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Method for Acquisition and Reconstruction of non-Cartesian 3-D fMRI / Metod för insamling och rekonstruktion av icke-kartesisk 3-D fMRIThyr, Per January 2008 (has links)
The PRESTO sequence is a well-known 3-D fMRI imaging sequence. In this sequence the echo planar imaging technique is merged with the echo-shift technique. This combination results in a very fast image acquisition, which is required for fMRI examinations of neural activation in the human brain. The aim of this work was to use the basic Cartesian PRESTO sequence as a framework when developing a novel trajectory using a non-Cartesian grid. Our new pulse sequence, PRESTO CAN, rotates the k-space profiles around the ky-axis in a non-Cartesian manner. This results in a high sampling density close to the centre of the k-space, and at the same time it provides sparser data collection of the part of the k-space that contains less useful information. This "can- or cylinder-like" pattern is expected to result in a much faster k-space acquisition without loosing important spatial information. A new reconstruction algorithm was also developed. The purpose was to be able to construct an image volume from data obtained using the novel PRESTO CAN sequence. This reconstruction algorithm was based on the gridding technique, and a Kaiser-Bessel window was also used in order to re-sample the data onto a Cartesian grid. This was required to make 3-D Fourier transformation possible. In addition, simulations were also performed in order to verify the function of the reconstruction algorithm. Furthermore, in vitro tests showed that the development of the PRESTO CAN sequence and the corresponding reconstruction algorithm were highly successful. In the future, the results can relatively easily be extended and generalized for in vivo investigations. In addition, there are numerous exciting possibilities for extending the basic techniques described in this thesis.
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A correção por pares através de ferramentas digitais como mediações formativas no ensino-aprendizagem do francês como língua estrangeira / Peer correction through digital tools as formative mediations in the teaching and learning of French as a second languageArthur Marra 28 September 2018 (has links)
Esta dissertação teve por objetivo estudar o desenvolvimento da produção escrita em francês baseada em gêneros textuais de alunos universitários brasileiros e a influência de correções feitas por alunos canadenses anglófonos através de ferramentas digitais nesse processo. Os dados foram coletados em um projeto de telecolaboração envolvendo a Universidade de São Paulo e a University of Victoria, no Canadá, ao longo de um semestre. O projeto propôs interações entre os alunos brasileiros e canadenses através de três ferramentas digitais: Facebook, GoogleDocs e Skype. Como parte das atividades de uma disciplina de francês como língua estrangeira, os alunos brasileiros escreveram textos pertencentes aos gêneros fait divers, récit de voyage e récit littéraire court, que foram corrigidos de maneira assíncrona, com o GoogleDocs, e síncrona, pelo Skype, pelos alunos canadenses. A pesquisa baseou-se no quadro teóricometodológico do interacionismo sociodiscursivo (ISD) (BRONCKART, 1999/2012, SCHNEUWLY; DOLZ, 2004, MACHADO, 2009), que se apoia, de forma geral, nos estudos propostos por Vigotski (1997, 1998; 2004; 2007; 2008). Servimo-nos, também, dos conceitos propostos pelo ISD e voltados para a didática das línguas, tais como: capacidades de linguagem (DOLZ; PASQUIER; BRONCKART, 1993) e modelo didático (DE PIETRO; SCHNEUWLY, 2003), além de outros propostos por Vigotski, como instrumento e zona de desenvolvimento próximo (VIGOTSKI, 2004, 2007, 2008) a fim de compreender as dificuldades e o desenvolvimento da produção escrita dos alunos brasileiros. Foram utilizados, paralelamente, estudos sobre correção propostos por Tapia (2016), ao lado de outras pesquisas sobre correção de erros e uso de tecnologia para o ensino de línguas, para compreender as correções linguageiras feitas pelos alunos canadenses e investigar seu papel no desenvolvimento das capacidades de linguagem dos alunos brasileiros. Os resultados das análises indicam que, de forma geral, os alunos brasileiros desenvolveram as capacidades de linguagem ao longo do projeto e que as correções linguageiras propostas pelos alunos canadenses agiram como um instrumento para tal desenvolvimento. Identificamos certa diferença entre a forma e o conteúdo das correções em relação às ferramentas digitais GoogleDocs e Skype e também constatamos que o léxico, a concordância nominal e a regência verbal apresentaram maior número de correções. Além disso, observamos que a influência das correções no desenvolvimento das capacidades de linguagem dos alunos brasileiros ocorreu, sobretudo, no que diz respeito a duas das operações linguageiras mais corrigidas: a coesão nominal e a coesão verbal. / This thesis aimed to study the development of writing in French as a Second Language based on textual genres of Brazilian university students and the influence of feedback given by anglophone Canadian students through digital tools. The data were collected in a telecollaboration project including the University of São Paulo and the University of Victoria, Canada, during a semester. The project proposed interactions between Brazilian and Canadian students through three digital tools: Facebook, GoogleDocs and Skype. As part of the activities of a French as a foreign language course, Brazilian students wrote three text genres: fait divers, récit de voyage and récit littéraire court, which were corrected by the Canadian students asynchronously, with GoogleDocs, and synchronously, by Skype. The research was based on the theoretical-methodological framework of sociodiscursive interactionism (SDI) (BRONCKART, 1999/2012, SCHNEUWLY; DOLZ, 2004, MACHADO, 2009), which is based on the studies proposed by Vigotski (1997, 1998; 2004; 2007). In order to understand the difficulties and the development of writing in French of Brazilian students, we also relied on the concepts proposed by SDI which focus on language didactics, such as language capacities (DOLZ, PASQUIER, BRONCKART, 1993) and didactic model (DE PIETRO, SCHNEUWLY, 2003), as well as on concepts proposed by Vigotski, such as instrument and zone of proximal development (VIGOTSKI, 2004, 2007, 2008). In addition, we used the studies about correction proposed by Tapia (2016), as well as other researches about correction and the use of technology for language teaching, to understand the feedback given by the Canadian students and to investigate its role in the development of language capacities of the Brazilian students. In our analysis we could observe that, in general, the Brazilian students developed the language capacities throughout the project and that the feedback proposed by the Canadian students acted as an instrument for such development. We identified a certain difference between the form and the content of the corrections in relation to the digital tools GoogleDocs and Skype. We also verified that the lexicon, the nominal and the verbal cohesion were more often corrected. Moreover, we observed that the influence of corrections on the development of the language capacities of the Brazilian students occurred, especially, in relation to two of the most corrected linguistic operations: nominal cohesion and verbal cohesion.
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USING A NUMERICAL ALGORITHM TO SEARCH FOR DECOHERENCE-FREE SUB-SYSTEMSThakre, Purva 01 December 2018 (has links)
In this paper, we discuss the need for quantum error correction. We also describe some basic techniques used in quantum error correction which includes decoherence-free subspaces and subsystems. These subspaces and subsystems are described in detail. We also introduce a numerical algorithm that was used previously to search for these decoherence-free subspaces and subsystems under collective error. It is useful to search for them as they can be used to store quantum information. We use this algorithm in some specific examples involving qubits and qutrits. The results of these algorithm are then compared with the error algebra obtained using Young tableaux. We use these results to describe how the specific numerical algorithm can be used for the search of approximate decoherence-free subspaces and subsystems and minimal noise subsystems.
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Design of Single Phase Boost Power Factor Correction Circuit and Controller Applied in Electric Vehicle Charging SystemLiu, Ziyong 14 July 2016 (has links)
"In this thesis, based on the existing researches on power factor correction technology, I analyze, design and study the Boost type power factor correction technology, which is applied in the in-board two-stage battery charger. First I analyzed the basic working principle of the active power factor corrector. By comparing several different topologies of PFC converter main circuit and control methods, I specified the research object to be the average current control (ACM) boost power factor corrector. Then I calculated and designed the PFC circuit and the ACM controller applied in the first level charging of EVs. And I run the design in Simulink and study the important features like power factor, the input current waveform and the output DC voltage and the THD and odd harmonic magnitude."
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A negra força da princesa: polícia, pena de morte e correção em Pelotas (1830-1857)Al-Alam, Caiuá Cardoso 18 April 2007 (has links)
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Previous issue date: 18 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Nesta dissertação abordamos a cidade de Pelotas durante o final da primeira metade do século XIX (1830-1857), a partir da perspectiva das práticas de justiça. Utilizamos os mais variados tipos de fontes, desde processos-crimes, percorrendo jornais, e documentos administrativos da Província e do município. Primeiramente buscamos estudar a forma como foi imposta a questão da pena de morte na cidade; logo partimos para a análise dos projetos e da construção da primeira Casa Correcional da localidade. Paralela a estas instituições, nascia também a Polícia, primeiramente como Guarda Municipal Permanente, depois como Força Policial. Procuramos observar, então, como foram postos em prática estes “modelos europeus de civilização” no que concerne às práticas de justiça, mais especificamente as de punição e disciplina, dando ênfase para as reações das pessoas que viviam na cidade, principalmente a chamada camada “popular”. / The present dissertation approaches Pelotas city during the middle of the XIXth century (1830-1857), from the perspective of justice practices. It makes use of several kinds of sources, since criminal lawsuits, journals, and administrative documents deriving from the Province and from the municipal district. In first place, it approaches the imposition of death penalty, then analyses projects to construct the first “Correction Place” in the area. The birth of the police came with these institutions, at the beginning as Permanent Municipal Guard, later as Police Force. It observes the imposition of these “European civilization models” to the justice practices, specifically the punishment and disciplinary measures, with focus on people´s reactions, mainly the so called “popular” layer of the society
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APLICAÇÃO DE MOLÉCULAS AUTO-ORGANIZÁVEIS (SAM) EM FILMES FINOS DE SnO2 / APPLICATION OF SELF ASSEMBLED MOLECULES (SAM) IN THIN FILMS SnO2Fáveri, Cintia de 06 August 2008 (has links)
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Previous issue date: 2008-08-06 / Thin films of tin dioxide (SnO2) with the addition of doping are widely used because its various applications, so develop a search on this subject is of great value technology, since
many different forms of doping, formulation and preparation, can be made and modified, intended to improve this material according to their physical and chemical properties.
This paper used for niobium oxide (Nb2O5) as doping, an important factor in the formulation, since Brazil has the largest reserves of natural element, found in various forms of
ore. The preparation of thin films is a process that requires great care and high quality control. However, care is not sufficient to avoid the appearance of defects in his deposition,
and subsequent calcination, as broken, deterioration, poor adhesion to the substrate, which are considered problems, undermining the efficiency of the material and its applicability. The addition of self assembled monolayers (SAM) on thin films of SnO2 aimed to reduce or correct this type of defect.
Different techniques were used experimentally, as: X-ray diffraction, fotochronoamperometric, eletrochemical impedance spectroscopy, electrochemistry, measures
of potential open circuit, optical microscopy optical, scanning electron microscopy and Infrared. The results of the measures to density of current and electrochemical impedance of
samples of thin films of SnO2 containing SAM showed positive results, confirming that the SAM not only improved the structure of films about the electrochemical properties and
photovoltaic, but also corrected the defects caused existing surface the techniques for the generation thin film.
The efficiency of photosensitive films studied increased in the following sequence: SnO2 + SAM < SnO2:Nb2O5(0.1) + SAM SnO2:Nb2O5(0.3) + SAM. The electrochemical impedance spectroscopy, showed that the addition of SAM to thin films studied in this work is diminishing Rtc, minimizing the resistance. The film of SnO2 containing 0.3 Nb2O5 + SAM presents a resistance around 1000 Wcm-1 less than the film
containing 0.1 Nb2O5. The thin films containing SAM showed that when immersed in the electrolyte solution, extending the capacitance of double layer electrical probably due to accumulation of cargo between the surface of films.
The scanning electron microscopy showed that the nucleation of SAM has a higher incidence of disruptions in the regions (of higher energy) in the form of needles and often mixed, needles and mushrooms, as observed for the film: SnO2: Nb2O5 (0.3 ) + SAM. / Filmes finos de dióxido de estanho (SnO2) com adição de dopantes são muito utilizados devido as suas diversas aplicações, assim o desenvolver de uma pesquisa sobre este
tema é de grande valia tecnológica, já que muitas formas diferentes de dopagem, formulação e preparação, podem ser feitas e modificadas, visando o melhoramento deste material em função de suas propriedades físicas e químicas.
Neste trabalho foi utilizado óxido de nióbio (Nb2O5) como dopante, um fator importante na formulação, já que o Brasil possui a maior reserva natural deste elemento, encontrado em várias formas de minérios. A preparação de filmes finos é um processo que exige muito cuidado e alto controle de qualidade. Porém, cuidados não são suficientes para evitar o aparecimento de defeitos em sua deposição e, posterior calcinação, como trincas, deteriorização, baixa aderência ao
substrato, que são considerados problemas, comprometendo a eficiência do material e sua aplicabilidade. A adição de moléculas auto-organizáveis (SAM) em filmes finos de SnO2 teve como objetivo reduzir ou corrigir este tipo de defeito.
Diferentes técnicas foram utilizadas experimentalmente, tais como: difração de raios X, fotocronoamperometria, espectroscopia de impedância eletroquímica, medidas de potencial de circuito aberto, micrografia óptica, microscopia eletrônica de varredura e Infravermelha. Os resultados das medidas de densidade de corrente e impedância eletroquímica das amostras dos filmes finos de SnO2 contendo SAM mostraram resultados positivos, confirmando que a SAM não só melhorou a estrutura dos filmes quanto às propriedades
eletroquímicas e fotovoltaicas, como também corrigiu os defeitos superficiais existentes provocados pelas técnicas de geração do filme fino. A eficiência fotossensível dos filmes
estudados aumentou na seguinte seqüência: SnO2 + SAM < SnO2:Nb2O5 (0,1) + SAM < SnO2:Nb2O5 (0,3) + SAM.
A espectroscopia de impedância eletroquímica mostrou que a adição de SAM aos filmes finos estudados neste trabalho diminui a Rtc, minimizando a resistência do mesmo. O
filme de SnO2 contendo 0,3 Nb2O5 + SAM apresenta uma resistência aproximadamente 1000 Wcm-1 menor do que o filme contendo 0,1 Nb2O5. Os filmes finos contendo SAM
mostraram que ao serem imersos na solução eletrolítica, ampliaram a capacitância da dupla camada elétrica devido provavelmente ao acúmulo de carga entre a superfície dos filmes. A microscopia eletrônica de varredura mostrou que a nucleação da SAM tem maior incidência nas regiões de rupturas (de maior energia) em forma de agulhas e muitas vezes mista, agulhas e cogumelos, como observado para o filme: SnO2:Nb2O5 (0,3) + SAM.
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How is an ant navigation algorithm affected by visual parameters and ego-motion?Ardin, Paul Björn January 2017 (has links)
Ants typically use path integration and vision for navigation when the environment precludes the use of pheromones for trails. Recent simulations have been able to accurately mimic the retinotopic navigation behaviour of these ants using simple models of movement and memory of unprocessed visual images. Naturally it is interesting to test these navigation algorithms in more realistic circumstances, particularly with actual route data from the ant, in an accurate facsimile of the ant world and with visual input that draws on the characteristics of the animal. While increasing the complexity of the visual processing to include skyline extraction, inhomogeneous sampling and motion processing was conjectured to improve the performance of the simulations, the reverse appears to be the case. Examining closely the assumptions about motion, analysis of ants in the field shows that they experience considerable displacement of the head which when applied to the simulation leads to significant degradation in performance. The family of simulations rely upon continuous visual monitoring of the scene to determine heading and it was decided to test whether the animals were similarly dependent on this input. A field study demonstrated that ants with only visual navigation cues can return the nest when largely facing away from the direction of travel (moving backwards) and so it appears that ant visual navigation is not a process of continuous retinotopic image matching. We conclude ants may use vision to determine an initial heading by image matching and then continue to follow this direction using their celestial compass, or they may use a rotationally invariant form of the visual world for continuous course correction.
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Práticas de correção e aprendizagem: produção de subjetividades na contemporaneidadeMorgenstern, Juliane Marschall 25 February 2016 (has links)
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Previous issue date: 2016-02-25 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / PROEX - Programa de Excelência Acadêmica / Ao tomar como referência os crescentes programas de correção de fluxo idade-série e de Aceleração da Aprendizagem atualmente divulgados no Brasil, a presente pesquisa propõe-se problematizar como operam as práticas de correção e seus efeitos no mundo contemporâneo. Mais especificamente, é analisado o funcionamento das práticas de correção e seus efeitos no âmbito da educação brasileira. Embora o conjunto de materiais mobilizados para a elaboração desta tese tenha sido bastante amplo, para a realização da investigação o corpus foi formado a partir dos materiais didáticos e da sistematização de programas de correção de fluxo escolar que atuam pela aceleração da aprendizagem, produzidos no Brasil, a partir da década de 1990. Também compõem o corpus, vinte depoimentos escritos de sujeitos que integram as atividades dos programas e discutem suas experiências. Constatou-se um deslocamento nos modos de praticar a correção nas últimas décadas, cuja centralidade se volta à regulação do fluxo escolar e não mais a uma ortopedia do corpo individual. As análises conduziram a investigação para a proveniência das práticas corretivas num contexto temporalmente mais amplo, a qual se efetivou por meio de uma historicização de inspiração genealógica. Ao traçar um mapa panorâmico, foram encontradas quatro ênfases de atuação distintas no que se refere à finalidade (télos) dos modos de correção. A primeira ênfase está localizada no contexto da Antiguidade Pagã; a segunda ênfase é encontrada na Antiguidade Cristã; a terceira, nos desdobramentos das tecnologias disciplinares instauradas na Modernidade; a quarta ênfase concerne à atuação das tecnologias de seguridade, cuja evidência é visível na Contemporaneidade. Constatou-se ainda, que no seu modo de funcionamento, as práticas corretivas contemporâneas convergem com a constituição de uma subjetividade aprendente (Homo discentis), produzida na passagem do século XIX para o século XX. Nas condições de uma aprendizagem ao longo da vida, há um redirecionamento nas práticas de correção, cuja proeminência se direciona à construção de subjetividades que se tornem autorrealizáveis. Ficou visível a produtividade dessas práticas ao posicionarem o aprendente em determinadas condições, produzindo-o como uma subjetividade investida de aceleração. Compreendeu-se que o indivíduo subjetivado para a aprendizagem permanente deve ser capaz de corrigir-se em qualquer circunstância e em qualquer momento, de modo a se ajustar a um mundo no qual a mudança é constante. Tal como a possibilidade de agir sobre si mesmo e de ser ativo colocou-se como condição que sempre esteve presente nas ações praticadas pelos alunos, a esses também esteve implicada a condição de ser corrigido ou de se corrigir. Analisou-se que a correção está presente como algo permanente e necessário na constituição de uma subjetividade aprendente. / Taking as reference the growing programs of age-grade flow correction and Accelerated Learning currently disclosed in Brazil, this research aims to discuss how the correction practices operate and their effects on contemporary world. More specifically, the operation of correction practices and their effects are analyzed in the Brazilian education nowadays. Although the materials mobilized for the preparation of this Thesis has been quite broad, to carry out the research the corpus was composed from the teaching materials and the systematization of school flow programs that work for accelerated learning, produced in Brazil, since the 1990s. Twenty depositions of subjects that integrate program activities and discuss their experiences also make up the corpus. It was found a shift in the ways of correction practices in recent decades, whose centrality turns to the regulation of school flow and not to an individual body orthopedics. Analyses conducted the investigation for the descent of corrective practices in a temporally broader context, which was accomplished through a historicizing of genealogical inspiration. In tracing a panoramic map, were found four distinct acting emphases with regard to the purpose (télos) of the correction modes. The first emphasis is located in the context of Pagan Antiquity; the second emphasis is found in Christian Antiquity; the third, in the unfolding of the disciplinary technologies introduced in Modernity; and the fourth emphasis concerns the actions of security technologies, whose evidence is visible in Contemporaneity. It found also that, in its mode of operation, the contemporary corrective practices converge with the creation of a learning subjectivity (Homo discentis), produced in the late 19th century to the 20th century. Under the conditions of learning through life (lifelong learning), there is a redirecting on correction practices, whose prominence is directed to the construction of subjectivities that become self-fulfilling. The productivity of these practices became visible when positioning the learner under certain conditions, producing him as a subjectivity invested by acceleration. Thus, it was found that the individual subjectivized to lifelong learning should be able to correct itself in any circumstances and at any time, in order to adjust himself to a world where change is constant. Such as the possibility to act on itself and being active is put as a condition that has always been present in the actions practiced by students, to these students was also implicated the condition to be corrected or to correct itself. It was found that the correction is present as something permanent and necessary in the constitution of a learning subjectivity.
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Classify-normalize-classify : a novel data-driven framework for classifying forest pixels in remote sensing images / Classifica-normaliza-classifica : um nova abordagem para classficar pixels de floresta em imagens de sensoriamento remotoSouza, César Salgado Vieira de January 2017 (has links)
O monitoramento do meio ambiente e suas mudanças requer a análise de uma grade quantidade de imagens muitas vezes coletadas por satélites. No entanto, variações nos sinais devido a mudanças nas condições atmosféricas frequentemente resultam num deslocamento da distribuição dos dados para diferentes locais e datas. Isso torna difícil a distinção dentre as várias classes de uma base de dados construída a partir de várias imagens. Neste trabalho introduzimos uma nova abordagem de classificação supervisionada, chamada Classifica-Normaliza-Classifica (CNC), para amenizar o problema de deslocamento dos dados. A proposta é implementada usando dois classificadores. O primeiro é treinado em imagens não normalizadas de refletância de topo de atmosfera para distinguir dentre pixels de uma classe de interesse (CDI) e pixels de outras categorias (e.g. floresta versus não-floresta). Dada uma nova imagem de teste, o primeiro classificador gera uma segmentação das regiões da CDI e então um vetor mediano é calculado para os valores espectrais dessas áreas. Então, esse vetor é subtraído de cada pixel da imagem e portanto fixa a distribuição de dados de diferentes imagens num mesmo referencial. Finalmente, o segundo classificador, que é treinado para minimizar o erro de classificação em imagens já centralizadas pela mediana, é aplicado na imagem de teste normalizada no segundo passo para produzir a segmentação binária final. A metodologia proposta foi testada para detectar desflorestamento em pares de imagens co-registradas da Landsat 8 OLI sobre a floresta Amazônica. Experimentos usando imagens multiespectrais de refletância de topo de atmosfera mostraram que a CNC obteve maior acurácia na detecção de desflorestamento do que classificadores aplicados em imagens de refletância de superfície fornecidas pelo United States Geological Survey. As acurácias do método proposto também se mostraram superiores às obtidas pelas máscaras de desflorestamento do programa PRODES. / Monitoring natural environments and their changes over time requires the analysis of a large amount of image data, often collected by orbital remote sensing platforms. However, variations in the observed signals due to changing atmospheric conditions often result in a data distribution shift for different dates and locations making it difficult to discriminate between various classes in a dataset built from several images. This work introduces a novel supervised classification framework, called Classify-Normalize-Classify (CNC), to alleviate this data shift issue. The proposed scheme uses a two classifier approach. The first classifier is trained on non-normalized top-of-the-atmosphere reflectance samples to discriminate between pixels belonging to a class of interest (COI) and pixels from other categories (e.g. forest vs. non-forest). At test time, the estimated COI’s multivariate median signal, derived from the first classifier segmentation, is subtracted from the image and thus anchoring the data distribution from different images to the same reference. Then, a second classifier, pre-trained to minimize the classification error on COI median centered samples, is applied to the median-normalized test image to produce the final binary segmentation. The proposed methodology was tested to detect deforestation using bitemporal Landsat 8 OLI images over the Amazon rainforest. Experiments using top-of-the-atmosphere multispectral reflectance images showed that the deforestation was mapped by the CNC framework more accurately as compared to running a single classifier on surface reflectance images provided by the United States Geological Survey (USGS). Accuracies from the proposed framework also compared favorably with the benchmark masks of the PRODES program.
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Evaluation of statistical methods, modeling, and multiple testing in RNA-seq studiesChoi, Seung Hoan 12 August 2016 (has links)
Recent Next Generation Sequencing methods provide a count of RNA molecules in the form of short reads, yielding discrete, often highly non-normally distributed gene expression measurements. Due to this feature of RNA sequencing (RNA-seq) data, appropriate statistical inference methods are required. Although Negative Binomial (NB) regression has been generally accepted in the analysis of RNA-seq data, its appropriateness in the application to genetic studies has not been exhaustively evaluated. Additionally, adjusting for covariates that have an unknown relationship with expression of a gene has not been extensively evaluated in RNA-seq studies using the NB framework. Finally, the dependent structures in RNA-Seq data may violate the assumptions of some multiple testing correction methods. In this dissertation, we suggest an alternative regression method, evaluate the effect of covariates, and compare various multiple testing correction methods. We conduct simulation studies and apply these methods to a real data set. First, we suggest Firth’s logistic regression for detecting differentially expressed genes in RNA-seq data. We also recommend the data adaptive method that estimates a recalibrated distribution of test statistics. Firth’ logistic regression exhibits an appropriately controlled Type-I error rate using the data adaptive method and shows comparable power to NB regression in simulation studies. Next, we evaluate the effect of disease-associated covariates where the relationship between the covariate and gene expression is unknown. Although the power of NB and Firth’s logistic regression is decreased as disease-associated covariates are added in a model, Type-I error rates are well controlled in Firth’ logistic regression if the relationship between a covariate and disease is not strong. Finally, we compare multiple testing correction methods that control family-wise error rates and impose false discovery rates. The evaluation reveals that an understanding of study designs, RNA-seq data, and the consequences of applying specific regression and multiple testing correction methods are very important factors to control family-wise error rates or false discovery rates. We believe our statistical investigations will enrich gene expression studies and influence related statistical methods.
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