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PubMed1993

Stepwise development of a clinical expert system in rheumatology.

The evaluation of computer expert systems, a promising diagnostic tool for future application in clinical medicine, is of great importance. We present here the evaluation of our expert system, "RHEUMA". It is stressed, that repeated retrospective testing and updating of an expert system and its subsequent repeated assessment in clinical use and surroundings is mandatory. This increases the diagnostic accuracy of the system. For our system this is demonstrated under three separate conditions. In the first study the information available for the computer system (mainframe) came from medical histories only. Here an error rate of about 25%--similar to that of physicians themselves using the same information--was observed in 358 outpatients, compared to the final diagnoses of physicians also relying solely on information from medical histories. In a second step a completely new system on a personal computer was developed with all relevant diagnostic information. The error rate of this system (0.4%) was much too optimistic because the knowledge base was changed during the study, affecting about 30% of the 282 prospectively recruited outpatients. In a third step the efficacy of the expert system was tested in an additional hospital without the diagnostic involvement of the first testing clinic. The error rate of the system without changing the knowledge base reached 11% in 51 outpatients in this rheumatology clinic. This result reflects the diagnostic accuracy of the system today. Its ability to specify the same diagnoses which clinical experts reached approached 90%. Considerable time is needed for such prospective testing, with repeated updating of the knowledge base--in our case for both the two systems and field studies of 2 years each.(ABSTRACT TRUNCATED AT 250 WORDS)

Computers↗
PubMed1992

The status of psychosocial research in the rehabilitation of the cancer patient.

This article has tried to describe the current status of psychosocial research in the rehabilitation of the cancer patient. It attempted to weave together the author's perspective of how decisions early in the history of sponsored research programs, particularly by the National Cancer Institute, combined with a limited knowledge base led to limited growth of the Rehabilitation Program. Thus, the current status of psychosocial cancer rehabilitation can be reasonably attributed to the decision at the National Cancer Institute to encourage the development of cancer rehabilitation services, rather than to aggressively expand the knowledge base. Although, in retrospect, it is possible to criticize these decisions, in fact, they were legitimate choices among a wide range of options. It was also not possible in this article to discuss many topics in psychosocial cancer rehabilitation, particularly differences in psychosocial adjustment as a function of type of cancer. What the study attempted to do was to confront the impression that cancer rehabilitation, in general, and psychosocial cancer rehabilitation, in particular, are ancillary activities that can receive a secondary level of resource allocation and support. The point was made that determining if psychosocial rehabilitation is possible raises as many basic research questions as does understanding how chemotherapy works or how a malignancy develops. All three areas ask legitimate basic research questions on how the body works and how behavior changes. Today, 10 years after the start of the original Rehabilitation Program, psychosocial cancer rehabilitation is an established field of study and an integral part of most major oncology services. Now, as stated, what is needed is an expansion of its knowledge base. Some of the issues that are deserving of support include studies on cosmesis, to what extent voluntary processes can compensate loss in speech and swallowing functions, functional evaluation following alternative surgical procedures, what is the quality of life following long-term survival of cancer, what are the group dynamics following return of a cancer patient to a work site, and so on. Each of these research questions can be guided by the same model developed for cancer control research by Greenwald and Cullen. Other more general approaches include recognizing and promoting the preventative dimension of cancer rehabilitation and developing the art and practice of psychometric assessment of psychosocial aspects of cancer rehabilitation, just to name two such areas. The American Cancer Society also recently sponsored a meeting to review and set new directions for psychosocial rehabilitation research.(ABSTRACT TRUNCATED AT 400 WORDS)

Health Services Needs and Demand↗
PubMed1996

Prediction of rodent carcinogenicity using the DEREK system for 30 chemicals currently being tested by the National Toxicology Program. The DEREK Collaborative Group.

DEREK is a knowledge-based expert system for the qualitative prediction of toxicity. The DEREK system has been used to predict the carcinogenicity in rodents of the 30 chemicals in the second National Toxicology Program (NTP) carcinogenicity prediction exercise. Seven of the chemicals were predicted to be carcinogens. For 23 chemicals, there was no evidence in the DEREK knowledge base to suggest carcinogenic activity. Supplementary data from a variety of sources have been evaluated by human experts to assess confidence in each DEREK prediction. These sources included standard toxicology reference texts, genotoxicity and subchronic toxicity assay results for each chemical, as well as Salmonella mutagenicity and carcinogenicity data for close structural analogues. This process has led to the proposal of a number of improvements to the DEREK carcinogenicity knowledge base.

Animals↗
PubMed1998

Hierarchical organization of molecular structure computations.

The task of computing molecular structure from combinations of experimental and theoretical constraints is expensive because of the large number of estimated parameters (the 3D coordinates of each atom) and the rugged landscape of many objective functions. For large molecular ensembles with multiple protein and nucleic acid components, the problem of maintaining tractability in structural computations becomes critical. A well-known strategy for solving difficult problems is divide-and-conquer. For molecular computations, there are two ways in which problems can be divided: (1) using the natural hierarchy within biological macromolecules (taking advantage of primary sequence, secondary structural subunits and tertiary structural motifs, when they are known); and (2) using the hierarchy that results from analyzing the distribution of structural constraints (providing information about which substructures are constrained to one another). In this paper, we show that these two hierarchies can be complementary and can provide information for efficient decomposition of structural computations. We demonstrate five methods for building such hierarchies--two automated heuristics that use both natural and empirical hierarchies, one knowledge-based process using both hierarchies, one method based on the natural hierarchy alone, and for completeness one random hierarchy oblivious to auxiliary information--and apply them to a data set for the procaryotic 30S ribosomal subunit using our probabilistic least squares structure estimation algorithm. We show that the three methods that combine natural hierarchies with empirical hierarchies create decompositions which increase the efficiency of computations by as much as 50-fold. There is only half this gain when using the natural decomposition alone, while the random hierarchy suggests that a speedup of about five can be expected just by virtue of having a decomposition. Although the knowledge-based method performs marginally better, the automatic heuristics are easier to use, scale more reliably to larger problems, and can match the performance of knowledge-based methods if provided with basic structural information.

Algorithms↗
PubMedDate not supplied

[Methodology of a study on insomnia in the general population].

The study of sleep disorders in the general population involves several methodological issues that need to be defined prior to proceeding to the epidemiological study. The rigor of the methodology is an important issue since it will determine the reliability of the data gathered. This paper describes the methodology used in an epidemiological study performed in the French general population using telephone interviews with the help of Sleep-EVAL, an expert system designed for this purpose. The study aimed to investigate the prevalence of insomnia disorders according to the DSM IV classification and the use of psychotropic medications in the general population. The methodological choices for this study were based on several considerations. First, the sample had to be representative of the French population. Second, the study had to be conducted in the shortest period of time. Third, the interviews had to be conducted with respect to a strict standardization and fourth, the realization costs had to be minimal for a maximum of data collected. The telephone interview procedure was chosen over postal and face-to-face interviews because it offered the possibility of conducting all the interviews from the same site. Supervision was easier. It also offered an absolute control in the application of the selection procedure. To draw the sample, a two-stage procedure was adopted. At the first stage, we pulled a random series of telephone numbers in each Nielsen region with respect to the size of the settlement. At the second stage, during the initial telephone contact, a household member was chosen using the Kish selection procedure. This method is based on the utilization of eight tables of selection that allows for the choice of the person to interview in a given household and keeps the representativeness of the sample. This technique is little used in telephone surveys because of its burden and its intrusive nature: the interviewer must collect the age and gender of all eligible subjects, to classify men from the oldest to youngest and then to classify women. However, it is the most rigorous selection method for epidemiological surveys. To reduce the refusal rates and to alleviate the work of interviewers, the Kish method was implanted in the computer software used for this study. For this study, the exclusion criteria were minimal. Only individuals younger than 15 years of age, those with a speech or hearing impairment and those who were too ill to perform the interview were not included. Subjects who refused to participate, those who hung up without speaking to the interviewer and those who hung up before completing at least half of the interview were tabulated as refusal. The participation rate was calculated by dividing the number of completed interviews by the number of eligible participants (completed interviews, refusals and telephone numbers where the interviewer was unable to determine if the individuals met an exclusion criterion). In this study, the participation rate was 80.8% (5 622 completed interviews/6 966 eligible households). The diagnostic tool used for this study was the Sleep-EVAL system, an expert system designed to conduct epidemiological studies in the general population. It is a level 2, non-monotonic system endowed with a causal reasoning able to provide sleep and mental disorders diagnoses according to the DSM IV classification for this study. Subsequent versions of Sleep-EVAL also included the International Classification of Sleep Disorders. System symbolic representation of the classifications was put in a compiled knowledge base. This knowledge base was read and interpreted by the inference engine at the beginning of the interview. During the interview, this interpretation changed as a function of the answers provided by the interviewee and by deductions made from the analysis of information the system already knew. All interviews began with a standard questionnaire about sociodemographic information and sleep habits. From these first answers, the Sleep-EVAL system emitted a series of diagnostic hypotheses that were confirmed or rejected with supplementary questions. The interview ended once all diagnostic possibilities were exhausted. The validity of the Sleep-EVAL system was demonstrated in different studies performed in sleep disorders clinics. There were several advantages in using such a tool to conduct epidemiological surveys. No special skills from the interviewers nor specific knowledge of sleep and mental disorders were required. All the questions were chosen and formulated by the Sleep-EVAL system. The interviewer had simply to read the questions as they appeared on the monitor screen and enter the interviewee's responses by clicking the appropriate answer or typing it on the keyboard. Missing answers were non-existent because there was no possibility of skipping a question or entering inconsistent answers. It also ensured the uniformity of the interviews. Furthermore, it allowed the exploration of infrequent diagnoses. In summary, the methodology used for this study allowed for the investigation of the sleep pathology of the French population in a short period of time: only three months were necessary to complete the 5 622 interviews. The use of a computerized tool greatly facilitated the training of the interviewers and also their work. Furthermore, it ensured a standardized administration of the interviews and the exploration of a broad range of disorders that could hardly be realized with traditional paper-pencil questionnaires.

Adolescent↗
PubMed2005

Discovery of ligands by a combination of computational and NMR-based screening: RNA as an example target.

NMR for screening of knowledge-based focused libraries of compounds provides an efficient, cost-effective method to develop promising drug leads that target functionally important RNA structures. A knowledge-based focused library may be constructed from virtual (i.e., computational) screening of commercial or proprietary databases of available compounds for binding to the three-dimensional structure of a selected RNA target. Alternatively, the library may be constructed from compounds with properties deemed desirable, e.g., molecular moiety commonly found in drugs or known to bind RNA. The library ideally should be composed of small water-soluble, nonpeptide, nonnucleotide organic compounds. Various simple, robust NMR experiments are described that enable experimental screening of such a library for binding to a selected RNA structure. Some of the NMR experiments enable rapid mapping of the interaction site on the RNA to verify that the targeted structure is hit rather than the double helical region or a commonly occurring tetraloop. Other experiments enable elucidation of the ligand's binding moiety. Of course, any compounds thus identified should represent promising scaffolds suitable for easy chemical modification to enhance their pharmaceutical properties for subsequent drug development.

Computational Biology↗
PubMed2003

Towards a broad-coverage biomedical ontology based on description logics.

We describe an ontology engineering methodology by which conceptual knowledge is extracted from an informal medical thesaurus (UMLS) and automatically converted into a formal description logics system (LOOM). Our approach consists of four steps: concept definitions are automatically generated from the UMLS, integrity checking of taxonomic and partonomic hierarchies is performed by LOOM's terminological classifier, cycles and inconsistencies are eliminated, as well as incremental refinement of the evolving knowledge base is performed by a domain expert. We report on experiments with a very large knowledge base composed of 164,000 concepts and 76,000 relations.

Artificial Intelligence↗
PubMed2004

Inter-residue and solvent-residue interactions in proteins: a statistical study on experimental structures.

A large set of protein structures resolved by X-ray or NMR techniques has been extracted from the Protein Data Bank and analyzed using statistical methods. In particular, we investigate the interactions between side chains and the interactions between solvent and side chains, pointing out on the possibility of including the solvent as part of a knowledge-based potential. The solvent-residue contacts are accounted for on the basis of the Voronoi's polyhedron analysis. Our investigation confirms the importance of hydrophobic residues in determining the protein stability. We observe that in general hydrophobic-hydrophobic interactions and, more specifically, aromatic-aromatic contacts tend to be increasingly distally separated in the primary sequence of proteins, thus connecting distinct secondary structure elements. A simple relation expressing the dependence of the protein free energy by the number of residues is proposed. Such a relation includes both the residue-residue and the solvent-residue contributions. The former is dominant for large size proteins, whereas for small sizes (number of residues less than 100) the two terms are comparable. Gapless threading experiments show that the solvent-residue knowledge-based potential yields a significant contribution with respect to discriminating the native structure of proteins. Such contribution is important especially for proteins of small size and is similar to that given by the most favorable residue-residue knowledge-based potential referring to hydrophobic-hydrophobic interactions such as isoleucine-leucine. In general, the inclusion of the solvent-residue interaction produces a relevant increase of the free energy gap between the native structures and decoys.

Amino Acids↗
PubMed2000

[Clinical nursing research. New standards for quality assurance for nursing and patient].

Nursing as a health-service has a long tradition, nursing research however, a relatively short history. Florence Nightingale was the first to publish about nursing research in the year 1858. Since Nightingale, the need to study and improve the efficacy and efficiency of nursing has steadily increased. More than ever before, society needs nursing based on scientific knowledge and not just on unchallenged rituals and traditions. This scientific knowledge base can be acquired by clinical research. Within multidisciplinary clinical research it is necessary to focus on nursing's unique function. Virginia Henderson (1955) and Dorothea Orem (1959) have clearly explicated this function. Designs for clinical nursing research can be (quasi-) experimental, correlational or descriptive. Descriptive research can be qualitative or quantitative. Effects of nursing interventions on decrease of self-care problems and improvement of self-care capability and behaviors, should be investigated by experimental or quasi-experimental studies. Some examples of clinical nursing research are given. The first example demonstrates the effect of quantity and quality of nursing staff on patient's capabilities for hygiene self-care. The second example explicates the relation between self-care and quality of life with breast-cancer patients under chemotherapy treatment. The last example shows the effect of diabetes education on self-care behaviour and metabolic control. The examples given demonstrate the importance of clinical research focused on nursing's unique function. In order to accomplish this, programs of research are needed as well as close co-operation with nursing services, physicians and hospitals. Only when research findings are discussed and implemented in multidisciplinary teams, nursing will become more evidence-based.

Clinical Nursing Research↗
PubMed2005

Simplified representation of concepts and relations on screen.

The fully automated generation of diagnostic codes requires a knowledge-based system which is capable of interpreting noun phrases. The sense content of the words must be analysed and represented for this purpose. The codes are then generated based on this representation.In comparison with other knowledge-based systems, a system of this kind places the emphasis on the data structures and not on the calculus; coding itself is a simple matter compared to the much more difficult task of incorporating the complex information contained in the words used in natural language in a systematic data model. Initial attempts were based on the assumption that each word was linked to one conceptual meaning, whereas such a naive viewpoint certainly no longer applies today. The notation of concepts and their relations is the task at hand.Existing notation methods include predicate logic, conceptual graphs (CGs) as proposed by J. F. Sowa [2], GRAIL as used by the GALEN Project [1] and methods developed as part of the WWW consortium, e.g. RDF's (Resource Description Frameworks). For the purpose of coding, we developed a notation system using "concept particles" back in 1989 [3]. In 1996, the resulting experience led us to represent "concept molecules" (CM), with which both complex data structures and multi-branched rules can be denoted in a simple manner [4]. In this paper we shall explain the principles behind this notation and compare it with another modern concept representation system, conceptual graphs.

Expert Systems↗
PubMed2003

The SBASE domain sequence library, release 10: domain architecture prediction.

SBASE (http://www.icgeb.trieste.it/sbase) is an on-line collection of protein domain sequences and related computational tools designed to facilitate detection of domain homologies based on simple database search. The 10th 'jubilee release' of the SBASE library of protein domain sequences contains 1 052 904 protein sequence segments annotated by structure, function, ligand-binding or cellular topology, clustered into over 6000 domain groups. Domain identification and functional prediction are based on a comparison of BLAST search outputs with a knowledge base of biologically significant similarities extracted from known domain groups. The knowledge base is generated automatically for each domain group from the comparison of within-group ('self') and out-of-group ('non-self') similarities. This is a memory-based approach wherein group-specific similarity functions are automatically learned from the database.

Animals↗
PubMed1997

Formalisation for decision support in anaesthesiology.

This paper reports on research for decision support for anaesthesiologists at the University Hospital in Groningen, the Netherlands. Based on CAROLA, an existing automated operation documentation system, we designed a support environment that will assist in real-time diagnosis. The core of the work presented here consists of a knowledge base (containing anaesthesiological knowledge) and a diagnosis system. The knowledge base is specified in the logic-based formal specification language AFSL. This leads to a powerful and precise treatment of knowledge structuring and data abstraction.

Anesthesiology↗
PubMed2005

Profiling Canadian nurses' preferred knowledge sources for clinical practice.

Several researchers have examined nurses' knowledge sources within the context of research utilization, but conclusions are equivocal. Common problems include a lack of replication, conflicting results, poor generalizability of results, and unclear implications for practice. The objectives of this study were to: (a) describe sources of knowledge and their frequency of use among staff nurses across 7 surgical units, (b) compare knowledge-source patterns across the units, (c) determine whether knowledge-source preferences correlate to research utilization scores, and (d) profile staff nurses' knowledge-source patterns over time. A total of 230 nurses in 5 adult and 2 pediatric surgical units from 4 hospitals in the Canadian provinces of Alberta and Ontario completed a self-administered survey. The results were compared to the findings of previous studies. Nurses' knowledge-source preferences were consistent across the 7 units despite differences in education and in research utilization scores. Across all units, nurses preferred to use knowledge gained through personal experience and interactions with co-workers and with individual patients rather than journal articles or textbooks. These findings are consistent with the longitudinal comparison in the 2 earlier studies. In contrast to the knowledge privileged by nurse clinicians, researchers tend to place greater value on research-based knowledge than on experience-based knowledge. To increase research utilization in the practice setting, researchers and others need first to understand the reasons behind clinicians' valuing of experiential and social knowledge sources and then to consider research dissemination and implementation strategies that are more closely aligned with clinician preferences.

Attitude of Health Personnel↗
PubMed1997

The rubber meets the road: integrating the Unified Medical Language System Knowledge Source Server into the computer-based patient record.

Ongoing improvements in the content of the Unified Medical Language System, coupled with the recent release of the Internet-based Knowledge Source Server (KSS), have prompted us to develop an interface between the KSS and our computer-based patient record. We confronted many challenges while developing a robust interface to an Internet-based server, and in integrating the process of codification into the workflow of clinicians. An initial evaluation of the interface in the clinical environment suggests that acceptable performance is attainable. The benefits of using an Internet-accessible tool in a clinical information system appear to justify the effort required.

Humans↗
PubMed1993

A Pathfinder analysis of pedagogical knowledge structures: a follow-up investigation.

This study is an extension of an earlier investigation of undergraduate students' acquisition of key pedagogical concepts in a physical education teaching methodology course. In that study, Pathfinder, a method for eliciting associative memory networks, was used to describe and compare the pedagogical knowledge structures of students to that of the course instructor. After the course, students' pedagogical knowledge structures corresponded more closely with that of the instructor, and students who corresponded the closest performed better in the course. The results raised an interesting issue regarding the acquisition of knowledge in undergraduate students. Did students acquire a generalizable body of pedagogical knowledge applicable beyond the context of the teaching methodology course or a highly contextualized reflection of their course instructor's knowledge base? In the present study the external validity of the pedagogical knowledge base was examined by using Pathfinder to compare the knowledge structures of students from the initial investigation with knowledge structures of five experienced teacher educators from five different teacher education programs. The findings indicated that students' knowledge structures became significantly more correspondent with that of the experienced teachers' structures from the beginning to the end of the course. Also, students' correspondence with teacher educators' structures following instruction was found to be significantly correlated with academic and teaching performance. The findings point to the external validity of the domain of knowledge under study and the robustness of Pathfinder for capturing pedagogical knowledge.

Adult↗
PubMed2005

An arrhythmia classification system based on the RR-interval signal.

OBJECTIVE: This paper proposes a knowledge-based method for arrhythmic beat classification and arrhythmic episode detection and classification using only the RR-interval signal extracted from ECG recordings. METHODOLOGY: A three RR-interval sliding window is used in arrhythmic beat classification algorithm. Classification is performed for four categories of beats: normal, premature ventricular contractions, ventricular flutter/fibrillation and 2 degrees heart block. The beat classification is used as input of a knowledge-based deterministic automaton to achieve arrhythmic episode detection and classification. Six rhythm types are classified: ventricular bigeminy, ventricular trigeminy, ventricular couplet, ventricular tachycardia, ventricular flutter/fibrillation and 2 degrees heart block. RESULTS: The method is evaluated by using the MIT-BIH arrhythmia database. The achieved scores indicate high performance: 98% accuracy for arrhythmic beat classification and 94% accuracy for arrhythmic episode detection and classification. CONCLUSION: The proposed method is advantageous because it uses only the RR-interval signal for arrhythmia beat and episode classification and the results compare well with more complex methods.

Algorithms↗
PubMed1998

An introductory-level companion animal care course: student perception and subsequent performance.

A survey and pre- and postcourse examinations were administered to students (n = 23) enrolled in a companion animal (dog and cat) care course. The course objectives were to assess a student's knowledge base and then help him or her gain the knowledge to maintain the health, well-being, and longevity of companion animals. Four teaching modules were used in this course: 1) general lectures by the instructor; 2) special topics presented by guest professors; 3) videos shown in class; and 4) out-of-class experiential learning projects. The examination questions were developed from these modules. At the end of the academic term (quarter), students evaluated the course and each teaching module using a scale of 1 (= poor) to 5 (= very good). Seventy percent of the students enrolled in the course were female. The disciplines represented were animal health/preveterinary medicine (34.8%), animal science (21.7%), arts and science (13.0%), education (8.7%), forestry (8.6%), nursing education (4.4%), and 8.7% undecided. Only 15% had been exposed to an animal and dairy science introductory course. Students rated the course good (4.2 +/- .83 with 5 = very good) and agreed (4.4 +/- .87 with 5 = strongly agree) that the course provided a valuable learning experience. Average student score on the precourse examination (38.6% correct answers) improved dramatically on the postcourse examination (92.0% correct answers; P < .001). A positive correlation was observed between students' evaluation of the teaching modules and their total postcourse examination score (P < .05). Results indicated that the companion animal care course attracted students from disciplines other than that of animal science. Students evaluated the course as favorable, and their knowledge base of companion animal care was significantly expanded.

Adult↗
PubMed2000

Cardiovascular exercise and wellness. Exercise training for cardiac rehabilitation patients: meeting the challenges of the millennium.

Exercise training for cardiac rehabilitation has evolved over the past decades in response to a growing knowledge base in exercise physiology, an expanding understanding to the knowledge base of coronary disease, and a change in the patients presenting for cardiac rehabilitation. The patient population has changed from a post myocardial infarction patient group, to patients who have had coronary artery revascularization (coronary artery bypass surgery or percutaneous transluminal coronary angioplasty) with the implantation of intraarterial stents. Program goals have evolved from enhancing endurance fitness in deconditioned patients to initiating the long-term adoption of an active exercising lifestyle with the use of strength training to complement endurance training. An increased understanding of behavioral issues in the adoption of an active lifestyle will influence the evolution of cardiac rehabilitation exercise training. During the next several years, it is anticipated that the patient population will change to include patients with significant left ventricular systolic dysfunction and congestive heart failure. The exercise training programs will then further evolve to reflect the successful exercise training formats utilized in the multicenter trials of exercise training for patients with congestive heart failure. (c) 2000 by CHF, Inc.

Journal Article↗