Path integrals for continuous-time Markov chains

This note presents a method of evaluating the distribution of a path integral for Markov chains on a countable state space.

Análise térmica e estrutural de barragens de BCC - (betão compactado com cilindros)

Dissertação para obtencão do Grau de Mestre em Engenharia Civil - Perfil Estruturas

Dying neurons in thalamus of asphyxiated term newborns and rats are autophagic.

OBJECTIVE: Neonatal hypoxic-ischemic encephalopathy (HIE) still carries a high burden by its mortality and long-term neurological morbidity in survivors. Apart from hypothermia, there is no acknowledged therapy for HIE, reflecting the lack of mechanistic understanding of its pathophysiology. (Macro)autophagy, a physiological intracellular process of lysosomal degradation, has been proposed to be excessively activated in excitotoxic conditions such as HIE. The present study examines whether neuronal autophagy in the thalamus of asphyxiated human newborns or P7 rats is enhanced and related to neuronal death processes. METHODS: Neuronal autophagy and cell death were evaluated in the thalamus (frequently injured in severe HIE) of both human newborns who died after severe HIE (n = 5) and P7 hypoxic-ischemic rats (Rice-Vannuci model). Autophagic (LC3, p62), lysosomal (LAMP1, cathepsins), and cell death (TUNEL, caspase-3) markers were studied by immunohistochemistry in human and rat brain sections, and by additional methods in rats (immunoblotting, histochemistry, and electron microscopy). RESULTS: Following severe perinatal asphyxia in both humans and rats, thalamic neurons displayed up to 10-fold (p < 0.001) higher numbers of autophagosomes and lysosomes, implying an enhanced autophagic flux. The highly autophagic neurons presented strong features of apoptosis. These findings were confirmed and elucidated in more detail in rats. INTERPRETATION: These results show for the first time that autophagy is enhanced in severe HIE in dying thalamic neurons of human newborns, as in rats. Experimental neuroprotective strategies targeting autophagy could thus be a promising lead to follow for the development of future therapeutic approaches. Ann Neurol 2014;76:695-711.

Evolutionary Games in Networked Populations: Models and Experiments

Cooperation and coordination are desirable behaviors that are fundamental for the harmonious development of society. People need to rely on cooperation with other individuals in many aspects of everyday life, such as teamwork and economic exchange in anonymous markets. However, cooperation may easily fall prey to exploitation by selfish individuals who only care about short- term gain. For cooperation to evolve, specific conditions and mechanisms are required, such as kinship, direct and indirect reciprocity through repeated interactions, or external interventions such as punishment. In this dissertation we investigate the effect of the network structure of the population on the evolution of cooperation and coordination. We consider several kinds of static and dynamical network topologies, such as Baraba´si-Albert, social network models and spatial networks. We perform numerical simulations and laboratory experiments using the Prisoner's Dilemma and co- ordination games in order to contrast human behavior with theoretical results. We show by numerical simulations that even a moderate amount of random noise on the Baraba´si-Albert scale-free network links causes a significant loss of cooperation, to the point that cooperation almost vanishes altogether in the Prisoner's Dilemma when the noise rate is high enough. Moreover, when we consider fixed social-like networks we find that current models of social networks may allow cooperation to emerge and to be robust at least as much as in scale-free networks. In the framework of spatial networks, we investigate whether cooperation can evolve and be stable when agents move randomly or performing Le´vy flights in a continuous space. We also consider discrete space adopting purposeful mobility and binary birth-death process to dis- cover emergent cooperative patterns. The fundamental result is that cooperation may be enhanced when this migration is opportunistic or even when agents follow very simple heuristics. In the experimental laboratory, we investigate the issue of social coordination between indi- viduals located on networks of contacts. In contrast to simulations, we find that human players dynamics do not converge to the efficient outcome more often in a social-like network than in a random network. In another experiment, we study the behavior of people who play a pure co- ordination game in a spatial environment in which they can move around and when changing convention is costly. We find that each convention forms homogeneous clusters and is adopted by approximately half of the individuals. When we provide them with global information, i.e., the number of subjects currently adopting one of the conventions, global consensus is reached in most, but not all, cases. Our results allow us to extract the heuristics used by the participants and to build a numerical simulation model that agrees very well with the experiments. Our findings have important implications for policymakers intending to promote specific, desired behaviors in a mobile population. Furthermore, we carry out an experiment with human subjects playing the Prisoner's Dilemma game in a diluted grid where people are able to move around. In contrast to previous results on purposeful rewiring in relational networks, we find no noticeable effect of mobility in space on the level of cooperation. Clusters of cooperators form momentarily but in a few rounds they dissolve as cooperators at the boundaries stop tolerating being cheated upon. Our results highlight the difficulties that mobile agents have to establish a cooperative environment in a spatial setting without a device such as reputation or the possibility of retaliation. i.e. punishment. Finally, we test experimentally the evolution of cooperation in social networks taking into ac- count a setting where we allow people to make or break links at their will. In this work we give particular attention to whether information on an individual's actions is freely available to poten- tial partners or not. Studying the role of information is relevant as information on other people's actions is often not available for free: a recruiting firm may need to call a job candidate's refer- ences, a bank may need to find out about the credit history of a new client, etc. We find that people cooperate almost fully when information on their actions is freely available to their potential part- ners. Cooperation is less likely, however, if people have to pay about half of what they gain from cooperating with a cooperator. Cooperation declines even further if people have to pay a cost that is almost equivalent to the gain from cooperating with a cooperator. Thus, costly information on potential neighbors' actions can undermine the incentive to cooperate in dynamical networks.

Spectral Analysis of Buffers in Communication Systems

Muokatun matriisi-geometrian tekniikan kehitys yleimmäksi jonoksi on esitelty tässä työssä. Jonotus systeemi koostuu useista jonoista joilla on rajatut kapasiteetit. Tässä työssä on myös tutkittu PH-tyypin jakautumista kun ne jaetaan. Rakenne joka vastaa lopullista Markovin ketjua jossa on itsenäisiä matriiseja joilla on QBD rakenne. Myös eräitä rajallisia olotiloja on käsitelty tässä työssä. Sen esitteleminen matriisi-geometrisessä muodossa, muokkaamalla matriisi-geometristä ratkaisua on tämän opinnäytetyön tulos.

Clippings - Births, Deaths, Marriage

Clipping of the obituary of Mrs. Mary Lanman Douw Ferris, widow of Morris Patterson Ferris, n.d. Clipping of the obituary of Alfred Sanderson Woodruff, March 20, 1926. Clipping describing the wedding of Margaret Julia Woodruff and Captain Percy Carruthers Band, n.d. Clipping of a birth announcement of a daughter to Mr. and Mrs. P.C. Band, 1924. Clipping of a birth announcement of a son to Mr. and Mrs. Percy C. Band, Sept. 11, 1927.

Algorithmes pour la réconciliation d’un arbre de gènes avec un arbre d’espèces

Une réconciliation entre un arbre de gènes et un arbre d’espèces décrit une histoire d’évolution des gènes homologues en termes de duplications et pertes de gènes. Pour inférer une réconciliation pour un arbre de gènes et un arbre d’espèces, la parcimonie est généralement utilisée selon le nombre de duplications et/ou de pertes. Les modèles de réconciliation sont basés sur des critères probabilistes ou combinatoires. Le premier article définit un modèle combinatoire simple et général où les duplications et les pertes sont clairement identifiées et la réconciliation parcimonieuse n’est pas la seule considérée. Une architecture de toutes les réconciliations est définie et des algorithmes efficaces (soit de dénombrement, de génération aléatoire et d’exploration) sont développés pour étudier les propriétés combinatoires de l’espace de toutes les réconciliations ou seulement les plus parcimonieuses. Basée sur le processus classique nommé naissance-et-mort, un algorithme qui calcule la vraisemblance d’une réconciliation a récemment été proposé. Le deuxième article utilise cet algorithme avec les outils combinatoires décrits ci-haut pour calculer efficacement (soit approximativement ou exactement) les probabilités postérieures des réconciliations localisées dans le sous-espace considéré. Basé sur des taux réalistes (selon un modèle probabiliste) de duplication et de perte et sur des données réelles/simulées de familles de champignons, nos résultats suggèrent que la masse probabiliste de toute l’espace des réconciliations est principalement localisée autour des réconciliations parcimonieuses. Dans un contexte d’approximation de la probabilité d’une réconciliation, notre approche est une alternative intéressante face aux méthodes MCMC et peut être meilleure qu’une approche sophistiquée, efficace et exacte pour calculer la probabilité d’une réconciliation donnée. Le problème nommé Gene Tree Parsimony (GTP) est d’inférer un arbre d’espèces qui minimise le nombre de duplications et/ou de pertes pour un ensemble d’arbres de gènes. Basé sur une approche qui explore tout l’espace des arbres d’espèces pour les génomes considérés et un calcul efficace des coûts de réconciliation, le troisième article décrit un algorithme de Branch-and-Bound pour résoudre de façon exacte le problème GTP. Lorsque le nombre de taxa est trop grand, notre algorithme peut facilement considérer des relations prédéfinies entre ensembles de taxa. Nous avons testé notre algorithme sur des familles de gènes de 29 eucaryotes.

Complexe de Morse et bifurcations

Soit une famille de couples (ft,Xt)t∈J , où J est un intervalle, ft est une fonction lisse à valeurs réelles définie sur une variété lisse et compacte V , et Xt est un pseudo-gradient associé à la fonction ft. L’objet de ce mémoire est l’étude des bifurcations subies par les complexes de Morse associés à ces couples. Deux approches sont utilisées : l’étude directe des bifurcations et l’approche par homotopie. On montre que finalement ces deux approches permettent d’obtenir les mêmes résultats d’un point de vue fonctoriel.

Studies on Inventory with Positive Service Time Under Local Purchase Driven by N/T- Policy

In this thesis, certain continuous time inventory problems with positive service time under local purchase guided by N/T-policy are analysed. In most of the cases analysed, we arrive at stochastic decomposition of system states, that is, the joint distribution of the system states is obtained as the product of marginal distributions of the components. The thesis is divided into ve chapters

Long-Term Culture of Mouse Embryonic Stem Cell-Derived Adherent Neurospheres and Functional Neurons

Innumerous protocols, using the mouse embryonic stem (ES) cells as model for in vitro study of neurons functional properties and features, have been developed. Most of these protocols are short lasting, which, therefore, does not allow a careful analysis of the neurons maturation, aging, and death processes. We describe here a novel and efficient long-lasting protocol for in vitro ES cells differentiation into neuronal cells. It consists of obtaining embryoid bodies, followed by induction of neuronal differentiation with retinoic acid of nonadherent embryoid bodies (three-dimensional model), which further allows their adherence and formation of adherent neurospheres (AN, bi-dimensional model). The AN can be maintained for at least 12 weeks in culture under repetitive mechanical splitting, providing a constant microenvironment (in vitro niche) for the neuronal progenitor cells avoiding mechanical dissociation of AN. The expression of neuron-specific proteins, such as nestin, sox1, beta III-tubulin, microtubule-associated protein 2, neurofilament medium protein, Tau, neuronal nuclei marker, gamma-aminobutyric acid, and 5-hydroxytryptamine, were confirmed in these cells maintained during 3 months under several splitting. Additionally, expression pattern of microtubule-associated proteins, such as lissencephaly (Lis1) and nuclear distribution element-like (Ndel1), which were shown to be essential for differentiation and migration of neurons during embryogenesis, was also studied. As expected, both proteins were expressed in undifferentiated ES cells, AN, and nonrosette neurons, although presenting different spatial distribution in AN. In contrast to previous studies, using cultured neuronal cells derived from embryonic and adult tissues, only Ndel1 expression was observed in the centrosome region of early neuroblasts from AN. Mature neurons, obtained from ES cells in this work, display ionic channels and oscillations of membrane electrical potential typical of electrically excitable cells, which is a characteristic feature of the functional central nervous system (CNS) neurons. Taken together, our study demonstrated that AN are a long-term culture of neuronal cells that can be used to analyze the process of neuronal differentiation dynamics. Thus, the protocol described here provides a new experimental model for studying neurological diseases associated with neuronal differentiation during early development, as well as it represents a novel source of functional cells that can be used as tools for testing the effects of toxins and/or drugs on neuronal cells.

Action of the chemical agent fipronil (active ingredient of acaricide Frontline (R)) on the liver of mice: An ultrastructural analysis

Fipronil, active ingredient of the acaricide Frontiline (R), is a phenyl-pyrazolic derivative, and its efficacy in the elimination of several plagues, even in low concentrations, has already been demonstrated; however, its effect on nontarget organisms has not been thoroughly explained. In this sense, the objective of this study was to evaluate the effects of different dosages of fipronil on the liver of mice in artificial conditions. Results showed that the animals exposed to fipronil present significant ultrastrucutural changes in hepatic cells with evident cellular and cytoplasm disorganization in hepatocytes characterized by an increase in the number of organelles, mainly mitochondria and rough endoplasmic reticulum, organelles that, in the case of the exposed animals, were probably responsible for the enzymes' synthesis that have the function of inactivating the toxic metabolites. A fat accumulation in the hepatocytes' cytoplasm (steatosis) was observed, in addition to extended vacuolated areas, mainly in regions next to the cell nucleus. Alterations observed in the nuclei of the hepatocytes pointed out cell death processes. Moreover, Kupffer cells increased in number (hyperplasia) suggesting an increase in the phagocytic activity of the liver in the exposed animals. Microsc. Res. Tech., 2011. (c) 2011 Wiley Periodicals, Inc.

An overview of biodiesel soil pollution: Data based on cytotoxicity and genotoxicity assessments

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Paródia e carnavalização no cancioneiro Chico Buarque de Hollanda

A pesquisa Paródia e carnavalização no cancioneiro Chico Buarque de Hollanda investiga os aspectos paródicos e carnavalescos presentes no repertório de Chico Buarque, enfatizando a carnavalização, inicialmente, como uma prática cultural medieval, baseada nas teorias de Mikhail Bakhtin, a cerca do carnaval medieval e renascentista analisado na obra do francês François Rabelais, proposições desenvolvidas no livro A cultura popular: na Idade Média e no. Desta análise, o presente estudo destaca os principais elementos constituintes dos ritos carnavalescos: 1) o dialogismo entre o discurso popular e o discurso poético, uma vez que toda comunicação é uma ação recíproca; 2) a ambivalência da linguagem carnavalesca que primava por estabelecer a ligação entre os pólos positivos e negativos referentes ao ciclo nascimento-morte; 3) o riso e as suas complexidades de significações e realizações que oscilam entre a ingenuidade e a sátira; e por fim 4) a paródia que incorpora todos os elementos citados anteriormente para sua realização. Partindo da apreensão destes conceitos, será traçado também um breve panorama histórico para compreender as múltiplas facetas artísticas de Chico Buarque e a sua relação com a vida social, a fim de percebê-lo por meio de sua produção como poeta lírico social. Para comprovar a importância do carnaval na cultura universal, dando ênfase à cultura brasileira, as canções Tem mais samba (1964), Sonho de um carnaval (1965), Amanhã, ninguém sabe (1966), Noite dos mascarados (1966), Roda-viva (1967), Ela desatinou (1968), Apesar de você (1970), Quando o carnaval chegar (1972) e Vai passar (1984) serão analisadas num estabelecimento comparativo entre o carnaval contemporâneo e o carnaval medieval, observando as confluências e dissonâncias, que ainda fazem parte desta festa popular. Desta apreciação, o presente estudo assinala a importância da obra de Chico Buarque pelo valor poético e cultural presente em todas as suas atividades artísticas. Os critérios de análise serão pautados num estudo bibliográfico entre as teorias carnavalescas de Bakhtin e as músicas de Chico Buarque, que aqui serão compreendidas como poemas-canções, destacando dessas a temática do carnaval.

Exposição à concentração subletal de metilmercúrio: genotoxicidade e alterações na proliferação celular

O mercúrio é um metal que se destaca dos demais por se apresentar líquido em temperatura e pressão normais. Este xenobiótico se apresenta como a maior fonte de poluição em várias partes do mundo e tem como característica ser altamente tóxico ao Sistema Nervoso Central (SNC). O despejo é na forma líquida diretamente no solo e leito dos rios. Este metal pesado é complexado com vários elementos presentes no solo ou sedimentos sendo convertido à metilmercúrio (MeHg) pela microbiota aquática. O MeHg apresenta a capacidade de se acumular ao longo da cadeia trófica, um evento conhecido como biomagnificação, o qual afeta diretamente a vida humana. Nesse sentido, a Região Amazônica se destaca por possuir todos os componentes necessários para a manutenção do ciclo biogeoquímico do mercúrio, além de populações cronicamente expostas a este metal pesado, sendo este fato considerado um problema de saúde pública. Tem-se conhecimento que este xenobiótico após a exposição aguda a altas doses promove desordens relacionadas ao surgimento de processos degenerativos no SNC, entretanto, os efeitos a baixas concentrações ainda não são totalmente conhecidos. Nesse sentido, se destacam as células gliais que atuam como mediadores no processo de neurotoxicidade desse metal, principalmente em baixas concentrações. Apesar de este tipo celular exibir um importante papel no processo de intoxicação mercurial, a ação deste metal sobre as células glias é pouco conhecida, principalmente sobre o genoma e a proliferação celular. Desta forma, este trabalho se propõe a avaliar o efeito da exposição a este xenobiótico em baixa concentração sobre o material genético e a proliferação celular em células da linhagem glial C6. As avaliações bioquímica (atividade mitocondrial – medida pelo ensaio de MTT –) e morfofuncional (integridade da membrana – avaliada pelo ensaio com os corantes BE e AA –) confirmaram a ausência de morte celular após a exposição ao metal pesado na concentração de 3 μM por um intervalo de 24 horas. Mesmo sem promover processos de morte celular, o tratamento com esta concentração subletal de MeHg foi capaz de aumentar significativamente os níveis dos marcadores de genotoxicidade (fragmentação do DNA, formação de micronúcleos, pontes nucleoplásmica e brotos nucleares). Ao mesmo tempo, foi possível observar uma alteração no ciclo celular através do aumento do índice mitótico e uma mudança no perfil do ciclo celular com aumento da população celular nas fases S e G2/M, sugerindo um aprisionamento nessa etapa. Esta mudança no ciclo celular, provocada por 24h de exposição ao MeHg, foi seguida de uma redução no número de células viáveis e confluência celular 24h após a retirada do MeHg e substituição do meio de cultura, além do aumento no tempo de duplicação da cultura do mesmo. Este estudo demonstrou pela primeira vez que a exposição ao metilmercúrio em concentração baixa e subletal é capaz de promover eventos genotóxicos e distúrbios na proliferação celular em células de origem glial.