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PubMed2003

A review of current knowledge on Electronic Vision Enhancement Systems for the visually impaired.

Magnification can be provided to assist those with visual impairment to make the best use of remaining vision. Electronic transverse magnification of an object was first conceived for use in low vision in the late 1950s, but has developed slowly and is not extensively prescribed because of its relatively high cost and lack of portability. Electronic devices providing transverse magnification have been termed closed-circuit television (CCTVs) because of the direct cable link between the camera imaging system and monitor viewing system, but this description generally refers to surveillance devices and does not indicate the provision of features such as magnification and contrast enhancement. Therefore, the term Electronic Vision Enhancement Systems (EVES) is proposed to better distinguish and describe such devices. This paper reviews current knowledge on EVES for the visually impaired in terms of: classification; hardware and software (development of technology, magnification and field-of-view, contrast and image enhancement); user aspects (users and usage, reading speed and duration, and training); and potential future development of EVES.

Persons with Disabilities↗

PubMedDate not supplied

Protocols for clinical care.

This paper describes the work of the DILEMMA project to provide protocol-based decision support in a variety of clinical domains. We give an outline of the generic protocol model that DILEMMA has produced, and the protocol task manager (PTM) software developed to assist protocol use in routine clinical practice. We summarise the validation of the model carried out to date, and take a quick look at the place of protocols in the wider context of clinical decision support.

Clinical Protocols↗

PubMed2006

dictyBase, the model organism database for Dictyostelium discoideum.

dictyBase (http://dictybase.org) is the model organism database (MOD) for the social amoeba Dictyostelium discoideum. The unique biology and phylogenetic position of Dictyostelium offer a great opportunity to gain knowledge of processes not characterized in other organisms. The recent completion of the 34 MB genome sequence, together with the sizable scientific literature using Dictyostelium as a research organism, provided the necessary tools to create a well-annotated genome. dictyBase has leveraged software developed by the Saccharomyces Genome Database and the Generic Model Organism Database project. This has reduced the time required to develop a full-featured MOD and greatly facilitated our ability to focus on annotation and providing new functionality. We hope that manual curation of the Dictyostelium genome will facilitate the annotation of other genomes.

Animals↗

PubMed1993

GenBank.

The GenBank sequence database has undergone an expansion in data coverage, annotation content and the development of new services for the scientific community. In addition to nucleotide sequences, data from the major protein sequence and structural databases, and from U.S. and European patents is now included in an integrated system. MEDLINE abstracts from published articles describing the sequences provide an important new source of biological annotation for sequence entries. In addition to the continued support of existing services, new CD-ROM and network-based systems have been implemented for literature retrieval and sequence similarity searching. Major releases of GenBank are now more frequent and the data are distributed in several new forms for both end users and software developers.

Amino Acid Sequence↗

PubMed2002

Promise and challenge of high-performance computing, with examples from molecular modelling.

Computational modelling is one of the most significant developments in the practice of scientific inquiry in the 20th century. During the past decade, advances in computing technologies have increased the speed of computers by a factor of 100; an increase of a factor of 1000 can be expected in the next decade. These advances have, however, come at a price, namely, radical change(s) in computer architecture. Will computational scientists and engineers be able to harness the power offered by these high-performance computers to solve the most critical problems in science and engineering? In this paper, we discuss the challenges that must be addressed if we are to realize the benefits offered by high-performance computing. The task will not be easy; it will require revision or replacement of much of the software developed for vector supercomputers as well as advances in a number of key theoretical areas. Because of the pace of computing advances, these challenges must be met by close collaboration between computational scientists, computer scientists and applied mathematicians. The effectiveness of such a multidisciplinary approach is illustrated in a brief review of NWCHEM, a general-purpose computational chemistry code designed for parallel supercomputers.

Algorithms↗

PubMed2006

The wildcat toolbox: a set of perl script utilities for use in peptide mass spectral database searching and proteomics experiments.

We describe in this communication a set of functional perl script utilities for use in peptide mass spectral database searching and proteomics experiments, known as the Wildcat Toolbox. These are all freely available for download from our laboratory Web site (http://proteomics.arizona.edu/toolbox.html) as a combined zip file, and can also be accessed via the Proteome Commons Web site (www.proteomecommons.org) in the tools section. We make them available to other potential users in the spirit of open source software development; we do not have the resources to provide any significant technical support for them, but we hope users will share both bugs and improvements with the community at large.

Algorithms↗

PubMed1998

Web-based resources for clinical protocol management.

The data monitoring regulatory procedures, and administrative tasks associated with protocol management have become increasingly complex. Relational database technology and Internet-based connectivity offer resources to improve the quality and efficiency of protocol operations. At Fox Chase Cancer Center, we have developed a suite of database applications for protocol management and tracking of patient accrual. All data transactions and reporting occur through a graphical web browser interface using standard Internet technology. Security and confidentiality have been addressed through encryption, user authentication, address restriction, and database authority. Database management has been tightly integrated with protocol operations to avoid duplication of resources and effort. Data query functions also extend to other institutional resources, such as tumor registry and the hospital clinical laboratory, to further reduce the need for redundant data storage. Newer components, such as chemotherapy orders and toxicity reporting, have been incorporated in a modular fashion. Although custom software development can be expensive and time-consuming, it offers the best opportunity for successful integration with existing resources, staff, and procedures, as well as collaboration with other institutions.

Clinical Protocols↗

PubMed2002

New computational approaches for analysis of cis-regulatory networks.

The investigation and modeling of gene regulatory networks requires computational tools specific to the task. We present several locally developed software tools that have been used in support of our ongoing research into the embryogenesis of the sea urchin. These tools are especially well suited to iterative refinement of models through experimental and computational investigation. They include: BioArray, a macroarray spot processing program; SUGAR, a system to display and correlate large-BAC sequence analyses; SeqComp and FamilyRelations, programs for comparative sequence analysis; and NetBuilder, an environment for creating and analyzing models of gene networks. We also present an overview of the process used to build our model of the Strongylocentrotus purpuratus endomesoderm gene network. Several of the tools discussed in this paper are still in active development and some are available as open source.

Chromosomes, Artificial, Bacterial↗

PubMed2006

Benchmarking a memetic algorithm for ordering microarray data.

This work introduces a new algorithm for "gene ordering". Given a matrix of gene expression data values, the task is to find a permutation of the gene names list such that genes with similar expression patterns should be relatively close in the permutation. The algorithm is based on a combined approach that integrates a constructive heuristic with evolutionary and Tabu Search techniques in a single methodology. To evaluate the benefits of this method, we compared our results with the current outputs provided by several widely used algorithms in functional genomics. We also compared the results with our own hierarchical clustering method when used in isolation. We show that the use of images, corrupted with known levels of noise, helps to illustrate some aspects of the performance of the algorithms and provide a complementary benchmark for the analysis. The use of these images, with known high-quality solutions, facilitates in some cases the assessment of the methods and helps the software development, validation and reproducibility of results. We also propose two quantitative measures of performance for gene ordering. Using these measures, we make a comparison with probably the most used algorithm (due to Eisen and collaborators, PNAS 1998) using a microarray dataset available on the public domain (the complete yeast cell cycle dataset).

Algorithms↗

PubMed1994

Quantification of cholesterol in all lipoprotein classes by the VAP-II method.

We have developed a high resolution microvolume Vertical Auto Profile (VAP) method for the simultaneous measurement of cholesterol in all lipoprotein classes, including lipoprotein[a] (Lp[a]) and intermediate density lipoprotein (IDL). This method, designated as VAP-II, uses a non-segmented continuous flow (controlled-dispersion flow) analyzer for the enzymatic analysis of cholesterol in lipoprotein classes separated by a short spin (47 min) single vertical ultracentrifugation. Cholesterol concentrations of high (HDL), low (LDL), very low (VLDL), and intermediate (IDL) density lipoproteins, as well as Lp[a], are determined by decomposing the spectrophotometric absorbance curve, obtained from the continuous analysis of the centrifuged sample, into its components using software developed in this laboratory. Analysis by VAP-II is rapid and sensitive (as little as 40 microliters plasma is required per assay). The resolution of lipoprotein peaks is considerably enhanced in the present analyzer compared to the previous analyzer (VAP-I, which used the Technicon AutoAnalyzer); improvement is especially noticeable for Lp[a] and IDL. Total and lipoprotein cholesterol values obtained by VAP-II correlated well with the values obtained by Northwest Lipid Research Laboratories (NWLRL). VAP-II Lp[a] cholesterol values also correlated well with the Lp[a] mass values obtained by an immunoassay technique performed at NWLRL (r = 0.907). The reproducibility and accuracy of the method are within the requirements of the CDC-NHLBI (Centers for Disease Control-National Heart, Lung, and Blood Institute) Lipid Standardization Program.

Blood Chemical Analysis↗

PubMed2006

Lineage-specific expansion of proteins exported to erythrocytes in malaria parasites.

BACKGROUND: The apicomplexan parasite Plasmodium falciparum causes the most severe form of malaria in humans. After invasion into erythrocytes, asexual parasite stages drastically alter their host cell and export remodeling and virulence proteins. Previously, we have reported identification and functional analysis of a short motif necessary for export of proteins out of the parasite and into the red blood cell. RESULTS: We have developed software for the prediction of exported proteins in the genus Plasmodium, and identified exported proteins conserved between malaria parasites infecting rodents and the two major causes of human malaria, P. falciparum and P. vivax. This conserved 'exportome' is confined to a few subtelomeric chromosomal regions in P. falciparum and the synteny of these and surrounding regions is conserved in P. vivax. We have identified a novel gene family PHIST (for Plasmodium helical interspersed subtelomeric family) that shares a unique domain with 72 paralogs in P. falciparum and 39 in P. vivax; however, there is only one member in each of the three species studied from the P. berghei lineage. CONCLUSION: These data suggest radiation of genes encoding remodeling and virulence factors from a small number of loci in a common Plasmodium ancestor, and imply a closer phylogenetic relationship between the P. vivax and P. falciparum lineages than previously believed. The presence of a conserved 'exportome' in the genus Plasmodium has important implications for our understanding of both common mechanisms and species-specific differences in host-parasite interactions, and may be crucial in developing novel antimalarial drugs to this infectious disease.

Amino Acid Sequence↗

PubMed1995

Reengineering materiel management using computer technology.

The Materiel Management Department in today's hospital is in a uniquely advantageous position. It can better support the hospital's mission by applying current techniques in material management systems automation together with current computing technology as part of a broad-based reengineering process. Materiel management executives, suppliers, software developers, and hardware manufacturers now have all the necessary tools to create and implement a flexible, cost-effective, complete, paperless system. The model system offers tremendous advantages in terms of increased productivity and reduced total cost. This article discusses the process and the tools and techniques that should be considered.

Hospital Restructuring↗

PubMed1998

Reproducibility of polar map generation and assessment of defect severity and extent assessment in myocardial perfusion imaging using positron emission tomography.

The purpose of this study was to determine the reliability of new software developed for the analysis of cardiac tomographic data. The algorithm delineates the long axis and defines the basal plane and subsequently generates polar maps to quantitatively and reproducibly assess the size and severity of perfusion defects. The developed technique requires an initial manual estimate of the left ventricular long axis and calculates the volumetric maximum myocardial activity distribution. This surface is used to map three-dimensional tracer accumulation onto a two-dimensional representation (polar map), which is the basis for further processing. The spatial information is used to compute geometrical and mechanical properties of a solid model of the left ventricle including the left heart chamber. A new estimate of the axis is determined from this model, and the previously outlined procedure is repeated together with an automated definition of the valve plane until differences between the polar maps can be neglected. This quantitative analysis software was validated in phantom studies with defects of known masses and in ten data sets from normals and patients with coronary artery disease of various severity. We investigated the reproducibility of the maps with the introduction of a similarity criterion where the ratio of two corresponding polar map elements lies within a 10% interval. The maps were also used to measure intra-and interobserver variability in respect of defect size and severity. In the phantom studies, it was possible to reliably assess mass information over a wide range of defects from 5 to 60 g (slope: 1.02, offset -0.68, r = 0.972). Patient studies revealed a statistically significant increase in the reproducibility of the automatic technique compared with the manual approach: 54%+/-19% (manual) compared with 88%+/-9% (automatic) for observer 1 and 61%+/-20% vs 82%+/-5% for observer 2, respectively. The intervariability analysis showed a significant improvement from 59%+/-14% to 83%+/-7% in similar polar map elements and a significantly improved correlation in the calculation of severity (from r = 0.908 to 0.989) and extent (from r = 0.963 to r = 0.992) of the perfusion defects when the automated procedure was applied. It is concluded that, assuming a constant wall thickness and tissue density, absolute defect mass can be reliably estimated. Furthermore, the proposed software demonstrates a significant improvement in the generation of volumetric polar maps for the quantitative assessment of perfusion defects.

Algorithms↗

PubMed2004

[Fully automatic detection and quantification of emphysema on thin section MD-CT of the chest by a new and dedicated software].

PURPOSE: Introduction of a novel software tool (YACTA -- yet another CT analyzer) for detection and quantification of pulmonary emphysema in thin-slice chest MDCT data sets. MATERIALS AND METHODS: Consisting of grey-level threshold-based algorithms (e. g., region-growing), expert rules and morphological image postprocessing YACTA segments the tracheobronchial tree prior to the detection and quantification of pulmonary emphysema. In addition to general parameters, such as the mean lung density (MLD) and the emphysema index (EI -- also described as pixel index PI), the previously described bullae index (BI) is transformed into a three-dimensional parameter for a morphological description of emphysema. A first evaluation of chest MDCT data sets of 11 patients was performed as well as a comparison of MLD, lung volume (LV), emphysema volume (EV) and PI calculated with two established commercial tools of Siemens Medical Solutions (Volume and Pulmo). Furthermore, the BI was calculated with YACTA. RESULTS: YACTA processed the image data without manual interaction and demonstrated more user-comfort than Volume and Pulmo software, which require manual correction especially for lung segmentation at the hilar regions to separate central airways from lung parenchyma. MLD, LV, and EV values calculated with YACTA were systematically higher (Pulmo: + 50 HU/+ 597 ml/+ 159 ml; Volume: + 32 HU/+ 110 ml/+ 155 ml). Different segmentation algorithms are responsible for this: YACTA includes areas not assessed by mere threshold-based techniques. Constantly lowered LV values of Pulmo are caused by a missing dilatation algorithm. The error correction as a special feature of YACTA results in increased emphysema volumes and indices. The segmentation of the tracheobronchial tree lowers the part of airways falsely classified as emphysema. CONCLUSION: The new developed software shows higher user comfort as established by semi-automated tools. RESULTS: of LV, EV, MLD and PI are comparable or moderately different. Automatic calculation of a BI is possible, providing information about bullous morphology of pulmonary emphysema. Further studies are necessary to correlate data with clinical or pathological parameters.

Adult↗

PubMed2005

A new three-dimensional automatic bodymarker system for transvaginal ultrasonography.

OBJECTIVE: To evaluate the accuracy and usefulness of a newly developed three-dimensional automatic bodymarker system for transvaginal ultrasonography. METHODS: A bodymarker system which utilizes an electromagnetic field to specify the probe position was developed. Software was written which enabled the positional information of the probe and the ultrasound image to be simultaneously displayed on a personal computer. The bodymarker was displayed as a three-dimensional graphic model. The differences between the estimated and the actual position--i.e. the error--for both position (x, y and z) and angles (azimuth, elevation and roll) of the probe were measured. The movement of the probe was then evaluated in healthy female volunteers and the comparative time required for ultrasound examination was determined. RESULTS: Both the position and the angles of the probe were accurately shown in the computer display. The errors were 1.0 mm and 0.7 degrees (median) for position and angle, respectively. The system was also shown to work well in healthy female volunteers. Calibration of the new system required only 5.0 seconds, compared with an average of 7.6 seconds for the conventional bodymarker. CONCLUSION: The newly developed three-dimensional automatic transvaginal bodymarker system provides an accurate indication of probe position and its tilting angle. It works well in healthy female volunteers and speeds up the examination time. It may be clinically useful for transvaginal ultrasound examination.

Calibration↗

PubMed2005

An online operational rainfall-monitoring resource for epidemic malaria early warning systems in Africa.

Periodic epidemics of malaria are a major public health problem for many sub-Saharan African countries. Populations in epidemic prone areas have a poorly developed immunity to malaria and the disease remains life threatening to all age groups. The impact of epidemics could be minimized by prediction and improved prevention through timely vector control and deployment of appropriate drugs. Malaria Early Warning Systems are advocated as a means of improving the opportunity for preparedness and timely response. Rainfall is one of the major factors triggering epidemics in warm semi-arid and desert-fringe areas. Explosive epidemics often occur in these regions after excessive rains and, where these follow periods of drought and poor food security, can be especially severe. Consequently, rainfall monitoring forms one of the essential elements for the development of integrated Malaria Early Warning Systems for sub-Saharan Africa, as outlined by the World Health Organization. The Roll Back Malaria Technical Resource Network on Prevention and Control of Epidemics recommended that a simple indicator of changes in epidemic risk in regions of marginal transmission, consisting primarily of rainfall anomaly maps, could provide immediate benefit to early warning efforts. In response to these recommendations, the Famine Early Warning Systems Network produced maps that combine information about dekadal rainfall anomalies, and epidemic malaria risk, available via their Africa Data Dissemination Service. These maps were later made available in a format that is directly compatible with HealthMapper, the mapping and surveillance software developed by the WHO's Communicable Disease Surveillance and Response Department. A new monitoring interface has recently been developed at the International Research Institute for Climate Prediction (IRI) that enables the user to gain a more contextual perspective of the current rainfall estimates by comparing them to previous seasons and climatological averages. These resources are available at no cost to the user and are updated on a routine basis.

Africa↗

PubMed1991

The benefits of the application of geographical information systems in public and environmental health.

One of the most important issues in public and environmental health today concerns the type of instruments that can be used to devise quick, reliable and scientifically valid methods of rapid assessment which, in turn, can be utilized in health research and in the planning, monitoring and evaluation of health programmes. As the applications of geographical information systems (GIS) relate to the collection, storage, integration, management, retrieval, analysis and display of spatial data, it is not surprising that the potential usefulness of this new technology in the fields of health research and policy is beginning to be realized. This article seeks to demonstrate the opportunities which the use of geographical information systems can offer to research and policy on health issues. The article first describes the principles and objectives of GIS before going on to discuss hardware and software developments as well as the variety of application fields, organizations and users. Some examples of current applications are provided to illustrate the type of work being undertaken. The final sections address issues specifically related to the application of GIS in health research and policies in the European context.

Computers↗

PubMed2003

Using a personal digital assistant enhances gathering of patient data on an acute pain management service: a pilot study.

PURPOSE: Handheld computer technology provides a unique opportunity for health care professionals to access real time or near real time patient information and evidence-based resources at the point-of-care. The purpose of this study was to assess one physician's experience using acute pain assessment software on a personal digital assistant (PDA) to assess patients on an acute pain management service (APMS). METHODS: Using a historical control and a "time and motion" study design, comparisons were made on acute pain assessment time and comprehensiveness when patient assessments are documented on a PDA vs the current paper-based method. RESULTS: The study physician (a PDA-user) reported feeling comfortable with the assessment software after five patient assessments. PDA assessments were more likely to contain documentation regarding pain and side effects (e.g., nausea, pruritus, hypotension) than the paper assessments. The median time of the "assessment only" component of the patient encounter was 53 sec longer using the PDA compared to paper (P < 0.00), however, the median "total encounter" (chart review, assessment, documentation) time was 74 sec shorter using the PDA vs paper (P < 0.00). DISCUSSION: The findings of this preliminary study suggest that the PDA is a reliable tool that meets the data management requirements within an APMS setting. This study found that patient assessments documented using acute pain software developed for use on a PDA were as efficient and content-rich as paper assessments. The PDA may even enhance the efficiency of the patient assessment process through the provision of more comprehensive digital data for research, clinical, and administrative needs.

Computers, Handheld↗