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PubMed2004

User acceptance of clinical information systems: a methodological approach to identify the key dimensions allowing a reliable evaluation framework.

The introduction of Computerized Information Systems (CIS) in clinical settings encountered difficulties. These difficulties highlight the lack of understanding of factors and mechanisms influencing user acceptance. The existing tools and research obtained contradictory results that point out the existence of neglected aspects, such as impacts of CIS, in computer science developments in complex settings. This paper proposes to identify key dimensions which make up user acceptance in clinical settings through the union of three methods. They define five main dimensions which require a concrete evaluation to validate the underlying proposed framework and to complete the description of the acceptance phenomenon. Identifying key dimensions opens the gate to comparative evaluation of many CIS and adds new indicators to evaluate the highlighted dimensions. A long-term aim is the development of longitudinal studies and to state priorities and guidelines for new CIS designs.

Attitude to Computers↗
PubMed1992

Optical imaging of architecture and function in the living brain sheds new light on cortical mechanisms underlying visual perception.

Long standing questions related to brain mechanisms underlying perception can finally be resolved by direct visualization of the architecture and function of mammalian cortex. This advance has been accomplished with the aid of two optical imaging techniques with which one can literally see how the brain functions. The upbringing of this technology required a multi-disciplinary approach integrating brain research with organic chemistry, spectroscopy, biophysics, computer sciences, optics and image processing. Beyond the technological ramifications, recent research shed new light on cortical mechanisms underlying sensory perception. Clinical applications of this technology for precise mapping of the cortical surface of patients during neurosurgery have begun. Below is a brief summary of our own research and a description of the technical specifications of the two optical imaging techniques. Like every technique, optical imaging also suffers from severe limitations. Here we mostly emphasize some of its advantages relative to all alternative imaging techniques currently in use. The limitations are critically discussed in our recent reviews. For a series of other reviews, see Cohen (1989).

Brain↗
PubMed1998

Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets.

An integrated understanding of molecular and developmental biology must consider the large number of molecular species involved and the low concentrations of many species in vivo. Quantitative stochastic models of molecular interaction networks can be expressed as stochastic Petri nets (SPNs), a mathematical formalism developed in computer science. Existing software can be used to define molecular interaction networks as SPNs and solve such models for the probability distributions of molecular species. This approach allows biologists to focus on the content of models and their interpretation, rather than their implementation. The standardized format of SPNs also facilitates the replication, extension, and transfer of models between researchers. A simple chemical system is presented to demonstrate the link between stochastic models of molecular interactions and SPNs. The approach is illustrated with examples of models of genetic and biochemical phenomena where the ULTRASAN package is used to present results from numerical analysis and the outcome of simulations.

Animals↗
PubMedDate not supplied

Acute NMR changes during MCA occlusion: a preliminary study in primates.

Advancements in computer science and magnet design have resulted in the recent development of high resolution NMR imaging systems. Using our primate model we evaluated the ability of NMR scanning to detect early changes following middle cerebral artery (MCA) occlusion. Serial NMR scans documented progressive changes secondary to edema and swelling beginning ninety minutes after MCA occlusion. NMR was also able to readily demonstrate the area of cerebral infarct 10 days after a six hour episode of MCA occlusion. Soft tissue contrast and image resolution were superb. Correlation with pathologic sections was excellent.

Animals↗
PubMedDate not supplied

Trends in computational biology: a summary based on a RECOMB plenary lecture, 1999.

Computational biology, a term coined from analogy to the role of computing in the physical sciences, is now coming into its own as a major element of contemporary biological and biomedical research. Information science and computational science provide essential tools for next generation biological science efforts, from focusing the direction of experimental studies to providing knowledge and insight that can not otherwise be obtained. Going beyond the revolution in biology reflected in the successes of the genome project and driven by the power of molecular biology techniques, computational approaches will provide an underpinning for the integration of broad disciplines for development of a quantitative systems approach to understanding the mechanisms in the life of the cell.

Cell Physiological Phenomena↗
PubMed2001

BioLayout--an automatic graph layout algorithm for similarity visualization.

UNLABELLED: Graph layout is extensively used in the field of mathematics and computer science, however these ideas and methods have not been extended in a general fashion to the construction of graphs for biological data. To this end, we have implemented a version of the Fruchterman Rheingold graph layout algorithm, extensively modified for the purpose of similarity analysis in biology. This algorithm rapidly and effectively generates clear two (2D) or three-dimensional (3D) graphs representing similarity relationships such as protein sequence similarity. The implementation of the algorithm is general and applicable to most types of similarity information for biological data. AVAILABILITY: BioLayout is available for most UNIX platforms at the following web-site: http://www.ebi.ac.uk/research/cgg/services/layout.

Algorithms↗
PubMed1997

[The organization of the database and data flow in mass screening for cervical cancer].

Mass screening, because of very many potential patients, requires storing and processing a great deal of medical and population information. That is why it should be supported not only by human resources but by computer techniques as well. The example of a computer science application in medicine is Populations Database System (PDB) which was designed and implemented in the Department of Institute of Mother and Child in Białystok. The aim of this work is to evaluate PDB System's effectiveness in mass screening for cervical cancer. Population database contains several standard database files (DBF) and indexes. All the data is organized as a relational database. Every data relationship is at least in 1NF (first normal form). Functional dependency holds for the structures of database. Because of great variety of stored data it was essential to design how to enter information and how to combine database files to avoid redundancy. It has particular importance for the special functions of system, for example printing and sending individual invitation for an examination. In addition the system can realize all standard database functions and some statistical analysis. Special attention was paid to the problem of data security which is particularly important for medical information. Thanks to PDB system we could realize mass and active screening for cervical cancer in Białystok. Without computer techniques it would be impossible to store, process and interpret so much data.

Databases as Topic↗
PubMed2006

A graph-based reflexive artificial chemistry.

The conceptual divide between formal systems of computation and abstract models of chemistry is considered. As an attempt to concretely bridge this divide, a formalism is proposed that describes a constructive artificial chemistry on a space of directed graph structures. The idea for the formalism originates in computer science theory, with the traditional abstraction of a physical machine, the finite-state machine (FSM). In the FSM, the machine (state-transition graph) and input string (series of binary digits) are fundamentally distinct objects, separated by nature of the underlying formalism. This distinction is dissolved in the proposed system, resulting in a construction process that is reflexive: graphs interact with their own topological structure to generate a product. It is argued that this property of reflexivity is a key element missing from earlier model chemistries. Examples demonstrate the continuous emergence complex self-similar topologies, novel reaction pathways, and seemingly open-ended diversity. Implications of these findings are discussed.

Chemical Phenomena↗
PubMed2006

Epigenetic acquisition of inducibility of type III cytotoxicity in P. aeruginosa.

BACKGROUND: Pseudomonas aeruginosa, an opportunistic pathogen, is often encountered in chronic lung diseases such as cystic fibrosis or chronic obstructive pneumonia, as well as acute settings like mechanical ventilation acquired pneumonia or neutropenic patients. It is a major cause of mortality and morbidity in these diseases. In lungs, P. aeruginosa settles in a biofilm mode of growth with the secretion of exopolysaccharides in which it is encapsulated, enhancing its antibiotic resistance and contributing to the respiratory deficiency of patients. However, bacteria must first multiply to a high density and display a cytotoxic phenotype to avoid the host's defences. A virulence determinant implicated in this step of infection is the type III secretion system (TTSS), allowing toxin injection directly into host cells. At the beginning of the infection, most strains isolated from patients' lungs possess an inducible TTSS allowing toxins injection or secretion upon in vivo or in vitro activation signals. As the infection persists most of the bacteria permanently loose this capacity, although no mutations have been evidenced. We name "non inducible" this phenotype. As suggested by the presence of a positive feedback circuit in the regulatory network controlling TTSS expression, it may be due to an epigenetic switch allowing heritable phenotypic modifications without genotype's mutations. RESULTS: Using the generalised logical method, we designed a minimal model of the TTSS regulatory network that could support the epigenetic hypothesis, and studied its dynamics which helped to define a discriminating experimental scenario sufficient to validate the epigenetic hypothesis. A mathematical framework based on formal methods from computer science allowed a rigorous validation and certification of parameters of this model leading to epigenetic behaviour. Then, we demonstrated that a non inducible strain of P. aeruginosa can stably acquire the capacity to be induced by calcium depletion for the TTSS after a short pulse of a regulatory protein. Finally, the increased cytotoxicity of a strain after this epigenetic switch was demonstrated in vivo in an acute pulmonary infection model. CONCLUSION: These results may offer new perspectives for therapeutic strategies to prevent lethal infections by P. aeruginosa by reverting the epigenetic inducibility of type III cytotoxicity.

Bacterial Proteins↗
PubMed1993

Multidimensional visualization in echocardiography: an introduction.

X-ray films depict three-dimensional objects as shadows in a two-dimensional plane; thus, objects become superimposed. Computed tomography and other types of tomographic imaging, such as ultrasonography, acquire two-dimensional images of a material property within a thin slice. Sequential adjacent two-dimensional tomograms can be used to construct three-dimensional displays of objects. Visualization, a field of computer science, enables scientists to measure image attributes (extraction of features), identify features (classification), separate objects from one another (segmentation), and produce comprehensible, information-dense images from three-dimensional data sets (rendering). A three-dimensional rendering of the heart can be used to represent only one component of the heart, such as the atrial septum or the ventricular chamber, and can be shaded or colored to enhance comprehension. Three-dimensional images rendered sequentially over time result in a dynamic four-dimensional display. This report describes multidimensional visualization of objects and tissues and specifically discusses examples from echocardiography.

Echocardiography↗
PubMedDate not supplied

A web application for recording and analyzing the clinical experiences of nursing students.

A primary focus in nursing education is to provide students with a diverse range of clinical experiences. Historically, the collection and assessment of data from students' clinical experiences have been paper-and-pencil tasks that are arduous for both students and nursing faculty. The volume of collected information also has made it difficult to produce ad hoc statistical reports without additional intensive manual labor. To facilitate recording and analysis of these data, the Nursing and Computer Science Departments at Indiana University-Purdue University Fort Wayne have collaborated to create a Web application: Essential Clinical Behaviors. The use of the Web-accessible database represents a major change in nursing education by alteration of format used by students to record their clinical experiences in nursing courses. The application was designed to enhance nursing students' learning and to assist faculty in making student assignments, evaluating student progress, and supporting curriculum decisions. This report discusses the rationale for the development of the Web application, a description of its data entry and reporting mechanisms, an overview of the system architecture, its use in the nursing curriculum, and planned enhancements.

Clinical Competence↗
PubMed1998

Controversy and the state: lord ARPA and intelligent computing.

This is a study of a well-known controversy in computer science, between artificial intelligence and neural networks researchers. It examines claims made by participants in the field that the controversy was triggered, shaped and finally resolved in connection to activities of state research agencies, particularly the US Department of Defense Advanced Research Projects Agency (ARPA). In contrast to these claims, this account concludes that, although ARPA's relations to the controversy among researchers were important, they were indirect. This study thus beings the analytical resources of studies of scientific controversy to bear on a domain which has so far gone largely unexamined in studies of 20th-century controversies - namely, state research policy and management. The account is based on contemporary documents, historical literatuare, and interviews with researchers and ARPA officials.

Artificial Intelligence↗
PubMed2003

Anatomy and the access grid: exploiting plastinated brain sections for use in distributed medical education.

Computerized animation is becoming an increasingly popular method to provide dynamic presentation of anatomical concepts. However, most animations use artistic renderings as the base illustrations that are subsequently altered to depict movement. In most cases, the artistic rendering is a schematic that lacks realism. Plastinated sections provide a useful alternative to artistic renderings to serve as a base image for animation. The purpose of this study is to describe a method for developing animations by using plastinated sections. This application is used in Project TOUCH as a supplemental learning tool for a problem-based learning case distributed over the National Computational Science Alliance's Access Grid. The case involves traumatic head injury that results in an epidural hematoma with transtentorial uncal herniation. In addition, a subdural hematoma is animated permitting the student to contrast the two processes for a better understanding of dural hematomas, in general. The method outlined uses P40 plastinated coronal brain sections that are digitized and to which contiguous anatomical structures are rendered. The base illustration is rendered, interpolated, and viewed while audio narration describes the event. This method demonstrates how realistic anatomical animations can be generated quickly and inexpensively for medical education purposes by using plastinated brain sections.

Anatomy, Cross-Sectional↗
PubMed1985

Computer assessment of left ventricular wall motion: the ALVEN expert system.

The current limited success of computer-assisted analysis of left ventricular (LV) dynamics is due to three main reasons: there is a strong tendency to remain within the realm of mathematical modeling for LV dynamics, and it is not at all clear that this is an adequate approach; in places where mathematical models alone may be insufficient, current computer science research into more sophisticated schemes is not yet complete, and thus, more basic research is required, particularly into artificial intelligence, representations of knowledge, and interpretation control structures, before applications such as LV performance can be solved, a view also stated in M. Boehm and K. Hoehne (in "Digital Image Processing in Medicine" (K. Hoehne, Ed.), Springer-Verlag, New York/Berlin, 1981); there is a distinct lack of knowledge about LV dynamics, in conjunction with disagreements about what is important to model and what terminology is to be used. Although each of these issues is addressed, the first two issues are concentrated on. Furthermore, a language for the expression of definitions for terminology has been designed, and a system for LV dynamics interpretation has been implemented.

Cineradiography↗
PubMed2001

"THE PILOT": a tool for connecting existing HIS to an extranet quickly, easily and smoothly.

Migrations and expansions of information systems are constantly at the front line of all the computer science problems to be overcome in medical / health informatics systems. It is shown here that one effective way to open the communication between heterogeneous systems is depending upon the ease of putting all the systems at work together using the middleware level to facilitate the interconnection between heterogeneous applications. However the most difficult application to migrate is certainly the ADT. It is shown here how the Pilot could facilitate the migration of applications namely with the migration of the ADT itself from a centralized platform to a full scale distributed system. Indeed the Pilot has been developed up to the stage of a pre-product and is on sale already. It has been experienced satisfactorily and is presented here.

Computer Communication Networks↗
PubMed1999

Global perceptual processing in problem solving: the case of the traveling salesperson.

The traveling salesperson problem (TSP) consists of finding the shortest tour around a set of locations and is an important task in computer science and operations research. In four experiments, the relationship between processes implicated in the recognition of good figures and the identification of TSP solutions was investigated. In Experiment 1, a linear relationship was found between participants' judgments of good figure and the optimality of solutions to TSPs. In Experiment 2, identification performance was shown to be a function of solution optimality and problem orientation. Experiment 3 replicated these findings with a forced-pace method, suggesting that global processing, rather than a local processing strategy involving point-by-point analysis of TSP solutions, is the primary process involved in the derivation of best figures for the presented TSPs. In Experiment 4, the role of global precedence was confirmed using a priming method, in which it was found that short (100 msec) primes facilitated solution identification, relative to no prime or longer primes. Effects of problem type were found in all the experiments, suggesting that local features of some problems may disrupt global processing. The results are discussed in terms of Sanocki's (1993) global-to-local contingency model. We argue that global perceptual processing may contribute more generally to problem solving and that human performance can complement computational TSP methods.

Adult↗
PubMed2002

Bionformation: untangling the networks of life.

The growth of numerous subdisciplines at the interface between biology and computer science paves the way for reconsidering the special relationship between information and life. In this sense, the term 'bioinformation' appears as an integrative notion that is useful to promote a new understanding of the heterogeneous networkings that characterize life. Two conceptual avenues are explored here: representation and symmetry. It is argued that the special organization of the living cell, based on the overlapping of both sequential and 'amorphous' architectures, endlessly strives to fill in the occurring 'functional voids' or symmetry breakings; and it endlessly produces physiological networkings and evolutionary novelties as a byproduct. Characterizing the special dynamics inherent in the living cell may be a precondition for understanding the information-production processes on which other emergent informational entities are based, particularly, nervous systems and societies.

Animals↗
PubMed1999

Nursing informatics. Issues for critical care medicine.

The demands of today's health care arena have forced the issue of automation and computerization. Nursing, as the major stakeholder in the collecting, managing, processing, transforming, and communicating of information regarding the patient, has developed a new approach to these tasks. Nursing informatics, which is the application of computer science and information science, is being used to manage and process the data, information, and knowledge necessary in the discipline. Although still in its infancy, nursing informatics has started to have a major effect on health care information gathering and clinical practice despite the multiple barriers to its advancement. Critical care is a data-rich environmental that can benefit from better management and processing of the data derived from the critically ill patient. Nursing and medical informatics joining together to organize the data, coupled with the introduction of good DSS and the addition of information retrieval systems at the bedside and the on-line medical record, will have a positive effect on the critical care environment and on the critical care patient outcomes.

Critical Care↗