Knowledge-based design of artificial worlds

We review the concepts of knowledge representation and modelling and simulation methodology which facilitate computer exploration of alternative artificial worlds, such as self-sufficient human habitats. An object-oriented computer environment which supports such simulation studies is briefly described. A simplified example of an artificial world model is given to demonstrate the power of the approach.     

基于网格的医学信息平台设计

针对目前医学信息应用模式的局限性,提出一种基于网格的平台技术,促进网络环境下的医学资源共享和互用。其中采用面向网格工具包的中间件设计,简化了服务集成和调用。实验模型的建立验证平台的可行性及实用价值。     

Evaluation of diallate and triallate herbicides for genotoxic effects in a battery of in vitro and short-term in vivo tests

Commercial-grade preparations of two thiocarbamate herbicides, diallate and triallate, were evaluated for their mutagenic potential in a battery of short-term bioassays. All in vitro bioassays were performed with and without mammalian metabolic activation, and all such tests were repeated after an interval of at least 1 week. Diallate and triallate were tested in the Salmonella/microsome assay over dose ranges of 0.59 to 118.0 micrograms/plate and 6.37 to 1273 micrograms/plate, respectively. Both diallate and triallate gave positive results in S. typhimurium strains TA1535, TA98, and TA100 only in the presence of a rat-liver metabolic activation system. In Saccharomyces cerevisiae strain D7, diallate was tested at concentrations from 1.18 to 29.50 micrograms/ml, and triallate was tested at 0.955 to 9.548 micrograms/ml. Both diallate and triallate gave negative results for mitotic gene conversion, mitotic crossing-over, and reverse mutation. In the mouse lymphoma L5178Y TK+/- assay, diallate was tested at concentrations ranging from 1 to 72 micrograms/ml, and triallate was tested at 0.5 to 60 micrograms/ml. Both herbicides produced mutagenic responses in the mouse lymphoma assay in the presence of metabolic activation. In the Drosophila sex-linked recessive lethal test, flies were exposed to 0.0004% diallate and 0.001% triallate. In this assay, diallate was considered mutagenic, whereas triallate did not produce a detectable mutagenic response.     

Utility of short-term tests for genetic toxicity

By definition, short-term tests (STTs) for genetic toxicity detect genotoxic agents, not carcinogens specifically. However, there is sufficient evidence, based on mechanistic considerations alone, to say that genotoxic agents are potential carcinogens. STTs have high statistical power, are almost always replicated, can be performed rather easily under various sets of experimental conditions, are relatively inexpensive, and detect a variety of endpoints relevant to carcinogenesis. In addition, several STTs have shown considerable utility in evaluating the genotoxic effects of real-world, environmental complex mixtures as well as the antimutagenic effects of various pure compounds and complex mixtures. STTs are likely to continue to be refined, resulting in STTs that are increasingly more relevant to human mutation and disease. Their utility should not be judged solely against the questionable standard of a rodent carcinogenicity assay.     

Knowledge-based design of reagentless fluorescent biosensors from recombinant antibodies

The possibility of obtaining from any antibody a fluorescent conjugate which responds to the binding of the antigen by a variation of its fluorescence, would be of great interest in the analytical sciences and for the construction of protein chips. This possibility was explored with antibody mAbD1.3 directed against hen egg white lysozyme. Rules of design were developed to identify the residues of the antibody to which a fluorophore could be chemically coupled, after changing them to cysteine by mutagenesis. These rules were based on: the target residue belonging to a topological neighbourhood of the antigen in the structure of the complex between antibody and antigen; its absence of functional importance for the interaction with the antigen; and its solvent accessibility in the structure of the free antibody. Seventeen conjugates between the single-chain variable fragment scFv of mAbD1.3 and an environment-sensitive fluorophore were constructed. For six of the ten residues which fully satisfied the design rules, the relative variation of the fluorescence intensity between the free and bound states of the conjugate was comprised between 12 and 75% (in non-optimal buffer), and the affinity of the conjugate for lysozyme remained unchanged relative to the parental scFv. In contrast, such results were true for only one of the seven residues which failed to satisfy one of the rules and were used as controls. One of the conjugates was studied in more detail. Its fluorescence increased proportionally to the concentration of lysozyme in a nanomolar range, up to 90% in a defined buffer, and 40% in serum. This increase was specific for hen egg lysozyme and it was not observed with a closely related protein, turkey egg lysozyme. The residues which gave operational conjugates (six in V(L) and one in V(H)), were located in the immediate vicinity of residues which are functionally important, along the sequence of FvD1.3. The results suggest rules of design for constructing antigen-sensitive fluorescent conjugates from any antibody, in the absence of structural data.     

Knowledge-based design of 7-azaindoles as selective B-Raf inhibitors

The synthesis of a 7-azaindole series of novel, potent B-Raf kinase inhibitors using knowledge-based design was carried out. Compound 6h exhibits not only excellent potency in both the enzyme assay (IC(50)=2.5 nM) and the cellular assay (IC(50)=63 nM), but also has an outstanding selectivity profile against other kinases.     

Genotoxicity of aniline derivatives in various short-term tests

Various substituted aniline derivatives were tested for genotoxicity in several short-term tests in order to examine the hypothesis that a substitution at both ortho positions (2,6-disubstitution) could prevent genotoxicity due to steric hindrance of an enzymatic activation to electrophilic intermediates. In the Salmonella/microsome assay, 2,6-dialkylsubstituted anilines and 2,4,6-trimethylaniline (2,4,6-TMA) were weakly mutagenic in strain TA100 when 20% S9 mix was used, although effects were small compared to those of 2,4-dimethylaniline and 2,4,5-trimethylaniline (2,4,5-TMA). In Drosophila melanogaster, however, 2,4,6-TMA and 2,4,6-trichloroaniline (TCA) were mutagenic in the wing spot test at 2-3 times lower doses than 2,4,5-TMA. In the 6-thioguanine resistance test in cultured fibroblasts, 2,4,6-TMA was again mutagenic at lower doses than 2,4,5-TMA. Two methylene-bis-aniline derivatives were also tested with the above methods: 4,4'-methylene-bis-(2-chloroaniline) (MOCA) was moderately genotoxic in all 3 test systems whereas 4,4'-methylene-bis-(2-ethyl-6-methylaniline) (MMEA) showed no genotoxicity at all. DNA binding studies in rats, however, revealed that both MOCA and MMEA produced DNA adducts in the liver at levels typically found for moderately strong genotoxic carcinogens. These results indicate that the predictive value of the in vitro test systems and particularly the Salmonella/microsome assay is inadequate to detect genotoxicity in aromatic amines. Genotoxicity seems to be a general property of aniline derivatives and does not seem to be greatly influenced by substitution at both ortho positions.     

Principal agent model based design and outsourcing of information value

IT outsourcing allows a business to reduce the cost of IT service delivery and improve the quality of IT service by taking advantage of the service provider’s economics of scale and technical expertise. However, the successful outsourcing of IT service is hampered by lack of guidance on how to design incentive contracts to encourage performance of the service provider, especially in the presence of information asymmetry and incentive divergence. In this article, we identify and characterize two asymmetric information factors: asymmetric effort information and asymmetric capability information. Depending on whether the service provider’s effort information and capability information is symmetric or not, we consider three information scenarios and characterize optimal incentive contracts for each scenario. We also introduce the concept of information value to quantify the adverse effects of the two asymmetric information factors. The results provide theoretical support for designing incentive contracts that mitigate the adverse effects of asymmetric information, and recommend effective guidance for activities so as to reduce the degree of information asymmetry.     

The influence of the proportion of carcinogens on the cost-effectiveness of short-term tests

The cost-effectiveness of using short-term genotoxicity tests to screen unknown chemicals for carcinogenicity depends upon the inherent reliability of the tests (sensitivity, or fraction of carcinogens giving positive results, and specificity, or fraction of non-carcinogens giving negative results) and also upon the proportion of carcinogens in the population of chemicals to be screened. Individual tests may be combined into batteries to improve reliability; however, this requires decision rules to declare the overall result positive or negative. A framework for developing such rules based upon minimizing costs of false-positives and false-negatives was presented in a seminal paper by Lave and Omenn (1986, Nature (London), 324, 29-34). We have extended their work, which is based on logit analysis, to consider, using Bayes' theorem, the influence of the proportion of carcinogens upon the decision rules for declaring a battery result positive or negative. If the proportion of carcinogens is high (20% or greater), then the most effective tests are those with high sensitivity, and if the proportion of carcinogens is low, then the most effective tests are those with high specificity.     

Lack of mutagenicity of diphenylhydantoin in in vitro short-term tests

The mutagenicity of diphenylhydantoin (DPH) and its major metabolite, 5-(p-hydroxyphenyl)-5-phenylhydantoin (HPPH), has been re-evaluated by the Ames test using Salmonella typhimurium and, for DPH only, by an in vitro cytogenetic test with human lymphocytes and a turbidimetric assay of tubulin polymerization. As negative results were obtained in all test systems used here, one has to conclude that DPH is devoid of mutagenic properties.     

Mutagenicity of methyl bromide in a series of short-term tests

Methyl bromide is commonly used as a soil fumigant in greenhouses. In the framework of a toxicological evaluation, it was tested for possible genotoxic properties in two bacterial test systems (the fluctuation test using Klebsiella pneumoniae and the plate test using Salmonella typhimurium TA100 and TA98), two systems using mammalian cells in vitro (forward mutations at the TK and HPRT loci in L5178Y mouse lymphoma cells and unscheduled DNA synthesis in primary rat-liver cells) and in the sex-linked recessive lethal test using Drosophila melanogaster. Methyl bromide was active in all tests except the DNA-repair assay. The results indicate a relatively low mutagenic efficiency of the compound, as expected from its alkylating properties.     

Scientific and cost-effectiveness criteria in selecting batteries of short-term tests

The scientific and cost-effectiveness criteria introduced in this paper can be applied to published datasets and current and proposed batteries of short-term tests. The reports in the current volume will provide a wealth of additional material for such evaluations, but more systematically obtained information will be necessary to assess both the internal and external validity of these tests. Individual tests and batteries of tests should be standardized, employ positive controls, generate results capable of quantitative analyses that may make dichotomous classification as "positive" and "negative" obsolete, be interpreted in light of mechanisms of action, and be cost-effective on a grand scale. For regulatory purposes our long-term goal should be to replace the whole animal lifetime bioassay with an appropriate and cost-effective set of short-term tests.     

Cluster analysis of short-term tests: a new methodological approach

A totally data-based approach to the evaluation of short-term tests is proposed. The performances of 22 tests over a range of 42 chemicals (data from literature) were studied by cluster analysis. The comparison between them was performed only on the basis of their responses to the chemicals. Two different clustering methods produced a coincident classification, pointing to a clear resolution of all tests into 3 groups with common characteristics. With respect to carcinogen discrimination, cluster 1 showed the highest sensitivity and the lowest specificity. Cluster 3 had opposite characteristics. The tests of cluster 2 showed intermediate features. As far as the membership to clusters is concerned, the literature data about the responses to chemicals indicated a strong test system specificity. This apparently overcame both phylogeny and end-point community. A major characteristic of the present approach is the ability to elicit underlying patterns, the knowledge of which can contribute both to hypothesis formulation and be useful for practical purposes.     

A comparison of performance of cebus and rhesus monkeys on a battery of behavioral tests

Cebus monkeys (C. apella, C. albifrons, andC. capuchin) and rhesus monkeys (Macaca mulatta) were compared with respect to their performance on a battery of 6 tests. The battery consisted of tests of delayed response, oddity problems, matching problems, contingent response and delayed alternation. A suggestive trend was noted, with cebus performing relatively better on long delay problems and the oddity problem, and rhesus performing relatively better on the delayed alternation, matching and contingency problems. However, no statistically significant differences were found between the two groups on any of the tests. It is suggested that a strict hierarchial arrangement of species on test performance, corresponding to phylogenetic classification may be a fantasy.Supported in part by: Grant No. N.S. 6552-04, from The National Institutes of Health.