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PubMedDate not supplied

A schema for representing medical language applied to clinical radiology.

OBJECTIVE: Develop a representational schema for clinical concepts and apply it to the task of encoding radiology reports of the chest. DESIGN: The schema was developed following a manual analysis of sample reports from the domain. The schema has two main components: the Medical Entities Dictionary (MED), which specifies the formal representation of the concepts in the domain and of their structures, and the natural-language processor, which specifies the linguistic expressions of the concepts. The schema was evaluated by applying it to a test set of 7,500 reports. Two-hundred reports from the test set were manually analyzed by a medical expert to determine the accuracy and success rate of the system. RESULTS: 82% of the 7,500 reports that contained relevant clinical information were successfully structured automatically. For the smaller set of 200 reports, 80% were structured successfully with an accuracy rate of 97%. CONCLUSIONS: The schema is a formal representation for clinical concepts in radiology reports, and provides domain coverage that is particularly well-suited for natural-language processing of radiology for use in a decision support system.

Decision Support Systems, Management↗
PubMedDate not supplied

A continuous-speech interface to a decision support system: I. Techniques to accommodate for misrecognized input.

OBJECTIVE: Develop a continuous-speech interface that allows flexible input of clinical findings into a medical diagnostic application. DESIGN: The authors' program allows users to enter clinical findings using their own vernacular. It displays from the diagnostic program's controlled vocabulary a list of terms that most closely matches the input, and allows the user to select the single best term. The interface program includes two components: a speech-recognition component that converts utterances into text strings, and a language-processing component that matches recognized text strings with controlled-vocabulary terms. The speech-recognition component is composed of commercially available speech-recognition hardware and software, and developer-created grammars, which specify the language to be recognized. The language-processing component is composed of a translator, which extracts a canonical form from both recognized text strings and controlled-vocabulary terms, and a matcher, which measures the similarity between the two canonical forms. RESULTS: The authors discovered that grammars constructed by a physician, who could anticipate how users might speak findings, supported speech recognition better than did grammars constructed programmatically from the controlled vocabulary. However, this programmatic method of grammar construction was more time efficient and better supported long-term maintenance of the grammars. The authors also found that language-processing techniques recovered some of the information lost due to speech misrecognition, but were dependent on the completeness of supporting synonym dictionaries. CONCLUSIONS: The authors' program demonstrated the feasibility of using continuous speech to enter findings into a medical application. However, improvements in speech-recognition technology and language-processing techniques are needed before natural continuous speech becomes an acceptable input modality for clinical applications.

Diagnosis, Computer-Assisted↗
PubMedDate not supplied

Managing attribute--value clinical trials data using the ACT/DB client-server database system.

ACT/DB is a client-server database application for storing clinical trials and outcomes data, which is currently undergoing initial pilot use. It stores most of its data in entity-attribute-value form. Such data are segregated according to data type to allow indexing by value when possible, and binary large object data are managed in the same way as other data. ACT/DB lets an investigator design a study rapidly by defining the parameters (or attributes) that are to be gathered, as well as their logical grouping for purposes of display and data entry. ACT/DB generates customizable data entry. The data can be viewed through several standard reports as well as exported as text to external analysis programs. ACT/DB is designed to encourage reuse of parameters across multiple studies and has facilities for dictionary search and maintenance. It uses a Microsoft Access client running on Windows 95 machines, which communicates with an Oracle server running on a UNIX platform. ACT/DB is being used to manage the data for seven studies in its initial deployment.

Clinical Trials as Topic↗
PubMedDate not supplied

Benefits of an object-oriented database representation for controlled medical terminologies.

OBJECTIVE: Controlled medical terminologies (CMTs) have been recognized as important tools in a variety of medical informatics applications, ranging from patient-record systems to decision-support systems. Controlled medical terminologies are typically organized in semantic network structures consisting of tens to hundreds of thousands of concepts. This overwhelming size and complexity can be a serious barrier to their maintenance and widespread utilization. The authors propose the use of object-oriented databases to address the problems posed by the extensive scope and high complexity of most CMTs for maintenance personnel and general users alike. DESIGN: The authors present a methodology that allows an existing CMT, modeled as a semantic network, to be represented as an equivalent object-oriented database. Such a representation is called an object-oriented health care terminology repository (OOHTR). RESULTS: The major benefit of an OOHTR is its schema, which provides an important layer of structural abstraction. Using the high-level view of a CMT afforded by the schema, one can gain insight into the CMT's overarching organization and begin to better comprehend it. The authors' methodology is applied to the Medical Entities Dictionary (MED), a large CMT developed at Columbia-Presbyterian Medical Center. Examples of how the OOHTR schema facilitated updating, correcting, and improving the design of the MED are presented. CONCLUSION: The OOHTR schema can serve as an important abstraction mechanism for enhancing comprehension of a large CMT, and thus promotes its usability.

Classification↗
PubMedDate not supplied

Studying the human-computer-terminology interface.

OBJECTIVE: To explore the use of an observational, cognitive-based approach for differentiating between successful, suboptimal, and failed entry of coded data by clinicians in actual practice, and to detect whether causes for unsuccessful attempts to capture true intended meaning were due to terminology content, terminology representation, or user interface problems. DESIGN: Observational study with videotaping and subsequent coding of data entry events in an outpatient clinic at New York Presbyterian Hospital. PARTICIPANTS: Eight attending physicians, 18 resident physicians, and 1 nurse practitioner, using the Medical Entities Dictionary (MED) to record patient problems, medications, and adverse reactions in an outpatient medical record system. MEASUREMENTS: Classification of data entry events as successful, suboptimal, or failed, and estimation of cause; recording of system response time and total event time. RESULTS: Two hundred thirty-eight data entry events were analyzed; 71.0 percent were successful, 6.3 percent suboptimal, and 22.7 percent failed; unsuccessful entries were due to problems with content in 13.0 percent of events, representation problems in 10.1 percent of events, and usability problems in 5.9 percent of events. Response time averaged 0.74 sec, and total event time averaged 40.4 sec. Of an additional 209 tasks related to drug dose and frequency terms, 94 percent were successful, 0.5 percent were suboptimal, and 6 percent failed, for an overall success rate of 82 percent. CONCLUSIONS: Data entry by clinicians using the outpatient system and the MED was generally successful and efficient. The cognitive-based observational approach permitted detection of false-positive (suboptimal) and false-negative (failed due to user interface) data entry.

Ambulatory Care Information Systems↗
PubMed1975

Dermatoglyphic findings in 54 triple-X females and a review of some general principles applying to the soles in sex chromosome aneuploidy.

The dermatoglyphic findings from 54 females with XXX sex chromosomes are reported. Sole prints were available for study in 33 cases. Compared with female controls, an excess of radial loops and arches and a reduced mean for total finger ridge-count were the main peculiarities on the fingers. On the palms, the absence of pattern in areas I and II, and wider ridges in the a-b interval were characteristics observed. Prevous findings by other authors with respect to: (1) zygodactylous tendency in the palms, (2) tendency for the ridge width to increase with the number of sex chromosomes, and (3) greater effect of an extra X chromosome in pattern size reduction but lesser influence on ridge width than an additional Y chromosome, were confirmed. On the soles, pattern intensity was above the control average. There was a significant deficit of proximal loops in area III but excess of proximal V together with triradius H. Triradius p" and zygodactylous z' were also significantly reduced in frequency. General findings with respect to the soles of patients with X,XXX,XXY, and XYY sex chromosomal abnormalities are also reviewed. Discrepancies are apparent and further studies are needed. Finally, a dictionary (Appendices 1 and 2) is provided which gives the frequencies of the complete pattern configurations on the palms and soles of XXX females.

Aneuploidy↗
PubMed2005

Study of effect of drug lexicons on medication extraction from electronic medical records.

Extraction of relevant information from free-text clinical notes is becoming increasingly important in healthcare to provide personalized care to patients. The purpose of this dictionary-based NLP study was to determine the effects of using varying drug lexicons to automatically extract medication information from electronic medical records. A convenience training sample of 52 documents, each containing at least one medication, and a randomized test sample of 100 documents were used in this study. The training and test set documents contained a total of 681 and 641 medications respectively. Three sets of drug lexicons were used as sources for medication extraction: first, containing drug name and generic name; second with drug, generic and short names; third with drug, generic and short names followed by filtering techniques. Extraction with the first drug lexicon resulted in 83.7% sensitivity and 96.2% specificity for the training set and 85.2% sensitivity and 96.9% specificity for the test set. Adding the list of short names used for drugs resulted in increasing sensitivity to 95.0%, but decreased the specificity to 79.2% for the training set. Similar results of increased sensitivity of 96.4% and 80.1% specificity were obtained for the test set. Combination of a set of filtering techniques with data from the second lexicon increased the specificity to 98.5% and 98.8% for the training and test sets respectively while slightly decreasing the sensitivity to 94.1% (training) and 95.8% (test). Overall, the lexicon with filtering resulted in the highest precision, i.e., extracted the highest number of medications while keeping the number of extracted non-medications low.

Electronic Data Processing↗
PubMed2001

Neural networks and logical reasoning systems: a translation table.

A correspondence is established between the basic elements of logic reasoning systems (knowledge bases, rules, inference and queries) and the structure and dynamical evolution laws of neural networks. The correspondence is pictured as a translation dictionary which might allow to go back and forth between symbolic and network formulations, a desirable step in learning-oriented systems and multicomputer networks. In the framework of Horn clause logics, it is found that atomic propositions with n arguments correspond to nodes with nth order synapses, rules to synaptic intensity constraints, forward chaining to synaptic dynamics and queries either to simple node activation or to a query tensor dynamics.

Logic↗
PubMed2003

Identification of biological relationships from text documents using efficient computational methods.

The biological literature databases continue to grow rapidly with vital information that is important for conducting sound biomedical research and development. The current practices of manually searching for information and extracting pertinent knowledge are tedious, time-consuming tasks even for motivated biological researchers. Accurate and computationally efficient approaches in discovering relationships between biological objects from text documents are important for biologists to develop biological models. The term "object" refers to any biological entity such as a protein, gene, cell cycle, etc. and relationship refers to any dynamic action one object has on another, e.g. protein inhibiting another protein or one object belonging to another object such as, the cells composing an organ. This paper presents a novel approach to extract relationships between multiple biological objects that are present in a text document. The approach involves object identification, reference resolution, ontology and synonym discovery, and extracting object-object relationships. Hidden Markov Models (HMMs), dictionaries, and N-Gram models are used to set the framework to tackle the complex task of extracting object-object relationships. Experiments were carried out using a corpus of one thousand Medline abstracts. Intermediate results were obtained for the object identification process, synonym discovery, and finally the relationship extraction. For the thousand abstracts, 53 relationships were extracted of which 43 were correct, giving a specificity of 81 percent. These results are promising for multi-object identification and relationship finding from biological documents.

Algorithms↗
PubMed1992

Introduction to the ACR-NEMA DICOM standard.

In 1982, the American College of Radiology (ACR) and the National Electrical Manufacturers Association (NEMA) formed a committee to develop standards for the interconnection of digital imaging devices. Version 1.0 of the standard, published in 1985, specifies a hardware interface supporting point-to-point (not network) image transmission, a data dictionary (a set of rules for encoding information), and a set of commands to initiate transactions. Version 2.0, published in 1988, also addresses point-to-point image transmission and provides semantic rules by which messages (streams of bits representing information in transit from one device to another) are organized. Version 3.0, also referred to as DICOM (Digital Imaging and Communications in Medicine), will be finalized in 1992. The DICOM standard encourages open systems interconnection of imaging equipment over standard networks, while maintaining compatibility with earlier point-to-point connection standards. The DICOM standard conforms fully with the International Standards Organization reference model for network communications (ISORM), addresses the issue of conformance, and incorporates the concept of object-oriented design.

Computer Communication Networks↗
PubMedDate not supplied

Informatics in Radiology (infoRAD): album of radiologic signs: a useful tool for training in radiologic semiology.

The importance of radiologic semiology can be seen from the large number of articles, books, and Web pages dealing with radiologic signs. Recognition of these signs forms an important part of the training process for radiologists. Computer-assisted instruction complements traditional techniques for teaching radiology and provides an appropriate method of collecting, organizing, and presenting radiologic signs. A computer application that includes more than 350 radiologic signs has been created with Microsoft PowerPoint (version 2002 for Windows). The user can navigate freely to see the signs from a menu that provides access according to anatomic region or from an interactive dictionary that includes 779 terms. From the presentation of each sign, the user can access one or more representative images, information about the examination wherein the sign appears, an explanation of the meaning of the sign and the corresponding diagnosis, additional comparative images (pathologic or normal), and relevant references. This album of radiologic signs is a useful tool for training in radiologic semiology and also allows a quick consultation based on the name of the sign. Although designed for interns and residents, it will also be useful in pregraduate teaching of radiology, as a reference, and in continuing medical education.

Databases, Factual↗
PubMed2003

Terminology for contractions of muscles during shortening, while isometric, and during lengthening.

Communication among scientists must be clear and concise to avoid ambiguity and misinterpretations. The selection of words must be based on accepted definitions. The fields of biomechanics, muscle physiology, and exercise science have had a particularly difficult time with terminology, arising from the complexity of muscle contractions and by the use of inappropriate terminology by scientists. The dictionary definition of the verb "contract," specifically for the case of muscle, is "to undergo an increase in tension, or force, and become shorter." Under all circumstances, an activated muscle generates force, but an activated muscle generating force does not invariably shorten! During the 1920s and 1930s, investigators recognized that the interaction between the force generated by the muscle and the load on the muscle results in either shortening, no length change (isometric), or lengthening of the muscle. The recognition that muscles perform three different types of "contractions" required that contraction be redefined as "to undergo activation and generate force." Modifiers of contraction are then needed to clarify the lack of movement or the directionality of movement. Despite the contradiction, for 75 years the lack of movement has been termed an "isometric contraction." The directionality of the movement is then best described by the adjectives "shortening" and "lengthening." The definitions of "concentric" as "having the same center" and of "eccentric" as "not having the same center" are consistent with hypertrophy, or remodeling of the heart muscle, but are inappropriate to describe the contractions of skeletal muscles.

Animals↗
PubMed1992

Sequences of C mu and the VH1 family in LG7, a clonable strain of Xenopus, homozygous for the immunoglobulin loci.

Twenty-eight heavy-chain variable (VH1) region genes and the immunoglobulin (IgM) heavy-chain constant region of an isogenic Xenopus hybrid, X. laevis/X. gilli, LG7, have been sequenced. The LG7 clone represents the first Xenopus hybrid that is homozygous for the IgH locus. The VH1 family was specifically investigated because VH1 genes are used by the antibodies produced during the Xenopus antidinitrophenol (DNP) response, These VH1 germ-line sequences establish a so-called "dictionary" that is available for studying somatic hypermutational mechanisms in immunized frogs.

Amino Acid Sequence↗
PubMed2000

Learning overcomplete representations.

In an overcomplete basis, the number of basis vectors is greater than the dimensionality of the input, and the representation of an input is not a unique combination of basis vectors. Overcomplete representations have been advocated because they have greater robustness in the presence of noise, can be sparser, and can have greater flexibility in matching structure in the data. Overcomplete codes have also been proposed as a model of some of the response properties of neurons in primary visual cortex. Previous work has focused on finding the best representation of a signal using a fixed overcomplete basis (or dictionary). We present an algorithm for learning an overcomplete basis by viewing it as probabilistic model of the observed data. We show that overcomplete bases can yield a better approximation of the underlying statistical distribution of the data and can thus lead to greater coding efficiency. This can be viewed as a generalization of the technique of independent component analysis and provides a method for Bayesian reconstruction of signals in the presence of noise and for blind source separation when there are more sources than mixtures.

Algorithms↗
PubMed1998

An Equivalence Between Sparse Approximation and Support Vector Machines.

This article shows a relationship between two different approximation techniques: the support vector machines (SVM), proposed by V. Vapnik (1995) and a sparse approximation scheme that resembles the basis pursuit denoising algorithm (Chen, 1995; Chen, Donoho, and Saunders, 1995). SVM is a technique that can be derived from the structural risk minimization principle (Vapnik, 1982) and can be used to estimate the parameters of several different approximation schemes, including radial basis functions, algebraic and trigonometric polynomials, B-splines, and some forms of multilayer perceptrons. Basis pursuit denoising is a sparse approximation technique in which a function is reconstructed by using a small number of basis functions chosen from a large set (the dictionary). We show that if the data are noiseless, the modified version of basis pursuit denoising proposed in this article is equivalent to SVM in the following sense: if applied to the same data set, the two techniques give the same solution, which is obtained by solving the same quadratic programming problem. In the appendix, we present a derivation of the SVM technique in one framework of regularization theory, rather than statistical learning theory, establishing a connection between SVM, sparse approximation, and regularization theory.

Journal Article↗
PubMed2006

What neuroscience can tell about intuitive processes in the context of perceptual discovery.

According to the Oxford English Dictionary, intuition is "the ability to understand or know something immediately, without conscious reasoning." Most people would agree that intuitive responses appear as ideas or feelings that subsequently guide our thoughts and behaviors. It is proposed that people continuously, without conscious attention, recognize patterns in the stream of sensations that impinge upon them. What exactly is being recognized is not clear yet, but we assume that people detect potential content based on only a few aspects of the input (i.e., the gist). The result is a vague perception of coherence which is not explicitly describable but instead embodied in a "gut feeling" or an initial guess, which subsequently biases thought and inquiry. To approach the nature of intuitive processes, we used functional magnetic resonance imaging when participants were working at a modified version of the Waterloo Gestalt Closure Task. Starting from our conceptualization that intuition involves an informed judgment in the context of discovery, we expected activation within the median orbito-frontal cortex (OFC), as this area receives input from all sensory modalities and has been shown to be crucially involved in emotionally driven decisions. Results from a direct contrast between intuitive and nonintuitive judgments, as well as from a parametric analysis, revealed the median OFC, the lateral portion of the amygdala, anterior insula, and ventral occipito-temporal regions to be activated. Based on these findings, we suggest our definition of intuition to be promising and a good starting point for future research on intuitive processes.

Adult↗
PubMed2006

The role of the striatum in processing language rules: evidence from word perception in Huntington's disease.

On the assumption that linguistic faculties reflect both lexical storage in the temporal cortex and combinatorial rules in the striatal circuits, several authors have shown that striatal-damaged patients are impaired with conjugation rules while retaining lexical knowledge of irregular verbs [Teichmann, M., Dupoux, E., Kouider, S., Brugières, P., Boissé, M. F., Baudic, S., Cesaro, P., Peschanski, M., & Bachoud-Lévi, A. C. (2005). The role of the striatum in rule application. The model of Huntington's disease at early stage. Brain, 128, 1155-1167; Ullman, M. T., Corkin, S., Coppola, M., Hickok, G., Growdon, J. H., Koroshetz, W. J., & Pinker, S. (1997). A neural dissociation within language: Evidence that the mental dictionary is part of declarative memory, and that grammatical rules are processed by the procedural system. Journal of Cognitive Neuroscience, 9, 266-276]. Yet, such impairment was documented only with explicit conjugation tasks in the production domain. Little is known about whether it generalizes to other language modalities such as perception and whether it refers to implicit language processing or rather to intentional rule operations through executive functions. We investigated these issues by assessing perceptive processing of conjugated verb forms in a model of striatal dysfunction, namely, in Huntington's Disease (HD) at early stages. Rule application and lexical processes were evaluated in an explicit task (acceptability judgments on verb and nonword forms) and in an implicit task (lexical decision on frequency-manipulated verb forms). HD patients were also assessed in executive functions, and striatal atrophy was evaluated with magnetic resonance imaging (bicaudate ratio). Results from both tasks showed that HD patients were selectively impaired for rule application but lexical abilities were spared. Bicaudate ratios correlated with rule scores on both tasks, whereas executive parameters only correlated with scores on the explicit task. We argue that the striatum has a core function in linguistic rule application generalizing to perceptive aspects of morphological operations and pertaining to implicit language processes. In addition, we suggest that the striatum may enclose computational circuits that underpin explicit manipulation of regularities.

Adult↗
PubMed2002

Beyond Wernicke's: a lexicon of eponyms in psychiatry.

Because no one has ever composed a glossary of psychiatry's numerous eponyms, the author collected eponymous signs and syndromes for a behavioral lexicon. Eponyms are included if they recall a real person, if they have special relevance to psychiatry, and if they describe an abnormal symptom or syndrome that we consider clinically important today, even if American physicians no longer favor the eponym. The author used MEDLINE and Campbell's Psychiatric Dictionary to locate candidates for the glossary. A brief definition and suggested reference accompany each entry.

Aphasia, Wernicke↗