Dynamic binary translation using run-time feedbacks

Dynamic binary translation is the process of translating, modifying and rewriting executable (binary) code from one machine to another at run-time. This process of low-level re-engineering consists of a reverse engineering phase followed by a forward engineering phase. UQDBT, the University of Queensland Dynamic Binary Translator, is a machine-adaptable translator. Adaptability is provided through the specification of properties of machines and their instruction sets, allowing the support of different pairs of source and target machines. Most binary translators are closely bound to a pair of machines, making analyses and code hard to reuse. Like most virtual machines, UQDBT performs generic optimizations that apply to a variety of machines. Frequently executed code is translated to native code by the use of edge weight instrumentation, which makes UQDBT converge more quickly than systems based on instruction speculation. In this paper, we describe the architecture and run-time feedback optimizations performed by the UQDBT system, and provide results obtained in the x86 and SPARC® platforms.

Spatial gene expression in the T-stage mouse metanephros

The E11.5 mouse metanephros is comprised of a T-stage ureteric epithelial tubule sub-divided into tip and trunk cells surrounded by metanephric mesenchyme (MM). Tip cells are induced to undergo branching morphogenesis by the MM. In contrast, signals within the mesenchyme surrounding the trunk prevent ectopic branching of this region. In order to identify novel genes involved in the molecular regulation of branching morphogenesis we compared the gene expression profiles of isolated tip, trunk and MM cells using Compugen mouse long oligo microarrays. We identified genes enriched in the tip epithelium, sim-1, Arg2, Tacstd1, Crlf-1 and BMP7; genes enriched in the trunk epithelium, Innp1, Itm2b, Mkrn1, SPARC, Emu2 and Gsta3 and genes spatially restricted to the mesenchyme surrounding the trunk, CSPG2 and CV-2, with overlapping and complimentary expression to BMP4, respectively. This study has identified genes spatially expressed in regions of the developing kidney involved in branching morphogenesis, nephrogenesis and the development of the collecting duct system, calyces, renal pelvis and ureter. (c) 2006 Elsevier B.V. All rights reserved.

Optimization of chemical plant simulation using double collocation

A method has been constructed for the solution of a wide range of chemical plant simulation models including differential equations and optimization. Double orthogonal collocation on finite elements is applied to convert the model into an NLP problem that is solved either by the VF 13AD package based on successive quadratic programming, or by the GRG2 package, based on the generalized reduced gradient method. This approach is termed simultaneous optimization and solution strategy. The objective functional can contain integral terms. The state and control variables can have time delays. Equalities and inequalities containing state and control variables can be included into the model as well as algebraic equations and inequalities. The maximum number of independent variables is 2. Problems containing 3 independent variables can be transformed into problems having 2 independent variables using finite differencing. The maximum number of NLP variables and constraints is 1500. The method is also suitable for solving ordinary and partial differential equations. The state functions are approximated by a linear combination of Lagrange interpolation polynomials. The control function can either be approximated by a linear combination of Lagrange interpolation polynomials or by a piecewise constant function over finite elements. The number of internal collocation points can vary by finite elements. The residual error is evaluated at arbitrarily chosen equidistant grid-points, thus enabling the user to check the accuracy of the solution between collocation points, where the solution is exact. The solution functions can be tabulated. There is an option to use control vector parameterization to solve optimization problems containing initial value ordinary differential equations. When there are many differential equations or the upper integration limit should be selected optimally then this approach should be used. The portability of the package has been addressed converting the package from V AX FORTRAN 77 into IBM PC FORTRAN 77 and into SUN SPARC 2000 FORTRAN 77. Computer runs have shown that the method can reproduce optimization problems published in the literature. The GRG2 and the VF I 3AD packages, integrated into the optimization package, proved to be robust and reliable. The package contains an executive module, a module performing control vector parameterization and 2 nonlinear problem solver modules, GRG2 and VF I 3AD. There is a stand-alone module that converts the differential-algebraic optimization problem into a nonlinear programming problem.

Mesenchymal stem cell-conditioned medium accelerates skin wound healing:an in vitro study of fibroblast and keratinocyte scratch assays

We have used in vitro scratch assays to examine the relative contribution of dermal fibroblasts and keratinocytes in the wound repair process and to test the influence of mesenchymal stem cell (MSC) secreted factors on both skin cell types. Scratch assays were established using single cell and co-cultures of L929 fibroblasts and HaCaT keratinocytes, with wound closure monitored via time-lapse microscopy. Both in serum supplemented and serum free conditions, wound closure was faster in L929 fibroblast than HaCaT keratinocyte scratch assays, and in co-culture the L929 fibroblasts lead the way in closing the scratches. MSC-CM generated under serum free conditions significantly enhanced the wound closure rate of both skin cell types separately and in co-culture, whereas conditioned medium from L929 or HaCaT cultures had no significant effect. This enhancement of wound closure in the presence of MSC-CM was due to accelerated cell migration rather than increased cell proliferation. A number of wound healing mediators were identified in MSC-CM, including TGF-beta1, the chemokines IL-6, IL-8, MCP-1 and RANTES, and collagen type I, fibronectin, SPARC and IGFBP-7. This study suggests that the trophic activity of MSC may play a role in skin wound closure by affecting both dermal fibroblast and keratinocyte migration, along with a contribution to the formation of extracellular matrix.

Simulação da destilação molecular de filme descendente para o petróleo

The heavy part of the oil can be used for numerous purposes, e.g. to obtain lubricating oils. In this context, many researchers have been studying alternatives such separation of crude oil components, among which may be mentioned molecular distillation. Molecular distillation is a forced evaporation technique different from other conventional processes in the literature. This process can be classified as a special distillation case under high vacuum with pressures that reach extremely low ranges of the order of 0.1 Pascal. The evaporation and condensation surfaces must have a distance from each other of the magnitude order of mean free path of the evaporated molecules, that is, molecules evaporated easily reach the condenser, because they find a route without obstacles, what is desirable. Thus, the main contribution of this work is the simulation of the falling-film molecular distillation for crude oil mixtures. The crude oil was characterized using UniSim® Design and R430 Aspen HYSYS® V8.5. The results of this characterization were performed in spreadsheets of Microsoft® Excel®, calculations of the physicochemical properties of the waste of an oil sample, i.e., thermodynamic and transport. Based on this estimated properties and boundary conditions suggested by the literature, equations of temperature and concentration profiles were resolved through the implicit finite difference method using the programming language Visual Basic® (VBA) for Excel®. The result of the temperature profile showed consistent with the reproduced by literature, having in their initial values a slight distortion as a result of the nature of the studied oil is lighter than the literature, since the results of the concentration profiles were effective allowing realize that the concentration of the more volatile decreases and of the less volatile increases due to the length of the evaporator. According to the transport phenomena present in the process, the velocity profile tends to increase to a peak and then decreases, and the film thickness decreases, both as a function of the evaporator length. It is concluded that the simulation code in Visual Basic® language (VBA) is a final product of the work that allows application to molecular distillation of petroleum and other similar mixtures.

Experiencias de danzaterapia de mujeres que han sufrido cáncer de mama. Un estudio fenomenológico

Objective: This essay aims at identifying, describing and analyzing possible changes both in the experience of the body and in interpersonal relations of women with breast cancer, which result from their participation in Dance Therapy group meetings.Method: This is a phenomenologically oriented qualitative research using Maria Fux´s dance therapy method for group experiences. Eight meetings are described here, and an analysis of descriptions based primarily on Merleau-Ponty and María Fux is provided.Results: The participants have been able to express pain and sorrow over the circumstances that breast cancer and its relational environments have brought to their lives. They have been able to go through moments of creation and surrender to the rhythmic body sensations and experiential environment with different emotions lived separately and jointly. They have revived memories and sensations of their childhood and adolescence, and finally, they have rediscovered their sensitive body through body resignifications marked by the absence of the breast, and by means of feelings of greater acceptance and integration of lived experiences in new gestalts.Conclusions: This project is still under way, but it is already possible to conclude that the life experiences provided in dance therapy have allowed these women to improve their integration and welfare. Likewise, they have felt positive changes in the perception of their corporality and in their way of being in the world and with other subjects, thus experiencing the body in a new and different way.

NOD2 mutations and colorectal cancer - Where do we stand?

Due to the overwhelming burden of colorectal cancer (CRC), great effort has been placed on identifying genetic mutations that contribute to disease development and progression. One of the most studied polymorphisms that could potentially increase susceptibility to CRC involves the nucleotide-binding and oligomerization-domain containing 2 (NOD2) gene. There is growing evidence that the biological activity of NOD2 is far greater than previously thought and a link with intestinal microbiota and mucosal immunity is increasingly sought after. In fact, microbial composition may be an important contributor not only to inflammatory bowel diseases (IBD) but also to CRC. Recent studies have showed that deficient NOD2 function confers a communicable risk of colitis and CRC. Despite the evidence from experimental models, population-based studies that tried to link certain NOD2 polymorphisms and an increase in CRC risk have been described as conflicting. Significant geographic discrepancies in the frequency of such polymorphisms and different interpretations of the results may have limited the conclusions of those studies. Since being first associated to IBD and CRC, our understanding of the role of this gene has come a long way, and it is tempting to postulate that it may contribute to identify individuals with susceptible genetic background that may benefit from early CRC screening programs or in predicting response to current therapeutic tools. The aim of this review is to clarify the status quo of NOD2 mutations as genetic risk factors to chronic inflammation and ultimately to CRC. The use of NOD2 as a predictor of certain phenotypic characteristics of the disease will be analyzed as well.

Développement d’une stratégie de modification du bois afin de limiter les variations dimensionnelles du produit lambris dans un contexte éco-responsable

Ce travail de thèse présente deux grands axes. Le premier axe, touche les traitements du bois dans le but principal de réduire les variations dimensionnelles et d’améliorer la résistance à l’attaque des champignons lignivores. Le second axe quant à lui, touche l’aspect environnemental du traitement acide citrique-glycérol. Ce dernier a pour but principal de démontrer que le prolongement de la durée de vie en service du produit lambris traité, compense les impacts environnementaux causés par ce traitement. Dans le premier axe, deux traitements ont été réalisés sur deux essences de pin (Pinus strobus L. et Pinus contorta D.). Un traitement à l’anhydride maléique et un autre traitement avec une solution d’acide citrique – glycérol brute (AC-G). Dans le premier cas, les effets de deux paramètres (la durée de séchage et la température d’estérification) sur les résultats des essais de stabilité dimensionnelle, de résistance à la dégradation fongique et de vieillissement accéléré ont été évalués. Trois niveaux de durée de séchage après imprégnation (12 h, 18 h et 24 h) et trois niveaux de température d’estérification (140 °C, 160 °C et 180 °C) ont été considérés. Dans le second cas, après identification du meilleur catalyseur (HCl) et du meilleur ratio acide citrique – glycérol (3/1) pendant les essais préliminaires, les performances de ce traitement sur la stabilité dimensionnelle, la résistance à la pourriture fongique, la dureté de surface et l’adhérence des couches de revêtement de peinture sur la surface du substrat bois ont été analysées. Les résultats obtenus ont été appuyés par une suite d’analyses qualitatives et quantitatives pour mieux comprendre et expliquer. Les analyses qualitatives sont : (i) la spectroscopie infrarouge à transformée de Fourier (IRTF) et (ii) la microscopie électronique à balayage (MEB) tandis que la quantitative, l’analyse par perte de masse a été faite par pesée. Dans le second axe, une analyse des impacts environnementaux du traitement AC-G a été effectuée par le biais du logiciel SimaPro v8. La base de données Ecoinvent v3 et la méthode d’analyse d’impact Impact 2002+ ont été utilisées dans cette partie du travail de thèse. Sur la base des résultats du second traitement (AC-G) et des travaux disponibles dans la littérature, nous avons estimé, une durée de vie en service des lambris traités. Les différents scénarios de la durée de vie du lambris traité mis sur pied par rapport à celle offerte aujourd’hui par l’industrie, nous permettent de modéliser les impacts environnementaux du traitement. A cette fin, l’analyse de cycle de vie (ACV) a été utilisée comme outil de conception. En conclusion, les paramètres, durée de séchage et température d’estérification influencent les résultats obtenus dans le cas du traitement du bois à l’anhydride maléique. La combinaison 24 h de séchage et 180 °C, température d’estérification, représente les paramètres qui offrent les meilleurs résultats de stabilité dimensionnelle, de résistance à la dégradation fongique et de vieillissement accéléré. Le traitement AC-G améliore la stabilité dimensionnelle, la résistance à la dégradation fongique et la dureté de surface des échantillons. Cependant, le traitement réduit l’adhérence des couches de peinture. Les impacts environnementaux produits par le traitement AC-G sont majoritairement liés à la consommation de la ressource énergie (électricité). Le traitement prolonge la durée de vie en service du lambris traité et il a été mis en évidence que le scénario de durée de vie qui permettrait que le lambris traité puisse se présenter comme un produit à faible impact environnemental par rapport au lambris non traité est celui d’une durée de vie de 55 ans.

The impact of Open Access outside of European Universities

The Open Access movement has encouraged the availability of publicly-funded research papers, data and learning content for barrier-free use of that content without payment by the user. The impact of increasing availability of content to researchers in European universities is understood in terms of easier access to previous research and greater exposure for new research results, bringing benefits to the research community itself. A new culture of informal sharing is evident within the teaching and learning communities and to some extent also within the research community, but as yet the growth in informal sharing has not had a major effect upon the use of formal publication choices. This briefing paper explores the impact of open access upon potential users of research outputs outside the walls of research-led European universities, where the economic value of open access may be even greater than the academic value within universities. The potential impact of open access is understood in many communities but requires a greater volume of open access content to be available for the full potential to be realised. More open access content will become available as the opportunities in open, internet-based digital scholarship are understood. This briefing paper was written in cooperation with SPARC Europe. All links provided in footnotes in this Briefing Paper are to studies available in open access.

NOD2 mutations and colorectal cancer - Where do we stand?

Due to the overwhelming burden of colorectal cancer (CRC), great effort has been placed on identifying genetic mutations that contribute to disease development and progression. One of the most studied polymorphisms that could potentially increase susceptibility to CRC involves the nucleotide-binding and oligomerization-domain containing 2 (NOD2) gene. There is growing evidence that the biological activity of NOD2 is far greater than previously thought and a link with intestinal microbiota and mucosal immunity is increasingly sought after. In fact, microbial composition may be an important contributor not only to inflammatory bowel diseases (IBD) but also to CRC. Recent studies have showed that deficient NOD2 function confers a communicable risk of colitis and CRC. Despite the evidence from experimental models, population-based studies that tried to link certain NOD2 polymorphisms and an increase in CRC risk have been described as conflicting. Significant geographic discrepancies in the frequency of such polymorphisms and different interpretations of the results may have limited the conclusions of those studies. Since being first associated to IBD and CRC, our understanding of the role of this gene has come a long way, and it is tempting to postulate that it may contribute to identify individuals with susceptible genetic background that may benefit from early CRC screening programs or in predicting response to current therapeutic tools. The aim of this review is to clarify the status quo of NOD2 mutations as genetic risk factors to chronic inflammation and ultimately to CRC. The use of NOD2 as a predictor of certain phenotypic characteristics of the disease will be analyzed as well.

Hydrometallurgical process modeling using advanced mathematical tools

Hydrometallurgical process modeling is the main objective of this Master’s thesis work. Three different leaching processes namely, high pressure pyrite oxidation, direct oxidation zinc concentrate (sphalerite) leaching and gold chloride leaching using rotating disc electrode (RDE) are modeled and simulated using gPROMS process simulation program in order to evaluate its model building capabilities. The leaching mechanism in each case is described in terms of a shrinking core model. The mathematical modeling carried out included process model development based on available literature, estimation of reaction kinetic parameters and assessment of the model reliability by checking the goodness fit and checking the cross correlation between the estimated parameters through the use of correlation matrices. The estimated parameter values in each case were compared with those obtained using the Modest simulation program. Further, based on the estimated reaction kinetic parameters, reactor simulation and modeling for direct oxidation zinc concentrate (sphalerite) leaching is carried out in Aspen Plus V8.6. The zinc leaching autoclave is based on Cominco reactor configuration and is modeled as a series of continuous stirred reactors (CSTRs). The sphalerite conversion is calculated and a sensitivity analysis is carried out so to determine the optimum reactor operation temperature and optimum oxygen mass flow rate. In this way, the implementation of reaction kinetic models into the process flowsheet simulation environment has been demonstrated.

Análisis de las simulaciones del proceso de deshidratación del gas natural con Aspen Hysys y Aspen Plus

El gas natural ha tomado un rol estratégico importante en el suministro de energía a nivel mundial como consecuencia de la creciente demanda global de energía. El agua es probablemente el componente indeseable más común en el gas natural no tratado ya que su presencia puede ocasionar la formación de hidratos y problemas de corrosión. Debido a las potenciales consecuencias costosas, el gas debe ser sometido a procesos de acondicionamiento a fin de alcanzar las especificaciones requeridas para su venta, transporte hacia los centros de distribución y consumo final. En los últimos años, la simulación de procesos está jugando un papel muy importante en la industria del gas y petróleo como una herramienta adecuada y oportuna para el diseño, caracterización, optimización y monitoreo del funcionamiento de procesos industriales. En el presente trabajo se describe el desarrollo de dos simulaciones estacionarias del proceso de deshidratación de gas natural por absorción con trietilenglicol (TEG), empleando los simuladores comerciales de procesos Aspen HYSYS V8.3 y Aspen PLUS V8.2. La composición del gas natural, la configuración del proceso y las condiciones de operación empleadas en los cálculos y la simulación son típicas de los yacimientos y plantas de acondicionamiento de la provincia de Salta (Argentina).

Diseño del proceso de una torre de vacío. Ventajas de la simulación

Los hidrocarburos pesados son el mayor recurso del petróleo en el mundo, sin embargo en el pasado se habían dejado de lado como recurso energético debido a las dificultades y costos asociados de su producción [1]. La industria financia estas investigaciones por la importancia del tema en producción y caracterización. Al trabajar con una torre de vacio los datos necesarios para los cálculos son las temperaturas ASTM (10mmHg) y la densidad del crudo con la cual se obtiene la curva TBP760 (True Boiling Point), también se necesita las especificaciones de los productos y los rendimientos respecto de la alimentación. Para poder correlacionar los distintos puntos de ebullición con los porcentajes de vaporizado para cada cambio de presión de los distintos productos, se construye un diagrama de fases con las temperaturas EFV760 (Equilibrium Flash Vaporization) y EFV10. El simulador a través de cálculos internos resuelve automáticamente el diagrama de fases, en comparación con la dificultad que representan los cálculos manuales del mismo, tal como son explicitados precedentemente. En este trabajo se desarrolla la simulación de una torre de vacío mediante el simulador Aspen HYSYS V8.3, empleando como alimentación un crudo pesado. Lo antes expuesto constituye una importante ventaja el uso del simulador frente al cálculo convencional, considerando los tiempos de resolución de los diseños de procesos.

Structure-function relationship of new crotamine isoform from the Crotalus durissus cascavella

In this work we isolated a novel crotamine like protein from the Crotalus durissus cascavella venom by combination of molecular exclusion and analytical reverse phase HPLC. Its primary structure was:YKRCHKKGGHCFPKEKICLPPSSDLGKMDCRWKRK-CCKKGS GK. This protein showed a molecular mass of 4892.89 da that was determined by Matrix Assisted Laser Desorption Ionization Time-of-flight (MALDI-TOF) mass spectrometry. The approximately pI value of this protein was determined in 9.9 by two-dimensional electrophoresis. This crotamine-like protein isolated here and that named as Cro 2 produced skeletal muscle spasm and spastic paralysis in mice similarly to other crotamines like proteins. Cro 2 did not modify the insulin secretion at low glucose concentration (2.8 and 5.6 mM), but at high glucose concentration (16.7 mM) we observed an insulin secretion increasing of 2.7-3.0-fold than to control. The Na+ channel antagonist tetrodoxin (6 mM) decreased glucose and Cro 2-induced insulin secretion. These results suggested that Na+ channel are involved in the insulin secretion. In this article, we also purified some peptide fragment from the treatment of reduced and carboxymethylated Cro 2 (RC-Cro 2) with cyanogen bromide and protease V8 from Staphylococcus aureus. The isolated pancreatic beta-cells were then treated with peptides only at high glucose concentration (16.7 mM), in this condition only two peptides induced insulin secretion. The amino acid sequence homology analysis of the whole crotamine as well as the biologically-active peptide allowed determining the consensus region of the biologically-active crotamine responsible for insulin secretion was KGGHCFPKE and DCRWKWKCCKKGSG.