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At least 649 records · Page 36Linked to original sources
PubMed1989

The principles and prototyping of a knowledge-based diabetes management system.

This paper describes the principles and prototyping of a computer-based system being developed to assist in the management of diabetes mellitus. Unlike other approaches based upon mathematical modelling or the use of computer algorithms, this system adopts one derived from artificial intelligence, seeking to incorporate the dynamics of glucose and insulin in a manner which reflects their clinical importance. The resultant logical model (qualitative algebra) defines the relationships between changes in insulin dose and site and time of injection and glycaemic response. In this manner the computer-based system, implemented in Prolog, can be used to provide advice concerning insulin therapy by means of making qualitative predictions of patient outcome of blood glucose profile resulting from alternative insulin regimens.

Blood Glucose↗
PubMed1989

PEPTY: a knowledge-based program for assisting medical reasoning in peptic diseases.

PEPTY is a program developed with the aim of providing a diagnostic and therapeutic assistance in managing peptic diseases. Its theoretical basis is an accurate analysis of current concepts in peptic disease diagnosis and treatment. This was done by reviewing recent literature and consulting skilled gastroenterologists. The decision tree includes three sections dealing with diagnostic, therapeutic and monitoring problems. The diagnostic section starts by evaluating clinical data from patient history and physical examination; the diagnostic hypotheses given at this level are refined and eventually confirmed by further information in the following section. Here the decision tree becomes modular in that a proper therapeutic and monitoring pathway is defined for four disease classes: gastroduodenal peptic ulcer and duodenitis, gastro-oesophageal reflux, erosive gastritis, and chronic antral gastritis. In the therapeutic section a cost-benefit analysis of possible therapeutic choices is always performed, but the final decision is made by the user. Complications, side effects and treatment efficacy are also considered and the program finally suggests the appropriate maintenance treatment. Patient data display, storage and retrieval, and explanation facilities are supplied. The system can provide a 'second opinion' in the medical practice and may be a useful learning tool for medical students.

Artificial Intelligence↗
PubMed1990

Application of a network structure in a knowledge-based system for medical diagnostics.

Systems supporting diagnostic decision making have been designed more often on the base of production rules than on semantic nets. One reason for that might be that concepts to process information on the latter structures are still rare. In this study the application of a semantic net is described. Via creation of various views, different sets of information are defined, depending on their meaning in the semantic net. Projections, which are in general a combination of mappings and set operations, are used to infer a set of information from another. The developed system was written in Pascal, the semantic net was implemented using a network-like pointer structure. The concept has been used to develop PROJECTOR, an expert system for differential diagnosis based on a semantic net. The structure has turned out to be fast and compact enough to allow large amounts of data to be handled easily even with a personal computer.

Diagnosis, Computer-Assisted↗
PubMed2005

Implementation of automated signal generation in pharmacovigilance using a knowledge-based approach.

Automated signal generation is a growing field in pharmacovigilance that relies on data mining of huge spontaneous reporting systems for detecting unknown adverse drug reactions (ADR). Previous implementations of quantitative techniques did not take into account issues related to the medical dictionary for regulatory activities (MedDRA) terminology used for coding ADRs. MedDRA is a first generation terminology lacking formal definitions; grouping of similar medical conditions is not accurate due to taxonomic limitations. Our objective was to build a data-mining tool that improves signal detection algorithms by performing terminological reasoning on MedDRA codes described with the DAML+OIL description logic. We propose the PharmaMiner tool that implements quantitative techniques based on underlying statistical and bayesian models. It is a JAVA application displaying results in tabular format and performing terminological reasoning with the Racer inference engine. The mean frequency of drug-adverse effect associations in the French database was 2.66. Subsumption reasoning based on MedDRA taxonomical hierarchy produced a mean number of occurrence of 2.92 versus 3.63 (p < 0.001) obtained with a combined technique using subsumption and approximate matching reasoning based on the ontological structure. Semantic integration of terminological systems with data mining methods is a promising technique for improving machine learning in medical databases.

Adverse Drug Reaction Reporting Systems↗
PubMed2005

International industry initiatives to improve the glycol ether health effects knowledge base.

Following the recognition in the early 1980s of the potential reproductive hazards of certain glycol ethers, industry organizations were formed in the US and Europe having a number of stated goals to: (1) provide hazard information by expanding the toxicity database for glycol ethers; (2) promote cooperation among scientists, governmental authorities, and industry; and (3) promote scientifically sound regulatory actions and to assist in the setting of scientifically defensible safety standards. This effort led to early recommendations that EGME, EGEE, and their acetates be removed from consumer products. Also, studies conducted by industry under US EPA test rules have led to a better understanding of the hazards associated with glycol ether constituents of brake fluids, paints, and other products. Industry-provided information has greatly assisted the setting of occupational and public safety standards in a number of countries. Hazard assessments for a number of large-volume glycol ethers have been performed under the OECD SIDS program. This work continues with the industry-funded ICCA/HPV testing initiative. To provide sound risk assessment data, industry continues to sponsor basic research aimed at better understanding human versus mouse versus rat sensitivities to certain glycol ethers. Industry has also prepared and supported the publication of toxicological data compendia for glycol ethers.

Animals↗
PubMed2001

A self-consistent knowledge-based approach to protein design.

A simple and very efficient protein design strategy is proposed by developing some recently introduced theoretical tools which have been successfully applied to exactly solvable protein models. The design approach is implemented by using three amino acid classes and it is based on the minimization of an appropriate energy function. For a given native state the results of the design procedure are compared, through a statistical analysis, with the properties of an ensemble of sequences folding in the same conformation. If the success rate is computed on those sites designed with high confidence, it can be as high as 80%. The method is also able to identify key sites for the folding process: results for 2ci2 and barnase are in very good agreement with experimental results.

Amino Acid Sequence↗
PubMed1997

AUDILAB: a knowledge-based quality audit simulator for testing laboratories.

In order to obtain an accreditation, a laboratory must be prepared to provide a point-by-point check of various activities against the chosen reference standard, both from a general point of view and in relation to details of application. This paper describes AUDILAB, a computerized simulator accessible by network, able to provide testing laboratories with realistic quality audits performed in a customized way. AUDILAB establishes a detailed list of strengths (compliance with corresponding requirements of established standards) and weaknesses (improvements needed for laboratory's accreditation). The standard used by AUDILAB is the EN 45001 "General criteria for the operation of testing laboratories". A preliminary validation has already been completed. AUDILAB became operational in September 1993.

Artificial Intelligence↗
PubMed2002

Intelligent automation of high-performance liquid chromatography method development by means of a real-time knowledge-based approach.

We describe the development, attributes and capabilities of a novel type of artificial intelligence system, called LabExpert, for automation of HPLC method development. Unlike other computerised method development systems, LabExpert operates in real-time, using an artificial intelligence system and design engine to provide experimental decision outcomes relevant to the optimisation of complex separations as well as the control of the instrumentation, column selection, mobile phase choice and other experimental parameters. LabExpert manages every input parameter to a HPLC data station and evaluates each output parameter of the HPLC data station in real-time as part of its decision process. Based on a combination of inherent and user-defined evaluation criteria, the artificial intelligence system programs use a reasoning process, applying chromatographic principles and acquired experimental observations to iteratively provide a regime for a priori development of an acceptable HPLC separation method. Because remote monitoring and control are also functions of LabExpert, the system allows full-time utilisation of analytical instrumentation and associated laboratory resources. Based on our experience with LabExpert with a wide range of analyte mixtures, this artificial intelligence system consistently identified in a similar or faster time-frame preferred sets of analytical conditions that are equal in resolution, efficiency and throughput to those empirically determined by highly experienced chromatographic scientists. An illustrative example, demonstrating the potential of LabExpert in the process of method development of drug substances, is provided.

Artificial Intelligence↗
PubMed2002

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.

Amino Acid Sequence↗
PubMed1990

Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins.

We present a prototype of a new approach to the folding problem of polypeptide chains. This approach is based on the analysis of known protein structures. It derives the energy potentials for the atomic interactions of all amino acid residue pairs as a function of the distance between the involved atoms. These potentials are then used to calculate the energies of all conformations that exist in the data base with respect to a given sequence. Then, by using only the most stable conformations, clusters of the most probable conformations for the given sequence are obtained. To discuss the results properly we introduce a new classification of segments based on their conformational stability. Special care is taken to allow for sparse data sets. The use of the method is demonstrated in the discussion of the identical oligopeptide sequences found in different conformations in unrelated proteins. VNTFV, for example, adopts a beta-strand in ribonuclease but it is found in an alpha-helical conformation in erythrocruorin. In the case of VNTFV the ensemble obtained consists of a single cluster of beta-strand conformations, indicating that this may be the preferred conformation for the pentapeptide. When the flanking residues are included in the calculation the hepapeptide P-VNTFV-H (ribonuclease) again yields an ensemble of beta-strands. However, in the ensemble of D-VNTFV-A (erythrocruorin) the major cluster is of alpha-helical type. In the present study we concentrate on the local aspects of protein conformations. However, the theory presented is quite general and not restricted to oligopeptides. We indicate extensions of the approach to the calculation of global conformations of proteins as well as conceivable applications to a number of molecular systems.

Amino Acid Sequence↗
PubMed2001

Protein structure determination by non-parametric regression and knowledge-based constraints.

We have devised a non-parametric regression-based approach for the estimation of small- and medium-range inter-residual three-dimensional (3d) distances in a protein using only the primary sequence as input. A multivariate analysis of variance technique is used to identify the attributes of the primary sequence that is most effective in determining the tertiary structure. Certain compactness and hydrophobic core building heuristics are used along with the estimated distances in a distance geometry program to predict the 3d-structure (tertiary fold). Our method is found to predict correctly the native topologies of small proteins having up to 150 residues. The sensitivity of the structures to long-range distance constraints is studied by incorporating a small number of NMR distance restraints. In terms of modularity, precision, accuracy and computational efficiency our method is found to be better in comparison with current computational methods like X-PLOR and DRAGON on the sample that was reported in the literature for the comparison of these two methods.

Algorithms↗