COMPUTATIONAL MODELS OF INFLAMMATION AND WOUND HEALING

The acute inflammatory response to biological stress involves a highly conserved cascade of events mediated by a large array of cells and molecules. While not intrinsically detrimental, inflammation can cause secondary or ancillary damage to tissues, which in turn leads to the production of molecules that amplify inflammatory response and, in extreme cases, promote organ dysfunction and death. Therefore, there is a need to identify and modulate dysregulated inflammatory processes while allowing healthy inflammation to carry on. While in vitro and in vivo studies have brought many insights into the components and dynamics of the inflammatory response, computational techniques are becoming increasingly relevant to tease out complex relationships and inter-dependencies that may not be directly measureable. In this dissertation, we explore a computational model of pressure ulcer formation that generates tissue-realistic output and clinically-relevant predictions. By simulating basic inflammatory mechanisms and ischemia/reperfusion injury to soft tissue, our model spontaneously produces both resolving and ulcerative inflammatory patterns from a single set of parameter values. We use statistical methods to explore which mechanisms in the model are responsible for this spontaneous bifurcation. We also use data-driven methods to examine dynamics of inflammatory mediators during in vitro murine hepatocellular stress. Our results lead to identification of MCP-1 as a clinically-predictive inflammatory mediator in human trauma patients

Infant Pain Management

Emphasis on infant pain management has recently become prominent in the medical field. Though it was once thought that infants do not feel pain or remember pain, this thinking has changed due to recent research on the subject. This research has found that infants’ underdeveloped nervous systems actually leads to increased pain rather than decreased pain as previously thought. Research has also found that there are long-term developmental risks associated with prolonged or unmanaged pain in infancy. However, this has not been applied to clinical practice. Studies show that infants are still being under-medicated, if medicated at all, for painful or invasive procedures. Infants in the neonatal intensive care unit are at a high-risk for complications related to unmanaged pain because of the frequency and abundance of invasive procedures performed on this unit. Reasons for this include lack of physician education on this subject, risk for adverse effects with opioid administration, and lack of adequate pain assessment tools for infants. There are some interventions that can be implemented to improve pain management in infants, which include non-pharmacological methods and educating medical staff on this subject

Thermalization and relaxation after a quantum quench in disordered Hamiltonians

In the present thesis we study the unitary dynamics and the thermalization properties of free-fermion-like Hamiltonians after a sudden quantum quench in presence of disorder. With analytical and numerical arguments, we show that the existence of a stationary state and its description with a generalized Gibbs ensemble (GGE) depend crucially on the observable considered (local versus extensive, one-body versus many-body) and on the localization properties of the final Hamiltonian. We then show an extension of the Wang-Landau algorithm which allows the computation of weighted distributions associated to quantum quenches, like the diagonal and the GGE ensemble expectation-value distributions. We present results on three one-dimensional models, the Anderson model, a disordered one-dimensional fermionic chain with long-range hopping, and the disordered Ising/XY spin chain

Kinetic pathways of topology simplification by Type-II topoisomerases in knotted supercoiled DNA

The topological state of covalently closed, double-stranded DNA is defined by the knot type $K$ and the linking-number difference $\\Delta Lk$ relative to unknotted relaxed DNA. DNA topoisomerases are essential enzymes that control the topology of DNA in all cells. In particular, type-II topoisomerases change both $K$ and $\\Delta Lk$ by a duplex-strand-passage mechanism and have been shown to simplify the topology of DNA to levels below thermal equilibrium at the expense of ATP hydrolysis. It remains a key question how small enzymes are able to preferentially select strand passages that result in topology simplification in much larger DNA molecules. Using numerical simulations, we consider the non-equilibrium dynamics of transitions between topological states $(K,\\Delta Lk)$ in DNA induced by type-II topoisomerases. For a biological process that delivers DNA molecules in a given topological state $(K,\\Delta Lk)$ at a constant rate we fully characterize the pathways of topology simplification by type-II topoisomerases in terms of stationary probability distributions and probability currents on the network of topological states $(K,\\Delta Lk)$. In particular, we observe that type-II topoisomerase activity is significantly enhanced in DNA molecules that maintain a supercoiled state with constant torsional tension. This is relevant for bacterial cells in which torsional tension is maintained by enzyme-dependent homeostatic mechanisms such as DNA-gyrase activity

DNA-Topology Simplification by Topoisomerases

The topological properties of DNA molecules, supercoiling, knotting, and catenation, are intimately connected with essential biological processes, such as gene expression, replication, recombination, and chromosome segregation. Non-trivial DNA topologies present challenges to the molecular machines that process and maintain genomic information, for example, by creating unwanted DNA entanglements. At the same time, topological distortion can facilitate DNA-sequence recognition through localized duplex unwinding and longer-range loop-mediated interactions between the DNA sequences. Topoisomerases are a special class of essential enzymes that homeostatically manage DNA topology through the passage of DNA strands. The activities of these enzymes are generally investigated using circular DNA as a model system, in which case it is possible to directly assay the formation and relaxation of DNA supercoils and the formation/resolution of knots and catenanes. Some topoisomerases use ATP as an energy cofactor, whereas others act in an ATP-independent manner. The free energy of ATP hydrolysis can be used to drive negative and positive supercoiling or to specifically relax DNA topologies to levels below those that are expected at thermodynamic equilibrium. The latter activity, which is known as topology simplification, is thus far exclusively associated with type-II topoisomerases and it can be understood through insight into the detailed non-equilibrium behavior of type-II enzymes. We use a non-equilibrium topologicalnetwork approach, which stands in contrast to the equilibrium models that are conventionally used in the DNA-topology field, to gain insights into the rates that govern individual transitions between topological states. We anticipate that our quantitative approach will stimulate experimental work and the theoretical/computational modeling of topoisomerases and similar enzyme systems

Projeto de um diferencial para veículo Fórmula SAE

Trabalho de Conclusão de Curso (graduação)—Universidade de Brasília, Faculdade de Tecnologia, Departamento de Engenharia Mecânica, 2017.Este trabalho apresenta o projeto de um diferencial para um veículo de Fórmula SAE. A equipe de Fórmula SAE da Universidade de Brasília, a Apuama Racing, tem como um de seus objetivos para a subárea de transmissão em 2018 a utilização de um diferencial concebido e projetado pela própria equipe. O projeto deve melhorar a dirigibilidade do veículo, possuir baixo peso, alta resistência e ser de fácil usinagem. Inicialmente foi feita uma revisão bibliográfica sobre diferenciais em seguida três alternativas foram analisadas levando-se em conta os critérios de: peso, redistribuição de torque, facilidade de manufatura e custo. Entre as alternativas propostas uma foi escolhida e projetada utilizando para o projeto das engrenagens a metodologia AGMA e para a carcaça e outros componentes utilizou-se análise por elementos finitos. Como resultado obteve-se um diferencial 25% mais leve que o projeto anterior, com 5,1 kg e 8,9 kg considerando a montagem do sistema com todos os componentes, TBR de 2,75:1, redução do volume do diferencial principalmente em razão da diminuição do comprimento total de 212,8 mm para 196,7 mm e os desenhos de fabricação bem como a especificação dos materiais e processos de fabricação a serem utilizados.This work presents the design of a differential for a FSAE vehicle. The Formula SAE team at the University of Brasilia, Apuama Racing, has as one of its objectives for the transmission subarea in 2018 the use of a differential designed by the team itself. The design should have low weight, improve vehicle handling, have high strength and easy machining. Initially, a literature review was carried out on differentials. Three alternatives were analyzed taking into account the criteria of: weight, redistribution of torque, ease of manufacture and cost. Among the proposed alternatives, one was chosen and designed using the AGMA methodology for the design of the gears and for the housing and other components was used finite element analysis. As a result, a differential 25% lighter than the previous design was obtained, with 5.1 kg and 8.9 kg considering the assembly of the system with all components, TBR of 2.75: 1, reduction of the differential volume mainly due to the reduction of the total length from 212.8 mm to 196.7 mm and the manufacturing drawings as well as the specification of the materials and manufacturing processes to be used

Problematika latiniziranja hangeula v slovenščino

Slovenian grammar does not deal with Korean language and words of Korean origin. Since the number of Korean words in newspapers and other media in Slovenia is increasing, and different writers romanize these words in different ways, a need exists for a uniform transliteration system as soon as possible in order to avoid misapprehensions.The romanization of Korean is not a problem only in Slovenia but also in Korea. There are several systems of romanization. At the moment the Republic of Korea is using the Revised Romanization system, which was approved in the year 2000, while the Democratic People’s Republic of Korea uses the McCune-Reischauer system. The Republic of Korea stopped using the McCune-Reischauer system because of the inconvenient usage of diacritics and apostrophes. The problem of romanization of Korean consists not only in the difficulty of transcription but also the fact that not everyone follows the approved system. When writing proper names typically none of the existing systems is followed. Geographical names are written according to the Revised Romanization system, while names of universities, festivals etc., which include geographical names as well, are still written according to the McCune-Reischauer system.Koreans are aware of the problem of romanization and recently there has been new discussion in the Republic of Korea about another revision and the unification of the romanization of personal names. There is, however, an established convention according to which each individual writes their own name as wished. Due to specific morphophonological characteristics of the Korean language, consistent Romanization is impossible without adequate knowledge of the language.Since there are currently few Korean words used in Slovenian language an opportunity exists to establish an agreed spelling convention without the excessive revision that might be required later.Slovenski pravopis korejskega jezika in iz korejščine prevzetih besed ne obravnava. Ker se v časopisih in drugje pojavlja vedno več tujk iz korejščine in jih avtorji zapisujejo po svoje, je potrebno zapis čim prej poenotiti, da ne bi prišlo do nesporazumov.Latinizacija korejskega jezika ni problem le v Sloveniji, temveč tudi v Koreji. Obstaja več različnih sistemov latinizacije. Trenutno je v Republiki Koreji v veljavi prenovljeni sistem iz leta 2000, v Demokratični ljudski republiki Koreji pa še vedno sistem McCune-Reischauer, katerega so na jugu zaradi prevelike uporabe diakritičnih znakov in apostrofov opustili. Problem pri latinizaciji korejskega jezika ni samo, da je vse glasove težko prečrkovati v latinico, ampak tudi, da se vsi ne držijo veljavnega sistema. Tako se pri zapisu lastnih imen večinoma ne držijo nobenega sistema, krajevna imena so zapisana po prenovljenem sistemu, imena raznih prireditev, univerz itd., v katerih se prav tako pojavljajo krajevna imena, so le-ta zapisana še po starem sistemu.Korejci se problema latinizacije svojega jezika zavedajo in Republiki Koreji znova potekajo razprave, da bi prenovili sistem in ga poenotili, predvsem kar se tiče zapisa lastnih imen. Podpirava pa pravilo, naj se lastna imena Korejcev in Korejk v slovenskem jeziku zapisujejo tako, kot jih zapisujejo sami. Zaradi morfofonoloških posebnosti brez primernega poznavanja korejskega jezika latiniziranje ni možno.Glede na to, da je v slovenščini število prevzetih besed iz korejskega jezika obvladljivo, bi se bilo smiselno čim prej dogovoriti, kako bomo te besede pravilno zapisovali

Photosensitizer Activation Drives Apoptosis by Interorganellar Ca2+ Transfer and Superoxide Production in Bystander Cancer Cells

In cells, photosensitizer (PS) activation by visible light irradiation triggers reactive oxygen species (ROS) formation, followed by a cascade of cellular responses involving calcium (Ca2+) and other second messengers resulting in cell demise. Cytotoxic effects spread to nearby cells not exposed to light by poorly characterized so-called \u201cbystander effects\u201d. To elucidate the mechanisms involved in bystander cell death, we used both genetically encoded biosensors and fluorescent dyes. In particular, we monitored the kinetics of interorganellar Ca2+ transfer and the production of mitochondrial superoxide anion (O2\uaf\uaf 19) and hydrogen peroxide (H2O2) in irradiated and bystander B16-F10 mouse melanoma cancer cells. We determined that focal PS photoactivation in a single cell triggers Ca2+ release from the endoplasmic reticulum (ER) also in the surrounding non-exposed cells, paralleled by mitochondrial Ca2+ uptake. Efficient Ca2+ efflux from ER was required to promote mitochondrial O2\uaf\uaf 19 production in these bystander cells. Our results support a key role for ER-mitochondria communication in the induction of ROS-mediated apoptosis both in direct and indirect photodynamical cancer cell killing

A Human-Derived Monoclonal Antibody Targeting Extracellular Connexin Domain Selectively Modulates Hemichannel Function

Connexin hemichannels, which are plasma membrane hexameric channels (connexons) composed of connexin protein protomers, have been implicated in a host of physiological processes and pathological conditions. A number of single point pathological mutations impart a "leaky" character to the affected hemichannels, i.e., make them more active or hyperactive, suggesting that normal physiological condition could be recovered using selective hemichannel inhibitors. Recently, a human-derived monoclonal antibody named abEC1.1 has been shown to inhibit both wild type and hyperactive hemichannels composed of human (h) connexin 26 (hCx26) subunits. The aims of this work were (1) to characterize further the ability of abEC1.1 to selectively modulate connexin hemichannel function and (2) to assess its in vitro stability in view of future translational applications. In silico analysis of abEC1.1 interaction with the hCx26 hemichannel identified critically important extracellular domain amino acids that are conserved in connexin 30 (hCx30) and connexin 32 (hCx32). Patch clamp experiments performed in HeLa DH cells confirmed the inhibition efficiency of abEC1.1 was comparable for hCx26, hCx30 and hCx32 hemichannels. Of note, even a single amino acid difference in the putative binding region reduced drastically the inhibitory effects of the antibody on all the other tested hemichannels, namely hCx30.2/31.3, hCx30.3, hCx31, hCx31.1, hCx37, hCx43 and hCx45. Plasma membrane channels composed of pannexin 1 were not affected by abEC1.1. Finally, size exclusion chromatography assays showed the antibody does not aggregate appreciably in vitro. Altogether, these results indicate abEC1.1 is a promising tool for further translational studies