Filogenia molecular das enzimas isocitrato liase e malato sintase e sua evolução em Viridiplanta

The plant metabolism consists of a complex network of physical and chemical events resulting in photosynthesis, respiration, synthesis and degradation of organic compounds. This is only possible due to the different kinds of responses to many environmental variations that a plant could be subject through evolution, leading also to conquering new surroundings. The glyoxylate cycle is a metabolic pathway found in glyoxysomes plant, which has unique role in the seedling establishment. Considered as a variation of the citric acid cycle, it uses an acetyl coenzyme A molecule, derived from lipids beta-oxidation to synthesize compounds which are used in carbohydrate synthesis. The Malate synthase (MLS) and Isocitrate lyase (ICL) enzyme of this cycle are unique and essential in regulating the biosynthesis of carbohydrates. Because of the absence of decarboxylation steps as rate-limiting steps, detailed studies of molecular phylogeny and evolution of these proteins enables the elucidation of the effects of this route presence in the evolutionary processes involved in their distribution across the genome from different plant species. Therefore, the aim of this study was to establish a relationship between the molecular evolution of the characteristics of enzymes from the glyoxylate cycle (isocitrate lyase and malate synthase) and their molecular phylogeny, among green plants (Viridiplantae). For this, amino acid and nucleotide sequences were used, from online repositories as UniProt and Genbank. Sequences were aligned and then subjected to an analysis of the best-fit substitution models. The phylogeny was rebuilt by distance methods (neighbor-joining) and discrete methods (maximum likelihood, maximum parsimony and Bayesian analysis). The identification of structural patterns in the evolution of the enzymes was made through homology modeling and structure prediction from protein sequences. Based on comparative analyzes of in silico models and from the results of phylogenetic inferences, both enzymes show significant structure conservation and their topologies in agreement with two processes of selection and specialization of the genes. Thus, confirming the relevance of new studies to elucidate the plant metabolism from an evolutionary perspective

SCAPHOID AND LUNATE CARPAL MECHANICS OVER THE SPECTRUM OF HEALTHY FUNCTION

When ligaments within the wrist are damaged, the resulting loss in range of motion and grip strength can lead to reduced earning potential and restricted ability to perform important activities of daily living. Left untreated, ligament injuries ultimately lead to arthritis and chronic pain. Surgical repair can mitigate these issues but current procedures are often non-anatomic and unable to completely restore the wrist’s complex network of ligaments. An inability to quantitatively assess wrist function clinically, both before and after surgery, limits the ability to assess the response to clinical intervention. Previous work has shown that bones within the wrist move in a similar pattern across people, but these patterns remain challenging to predict and model. In an effort to quantify and further develop the understanding of normal carpal mechanics, we performed two studies using 3D in vivo carpal bone motion analysis techniques. For the first study, we measured wrist laxity and performed CT scans of the wrist to evaluate 3D carpal bone positions. We found that through mid-range radial-ulnar deviation range of motion the scaphoid and lunate primarily flexed and extended; however, there was a significant relationship between wrist laxity and row-column behaviour. We also found that there was a significant relationship between scaphoid flexion and active radial deviation range of motion. For the second study, an analysis was performed on a publicly available database. We evaluated scapholunate relative motion over a full range of wrist positions, and found that there was a significant amount of variation in the location and orientation of the rotation axis between the two bones. Together the findings from the two studies illustrate the complexity and subject specificity of normal carpal mechanics, and should provide insights that can guide the development of anatomical wrist ligament repair surgeries that restore normal function.

Applying complexity science to air traffic management

Complexity science is the multidisciplinary study of complex systems. Its marked network orientation lends itself well to transport contexts. Key features of complexity science are introduced and defined, with a specific focus on the application to air traffic management. An overview of complex network theory is presented, with examples of its corresponding metrics and multiple scales. Complexity science is starting to make important contributions to performance assessment and system design: selected, applied air traffic management case studies are explored. The important contexts of uncertainty, resilience and emergent behaviour are discussed, with future research priorities summarised.

On the multi-dimensionality and sampling of air transport networks

Complex network theory is a framework increasingly used in the study of air transport networks, thanks to its ability to describe the structures created by networks of flights, and their influence in dynamical processes such as delay propagation. While many works consider only a fraction of the network, created by major airports or airlines, for example, it is not clear if and how such sampling process bias the observed structures and processes. In this contribution, we tackle this problem by studying how some observed topological metrics depend on the way the network is reconstructed, i.e. on the rules used to sample nodes and connections. Both structural and simple dynamical properties are considered, for eight major air networks and different source datasets. Results indicate that using a subset of airports strongly distorts our perception of the network, even when just small ones are discarded; at the same time, considering a subset of airlines yields a better and more stable representation. This allows us to provide some general guidelines on the way airports and connections should be sampled.

A systematic literature review of university technology transfer from a quadruple helix perspective: Towards a research agenda

Within recent years, there has been a rapid expansion of the University's role in economic development. This has resulted in University Technology Transfer (UTT) taking place within an increasingly complex network of regional stakeholders. This complexity has resulted in quadruple helix models where the triple helix model of academia, industry and regional government now includes societal based innovation users as a fourth helix. Despite this development, extant research is fragmented and lacks coherent frameworks and conceptualisations which fully depict the dynamic and evolving nature of UTT. Accordingly, this article reviews Mode 2 UTT from a quadruple helix perspective to identify key themes to develop a research agenda which reflects progression from a triple into a quadruple helix ecosystem.

Sex steroid feedback regulation of pituitary gonadotropins during early secondary oocyte growth in coho salmon (Oncorhynchus kisutch) – a potential target of endocrine disruption.

Thesis (Ph.D.)--University of Washington, 2016-06

Regenerative Cues of Myeloid Cells on Pancreatic Epithelium

Thesis (Ph.D.)--University of Washington, 2016-07

Computer simulations of soft particles in flow

Understanding the dynamics of blood cells is a crucial element to discover biological mechanisms, to develop new efficient drugs, design sophisticated microfluidic devices, for diagnostics. In this work, we focus on the dynamics of red blood cells in microvascular flow. Microvascular blood flow resistance has a strong impact on cardiovascular function and tissue perfusion. The flow resistance in microcirculation is governed by flow behavior of blood through a complex network of vessels, where the distribution of red blood cells across vessel cross-sections may be significantly distorted at vessel bifurcations and junctions. We investigate the development of blood flow and its resistance starting from a dispersed configuration of red blood cells in simulations for different hematocrits, flow rates, vessel diameters, and aggregation interactions between red blood cells. Initially dispersed red blood cells migrate toward the vessel center leading to the formation of a cell-free layer near the wall and to a decrease of the flow resistance. The development of cell-free layer appears to be nearly universal when scaled with a characteristic shear rate of the flow, which allows an estimation of the length of a vessel required for full flow development, $l_c \approx 25D$, with vessel diameter $D$. Thus, the potential effect of red blood cell dispersion at vessel bifurcations and junctions on the flow resistance may be significant in vessels which are shorter or comparable to the length $l_c$. The presence of aggregation interactions between red blood cells lead in general to a reduction of blood flow resistance. The development of the cell-free layer thickness looks similar for both cases with and without aggregation interactions. Although, attractive interactions result in a larger cell-free layer plateau values. However, because the aggregation forces are short-ranged at high enough shear rates ($\bar{\dot{\gamma}} \gtrsim 50~\text{s}^{-1}$) aggregation of red blood cells does not bring a significant change to the blood flow properties. Also, we develop a simple theoretical model which is able to describe the converged cell-free-layer thickness with respect to flow rate assuming steady-state flow. The model is based on the balance between a lift force on red blood cells due to cell-wall hydrodynamic interactions and shear-induced effective pressure due to cell-cell interactions in flow. We expect that these results can also be used to better understand the flow behavior of other suspensions of deformable particles such as vesicles, capsules, and cells. Finally, we investigate segregation phenomena in blood as a two-component suspension under Poiseuille flow, consisting of red blood cells and target cells. The spatial distribution of particles in blood flow is very important. For example, in case of nanoparticle drug delivery, the particles need to come closer to microvessel walls, in order to adhere and bring the drug to a target position within the microvasculature. Here we consider that segregation can be described as a competition between shear-induced diffusion and the lift force that pushes every soft particle in a flow away from the wall. In order to investigate the segregation, on one hand, we have 2D DPD simulations of red blood cells and target cell of different sizes, on the other hand the Fokker-Planck equation for steady state. For the equation we measure force profile, particle distribution and diffusion constant across the channel. We compare simulation results with those from the Fokker-Planck equation and find a very good correspondence between the two approaches. Moreover, we investigate the diffusion behavior of target particles for different hematocrit values and shear rates. Our simulation results indicate that diffusion constant increases with increasing hematocrit and depends linearly on shear rate. The third part of the study describes development of a simulation model of complex vascular geometries. The development of the model is important to reproduce vascular systems of small pieces of tissues which might be gotten from MRI or microscope images. The simulation model of the complex vascular systems might be divided into three parts: modeling the geometry, developing in- and outflow boundary conditions, and simulation domain decomposition for an efficient computation. We have found that for the in- and outflow boundary conditions it is better to use the SDPD fluid than DPD one because of the density fluctuations along the channel of the latter. During the flow in a straight channel, it is difficult to control the density of the DPD fluid. However, the SDPD fluid has not that shortcoming even in more complex channels with many branches and in- and outflows because the force acting on particles is calculated also depending on the local density of the fluid.

An overview of the effect of probiotics and exercise on mood and associated health conditions

The present paper provides a review of the current knowledge relating to the health benefits of probiotics, specially focused on the effects they may have together with physical exercise on mood disorders and related chronic medical conditions. With both these conditions being a substantial contributor to the global disease burden any alternative therapy must be considered. Probiotics influence the gut microbiota through a complex network of events which can influence mechanisms leading to development of mood disorders such as depression and anxiety. Similarly, through a complex interaction between psychological and neurobiological mechanisms, exercise has been found to play a key role in mood enhancement.

Apicomplexans pulling the strings: manipulation of the host cell cytoskeleton dynamics

Invasive stages of apicomplexan parasites require a host cell to survive, proliferate and advance to the next life cycle stage. Once invasion is achieved, apicomplexans interact closely with the host cell cytoskeleton, but in many cases the different species have evolved distinct mechanisms and pathways to modulate the structural organization of cytoskeletal filaments. The host cell cytoskeleton is a complex network, largely, but not exclusively, composed of microtubules, actin microfilaments and intermediate filaments, all of which are modulated by associated proteins, and it is involved in diverse functions including maintenance of cell morphology and mechanical support, migration, signal transduction, nutrient uptake, membrane and organelle trafficking and cell division. The ability of apicomplexans to modulate the cytoskeleton to their own advantage is clearly beneficial. We here review different aspects of the interactions of apicomplexans with the three main cytoskeletal filament types, provide information on the currently known parasite effector proteins and respective host cell targets involved, and how these interactions modulate the host cell physiology. Some of these findings could provide novel targets that could be exploited for the development of preventive and/or therapeutic strategies.

Markov Random Fields in Cancer Mutation Dependencies

Even though a large amount of evidence would suggest that PP2A serine/threonine protein phosphatase acts as a tumour suppressor the genomics data to support this claim is limited. We fit a sparse binary Markov random field with individual sample's total mutational frequency as an additional covariate to model the dependencies between the mutations occurring in the PP2A encoding genes. We utilize the data from recent large scale cancer genomics studies, where the whole genome from a human tumour biopsy has been analysed. Our results show a complex network of interactions between the occurrence of mutations in our twenty examined genes. According to our analysis the mutations occurring in the genes PPP2R1A, PPP2R3A, and PPP2R2B are identified as the key mutations. These genes form the core of the network of conditional dependency between the mutations in the investigated twenty genes. Additionally, we note that the mutations occurring in PPP2R4 seem to be more influential in samples with higher number of total mutations. The mutations occurring in the set of genes suggested by our results has been shown to contribute to the transformation of human cells. We conclude that our evidence further supports the claim that PP2A acts as a tumour suppressor and restoring PP2A activity is an appealing therapeutic strategy.

Uma abordagem evolucionária e espacial para o jogo da autorregulação de processos de trocas sociais em sistemas multiagentes

Interações sociais são frequentemente descritas como trocas sociais. Na literatura, trocas sociais em Sistemas Multiagentes são objeto de estudo em diversos contextos, nos quais as relações sociais são interpretadas como trocas sociais. Dentre os problemas estudados, um problema fundamental discutido na literatura e a regulação¸ ao de trocas sociais, por exemplo, a emergência de trocas equilibradas ao longo do tempo levando ao equilíbrio social e/ou comportamento de equilíbrio/justiça. Em particular, o problema da regulação de trocas sociais e difícil quando os agentes tem informação incompleta sobre as estratégias de troca dos outros agentes, especificamente se os agentes tem diferentes estratégias de troca. Esta dissertação de mestrado propõe uma abordagem para a autorregulacao de trocas sociais em sistemas multiagentes, baseada na Teoria dos Jogos. Propõe o modelo de Jogo de Autorregulacão ao de Processos de Trocas Sociais (JAPTS), em uma versão evolutiva e espacial, onde os agentes organizados em uma rede complexa, podem evoluir suas diferentes estratégias de troca social. As estratégias de troca são definidas através dos parâmetros de uma função de fitness. Analisa-se a possibilidade do surgimento do comportamento de equilíbrio quando os agentes, tentando maximizar sua adaptação através da função de fitness, procuram aumentar o numero de interações bem sucedidas. Considera-se um jogo de informação incompleta, uma vez que os agentes não tem informações sobre as estratégias de outros agentes. Para o processo de aprendizado de estratégias, utiliza-se um algoritmo evolutivo, no qual os agentes visando maximizar a sua função de fitness, atuam como autorregulares dos processos de trocas possibilitadas pelo jogo, contribuindo para o aumento do numero de interações bem sucedidas. São analisados 5 diferentes casos de composição da sociedade. Para alguns casos, analisa-se também um segundo tipo de cenário, onde a topologia de rede é modificada, representando algum tipo de mobilidade, a fim de analisar se os resultados são dependentes da vizinhança. Alem disso, um terceiro cenário é estudado, no qual é se determinada uma política de influencia, quando as medias dos parâmetros que definem as estratégias adotadas pelos agentes tornam-se publicas em alguns momentos da simulação, e os agentes que adotam a mesma estratégia de troca, influenciados por isso, imitam esses valores. O modelo foi implementado em NetLogo.

Um olhar sobre o castelo de Noudar: do castelo medieval à ruína: Proposta de valorização do lugar

O Castelo de Noudar está implantado num íngreme promontório da herdade da Coitadinha, a Noroeste de Barrancos, integrando o atual Parque da Natureza de Noudar. Construído a partir de 1303, foi alvo de diversas transformações ao longo do tempo, para responder às exigências militares de cada época, e chega aos nossos dias num avançado estado de decadência física. A investigação desenvolvida assenta, em grande parte, no desenho: de Noudar a uma escala territorial, como elemento que participa numa rede fortificada complexa; da evolução morfológica e funcional, que nos permite ter noção das várias configurações do castelo ao longo dos séculos; num desenho propositivo que desenvolve uma estratégia para valorização do lugar e do seu património material e imaterial. Hoje é fundamental compreender como as valências do Parque e da fortaleza se podem cruzar? Este trabalho pretende refletir sobre possibilidades de valorização para contrariar a degradação em que a fortaleza se encontra; ABSTRACT: The Noudar Castle is located in a steep promontory in the herdade da Coitadinha, Northeast from Barrancos, part of the Natural Park of Noudar. Its construction began in 1303, and underwent several transformations throughout its existence, adapting to the military advancements thru out the ages. Today, it shows an advanced state of decay. The investigation is focused on the design of Noudar on a territorial scale, taking part in a complex network of fortified systems; its functional and morphological evolution, which allows us to comprehend the configurations of the castle throughout the centuries; and on a proposed design that develops a strategy to enhance and bring value to this place and its material and non-material heritage. Today it's crucial to comprehend how can the values of the Park and fortress intertwine. This thesis reflects on the possibilities of valuing this site, counter acting the decay which has fallen upon it.

The ways behind the railways: Algarve's railway line. Technique transfers and transport development in Southern Portugal

Esta dissertação pretende contribuir para um melhor conhecimento da complexidade das redes de transferência de conhecimentos e técnicas, no domínio da engenharia civil e mais concretamente através dos caminhos-de-ferro, nos séculos XIX e XX. Em Portugal, os caminhos-de-ferro estiveram no cerne de um vasto debate, sobretudo político, concomitante com uma instabilidade crescente no cenário político e uma fase de fragilidade económica. É neste contexto que a Linha do Sul e Sueste vai ser construída (seguida pela sua extensão até Vila Real de Santo António e pela construção do ramal de Portimão, que chegará a Lagos). Este empreendimento é uma clara ilustração da realidade portuguesa de então, no que concerne ao desenvolvimento desta rede de transportes, que nos permite, igualmente, conhecer e compreender quem interveio no processo de construção da linha (os engenheiros, as empresas, entre outros aspectos) e assim determinar quais as influências e transferências técnicas que tiveram lugar; RESUMEE: Cette mémoire attire à la contribution pour une meilleure connaissance de la complexité des réseaux de transfert de techniques et connaissances qui ont eu lieu dans le domaine de l’ingénierie civile, surtout dans les chemins de fer, au XIXème et XXème siècles. Au Portugal, les chemins de fer sont été le cerne d’un très vaste débat, coïncidant avec une croissante instabilité dans le scenario politique et aussi une phase économique fragile. C’est dans ce contexte que la Ligne du Sud et Sud-est va être bâti (suivi par l’extension jusqu’à Vila Real de Santo António et la construction de l’embranchement ferroviaire Portimão). Cette entreprise c’est une illustration claire de la réalité portugaise, en concernant l’implémentation de cette réseau de transport, que nous permettre de comprendre et également bien connaitre qui a intervenu dans le processus de construction de la ligne (les ingénieurs, entreprises, etcetera), ainsi que déterminer les influences et les transferts techniques qui ont eu lieu; ABSTRACT: With this master’s thesis, the aim is to be able to contribute to a better understanding of the complex network of technique’s and knowledge transfers, that took place within the field of civil engineering, in the 19th and 20th centuries, namely on the railways. In Portugal, railways take-up was a wide and ample debate, coinciding with an uprising turmoil on the Portuguese political outskirt and a phase of economic frailty. It’s in this context that the construction of the South and Southeast Line took place (followed, later on, by its extension until Vila Real de Santo António and by the construction of the Portimão’s branch). This enterprise is, as we pretend to prove in this master’s thesis, a clear example of the Portuguese reality, enabling us to understand and to get to know those who intervened in the construction’s process (the engineers and the companies) as well as determining influences and technique transfers that have taken place.

Método de análise de vulnerabilidade utilizando redes complexas : aplicação na rede de transporte aéreo brasileira

Dissertação (mestrado)—Universidade de Brasília, Faculdade de Tecnologia, Departamento de Engenharia Civil e Ambiental, 2016.