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We have looked at general descriptions and illustrations of several software development tools, such as tools for prototyping, developing DFDs, testing, and maintenance. Many others are available, and new ones are being developed. However, you have at least seen some examples of powerful CASE tools for systems development.
Most image guided Neurosurgery employs adhesively mounted external fiducials for registration of medical images to the surgical workspace. Due to high logistical costs associated with these artificial landmarks, we strive to eliminate the need for these markers. At our institution, we developed a handheld laser stripe triangulation device to capture the surface contours of the patient's head while oriented for surgery. Anatomical surface registration algorithms rely on the assumption that the patient's anatomy bears the same geometry as the 3D model of the patient constructed from the imaging modality employed. During the time interval from which the patient is imaged and placed in the Mayfield head clamp in the operating room, the skin of the head bulges at the pinsite and the skull fixation equipment itself optically interferes with the image capture laser. We have developed software to reject points belonging to objects of known geometry while calculating the registration. During the course of development of the laser scanning unit, we have acquired surface contours of 13 patients and 2 cadavers. Initial analysis revealed that this automated rejection of points improved the registrations in all cases, but the accuracy of the fiducial method was not surpassed. Only points belonging to the offending instrument are removed. Skin bulges caused by the clamps and instruments remain in the data. We anticipate that careful removal of the points in these skin bulges will yield registrations that at least match the accuracy of the fiducial method.
Two economic analyses of immunization programmes, one from Denmark and one from Kenya, are described with emphasis on practical problems in relation to the collection of data. The Danish study was performed by a study group with participation of experts within health economics and epidemiology and a specifically designed computer programme was developed. The Kenyan study was performed by the management unit of the Kenyan immunization programme using standard computer software developed by WHO (EPICost) and without external assistance. Both studies yielded results of significant relevance for the dialogue with the administration and politicians.
A common problem for developers of clinical applications is coping with the diversity of medical language. Medical language as it is used all over the world varies widely, while the referents for these words stay essentially the same. Software developers must reconcile this diversity with the practical necessity of producing applications that are usable in a variety of hospitals, while ensuring that information can be shared between applications. Existing approaches center around coding and classification schemes, but these approaches must be supplemented by a range of sophisticated terminological services in order for the language barriers to be overcome. To address this, the GALEN project is developing an application called the Terminology Server to provide such a range of terminological services (e.g., conceptual and multilingual services). The software is built upon a re-usable core model of medical terminology. This paper reports on the development of a clinical application called the SCUI (Structured Clinical User Interface) which draws on these GALEN technologies and illustrates an innovative approach to the construction of future clinical applications. The SCUI was specifically developed and tested in the context of infectious diseases to satisfy the demands made by the medical intensive care unit on the Geneva Hospital's microbiology laboratory.
OBJECTIVE: To estimate mean level of trans fatty acid intakes using a representative sample of the US population. DESIGN: The study used food intake data from the 1989-1991 Continuing Survey of Food Intakes by Individuals (CSFII) and the trans fatty acid contents of specific foods calculated from a database compiled by the US Department of Agriculture (USDA) to estimate the mean level and deciles of trans fatty acid intake of the representative US population. SUBJECTS/SETTING: Trans fatty acid intakes were estimated for each subject (N = 11,258) in the CSFII data who completed both a 24-hour recall and a 2-day food record. STATISTICAL ANALYSES PERFORMED: Weights developed by USDA for the survey were used for all data analyses. The Technical Assessment Systems (TAS) International Diet Research System (TAS-DIET), software developed by TAS, was used to derive weighted estimates of the mean and percentiles of the intake distribution. PC CARP, software designed by Iowa State University, was used to estimate standard errors. RESULTS: Mean percentage of energy ingested as trans fatty acids was 2.6% and the mean percentage of total fat ingested as trans fatty acids was 7.4%. Across all age and gender groups examined, estimates ranged from 2.6% to 2.8% and 7.1% to 7.9%, respectively. APPLICATIONS/CONCLUSIONS: Dietetics practitioners can use the representative data of this study to help clients achieve desired changes in consumption levels of trans fatty acids.
Computer support for research in biotechnology has developed rapidly and has provided several tools to aid the researcher. This report describes the capabilities of new computer software developed in this laboratory to aid in the documentation and planning of experiments in molecular biology. The program, POLLUX, provides a graphical medium for the entry, edit and manipulation of DNA constructs and a textual format for display and edit of construct descriptive data. Program operation and procedures are designed to mimic the actual laboratory experiments with respect to capability and the order in which they are performed. Flexible control over the content of the computer-generated displays and program facilities is provided by a mouse-driven menu interface. Programmed facilities for mutagenesis, simulated cloning and searching of the database from networked workstations are described.
The combination of volumetric MRI and multivoxel localized MR spectroscopic imaging (MRSI) data provides the potential for quantifying variations in tissue morphology and function. These techniques have numerous applications for the evaluation of neurological diseases. While state-of-the-art whole-body MR scanners are able to acquire both types of data, there have been relatively few reports which have presented clinical applications of the technology. One of the reasons for this has been the need to develop software for reconstruction and reliable interpretation of 3D imaging and spectral data. In this article, we describe the strategy developed for quantitative analysis of combined MRI and MRSI examinations from patients with brain tumors and evaluate the key components of this procedure using both simulations and empirical data from phantoms, normal volunteers, and patients. Important factors are the use of volume or interleaved multislice anatomic images as a reference, the reconstruction and correction of the spectral data for frequency, phase, and baseline distortions and consideration of the characteristics of the coil, RF pulses used for spatial selection, and phase encoding procedures. These studies show that the metabolic parameters most critical for distinguishing tumor from normal and necrotic tissue were relative levels of choline and NAA. Levels of creatine and lactate were found to be variable, both in terms of their spatial distribution within individual lesions and between different patients.
The potential of matrix-assisted laser desorption ionization (MALDI) and MALDI-post-source decay (PSD) time-of-flight mass spectrometry for the characterization of peptides and proteins is discussed. Recent instrumental developments provide for levels of sensitivity and accuracy that make these techniques major analytical tools for proteome analysis. New software developments employing protein database searches have greatly enhanced the fields of application of MALDI-PSD. Peptides and proteins can be easily identified even if only a partial sequence information is determined. Derivatization procedures have been optimized for MALDI-PSD to increase the structural information and to obtain a complete peptide sequence even in critical cases. They are fast, simple and can be performed on target. MALDI-PSD is also a very powerful tool to characterize or elucidate post-translational or chemically induced modifications. In association with database searches, proteins issued from electrophoretic gels can be identified after specific enzymatic cleavages and peptide mapping.
The availability of the genome sequences of human and mouse, human sequence variation data and other large genetic data sets will lead to a revolution in understanding of the human machine and the treatment of its diseases. The success of the international genome sequencing consortiums shows what can be achieved by well coordinated large scale public domain projects and the benefits of data access to all. It is already clear that the availability of this sequence is having a huge impact on research worldwide. Complete genome sequences provide a framework to pull all biological data together such that each piece has the potential to say something about biology as a whole. Biology is too complex for any organisation to have a monopoly of ideas or data, so the collection, analysis and access to this data can be contributed to by research institutes around the world. However, although it is possible for all this data to be accessible to all through the internet, the more organisations provide data or analysis separately, the harder it becomes for anyone to collect and integrate the results. To address these problems of intergration of data, open standards for biological data exchange, such as the 'Distributed Annotation System' (DAS) are being developed and bioinformatics (Dowell et al., 2001) as a whole is now being strongly driven by the open source software (OSS) model for collaborative software development (Hubbard and Birney, 1999). The leading provider of human genome annotation, the Ensembl project (http://www.ensembl.org), is entirely an OSS project and has been widely adopted by academic and commerical organisations alike (Hubbard et al., 2002). Accurate automatic annotation of features such as genes in vertebrate genomes currently relies on supporting evidence in the form of homologies to mRNAs, ESTs or protein. However, it appears that sufficient high quality experimentally curated annotation now exists to be used as a substrate for machine learning algorithms to create effective models of biological signal sequences (Down and Hubbard, 2002). Is there hope for ab initio prediction methods after all?
A multiterminal system --NUMEDICS--has been developed to study the problems of on-line acquisition, processing, and display of scintigraphic data. The hardware-software configuration of NUMEDICS permits simultaneous and independent operation of terminals in the Division of Nuclear Medicine, the Physics Research Laboratory, and the Cyclotron Laboratory of the Massachusetts General Hospital. This paper describes the hardware and software developments in NUMEDICS which have been proven to be of value in clinical and research applications. These features are illustrated by applications to the evaluation of left ventricular performance, three-dimensional imaging, and functional imaging of rCBF.
We describe the development and approach to clinical application of the neurosurgical robot Minerva, including the mechanical structure of the robot and the software developed to perform intracranial neurosurgical operations with accuracy, smoothness, and safety. The first eight operations have been undertaken on patients requiring stereotactic brain biopsy. We describe the ongoing developments, including improved sterilization features, force sensors, nonlinear electrostimulation probe, and implantation of living encapsulated cells, all of which have entered a test phase. The goals are increased safety and capability to perform simple three-dimensional operations. This research should ease the way for new complex operations that are difficult to perform manually today.
The internet, is an informational tool of impressive proportions and capabilities. New software developments puts the use of this informational technology into the hands of all physicians. The use of Internet informational resources allows the intensivist to stay abreast of new developments in critical care medicine, communicate in a matter of seconds with colleagues half a world away, acquire medically related software, access remote database structures, obtain continuing medical education, and in the near future to "see' patients and obtain physiological data in real time. This tutorial will introduce the Internet and it's current tool suite.
A new system for computing brain electrical activity maps on a standard IBM-compatible computer has been developed. The EEG is recorded using a CED1401 intelligent laboratory interface and stored in the computer; colour coded maps are generated using software developed in Turbo PASCAL and displayed on the EGA graphics screen. An acceptable computation time of 1.2 s for a 64 x 64 map displayed as a 128 x 128 pixel image has been achieved by incorporating assembly language routines and a maths coprocessor. The system may be readily upgraded as improved hardware becomes available and further software can be added. In addition to triggering auditory, visual and somatosensory stimulators, it provides the potential for the generation of complex stimuli for cognitive experiments by means of mass RAM and digital-to-analogue converters.
The objective of this study was to evaluate the feasibility and accuracy of a novel surgical computer-aided navigation system for the placement of endosseous implants in patients after ablative tumour surgery. Pre-operative planning was performed by developing a prosthetic concept and modifying the implant position according to surgical requirements after high-resolution computed tomography (HRCT) scans with VISIT, a surgical planning and navigation software developed at the Vienna General Hospital. The pre-operative plan was transferred to the patients intraoperatively using surgical navigation software and optical tracking technology. The patients were HRCT-scanned again to compare the position of the implants with the pre-operative plan on reformatted CT-slices after matching of the pre- and post-operative data sets using the mutual information-technique. A total of 32 implants was evaluated. The mean deviation was 1.1 mm (range: 0-3.5 mm). The mean angular deviation of the implants was 6.4 degrees (range: 0.4 degrees - 17.4 degrees, variance: 13.3 degrees ). The results demonstrate, that adequate accuracy in placing endosseous oral implants can be delivered to patients with most difficult implantologic situations.
Most people involved in medical photography and illustration are aware of the difficulties of efficient archiving and retrieval of picture information. The recent developments in Photo CD now enable cost effective storage of high resolution images. Applications already exist for easy archive management and new software developments make it simple to tailor standard systems for professional people in very specific fields without the necessity of commissioning programmers and system developers with the consequential cost implications.
Gas chromatography/mass spectrometry (GC/MS) is the method of choice for confirming the presence of drugs tentatively identified in urine or serum by thin-layer chromatography, gas chromatography, or immunoassay. One of the most widely used GC/MS systems is the Hewlett-Packard (HP) Model 5970 mass selective detector equipped with a work station programmed in Pascal. Searching of mass spectra after a GC/MS run must be done manually, and this can take hours, especially when there are many peaks in a chromatogram to check. I have developed software that allows the unattended searching of all peaks in a run, using a forward search algorithm with a custom-made drug library developed over a period of 5 years, and a reverse search with a 1600+ drug library from HP or another in-house drug library. Using these libraries with the two algorithms maximizes the chances of finding a drug peak and identifying it correctly. Individual searches take about 5 seconds each. Overall search time of nearly 200 mass spectra per run takes about 40 minutes, including printing time. This software has proven to be both labor saving and effective in positively identifying drugs.
One of the nation's largest academic medical centers is benchmarking its operations using internally developed software to improve privacy/confidentiality of protected health information (PHI) and to enhance data security to comply with HIPAA regulations. It is also coordinating the development of a web-based interactive product that can help hospitals, physician practices, and managed care organizations measure their compliance with HIPAA regulations.
Advances in computational, and imaging techniques have enabled the rapid development of three-dimensional (3-D) models of biological systems in unprecedented detail. Using these advances, 3-D models of the lungs and nasal passages of the rat and human are being developed to ultimately improve predictions of airborne pollutant dosimetry. Techniques for imaging the respiratory tract by magnetic resonance imaging (MRI) were developed to improve the speed and accuracy of geometric data collection for mesh reconstruction. The MRI resolution is comparable to that obtained by manual measurements but at much greater speed and accuracy. Newly developed software (NWGrid) was utilized to translate imaging data from MR into 3-D mesh structures. Together, these approaches significantly reduced the time to develop a 3-D model. This more robust airway structure will ultimately facilitate modeling gas or vapor exchange between the respiratory tract and vasculature as well as enable linkages of dosimetry with cell response models. The 3-D, finite volume, viscoelastic mesh structures form the geometric basis for computational fluid dynamics modeling of inhalation, exhalation and the delivery of individual particles (or concentrations of gas or vapors) to discrete regions of the respiratory tract. The ability of these 3-D models to resolve dosimetry at such a high level of detail will require new techniques to measure regional airflows and particulate deposition for model validation.