Conformational selection of inhibitors and substrates by proteolytic enzymes: Implications for drug design and polypeptide processing

Inhibitors of proteolytic enzymes (proteases) are emerging as prospective treatments for diseases such as AIDS and viral infections, cancers, inflammatory disorders, and Alzheimer's disease. Generic approaches to the design of protease inhibitors are limited by the unpredictability of interactions between, and structural changes to, inhibitor and protease during binding. A computer analysis of superimposed crystal structures for 266 small molecule inhibitors bound to 48 proteases (16 aspartic, 17 serine, 8 cysteine, and 7 metallo) provides the first conclusive proof that inhibitors, including substrate analogues, commonly bind in an extended beta-strand conformation at the active sites of all these proteases. Representative superimposed structures are shown for (a) multiple inhibitors bound to a protease of each class, (b) single inhibitors each bound to multiple proteases, and (c) conformationally constrained inhibitors bound to proteases. Thus inhibitor/substrate conformation, rather than sequence/composition alone, influences protease recognition, and this has profound implications for inhibitor design. This conclusion is supported by NMR, CD, and binding studies for HIV-1 protease inhibitors/ substrates which, when preorganized in an extended conformation, have significantly higher protease affinity. Recognition is dependent upon conformational equilibria since helical and turn peptide conformations are not processed by proteases. Conformational selection explains the resistance of folded/structured regions of proteins to proteolytic degradation, the susceptibility of denatured proteins to processing, and the higher affinity of conformationally constrained 'extended' inhibitors/substrates for proteases. Other approaches to extended inhibitor conformations should similarly lead to high-affinity binding to a protease.

Design of the multicenter Australian study of epidural anesthesia and analgesia in major surgery: The MASTER Trial

The Multicenter Australian Study of Epidural Anesthesia and Analgesia in Major Surgery (The MASTER Trial) was designed to evaluate the possible benefit of epidural block in improving outcome in high-risk patients. The trial began in 1995 and is scheduled to reach the planned sample size of 900 during 2001. This paper describes the trial design and presents data comparing 455 patients randomized in 21 institutions in Australia, Hong Kong, and Malaysia, with 237 patients from the same hospitals who were eligible but not randomized. Nine categories of high-risk patients were defined as entry criteria for the trial. Protocols for ethical review, informed consent, randomization, clinical anesthesia and analgesia, and perioperative management were determined following extensive consultation with anesthesiologists throughout Australia. Clinical and research information was collected in participating hospitals by research staff who may not have been blind to allocation. Decisions about the presence or absence of endpoints were made primarily by a computer algorithm, supplemented by blinded clinical experts. Without unblinding the trial, comparison of eligibility criteria and incidence of endpoints between randomized and nonrandomized patients showed only small differences. We conclude that there is no strong evidence of important demographic or clinical differences between randomized and nonrandomized patients eligible for the MASTER Trial. Thus, the trial results are likely to be broadly generalizable. Control Clin Trials 2000;21:244-256 (C) Elsevier Science Inc. 2000.

Decentralized control design for nonlinear plants: a v-metric approach

In this paper, a new v-metric based approach is proposed to design decentralized controllers for multi-unit nonlinear plants that admit a set of plant decompositions in an operating space. Similar to the gap metric approach in literature, it is shown that the operating space can also be divided into several subregions based on a v-metric indicator, and each of the subregions admits the same controller structure. A comparative case study is presented to display the advantages of proposed approach over the gap metric approach. (C) 2000 Elsevier Science Ltd. All rights reserved.

Incubation of eggs of the Australian broad-shelled turtle, Chelodina expansa (Testudinata : Chelidae), at different temperatures: effects on pattern of oxygen consumption and hatchling morphology

Incubation temperature influences embryonic development and the morphology of resultant hatchlings in many species of turtle but few studies have addressed its effect on oxygen consumption and total embryonic energy expenditure. Eggs of the Australian broad-shelled river turtle, Chelodina expansa, were incubated at constant temperatures of 24 degrees C and 28 degrees C to determine the effect of temperature on oxygen consumption, embryonic energy expenditure and hatchling morphology. All embryos at both incubation temperatures experienced a period of developmental diapause immediately after oviposition. Once this initial diapause was broken, embryos underwent a further period of developmental arrest when the embryo was still very small and had minimal oxygen consumption (

Investigation of threat-related attentional bias in anxious children using the startle eyeblink modification paradigm

We used the startle eyeblink modification paradigm to investigate whether clinically anxious children, like high trait-anxious adults, display a bias in favour of threat words compared to neutral words. The present study included 16 clinically anxious children whose diagnostic status was determined using the parent version of a semistructured diagnostic interview as part of a larger childhood anxiety study. The children were presented with threat and neutral words fur 6 s each. A startle-eliciting auditory stimulus - a 100 dBA burst of white noise of 50 ms duration - was presented during the words at lead intervals of 60, 120, 240, or 3500 ms and during intertrial intervals. The overall pattern of startle eyeblink modification indicated inhibition at the 120 and 240 ms lead intervals and facilitation at the 3500 ms lead interval. startle-latency shortening during threat words at the :60 ms lead interval was larger than at other intervals, whereas there was no difference during neutral words. This result reflects an anxiety-related bias in favour of threat words occurring at a very early - and possibly preattentive stage - of information processing.

Eye design and color signaling in a stomatopod crustacean Gonodactylus smithii

Many species of stomatopod crustaceans have multiple spectral classes of photoreceptors in their retinas. Behavioral evidence also indicates that stomatopods are capable of discriminating objects by their spectral differences alone, Most animals use only two to four different types of photoreceptors in their color vision systems, typically with broad sensitivity functions, but the stomatopods apparently include eight or more narrowband photoreceptor classes for color recognition. It is also known that stomatopods use several colored body regions in social interactions. To examine why stomatopods may be so 'concerned' with color, we measured the absorption spectra of visual pigments and intrarhabdomal filters, and the reflectance spectra from different parts of the bodies of several individuals of the gonodactyloid stomatopod species, Gonodactylus smithii. We then applied a model of multiple dichromatic channels for color encoding to examine whether the finely tuned color vision was specifically co-evolved with their complex color signals. Although the eye design of stomatopods seems suitable for detecting color signals of their own, the detection of color signals from other animals, such as reef fishes, can be enhanced as well. Color vision in G. smithii is therefore not exclusively adapted to detect its own color signals, but the spectral tuning of some photoreceptors (e.g. midband Rows 2 and 3) enhances the contrast of certain color signals to a large enough degree to make co-evolution between color vision and these rather specific color signals likely. Copyright (C) 2000 S. Karger AG, Basel.

Simultaneous steady state and dynamic design of process systems using structural indicators

The simultaneous design of the steady-state and dynamic performance of a process has the ability to satisfy much more demanding dynamic performance criteria than the design of dynamics only by the connection of a control system. A method for designing process dynamics based on the use of a linearised systems' eigenvalues has been developed. The eigenvalues are associated with system states using the unit perturbation spectral resolution (UPSR), characterising the dynamics of each state. The design method uses a homotopy approach to determine a final design which satisfies both steady-state and dynamic performance criteria. A highly interacting single stage forced circulation evaporator system, including control loops, was designed by this method with the goal of reducing the time taken for the liquid composition to reach steady-state. Initially the system was successfully redesigned to speed up the eigenvalue associated with the liquid composition state, but this did not result in an improved startup performance. Further analysis showed that the integral action of the composition controller was the source of the limiting eigenvalue. Design changes made to speed up this eigenvalue did result in an improved startup performance. The proposed approach provides a structured way to address the design-control interface, giving significant insight into the dynamic behaviour of the system such that a systematic design or redesign of an existing system can be undertaken with confidence.

Minimum-order stable recursive filter design via the genetic algorithm approach

In this paper, the minimum-order stable recursive filter design problem is proposed and investigated. This problem is playing an important role in pipeline implementation sin signal processing. Here, the existence of a high-order stable recursive filter is proved theoretically, in which the upper bound for the highest order of stable filters is given. Then the minimum-order stable linear predictor is obtained via solving an optimization problem. In this paper, the popular genetic algorithm approach is adopted since it is a heuristic probabilistic optimization technique and has been widely used in engineering designs. Finally, an illustrative example is sued to show the effectiveness of the proposed algorithm.

The advantages of theft over toil: The design inference and arguing from ignorance

Intelligent design theorist William Dembski has proposed an explanatory filter for distinguishing between events due to chance, lawful regularity or design. We show that if Dembski's filter were adopted as a scientific heuristic, some classical developments in science would not be rational, and that Dembski's assertion that the filter reliably identifies rarefied design requires ignoring the state of background knowledge. If background information changes even slightly, the filter's conclusion will vary wildly. Dembski fails to overcome Hume's objections to arguments from design.

Suicidal ideation and suicide attempts as predictors of mental health service use

Objective: To examine the extent to which suicidal ideation and suicide attempts are predictive of service use. Design and setting: The National Survey of Mental Health and Wellbeing considered service utilisation in relation to self-reported mental health problems. Service utilisation was inquired of in relation to hospital-based care (including both specialist mental health and general care settings), as well as consultations with a range of health professionals (both specialist and non-specialist mental health professionals, including psychiatrists, psychologists and general practitioners) on an outpatient basis. Participants: Secondary analysis of self-report data from 10 641 randomly selected Australian adults who participated in the National Survey of Mental Health and Wellbeing in 1997. The key predictor variables were reported suicidal ideation and suicide attempts over the past 12 months. Main outcome measures: Use of services for mental health problems (past 12 months). Results: When considered in isolation, individuals reporting suicidal ideation were more likely to make use of at least one type of service for mental health problems than non-suicidal individuals (OR, 17.3; 95% Cl, 13.2-22.6), and individuals reporting suicide attempts were even more likely to do so (OR, 32.3; 95% CI, 9.0-115.4). In the case of suicidal ideation, this effect remained significant after controlling for a range of potential confounders. For suicide attempts, the effect of mental health service use was no longer significant after other variables were taken into account. Conclusions: Suicidal individuals are likely to make use of services, and a high proportion of suicides may be preventable through appropriate healthcare system responses.

A time-harmonic inverse methodology for the design of RF coils in MRI

An inverse methodology is described to assist in the design of radio-frequency (RF) coils for magnetic resonance imaging (MRI) applications. The time-harmonic electromagnetic Green's functions are used to calculate current on the coil and shield cylinders that will generate a specified internal magnetic field. Stream function techniques and the method of moments are then used to implement this theoretical current density into an RF coil. A novel asymmetric coil operating for a 4.5 T MRI machine was designed and constructed using this methodology and the results are presented.

The VITATOPS (vitamins to prevent stroke) Trial: Rationale and design of an international, large, simple, randomised trial of homocysteine-lowering multivitamin therapy in patients with recent transient ischaemic attack or stroke

Background: Epidemiological studies suggest that raised plasma concentrations of total homocysteine (tHcy) may be a common, causal and treatable risk factor for atherothromboembolic ischaemic stroke. Although tHcy can be lowered effectively with small doses of folic acid, vitamin B-12 and vitamin B-6, it is not known whether lowering tHcy, by means of multivitamin therapy, can prevent stroke and other major atherothromboembolic vascular events. Purpose: To determine whether vitamin supplements (folic acid 2 mg, B-6 25 Mg, B-12 500 mug) reduce the risk of stroke, and other serious vascular events, in patients with recent stroke or transient ischaemic attacks of the brain or eye (TIA). Methods: An international, multi-centre, randomised, double-blind, placebo-controlled clinical trial. Results: As of November 2001, more than 1,400 patients have been randomised from 10 countries in four continents. Conclusion: VITATOPS aims to recruit and follow up 8,000 patients between 2000 and 2004, and provide a reliable estimate of the safety and effectiveness of dietary supplementation with folic acid, vitamin B-12, and vitamin B-6 in reducing recurrent serious vascular events among a wide range of patients with TIA and stroke. Copyright (C) 2002 S. Karger AG, Basel.

The demise of a planned randomised controlled trial in an urban Aboriginal medical service

To fill a gap in knowledge about the effectiveness of brief intervention for hazardous alcohol use among Indigenous Australians, we attempted to implement a randomised controlled trial in an urban Aboriginal Medical Service (AMS) as a joint AMS-university partnership. Because of low numbers of potential participants being screened, the RCT was abandoned in favour of a two-part demonstration project. Only 16 clients were recruited for follow-up in six-months, and the trial was terminated. Clinic, patient, Aboriginal health worker, and GP factors, interacting with study design factors, all contributed to our inability to implement the trial as designed. The key points to emerge from the study are that alcohol misuse is a difficult issue to manage in an Indigenous primary health care setting; RCTs involving inevitably complex study protocols may not be acceptable or sufficiently adaptable to make them viable in busy, Indigenous primary health care settings; and gold-standard RCT-derived evidence for the effectiveness of many public health interventions in Indigenous primary health care settings may never be available, and decisions about appropriate interventions will often have to be based on qualitative assessment of appropriateness and evidence from other populations and other settings.

NMR shim coil design utilising a rapid spherical harmonic calculation method

A rapid spherical harmonic calculation method is used for the design of Nuclear Magnetic Resonance shim coils. The aim is to design each shim such that it generates a field described purely by a single spherical harmonic. By applying simulated annealing techniques, coil arrangements are produced through the optimal positioning of current-carrying circular arc conductors of rectangular cross-section. This involves minimizing the undesirable harmonies in relation to a target harmonic. The design method is flexible enough to be applied for the production of coil arrangements that generate fields consisting significantly of either zonal or tesseral harmonics. Results are presented for several coil designs which generate tesseral harmonics of degree one.

Evaluating design proposals for complex systems with work domain analysis

In this paper we propose a new framework for evaluating designs based on work domain analysis, the first phase of cognitive work analysis. We develop a rationale for a new approach to evaluation by describing the unique characteristics of complex systems and by showing that systems engineering techniques only partially accommodate these characteristics. We then present work domain analysis as a complementary framework for evaluation. We explain this technique by example by showing how the Australian Defence Force used work domain analysis to evaluate design proposals for a new system called Airborne Early Warning and Control. This case study also demonstrates that work domain analysis is a useful and feasible approach that complements standard techniques for evaluation and that promotes a central role for human factors professionals early in the system design and development process. Actual or potential applications of this research include the evaluation of designs for complex systems.