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PubMed1999

Merging multiple institutions: information architecture problems and solutions.

Amalgamating organizations face great challenges when trying to merge their formerly separate information systems. An architectural approach is essential in order to understand the business process and data implications of the new organization's business decisions and application choices. HL7 is useful as a common messaging standard, but does not help to reconcile conflicting local identifier coding systems. The Information Services department has an important role in catalyzing decisions about inconsistent business processes and conflicting universal coding systems within an enterprise framework.

Computer Systems↗

PubMed2001

End-user support: a necessary issue in the implementation and use of EPR systems.

A successful integration of an IT-system is dependent not only of the quality of the information and the user interface features of the system but also of the organizations ability to support the users learning process. As IT is becoming more and more pervasive in the Health Care sector as such there is a need for a systematic approach to the question on how to support end-users. Based on an empirical study of an implementation process in a Danish Primary Health Care Services the concept of end-user support is discussed and it is argued that there is a need for a distinction between different kinds of support depending of the type of activity involved. First the organizations strategy for learning when the system was implemented is described. The evaluation of the learning strategy revealed that there was a need for different kinds of knowledge involving qualitatively different kinds of learning. Second the area of end-user support is discussed and it is argued that the common understanding of end-user support as something provided by DP staff, vendors or manuals are to narrow. Third a more differentiated way of thinking of support that link the need for different kind of knowledge and learning processes to different kinds of support is proposed. Finally Activity Theory is put forward as a possible basis that provide the opportunity of discussing issues belonging to different kinds of end-user support within an integrated framework.

Computer User Training↗

PubMed2003

Neural representation of probabilistic information.

It has been proposed that populations of neurons process information in terms of probability density functions (PDFs) of analog variables. Such analog variables range, for example, from target luminance and depth on the sensory interface to eye position and joint angles on the motor output side. The requirement that analog variables must be processed leads inevitably to a probabilistic description, while the limited precision and lifetime of the neuronal processing units lead naturally to a population representation of information. We show how a time-dependent probability density rho(x; t) over variable x, residing in a specified function space of dimension D, may be decoded from the neuronal activities in a population as a linear combination of certain decoding functions phi(i)(x), with coefficients given by the N firing rates a(i)(t) (generally with D << N). We show how the neuronal encoding process may be described by projecting a set of complementary encoding functions phi;(i)(x) on the probability density rho(x; t), and passing the result through a rectifying nonlinear activation function. We show how both encoders phi;(i)(x) and decoders phi(i)(x) may be determined by minimizing cost functions that quantify the inaccuracy of the representation. Expressing a given computation in terms of manipulation and transformation of probabilities, we show how this representation leads to a neural circuit that can carry out the required computation within a consistent Bayesian framework, with the synaptic weights being explicitly generated in terms of encoders, decoders, conditional probabilities, and priors.

Models, Neurological↗

PubMedDate not supplied

Medical informatics and the science of cognition.

Recent developments in medical informatics research have afforded possibilities for great advances in health care delivery. These exciting opportunities also present formidable challenges to the implementation and integration of technologies in the workplace. As in most domains, there is a gulf between technologic artifacts and end users. Since medical practice is a human endeavor, there is a need for bridging disciplines to enable clinicians to benefit from rapid technologic advances. This is turn necessitates a broadening of disciplinary boundaries to consider cognitive and social factors pertaining to the design and use of technology. The authors argue for a place of prominence for cognitive science. Cognitive science provides a framework for the analysis and modeling of complex human performance and has considerable applicability to a range of issues in informatics. Its methods have been employed to illuminate different facets of design and implementation. This approach has also yielded insights into the mechanisms and processes involved in collaborative design. Cognitive scientific methods and theories are illustrated in the context of two examples that examine human-computer interaction in medical contexts and computer-mediated collaborative processes. The framework outlined in this paper can be used to refine the process of iterative design, end-user training, and productive practice.

Cognitive Science↗

PubMed1992

[Acute abdominal pain--standardized findings as diagnostic support. Results of a prospective multicenter intervention study and testing of a computer-assisted diagnosis system].

Despite powerful diagnostic tools (e.g. ultrasound, special laboratory investigations), the diagnosis of acute abdominal pain is still a considerable problem. Several studies in the UK have shown that the diagnostic accuracy can be improved by structured and standardized history taking and clinical examination and by computer-aided diagnosis. In the framework of a concerted action of the European Community we have conducted a prospective multicenter interventional trial comparing two consecutive phases: a) a baseline phase in clinical routine without additional intervention, b) a test phase with structured and standardized history and clinical examination (questionnaire, documentation programme). In addition, a computer-aided diagnostic system developed in the UK was applied to the cases in the test phase. Outcome criteria were the diagnostic accuracy of the initial and the final examiner, the perforated appendix rate, the negative appendectomy rate, the negative laparotomy rate and the rates of diagnostic errors with missing indication to operation and of delayed urgent operations. No differences could be found between the phases with respect to the outcome criteria. In the baseline phase (test phase) diagnostic accuracy was 59% (59%), diagnostic accuracy after investigation (senior examiner) was 77% (78%), perforated appendix rate was 11% (16%), negative appendectomy rate was 13% (15%), negative laparotomy rate was 7% (8%), the rate of missed urgent indications to operation was 1.1% (1.9%) and the rate of delayed urgent operations was 3.4% (2.4%). Major differences between the centers were recorded. Computer-aided diagnosis resulted in a diagnostic accuracy of 51%. The introduction of structured and standardized history taking and clinical examination has not brought any improvement of the good results in clinical routine. It is doubtful, whether existing systems of computer-aided diagnosis are able to significantly decrease the still remaining error rate of 20%.

Abdomen, Acute↗

PubMed2001

Reinventing patient-centered computing for the twenty-first century.

Despite evidence over the past decade that patients like and will use patient-centered computing systems in managing their health, patients have remained forgotten stakeholders in advances in clinical computing systems. We present a framework for patient empowerment and the technical realization of that framework in an architecture called CareLink. In an evaluation of the initial deployment of CareLink in the support of neonatal intensive care, we have demonstrated a reduction in the length of stay for very-low birthweight infants, and an improvement in family satisfaction with care delivery. With the ubiquitous adoption of the Internet into the general culture, patient-centered computing provides the opportunity to mend broken health care relationships and reconnect patients to the care delivery process. CareLink itself provides functionality to support both clinical care and research, and provides a living laboratory for the further study of patient-centered computing.

Humans↗

PubMed2004

Medical privacy protection based on granular computing.

Based on granular computing methodology, we propose two criteria to quantitatively measure privacy invasion. The total cost criterion measures the effort needed for a data recipient to find private information. The average benefit criterion measures the benefit a data recipient obtains when he received the released data. These two criteria remedy the inadequacy of the deterministic privacy formulation proposed in Proceedings of Asia Pacific Medical Informatics Conference, 2000; Int J Med Inform 2003;71:17-23. Granular computing methodology provides a unified framework for these quantitative measurements and previous bin size and logical approaches. These two new criteria are implemented in a prototype system Cellsecu 2.0. Preliminary system performance evaluation is conducted and reviewed.

Computing Methodologies↗

PubMed1998

A proposed bioactive conformation of peptide T.

The conformational profiles of Peptide T, (5-8)Peptide T, [Abu5](4-8)Peptide T and (4-8)Peptide T were computed independently to assess the geometrical characteristics of the bioactive conformation of Peptide T. The conformational profiles of the peptides were computed within the molecular mechanics framework using an effective dielectric constant of 80. The conformational space was thoroughly sampled using an iterative simulated annealing protocol. The bioactive conformation was assessed by pairwise cross comparisons of each of the unique low energy conformations found for each of the different analogs studied. After a putative bioactive conformation was selected, in order to further validate our hypothesis the conformational profile of the potent compound cyclo(Thr-Thr-Asn-Tyr-Thr-Asp) was computed and the putative bioactive conformation was found. The conformation exhibits a pseudo beta-turn involving the side chain of Thr5 and the carbonyl oxygen of Tyr7 forming a C12 ring.

Amino Acid Sequence↗

PubMed2004

A computational model of auditory selective attention.

The human auditory system is able to separate acoustic mixtures in order to create a perceptual description of each sound source. It has been proposed that this is achieved by an auditory scene analysis (ASA) in which a mixture of sounds is parsed to give a number of perceptual streams, each of which describes a single sound source. It is widely assumed that ASA is a precursor of attentional mechanisms, which select a stream for attentional focus. However, recent studies suggest that attention plays a key role in the formation of auditory streams. Motivated by these findings, this paper presents a conceptual framework for auditory selective attention in which the formation of groups and streams is heavily influenced by conscious and subconscious attention. This framework is implemented as a computational model comprising a network of neural oscillators, which perform stream segregation on the basis of oscillatory correlation. Within the network, attentional interest is modeled as a Gaussian distribution in frequency. This determines the connection weights between oscillators and the attentional process, which is modeled as an attentional leaky integrator (ALI). Acoustic features are held to be the subject of attention if their oscillatory activity coincides temporally with a peak in the ALI activity. The output of the model is an "attentional stream," which encodes the frequency bands in the attentional focus at each epoch. The model successfully simulates a range of psychophysical phenomena.

Action Potentials↗

PubMed2003

BioSPICE: access to the most current computational tools for biologists.

The goal of the BioSPICE program is to create a framework that provides biologists access to the most current computational tools. At the program midpoint, the BioSPICE member community has produced a software system that comprises contributions from approximately 20 participating laboratories integrated under the BioSPICE Dashboard and a methodology for continued software integration. These contributed software modules are the BioSPICE Dashboard, a graphical environment that combines Open Agent Architecture and NetBeans software technologies in a coherent, biologist-friendly user interface. The current Dashboard permits data sources, models, simulation engines, and output displays provided by different investigators and running on different machines to work together across a distributed, heterogeneous network. Among several other features, the Dashboard enables users to create graphical workflows by configuring and connecting available BioSPICE components. Anticipated future enhancements to BioSPICE include a notebook capability that will permit researchers to browse and compile data to support model building, a biological model repository, and tools to support the development, control, and data reduction of wet-lab experiments. In addition to the BioSPICE software products, a project website supports information exchange and community building.

Computational Biology↗

PubMedDate not supplied

A neurocomputational approach to delusions.

Neuronal networks process information in parallel. The cortex can be viewed as a computational surface that creates and maintains dynamic maps of representations of important sensorimotor and higher-level aspects of the environment and the organism. Its functions can be modeled by a particular type of neural network, the self-organizing feature map. Most importantly, representations of information in the cortex and in these maps have been demonstrated to change dynamically according to the salience and frequency of the input. This feature is referred to as neuroplasticity. The fact that general operational characteristics of computational maps in the cortex can be fine-tuned according to specific processing needs is referred to as neuromodulation. Within this framework of cortical maps and their computational models, acute and chronic delusions are discussed in terms of neuromodulation and neuroplasticity. This neurocomputational approach provides new insights into the phenomena in question, is detailed enough to allow empirical testing, and has therapeutic implications.

Brain↗

PubMed1981

A computer model for epidermal cellular interactions.

A model has been constructed of an assembly of mammalian epidermal cells. The model, simulated by computer, has served as a framework by which experiments can be performed "in machina". Relationships between the various parameters considered have been established. Hypotheses referring to the time at which cells leave the basal layer, and to the simultaneous occurrence of folded basal layer and of a significant number of vertical mitosis in some hyperplastic conditions have been implemented and examined.

Animals↗

PubMed2005

Efficient decoding algorithms for generalized hidden Markov model gene finders.

BACKGROUND: The Generalized Hidden Markov Model (GHMM) has proven a useful framework for the task of computational gene prediction in eukaryotic genomes, due to its flexibility and probabilistic underpinnings. As the focus of the gene finding community shifts toward the use of homology information to improve prediction accuracy, extensions to the basic GHMM model are being explored as possible ways to integrate this homology information into the prediction process. Particularly prominent among these extensions are those techniques which call for the simultaneous prediction of genes in two or more genomes at once, thereby increasing significantly the computational cost of prediction and highlighting the importance of speed and memory efficiency in the implementation of the underlying GHMM algorithms. Unfortunately, the task of implementing an efficient GHMM-based gene finder is already a nontrivial one, and it can be expected that this task will only grow more onerous as our models increase in complexity. RESULTS: As a first step toward addressing the implementation challenges of these next-generation systems, we describe in detail two software architectures for GHMM-based gene finders, one comprising the common array-based approach, and the other a highly optimized algorithm which requires significantly less memory while achieving virtually identical speed. We then show how both of these architectures can be accelerated by a factor of two by optimizing their content sensors. We finish with a brief illustration of the impact these optimizations have had on the feasibility of our new homology-based gene finder, TWAIN. CONCLUSIONS: In describing a number of optimizations for GHMM-based gene finders and making available two complete open-source software systems embodying these methods, it is our hope that others will be more enabled to explore promising extensions to the GHMM framework, thereby improving the state-of-the-art in gene prediction techniques.

Algorithms↗

PubMed1993

Virtual trajectory and stiffness ellipse during multijoint arm movement predicted by neural inverse models.

We predict the virtual trajectories and stiffness ellipses during multijoint arm movements by computer simulations. A two-link manipulator with four single-joint muscles and two double-joint muscles is used as a model of the human arm. Physical parameters of the model are derived from several experimental data. Among them, special emphasis is put on low values of the dynamic hand stiffness recently measured during single-joint and multijoint movements. The feedback-error-learning scheme to acquire the inverse dynamics model and the inverse statics model is utilized for this prediction. The virtual trajectories are much more complex than the actual trajectories. This indicates that planning the virtual trajectory is as difficult as solving the inverse dynamics problem for medium and fast movements, and simply falsifies the advocated computational advantage of the virtual trajectory control hypothesis. Thus, we conclude that learning inverse models is essential even in the virtual trajectory control framework. Finally, we propose a new computational model to learn the complicated shape of the virtual trajectories by integrating the virtual trajectory control and the feedback-error-learning scheme.

Arm↗

PubMed2003

A software tool for specifying voxel models for dosimetry estimation.

Many dose estimation problems can be conveniently formulated in terms of finding the energy emitted and absorbed by a set of homogeneous volume elements (voxels) arranged in a rectilinear grid. The solution of these problems requires an accurate model of the source and target geometry to be established, whereupon conventional Monte Carlo simulation of radiation transport can be employed to determine energy deposition. A software application ("MrVoxel") has been developed to assist in the specification of the source and target models. This application includes tools for image segmentation and image registration (2D and 3D, intra- and inter-modality, interactive, and automatic). It employs a plug-in architecture to facilitate customization and future expansion: plug-ins can be written to perform image import and export as well as to implement specialized image processing routines. Using plug-ins, the package can, for example, import DICOM 3.10 files and export input files for a voxel-based Monte Carlo package. Standard dosimetric tools such as the geometric mean method, transmission based attenuation correction, and MIRD-style voxel dose kernel convolution are also implemented as plug-ins. MrVoxel was implemented on a Macintosh computer using a commercial software framework to produce a conventional document-centric application. Hence it includes useful features such as the ability to undo an operation or to save a processed image set at any point. This latter feature enables the production of a processing trail, to allow post-hoc auditing of the analysis process. This paper describes the MrVoxel application and its role in the analysis of a particular dosimetry problem.

Algorithms↗

PubMedDate not supplied

Attitudes of Australian nurses toward the implementation of a clinical information system.

A computerized clinical information system (CIS) used for the majority of patient charting and medical records was installed in six of 15 beds in the intensive care unit (ICU) of a large Australian hospital in November 1993. Staff acceptance was identified as integral to the success of the system. A survey was issued to all nursing staff of the ICU to identify factors that affected attitude toward computers in the critical care environment. Factors resulting in negative attitudes then could be targeted through training and support for users. The factors considered that potentially could influence attitudes were age, nursing experience, intensive care nursing experience, and education. The study showed that nursing experience had a statistically significant effect on motivation to use computers. A strong relation was evident between the concepts of beliefs, attitudes, and motivation. A less apparent association was present between knowledge and the other concepts. Orientation and in-service education programs should provide appropriate and applied information to optimize the motivation, beliefs, and computer literacy of nurses using CIS frameworks.

Adult↗

PubMed2026

Endothelial cell-specific DNA methylation alterations in breast cancer.

DNA methylation alterations are well-established contributors to carcinogenesis, yet, in the tumor microenvironment (TME), patterns of lineage and cell-specific methylation alterations are not well understood. Single-cell DNA methylation profiling in the TME is limited by technical challenges and high costs. Here, we use bulk DNA methylation, cell type deconvolution (HiTIMED), and an interaction testing framework (CellDMC) to identify reproducible, computationally inferred lineage-specific epigenetic alterations in the TME supported by orthogonal data sources. Tumor endothelial cells (TECs), critical regulators of angiogenesis, vascular permeability, and immune cell trafficking, acquire structural and functional abnormalities that promote tumor growth. We hypothesize that TECs have altered DNA methylation compared with endothelial cells in non-tumor tissues. In genome-scale methylation data from discovery and validation datasets (tumor n = 1071; non-tumor n = 415), we identify and validate >4500 TEC-specific CpGs with altered methylation, many mapping to genes involved in angiogenesis and endothelial function. Integration with gene expression data indicates that TEC-specific methylation alterations may reprogram transcriptional networks controlling angiogenesis. High-resolution, cell lineage-specific epigenetic landscapes can be inferred from bulk methylation data, implicating TEC-specific DNA methylation alterations as potential drivers of cancer angiogenesis and vascular dysfunction and providing a framework for future mechanistic and translational studies of the tumor vasculature.

DNA Methylation↗

PubMed2000

Shape analysis of hippocampal surface structure in patients with unilateral mesial temporal sclerosis.

Structural hippocampal magnetic resonance (MR) imaging-based analysis is helpful in the diagnosis and treatment of mesial temporal epileptic seizures. Computational anatomic techniques provide a framework for objective assessment of three-dimensional hippocampal structure. We applied a previously validated technique of deformation-based hippocampal segmentations in 20 subjects with documented unilateral mesial temporal sclerosis (MTS) and temporal lobe epilepsy. Using composite images, we then measured shape differences between the epileptogenic, smaller hippocampus, and contralateral hippocampus. Final shape differences were projected on the contralateral "normal" side. We calculated results for the left MTS group (10 patients) and right MTS group (10 patients) separately. Both groups showed similar regions of maximal inward deformation in the affected hippocampus, which were the medial and lateral aspect of the head, and posterior aspect of the tail. These results suggest that there are specific three-dimensional patterns of volume loss in patients with mesial temporal epilepsy.

Dominance, Cerebral↗