[pt] Os problemas de alocação de recurso procuram encontrar uma repartição ideal de recursos a um número fixo de áreas. Nesta dissertação, consideramos um problema de alocação de recurso com uma função objetiva linear e dois conjuntos distintos de restrições: um conjunto de restrições aninhados, onde as somas parciais das variáveis de decisão são limitadas por cima e uma restrição linear que define um hiperplano. Propomos um algoritmo fracamente e um fortemente polinomial. O algoritmo fracamente polinomial requer algumas suposições sobre os dados e possui complexidade de O(n log n log |Λ|/|I|), onde n é o número de variáveis, Λ é um intervalo no espaço dual, e |I| está relacionado com a precisão dos dados. O algoritmo fortemente polinomial é baseado na técnica de busca paramétrica de Megiddo e obtém uma complexidade O(n log n). As complexidades obtidas são superiores à complexidade do método genérico de Pontos Interiores, O(n 3/ log n). Além disso, uma análise experimental foi realizada e os algoritmos mostraram-se mais eficientes e produziram soluções ótimas para instâncias de problemas com até 1.000.000 variáveis. / [en] The Resource Allocation Problems seek to find an optimal repartition of resources into a fixed number of areas. In this thesis, we consider a resource allocation problem with a linear objective and two distinct sets of constraints: a set of nested constraints, where the partial sums of the decision variables are limited from above and a linear constraint that defines a hyperplane. We propose a weakly and a strongly polynomial algorithm. The weakly polynomial algorithm requires certain assumptions of the data and runs in O(n log n log |Λ|/|I|) time, where n is the number of decision variables, Λ is an interval in the dual space, and |I| relates to the precision of the data. The strongly polynomial algorithm is based on Megiddo s parametric search technique, and obtains a complexity of O(n log n). These are large improvements upon the O(n 3/ log n) complexity of the generic Interior Point Method. In addition, an experimental analysis was carried out and the algorithms showed to be more efficient and produced optimal solutions for problem instances with up to 1,000,000 variables.

This dissertation focuses on studying various network formation games in Economics. We explore a different model in each chapter to capture various aspects of networks. Chapter 1provides an overview of this dissertation. Chapter 2 studies the possible Nash equilibrium configurations in a model of signed network formation as proposed by Hiller (2017). We specify the Nash equilibria in the case of heterogeneous agents. We find 3 possible Nash equilibrium configurations: Utopia network, positive assortative matching, and disassortative matching. We derive the specific conditions under which they arise in a Nash equilibrium. In Chapter 3, we study a generalized model of signed network formation game where the players can choose not only positive and negative links but also neutral links. We check whether the results of the signed network formation model in the literature still hold in our generalized framework using the notion of pairwise Nash equilibrium. Chapter 4 studies inequality in a weighted network formation model using the notion of Nash equilibrium. As a factor of inequality, there are two types of players: Rich players and poor players. We show that both rich and poor players designate other rich players as their best friends. As a result, We present that nested split graphs are drawn from survey data because researchers tend to ask respondents to list only a few friends. / Doctor of Philosophy / This dissertation focuses on studying various network formation games in Economics. We explore a different model in each chapter to capture various aspects of networks. Chapter 1 provides an overview of this dissertation. Chapter 2 studies the possible singed network configurations in equilibrium. In the signed network, players can choose a positive (+) relationship or a negative (-) relationship toward each other player. We study the case that the players are heterogeneous. We find 3 possible categories of networks in equilibrium: Utopia network, positive assortative matching, and disassortative matching. We derive the specific conditions under which they arise in equilibrium. In Chapter 3, we study a generalized model of signed network formation game where the players can choose not only positive and negative links but also neutral links. We check whether the results of the signed network formation model in the literature still hold in our generalized framework. Chapter 4 studies inequality in a weighted network formation model using the notion of Nash equilibrium. In this weighted network model, each player can choose the level of relationship. As a factor of inequality, there are two types of players: rich players and poor players. We show that both rich and poor players choose other rich players as their best friends. As a result, we present that nested split graphs are drawn from survey data because these social network data are censored due to the limit of the number of responses.

<p dir="ltr">Uncovering the mechanisms of senescence in maize will give us a deeper understanding needed to drive future yield increases. Previous work on senescence response to sink disruption has identified a set of genes and biochemical mechanisms. Still, little is understood about the impact of this phenotype on yield and other commercially relevant traits. Uncovering the genetic basis of senescence in maize and testing the effect of these alleles on yield will provide a mechanistic framework for considering this trait to drive future yield increases.</p><p dir="ltr">Ear removal experiments demonstrated that senescence timing is insensitive to the presence or absence of an ear outside a critical window from 10 to 45 days after pollination. Nitrogen fertilization did not impact the SSRS response measured in the upper canopy. In further characterizing the SSRS phenotype, we have provided a spatial and temporal map of the B73 senescence response to sink disruption from the top of the plant to the ear leaf and discovered that this phenomenon is dose dependent and proportional to the size of the sink across two genotypes and years. This relationship was successfully used to predict kernel numbers and grain weight from spectral leaf properties as early as 4 weeks after pollination using remote sensing under agronomic conditions.</p><p dir="ltr">A population of 343 exPVP inbred lines was evaluated for source-sink regulated senescence and hybrid testcrosses were made for a subset of 200 inbred lines to testers for measurement of yield and ear photometry phenotypes. Source-sink regulated senescence of inbred parents was correlated with the yield of intra-family hybrids but was not generally correlated with the yield of hybrids made from crosses between two heterotic groups. The presence of multiple significant SNP association at the Bonferroni-corrected threshold at loci that are associated both with kernel traits and SSRS suggests shared genetic regulation of two traits that is likely driving the observed trait correlations of SSRS with kernel size and yield.</p><p dir="ltr">The maize nested association mapping (NAM) parents reveal a previously unknown breadth of SSRS phenotypes in the global diversity of maize germplasm. Mapping genes for SSRS in the NAM populations supports previously reported loci with large, dominant effects as well as evidence for previously unreported modifiers that are capable of suppressing the dominant alleles and producing a quantitative distribution in SSRS phenotypes. There are distinct alleles within sub-populations worth further study such as sweetcorn populations with non-senescence responses to sink disruption. A multi-factor analysis for QTL mapping, GWAS, and mutant variant sequencing identified highly significant loci on chromosomes 1 from 30.4Mbp to 35.8Mbp, chromosome 2 from 183.2Mbp to 190.8Mbp, chromosome 4 from 38.2Mbp to 134.8Mbp (crosses a centromere), chromosome 5 from 140.8Mbp to 233.9Mbp, chromosome 8 from 112.5Mbp to 123.8Mbp, and chromosome 8 from 155.7Mbp to 163.9Mbp. Candidate genes co-located with Bonferroni SNP in these regions may contribute to SSRS phenotypes through regulation of autophagy, accumulation of flavonoids, and sequestration of sugar in cell walls as an alternative sink. It is possible that co-regulation of these genes could cause all of them to be involved in the stress response of B73 to sugar accumulation. To find the causal variants for these traits, fine mapping and comparisons of near-isogenic lines will be required to narrow the list of candidate genes. Uncovering the alleles responsible for SSRS in global maize diversity could provide the building blocks for a physiological approach to increasing yields through optimizing the senescence responses to elevated sugar levels during grain-fill.</p>

This study compared 3 approaches for handling a fourth level of nesting structure when analyzing data from a cluster-randomized trial (CRT). CRTs can include 3 levels of nesting: repeated measures, individual, and cluster levels. However, above the cluster level, there may sometimes be an additional potentially important fourth level of nesting (e.g., schools, districts, etc., depending on the design) that is typically ignored in CRT data analysis. The current study examined the impact of ignoring this fourth level, accounting for it using a model-based approach, and accounting it using a design-based approach on parameter and standard error (SE) estimates. Several fixed effect and random effect variance parameters and SEs were biased across all 3 models. In the 4-level model, most SE biases decreased as the number of level 3 clusters increased and as the number of level 4 clusters decreased. Also, random effect variance biases decreased as the number of level 3 clusters increased. In the 3-level and complex models, SEs became more biased as the weight level 4 carried increased (i.e., larger intraclass correlation, more clusters at that level). The current results suggest that if a meaningful fourth level of nesting exists, future researchers should account for it using design-based approach; the model-based approach is not recommended. If the fourth level is not practically important, researchers may ignore it altogether.

O vírus linfotrópico das células T humanas tipo 1 (HTLV-1), é responsável por patologias como a mielopatia associada ao HTLV-1 ou paraparesia espástica tropical (HAM/TSP) e a leucemia/linfoma das células T do adulto (ATL) dentre outras. As vias de replicação até hoje demonstradas, não suportam a hipótese de um estado virêmico. Neste estudo, a detecção de partículas virais plasmáticas foi executada, por PCR em Tempo Real e Nested PCR em 190 amostras de pacientes infectados pelo HTLV-1(assintomáticos ou com HAM/TSP), em acompanhamento, no Instituto de Infectologia Emílio Ribas. 12 indivíduos (8%) testados por PCR em tempo real (n=150) e 6 indivíduos (18%) testados por Nested PCR (n=33, dado que sete amostras foram excluídas da análise) apresentaram RNA do HTLV-1 detectável no plasma. Em conclusão, foi possível identificar RNA plasmático do HTLV-1, tanto em pessoas assintomáticas quanto com HAM/TSP. Esta detecção abre novas possibilidades de discussão sobre a replicação do HTLV-1 e das vias de transmissão, sugerindo maiores investigações para elucidar o assunto. / The human T-cell lymphotropic virus type1 (HTLV-1) is responsible for some pathologies such as HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) and Adult T-cell Leukemia/ Lymphoma (ATL) among others. Its ways of replication so far presented do not support the hypothesis of a viremic stage. In this study, the detection of the plasmatic viral load was performed by real time PCR and Nested PCR in 190 samples from HTLV-1 infected individuals (Either Asymptomatic or HAM/TSP cases) following up at Instituto de Infectologia Emílio Ribas. 12 individuals (8%) tested by Real time PCR (n= 150) and 6 individuals (18%) tested by Nested PCR (n= 33, given that 7 samples were excluded from the analysis) presented detectable HTLV-1 RNA in the plasma. In conclusion, it was possible to indentify HTLV-1 plasmatic RNA in asymptomatic carriers as well as in HAM/TSP cases. This detection opens new possibilities of discussion about HTLV-1 replication and transmission pathways, suggesting further investigation for clarifying this matter.

This thesis is concerned with methods for Bayesian inference and their applications in astrophysics. We principally discuss two related themes: advances in nested sampling (Chapters 3 to 5), and Bayesian sparse reconstruction of signals from noisy data (Chapters 6 and 7). Nested sampling is a popular method for Bayesian computation which is widely used in astrophysics. Following the introduction and background material in Chapters 1 and 2, Chapter 3 analyses the sampling errors in nested sampling parameter estimation and presents a method for estimating them numerically for a single nested sampling calculation. Chapter 4 introduces diagnostic tests for detecting when software has not performed the nested sampling algorithm accurately, for example due to missing a mode in a multimodal posterior. The uncertainty estimates and diagnostics in Chapters 3 and 4 are implemented in the $\texttt{nestcheck}$ software package, and both chapters describe an astronomical application of the techniques introduced. Chapter 5 describes dynamic nested sampling: a generalisation of the nested sampling algorithm which can produce large improvements in computational efficiency compared to standard nested sampling. We have implemented dynamic nested sampling in the $\texttt{dyPolyChord}$ and $\texttt{perfectns}$ software packages. Chapter 6 presents a principled Bayesian framework for signal reconstruction, in which the signal is modelled by basis functions whose number (and form, if required) is determined by the data themselves. This approach is based on a Bayesian interpretation of conventional sparse reconstruction and regularisation techniques, in which sparsity is imposed through priors via Bayesian model selection. We demonstrate our method for noisy 1- and 2-dimensional signals, including examples of processing astronomical images. The numerical implementation uses dynamic nested sampling, and uncertainties are calculated using the methods introduced in Chapters 3 and 4. Chapter 7 applies our Bayesian sparse reconstruction framework to artificial neural networks, where it allows the optimum network architecture to be determined by treating the number of nodes and hidden layers as parameters. We conclude by suggesting possible areas of future research in Chapter 8.

臺灣的連鎖式便利商店密度居世界之冠，為數眾多的門市使得便利商店與臺灣人 民的生活息息相關，就直覺來說，便利商店門市的數量也影響了廠商設立新門市 的決策。本研究建構了一離散選擇的動態賽局，分析臺北市各個行政區便利商店 門市數量對不同廠商設立新門市的影響。實證結果顯示當競爭對手門市數量剛開 始增加時，門市數量對便利商店的利潤有正向的影響，但是當對手門市數量太多 時，此數量的增加對便利商店的利潤產生負向影響。這結果表示一開始門市之間 的互補效果大於替代效果，但是門市數量太多造成過度競爭，此時門市之間的替 代效果大於互補效果。而同品牌的門市數量對於廠商的總利潤也有類似的影響。 另外，本研究也估計便利商店歷年來在臺北市各行政區展店的機率，其中大安區 和中山區是便利商店廠商最想展店的行政區，相對而言，南港區、大同區和萬華 區則是展店機率較低的行政區。 / The density of convenience stores (CVS) in Taiwan is ranked as number one in the world. The highly concentrated market of convenience stores has dramatically changed the lifestyle of Taiwanese people. The number of existing outlets in a region is also an important factor in regard to the entry decisions of new outlets. In this study, we construct a model of the dynamic discrete game, and examine the influence of the rival outlet number on CVS entry decisions in Taipei, Taiwan. The empirical evidence we find is that the CVS profits first rise and then decline as the own or rival outlet number increases. This result implies that the complement and substitution effects vary with the number of the CVS outlets in a specific region. Furthermore, we estimate the probabilities that the CVS companies will set up additional outlets in any district of Taipei during the data period. The results show that it is most likely for the companies to enter the Da’an and Zhongshan districts, while Nangang, Datong and Wanhua are districts with low entry probabilities.

O vírus linfotrópico das células T humanas tipo 1 (HTLV-1), é responsável por patologias como a mielopatia associada ao HTLV-1 ou paraparesia espástica tropical (HAM/TSP) e a leucemia/linfoma das células T do adulto (ATL) dentre outras. As vias de replicação até hoje demonstradas, não suportam a hipótese de um estado virêmico. Neste estudo, a detecção de partículas virais plasmáticas foi executada, por PCR em Tempo Real e Nested PCR em 190 amostras de pacientes infectados pelo HTLV-1(assintomáticos ou com HAM/TSP), em acompanhamento, no Instituto de Infectologia Emílio Ribas. 12 indivíduos (8%) testados por PCR em tempo real (n=150) e 6 indivíduos (18%) testados por Nested PCR (n=33, dado que sete amostras foram excluídas da análise) apresentaram RNA do HTLV-1 detectável no plasma. Em conclusão, foi possível identificar RNA plasmático do HTLV-1, tanto em pessoas assintomáticas quanto com HAM/TSP. Esta detecção abre novas possibilidades de discussão sobre a replicação do HTLV-1 e das vias de transmissão, sugerindo maiores investigações para elucidar o assunto. / The human T-cell lymphotropic virus type1 (HTLV-1) is responsible for some pathologies such as HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) and Adult T-cell Leukemia/ Lymphoma (ATL) among others. Its ways of replication so far presented do not support the hypothesis of a viremic stage. In this study, the detection of the plasmatic viral load was performed by real time PCR and Nested PCR in 190 samples from HTLV-1 infected individuals (Either Asymptomatic or HAM/TSP cases) following up at Instituto de Infectologia Emílio Ribas. 12 individuals (8%) tested by Real time PCR (n= 150) and 6 individuals (18%) tested by Nested PCR (n= 33, given that 7 samples were excluded from the analysis) presented detectable HTLV-1 RNA in the plasma. In conclusion, it was possible to indentify HTLV-1 plasmatic RNA in asymptomatic carriers as well as in HAM/TSP cases. This detection opens new possibilities of discussion about HTLV-1 replication and transmission pathways, suggesting further investigation for clarifying this matter.

This diploma thesis deals with adjusting the reverberation time of enclosed spaces. It is divided into two thematic areas. The first thematic area deals with active systems that adjust the reverberation time, with a stronger focus on usage of reverberators to simulate secondary spaces. The second thematic area is the implementation of reverberators and their fundamental building blocks in Matlab.

Historically, wireless communication security solutions have heavily relied on computational methods, such as cryptographic algorithms implemented in the upper layers of the network stack. Although these methods have been effective, they may not always be sufficient to address all security threats. An alternative approach for achieving secure communication is the physical layer security approach, which utilizes the physical properties of the communication channel through appropriate coding and signal processing. The goal of this Ph.D. dissertation is to leverage the foundations of information-theoretic security to develop innovative and secure schemes, as well as code design techniques, that can enhance security and reliability in wireless communication networks. This dissertation includes three main phases of investigation. The first investigation analyzes the finite blocklength coding problem for the wiretap channel model which is equipped with the cache. The objective was to develop and analyze a new wiretap coding scheme that can be used for secure communication of sensitive data. Secondly, an investigation was conducted into information-theoretic security solutions for aeronautical mobile telemetry (AMT) systems. This included developing a secure coding technique for the integrated Network Enhanced Telemetry (iNET) communications system, as well as examining the potential of post-quantum cryptography approaches as future secrecy solutions for AMT systems. The investigation focused on exploring code-based techniques and evaluating their feasibility for implementation. Finally, the properties of nested linear codes in the wiretap channel model have been explored. Investigation in this phase began by exploring the duality relationship between equivocation matrices of nested linear codes and their corresponding dual codes. Then a new coding algorithm to construct the optimum nested linear secrecy codes has been invented. This coding algorithm leverages the aforementioned duality relationship by starting with the worst nested linear secrecy codes from the dual space. This approach enables us to derive the optimal nested linear secrecy code more efficiently and effectively than through a brute-force search for the best nested linear secrecy codes directly.