Synthesis, stability, antiviral activity, and protease-bound structures of substrate-mimicking constrained macrocyclic inhibitors of HIV-1 protease

Three new peptidomimetics (1-3) have been developed with highly stable and conformationally constrained macrocyclic components that replace tripeptide segments of protease substrates. Each compound inhibits both HIV-1 protease and viral replication (HIV-I, HIV-2) at nanomolar concentrations without cytotoxicity to uninfected cells below 10 mu M. Their activities against HIV-1 protease (K-i 1.7 nM (1), 0.6 nM (2), 0.3 nM (3)) are 1-2 orders of magnitude greater than their antiviral potencies against HIV-1-infected primary peripheral blood mononuclear cells (IC50 45 nM (1), 56 nM (2), 95 nM (3)) or HIV-1-infected MT2 cells (IC50 90 nM (1), 60 nM (2)), suggesting suboptimal cellular uptake. However their antiviral potencies are similar to those of indinavir and amprenavir under identical conditions. There were significant differences in their capacities to inhibit the replication of HIV-1 and HIV-2 in infected MT2 cells, 1 being ineffective against HIV-2 while 2 was equally effective against both virus types. Evidence is presented that 1 and 2 inhibit cleavage of the HIV-1 structural protein precursor Pr55(gag) to p24 in virions derived from chronically infected cells, consistent with inhibition of the viral protease in cells. Crystal structures refined to 1.75 Angstrom (1) and 1.85 Angstrom (2) for two of the macrocyclic inhibitors bound to HIV-1 protease establish structural mimicry of the tripeptides that the cycles were designed to imitate. Structural comparisons between protease-bound macrocyclic inhibitors, VX478 (amprenavir), and L-735,524 (indinavir) show that their common acyclic components share the same space in the active site of the enzyme and make identical interactions with enzyme residues. This substrate-mimicking minimalist approach to drug design could have benefits in the context of viral resistance, since mutations which induce inhibitor resistance may also be those which prevent substrate processing.

Visual Biology of Hawaiian Coral Reef Fishes. III. Environmental Light and an Integrated Approach to the Ecology of Reef Fish Vision

In the previous two papers in this three-part series, we have examined visual pigments, ocular media transmission, and colors of the coral reef fish of Hawaii. This paper first details aspects of the light field and background colors at the microhabitat level on Hawaiian reefs and does so from the perspective and scale of fish living on the reef. Second, information from all three papers is combined in an attempt to examine trends in the visual ecology of reef inhabitants. Our goal is to begin to see fish the way they appear to other fish. Observations resulting from the combination of results in all three papers include the following. Yellow and blue colors on their own are strikingly well matched to backgrounds on the reef such as coral and bodies of horizontally viewed water. These colors, therefore, depending on context, may be important in camouflage as well as conspicuousness. The spectral characteristics of fish colors are correlated to the known spectral sensitivities in reef fish single cones and are tuned for maximum signal reliability when viewed against known backgrounds. The optimal positions of spectral sensitivity in a modeled dichromatic visual system are generally close to the sensitivities known for reef fish. Models also predict that both UV-sensitive and red-sensitive cone types are advantageous for a variety of tasks. UV-sensitive cones are known in some reef fish, red-sensitive cones have yet to be found. Labroid colors, which appear green or blue to us, may he matched to the far-red component of chlorophyll reflectance for camouflage. Red cave/hole dwelling reef fish are relatively poorly matched to the background they are often viewed against but this may be visually irrelevant. The model predicts that the task of distinguishing green algae from coral is optimized with a relatively long wavelength visual pigment pair. Herbivorous grazers whose visual pigments are known possess the longest sensitivities so far found. Labroid complex colors are highly contrasting complementary colors close up but combine, because of the spatial addition, which results from low visual resolution, at distance, to match background water colors remarkably well. Therefore, they are effective for simultaneous communication and camouflage.

Quadriceps activation in closed and in open kinetic chain exercise

Purpose: For treatment of various knee disorders, muscles are trained in open or closed kinetic chain tasks. Coordination between the heads of the quadriceps muscle is important for stability and optimal joint loading for both the tibiofemoral and the patellofemoral joint. The aim of this study was to examine whether the quadriceps femoris muscles are activated differently in open versus closed kinetic chain tasks. Methods: Ten healthy men and women (mean age 28.5 +/- 0.7) extended the knees isometrically in open and closed kinetic chain tasks in a reaction time paradigm using moderate force. Surface electromyography (EMG) recordings were made from four different parts of the quadriceps muscle. The onset and amplitude of EMG and force data were measured. Results: In closed chain knee extension, the onset of EMG activity of the four different muscle portions of the quadriceps was more simultaneous than in the open chain. In open chain, rectus femoris (RF) had the earliest EMG onset while vastus medialis obliquus was activated last (7 +/- 13 ms after RF EMG onset) and with smaller amplitude (40 +/- 30% of maximal voluntary contraction (MVC)) than in closed chain (46 +/- 43% MVC). Conclusions: Exercise in closed kinetic chain promotes more balanced initial quadriceps activation than does exercise in open kinetic chain. This may be of importance in designing training programs aimed toward control of the patellofemoral joint.

A genetic algorithm/method of moments approach to the optimization of an RF coil for MRI applications - Theoretical considerations - Abstract

A Combined Genetic Algorithm and Method of Moments design methods is presented for the design of unusual near-field antennas for use in Magnetic Resonance Imaging systems. The method is successfully applied to the design of an asymmetric coil structure for use at 190MHz and demonstrates excellent radiofrequency field homogeneity.

An approach to verifying and debugging simulation models governed by ordinary differential equations: Part 1. Methodology for residual generation

For dynamic simulations to be credible, verification of the computer code must be an integral part of the modelling process. This two-part paper describes a novel approach to verification through program testing and debugging. In Part 1, a methodology is presented for detecting and isolating coding errors using back-to-back testing. Residuals are generated by comparing the output of two independent implementations, in response to identical inputs. The key feature of the methodology is that a specially modified observer is created using one of the implementations, so as to impose an error-dependent structure on these residuals. Each error can be associated with a fixed and known subspace, permitting errors to be isolated to specific equations in the code. It is shown that the geometric properties extend to multiple errors in either one of the two implementations. Copyright (C) 2003 John Wiley Sons, Ltd.

An approach to verifying and debugging simulation models governed by ordinary differential equations: Part 2. Residuals analysis and a case study

In Part 1 of this paper a methodology for back-to-back testing of simulation software was described. Residuals with error-dependent geometric properties were generated. A set of potential coding errors was enumerated, along with a corresponding set of feature matrices, which describe the geometric properties imposed on the residuals by each of the errors. In this part of the paper, an algorithm is developed to isolate the coding errors present by analysing the residuals. A set of errors is isolated when the subspace spanned by their combined feature matrices corresponds to that of the residuals. Individual feature matrices are compared to the residuals and classified as 'definite', 'possible' or 'impossible'. The status of 'possible' errors is resolved using a dynamic subset testing algorithm. To demonstrate and validate the testing methodology presented in Part 1 and the isolation algorithm presented in Part 2, a case study is presented using a model for biological wastewater treatment. Both single and simultaneous errors that are deliberately introduced into the simulation code are correctly detected and isolated. Copyright (C) 2003 John Wiley Sons, Ltd.

A metalinguistic approach to deconstructing the concepts of 'face' and 'politeness' in Chinese, English and Japanese

In this paper we investigate the concepts of 'face' and 'politeness'. We introduce a metalanguage which we believe is a framework for simplifying the analysis of 'face' and 'politeness'. This metalanguage is based on the observation that both 'face' and 'politeness' involve external evaluations of people. This common element is represented in the metalanguage as B what A shows A thinks of B and what B thinks A thinks of B. The implications of the metalanguage for the analysis of Chinese mian and lion ('face') and English face are then discussed. This is followed by an analysis of examples of politeness in English and teineisa ('politeness') in Japanese. We conclude that the metalanguage may be further developed for use in comparisons of 'face' and 'politeness' across cultures. (C) 2003 Elsevier B.V. All rights reserved.

Balancing the number and size of sites: An economic approach to the optimal design of cluster samples

The design of randomized controlled trials entails decisions that have economic as well as statistical implications. In particular, the choice of an individual or cluster randomization design may affect the cost of achieving the desired level of power, other things being equal. Furthermore, if cluster randomization is chosen, the researcher must decide how to balance the number of clusters, or sites, and the size of each site. This article investigates these interrelated statistical and economic issues. Its principal purpose is to elucidate the statistical and economic trade-offs to assist researchers to employ randomized controlled trials that have desired economic, as well as statistical, properties. (C) 2003 Elsevier Inc. All rights reserved.

Simultaneous FT-NIR and ESR analyses to yield propagation rate coefficients for polymerization of methyl methacrylate based monomers

A hyphenated instrumental approach has been used to obtain reliable values for the propagation rate coefficients as a function of conversion for polymerizations of methyl methacrylate (MMA) and a mixture of MMA and ethyleneglycol dimethacrylate (EGDMA) with a 1:1 concentration of double bonds, from near the onset of the Trommsdorf region into the glass region. ESR spectroscopy was used to measure the radical concentration while FT-NIR fibre-optic spectroscopy was employed to measure instantaneously the double-bond concentration within the temperature-controlled cavity of the ESR instrument during polymerization. The advantage of this approach to the measurement of the rate coefficient is that it is equally applicable to branching and linear polymerizations. For the polymerization of methyl methacrylate, the values of the rate coefficient at the lowest conversions at which reliable values could be obtained were in agreement with recently reported values obtained by the PLP-SEC method. For the lowest conversions, the values obtained were 403 1 mol(-1) s(-1) at 306 K for MMA and 5201 mol(-1) s(-1) at 310 K for a 1:1 mixture of MMA and EGDMA. (C) 2003 Society of Chemical Industry.

A kinetic study of the thermally initiated free radical reactions of styrene with octanedithiol as a model for the reactions of multifunctional thiols with divinylbenzene

The kinetics of chain reactions of octanedithiol with styrene, thermally initiated with TX29B50 (a 50:50 wt% solution of TX29 diperoxy initiator in a phthalate plasticizer), have been studied over a range of initiator concentrations, a range of mixture formulations and a range of temperatures. This system has been investigated as a model system for the reactions of polyfunctional thiols with divinyl benzene. The reactions have been shown to follow first-order kinetics for both the thiol and the ene species and to be characterized by a dependence on the initiator concentration to the power of one half. The kinetic rate parameters have been shown to adhere to Arrhenius behaviour. A kinetic model for the chain reactions for this system has been proposed. (C) 2003 Society of Chemical Industry.

Quantum theory of the far-off-resonance continuous-wave Raman laser: Heisenberg-Langevin approach

We present the quantum theory of the far-off-resonance continuous-wave Raman laser using the Heisenberg-Langevin approach. We show that the simplified quantum Langevin equations for this system are mathematically identical to those of the nondegenerate optical parametric oscillator in the time domain with the following associations: pump pump, Stokes signal, and Raman coherence idler. We derive analytical results for both the steady-state behavior and the time-dependent noise spectra, using standard linearization procedures. In the semiclassical limit, these results match with previous purely semiclassical treatments, which yield excellent agreement with experimental observations. The analytical time-dependent results predict perfect photon statistics conversion from the pump to the Stokes and nonclassical behavior under certain operational conditions.

Representing organizational structures in enterprise architecture : an ontology-based approach

Arquitetura Corporativa promove o estabelecimento de uma visão holística da estrutura e forma de trabalho de uma organização. Um dos aspectos abordados em Arquitetura Corporativa está associada a "estrutura ativa" da organização, que diz respeito a “quem" realiza as atividades organizacionais. Várias abordagens têm sido propostas a fim de proporcionar um meio para a representação de Arquitetura Corporativa, entre as quais ARIS, RM-ODP, UPDM e ArchiMate. Apesar da aceitação por parte da comunidade, as abordagens existentes se concentram em propósitos diferentes, têm limitações de escopo e algumas não têm semântica de mundo real bem definida. Além das abordagens de modelagem, muitas abordagens de ontologias têm sido propostas, a fim de descrever o domínio de estrutura ativa, incluindo as ontologias de SUPER Project, TOVE, Enterprise Ontology e W3C Org Ontology. Embora especificadas para fundamentação semântica e negociação de significado, algumas das abordagens propostas têm fins específicos e cobertura limitada. Além disso, algumas das abordagens não são definidas usando linguagens formais e outras são especificadas usando linguagens sem semântica bem definida. Este trabalho apresenta uma ontologia de referência bem fundamentada para o domínio organizacional. A ontologia organizacional de referência apresentada abrange os aspectos básicos discutidos na literatura organizacional, tais como divisão do trabalho, relações sociais e classificação das unidades estruturais. Além disso, também abrange os aspectos organizacionais definidos em abordagens existentes, levando em consideração tanto abordagens de modelagem quanto abordagens ontológicas. A ontologia resultante é especificada em OntoUML e estende os conceitos sociais de UFO-C.

Rendering peacekeeping instrumental? The Brazilian approach to United Nations peacekeeping during the Lula da Silva years (2003-2010)

The article analyses how Brazilian state actions and policies regarding peace operations during the Presidency of Lula da Silva relate to the country's positions and attitudes towards United Nations peacekeeping. It argues that the inconsistencies identified on the Brazilian positions reflect the lack of a clear strategic horizon guiding the country's participation in UN peacekeeping, which consequentially hinders the country emergence as a great power.