Submitted by Geandra Rodrigues (geandrar@gmail.com) on 2018-03-27T12:00:11Z No. of bitstreams: 0 / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2018-03-27T13:49:39Z (GMT) No. of bitstreams: 0 / Made available in DSpace on 2018-03-27T13:49:39Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-03-02 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / O queijo Minas Frescal (QMF) representa um dos queijos mais consumidos no Brasil. Diversos fatores do seu processamento influenciam suas características microbiológicas, e consequentemente, sua qualidade e propriedades organolépticas. Seu alto teor de umidade e os riscos de contaminação durante a cadeia produtiva favorecem a ocorrência de microrganismos contaminantes, muitas vezes apresentando resistência aos antimicrobianos. Dessa forma, do ponto de vista da segurança alimentar e frente ao crescente fenômeno da resistência bacteriana às drogas, torna-se importante a investigação sobre a estrutura da comunidade bacteriana em QMF, bem como a avaliação da ocorrência de marcadores genéticos microbianos relacionados à resistência a drogas e seu potencial de mobilização. Neste estudo foram obtidas 5 amostras de um mesmo lote de 7 marcas de QMF identificadas de A a G, totalizando 35 amostras. Após a extração de DNA total microbiano das amostras, foram utilizadas abordagens de DNA fingerprint, pela amplificação de sequências palindrômicas extragênicas repetitivas (rep-PCR) para avaliação comparativa da similaridade da estrutura global da comunidade bacteriana. Posteriormente, PCR-DGGE foi utilizada para avaliar o perfil e a riqueza das amostras com relação a grupos de bactérias láticas. Matrizes de similaridade foram obtidas utilizando o método de agrupamento UPGMA. Os resultados obtidos pela técnica de rep-PCR revelaram que as amostras de queijos foram claramente agrupadas de acordo com as suas respectivas marcas. Além disso, perfis semelhantes entre amostras de marcas diferentes foram observados, indicando a presença de um núcleo microbiano comum. As amostras avaliadas também foram agrupadas de acordo com suas respectivas marcas de fabricação de acordo com os padrões de DGGE obtidos para bactérias láticas. A elevada similaridade entre a maioria das amostras do mesmo lote obtida nas técnicas de fingerprint sugere a reprodutibilidade e aplicabilidade das técnicas, e controle no processamento dos queijos ao longo da cadeia produtiva. Para a avaliação do resistoma clínico, a presença de 40 marcadores de resistência a diferentes classes de antibióticos foi avaliada por reação de PCR. Um núcleo comum de marcadores genéticos em todas as marcas foi detectado, associado à resistência aos beta-lactâmicos, tetraciclinas, quinolonas e sulfonamidas. Outros marcadores, incluindo aqueles relacionados a bombas de efluxo e resistência aos aminoglicosídeos, também foram observados. Integrons de classes 1 e 2 foram detectados, respectivamente, em 77% e 97% das amostras. As diferentes amostras de QMF puderam ser agrupadas de acordo com seu perfil de marcadores genéticos de resistência aos antimicrobianos, o que sugere epidemiologia peculiar que pode estar relacionada a qualidade e aos níveis de contaminação dos queijos ao longo da cadeia produtiva. Em conjunto, os dados sugerem que embora a cadeia produtiva do QMF seja controlada na indústria, riscos sanitários são inerentes pela contaminação dos queijos por bactérias putativas resistentes a antimicrobianos. Como um todo, os dados apontam para a necessidade de discussão dos parâmetros de qualidade microbiológica na produção, armazenamento e distribuição de QMF. Além disso, a detecção de integrons de classe 1 e 2 levanta questões a respeito do potencial de transferência horizontal de genes de resistência para a microbiota humana através do consumo destes alimentos. / Minas Frescal cheese (QMF) represents one of the most consumed cheeses in the country. Several factors of its processing influence its microbiological characteristics, and, consequently, its quality and properties. Its high moisture content and the risks of contamination during the production chain favor the occurrence of contaminating microorganisms, often presenting antimicrobial resistance. Thus, from the point of view of food safety and the growing phenomenon of bacterial resistance to drugs, it is important to investigate the structure of the bacterial community in Minas Frescal cheese, as well as the evaluation of the occurrence of microbial genetic markers related to drug resistance and its potential for mobilization. In this study 5 samples from the same batch of 7 brands of Minas Frescal cheeses were identified from A to G, totaling 35 samples. After the extraction of total DNA from the samples, DNA fingerprint approaches were used, by the amplification of repetitive extragenic palindromic sequences (rep-PCR) to evaluate the similarity of the global structure of the bacterial community. Afterwards, PCR-DGGE was used to evaluate the profile and richness of the samples in relation to groups of lactic bacteria. Similarity matrices were obtained using the UPGMA clustering method. The results obtained by the rep-PCR technique revealed that the cheese samples were clearly brand-clustered. In addition, similar profiles among samples of different brands were observed, indicating the presence of a common microbial nucleus. The evaluated samples were also separated according to their respective manufacturing brands by the DGGE for lactic acid bacteria. The high similarity among the majority of the samples from the same batch obtained in the fingeprint techniques suggests the reproducibility and applicability of the techniques, and control in the cheese processing along the production chain. For the evaluation of clinical resistance, the presence of resistance markers to different classes of antibiotics was evaluated by PCR reaction. A common core of genetic markers was detected, associated with resistance to beta-lactams, tetracyclines, quinolones and sulfonamides. Other markers, including those related to efflux pumps and aminoglycoside resistance, have also been observed, but not in all brands. Integrons of classes 1 and 2 were detected, respectively, in 77% and 97% of the samples. The different QMF samples could be grouped according to their profile of genetic markers of antimicrobial resistance, which suggests peculiar epidemiology that may be related to the quality and levels of contamination of the cheeses along the production chain. Taken together, the data suggest that although the productive chain of QMF is controlled in the industry, health risks are inherent in the contamination of cheeses by putative antimicrobial resistant bacteria. As a whole, the data point to the need to discuss the parameters of microbiological quality in the production, storage and distribution of QMF. In addition, the detection of class 1 and 2 integrons raises questions about the potential for horizontal transfer of resistance genes to the human microbiota through the consumption of these foods.

Kritickým prvkem biometrického systému pro rozpoznávání otisků prstů je proces snímání. Kvalita snímku totiž ovlivňuje všechny další části systému počínaje zpracováním obrazu, přes extrakci rysů až po samotné rozhodnutí. Přestože bylo navrženo několik metod určování kvality snímku, chybějící formální specifikace kvality otisku nedovoluje ověřit jejich přesnost. Tato diplomová práce se zabývá hodnocením metod určujících kvalitu biometrického signálu otisku prstu. Popisuje jednotlivé faktory ovlivňující kvalitu spolu se současnými přístupy používanými pro její odhad. V práci je rovněž vysvětlena evaluační technika navržená za účelem porovnání schopnosti jednotlivých metod předpovědět výkon biometrického systému. Několik metod pro odhad kvality bylo implementováno a ohodnoceno touto technikou.

This master's thesis deals with proposal and implementation of system for detection of fingerprint area in image. The first task was to elaborate the theory which is necessary for understanding the image fingerprint area detection problems. It is also necessary to propose a specific system for image fingerprint area detection where it is possible to enhance or improve present methods or design a new one. The proposed system making use of selected method will be able to avoid all problems arising during fingerprint area detection. Description of proposed system implementation and testing on the fingerprint database is described in following part. In last part all the achieved results are discussed.

The thesis deals with design and implementation of a tool for simulating marks of chosen skin diseases into a synthetic fingerprint. The diseases selected to work with are warts and atopic eczema. The marks of diseases are generated into a synthetic fingerprint image created by the SFinGe application. Existing disesase-affected fingerprints from the STRaDe database are analysed in detail. Then, methods for simulating the diseases into a synthetic fingerprint are proposed, implemented, and the results are evaluated.

Les empreintes papillaires sont principalement utilisées à des fins d'identification par les forces policières, chez les individus vivants et décédés. Dans les contextes forensiques, l'étendue de la conservation/décomposition de restes peut avoir un impact sur la capacité de restaurer et prélever les empreintes papillaires, et par conséquent, sur les méthodes utilisées. L’application de ces méthodes sur le terrain (p. ex. en cas de catastrophes de masse ou fosses communes) ne peut pas compter sur les mêmes installations/ressources de laboratoire, et nécessite des adaptations pratiques. Ce travail de recherche représente la première application et comparaison dans un cadre expérimental des méthodes de restauration et prélèvement des empreintes papillaires à partir de restes humains en décomposition dans des conditions contrôlées au Québec. Deux essais ont été menés sur quatre donneurs au site de Recherche en Sciences Thanatologiques Expérimentales et Sociales (REST[ES]); un à l’été 2021 et un à l’automne/hiver 2021-2022. Au total, cinq méthodes existantes de restauration et trois méthodes de prélèvement, développées sous d'autres climats, ont été expérimentées. Les résultats ont montré que les méthodes pouvaient être adaptées pour une application sur le terrain, de manière simple, rapide et économique. Les restaurations et prélèvements après l'hiver ont été réalisées de façon moins invasive et destructrice qu'en été, où des variables incontrôlables ont limité leur application. Basé sur ces résultats, deux outils ont été développés pour soutenir la prise de décision des praticiens du Québec (Canada) lors du choix des méthodes à prioriser dans les cas réels forensiques. / Fingerprints are primarily used for identification purposes by law enforcement, for both living and deceased individuals. In forensic contexts, the extent of preservation or decomposition of remains can impact the ability to restore and collect fingerprints, and subsequently the methods used. Additionally, implementation of these methods in the field in cases of mass disasters or mass graves cannot rely on laboratory facilities and resources, and therefore require practical adaptations. This research work represents the first application and comparison in an experimental setting of fingerprints restoration and collection methods from decomposing remains under controlled conditions in Quebec. Two trials were conducted on four donors at the site for Research in Experimental and Social Thanatology (REST[ES]); one in summer 2021 and one in fall/winter 2021-2022. In total, five existing restoration methods and three collection methods, developed in other climates, were tested. Results showed that fingerprint restoration and collection methods could be adapted for practical applications in real forensic contexts, in a simple, rapid, and cost-effective way. Fingerprints restorations and collections after winter were achieved in less invasive and destructive manners than in summer, where uncontrollable variables limited their application. Based on these results, two tools have been developed to support the decision-making of forensic practitioners in Quebec (Canada) when choosing which methods to prioritize in real forensic cases.

The objective of the proposed research is the design and fabrication of a novel stand-alone wireless robust system with enhanced hardware-enabled authentication and anti-counterfeiting capabilities. The system consists of two major components; the near-field certificates of authenticity (CoA), which serve as authenticity vouchers of the products they are attached to, and a microcontroller-enabled, low-power and low-cost reader. Small-sized passive physical three-dimensional structures that are composed of extremely cheap conductive and dielectric materials are shown to yield a unique and repeatable RF signature in a small portion of the frequency spectrum when brought in the reactive and radiating near-field regions of an array of miniature antennas. The multidimensional features of these CoAs, or in other words their signature or fingerprint, are cryptographically signed and digitally stored. The contactless signature validation procedure, in which an attempt to associate the near-field signature response of the physical CoA with the digitized signature, is carried out by the reader designed and fabricated. This low-cost reader operates autonomously and in an offline fashion. The feasibility and performance robustness of the system, in terms of accuracy, consistency and speed of capturing of the signatures, is rigorously assessed with a wide array of tests. Moreover, the entropy, or uncertainty, of the signatures generated by the system are empirically quantified and verified to achieve a virtually impossible false alarm. The aforementioned characteristics of the realized authentication system make it applicable to a vast array of physical objects that needs protection against counterfeiters.

Doctor of Philosophy / Department of Computing Science / David Gustafson / The web is no longer composed of static resources. Technology and demand have driven the web towards a complex, dynamic model that tailors content toward specific client fingerprints. Servers now commonly modify responses based on the browser, operating system, or location of the connecting client. While this information may be used for legitimate purposes, malicious adversaries can also use this information to deliver misinformation or tailored exploits. Currently, there are no tools that allow a user to detect when a response contains tailored content. Developing an easily configurable multiplexing system solved the problem of detecting tailored web content. In this solution, a custom proxy receives the initial request from a client, duplicating and modifying it in many ways to change the browser, operating system, and location-based client fingerprint. All of the requests with various client fingerprints are simultaneously sent to the server. As the responses are received back at the proxy, they are aggregated and analyzed against the original response. The results of the analysis are then sent to the user along with the original response. This process allowed the proxy to detect tailored content that was previously undetectable through casual browsing. Theoretical and empirical analysis was performed to ensure the multiplexing proxy detected tailored content at an acceptable false alarm rate. Additionally, the tool was analyzed for its ability to provide utility to open source analysts, cyber analysts, and reverse engineers. The results showed that the proxy is an essential, scalable tool that provides capabilities that were not previously available.

This thesis is a critical analysis of the processes, concepts and imagery of my artwork. In my art, I intended to explore death anxieties, individuality and the uncanny. I am interested in what we leave behind after we are gone as proof of existing post mortem. My themes include procreation, forensic science, and religion among others. My imagery includes fragmented bodies, reliquaries, and forensic evidence. I use traditional and non-traditional sculpture materials and processes that are intended to conceptually inform the viewer further.

Les techniques de micromanipulation de molécules d’ADN uniques offrent des perspectives nouvelles pour lire et exploiter l’information contenue dans les génomes. Cela inclut le séquençage, la cartographie, le dénombrement de molécules et l'identification de modifications chimiques de l'ADN. Dans ce contexte, l'Équipe ABCDLab de l'ENS a développé une méthode utilisant l’ouverture et la fermeture mécanique répétée d’une molécule d’ADN en épingle à cheveux par pince magnétique. Cet outil permet de déterminer la position d'hybridation de petits oligonucléotides ainsi que celle d'anticorps révélant la position de marques épigénétiques. Un avantage de cette approche est de pouvoir travailler sur la même molécule pour d’une part identifier les marques épigénétiques et d'autre part réaliser une cartographie de sa position dans le génome. Mon travail de thèse consiste à développer un ensemble de méthodes bio-informatique visant à réaliser cette étape de cartographie. Le signal expérimental consiste en lecture des positions d’hybridation d’un, ou de plusieurs petits oligonucléotides sur la molécule étudiée. Cette mesure permet de construire une signature spécifique de la molécule que l’on peut rechercher dans le génome d’origine. Dans ce travail de thèse, j'ai réalisé des expériences avec sur pinces magnétiques pour acquérir des signatures moléculaires sur des molécules sélectionnées en aveugle dans E. coli. J'ai développé un logiciel capable de faire la recherche de ces signatures dans un génome et ensuite effectué l’ensemble du traitement des données pour tester le logiciel. Après plusieurs étapes d’optimisation, j’ai pu retrouver la position génomique des molécules étudiées, établissant ainsi une preuve de concept de cette stratégie de cartographie. Le travail a concerné l'ensemble de la chaîne de mesure : (1) le choix des sondes utilisées pour constituer la signature d’une molécule observée en optimisant un ensemble de critères liés aux conditions expérimentales et à la combinatoire des motifs de séquence. (2) la mise au point d’algorithmes de cartographie adaptés aux caractéristiques expérimentales des mesures. Enfin, j'ai testé ces algorithmes, à la fois sur des données simulées in silico et in vitro sur de l'ADN d'origine bactérienne. Je discuterais en quoi les performances des solutions de cartographie développées ici sont influencées par, d’une part les limites du montage expérimental actuel, et d’autre part les limites des approches bioinformatiques. Je présenterais les voies d’amélioration possibles de ces dernières. Mes travaux établissent qu'identifier des molécules d’ADN uniques par pinces magnétiques est possible dans le contexte d’application épigénétique et en génomique. / Single molecule micromanipulations technic offer new perspectives to read and unravel genome information. This includes sequencing, mapping, molecule counting and identification of DNA modifications. In this respect, ABCDLab team has developed a cutting edge method using repeated mechanical opening and closing of a DNA molecule with a hairpin shape using magnetic tweezers. This tool allows measuring along the DNA molecule the hybridization positions of oligonucleotides a few bases long and also to locate specific antibodies transiently bound to epigenetic markers. With this approach we can identify with the single molecule level epigenetics markers and localized them on the genome. My PhD work consisted of developing a set of bioinformatics methods to perform DNA mapping using magnetics tweezer signal consisting of hybridization positions along the studied molecule. This measurement may be viewed as a fingerprint of the molecule which can be searched on the reference genome. During my thesis, I have realized an experimental test using magnetic tweezers to acquire a set fingerprint data on a set of blinded selected molecules in the E. coli genome. I have developed a software performing a rapid search of these fingerprints inside the genome. Then I have performed the whole data treatment to check the software on the selected molecules. After several rounds of optimization, I have recovered the genetic position of the studied molecules, establishing a proof of concept of this cartography strategy. The work has addressed the whole measuring chain; (1) by choosing the oligonucleotides best adapted to obtain the molecular signature by optimizing the set of experimental constrains and combinatorial motifs of the sequence. (2) by tuning the cartography algorithm to adapt to the experimental measurement constrains. Finally, I have tested these algorithms, both on simulated data in silico and on experimental fingerprint in vitro. I shall discuss how the performances of these cartography solutions that have been developed here are impacted by the experimental limitations of the present technique, and by the bioinformatics limits. I shall present possible improvements to these methods. My studies constitute a proof of concept for genomic and epigenetic applications.

O objetivo deste trabalho é apresentar algoritmos aplicados para extração de características invariantes à rotação em imagens de impressões digitais. No pré-processamento da imagem utiliza-se detecção de bordas pelo detector de Canny tendo como resultado uma imagem binarizada e afinada. Na extração das minúcias a metodologia adotada é o número de cruzamentos (CN), que extrai os aspectos locais, tais como, as minúcias fim de linha e bifurcações. A direção das cristas locais não é utilizada porque nas imagens rotacionadas a condição de permanência das propriedades biométricas não são satisfeitas. A comparação das impressões digitais utiliza os vetores gerados pela extração de minúcias considerando a posição (x,y) da minúcia armazenada em um vetor por tipo de minúcia (um vetor para crista final e outro vetor para crista bifurcada) e calculando a distância Euclidiana dessa posição (x,y) ao centro de massa da distribuição de minúcias para cada tipo de minúcia. Assim, as duas imagens são similares quando a distância Euclidiana entre os vetores de cada imagem e por tipo de minúcia forem mínimas. São discutidas as limitações de outros trabalhos existentes envolvendo rotação, translação e distorção da imagem de impressão digital, mostrando que os poucos trabalhos que tratam o problema possuem resultados não satisfatórios. Os maiores problemas ocorridos foram a extração de minúcias espúrias, mas foram resolvidos com os métodos sugeridos por Dixon (1979), tendo resultados satisfatórios em duas metodologias. No método média, a precisão para encontrar uma imagem foi de 100%, duas imagens 97,32%, três imagens 92,35%, quatro imagens 86,41% e cinco imagens 71,86%. E no método normal, a precisão para encontrar uma imagem foi de 100%, duas imagens 99,20%, três imagens 96,95%, quatro imagens 94,00% e cinco imagens 76,43%. / The objective of this research is to present algorithms that can be applied in fingerprints images in order to extract certain features, which are invariant to an likely rotation in the given image. In the preprocessing stage, the Canny border detector is used, resulting in a binary, fine tuned image. For the minutiae extraction, the crossing number method is used, which extracts local aspects such as minutiae endings and bifurcations. The direction of local ridges is ignored because, in rotated images, the permanence conditions of the biometric attributes are not fulfilled. The process of matching fingerprints uses two arrays (one for ridge endings and the other for bifurcations), which are generated by the extraction of the minutiae, considering the (x,y) coordinate of the given minutiae stored in the arrays, and calculating its Euclidian distance relating to the center of mass of the minutiae distribution, for each of its types (ending or bifurcation). Thus, both images are similar when the Euclidian distance between the arrays of each image, distinct by the type of each minutiae, is minimal. The limitations of other pieces of research works concerning fingerprint image rotation, translation and distortion are discussed, indicating that the only few ones that deal with these kinds of problems give unsatisfactory results.