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PubMed1992

Validation of computerized three-dimensional reconstruction of intravascular ultrasound: measurements of absolute luminal diameter and cross-sectional area in ex vivo human coronary arteries.

UNLABELLED: Computer based 3-dimensional reconstruction transforms 2-dimensional intravascular ultrasound images into a longitudinal format facilitating analysis of luminal narrowing. To validate the accuracy of current software in measuring coronary artery diameter and cross-sectional area, in arteries with atherosclerosis, we performed 3-dimensional reconstruction in 10 human pathologic coronary arterial segments of 10-25mm length. Images were obtained using a 4.8 French catheter with pullback speed of 1mm/sec acquired at 3 frames/sec onto VHS tape. The data were digitized and intraluminal 3-dimensional reconstruction performed using a voxel-based program. Pathologic sections were obtained every 3mm, and dimensions were measured with a resolution of 0.01 mm. Maximum, minimum, and 3 other representative diameters were recorded by an observer blinded to the ultrasound diameters. Average histo-pathologic diameters were reported, and specimen cross-sectional area was then calculated. RESULTS: In 53 sections, pathological diameters ranged from 1.4-4.5mm (mean 2.7 +/- 0.68mm) while 3-dimensional reconstructed diameters were 1.9 to 3.8mm (mean 2.6 +/- 0.54mm). Pathologic and ultrasound derived 3-dimensional reconstruction diameters had an excellent correlation (r=0.86, SEE=+/-0.36). Pathology and 3-dimensional reconstruction cross-sectional area also correlated closely (r=0.88, SEE=+/-1.50). Diameters less than 2.0mm were systematically overestimated and diameters greater than 3.5mm underestimated by 3-dimensional reconstruction. Most 3 dimensional reconstruction values were within +/- 10% of pathology, but diverged at each diameter extreme, approaching +/- 20%. Thus, computerized 3-dimensional reconstruction of ultrasound images shows excellent quantification of luminal size in the 2.0-3.5mm range, suggesting important investigative and clinical applications.

Arteries↗

PubMed2003

Performance evaluation of two multiplexes used in fluorescent short tandem repeat DNA analysis.

The performance of two commercial multiplex kits that together amplify the 13 core short tandem repeat (STR) loci currently in use by forensic laboratories and the U.S. national Combined DNA Indexing System (CODIS) were evaluated. The typing systems examined were AmpFlSTR Profiler Plus and AmpFlSTR COfiler (PE Applied Biosystems, Foster City, CA). Electrophoretic separation and detection of the fluorescent PCR products was achieved by capillary electrophoresis (CE) using an ABI Prism 310 Genetic Analyzer. The studies addressed the on-site validation of the instrument, the software, and each typing system. These studies included instrument sensitivity, resolution, precision, binning, peak height ratios, mixtures, stutter, and the amplification of non-probative and simulated forensic samples. Other additional developmental-type work is also reported herein, such as species specificity testing and amplification of environmentally insulted samples. Amplification conditions were found to be robust and the primer sets shown to be specific to human DNA. Stutter and peak height ratios fell within limits published by the manufacturer and other laboratories. The data demonstrate that the CE instrument can consistently resolve fragments differing in length by one base and that the +/-0.5 base bin used by the Genotyper software is acceptable for making accurate allele calls. Correct typing results were obtained from non-probative and simulated case samples, as well as samples exposed to outdoor environmental conditions. The results support the conclusion that DNA extracted from biological samples routinely encountered in the forensic laboratory can be reliably analyzed with AmpFlSTR Profiler Plus and COfiler using CE.

Alleles↗

PubMed2006

Telemicrobiology: a novel telemedical module for mission support in the field of infectious medicine.

Infectious diseases are among the most common diseases suffered by soldiers while serving in missions away from their home countries. The diagnosis of theses diseases requires special procedures and expertise, both of which are provided by field microbiological laboratories. In order to support the diagnostic process by means of telemedicine, a modification of the standard telemedicine workstation, i.e. a telemicrobiology module with special equipment, camera and software, has been designed and validated. This module, currently in use in two operational theaters, has stood the test in routine practice. It enables the transmission of high-quality static images of microscopic specimens or overgrown nutrient media in a matter of seconds. The inclusion of experts into diagnostic analysis through the use of telemedicine improves diagnostic specificity by avoiding false positive results and, particularly in medical parasitology, allows a treatment-essential diagnosis without the dispatch of specimens to Germany. Telemicrobiology allows the control of the entire microbiology diagnostic process by expert workstation even with only a microbiological technician on site.

Communicable Diseases↗

PubMed1993

[Transmission of neurosurgical medical records through computers. Simple reality, considerable progress].

Tests on the transmission of view data processing images were undertaken for 5 months from two experimental micro-processing sites specialized in medical imagery and linked to the R.N.I.S. network. The aim of the research was to validate the equipment and the software, and to find a way of working with regard problems related to long-distance diagnosis. Using an everyday equipment like Apple Macintosh II fx, 75 files were transferred corresponding in 375 images (1% conventional X-ray, 5% digital angiography, 31% scanner and 63% M.R.I.). It has been found that the transfer of medical data is reliable (the images do not deteriorate), easy (less than 3 hours to be familiar with the program) and above all fast (actual transfer time: 8.72 Ko per second). Neurosurgeon and neuroradiologist writers talk about their experience in this field.

Computer Communication Networks↗

PubMed2004

Brief report: validation of a system for automated measurement of knee laxity.

OBJECTIVE: To determine the accuracy and repeatability of an automated quantitative fluoroscopic imaging system for measuring knee laxity. DESIGN: Cadaveric validation study. BACKGROUND: Current methods of measuring anterior-posterior laxity lack sufficient accuracy and repeatability. A commercially developed fluoroscopic software package, capable of measuring laxity, required validation. METHODS: Five human cadaveric knees were used. A constant force of 130 N was applied anteriorly and posteriorly in turn to the tibia of each knee with the femur fixed in 30 degrees and 90 degrees of flexion. Quantitative fluoroscopic measurements of anterior-posterior laxity were determined using image analysis software. Fluoroscopic results were compared to the true anterior-posterior displacements of the tibia, which were simultaneously recorded using linear transducers directly attached to the cadaveric specimens. RESULTS: The quantitative fluoroscopic method underestimated laxity by an average of 0.40 mm with a root mean square error of 0.49 mm. The 95% confidence intervals for anterior and posterior laxity error were calculated to be -0.99 to 0.25 mm and -0.89 to 0.03 mm, respectively, where a negative error represents an underestimation. CONCLUSIONS: The quantitative fluoroscopic method offers a dramatic improvement in accuracy over current laxity measurement techniques and acceptable repeatability for assessing ligament damage. RELEVANCE: The considerably more accurate, validated measurement system of this study could improve ligament assessment and diagnosis, and the recognition of injuries otherwise undetected with current methods.

Fluoroscopy↗

PubMed2003

Automated quality checks on repeat prescribing.

BACKGROUND: Good clinical practice in primary care includes periodic review of repeat prescriptions. Markers of prescriptions that may need review have been described, but manually checking all repeat prescriptions against the markers would be impractical. AIM: To investigate the feasibility of computerising the application of repeat prescribing quality checks to electronic patient records in United Kingdom (UK) primary care. DESIGN OF STUDY: Software performance test against benchmark manual analysis of cross-sectional convenience sample of prescribing documentation. SETTING: Three general practices in Greater Manchester, in the north west of England, during a 4-month period in 2001. METHOD: A machine-readable drug information resource, based on the British National Formulary (BNF) as the 'gold standard' for valid drug indications, was installed in three practices. Software raised alerts for each repeat prescribed item where the electronic patient record contained no valid indication for the medication. Alerts raised by the software in two practices were analysed manually. Clinical reaction to the software was assessed by semi-structured interviews in three practices. RESULTS: There was no valid indication in the electronic medical records for 14.8% of repeat prescribed items. Sixty-two per cent of all alerts generated were incorrect. Forty-three per cent of all incorrect alerts were as a result of errors in the drug information resource, 44% to locally idiosyncratic clinical coding, 8% to the use of the BNF without adaptation as a gold standard, and 5% to the inability of the system to infer diagnoses that, although unrecorded, would be 'obvious' to a clinical reading the record. The interviewed clinicians supported the goals of the software. CONCLUSION: Using electronic records for secondary decision support purposes will benefit from (and may require) both more consistent electronic clinical data collection across multiple sites, and reconciling clinicians' willingness to infer unstated but 'obvious' diagnoses with the machine's inability to do the same.

Clinical Pharmacy Information Systems↗

PubMed2005

Validation of a high-throughput absorption, distribution, metabolism, and excretion (ADME) system and results for 60 literature compounds.

A high-throughput analytical system for the support of absorption, distribution, metabolism, and excretion (ADME) was constructed in collaboration with Gubbs Inc. to commercialize corresponding software. We sought to quickly build and validate this system for microsomal clearance assessment using 60 commercially available non-proprietary compounds that are non-DEA-restricted in addition to 36 proprietary Millennium compounds that had already been assessed using a low-throughput infrastructure. The system was constructed such that a approximately 45 second total cycle time was achieved injection-to-injection. Software was successfully coded to enable the analyst to submit multiple batches, and modify multiple methods very quickly for use with Applied Biosystems Analyst 1.3. After acquisition the software was used to simultaneously integrate multiple injection chromatograms, regress the data, and calculate clearance such that all of the data could be easily and immediately reviewed by both bioanalytical and enzymology personnel. Unfortunately, despite an exhaustive search of the literature, we were unable to find a large number of non-proprietary compound data for validation, so we provide such a source of data here. Results are presented for the 60 literature compounds that were assessed. A good correlation was observed between literature results for 16 compounds that we were able to find and the results obtained using the system. The Millennium proprietary compounds that we assessed using both low- and high-throughput approaches also correlated well. We present here a system for the support of high-throughput in vitro ADME analysis and also present the results of 60 non-proprietary, non-DEA-scheduled compounds to facilitate the validation efforts of others. Finally, we present commercially available software to facilitate high-throughput ADME systems in the community.

Absorption↗

PubMed2006

GO-Diff: mining functional differentiation between EST-based transcriptomes.

BACKGROUND: Large-scale sequencing efforts produced millions of Expressed Sequence Tags (ESTs) collectively representing differentiated biochemical and functional states. Analysis of these EST libraries reveals differential gene expressions, and therefore EST data sets constitute valuable resources for comparative transcriptomics. To translate differentially expressed genes into a better understanding of the underlying biological phenomena, existing microarray analysis approaches usually involve the integration of gene expression with Gene Ontology (GO) databases to derive comparable functional profiles. However, methods are not available yet to process EST-derived transcription maps to enable GO-based global functional profiling for comparative transcriptomics in a high throughput manner. RESULTS: Here we present GO-Diff, a GO-based functional profiling approach towards high throughput EST-based gene expression analysis and comparative transcriptomics. Utilizing holistic gene expression information, the software converts EST frequencies into EST Coverage Ratios of GO Terms. The ratios are then tested for statistical significances to uncover differentially represented GO terms between the compared transcriptomes, and functional differences are thus inferred. We demonstrated the validity and the utility of this software by identifying differentially represented GO terms in three application cases: intra-species comparison; meta-analysis to test a specific hypothesis; inter-species comparison. GO-Diff findings were consistent with previous knowledge and provided new clues for further discoveries. A comprehensive test on the GO-Diff results using series of comparisons between EST libraries of human and mouse tissues showed acceptable levels of consistency: 61% for human-human; 69% for mouse-mouse; 47% for human-mouse. CONCLUSION: GO-Diff is the first software integrating EST profiles with GO knowledge databases to mine functional differentiation between biological systems, e.g. tissues of the same species or the same tissue cross species. With rapid accumulation of EST resources in the public domain and expanding sequencing effort in individual laboratories, GO-Diff is useful as a screening tool before undertaking serious expression studies.

Animals↗

PubMed1999

MABDOSE. II: Validation of a general purpose dose estimation code.

UNLABELLED: The MABDOSE software represents a general tool to assess internal radiation dose. A suite of tests are described that validate the dosimetry system's implementation. METHODS: The validation suite is divided among tests that verify target digitalization, tumor digitalization and organ replacement, cumulated activity calculation, random number generation, radiation transport, and dose calculation. RESULTS: A comparison between Reference Man organ volumes and MABDOSE organ volumes at (5 mm)3 resolution demonstrates volume correspondence within 10% save for ten organs having dimensions smaller than the target lattice resolution. An accounting of normal organ volume replaced by an arbitrary tumor volume indicates mass is conserved. A comparison between cumulated activities generated by MABDOSE and solutions obtained analytically demonstrates exact correspondence for curve-fitting algorithms. For mathematical modeling algorithms, cumulated activity solutions converge to their correct values provided sufficient data of high precision are input, accompanied by reasonable initial estimates of rate constants. A comparison of MABDOSE results with the MIRD 3 report demonstrates good agreement (<8% difference) in absorbed fractions for spheres at energies from 20 keV to 2.75 MeV. A comparison of MABDOSE results with the Cristy-Eckerman report demonstrates marginal agreement (specific absorbed fractions within a factor of 2 for all Reference Man organs) at simulation energies of 20, 50, and 100 keV. Lack of exact correspondence is attributed to volume digitalization errors, and to differences in cross-section libraries, interpolation schemes between cross-section data points, and random number generators. Finally, the doses reported by MABDOSE correspond to the correct algebraic combination of paired cumulated activities and "S" values. CONCLUSIONS: The MABDOSE program has been validated as a general purpose computation tool for use in internal radionuclide dosimetry.

Humans↗

PubMed2004

A graphical user interface for automatic image registration software designed for radiotherapy treatment planning.

Medical imaging forms a vital component of radiotherapy treatment planning and its evaluation. The integration of the useful data obtained from multiple imaging modalities for radiotherapy planning is achieved by image registration softwares. In radiotherapy planning systems, normally the computed tomography (CT) slices are kept as a standard upon which other modality images (magnetic resonance imaging [MRI], single photon emission computed tomography [SPECT], positron emission tomography [PET], etc.) are aligned--automatically or interactively. Following validation of successful registration, they are resampled and reformatted, as per the requirements. This paper defines the minimum requirements of automatic image registration software for 3-dimensional (3D) radiotherapy planning and describes the implementation of a suitable graphical user interface developed in Visual Basic (version 5). The automatic image registration (AIR) routines freely available from Dr. Roger P. Woods, UCLA, (USA) were used in this software. This software could be easily implemented and was easy to use for image processing suitable for radiotherapy planning systems.

Algorithms↗

PubMed1995

Automating the sleep laboratory: implementation and validation of digital recording and analysis.

OBJECTIVES: We report on the implementation of digital processing in a large clinical and research sleep laboratory. The system includes the digital collection, display, analysis, and repository of physiological signals collected during sleep. METHODS: After describing the original analog system, the computer equipment and software necessary for the digital implementation are presented and we explain our algorithms for rapid eye movement (REM) and delta-wave detection. Finally, we describe an experiment validating the digital system of display and analyses. CONCLUSIONS: The digital processing of sleep signals saves computer operator, polysomnographic technologist, and computer time. It also saves resources such as polysomnographic paper and FM tape. The digital signals lend themselves to a large array of analysis techniques and result in improved signal quality. Automated REM and delta-wave detection via digital processing correlate highly with visual counts of rapid eye movements and delta waves.

Algorithms↗

PubMed2004

[Logical-mathematical "ND" software development].

In this article, we propose a mathematical analysis model for the generation of a proportional value of defining characteristics in nursing diagnoses. The study results are based on the logical-mathematical development of software specifically built for the generation of diagnosis hypotheses. The final calculation creates the sum of all defining characteristics found in each diagnosis, comparing it with the value of the V variable of the diagnosis, according to a mathematical rule that was set. It is concluded that the software needs to go through clinical validation in order to evaluate the pertinence of the rule proposed here.

Models, Theoretical↗

PubMed1996

Radiology systems architecture.

This article focuses on the software requirements for enterprise integration in radiology. The needs of a future radiology systems architecture are examined, both at a concrete functional level and at an abstract system-properties level. A component-based approach to software development is described and is validated in the context of each of the abstract system requirements for future radiology computing environments.

Computer Systems↗

PubMed2005

Toward supportive data collection tools for plant metabolomics.

Over recent years, a number of initiatives have proposed standard reporting guidelines for functional genomics experiments. Associated with these are data models that may be used as the basis of the design of software tools that store and transmit experiment data in standard formats. Central to the success of such data handling tools is their usability. Successful data handling tools are expected to yield benefits in time saving and in quality assurance. Here, we describe the collection of datasets that conform to the recently proposed data model for plant metabolomics known as ArMet (architecture for metabolomics) and illustrate a number of approaches to robust data collection that have been developed in collaboration between software engineers and biologists. These examples also serve to validate ArMet from the data collection perspective by demonstrating that a range of software tools, supporting data recording and data upload to central databases, can be built using the data model as the basis of their design.

Arabidopsis↗

PubMed1994

Revision of dietary analysis software for the Health Habits and History Questionnaire.

The software for analysis of the Health Habits and History Questionnaire (HHHQ) has been revised and is available to researchers. As in earlier versions of the software, questionnaires other than the standard National Cancer Institute versions can be analyzed. Foods can be added or dropped, nutrients can be added or changed, and many other revisions and options are facilitated. Estimates of 33 nutrients and up to 20 user-defined food groups are produced. The validity is unchanged from the previous software. Other features include a data entry key-and-verify system, standardized editing, a computer-assisted interview, and the calculation of health indices including pack-years of smoking and social network index.

Data Collection↗

PubMed1996

Validation of the EINTHOVEN model-based computerized electrocardiogram rhythm analysis system with three classes of clinical arrhythmias.

Rhythm analysis by commercial systems does not meet clinical needs well, because (1) differential diagnosis of complex rhythms is not performed, (2) common rhythms are often misdiagnosed, and (3) transitions between rhythms are not described. We have developed a model-based diagnostic software system named EINTHOVEN that is designed to address the above limitations. A demonstration is available on the World Wide Web at http:@einthoven.uokhsc.edu. The system has been validated using simple rhythms from introductory electrocardiogram (ECG) textbooks. We present here the results of evaluation with more complex rhythm strips taken from clinical records and intermediate-level ECG textbooks. Rhythm strips were described by the onset and offset of each electrical event (P wave, QRS complex, and T wave) and by a morphology classification for each event. The rhythms included a variety of supraventricular and ventricular rhythms. The analysis was considered correct if it named all correct diagnoses in a rhythm strip, incorrect if it completed the analysis and failed to name the correct diagnoses, and indeterminate if it failed to complete the analysis. The system was designed not to complete an analysis if it could not explain an entire rhythm by at least 1 pathophysiological model. The test rhythms were not used to develop the system. Forty-six of 56 test rhythms were diagnosed correctly, and 8 were not analyzed completely. The 2 incorrect diagnoses were atrial tachycardia with variable conduction (diagnosed as intermittent complete heart block) and atrial fibrillation (diagnosed as irregular junctional tachycardia). All 56 rhythms were diagnosed correctly after minor technical improvements to the system. The processing time of the system was 7.6-fold (range 1.5-to 16.9-fold) faster than the elapsed time of the individual records. These preliminary results suggest (1) that computer-based interpretation of complex rhythms is possible, (2) that further software development is necessary to reach a clinical level of accuracy, and (3) that there are no theoretical obstacles to achieving this goal.

Arrhythmias, Cardiac↗

PubMed2004

Systematic differences in electropherogram peak heights reported by different versions of the GeneScan software.

DNA profiling using STRs on the 310 and 3100 Genetic Analyzers routinely generates electropherograms that are analyzed with the GeneScan software available from the instrument's manufacturer, Applied Biosystems. Users have been able to choose from three different smoothing options that have been known to result in significant differences in the peak heights that are reported. Improvements in the underlying algorithm of the most recent version of the software also result in significant and somewhat predictable differences in peak height values. Laboratories that have performed validation studies using older versions of GeneScan should either reanalyze the data generated in those validation studies with the newest version of the software or otherwise take into consideration the systematically higher peak height values obtained as they begin following the recommendation of the manufacturer and use the new algorithm.

Algorithms↗

PubMed2004

MONSTER: inferring non-covalent interactions in macromolecular structures from atomic coordinate data.

A web application for inferring potentially stabilizing non-bonding interactions in macromolecular structures from input atomic coordinate data is described. The core software, called Monster, comprises a PERL wrapper that takes advantage of scripts developed in-house as well as established software in the public domain to validate atomic coordinate files, identify interacting residues and assign the nature of these interactions. The results are assembled and presented in an intuitive and interactive graphical format. Potential applications of Monster range from mining and validating experimentally determined structures to guiding functional analysis. Non-commercial users can perform Monster analysis free of charge at http://monster.northwestern.edu.

Internet↗