Today, eavesdropping is becoming a common issue in the rapidly growing digital network and has foreseen the need for secret communication channels embedded in digital media. In this paper, a novel steganography technique designed for Standard Definition Digital Television (SDTV) H.264/AVC encoded video sequences is presented. The algorithm introduced here makes use of the compression properties of the Context Adaptive Variable Length Coding (CAVLC) entropy encoder to achieve a low complexity and real-time inserting method. The chosen scheme hides the private message directly in the H.264/AVC bit stream by modifying the AC frequency quantized residual luminance coefficients of intrapredicted I-frames. In order to avoid error propagation in adjacent blocks, an interlaced embedding strategy is applied. Likewise, the steganography technique proposed allows self-detection of the hidden message at the target destination. The code source was implemented by mixing MATLAB 2010 b and Java development environments. Finally, experimental results have been assessed through objective and subjective quality measures and reveal that less visible artifacts are produced with the technique proposed by reaching PSNR values above 40.0 dB and an embedding bit rate average per secret communication channel of 425 bits/sec. This exemplifies that steganography is affordable in digital television.

A correta adoção de medidas de manejo de resistência de insetos-pragas é motivo de preocupação constante, inclusive para as novas tecnologias disponíveis, como as plantas geneticamente modificadas para a expressão de toxinas da bactéria Bacillus thuringiensis (Bt). Portanto, para manter a eficiência das plantas-Bt comercialmente disponíveis, é preconizada a manutenção de áreas de refúgio (livres de plantas Bt) para evitar a rápida seleção de insetos resistentes. No caso de insetos polífagos, a determinação das áreas de refúgio pode levar em consideração a contribuição que fontes não-comerciais e/ou não-transgênicas têm na produção de adultos colonizadores que não sofreram seleção para o evento de transgenia de interesse. A identificação da fonte alimentar pode determinar a procedência de insetos e tornar mais eficiente e segura a implementação de zonas de refúgio e a determinação dos riscos de desenvolvimento de resistência pelo inseto-praga alvo. O objetivo deste trabalho foi o de avaliar o potencial de dois marcadores biológicos, a assinatura isotópica e a microbiota intestinal, para a identificação da fonte de alimento do imaturo pela análise de adultos de Spodoptera frugiperda (J.E. Smith) (Lepidoptera, Noctuidae), como subsídio para o monitoramento da origem de insetos migrantes em áreas de cultivo Bt para a adoção de estratégias adequadas de manejo de resistência. A análise isotópica de adultos foi realizada utilizando-se insetos criados em 12 plantas hospedeiras distintas, seis de metabolismo C3 e seis de metabolismo C4. Parte dos adultos provenientes dessa criação foram liofilizados, macerados e submetidos à análise isotópica para a determinação dos níveis de ?13C e ?15N. Amostras das plantas utilizadas na alimentação desses insetos também foram submetidas ao mesmo processo de análise. A outra parte dos adultos recémemergidos de S. frugiperda foi utilizada para a determinação da microbiota intestinal pela análise de região do gene do 16S rRNA após sequenciamento em plataforma 454. Os resultados da análise isotópica de carbono para as plantas utilizadas como fonte alimentar apresentaram médias entre -31,37? e -25,07? para plantas C3 e entre -13,03? e -12,26? para plantas C4. Adultos de S. frugiperda oriundos de lagartas criadas em plantas do grupo C3 apresentaram média de ?13C entre - 30,36? e -23,72?, enquanto aqueles do grupo C4 apresentaram média entre - 18,25? e -13,28?. O sequenciamento da microbiota via metagenômica produziu 126,970 sequências com cerca de 421 pb. O alimento influenciou substancialmente a diversidade da microbiota intestinal associada ao intestino de adultos, independentemente do metabolismo fotossintético da planta hospedeira. Análises comparativas de diversidade em que a abundância relativa dos diferentes componentes foi considerada (Unifrac ponderado) permitiu a distinção de praticamente todas as microbiotas. Foram identificadas várias UTOs exclusivamente associadas à microbiota intestinal de adultos provenientes de cada fonte de alimento, mas a maioria apresentou abundância relativa extremamente baixa. Apenas as UTOs 1199 e 2255 foram exclusivamente associados ao milho com abundância relativa superior a 2,5%. / The correct insect resistant management has been a topic of constant concern, even for the newer technologies available, such as genetically modified crops expressing Bacillus thuringiensis (Bt) toxins. The use of refuge areas with non-Bt crops to avoid the fast selection for resistant insects is proposed for maintaining the efficiency of Bt-crops. The implementation of refuge areas for polyphagous insects can consider non-commercial and non-Bt crops as sources of susceptible insects. The identification of the food source used during immature development can make the implementation of refuge areas safer and more efficient and allow for better estimates of risk assessment for insect resistance development. The objective of this study is to determine the potential use of, the isotopic signature and gut microbiota of adults as biological markers to allow for the identification of the food source during the larval stage of Spodoptera frugiperda (J.E. Smith) (Lepidoptera, Noctuidae). Adults were obtained from larval rearing on 12 food sources, six host-plants with a C3 photosynthetic metabolism and six host-plants with a C4 metabolism. Part of the adults obtained and the food source used during their immature development were lyophilized and macerated, and subjected to ?13C e ?15N isotopic analysis. The remaining adults of S. frugiperda were used to determine the composition of the gut microbiota by metagenomic analysis of the V1-V3 region of the 16S rRNA gene using a 454 sequencing platform. The carbon isotopic signatures obtained for the hostplants used as food source were between -31.37? and -25.07? for C3 plants, and - 13.03? and -12.26? for C4 plants. Adults of S. frugiperda obtained from larval rearing on C3 plants had a carbon isotopic signature between -30.36? and -23.72?, while those from C4 host-plants has between -18.25? and -13.28?. The metagenomic sequencing yielded 126,970 reads with an average of 421bp. The larval food source substantially influenced the diversity of the adult gut microbiota regardless of the plant\'s photosynthesis metabolism. Comparative analysis among gut microbiota in which the relative abundance was taken into account (weight- Unifrac) allowed the discrimination of the majority of the communities. Several OTUs were identified as exclusive to the adult gut microbiota from different food sources, but most of these OTUs were minor components of the community. OTUs 1199 and 2255, both exclusively associated with corn, were the only ones to represent at least 2.5% of their community.

Since the discovery of X-rays over a century ago the techniques applied to the engineering of X-ray sources have remained relatively unchanged. From the inception of thermionic electron sources, which, due to simplicity of fabrication, remain central to almost all X-ray applications at this time, there have been few fundamental technological advances. The emergence of new materials and manufacturing techniques has created an opportunity to replace the traditional thermionic devices with those that incorporate Field Emission electron sources. One of the most important attributes of Field Emission X-ray sources is their controllability, and in particular the fast response time, which opens the door to applying techniques which have formerly been the preserve of optical systems. The work in this thesis attempts to bridge the gap between the fabrication and optimisation of the vacuum electronic devices and image processing aspects of a new approach to high speed radiographic imaging, particularly with a view to addressing practical real-world problems. Off the back of a specific targeted application, the project has involved the design of a viable field emission X-ray source, together with the development of an understanding of the failure modes in such devices, both by analysis and by simulation. This thesis reviews the capabilities and the requirements of X-ray sources, the methods by which nano-materials may be applied to the design of those devices and the improvements and attributes that can be foreseen. I study the image processing methods that can exploit these attributes, and investigate the performance of X-ray sources based upon electron emitters using carbon nanotubes. Modelling of the field emission and electron trajectories of the cathode assemblies has led me to the design of equipment to evaluate and optimise the parameters of an X-ray tube, which I have used to understand the performance that is achievable. Finally, I draw conclusions from this work and outline the next steps to provide the basis for a commercial solution.

Due to the continuously decreasing feature sizes and the increasing complexity of integrated circuits, commercial off-the-shelf (COTS) hardware is becoming less and less reliable. However, dedicated reliable hardware is expensive and usually slower than commodity hardware. Thus, economic pressure will most likely result in the usage of unreliable COTS hardware in safety-critical systems. The usage of unreliable, COTS hardware in safety-critical systems results in the need for software-implemented solutions for handling execution errors caused by this unreliable hardware. In this thesis, we provide techniques for detecting hardware errors that disturb the execution of a program. The detection provided facilitates handling of these errors, for example, by retry or graceful degradation. We realize the error detection by transforming unsafe programs that are not guaranteed to detect execution errors into safe programs that detect execution errors with a high probability. Therefore, we use arithmetic AN-, ANB-, ANBD-, and ANBDmem-codes. These codes detect errors that modify data during storage or transport and errors that disturb computations as well. Furthermore, the error detection provided is independent of the hardware used. We present the following novel encoding approaches: - Software Encoded Processing (SEP) that transforms an unsafe binary into a safe execution at runtime by applying an ANB-code, and - Compiler Encoded Processing (CEP) that applies encoding at compile time and provides different levels of safety by using different arithmetic codes. In contrast to existing encoding solutions, SEP and CEP allow to encode applications whose data and control flow is not completely predictable at compile time. For encoding, SEP and CEP use our set of encoded operations also presented in this thesis. To the best of our knowledge, we are the first ones that present the encoding of a complete RISC instruction set including boolean and bitwise logical operations, casts, unaligned loads and stores, shifts and arithmetic operations. Our evaluations show that encoding with SEP and CEP significantly reduces the amount of erroneous output caused by hardware errors. Furthermore, our evaluations show that, in contrast to replication-based approaches for detecting errors, arithmetic encoding facilitates the detection of permanent hardware errors. This increased reliability does not come for free. However, unexpectedly the runtime costs for the different arithmetic codes supported by CEP compared to redundancy increase only linearly, while the gained safety increases exponentially.

A correta adoção de medidas de manejo de resistência de insetos-pragas é motivo de preocupação constante, inclusive para as novas tecnologias disponíveis, como as plantas geneticamente modificadas para a expressão de toxinas da bactéria Bacillus thuringiensis (Bt). Portanto, para manter a eficiência das plantas-Bt comercialmente disponíveis, é preconizada a manutenção de áreas de refúgio (livres de plantas Bt) para evitar a rápida seleção de insetos resistentes. No caso de insetos polífagos, a determinação das áreas de refúgio pode levar em consideração a contribuição que fontes não-comerciais e/ou não-transgênicas têm na produção de adultos colonizadores que não sofreram seleção para o evento de transgenia de interesse. A identificação da fonte alimentar pode determinar a procedência de insetos e tornar mais eficiente e segura a implementação de zonas de refúgio e a determinação dos riscos de desenvolvimento de resistência pelo inseto-praga alvo. O objetivo deste trabalho foi o de avaliar o potencial de dois marcadores biológicos, a assinatura isotópica e a microbiota intestinal, para a identificação da fonte de alimento do imaturo pela análise de adultos de Spodoptera frugiperda (J.E. Smith) (Lepidoptera, Noctuidae), como subsídio para o monitoramento da origem de insetos migrantes em áreas de cultivo Bt para a adoção de estratégias adequadas de manejo de resistência. A análise isotópica de adultos foi realizada utilizando-se insetos criados em 12 plantas hospedeiras distintas, seis de metabolismo C3 e seis de metabolismo C4. Parte dos adultos provenientes dessa criação foram liofilizados, macerados e submetidos à análise isotópica para a determinação dos níveis de ?13C e ?15N. Amostras das plantas utilizadas na alimentação desses insetos também foram submetidas ao mesmo processo de análise. A outra parte dos adultos recémemergidos de S. frugiperda foi utilizada para a determinação da microbiota intestinal pela análise de região do gene do 16S rRNA após sequenciamento em plataforma 454. Os resultados da análise isotópica de carbono para as plantas utilizadas como fonte alimentar apresentaram médias entre -31,37? e -25,07? para plantas C3 e entre -13,03? e -12,26? para plantas C4. Adultos de S. frugiperda oriundos de lagartas criadas em plantas do grupo C3 apresentaram média de ?13C entre - 30,36? e -23,72?, enquanto aqueles do grupo C4 apresentaram média entre - 18,25? e -13,28?. O sequenciamento da microbiota via metagenômica produziu 126,970 sequências com cerca de 421 pb. O alimento influenciou substancialmente a diversidade da microbiota intestinal associada ao intestino de adultos, independentemente do metabolismo fotossintético da planta hospedeira. Análises comparativas de diversidade em que a abundância relativa dos diferentes componentes foi considerada (Unifrac ponderado) permitiu a distinção de praticamente todas as microbiotas. Foram identificadas várias UTOs exclusivamente associadas à microbiota intestinal de adultos provenientes de cada fonte de alimento, mas a maioria apresentou abundância relativa extremamente baixa. Apenas as UTOs 1199 e 2255 foram exclusivamente associados ao milho com abundância relativa superior a 2,5%. / The correct insect resistant management has been a topic of constant concern, even for the newer technologies available, such as genetically modified crops expressing Bacillus thuringiensis (Bt) toxins. The use of refuge areas with non-Bt crops to avoid the fast selection for resistant insects is proposed for maintaining the efficiency of Bt-crops. The implementation of refuge areas for polyphagous insects can consider non-commercial and non-Bt crops as sources of susceptible insects. The identification of the food source used during immature development can make the implementation of refuge areas safer and more efficient and allow for better estimates of risk assessment for insect resistance development. The objective of this study is to determine the potential use of, the isotopic signature and gut microbiota of adults as biological markers to allow for the identification of the food source during the larval stage of Spodoptera frugiperda (J.E. Smith) (Lepidoptera, Noctuidae). Adults were obtained from larval rearing on 12 food sources, six host-plants with a C3 photosynthetic metabolism and six host-plants with a C4 metabolism. Part of the adults obtained and the food source used during their immature development were lyophilized and macerated, and subjected to ?13C e ?15N isotopic analysis. The remaining adults of S. frugiperda were used to determine the composition of the gut microbiota by metagenomic analysis of the V1-V3 region of the 16S rRNA gene using a 454 sequencing platform. The carbon isotopic signatures obtained for the hostplants used as food source were between -31.37? and -25.07? for C3 plants, and - 13.03? and -12.26? for C4 plants. Adults of S. frugiperda obtained from larval rearing on C3 plants had a carbon isotopic signature between -30.36? and -23.72?, while those from C4 host-plants has between -18.25? and -13.28?. The metagenomic sequencing yielded 126,970 reads with an average of 421bp. The larval food source substantially influenced the diversity of the adult gut microbiota regardless of the plant\'s photosynthesis metabolism. Comparative analysis among gut microbiota in which the relative abundance was taken into account (weight- Unifrac) allowed the discrimination of the majority of the communities. Several OTUs were identified as exclusive to the adult gut microbiota from different food sources, but most of these OTUs were minor components of the community. OTUs 1199 and 2255, both exclusively associated with corn, were the only ones to represent at least 2.5% of their community.

Made available in DSpace on 2014-06-12T18:28:51Z (GMT). No. of bitstreams: 2 arquivo4264_1.pdf: 8529909 bytes, checksum: 0a958aa0c57b9a6b54d2a7542dbf9476 (MD5) license.txt: 1748 bytes, checksum: 8a4605be74aa9ea9d79846c1fba20a33 (MD5) Previous issue date: 2007 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Um blink é um grafo plano onde cada aresta ou é vermelha ou é verde. Um espaço 3D ou, simplesmente, um espaço é uma variedade 3-dimensional conexa, fechada e orientada. Neste trabalho exploramos pela primeira vez em maiores detalhes o fato de que todo blink induz um espaço e todo espaço é induzido por algum blink (na verdade por infinitos blinks). Qual o espaço de um triângulo verde? E de um quadrado vermelho? São iguais? Estas perguntas foram condensadas numa pergunta cuja busca pela resposta guiou em grande parte o trabalho desenvolvido: quais são todos os espaços induzidos por blinks pequenos (poucas arestas)? Nesta busca lançamos mão de um conjunto de ferramentas conhecidas: os blackboard framed links (BFL), os grupos de homologia, o invariante quântico de Witten-Reshetikhin-Turaev, as 3-gems e sua teoria de simplificação. Combinamos a estas ferramentas uma teoria nova de decomposição/composição de blinks e, com isso, conseguimos identificar todos os espaços induzidos por blinks de até 9 arestas (ou BFLs de até 9 cruzamentos). Além disso, o nosso esforço resultou também num programa interativo de computador chamado BLINK. Esperamos que ele se mostre útil no estudo de espaços e, em particular, na descoberta de novos invariantes que complementem o invariante quântico resolvendo as duas incertezas deixadas em aberto neste trabalho

Mass production of translationally optimized bacteriophages (hereafter referred to as phages) is the need of the hour in the application of phages to therapy. Understanding translational efficiency of phages is the major preliminary step for mass producing efficient phages. The objective of this thesis is to understand factors affecting translational efficiency of phages. In chapter two, we hypothesized that weak translation initiation efficiency is responsible for weak codon concordance of Escherichia coli lambdoid phages with that of their hosts. We measured the strength of translation initiation using two indices namely minimum folding energy (MFE) and proportion of Shine-Dalgarno sequence (PSD). Empirical results substantiate our hypothesis suggesting lack of strong selection for improving codon adaptation in these phages is due to their weak translation initiation. In chapter three, we measured codon usage concordance between GC-rich and GC-poor Aeromonas phages with their GC-rich host Aeromonas salmonicida. We found low codon usage concordance in the GC-poor Aeromonas phages. We were interested in testing for the role of tRNAs in the GC-poor phages. We observed that the GC-poor phages carry tRNAs for codons that are overused by the phages and underused by the host. These findings suggest that the GC-poor Aeromonas phages carry their own tRNAs for compensating for the compositional difference between their genomes and that of their host. Previously several studies have reported observed avoidance of stable secondary structures in start site of mRNA in a wide range of species. We probed the genomes of 422 phage species and measured their secondary structure stability using MFE. We observed strong patterns of secondary structure avoidance (less negative MFE values) in the translation initiation region (TIR) and translation termination region (TTR) of all analyzed phages. These findings imply selection is operating at these translationally important sites to control stable secondary structures in order to maintain efficient translation.

<p>Protein kinases are essential in cell signaling pathways and are well-validated targets for cancer therapeutics and detection of activity levels. Yet, there remains a critical need for kinase inhibitors with high specificity and potency. The development of DNA-encoded library (DEL) technology dramatically facilitates the discovery of ligands to therapeutically relevant proteins. The preparation of combinatorial libraries followed by stringent selections can be exploited to rapidly generate hit molecules that bind to a large variety of targets.</p> <p>A combinatorial library of peptidomimetics is prepared and subjected to a selection for enriching molecules that can serve as substrates for tyrosine kinase Src. Non-natural substrate molecules are recognized by the anti-phosphotyrosine antibody during the selection. Using biophysical characterization assays including ADP-Glo and NMR, the resulting hits are investigated as novel peptide-substrate competitive inhibitors, as well as specific chemical probes that would benefit kinase activity detection. An ester derivative of the lead compound SrcDEL10 demonstrates cellular activity with inhibition of Src-dependent signaling in cell culture. Subsequently, our effort extends to parallel selections with a highly diverse-scaffold DEL on three cancer-related tyrosine kinases. Several hit molecules are validated with differential phosphotransfer activities among Src, Lyn, and Syk. Studies on the structure activity relationship of hit molecules produce selective kinase substrates with the lowest molecular weights reported to date. Potential bisubstrate inhibitors, showing above 8-fold Src selectivity over Lyn, are designed based on structures of selective substrates.</p> <p>Meanwhile, high sensitivity of DNA sequence analysis enables the development of specific and multiplexed activity assays. Using the substrate selection strategy, we develop a DNA-based kinome activity profiling assay using DNA conjugates of tyrosine kinase peptide substrates. Selective enrichment of phosphorylated probes enables activity detection by either quantitative PCR (qPCR) or parallel DNA sequencing. Results with detecting recombinant kinases demonstrated a low (~50 pM kinase) limit of detection. A library of 96 DNA-substrate conjugates enabled multiplexed tyrosine kinase assays in cell lysates in a manner analogous to peptide microarrays. This DNA-based assay potentially empowers the detection of tumor biomarkers with high specificity, lower detection limit, multiplexing capability, and high cost-effectiveness.</p> <p>Together, this research uses DNA-based technologies to assist developing new therapeutics and diagnostics, drug target validation, unveiling drug mechanisms of action, and understanding the role of protein phosphorylation in disease progression.</p>

No description available.

Yes / Virus-encoded miRNAs are emerging as key regulators of persistent infection and host-cell immune evasion. Merkel cell polyomavirus (MCPyV), the predominant aetiological agent of Merkel cell carcinoma (MCC), encodes a single miRNA, MCV-miR-M1, which targets the oncogenic MCPyV large T antigen (LT). MCV-miR-M1 has previously been shown to play an important role in establishment of long-term infection, however, the underlying mechanism is not fully understood. A key unanswered question is whether, in addition to auto-regulating LT, MCV-miR-M1 also targets cellular transcripts to orchestrate an environment conducive for persistent infection. To address this, we adopted an RNA-Seq-based approach to identify cellular targets of MCV-miR-M1. Intriguingly, bioinformatics analysis of transcripts that are differentially expressed in cells expressing MCV-miR-M1 revealed several genes implicated in immune evasion. Subsequent target validation led to the identification of the innate immunity protein, SP100, as a direct target of MCV-miR-M1. Moreover, MCV-miR-M1-mediated modulation of SP100 was associated with a significant decrease in CXCL8 secretion, resulting in the attenuation of neutrophil chemotaxis towards Merkel cells harbouring synthetic MCPyV. Based on these observations we propose that MCV-miR-M1 targets key immune response regulators to help facilitate persistent infection, which is a pre-requisite for cellular transformation in MCC. / Funded in part by a University of Bradford studentship to PA and a Royal Society research award to JRB.