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At least 415 records · Page 23Linked to original sources
PubMed1997

Design considerations in migrating an obstetrics clinical record to the Web.

Recently the American College of Obstetricians and Gynecologists (ACOG) embarked on an effort to promote the development of nationally networked obstetrical records. The Laboratory of Computer Science (LCS) is collaborating with them to help achieve this goal through the development of a web-based prototype of an electronic medical record (EMR) which would allow the entry and display of typical clinical information for the obstetric patient. The process of porting a stand alone application to the web environment necessitated the development of a robust software scheme that could exploit the strengths of Web-based technologies and avoid some of the drawbacks inherent in a stateless environment.

Computer Communication Networks↗
PubMed2007

The use of evolutionary biology concepts for genome annotation.

The past decade has seen the completion of numerous whole-genome sequencing projects, began with bacterial genomes and continued with eukaryotic species from different phyla: fungi, plants and animals. Besides, more biological information are produced and are shared thanks to information exchange systems, and more biological concepts, as well as more bioinformatics tools, are available. In this article, we will describe how the evolutionary biology concepts, as well as computer science, are useful for a better understanding of biology in general and genome annotation in particular. The genome annotation process consists of taking the raw DNA produced, for example, by the genome sequencing projects, adding the layers of analysis and interpretation necessary to extract its biological significance and placing it in the context of our understanding of biological processes. Genome annotation is a multistep process falling into two broad categories: structural and functional annotation.

Amino Acid Sequence↗
PubMed1999

A JAVA implementation of a medical knowledge base for decision support.

Distributed decision support is a challenging issue requiring the implementation of advanced computer science techniques together with tools of development which offer ease of communication and efficiency of searching and control performance. This paper presents a JAVA implementation of a knowledge base model called ARISTOTELES which may be used in order to support the development of the medical knowledge base by clinicians in diverse specialised areas of interest. The advantages that are evident by the application of such a cognitive model are ease of knowledge acquisition, modular construction of the knowledge base and greater acceptance from clinicians.

Artificial Intelligence↗
PubMed2001

Set of novel tools for PCR primer design.

We have developed a new package of computer programs and algorithms for different PCR applications, including allele-specific PCR, multiplex PCR, and long PCR. The package is included in the upcoming VectorNTI suite software and attempts to incorporate most of the current knowledge about PCR primer design. A wide range of primer characteristics is available for user manipulation to provide improved efficiency and increased flexibility of primer design. To accelerate the primer calculations, we have optimized algorithms using recent advances in computer science such as dynamic trees and lazy evaluation. Proper structural organization of input parameters provides further program acceleration. New Vector NTI primer design software allows calculations of primer pairs for long PCR amplification of 120-kb genomic DNA in 5 min under most stringent input parameters and clustering 435 primer pairs for multiplex PCR within 30 min on a standard Pentium III PC. Our program allows the user to take advantage of molecule annotation by applying different kinds of filtering features during PCR primer design.

Algorithms↗
PubMed1990

Validating nursing theory for use within a computerized nursing information system.

Computerized nursing information systems (CNISs) exemplify the application of computer science to nursing knowledge. For nursing knowledge to be a basis for CNIS development, variable relationships must be clearly defined, thus allowing transformation of data into knowledge. Nursing theories define variable relationships; these definitions, however, often are not specific enough on which to base data-based nursing information systems. This article describes how a nursing process model was derived from Self-Care Deficit Nursing Theory, the process model validated, and data relationships established within the model prior to its use as a structure for a CNIS.

Computer Simulation↗
PubMed2001

Metaphors of movement: a visualization and user interface for time-oriented, skeletal plans.

Therapy planning plays an increasingly important role in the everyday work of physicians. Clinical protocols or guidelines are typically represented using flow-charts, decision tables, or plain text. These representations are badly suited, however, for complex medical procedures.One representation method that overcomes these problems is the language Asbru. But because Asbru has a LISP-like syntax (and also incorporates many concepts from computer science), it is not suitable for physicians.Therefore, we developed a visualization and user interface to deal with treatment plans expressed in Asbru. We use graphical metaphors to make the underlying concepts easier to grasp, employ glyphs to communicate complex temporal information and colors to make it possible to understand the connection between the two views (Topological View and Temporal View) available in the system. In this paper, we present the design ideas behind AsbruView, and discuss its usefulness based on the results of a usability study we performed with six physicians.

Decision Making, Computer-Assisted↗
PubMed2003

Integration of advanced technologies to enhance problem-based learning over distance: Project TOUCH.

Distance education delivery has increased dramatically in recent years as a result of the rapid advancement of communication technology. The National Computational Science Alliance's Access Grid represents a significant advancement in communication technology with potential for distance medical education. The purpose of this study is to provide an overview of the TOUCH project (Telehealth Outreach for Unified Community Health; http://hsc.unm.edu/touch) with special emphasis on the process of problem-based learning case development for distribution over the Access Grid. The objective of the TOUCH project is to use emerging Internet-based technology to overcome geographic barriers for delivery of tutorial sessions to medical students pursuing rotations at remote sites. The TOUCH project also is aimed at developing a patient simulation engine and an immersive virtual reality environment to achieve a realistic health care scenario enhancing the learning experience. A traumatic head injury case is developed and distributed over the Access Grid as a demonstration of the TOUCH system. Project TOUCH serves as an example of a computer-based learning system for developing and implementing problem-based learning cases within the medical curriculum, but this system should be easily applied to other educational environments and disciplines involving functional and clinical anatomy. Future phases will explore PC versions of the TOUCH cases for increased distribution.

Craniocerebral Trauma↗
PubMedDate not supplied

Comparative evaluation of the use of artificial neural networks for modelling the epidemiology of schistosomiasis mansoni.

There has been a marked increase in the application of approaches based on artificial intelligence (AI) in the field of computer science and medical diagnosis, but AI is still relatively unused in epidemiological settings. In this study we report results of the application of neural networks (NN; a special category of AI) to schistosomiasis. It was possible to design an NN structure which can process and fit epidemiological data collected from 251 schoolchildren in Egypt using the first year's data to predict second and third years' infection rates. Data collected over 3 years included age, gender, exposure to canal water and agricultural activities, medical history and examination, and stool and urine parasitology. Schistosoma mansoni infection rates were 50%, 78% and 66% at the baseline and the 2 follow-up periods, respectively. NN modelling was based on the standard back-propagation algorithm, in which we built a suitable configuration of the network, using the first year's data, that optimized performance. It was implemented on an IBM compatible computer using commercially available software. The performance of the NN model in the first year compared favourably with logistic regression (NN sensitivity = 83% (95% confidence interval [CI] 78-88%) and positive predictive value (PPV) = 63% (95% CI 57-69%); logistic regression sensitivity = 66% (95% CI 60%-72%) and PPV = 59% (95% CI 53%-65%). The NN model generalized the criteria for predicting infection over time better than logistic regression and showed more stability over time, as it retained its sensitivity and specificity and had better false positive and negative profiles than logistic regression. The potential of NN-based models to analyse and predict wide-scale control programme data, which are inevitably based on unstable egg excretion rates and insensitive laboratory techniques, is promising but still untapped.

Adolescent↗
PubMed2004

Application of knowledge information processing methods to biochemical engineering, biomedical and bioinformatics fields.

In biochemical and biomedical engineering fields there are a variety of phenomena with many complex chemical reactions, in which many genes and proteins affect transcription or enzyme activity of others. It is difficult to analyze and estimate many of these phenomena using conventional mathematical models. Recently some knowledge information processing methods, such as the artificial neural network (ANN), fuzzy reasoning, fuzzy neural network (FNN), fuzzy adaptive resonance theory (fuzzy ART) and the genetics algorithm (GA), were developed in the computer science field and have been applied to analysis in a variety of research fields. In this chapter, these methods will be briefly reviewed. Next, the application of these methods in the biochemical field will be introduced, instancing two examples in actual industrial processes. In addition, the application in the biomedical and bioinformatics field as another attractive field will be reviewed. Two examples are our research such as the prediction of prognosis for cancer patients from DNA microarray data using FNN and gene clustering for DNA microarray data using fuzzy ART.

Artificial Intelligence↗
PubMed2006

Rules for modeling signal-transduction systems.

Formalized rules for protein-protein interactions have recently been introduced to represent the binding and enzymatic activities of proteins in cellular signaling. Rules encode an understanding of how a system works in terms of the biomolecules in the system and their possible states and interactions. A set of rules can be as easy to read as a diagrammatic interaction map, but unlike most such maps, rules have precise interpretations. Rules can be processed to automatically generate a mathematical or computational model for a system, which enables explanatory and predictive insights into the system's behavior. Rules are independent units of a model specification that facilitate model revision. Instead of changing a large number of equations or lines of code, as may be required in the case of a conventional mathematical model, a protein interaction can be introduced or modified simply by adding or changing a single rule that represents the interaction of interest. Rules can be defined and visualized by using graphs, so no specialized training in mathematics or computer science is necessary to create models or to take advantage of the representational precision of rules. Rules can be encoded in a machine-readable format to enable electronic storage and exchange of models, as well as basic knowledge about protein-protein interactions. Here, we review the motivation for rule-based modeling; applications of the approach; and issues that arise in model specification, simulation, and testing. We also discuss rule visualization and exchange and the software available for rule-based modeling.

Computer Simulation↗
PubMed2004

[FRAP, FLIP, FRET, BRET, FLIM, PRIM...new techniques for a colourful life].

Cell and tissue imaging provides scientists with wonderful tools, thanks to a fruitful dialog between chemistry, optical, mechanical, computational sciences and biology. Confocal microscopy, videomicroscopy together with a new generation of fluorochromes (especially those derived from green fluorescent protein, GFP) and image analysis software allow to visualize life in all its dimensions (space and time). Cell imaging also allows to quantify biological processes at the cellular level, to analyse both stoechiometry and dynamics of molecular interactions involved in cell and tissue regulations. Entering the new era of post-genomics requires a better knowledge of advantages and limitations of these new approaches.

Cell Physiological Phenomena↗
PubMed2004

A general framework for learning rules from data.

With the aim of getting understandable symbolic rules to explain a given phenomenon, we split the task of learning these rules from sensory data in two phases: a multilayer perceptron maps features into propositional variables and a set of subsequent layers operated by a PAC-like algorithm learns Boolean expressions on these variables. The special features of this procedure are that: i) the neural network is trained to produce a Boolean output having the principal task of discriminating between classes of inputs; ii) the symbolic part is directed to compute rules within a family that is not known a priori; iii) the welding point between the two learning systems is represented by a feedback based on a suitability evaluation of the computed rules. The procedure we propose is based on a computational learning paradigm set up recently in some papers in the fields of theoretical computer science, artificial intelligence and cognitive systems. The present article focuses on information management aspects of the procedure. We deal with the lack of prior information about the rules through learning strategies that affect both the meaning of the variables and the description length of the rules into which they combine. The paper uses the task of learning to formally discriminate among several emotional states as both a working example and a test bench for a comparison with previous symbolic and subsymbolic methods in the field.

Algorithms↗
PubMed1994

A software engineering approach for medical workstations development.

Multimedia medical workstations represent the natural tool for accessing the hospital information system environment. They are complex medical systems that have to gather, in a single framework, a large collection of components dealing with multimedia medical objects. To remain current with both medical practice and with advances in the computer science field, they have to allow the iterative addition of new functions to the set of existing ones. In this paper, after a survey of commonly required medical workstation functional components, we shall try to discuss how a software engineering approach can streamline the development of a medical workstation. Different software engineering tools needed to build the functional components of a workstation are described. Their integration in a single dedicated environment is considered through four perspectives: data, presentation, communication and control. Benefits and limitations of an object-oriented approach are discussed.

Computer Communication Networks↗
PubMedDate not supplied

Noviceware: a model for learning the software development process.

Students and nursing faculty without formal computer science training can collaborate within an independent study structure to assist the student in gaining experience with the fundamentals of software development. The systems development life cycle approach provides an essential map to structure such independent studies. This article describes the development within an academic setting of a computerized research management system. The software builds a database of research case demographic data and data from a 65-item tool used in scoring videotapes of caregiver-infant interactions. For students and faculty contemplating similar projects, recommendations about planning software development experiences and securing hardware, software, and expert resources are provided.

Algorithms↗
PubMed2002

Theory of DNA electrophoresis (approximately 1999-2002(1/2)).

Over the last two decades, the introduction of new methods such as pulsed-field gel electrophoresis and capillary array electrophoresis has made it possible to map and sequence entire genomes, including our own. The development of these experimental methods has been helped by the progress of theoretical and computational sciences, and the interactions between these three modi operandi of modern science are still pushing the limits of our technologies. We now see a clear trend towards proteomics and microfluidic (even nanofluidic!) devices. In this review, we take a look at the progress of the field over the last 3 years using the glasses of the theoretical scientist and focusing mostly on new ideas and concepts. About a dozen different subfields are discussed and reviewed. We conclude by giving a commented list of some of the best review articles published over the last 2-3 years.

Animals↗
PubMed1993

Designing a connectionist network supercomputer.

This paper describes an effort at UC Berkeley and the International Computer Science Institute to develop a supercomputer for artificial neural network applications. Our perspective has been strongly influenced by earlier experiences with the construction and use of a simpler machine. In particular, we have observed Amdahl's Law in action in our designs and those of others. These observations inspire attention to many factors beyond fast multiply-accumulate arithmetic. We describe a number of these factors along with rough expressions for their influence and then give the applications targets, machine goals and the system architecture for the machine we are currently designing.

Algorithms↗
PubMed1995

Selecting a pharmacy computer system for the future.

Major advances are occurring in the field of computer science that have placed us at the threshold of a significant revolution in the management and application of clinical data. These advances will have a profound effect on the practice of pharmacy and are occurring at a time when many hospital pharmacies are deciding whether to enhance or replace their current systems. To best position your department for the future, it is essential that you are knowledgeable of the advances being made, have a vision for how they will affect your practice, and undergo a well-organized and thorough selection process.

Clinical Pharmacy Information Systems↗
PubMed1995

Introduction to perceptual linearization of video display systems for medical image presentation.

The perceptual linearization of video display systems should play a significant role in medical image presentation. It maximizes the faithfulness of information transfer to the human observer; it provides a method for standardizing the appearance of images across different display devices; and it allows for calculation of the inherent contrast resolution of different display devices. This paper provides insight into the process of perceptual linearization by decomposing it into the digital driving level-to-monitor luminance relationship, the monitor luminance-to-human brightness perception relationship, and the construction of a linearization function derived from these two relationships. A discussion of previous work in these areas is given. We then compare and contrast the results of previous work with recent experiments in our laboratory and related work in vision and computer science. We conclude that (1) sufficiently good visual models exist for agreeing on a standard method of calculating the perceptual linearization function; (2) improvements in the resolution and luminance distribution of the digital-to-analog circuitry in display systems are required for medical imaging; and (3), methods for calculating a linearization remapping from a perceptual linearization function currently have significant error and should be replaced with methods that minimize perceptual error.

Analog-Digital Conversion↗