Reproductive division of labor is the most distinctive characteristic of the social Hymenoptera; some individuals reproduce and others forego their own reproduction to raise non-descendant offspring. In species where females are reproductively totipotent and lack morphologically distinct castes, there is potential for reproductive conflict because more than one female in a colony may attempt direct reproduction. I focused my dissertation research on a subtropical population of the primitively eusocial paper wasp, Mischocyttarus mexicanus, to investigate the initiation, establishment, and development of the colony before the emergence of adult offspring. Female M. mexicanus exhibit variation in behavior and task performance, and switch between reproductive and non-reproductive roles. These changes in behavior and reproduction may be influenced by social context. In three studies, I investigated the role of social context on reproduction, behavior, and brain structure. In the first study, I tested the role of body size, reproductive potential, and immediate egg-laying potential on the reproductive tactic employed by females. I found that large females either became solitary foundresses or became part of a group-initiated colony. In contrast, small females left their natal colony and pursued joining other colonies. This joiner tactic is unique to this population and has not been observed in temperate zone populations. I also found that subordinate females had the potential to lay eggs if given the opportunity. This suggests an incentive to remain in a colony for future opportunities of direct reproduction. In the second study, I investigated the effect of three variables on non-nestmate acceptance: non-nestmate age, stage of colony development, and non-nestmate aggressive behavior. I demonstrated that non-nestmate acceptance was context-dependent. Both non-nestmate age and stage of colony development had an effect on the proportion of accepted non-nestmates. Although, non-nestmate aggressive behavior did not affect non-nestmate acceptance, it did trigger an aggressive response from colony nestmates. In the third study, I assessed the relationship of Mushroom Bodies (MB) volume, the brain neuropils associated with learning and memory, to environmental conditions and social interactions. I compared MB volume of newly-established colonies initiated by solitary foundresses to groups of foundresses. In addition, I performed laboratory experiments to differentiate between the effect of environmental conditions and social interactions. I found a positive relationship between MB volume and environmental conditions including light intensity and foraging experience. In contrast to previous studies, I found no association between MB volume and social interactions. Ovary development was positively correlated with MB development. This result suggests that although reproductive dominance is established in newly-initiated colonies, social dominance may not yet be established. In summary, my studies found an effect of social context on behavior, adoption of reproductive tactics and brain structure in colonies of M. mexicanus during the offspring pre-emergence phase.

A comprehensive understanding of how the body and all its components function is essential when this knowledge is exploited for medical purposes. The achievements in biological and medical research during last decades has provided us with the complete human genome and identified signaling pathways that governs the cellular processes that facilitates the development and maintenance of higher order organisms. This has brought about the realization that diseases such as cancer is a consequence of genomic aberrations that effects these signaling pathways, endowing cancer cells with the capacity to circumvent homeostasis by acquiring features like self-sustained proliferation and insensitivity to apoptosis. The increased understanding of biology and medicine has been made possible by the development of advanced methods to carry out biological and clinical analyses. The demands of a method often differ regarding in what context it will be applied. It may be acceptable for method to be laborious and time consuming if it is used in basic research, but for medical purposes molecular methods need to be fast and straightforward to perform. Innovative technologies should preferentially address the demands of both researchers and clinicians and provide data not possible to obtain by other methods. An example of such a method is the in situ proximity ligation assay (in situ PLA). In this thesis I have used this method to determine the activity status, at the single-cell level, of the transforming growth factor-β (TGF-β) signaling pathway and activating protein-1 (AP-1) family of transcription factors.  Both of these pathways are frequently involved in cancer development and progression. In addition to this research I herein also present further modifications of in situ PLA, and analyses thereof, to increase the utility and resolution of this assay.

Source transformation systems are special-purpose programming languages, or in some cases suites of languages, that are designed for the analysis and transformation of computer languages. They enable rapid prototyping of programming languages, source code renovation, language-to-language translation, design recovery, and other custom analysis techniques. With the emergence of these systems a serious problem is evident: expressing a parser for common computer languages is sometimes very difficult. Source transformation systems employ generalized parsing algorithms, and while these are well suited for the kind of agile parsing techniques in use by transformation practitioners, they are not well suited for parsing languages that are context-dependent. Traditional deterministic parser generators do not stumble in this area, but they sacrifice the generalized parsing abilities that transformation systems depend on. When it is hard to get the input into the system as a correct and accurate parse tree the utility of the unified transformation environment is degraded and more ad hoc approaches become attractive for processing input. This thesis is about the design of a new computer language transformation system with a focus on enhancing the parsing system to support generalized context-dependent parsing. We argue for the use of backtracking LR as the generalized parsing algorithm. We present an enhancement to backtracking LR that allows us to control the parsing of an ambiguous grammar by ordering the productions of the grammar definitions. We add a grammar-dependent lexical solution and integrate it with our ordered choice parsing strategy. We design a transformation language that is closer to general-purpose programming languages, yet enables common transformation techniques. We add semantic actions to our backtracking LR parsing engine and encourage the modification of global state in support of context-dependent parsing. We introduce semantic undo actions for reverting changes to global state during backtracking, thereby enabling generalized context-dependent parsing. Finally, we free the user from having to write undo actions by employing automatic reverse execution. The resulting system allows a wider variety of computer languages to be analyzed. By focusing on improving parsing abilities and moving to a transformation language that resembles general-purpose languages, we aim to extend the transformation paradigm to allow greater use by practitioners who face an immediate need to parse, analyze and transform computer languages. / Thesis (Ph.D, Computing) -- Queen's University, 2008-12-15 21:01:24.236

O presente trabalho desenvolve um modelo capaz de descrever preferências dependentes de contexto, buscando superar as limitações impostas pela abordagem da preferência revelada. O espaço informacional no ato da escolha é ampliado através da incorporação de uma segunda dimensão, na forma de um novo tipo de utilidade, dita social ou moral, representativa do contexto no qual a escolha é realizada. As dimensões são assumidas incomensuráveis entre si, uma característica típica de escolhas que envolvem questões morais. A impossibilidade de comparação entre duas alternativas, cada qual superior à outra em uma dimensão distinta, é resolvida através de uma simetria rotacional capaz de preservar a relação sujacente entre ambas utilidades. O modelo é baseado, fundamentalmente, nos trabalhos de Amartya Sen (1974, 1977, 1993, 1997) e Amitai Etzioni (1986), incorporando conceitos de utilidade moral (ETZIONI, 1986), dependência de contexto no ato da escolha (SEN, 1993, 1997), inescapabilidade ou urgência da escolha (SEN, 1997), auto-imposição de limites à escolha (SEN, 1997; ETZIONI, 1986), commitment, entendido como divisão entre escolha e bem-estar (SEN, 1977) e flexibilidade cognitiva dos indivíduos (ARIELY, 2012). / In this work, we develop a model that is able to describe context-dependent preferences, trying to overcome the limitations given by the revealed preference approach. The informational space in the act of choice is broadened by incorporating a second dimension, as a new type of utility, called social or moral, representing the context within the choice is made. The dimensions are deemed incommensurable, a typical characteristic of moral-related choices. The impossibility of comparison between two alternatives, where each alternative is the superior one in a different dimension, is resolved through a rotational symmetry able to preserve the underlying relationship between the two utilities. The model is fundamentally based on the works of Amartya Sen (1974, 1977, 1993, 1997) and Amitai Etzioni (1986), making use of the concepts of moral utility (ETZIONI, 1986), context-dependency in the act of choice (SEN, 1993, 1997), inescapability or urgency of the choice (SEN, 1997), self-imposing limits to choice (SEN, 1997; ETZIONI, 1986), commitment, understood as a wedge between choice and welfare (SEN, 1977) and the cognitive flexibility of the individuals (ARIELY, 2012).

O presente trabalho desenvolve um modelo capaz de descrever preferências dependentes de contexto, buscando superar as limitações impostas pela abordagem da preferência revelada. O espaço informacional no ato da escolha é ampliado através da incorporação de uma segunda dimensão, na forma de um novo tipo de utilidade, dita social ou moral, representativa do contexto no qual a escolha é realizada. As dimensões são assumidas incomensuráveis entre si, uma característica típica de escolhas que envolvem questões morais. A impossibilidade de comparação entre duas alternativas, cada qual superior à outra em uma dimensão distinta, é resolvida através de uma simetria rotacional capaz de preservar a relação sujacente entre ambas utilidades. O modelo é baseado, fundamentalmente, nos trabalhos de Amartya Sen (1974, 1977, 1993, 1997) e Amitai Etzioni (1986), incorporando conceitos de utilidade moral (ETZIONI, 1986), dependência de contexto no ato da escolha (SEN, 1993, 1997), inescapabilidade ou urgência da escolha (SEN, 1997), auto-imposição de limites à escolha (SEN, 1997; ETZIONI, 1986), commitment, entendido como divisão entre escolha e bem-estar (SEN, 1977) e flexibilidade cognitiva dos indivíduos (ARIELY, 2012). / In this work, we develop a model that is able to describe context-dependent preferences, trying to overcome the limitations given by the revealed preference approach. The informational space in the act of choice is broadened by incorporating a second dimension, as a new type of utility, called social or moral, representing the context within the choice is made. The dimensions are deemed incommensurable, a typical characteristic of moral-related choices. The impossibility of comparison between two alternatives, where each alternative is the superior one in a different dimension, is resolved through a rotational symmetry able to preserve the underlying relationship between the two utilities. The model is fundamentally based on the works of Amartya Sen (1974, 1977, 1993, 1997) and Amitai Etzioni (1986), making use of the concepts of moral utility (ETZIONI, 1986), context-dependency in the act of choice (SEN, 1993, 1997), inescapability or urgency of the choice (SEN, 1997), self-imposing limits to choice (SEN, 1997; ETZIONI, 1986), commitment, understood as a wedge between choice and welfare (SEN, 1977) and the cognitive flexibility of the individuals (ARIELY, 2012).

Wolbachia is a maternally inherited, endosymbiotic bacterium that infects at least 40% of terrestrial arthropods. As a facultative symbiont in the majority of its hosts, Wolbachia commonly act as a reproductive parasite; however, there are a number of Wolbachia strains that do not cause reproductive manipulations in their hosts and have no apparent fitness enhancement, yet are stably maintained in populations at low to intermediate frequencies. How these strains of Wolbachia persist in nature has been a long-standing question and is still unresolved. One explanation for the persistence of such strains is that they provide a context-dependent fitness advantage to their hosts. In this thesis, I investigate one such strain of Wolbachia, wSuz, which infects the agricultural pest, Drosophila suzukii, also known as spotted wing Drosophila. To explore the possibility that wSuz may be involved in pathogen protection, I screened wild flies for Wolbachia and two naturally occurring RNA viruses, Teise Virus and a recently discovered virus related to Motts Mill Virus. I did not find an association between Wolbachia and virus infection. Additionally, I designed an experiment to test whether Wolbachia increases host fitness at high larval densities. Intriguingly, although there was no effect of density, the frequency of Wolbachia infection changed dramatically in just one generation, but in opposite directions in replicate experiments that were performed a month apart. These results support the hypothesis that Wolbachia frequencies can change quickly across generations and provide some type of condition-dependent benefit. The maintenance of Wolbachia remains a mystery, but my study provides some exciting clues about what conditions may be playing a role. / Graduate / 2022-05-10

京都大学 / 0048 / 新制・論文博士 / 博士(医学) / 乙第13139号 / 論医博第2139号 / 新制||医||1026(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 松田 道行, 教授 中川 一路, 教授 原田 浩 / 学位規則第4条第2項該当 / Doctor of Medical Science / Kyoto University / DFAM

In this study we have focused on the codon usage bias in E. coli. In chapter 3, we use the population genetics model and the data available on the protein and mRNA levels of the E. coli genes to understand the pattern of codon usage in different genes with different expression levels and see which measure best explains the codon usage pattern. Besides codon bias, by testing for the over-parametrization of the model, we are able to test for the existence of context dependent mutation. We have also fitted the model for the codon usage patter in the Yeast and also tested for the context dependent mutation in this organism. In chapter 4, we focus on the first 10-15 codons in the genes of E. coli. Motivated by the fact that in this region we observe two phenomena, reduction in translation efficiency and suppression of mRNA secondary structures, we investigate whether the former is a side effect of selection for the latter. For this matter we have generated a set of synonymous randomized sequences, and then by selecting the ones which show weak secondary structures in the mentioned region, we would be able to test the theory. We will also look at the frequencies of the amino acids in E. coli genes and see whether the selection for weak secondary structures in the translation initiation region could be strong enough to not only affect the codon usage, but also the choice of amino acids. We would also provide information on the correlation between the strength of the mRNA secondary structure in the first 13 codons and the overall translation efficiency of the genes. / Thesis / Master of Science (MSc)

Variability in the brain’s functional network connectivity is associated with differences in cognition. The degree to which brain networks flexibly reconfigure, or alternatively remain stable, can differ across regions of cortex, across time, and across individuals. The goal of this dissertation was to investigate how the brain’s functional network architecture is reconfigured to support abstract reasoning and rule learning. I proposed that flexibility within frontoparietal cortex, combined with a stable network core, is beneficial for effective reasoning and rule learning. Experiment One investigated the activation patterns and dynamic community structure of brain networks associated with shifting task demands during abstract reasoning. Twenty-seven subjects underwent fMRI scanning during resting state and during a subsequent abstract reasoning task. When quantifying network reconfiguration between resting and task states, I found a stable system within default and somatomotor networks alongside a more flexible frontoparietal control network. The results motivated a novel understanding of how the brain performs reasoning tasks: an underlying stable functional network acts as a cognitive control mechanism, priming task-active nodes within frontoparietal cortex to variably activate for unique task conditions. Experiment Two used a dynamic network analysis to identify changes in functional brain networks that were associated with context-dependent rule learning. During fMRI scanning, twenty-nine naïve subjects were challenged to learn a set of context-dependent rules. Successful learners showed greater stability in ventral attention and somatomotor regions, increased assortative mixing of cognitive control regions as rules were learned, and greater segregation of attention networks throughout the entire task. The results suggested that a stable ventral attention network and a flexible frontoparietal control network support sustained attention and the formation of rule representations. In Experiment Three, I carried out a separate analysis of data from Experiment 2 to characterize the functional connectivity patterns with the hippocampus that emerged during successful rule learning. The results demonstrated that the hippocampal head became increasingly functionally connected to the lateral frontal pole and caudate in successful learners. Additionally, the entire hippocampus exhibited decreased functional connectivity with the mid-cingulate and precuneus in successful learners. These three experiments demonstrated that stable functional connectivity in somatomotor and ventral attention networks, combined with flexible reconfiguration of frontoparietal cortex, is advantageous for successful rule learning and abstract reasoning. Altogether, this dissertation demonstrated that individual differences in dynamic functional connectivity are associated with learning, and that stability of brain networks across time and tasks supports higher order cognition. / 2025-01-23T00:00:00Z

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