An Enhanced Spatial Reasoning Ontology for Maritime Anomaly Detection

International audienceAlthough originally conceived as a conceptual object for modelling knowledge, current ontologies do not make it possible to manipulate spatial knowledge. However, spatial knowledge is an essential component of any modelling specification. This problem provided the motivation for the creation of an expert system driven by an ontology. The system enables experts in the maritime domain to characterise abnormal ship behaviour based on formal semantic properties. Users are able to specify and execute spatial rules that are directly integrated into the ontology and a map interface linked to the ontology displays the results of the inferences obtained

Estudo da influência de alta pressão hidrostática nas características químicas e sensoriais de vinho

Doutoramento em QuímicaDuring the last years, the use of high hydrostatic pressure (HHP) as a non-thermal technology for preservation or aging of wine has increased substantially in the academic community. However, HHP treated wine has been only analysed after the pressure treatment, with no knowledge available on the effects of HHP during subsequent storage. The results presented in this thesis showed that HHP treatments influence the chemical and sensorial properties of wine during storage. The application of high hydrostatic pressure treatments in winemaking for wine preservation, as an alternative to sulphur dioxide, was evaluated studying the effect of HHP in the physicochemical and sensorial properties of red and white wines during bottle storage. High pressure treatments with 5 min of processing time and pressures of 425 and 500 MPa were shown to influence on both red and white wine physicochemical and sensorial characteristics. However, the effects were only perceptible after, at least, 6 months of storage. The alterations that occurred on the pressurized red wine characteristics, such as the more orange-red colour and the lower antioxidant activity (15-27% less), total phenolic content (9% less), and anthocyanins content (45–61% less), were due to an increase of condensation reactions of phenolic compounds. The increase of these condensation reactions lead to the formation of compounds with higher degree of polymerisation that became insoluble along storage, increasing consequently the amount of wine deposits in the pressurized wines. In terms of white wines, pressurized wines showed, after one year of storage, a more brownish colour and a lower antioxidant activity (15% less) and total content of phenolic compounds (10% less) when compared to the unpressurized wines. These results, together with the lower content of free amino acids (15-20% less) and higher content of furans (up to 70% more), present in the pressurized wines after nine months of storage, led to propose an effect of HHP treatments in the acceleration of Maillard reactions that occur during the wine storage period. Therefore, contrary to the pressurized sulphur dioxide-free red wine, the pressurized white wines were not considered suitable for commercialization as table wines due to the higher brownish colour and cooked fruit aroma, characteristics of an aged or thermally treated wine.Additionally, the impact of the pressure treatments on the volatile composition of sulphur dioxide-free red and white wines, during bottle storage, was evaluated. More than 160 volatile compounds, distributed by 12 chemical groups, were identified in both wines. At the end of storage, the pressurized wines presented a higher content of furans, aldehydes, ketones, and acetals when compared to the unpressurized wines. These results indicate that pressure influences the white and red wine long term volatile composition, being this particularly evident for longer storage periods. The changes on the volatile composition of the pressurized wines, indicated that the HHP treatments accelerate the Maillard reactions, and the oxidation of alcohols and fatty acids, leading to wines with a volatile composition network approaching the characteristic of faster aged and/or thermally treated wines. The acceleration of Maillard reactions and phenolic compounds condensation by HHP treatments was also studied in model wine solutions (hydro alcoholic solution at acidic pH). The results showed that the high pressure treatment accelerated the Maillard reaction and this effect was quantifiable, mainly, after 6 months of storage. Pressurized model solutions presented higher concentration of 2-furfural, phenylacetaldehyde and benzaldehyde, when compared to the controls. In terms of phenolic compounds condensation reactions, the pressurized model wine solutions showed no relevant differences, when compared to controls. Therefore, it seems that the pressure treatment had a higher impact in terms of kineticks of reactions and in less extent in terms of different compounds formed. Lastly, the application of HHP treatments in winemaking to improve the properties of young wines was evaluated. For this propose, the effect of HHP treatments in the phenolic composition of a red wine was studied and compared with the effect of different oenological practices. Wines pressurized at 500 MPa for 5 min, and 600 MPa for 20 min, at 20 ºC, showed, after 5 months of storage, a lower monomeric anthocyanins (8-14%), phenolic acids (8-11%) and flavonols (14-22%) content, when compared to the unpressurized ones. The wine pressurized at 500 MPa presented a flavanols content and a degree of polymerization very similar to the wines treated by traditional aging processes. In terms of sensorial properties, the pressure treatments increased the cooked fruit aroma and decreased the floral and fruit odours and, in the case of the 600 MPa treatment, increased the bitterness. Therefore, the HHP treatments seem to promote reactions that are similar to those observed in wines treated with wood aging processes. In conclusion, the results presented in this thesis showed that HHP treatments accelerated the Maillard reaction and the polymerization reactions between phenolic compounds present in the wine, influencing the chemical and sensorial properties of wine. HHP can be potentially used to preserve or accelerate the wine aging process, producing wines with pleasant and distinct characteristics.Durante os últimos anos, o uso de alta pressão hidrostática (APH) como tecnologia não-térmica para a preservação ou envelhecimento de vinho tem aumentado substancialmente na comunidade académica. No entanto, os vinhos tratados por APH têm sido analisados após o tratamento de pressão, não havendo referências sobre as suas propriedades durante o armazenamento. Os resultados apresentados nesta tese mostram que a aplicação de tratamentos de APH altera as propriedades químicas e sensoriais de vinhos ao longo do armazenamento. Os tratamentos de alta pressão hidrostática foram aplicados na vinificação para a preservação de vinho, como alternativa ao dióxido de enxofre, sendo o seu efeito avaliado nas propriedades físico-químicas e sensoriais de vinhos tintos e brancos durante o armazenamento em garrafa. Os tratamentos de alta pressão com 5 min de processamento e pressões de 425 e 500 MPa mostraram influenciar as características físico-químicas e sensoriais de vinhos tintos e brancos. No entanto, o efeito foi apenas percetível após pelo menos 6 meses de armazenamento. As alterações que ocorreram nas características do vinho tinto pressurizado, tais como a cor mais laranja-vermelho, menor atividade antioxidante (menos 15 a 27%), menor conteúdo de compostos fenólicos totais (menos 9%) e menor teor de antocianinas (menos 45-61%), foram devidas a um aumento das reacções de condensação de compostos fenólicos. O aumento destas reações de condensação levou à formação de compostos com maior grau de polimerização que se tornaram insolúveis no vinho ao longo do armazenamento, aumentando consequentemente a quantidade de depósito nos vinhos pressurizados. Em relação ao vinho branco, os vinhos pressurizados mostraram, depois de um ano de armazenamento, uma cor mais acastanhada, menor atividade antioxidante (menos 15%) e menor teor de compostos fenólicos totais (menos 10%) comparando com os vinhos não pressurizados. Estes resultados, juntamente com o baixo teor de aminoácidos livres (menos 15 a 20%) e um maior teor de furanos (até 70% mais) para os vinhos pressurizados após nove meses de armazenamento, levam a propor que os tratamentos de APH aceleraram as reações de Maillard que ocorrem durante o período de armazenamento do vinho. No entanto, ao contrário dos vinhos tintos pressurizados, os vinho brancos pressurizados não foram considerados adequados para comercialização como vinhos de mesa, visto que apresentavam uma cor acastanhada e um elevado aroma a fruta cozida, características estas de vinhos envelhecidos ou tratados termicamente.Adicionalmente, foi avaliado o impacto dos tratamentos de APH sobre a composição volátil dos vinhos tintos e brancos sem dióxido de enxofre durante o armazenamento em garrafas. Mais de 160 compostos voláteis, distribuídos por 12 grupos químicos, foram identificados em ambos os vinhos. No final do armazenamento, os vinhos pressurizados apresentaram um teor mais elevado de furanos, aldeídos, cetonas e acetais quando comparados com os vinhos não pressurizados. Estes resultados indicam que os tratamentos de APH influenciam a composição volátil de vinhos brancos e tintos, , sendo mais evidente em longos períodos de armazenamento. As mudanças na composição volátil dos vinhos indicaram que os tratamentos de APH aceleraram as reações de Maillard e também a oxidação de álcoois e ácidos gordos, originando vinhos com uma composição volátil próxima de vinhos com envelhecimento acelerado ou tratados termicamente. A aceleração das reações de Maillard e de polimerização dos compostos fénolicos causada pelos tratamentos de APH foi também estudada em soluções modelo de vinho (solução hidroalcoólica com pH ácido). Os resultados mostraram que o tratamento de APH acelera a reação de Maillard , sendo este efeito quantificado, apenas, após 6 meses de armazenamento. As soluções modelo de vinho pressurizadas apresentaram concentrações mais elevadas de 2-furfuraldeído, fenilacetaldeído e benzaldeído, em comparação com os controlos. Em termos de polimerização dos compostos fénolicos, as soluções modelo pressurizadas não apresentaram diferenças relevantes, em comparação com os controlos. Por conseguinte, os tratamentos de APH aparentem ter mais impacto em termos de modificações nas cineticas de reação do que na formação de novos compostos. Por último, a aplicação de tratamentos de APH foi estudada para melhorar as propriedades de vinhos jovens. Para este propósito, o efeito de tratamentos de APH na composição fenólica de um vinho tinto foi estudado e comparado com o efeito de diferentes práticas enológicas. Vinhos pressurizados a 500 MPa durante 5 min e a 600 MPa durante 20 min, a 20 ºC, mostraram depois de 5 meses de armazenamento um menor teor de antocianinas monoméricas (8-14%), ácidos fenólicos (8-11%) e flavonóis (14 -22%), quando comparados com os vinhos não-pressurizados. O vinho pressurizado a 500 MPa apresentou um teor de flavonóis e um grau de polimerização de taninos muito semelhante aos vinhos tratados por processos de envelhecimento tradicionais. Em termos de propriedades sensoriais, os tratamentos de pressão aumentaram o aroma de fruta cozida e diminuiram os aromas florais e frutados, tendo no caso do tratamento de 600 MPa sido verificado também um aumento da amargura. Assim sendo, os tratamentos de APH parecem promover reações que são semelhantes às observadas em vinhos tratados com processos de envelhecimento em madeira. Em conclusão, os resultados apresentados nesta tese mostram que a aplicação de tratamentos de APH acelera as reações de Maillard e a polimerização dos compostos fenólicos presentes no vinho, ao longo do armazenamento, alterando assim as propriedades químicas e sensoriais dos vinhos. A APH pode ser potencialmente utilizada para preservar ou acelerar o processo de envelhecimento de vinho tinto produzindo vinhos com características agradáveis e distintas

BIOFILM PRODUCTION UNDER STATIC AND DYNAMIC CONDITIONS BY GENETICALLY CHARACTERIZED S. AUREUS CAUSING DAIRY COW MASTITIS.

Staphylococcus aureus (S. aureus) biofilm formation has been pointed out as an important factor in the establishment of bovine mastitis, particularly in its chronic form. Biofilm characterization of bovine isolates generally applies static systems and matrices other than milk, which is probably not adequate to access the potential of this bacterial trait in the pathogenesis of mastitis. The objectives of the study were: (1) to investigate the occurrence of biofilm associated genes icaA/D and bap in Italian S. aureus strains; (2) to characterize biofilm formation using a static and a dynamic assay and (3) to look for genetic markers to identify strains capable of biofilm formation in the dynamic system. Out of 112 PCR tested S. aureus strains, 73 (65.18%) carried both icaA and icaD, 2 (1.79%) only icaA, 15 (13.39%) only icaD, 22 (19.64%) were negative for both genes and only 7 (6.25%) carried the bap gene. Biofilm characterization of the same 112 strains using a standard static method (TCP) classified 88 (78.57%) as non-biofilm forming and 24 (21.43%) as biofilm forming. Twelve biofilm-forming and 18 non biofilm-forming strains, selected out of the 112 TCP tested strains, were further characterized by a dynamic, milk flow based assay (MFC). Six strains (20%) formed biofilm in the dynamic system and only a limited number of genes (n= 14), according to microarray results, was statistically related to strain ability to form biofilm in milk. This study indicates that the biofilm-forming potential of S. aureus strains should be critically evaluated and tested applying conditions similar to mammary environment

Interrogation d'un réseau sémantique de documents : l'intertextualité dans l'accès à l'information juridique

A collection of documents is generally represented as a set of documents but this simple representation does not take into account cross references between documents, which often defines their context of interpretation. This standard document model is less adapted for specific professional uses in specialized domains in which documents are related by many various references and the access tools need to consider this complexity. We propose two models based on formal and relational concept analysis and on semantic web techniques. Applied on documentary objects, these two models represent and query in a unified way documents content descriptors and documents relations.Une collection documentaire est généralement représentée comme un ensemble de documents mais cette modélisation ne permet pas de rendre compte des relations intertextuelles et du contexte d'interprétation d'un document. Le modèle documentaire classique trouve ses limites dans les domaines spécialisés où les besoins d'accès à l'information correspondent à des usages spécifiques et où les documents sont liés par de nombreux types de relations. Ce travail de thèse propose deux modèles permettant de prendre en compte cette complexité des collections documentaire dans les outils d'accès à l'information. Le premier modèle est basée sur l'analyse formelle et relationnelle de concepts, le deuxième est basée sur les technologies du web sémantique. Appliquées sur des objets documentaires ces modèles permettent de représenter et d'interroger de manière unifiée les descripteurs de contenu des documents et les relations intertextuelles qu'ils entretiennent

The energy cost of primary metabolism vacuole expansion: central to shape toamto leaf development under ammonium nutrition

231 p.Ammonium (NH4+) is a nitrogen source of great interest in the context of sustainable agriculture. Its application in the field together with nitrification inhibitors has been extensively proven efficient to limit detrimental N losses compared to the use of nitrate (N03). NH4+ is a common intermediate involved in numerous metabolic routes. However, high NH4 concentrations may lead to a stress situation provoking a set of symptoms collectively known as "ammonium syndrome" mainly characterized by growth retardation. Those symptoms are caused by a combination of, among others, a profound metabolic reprogramming, disruption of photosynthesis, pH deregulation and ion imbalance. Numerous studies have described the way plant copes to ammonium nutrition. However, the organ developmental stage has been generally neglected.To fill in this gap, in the first chapter we first aimed studying how the metabolism is adapted in function of the leaf position in the vertical axis of the tomato plants (Solanum lycopersicum) grown with NH4+, N03- or NH4N03 supply. To do so, we dissected leaf biomass composition and metabolism through a complete analysis of metabolites, ions and enzyme activities. The results showed that C and N metabolic adjustment in function of the nitrogen source was more intense in older leaves compared to younger ones. Importantly, we propose a trade-off between NH4+ accumulation and assimilation to preserve young leaves from ammonium stress. Besides, NH4+-fed plants exhibited a rearrangement of carbon skeletons with a higher energy cost respect to plants supplied with N03-. We explain such reallocation by the action of the biochemical pH-stat, to compensate the differential proton production that depends on the nitrogen form provided.Ammonium nutrition may limit cell expansion, suggesting that the cellular processes involved would be altered. Among others, cell growth is largely dependent of the internal pressure exerted on the cell wall by the vacuole. However, the role of the vacuole in ammonium stress has been rarely addressed. In the second chapter, we evaluated the effect of ammonium stress on leaf development with a special focus on vacuole expansion and metabolism. To carry out this aim, we monitored the leaf development from its appearance until its complete expansion in plants grown under NH4+ or NO/ as unique nitrogen source. Cytological analysis evidenced that the reduced cell expansion under ammonium nutrition was associated with smaller vacuole size. Besides, we reported an acidification of the vacuole of NH4+-fed plants compared to nitrate nutrition. Moreover, a model was built to predict the thermodynamic equilibrium of different soluble species across the tonoplast. The model was set up through an extensive reviewing of vacuolar transporters and integrated subcellular volumes, vacuolar electrochemical gradients and the formation of ionic complex in the vacuole to fit the subcellular concentration of ions, organic acids and sugars measured in the leaf. Further, predictions obtained with the model were cross validated with data from non-aqueous fractionation. Firstly, the entrance of solutes was higher in vacuoles of N03--fed leaves but was not associated with higher vacuolar osmolarity likely because of the adjustment of the vacuolar volume. In this sense, we proposed that the lack of malate in cells of ammonium-fed leaves was central in the limitation of vacuolar expansion. Secondly, we conclude that the energy cost of solute transport into the vacuole is higher under NH4+ based nutrition because of the higher electrochemical gradient generated by the proton pumps across tonoplast.This work highlights the importance of considering leaf phenological state when studying nitrogen metabolism. In addition, our integrated approach place cytosolic pH control and vacuole expansion in the center of tomato leaf adaptation to ammonium stress and pave the way for future studies in the field of ammonium nutrition

Intellektipuude genoomsed põhjused: kogu-genoomi SNP genotüpiseerimisanalüüs Eesti patsientidel ja üldpopulatsioonis

Väitekirja elektrooniline versioon ei sisalda publikatsioone.Intellektipuue on raske arenguhäire, mis arenenud riikides esineb ligikaudse sagedusega 2% üldpopulatsioonist. Intellektipuude tekkepõhjused võivad olla väga erinevad ning ligi pooltel patsientidest on häire põhjus jäänud koguni teadmata. Viimastel aastatel teaduses kasutusele võetud kogu-genoomi analüüsimeetodid on näidanud, et inimgenoomis esinevad laialdaselt DNA koopiaarvu variatisoonid (CNV) - kromosoomsegmendid, mille koopiate arv on ümberkorralduse tõttu genoomis tavapärasest suurem või väiksem. On leitud, et CNV-d võivad olulisel osal patsientidest vastutada intellektipuude ja teiste kaasasündinud arenguhäirete eest ning olla riskifaktoriks erinevate komplekshaiguste kujunemisel. Samas esinevad CNV-d ka (näiliselt) tervetel inimestel, mis muudab nende kliinilise tähtsuse hindamise sageli keeruliseks ning enamuse CNV-de mõju inimese tervisele ja arengule on praegusel ajal veel ebaselge. Käesolev töö on esimene ulatuslik uurimus CNV-de haigusseoselisest rollist intellektipuudega Eesti perekondades. Kuna rea genoomsete muutuste puhul võib nende mõju haigustunnuste avaldumisele olla varieeruv, teostati CNV-de täpsema rolli analüüsimiseks sama uuring ka Tartu Ülikooli Eesti Geenivaramu geenidoonoritele. Töö tulemusena leiti 18 peres intellektipuuet põhjustav CNV ehk geneetiline diagnoos määrati 23% uuritud patsientidest, kellel seni oli nende haiguse põhjus teadmata. Eesti Geenivaramu geenidoonorite hulgast leiti neuropsühholoogiliste häiretega seotud CNV-d 19 indiviidil. Vastavalt Eesti Geenivaramu küsimustikule on enamus neist inimestest kannatanud aastaid erinevate tervisehäirete (näiteks tugev rasvumine, epilepsia, kõnearengu häired, depressioon, teised neuroloogilised ja psühhiaatrilised probleemid) teadmata, et nende genoomis esineb vastavate haiguste riski suurendavaid variatsioone. Samuti oli uuringuandmetel oluline roll kahe kromosoomregiooniga, 7q11.23 ja 16p11.2, seotud uute genoomsete sündroomide iseloomustamisel. Kokkuvõtlikult näitas käesolev uuring CNV-de olulist rolli neuropsühholoogiliste häirete kujunemisel ning genoomse analüüsi efektiivsust teaduses ja diagnostikas.Intellectual disability (ID) is a neurodevelopmental disorder with a population prevalence of approximately 2% and high socio-economical burden on the patients’ families and the society. Due to the heterogeneous aetiology of ID, disease-causative factors have remained unknown in about half of patients with cognitive impairment. Over the recent years, the biotechnological progress in human genomics has enabled a whole-genome approaches to study the genetic background of diseases and revealed small chromosomal gains and losses - DNA copy number variations (CNVs) - as one of the major contributors to the aetiology of developmental disorders. However, these CNVs can also be harmless variants in the human genome or act as susceptibility factors for common diseases and phenotypic traits. Moreover, numerous CNVs initially detected in patients with brain-related disorders also occur with lower frequency in apparently normal individuals. Thus, challenging the assessment of the consequence of CNVs on individual’s health and development. The current study was the first comprehensive effort to investigate genomic causes of cognitive impairment and associated complex phenotypes in Estonian patients with unexplained ID and general population individuals. As a result of the study, genetic diagnosis was established in 18 investigated families (the diagnostic yield of 23%) and rare CNVs of neuropsychological relevance were found in 19 Estonian general population individuals. By participating in collaborative investigations, the core clinical features were established for novel genomic disorders associated with regions 7q11.23 and 16p11.2 in the human genome. In summary, the results of this study demonstrated the importance of rare CNVs in the aetiology of neurodevelopmental disorders and proved that whole-genome screening for genomic rearrangments is an effective tool in research and diagnostics