosome VII contains four previously unknown open reading frames

We report the sequence of a 9000 bp fragment from the right arm of Saccharomyces cerevisiae chromosome VII. Analysis of the sequence revealed four complete previously unknown open reading frames, which were named G7587, G7589, G7591 and G7594 following standard rules for provisional nomenclature. Outstanding features of some of these proteins were the homology of the putative protein coded by G7589 with proteins involved in transcription regulation and the transmembrane domains predicted in the putative protein coded by G7591.

Estudo e desenvolvimento de eléctrodos de superfície para electrocardiografia

Mestrado em Engenharia Electrotécnica e de Computadores – Ramo Automação e Sistemas.

Contribution of different vegetable types to exogenous nitrate and nitrite exposure

This study reports the levels of nitrate and nitrite of 34 vegetable samples, including different varieties of cabbage, lettuce, spinaches, parsley and turnips, collected in several locations of an intensive agricultural area (Modivas, Vila do Conde, northern Portugal). Nitrate levels ranged between 54 and 2440 mg NO-3 kg-1, while nitrite levels ranged between 1.1 and 57 mg NO-2 kg-1. The maximum residue levels established for nitrate in spinach and lettuce samples were not exceeded. Nitrate and nitrite levels reported in the literature for the same type of samples are reviewed, as well as the contribution of vegetables to nitrate and nitrite dietary exposure of populations.

Brewer's spent grain from different types of malt: Evaluation of the antioxidant activity and identification of the major phenolic compounds

The antioxidant activity and phenolic composition of brewer's spent grain (BSG) extracts obtained by microwave-assisted extraction from twomalt types (light and darkmalts) were investigated. The total phenolic content (TPC) and antioxidant activity among the light BSG extracts (pilsen, melano, melano 80 and carared)were significantly different (p b 0.05) compared to dark extracts (chocolate and black types), with the pilsen BSG showing higher TPC (20 ± 1 mgGAE/g dry BSG). In addition, the antioxidant activity assessed by 2,2-diphenyl- 1-picrylhydrazyl, 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) and deoxyribose assays decreased as a result of increasing kilning temperatures in the following order: pilsen N melano N melano 80 N carared N chocolate N black. HPLC-DAD/ESI-MS/MS analysis indicated the presence of phenolic acids, such as ferulic, p-coumaric and syringic acids, as well as several isomeric ferulate dehydrodimers and one dehydrotrimer. Chocolate and black extracts, obtained frommalts submitted to the highest kilning temperatures, showed the lowest levels of ferulic and p-coumaric acids. These results suggested that BSG extracts from pilsen malt might be used as an inexpensive and good natural source of antioxidants with potential interest for the food, pharmaceutical and/or cosmetic industries after purification.

Response surface methodology applied to SPE for the determination of ibuprofen in various types of water samples

Over the last few years, there has been a growing concern about the presence of pharmaceuticals in the environment. The main objective of this study was to develop and validate an SPE method using surface response methodology for the determination of ibuprofen in different types of water samples. The influence of sample pH and sample volume on the ibuprofen recovery was studied. The effect of each studied independent variable is pronounced on the dependent variable (ibuprofen recovery). Good selectivity, extraction efficiency, and precision were achieved using 600 mL of sample volume with the pH adjusted to 2.2. LC with fluorescence detection was employed. The optimized method was applied to 20 water samples from the North and South of Portugal.

Assigning real-time tasks on heterogeneous multiprocessors with two unrelated types of processors

A preliminary version of this paper appeared in Proceedings of the 31st IEEE Real-Time Systems Symposium, 2010, pp. 239–248.