Made available in DSpace on 2015-07-22T20:50:04Z (GMT). No. of bitstreams: 0 Previous issue date: 2010-07-28 / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Os cromossomos em anel geralmente resultam de quebras em seus braços curto e longo seguidas pela fusão das extremidades fraturadas, causando a perda de material genético. Atualmente, com o surgimento de técnicas moleculares mais sensíveis é possível definir os pontos de quebra com precisão e descrever o mecanismo de formação de cada anel. No presente trabalho, foram analisados 13 pacientes com cromossomos autossomos em anel. Para avaliação da instabilidade do cromossomo em anel foram avaliadas 300 metáfases de cada paciente, por meio de bandamento G e de FISH com sonda centromérica. Os pacientes portadores de r(14) e r(15) foram avaliados em dois períodos diferentes, com um intervalo de 19 anos, para a realização do estudo longitudinal. Somente os anéis dos cromossomos 4 (caso II) e 22 (casos XII e XIII) apresentaram-se estáveis de acordo com os critérios de Kosztolanyi (1987), enquanto os demais foram considerados instáveis. O estudo longitudinal mostrou que os r(14) e r(15) passaram de estáveis a instáveis no intervalo de tempo analisado. Apesar da instabilidade dos cromossomos em anel ter aumentado ao longo dos anos, esses dois pacientes não apresentaram agravamento no seu quadro clínico, tendo este se mantido estável. Através da técnica de SNP-array foram definidos os pontos de quebra e os mecanismos de formação dos anéis em 12 pacientes. Para os anéis nos quais não foram observadas perdas de material genético no braço curto e nem no braço longo foram utilizadas as técnicas de MLPA e de FISH com sondas subteloméricas e teloméricas, respectivamente. Assim, os cariótipos dos pacientes foram determinados como: 46,XY,r(3)(p26.1q29), 46,XX,r(4)(p16.3q35.2), 46,XY,r(10)(p15.3q26.2), 46,XX,r(10)(p15.3q26.13), 46,XY,r(13)(p13q31.1), 46,XY,r(14)(p13q32.33), 46,XX,r(15)(p13q26.2), 46,XY,r(18)(p11.32q22.2), 46,XX,r(18)(p11.32q21.33), 46,XX,r(18)(p11.21q23), 46,XY,r(22)(p13q13.33) e 46,XX,r(22)(p12q13.2). Verificamos que os anéis cromossômicos foram formados por meio de diferentes mecanismos: quebras em ambos os braços cromossômicos seguidas pela fusão das extremidades fraturadas (pacientes IV, VIII e X); quebra em um dos braços cromossômicos seguida pela fusão com região subtelomérica do outro braço (pacientes I, II, VII e XII); quebra em um dos braços cromossômicos seguida pela fusão com a região telomérica oposta (pacientes III e IX); fusão de regiões subteloméricas (paciente VI) e fusão de regiões teloméricas (paciente XI). Assim, os r(14) e um r(22) podem ser considerados anéis completos, uma vez que não houve perda de material genético relevante. O r(13) apresentou um mecanismo de formação mais complexo resultante da deleção de 11,1 Mb concomitante com uma duplicação intersticial de 1,5 Mb. Seu cariótipo foi definido como 46,XY,r(13)(p13q33.1).arr13q33.1(101,543,509-103,001,462)x3,13q33.1q34(103,003,268-114,142,980)x1 dn. Nós concluímos que o fenótipo dos pacientes portadores de cromossomos em anel podem estar relacionados a diferentes fatores, entre eles instabilidade do cromossomo em anel e a haploinsuficiência gênica. Além disso, fatores epigenéticos relacionados à configuração do cromossomo em anel poderiam alterar a expressão gênica, uma vez que os pacientes com r(14) e r(22) apresentam alterações fenotípicas apesar serem portadores de anéis completos. / Ring chromosomes usually result from breaks in their short and long arms followed by fusion of both ends causing genetic material loss. Nowadays with more sensible molecular techniques it is possible to better define the breakpoints and mechanism of ring chromosome formation. In this study we analyzed 13 patients with autosome ring chromosomes. We scored 300 metaphases from each patient lymphocyte cultures, using G banding and FISH with centromeric probes, in order to investigate the ring chromosome instability. A longitudinal study was done in patient VI with r(14) and in patient VII with r(15). They were investigated in two different periods with 19 years difference. Only the ring chromosomes 4 (case II) and 22 (cases XII and XIII) were considered stable since they present al lest 95% metaphases cells with only one monocentric ring, while the others were considered unstable. The longitudinal study showed that the r(14) and r(15) turned unstable during the period analyzed. In spite of the ring chromosomes instability had increased over the years, these patients did not present worse in clinical findings. Using the SNP-array technique, breakpoints and mechanisms of ring chromosome formation were determined in 12 patients. For the rings that we did not observe loss of genetic material in the short neither in the long arm MLPA and FISH techniques with subtelomeric and pantelomeric probes, respectively, were used. Thus, the patients´ karyotypes were determined as: 46,XY,r(3)(p26.1q29), 46,XX,r(4)(p16.3q35.2), 46,XY,r(10)(p15.3q26.2), 46,XX,r(10)(p15.3q26.13), 46,XY,r(13)(p13q31.1), 46,XY,r(14)(p13q32.33), 46,XX,r(15)(p13q26.2), 46,XY,r(18)(p11.32q22.2), 46,XX,r(18)(p11.32q21.33), 46,XX,r(18)(p11.21q23), 46,XY,r(22)(p13q13.33) and 46,XX,r(22)(p12q13.2). Different mechanisms were found to be involved in ring chromosome formation: from breaks in both chromosome arms, followed by end-to-end reunion (patients IV, VII-X and XII); from a break in one chromosome arm followed by fusion with the subtelomeric region of the other (patients I-II); from a break in one chromosome arm followed by fusion with the opposite telomeric region (patients III and IX); from fusion of two subtelomeric regions (patient VI); from telomere-telomere fusion (patient XI). Thus, the r(14) and one r(22) can be considered complete rings, since there was no loss of relevant genetic material. The r(13) showed a more complex mechanism of formation resulting in a deletion of 11.1 Mb concomitant with an interstitial duplication of 1.5 Mb with karyotype determined as 46,XY,r(13)(p13q33.1).arr13q33.1(101,543,509-103,001,462)x3,13q33.1q34(103,003,268-114,142,980)x1 dn. We concluded that the phenotypes of ring chromosome patients can be related with different factors, including gene haploinsufficiency, gene duplication and ring instability. Epigenetic factors related to gene expression changes due to the circular architecture of the ring chromosome must also be considered, since even patients with complete ring chromosomes can present associated phenotypic alterations, as observed in our patients with complete r(14) and r(22). / FAPESP: 2007/58735-5 / TEDE / BV UNIFESP: Teses e dissertações

abstract: Peptide microarrays have been used in molecular biology to profile immune responses and develop diagnostic tools. When the microarrays are printed with random peptide sequences, they can be used to identify antigen antibody binding patterns or immunosignatures. In this thesis, an advanced signal processing method is proposed to estimate epitope antigen subsequences as well as identify mimotope antigen subsequences that mimic the structure of epitopes from random-sequence peptide microarrays. The method first maps peptide sequences to linear expansions of highly-localized one-dimensional (1-D) time-varying signals and uses a time-frequency processing technique to detect recurring patterns in subsequences. This technique is matched to the aforementioned mapping scheme, and it allows for an inherent analysis on how substitutions in the subsequences can affect antibody binding strength. The performance of the proposed method is demonstrated by estimating epitopes and identifying potential mimotopes for eight monoclonal antibody samples. The proposed mapping is generalized to express information on a protein's sequence location, structure and function onto a highly localized three-dimensional (3-D) Gaussian waveform. In particular, as analysis of protein homology has shown that incorporating different kinds of information into an alignment process can yield more robust alignment results, a pairwise protein structure alignment method is proposed based on a joint similarity measure of multiple mapped protein attributes. The 3-D mapping allocates protein properties into distinct regions in the time-frequency plane in order to simplify the alignment process by including all relevant information into a single, highly customizable waveform. Simulations demonstrate the improved performance of the joint alignment approach to infer relationships between proteins, and they provide information on mutations that cause changes to both the sequence and structure of a protein. In addition to the biology-based signal processing methods, a statistical method is considered that uses a physics-based model to improve processing performance. In particular, an externally developed physics-based model for sea clutter is examined when detecting a low radar cross-section target in heavy sea clutter. This novel model includes a process that generates random dynamic sea clutter based on the governing physics of water gravity and capillary waves and a finite-difference time-domain electromagnetics simulation process based on Maxwell's equations propagating the radar signal. A subspace clutter suppression detector is applied to remove dominant clutter eigenmodes, and its improved performance over matched filtering is demonstrated using simulations. / Dissertation/Thesis / Doctoral Dissertation Electrical Engineering 2014

abstract: Currently in the US, many patients with cancer do not benefit from the population-based screening, due to challenges associated with the existing cancer screening scheme. Blood-based diagnostic assays have the potential to detect diseases in a non-invasive way. Proteins released from small early tumors may only be present intermittently and get diluted to tiny concentrations in the blood, making them difficult to use as biomarkers. However, they can induce autoantibody (AAb) responses, which can amplify the signal and persist in the blood even if the antigen is gone. Circulating autoantibodies is a promising class of molecules that have potential to serve as early detection biomarkers for cancers. This Ph.D thesis aims to screen for autoantibody biomarkers for the early detection of two deadly cancer, basal-like breast cancer and lung adenocarcinoma. First, a method was developed to display proteins in both native and denatured conformation on protein array. This method adopted a novel protein tag technology, called HaloTag, to covalently immobilize proteins on glass slide surface. The covalent attachment allowed these proteins to endure harsh treatment without getting dissociated from slide surface, which enabled the profiling of antibody responses against both conformational and linear epitopes. Next, a plasma screening protocol was optimized to significantly increase signal to noise ratio of protein array based AAb detection. Following this, the AAb responses in basal-like breast cancer were explored using nucleic acid programmable protein arrays (NAPPA) containing 10,000 full-length human proteins in 45 cases and 45 controls. After verification in a large sample set (145 basal-like breast cancer cases / 145 controls / 70 non-basal breast cancer) by ELISA, a 13-AAb classifier was developed to differentiate patients from controls with a sensitivity of 33% at 98% specificity. Similar approach was also applied to the lung cancer study to identify AAbs that distinguished lung cancer patients from computed-tomography positive benign pulmonary nodules (137 lung cancer cases, 127 smoker controls, 170 benign controls). In this study, two panels of AAbs were discovered that showed promising sensitivity and specificity. Six out of eight AAb targets were also found to have elevated mRNA level in lung adenocarcinoma patients using TCGA data. These projects as a whole provide novel insights on the association between AAbs and cancer, as well as general B cell antigenicity against self-proteins. / Dissertation/Thesis / Doctoral Dissertation Biological Design 2015

abstract: For a sensor array, part of its elements may fail to work due to hardware failures. Then the missing data may distort in the beam pattern or decrease the accuracy of direction-of-arrival (DOA) estimation. Therefore, considerable research has been conducted to develop algorithms that can estimate the missing signal information. On the other hand, through those algorithms, array elements can also be selectively turned off while the missed information can be successfully recovered, which will save power consumption and hardware cost. Conventional approaches focusing on array element failures are mainly based on interpolation or sequential learning algorithm. Both of them rely heavily on some prior knowledge such as the information of the failures or a training dataset without missing data. In addition, since most of the existing approaches are developed for DOA estimation, their recovery target is usually the co-variance matrix but not the signal matrix. In this thesis, a new signal recovery method based on matrix completion (MC) theory is introduced. It aims to directly refill the absent entries in the signal matrix without any prior knowledge. We proposed a novel overlapping reshaping method to satisfy the applying conditions of MC algorithms. Compared to other existing MC based approaches, our proposed method can provide us higher probability of successful recovery. The thesis describes the principle of the algorithms and analyzes the performance of this method. A few application examples with simulation results are also provided. / Dissertation/Thesis / Masters Thesis Electrical Engineering 2016

abstract: The Kilopixel Array Pathfinder Project (KAPPa) advances the number of coherent high-frequency terahertz (THz) receivers that could be packed into a single focal plane array on existing submm telescopes. The KAPPa receiver, at 655-695 GHz, is a high frequency heterodyne receiver that can achieve system temperatures of less than 200 K, the specification for ALMA band-9. The KAPPa receiver uses a novel design of a permanent magnet to suppress the noise generated by the DC Josephson effect. This is in stark contrast to the benchmark solution of an electromagnet that is both too expensive and too large for use in kilo-pixel arrays. I present a simple, robust design for a single receiver element that can be tessellated throughout a telescope's focal plane to make a ~1000 pixel array, which is much larger than the current state-of-the-art array, SuperCam, at 64 pixels and ~345 GHz. While the original goal to develop receiver technologies has been accomplished, the path to this accomplishment required a far more holistic approach than originally anticipated. The goal of the present work has expended exponentially from that of KAPPas promised technical achievements. In the present work, KAPPa and its extension, I present solutions ranging from 1) the creation of large scale astronomical maps, 2) metaheuristic algorithms that solve tasks too complex for humans, and 3) detailed technical assembly of microscopic circuit components. Each part is equally integral for the realization of a ~1000 pixel THz arrays. Our automated tuning algorithm, Alice, uses differential evolution techniques and has been extremely successful in its implementation. Alice provides good results for characterizing the extremely complex tuning topology of THz receivers. More importantly, it has accomplished rapid optimization of an entire array without human intervention. In the age of big data astronomy, I have prepared THz heterodyne receiver arrays by making cutting edge community-oriented data analysis tools for the future of large-scale discovery. I present a from-scratch reduction and analysis architecture developed for observations of 100s of square degree on-the-sky maps with SuperCam to address the gulf between observing with single dish antennas versus a truly integrated focal plane array. / Dissertation/Thesis / Doctoral Dissertation Astrophysics 2016

abstract: Gene manipulation techniques, such as RNA interference (RNAi), offer a powerful method for elucidating gene function and discovery of novel therapeutic targets in a high-throughput fashion. In addition, RNAi is rapidly being adopted for treatment of neurological disorders, such as Alzheimer's disease (AD), Parkinson's disease, etc. However, a major challenge in both of the aforementioned applications is the efficient delivery of siRNA molecules, plasmids or transcription factors to primary cells such as neurons. A majority of the current non-viral techniques, including chemical transfection, bulk electroporation and sonoporation fail to deliver with adequate efficiencies and the required spatial and temporal control. In this study, a novel optically transparent biochip is presented that can (a) transfect populations of primary and secondary cells in 2D culture (b) readily scale to realize high-throughput transfections using microscale electroporation and (c) transfect targeted cells in culture with spatial and temporal control. In this study, delivery of genetic payloads of different sizes and molecular characteristics, such as GFP plasmids and siRNA molecules, to precisely targeted locations in primary hippocampal and HeLa cell cultures is demonstrated. In addition to spatio-temporally controlled transfection, the biochip also allowed simultaneous assessment of a) electrical activity of neurons, b) specific proteins using fluorescent immunohistochemistry, and c) sub-cellular structures. Functional silencing of GAPDH in HeLa cells using siRNA demonstrated a 52% reduction in the GAPDH levels. In situ assessment of actin filaments post electroporation indicated a sustained disruption in actin filaments in electroporated cells for up to two hours. Assessment of neural spike activity pre- and post-electroporation indicated a varying response to electroporation. The microarray based nature of the biochip enables multiple independent experiments on the same culture, thereby decreasing culture-to-culture variability, increasing experimental throughput and allowing cell-cell interaction studies. Further development of this technology will provide a cost-effective platform for performing high-throughput genetic screens. / Dissertation/Thesis / Ph.D. Bioengineering 2012

abstract: Multidimensional data have various representations. Thanks to their simplicity in modeling multidimensional data and the availability of various mathematical tools (such as tensor decompositions) that support multi-aspect analysis of such data, tensors are increasingly being used in many application domains including scientific data management, sensor data management, and social network data analysis. Relational model, on the other hand, enables semantic manipulation of data using relational operators, such as projection, selection, Cartesian-product, and set operators. For many multidimensional data applications, tensor operations as well as relational operations need to be supported throughout the data life cycle. In this thesis, we introduce a tensor-based relational data model (TRM), which enables both tensor- based data analysis and relational manipulations of multidimensional data, and define tensor-relational operations on this model. Then we introduce a tensor-relational data management system, so called, TensorDB. TensorDB is based on TRM, which brings together relational algebraic operations (for data manipulation and integration) and tensor algebraic operations (for data analysis). We develop optimization strategies for tensor-relational operations in both in-memory and in-database TensorDB. The goal of the TRM and TensorDB is to serve as a single environment that supports the entire life cycle of data; that is, data can be manipulated, integrated, processed, and analyzed. / Dissertation/Thesis / Doctoral Dissertation Computer Science 2014

Orientador: Alice Maria Bastos Hubinger Tokarnia / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia Elétrica e de Computação / Made available in DSpace on 2018-08-16T03:05:57Z (GMT). No. of bitstreams: 1 Tachibana_Marina_M.pdf: 2745315 bytes, checksum: 91aeb0d6708948d94d06a63e21b98ad6 (MD5) Previous issue date: 2010 / Resumo: Um sistema embarcado executa um único programa ou um conjunto pré-definido de programas repetidamente e, muitas vezes, seus componentes podem ser customizados para satisfazer uma especificação com requisitos referentes à área, desempenho e consumo de energia. Caches on-chip, em particular, são alvos de muitos algoritmos de customização por terem uma contribuição importante no desempenho e no consumo de energia de processadores embarcados. Várias aplicações embarcadas processam estruturas de dados cujos padrões de acesso distintos tornam difícil encontrar uma configuração para o cache que garanta desempenho e baixo consumo. Propomos, neste trabalho, uma metodologia para projetar caches de matrizes particionados que satisfaçam uma restrição de tamanho total e em cujas partições estão mapeadas as matrizes da aplicação. Estas partições exploram a diferença de localidade espacial entre as matrizes. Com base na simulação de rastros de acesso à memória para entradas típicas, definimos uma métrica que quantifica o uso que as matrizes fazem das metades das linhas de um cache de matrizes unificado, associativo por conjunto, que satisfaz uma restrição de tamanho. Esta métrica é usada para dividir as matrizes em dois grupos, que são mapeados em duas partições de cache, uma com mesmo tamanho de linha, e outra com metade do tamanho de linha do cache de matrizes unificado. Este procedimento é repetido para várias organizações de cache de matrizes unificados com um tamanho especificado. No final, os caches de matrizes particionados baseados em rastros de acesso à memória com menor tempo médio de acesso à memória são selecionados. Para um decodificador MPEG-2, dependendo do paralelismo dos acessos de dados, os resultados das simulações mostram que o tempo médio de acesso à memória de um cache de matrizes particionado baseado em rastros de 8K bytes apresenta uma redução de 26% a 60%, quando comparado com o cache de matrizes unificado, associativo por conjunto, de mesmo tamanho, com menor tempo médio de acesso à memória. Existe também uma redução de 46% no consumo de energia entre estes caches / Abstract: An embedded system executes a single application or a pre-defined set of applications repeatedly and, frequently, its components can be fine-tuned to satisfy a specification with requirements related to area, performance, and energy consumption. On-chip caches, in particular, are the target of several customization algorithms due to its important contribution to the performance and energy consumption of embedded processors. Several embedded applications process data structures whose access patterns turn it difficult to find a cache configuration that guarantees performance and low energy consumption. In this work, we propose a methodology for designing a split array cache that satisfies a total size constraint and in whose partitions the arrays of an application are mapped. Those partitions explore the difference in spatial locality among the matrices. Using traces of memory accesses, obtained for typical input patterns, we define a metric that quantifies the use of the two halves of the lines by array accesses in a unified array set-associative cache that satisfies a size constraint. We use this metric to split the arrays in two groups that are mapped to two cache partitions, one with the same line size, and the other with half line size of that of the unified array cache. This procedure is repeated for several unified array cache organizations of a specified size. In the end, the trace based split array caches with lowest average memory access time are selected. For a MPEG-2 decoder, depending on the parallelism of array accesses, simulation results show that the average memory access time of an 8K byte split array cache is reduced from 26% to 60% as compared to that of the unified set associative array cache of same size with the lowest average memory access time. There is also a reduction of 46% in the consumption of energy / Mestrado / Engenharia de Computação / Mestre em Engenharia Elétrica

M.Ing. / This work considers a dual band electronically steerable parasitic array radiator (ESPAR) antenna system. This system is designed with one actively fed radiating element and N-parasitic radiating elements. The radiation pattern can be electronically controlled by means of the loads terminating the parasitic elements. The antenna system is designed as ESPAR to have a minimum number of controlling elements thereby minimising the power consumed. The dual band operation of this antenna is for the frequency bands of the wireless local area network (WLAN), which are 2.412-2.482 GHz for IEEE 802.11b/g (known as the 2.4 GHz band) and 5.15-5.825 GHz for IEEE 802.11a (known as the 5 GHz band). In the upper band, only the 5.8 GHz sub-band was considered. The dual-band capability was targeted by conducting a structural parameter modification on the antenna system. The structural modification involves optimisation of the length of the active element, the length of the parasitic element, the distance of the parasitic element from the active element and most importantly, by application of a loading technique on the elements. The loading was done by using optimisation tools, such as fminsearch, fminbnd and the genetic algorithm. The specific circuit that was used for the loading was a series connection inductors inserted into the antenna’s elements at positions found via a global optimization.. The method used was to first identify the optimal length per specific resonant frequency and consider the optimal length with respect to both resonant frequencies. The second step was to load the three resulting optimised different monopoles, and the loading with results closest to the requirements. The optimum monopole of the three in the second step was then used as the fixed input parameter for the main optimisation of ESPAR antenna. Using a ground plane with a skirt, an acceptable return loss performance has been achieved for the antenna's main building M.J. Bembe ii block, a monopole element, in both frequency bands. The challenge was found in steering of the beam in different directions; it was then concluded that the usage of more elements could provide the necessary freedom for the optimisation process. Six elements were arranged symmetrically close to the active fed element in order to achieve a dual band resonance, with different designs meeting the requirements differently. This is the first report showing an ESPAR antenna optimisation which includes the loading of elements with lengths and distance optimisation.

Metasurfaces which emerged as two-dimensional counterparts of metamaterials, facilitate the realization of arbitrary phase distributions using large arrays with subwavelength and ultra-thin features. Even if metasurfaces are ultra-thin, they still effectively manipulate the phase, amplitude, and polarization of light in transmission or reflection mode. In contrast, conventional optical components are bulky, and they lose their functionality at sub-wavelength scales, which requires conceptually new types of nanoscale optical devices. On the other hand, as the optical systems shrink in size day by day, conventional bulky optical components will have tighter alignment and fabrication tolerances. Since metasurfaces can be fabricated lithographically, alignment can be done during lithographic fabrication, thus eliminating the need for post-fabrication alignments. In this work, various types of metasurface applications are thoroughly investigated for robust wavefront engineering with enhanced characteristics in terms of broad bandwidth, high efficiency and active tunability, while beneficial for application. Plasmonic metasurfaces are not compatible with the CMOS process flow, and, additionally their high absorption and ohmic loss is problematic in transmission based applications. Dielectric metasurfaces, however, offer a strong magnetic response at optical frequencies, and thus they can offer great opportunities for interacting not only with the electric component of a light field, but also with its magnetic component. They show great potential to enable practical device functionalities at optical frequencies, which motivates us to explore them one step further on wavefront engineering and imaging sensor platforms. Therefore, we proposed an efficient ultra-thin flat metalens at near-infrared regime constituted by silicon nanodisks which can support both electric and magnetic dipolar Mie-type resonances. These two dipole resonances can be overlapped at the same frequency by varying the geometric parameters of silicon nanodisks. Having two resonance mechanisms at the same frequency allows us to achieve full (0-2π) phase shift on the transmitted beam. To enable the miniaturization of pixel size for achieving high-resolution, planar, compact-size focal plane arrays (FPAs), we also present and explore the metasurface lens array-based FPAs. The investigated dielectric metasurface lens arrays achieved high focusing efficiency with superior optical crosstalk performance. We see a magnificent application prospect for metasurfaces in enhancing the fill factor and reducing the pixel size of FPAs and CCD, CMOS imaging sensors as well. Moreover, it is of paramount importance to design metasurfaces possessing tunable properties. Thus, we also propose a tunable beam steering device by combining phase manipulating metasurfaces concept and liquid crystals. Tunability feature is implemented by nematic liquid crystals infiltrated into nano holes in SiO2. Using electrically tunable nematic liquid crystals, dynamic beam steering is achieved