Video Registration in Egocentric Vision under Day and Night Illumination Changes

With the spread of wearable devices and head mounted cameras, a wide range of application requiring precise user localization is now possible. In this paper we propose to treat the problem of obtaining the user position with respect to a known environment as a video registration problem. Video registration, i.e. the task of aligning an input video sequence to a pre-built 3D model, relies on a matching process of local keypoints extracted on the query sequence to a 3D point cloud. The overall registration performance is strictly tied to the actual quality of this 2D-3D matching, and can degrade if environmental conditions such as steep changes in lighting like the ones between day and night occur. To effectively register an egocentric video sequence under these conditions, we propose to tackle the source of the problem: the matching process. To overcome the shortcomings of standard matching techniques, we introduce a novel embedding space that allows us to obtain robust matches by jointly taking into account local descriptors, their spatial arrangement and their temporal robustness. The proposal is evaluated using unconstrained egocentric video sequences both in terms of matching quality and resulting registration performance using different 3D models of historical landmarks. The results show that the proposed method can outperform state of the art registration algorithms, in particular when dealing with the challenges of night and day sequences

Genome editing to be applied in functional characterization of genetic variants in familial breast cancer patients

RESUMO: O cancro da mama (CM) familiar representa 15% de todos os casos de CM, estando principalmente relacionado a variantes hereditárias nos genes BRCA. Vários genes ligados ao CM estão sobretudo relacionados com a Recombinação Homóloga (RH), a principal via de reparação de quebras de cadeia-dupla de DNA. A presença de variantes genéticas nestes genes, como o BRCA1 e BRCA2, pode comprometer a RH e consequentemente o desenvolvimento da doença. No cancro da mama familiar, o aconselhamento genético e a triagem através de testes genéticos têm se tornado padrão, aumentando a deteção de variantes de significado desconhecido (VUS). O efeito biológico atribuído às VUS é pouco claro, sendo necessários ensaios funcionais para caracterizar o seu significado clínico. Num estudo anterior, uma VUS foi identificada no gene BRCA1 em pacientes saudáveis, mas com histórico familiar de cancro relevante. Para estudar a sua relevância funcional, implementamos um modelo in vitro com linhas celulares de mama (MCF10-A e MCF-7) para introduzir a VUS de interesse com uma ferramenta de edição genómica, CRISPR-Cas9 e avaliar a resposta celular através de um desafio genotóxico com doxorrubicina (DOX). Introduzimos com sucesso a VUS como clone heterozigoto nas MCF10-A. Várias metodologias foram selecionadas para avaliar e comparar a resposta celular às lesões genéticas: ensaios do Cometa, ɣ-H2AX e Anexina V. Adicionalmente, avaliamos a expressão relativa da proteína através de Western Blot. Os resultados do ensaio do cometa mostram uma diminuição da sensibilidade à DOX no MCF10-A VUS, porém, no ensaio ɣ-H2AX, observamos um maior % de quebras e cadeia-dupla. Na Anexina V, o MCF10- A VUS apresentou menor % de células em necrose. Por último, a expressão da proteína BRCA1 encontra-se diminuída nas MCF10-A VUS. No geral, os resultados mostram uma diminuição da suscetibilidade à DOX para a linha celular com a VUS, sugerindo um efeito benigno. No entanto, são necessários mais ensaios funcionais para entender o seu papel no risco de cancro.ABSTRACT: Familial breast cancer (BC) is responsible for 15% of all BC cases being mainly linked to inherited variants in BRCA genes. Several genes associated with BC are mostly related to Homologous Recombination (HR), the main pathway to repair DNA double-strand breaks. The occurrence of genetic variants in these genes, such as BRCA1 and BRCA2, might compromise the HR, thus the development of disease. In familial breast cancer the genetic counselling and the screening through genetic testing has been widespread increasing detection of variants of unknown significance (VUS). The biologic effect attributed to those VUS is mostly unclear, so functional assays need to be performed to characterize their mutational status. In a previous study a VUS was identified in the BRCA1 gene in healthy patients but with a relevant familial history of cancer. To study its functional relevance, we implemented an in vitro model using breast cell lines (MCF10-A and MCF-7). to introduce the VUS of interest with a genome editing tool, CRISPR-Cas9 and assess the cellular response through a genotoxic challenge with doxorubicin (DOX). We successfully established MCF10-A heterozygous clone for the VUS. Several methodologies were selected to evaluate and compare the cellular response to genetic lesions: Comet, ɣ-H2AX and Annexin V assays. Also, we assessed the protein relative expression using Western Blot. The comet assay results showed a decreased sensitivity to DOX in MCF10-A VUS, yet, in ɣ-H2AX assay, we observed a higher % DSB. In Annexin V, MCF10-A VUS showed lower % of cells in necrosis. Lastly, the expression of BRCA1 protein was decreased in MCF10-A VUS. Overall, the results show a decreased susceptibility to DOX for the VUS cell line, suggesting a benign behaviour. Nonetheless more functional assays need to be performed to understand their role on cancer risk

Penicillium astrolabium and penicillium neocrassum, two new species isolated from grapes and their phylogenetic placement in the P. olsonii and P. brevicompactum clade

We describe two new terverticillate Penicillium species isolated from grapes on the basis of phenotypic and phylogenetic differences from known species. The strains were isolated in the course of a study to establish the mycobiota of grapes in Portugal. Penicillium astrolabium is phenotypically similar to P. olsonii but differs from it by two cultural characters, growth rates and the colony reverse color. P. neocrassum is similar to P. brevicompactum but is readily distinguished by sclerotia production. Phylogenetically P. astrolabium and P. neocrassum are placed respectively in the P. olsonii and P. brevicompactum clade. Multilocus analysis confirmed the genetic distinctiveness of both species. The parsimony trees obtained for ITS-lsu rDNA region and two protein coding genes, calmodulin and b-tubulin, show congruence for all the species in the Olsonii series: P. brevicompactum, P. bialowiezense, P. olsonii, P. astrolabium and P. neocrassum, indicating that these taxa are genetically well isolated.Fundação para a Ciência e a Tecnologia (FCT

Propagation and Molecular Characterization of Chlamydia trachomatis strains isolated in Portugal

Chlamydia trachomatis é uma bactéria intracelular que infeta exclusivamente o Homem. Constitui o principal agente etiológico bacteriano de infeções sexualmente transmissíveis e, na ausência de tratamento, pode evoluir para complicações clínicas graves, como a infertilidade tubária. C. trachomatis foi classificada em 15 genótipos, os quais causam preferencialmente infeções oculares (A-C), infeções genitais (D-K) ou linfogranuloma venéreo (LGV) (L1-L3). A tipagem das estirpes de clamídia baseia-se na principal proteína da membrana externa (MOMP) codificada pelo gene ompA. O estudo do genoma de C. trachomatis tem permitido identificar diferenças genéticas entre estirpes; no entanto, os mecanismos de adaptação e virulência não estão ainda bem definidos mas, tal tem sido observado noutras bactérias, podendo decorrer de mecanismos de variação de fase. No presente estudo foi realizada a tipagem de 278 amostras clínicas com base na sequência do gene ompA, através de técnicas de nested-PCR, de sequenciação pelo método de Sanger e de análise de similaridades das sequências obtidas relativamente a sequências de estirpes protótipo de C. trachomatis; tal processo possibilitou identificar variantes genotípicas previamente descritas assim como novas variantes, sugerindo a existência de um contínuo processo de adaptação na bactéria. Os genótipos mais frequentes foram o E, D e F, tal como descrito na maioria dos estudos em populações heterossexuais femininas; contudo um número apreciável (26) de estirpes do genótipo L2 foi igualmente detetado, em particular em amostras anorretais masculinas, o que está igualmente de acordo com o descrito em populações de homens que têm sexo com homens. Tal constatação revela a necessidade de um método de identificação expedita dos genótipos LGV, pelo que contribuímos para a implementação de uma metodologia mais rápida que a tradicional genotipagem-ompA. Pretendemos ainda contribuir para a avaliação da virulência das estirpes de C. trachomatis e para tal, realizamos um estudo preliminar de identificação de potenciais alvos genéticos sujeitos a variação de fase, com recurso à sequenciação de nova geração (NGS). Este estudo constitui um contributo para a vigilância epidemiológica das infeções por C. trachomatis em Portugal, uma situação pouco conhecida, um contributo para a celeridade da identificação de casos de LGV e um contributo para a avaliação da virulência das estirpes de C. trachomatis, pela identificação de alterações em genes potencialmente relacionados com a variação de fase.Chlamydia trachomatis is an intracellular bacterium that exclusively infects humans. It is the main bacterial etiological agent of sexually transmitted infections and, in the absence of treatment, may lead to serious clinical complications such as tubal infertility. C. trachomatis was classified into 15 genotypes, which preferentially cause ocular infections (A-C), genital infections (D-K) or lymphogranuloma venereum (LGV) (L1-L3). Typing of chlamydial strains is based on the major outer membrane protein (MOMP), which is encoded by the ompA gene. The study of the genome of C. trachomatis allowed identifying genetic differences between strains, and although the mechanisms of adaptation and virulence still require proper definition, these mechanisms may derive from mechanisms of phase variation, as has been observed in other bacteria. In the present study, 278 clinical samples were typed based on their ompA gene sequence, determined by using a nested-PCR technique, Sanger method sequencing and gene sequence similarity analysis regarding the ompA-sequence of C. trachomatis prototype strains. This procedure allowed to identify genotypic variants previously described, as well as new variants, suggesting the existence of a continuous process of adaptation in the bacterium. The most frequent genotypes in our study were E, D and F; this finding is in accordance to the described in most of the studies held in female heterosexual populations. However, an appreciable number (26) of L2 strains was also detected, in particular in male anorectal samples, which is an in agreement with the described for men who have sex with men. The number of L2 strains reveals the need for an expeditious LGV-genotype identification method. Thus, we contributed to the implementation of a methodology that should provide faster identification of LGV strains in comparison to the traditional ompA-genotyping. We also intended to contribute to the evaluation of the virulence of C. trachomatis strains and for this, we participated in a preliminary study of identification of potential genetic targets subjected to phase variation, using a new generation sequencing (NGS) approach This study contributes to the epidemiological surveillance of C. trachomatis infections in Portugal, a poorly known situation, contributes to a faster identification of LGV cases, and contributes to the evaluation of virulence of C. trachomatis strains by identifying changes in genes potentially related to phase variation

Fungi and ochratoxin A detected in healthy grapes for wine production

Aims: The mycoflora of healthy grapes (i.e. without visible symptoms of rot) for wine production in Portuguese winemaking regions was assessed and its potential for ochratoxin A (OTA) production evaluated. The OTA content of grapes was also determined. Methods and Results: A total of 386 fungal strains were isolated by plating methods. The most frequent genera found in grapes were non-ochratoxigenic species: Cladosporium (28%), Penicillium (24%), Botrytis (13%) and Aspergillus (9%). Two OTA-producing strains were isolated, belonging to the species Aspergillus carbonarius and Aspergillus ochraceus. OTA was detected in three of four grape samples, up to 116 ng lֿ¹. Conclusions: OTA is being produced in healthy berries by Aspergillus species, namely A. carbonarius, at levels below the maximum recommended limit of 2000 ng lֿ¹ in wine. Significance and Impact of the Study: The OTA concentration detected in healthy Portuguese grapes does not represent a risk to wine regarding the legal limit established.EC, Quality of Life Program (QoL), Key Action 1 (KA1) on Food, Nutrition and Health; Fundação para a Ciência e a Tecnologia (FCT

Biodegradation of Ochratoxin A by fungi isolated from grapes

Ochratoxin A is a mycotoxin present in several food products for which levels should be reduced. Chemical, physical, and biological methods have been proposed for the detoxification of mycotoxins, biological methods being the more promising ones. In this report, filamentous fungi isolated from Portuguese grapes were assessed for ochratoxin A degradation capabilities. It was observed that 51 of the 76 tested strains, predominantly aspergillus species, were able to degrade more than 80% of ochratoxin A added to the culture medium and that the most potent species (more than 95% of initial amount) were the black aspergilli, A. clavatus, A. ochraceus, A. versicolor, and A. wentii. Other fungi frequently isolated from grapes, such as Alternaria, Botrytis, Cladosporium, and Penicillium, also showed significant degradation capabilities. It was observed that the compounds obtained from the degradation of ochratoxin A by black aspergilli and by A. ochraceus and A. wentii strains were different.Fundação para a Ciência e a Tecnologia (FCT) - grant SFRH/ BD/1436/2000.Comunidade Europeia (CE) - Quality of Life Program (QoL), Key Action 1 (KA1) on Food, Nutrition and Health; contract number QLK1-CT-2001-01761-Wine-Ochra Risk

Egocentric Video Summarization of Cultural Tour based on User Preferences

In this paper, we propose a new method to obtain customized video summarization according to specific user preferences. Our approach is tailored on Cultural Heritage scenario and is designed on identifying candidate shots, selecting from the original streams only the scenes with behavior patterns related to the presence of relevant experiences, and further filtering them in order to obtain a summary matching the requested user's preferences. Our preliminary results show that the proposed approach is able to leverage user's preferences in order to obtain a customized summary, so that different users may extract from the same stream different summaries

Ochratoxin A occurrence and formation in Portuguese wine grapes at various stages of maturation

A total of 93 Portuguese grape samples destined for wine production were examined for the presence of ochratoxin A (OTA) and the OTA producing fungi Aspergillus carbonarius and A. niger aggregate. Samples came from 11 vineyards from four winemaking regions in the North and South of the Portuguese mainland, during the harvest seasons of 2001, 2002 and 2003. Grapes were examined at 3 maturation stages, from setting to the harvesting period, to evaluate when contamination with OTA producing fungi and OTA synthesis occur. The detection of fungi in grape samples was made by plating methods with and without surface disinfection. OTAwas formed by 14% of the 650 isolates tested. Most of the OTA producing strains (96%) were isolated at harvest time. At this stage, the percentage of grape samples with OTA producing strains detected without surface disinfection was 56%. With surface disinfection, A. carbonarius was isolated from 10% of the samples. OTAwas detected in grapes at the 3 maturation stages. The average OTA concentrations in 60 samples at pea berry (28 samples), early veraison (22 samples) and ripe berry (20 samples) were 263, 149 and 35 ng/kg, respectively. Experiments with an A. carbonarius strain demonstrated that OTA production differs significantly with the composition of the berries at different maturation stages (P<0.001), with a mean value of OTA production at pea berry, early veraison and ripe berry of 3402, 1530 and 22 μg/kg, respectively. The production of OTA by A. carbonarius was correlated positively and negatively with the total acidity of grapes (rs=0.855, P<0.001) and reducing sugars content (rs=−0.835, P<0.001), respectively. Our data demonstrate that OTA synthesis in grapes occurs since early maturation stages.The EC Quality of Life Programme (QoL), Key. Action 1 – Food, Nutrition & Health.Fundação para a Ciência e a Tecnologia (FCT) - grant SFRH/BPD/2827/2004