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The rational design of potential chemotherapeutic agents: synthesis of bryostatin analogues.

The bryostatins are a unique family of cancer chemotherapeutic candidates isolated from marine bryozoa. While their molecular mode of action is not known, these macrolactones exhibit high affinities for protein kinase C (PKC) isozymes, compete for the phorbol ester binding site on PKC, and stimulate kinase activity in vitro and in vivo. Unlike the phorbol esters, they do not act as tumor promoters. Despite promising biological properties, the supply of these compounds is limited by the difficulty of their isolation from natural sources and their synthetic complexity. A new class of bryostatin analogues which retain the putative recognition domain of the bryostatins but are simplified through deletions and modifications in the C1-C14 spacer domain have been designed using computer models. A convergent synthesis has been realized for the production, in gram quantities, of these recognition and spacer domains whose coupling allows for the generation of a range of analogues. The final closure process involves a novel macrotransacetalization reaction which proceeds with complete stereoselectivity. The solution structures of two synthetic analogues were determined by NMR spectroscopy and found to be very similar to the previously reported structures of bryostatins 1 and 10. In addition, these structures appear to indicate that the stereochemistry of the C3 hydroxyl group plays a significant role in the conformation of the macrolactone. All analogues bound strongly to a mixture of PKC isozymes, and several exhibited significant levels of in vitro growth inhibitory activity against human cancer cell lines. Taken together, this work provides important steps toward the development and understanding of simplified, synthetically accessible analogues of the bryostatins as potential chemotherapeutic agents.

Adjuvants, Immunologic↗

Modelling photon transport in non-uniform media for SPECT with a vectorized Monte Carlo code.

A vectorized Monte Carlo code has been developed for modelling photon transport in non-uniform media for single-photon-emission computed tomography (SPECT). The code is designed to compute photon detection kernels, which are used to build system matrices for simulating SPECT projection data acquisition and for use in matrix-based image reconstruction. Non-uniform attenuating and scattering regions are constructed from simple three-dimensional geometric shapes, in which the density and mass attenuation coefficients are individually specified. On a Stellar GS1000 computer, Monte Carlo simulations are performed between 1.6 and 2.0 times faster when the vector processor is utilized than when computations are performed in scalar mode. Projection data acquired with a clinical SPECT gamma camera for a line source in a non-uniform thorax phantom are well modelled by Monte Carlo simulations. The vectorized Monte Carlo code was used to stimulate a 99Tcm SPECT myocardial perfusion study, and compensations for non-uniform attenuation and the detection of scattered photons improve activity estimation. The speed increase due to vectorization makes Monte Carlo simulation more attractive as a tool for modelling photon transport in non-uniform media for SPECT.

Humans↗

Biologically inspired walking machines: design, control and perception.

This article presents a set of methods used to support the design and control of biologically inspired walking machines. Starting with a description of the general system design idea, an example for the design of the mechanical construction, a computer supported design procedure for the control architecture and the description of a three-dimensional world model to be used as knowledge base is given. The focus of this paper is on the engineering and integration process and the interrelation between the different phases of the design process.

Animals↗

Cerebral herniation during bacterial meningitis in children.

OBJECTIVE: To see whether the incidence of cerebral herniation is increased immediately after lumbar puncture in children with bacterial meningitis and whether any children with herniation have normal results on cranial computed tomography. DESIGN: Retrospective review of case notes; computed tomograms were read again. SETTING: Large paediatric teaching hospital. SUBJECTS: 445 children over 30 days old admitted to hospital with bacterial meningitis. MAIN OUTCOME MEASURES: Timing of herniation in relation to lumbar puncture; findings on computed tomography in children with herniation. RESULTS: Cerebral herniation was detected in 19 (4.3%) of the 445 children (21 episodes; herniation occurred twice in two children). Herniation occurred in 14 (45%) of the 31 children who died. Nineteen episodes of herniation occurred in the 17 children who had a lumbar puncture; 12 of the episodes occurred in the first 12 hours after the lumbar puncture and seven over six other 12 hour periods (odds ratio 32.6 (95% confidence interval 8.5 to 117.3); p < 0.001). The results of cranial computed tomography were normal in five (36%) of the 14 episodes of herniation in which scanning was performed at about the time of herniation. CONCLUSIONS: The temporal relation between lumbar puncture and herniation strongly suggests that a lumbar puncture may cause herniation in some patients, and normal results on computed tomography do not mean that it is safe to do a lumbar puncture in a child with bacterial meningitis.

Adolescent↗

Enhancing design of immobilized enzymatic microbioreactors using computational simulation.

In continuous-flow enzymatic microbioreactors, enzymes on the channel walls catalyze reaction(s) among feed chemicals, resulting in the production of some desirable material or the destruction of some undesirable material. Computational models of microbioreactors were developed using the CFD-ACE+ multiphysics simulation package. These models were validated via comparison with experimental data for the destruction of urea, catalyzed by urease. Similar models were then used to assess the impact of internal features on destruction efficiency. It was found that triangular features within the channels enhanced the destruction efficiency more than could be attributed to the increase in surface area alone.

Catalysis↗

[Online CRT visual masking system].

To analyse the human visual perception process by backward masking, thousands of TS's and MS's must be exposed even in an experiment. If a mechanical tachistoscope should be used, labors for making such stimuli, for changing them at each exposure and for arranging data of the S's reaction would be exceedingly great. In order to save the lavors, a computer-controlled visual masking system is designed. The computer generates the TS and MS, exposes them on the CRT and collects the S's reaction. A command language named OLM-1 is used to described forms of TS's and MS's and other parameters of backward masking. Using this system one thousand TS's can be exposed within an hour or so.

Computers↗

Effect of alphabet size and foldability requirements on protein structure designability.

A number of investigators have addressed the issue of why certain protein structures are especially common by considering structure designability, defined as the number of sequences that would successfully fold into any particular native structure. One such approach, based on foldability, suggested that structures could be classified according to their maximum possible foldability and that this optimal foldability would be highly correlated with structure designability. Other approaches have focused on computing the designability of lattice proteins written with reduced two-letter amino acid alphabets. These different approaches suggested contrasting characteristics of the most designable structures. This report compares the designability of lattice proteins over a wide range of amino acid alphabets and foldability requirements. While all alphabets have a wide distribution of protein designabilities, the form of the distribution depends on how protein "viability" is defined. Furthermore, under increasing foldability requirements, the change in designabilities for all alphabets are in good agreement with the previous conclusions of the foldability approach. Most importantly, it was noticed that those structures that were highly designable for the two-letter amino acid alphabets are not especially designable with higher-letter alphabets.

Amino Acids↗

Immunoinformatics and the prediction of immunogenicity.

Immunoinformatics is the application of informatics techniques to molecules of the immune system. One of the key goals of immunoinformatics is the development of computer aided vaccine design (CAVD), or computational vaccinology, and its application to the search for new vaccines. Key to solving this challenge is the prediction of immunogenicity, be that at the level of epitope, subunit vaccine or attenuated pathogen. This paper reviews the current state of play in the prediction of immunogenicity and focuses on well developed methods for the prediction of peptide binding affinity to major histocompatibility complexes, which are the necessary preliminary to the in silico identification of T cell epitopes.

Allergy and Immunology↗

High performance GRID based implementation for genomics and protein analysis.

Starting from the genomic and proteomic sequence data, a complex computational infrastructure as been established with the objective to develop a GRID based system to to automate the analysis, prediction and annotation processes of genomic DNA. To support of this type of analysis, several algorithms as been used to recognize biological signals involved in the identification of genes and proteins. The system implemented can be use to analyse the content of the large number of genomic sequences. For this reason, the system realized is capable of using a computational architecture specifically designed for intensive computing based on GRID technologies developed throughout the BIOINFOGRID European project. We developed a GRID based workflow to correlate different kind of Bioinformatics data, going from the Genomics Nucleotide to the Protein Sequence. The first step in the workflow consists of submitting a nucleotide sequence that is elaborated by a specific software for gene prediction. In particular this tool performs a search in the nucleotide sequence to find out the key components of gene. The predicted gene is then translated in the corresponding protein sequence. Based on protein sequence is then possible to identify the domains that characterize the protein functionality using specific tools of domain prediction. Protein domains classification are very important in the analysis of the macromolecular functionality. To analyze a whole protein family from large genome of various organism means to elaborate a large amount of data that requires huge computational resources. To analyze all this data we suggest the use of a high performance platform based on grid technology. We have implemented our applications on a wide area grid platform for scientific applications [http://www.grid.it and http://grid-it.cnaf.infn.it] composed of about 1000 CPU's. The grid infrastructure consists in a collection of computing elements and storage elements that jointly concur to define a platform for high performance elaboration. In this study a grid based application is presented to compute the protein domain analysis in a distributed way. This approach has high performance because the protein domains are checked with different software in parallel in different grid sites.

Computational Biology↗

Current computational tools for de novo ligand design.

Several new algorithms have been proposed recently for computational de novo ligand design. Empirical scoring functions are now available to prioritize the suggested structures. The first successful applications have been reported.

Algorithms↗

Computer-aided human modelling programs for workstation design.

In designing a workstation, computer-aided human modelling programs can be used advantageously to analyse human-fit to the workstation components. The analysis is performed within a three-dimensional computer graphics environment. To illustrate the current state of development, six representative programs were selected: CYBERMAN, COMBIMAN, CREW CHIEF, JACK, SAMMIE, and MANNEQUIN. The programs differ considerably in terms of system requirement, operating characteristics, applicability and the various ergonomic evaluation functions available in the human modelling programs. The comparative analysis of the programs will aid the user to select the appropriate program for a particular workstation design.

Anthropometry↗

Computational modelling of blood flow through curved stenosed arteries.

A computational model of three-dimensional blood flow in curved arteries with elliptic stenosis was developed. Two groups of models, (a) different angles of curvature and (b) degrees of stenosis, have been studied under typical conditions for stenosed coronary artery. Useful information on the haemodynamics has been obtained. Results of pressure drop show that the presence of the curvature augments the increased flow resistance due to stenotic lesions. The study also demonstrates the significant presence of secondary flow in a curved artery. In addition, the results have shown that the secondary flow in a curved artery brings about elevated shear stress on the vessel wall. These results indicated that both curvature and stenosis should be considered together by cardiologists to assess or quantify the severity of the stenosis. This study employed a powerful computer-aided design (CAD) package to construct the model and a commercial computational fluid dynamics (CFD) code for the analysis of blood flow in stenosed arteries. The long-term application of this form of research promises to be an effective tool for gaining insights into the pathology of arterial diseases.

Arteries↗

Logic-based integrity constraints and the design of dental prostheses.

This paper describes the ongoing development of a design assistant, RaPiD, for use in prosthetic dentistry. RaPiD integrates computed-aided design, knowledge-based systems and databases, employing a logic-based representation as the unifying medium. The user's manipulation of icons representing the developing design is interpreted as a set of transactions on a logic database of design components. The rules of design expertise are represented as constraints in first order predicate logic and design alterations are subject to the checking of the constraints. When design rules are contravened as the result of some proposed alteration, a suitable critique is presented to the user. RaPiD is being developed for use in both dental education and practice.

Artificial Intelligence↗

Medical plan-analysis by computer.

The traditional approach to computer-assisted medical decision-making involves designing a computer system which simulates a physician's decision-making process. This paper describes a different approach: Medical Plan-Analysis (MPA). Instead of trying to tell a physician how best to manage a patient, an MPA system critiques a physician's management plan. It is anticipated that this approach may have a number of potential social, medical, and medicolegal advantages. The MPA approach has been implemented in ATTENDING, a system designed using Artificial Intelligence techniques to critique a physician's plan for anesthetic management.

Anesthesiology↗

Drug Guru: a computer software program for drug design using medicinal chemistry rules.

Drug Guru (drug generation using rules) is a new web-based computer software program for medicinal chemists that applies a set of transformations, that is, rules, to an input structure. The transformations correspond to medicinal chemistry design rules-of-thumb taken from the historical lore of drug discovery programs. The output of the program is a list of target analogs that can be evaluated for possible future synthesis. A discussion of the features of the program is followed by an example of the software applied to sildenafil (Viagra) in generating ideas for target analogs for phosphodiesterase inhibition. Comparison with other computer-assisted drug design software is given.

Chemistry, Organic↗