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PubMedDate not supplied

Cellular vaccines.

This project is devoted to the development of novel cellular vaccines designed to treat cancer patients. These cellular vaccines present and enhance immunogens, which will elicit a potent immune response. The goal is to achieve safe and effective immune reaction against the patient's own tumour. (1) Autologous cellular vaccines are prepared by processing circulating blood mononuclear cells outside of the patient's body (ex vivo) to differentiate them into antigen-presenting cells (APCs). Monocyte-derived APCs (MD-APCs) are then grown in the presence of exogenous target antigens (tumour cell debris, or apoptotic bodies) to become fully mature APCs. (2) Functionality for antigen presentation to T cells of ex vivo MD-APCs is evaluated in vivo. (3) Cellular vaccines are tested in selected rodent animal models. Efficiency and immune response are monitored in pertinent experimental systems for cancer. Pharmacological data are generated for clinical investigation. Tolerance and biologic effects are documented in primates. (4) The first clinical trials on cancer patients are taking place in 1998 on melanoma and prostate cancer to validate the concept. Specialized cell processors with dedicated software and standardized controls are being developed and used for the preparation of cellular vaccines. (5) The evaluation of new non-viral vectors and the validation of new non-viral transfection methods of mononuclear cells with marker genes is in progress and will lead to the ex vivo transfection of genes coding for immunostimulating cytokines or for tumour antigens in MD-APCs. Efficiency will be validated in vitro and in animal models. The ex vivo and animal model studies validate the clinical relevance of this new cellular immunotechnology. Clinical validation of individual autologous cellular vaccines in specific indications for which no treatment is presently available will allow the development of cellular and gene immunotherapy for other types of cancers.

Animals↗
PubMed1998

Economic modeling and sensitivity analysis.

The field of pharmacoeconomics (PE) faces serious concerns of research credibility and bias. The failure of researchers to reproduce similar results in similar settings, the inappropriate use of clinical data in economic models, the lack of transparency, and the inability of readers to make meaningful comparisons across published studies have greatly contributed to skepticism about the validity, reliability, and relevance of these studies to healthcare decision-makers. Using a case study in the field of lipid PE, two suggestions are presented for generally applicable reporting standards that will improve the credibility of PE. Health economists and researchers should be expected to provide either the software used to create their PE model or a multivariate sensitivity analysis of their PE model. Software distribution would allow other users to validate the assumptions and calculations of a particular model and apply it to their own circumstances. Multivariate sensitivity analysis can also be used to present results in a consistent and meaningful way that will facilitate comparisons across the PE literature. Using these methods, broader acceptance and application of PE results by policy-makers would become possible. To reduce the uncertainty about what is being accomplished with PE studies, it is recommended that these guidelines become requirements of both scientific journals and healthcare plan decision-makers. The standardization of economic modeling in this manner will increase the acceptability of pharmacoeconomics as a practical, real-world science.

Journal Article↗
PubMed1993

Trends in computer hardware and software.

Previously identified and current trends in the development of computer systems and in the use of computers for health care applications are reviewed. Trends identified in a 1982 article were increasing miniaturization and archival ability, increasing software costs, increasing software independence, user empowerment through new software technologies, shorter computer-system life cycles, and more rapid development and support of pharmaceutical services. Most of these trends continue today. Current trends in hardware and software include the increasing use of reduced instruction-set computing, migration to the UNIX operating system, the development of large software libraries, microprocessor-based smart terminals that allow remote validation of data, speech synthesis and recognition, application generators, fourth-generation languages, computer-aided software engineering, object-oriented technologies, and artificial intelligence. Current trends specific to pharmacy and hospitals are the withdrawal of vendors of hospital information systems from the pharmacy market, improved linkage of information systems within hospitals, and increased regulation by government. The computer industry and its products continue to undergo dynamic change. Software development continues to lag behind hardware, and its high cost is offsetting the savings provided by hardware.

Clinical Pharmacy Information Systems↗
PubMed1999

Comparison of two techniques for measurement of visceral adipose tissue cross-sectional areas by computed tomography.

Most computed tomography (CT) scanners used today are able to accurately measure adipose tissue (AT) areas at any site of the body. However, first generation CT scanners used by some medical centers are not equipped with appropriate software allowing the measurements of AT areas. The aim of this study was to validate a technique of AT area measurements independent from CT scanner software. Abdominal AT areas were recorded with CT in a sample of 30 men. Areas were thereafter calculated using the standard CT software technique. Total and visceral AT areas were then remeasured using another technique for which X-ray film of each subject's scan was analysed by a system completely independent from the CT scanner (imaging densitometer and NIH image analysis software). Correlations between measurements obtained with the two techniques were very strong for both total (n = 0.99; SEE = 11.7 cm(2)) and visceral AT areas (r = 0.99; SEE = 5.3 cm(2)). Values obtained with the image analysis method were generally higher than with the conventional CT software technique (cross-sectional areas of AT were overestimated by 4.7% for total abdominal and 8.5% for visceral AT respectively). In conclusion, the results indicate that measurements obtained with this image analysis technique would be adequate to correctly rank subjects according to levels of total or visceral AT areas. However, since this method appears to slightly overestimate AT areas, a standardized correction should be performed before comparing subjects with AT areas measured with this technique to subjects whose AT areas have been obtained with the conventional CT software technique. Am. J. Hum. Biol. 11:61-68, 1999. Copyright 1999 Wiley-Liss, Inc.

Journal Article↗
PubMed2005

A new three-dimensional method of assessing facial volumetric changes after orthognathic treatment.

OBJECTIVE: To validate a new method of facial volumetric assessment that is dependent on the use of stereophotogrammetric models and a software-based Facial Analysis Tool. DESIGN: The method was validated in vitro with three-dimensional (3D) models of a lifelike plastic female dummy head and in vivo with a male-subject head. METHODS: Thirty facial silicone explants were added in the nasal and perioral regions of each head, and their volumes were obtained by three different algorithms. These were compared with the actual values obtained by a "water displacement" method. RESULTS: The least mean error was found with the "tetrahedron formation" method followed by the "projection" method and the "back-plane construction" method. The error with the tetrahedron formation method was 0.071 cm(3) (95% confidence interval [CI]: -0.074 to 0.2161 cm3) with the in vitro models and 0.314 cm3 (95% CI: -0.080 to 0.708 cm3) with the in vivo models. The increased volumetric assessment error observed in vivo was attributed to the registration procedure and possible changes in facial expression. CONCLUSIONS: These results encourage the use of this method in the 3D assessment of orthognathic surgical outcome, provided a standardized facial expression is used for image acquisition.

Algorithms↗
PubMed2005

Analytical technique for quantification of selected resorbable calcium phosphate bone void fillers with the use of polarized-light microscopy.

Synthetic calcium phosphate bone void fillers promote varying rates of bone formation and material resorption depending on chemistry, porosity, pore structure, and implant site. The objective of this study was to quantify the resorption of a novel ultraporous beta-tricalcium phosphate cancellous bone void filler with simultaneous quantification of bone formation in a canine humerus model. Potential measurement error involved in conventional histomorphometry using Von Kossa stains inspired the development of a new technique. This technique utilizes bright-field and polarized-light microscopy in conjunction with image analysis software, allowing more accurate histomorphometry. This technique was validated with two separate controlled experiments. Scanning electron microscopy further supported the results. The findings suggest that the use of polarized-light microscopy combined with image analysis software can be an effective tool in simultaneously quantifying calcium phosphate resorption and bone formation.

Animals↗
PubMed2003

Preliminary evaluation of a fuzzy logic-based automatic quantitative analysis in myocardial SPECT.

UNLABELLED: This study validates a new quantitative myocardial perfusion SPECT software. METHODS: The processing starts with the extraction of the morphologic skeleton of the left ventricular myocardium from reconstructed transverse sections. Fuzzy logic is used to decide whether a pixel belongs to the myocardium and any perfusion defect is filled according to a truncated bullet model. The resulting image is partitioned in 18 isovolumetric sectors. Sex-matched normal limits, criteria of abnormality for rest (201)Tl and (99m)Tc-labeled perfusion tracers, reproducibility studies, and detection of coronary artery disease were developed and validated in an overall population of 343 patients. The sex- and tracer-matched means and SDs of a normal response were calculated in 93 male and 93 female patients with a <5% likelihood of coronary artery disease. Reproducibility measurements and assignment of different sectors of the myocardium to a specific coronary were performed from data collected in 49 and 60 patients, respectively. The accuracy of the detection of a coronary artery occlusion was assessed in 48 patients who also underwent coronary angiography. RESULTS: The intra- and interoperator reproducibility of the sectorial activity was high with a linear regression coefficient of 0.97 and a SD of the difference measurement at 4.4% and 3.8%, respectively. Overall sensitivity and specificity for the detection of occluded coronary artery were 90% and 80%, respectively. For the detection of left anterior descending, left circumflex, and right artery coronary occlusion, sensitivity was 92%, 75%, and 92.5%, respectively, and specificity was 75%, 78%, and 90%, respectively. CONCLUSION: The new quantitative myocardial perfusion SPECT software appears to be a very helpful program for the objective analysis of perfusion tracer distribution in myocardial SPECT and a very accurate tool in the detection and localization of coronary artery occlusion.

Algorithms↗
PubMed1999

Evaluation of gene prediction software using a genomic data set: application to Arabidopsis thaliana sequences.

MOTIVATION: The annotation of the Arabidopsis thaliana genome remains a problem in terms of time and quality. To improve the annotation process, we want to choose the most appropriate tools to use inside a computer-assisted annotation platform. We therefore need evaluation of prediction programs with Arabidopsis sequences containing multiple genes. RESULTS: We have developed AraSet, a data set of contigs of validated genes, enabling the evaluation of multi-gene models for the Arabidopsis genome. Besides conventional metrics to evaluate gene prediction at the site and the exon levels, new measures were introduced for the prediction at the protein sequence level as well as for the evaluation of gene models. This evaluation method is of general interest and could apply to any new gene prediction software and to any eukaryotic genome. The GeneMark.hmm program appears to be the most accurate software at all three levels for the Arabidopsis genomic sequences. Gene modeling could be further improved by combination of prediction software. AVAILABILITY: The AraSet sequence set, the Perl programs and complementary results and notes are available at http://sphinx.rug.ac.be:8080/biocomp/napav/. CONTACT: Pierre.Rouze@gengenp.rug.ac.be.

Alternative Splicing↗
PubMed2001

GOBASE: the organelle genome database.

GOBASE (http://megasun.bch.umontreal.ca/gobase/) is a network-accessible biological database, which is unique in bringing together diverse biological data on organelles with taxonomically broad coverage, and in furnishing data that have been exhaustively verified and completed by experts. So far, we have focused on mitochondrial data: GOBASE contains all published nucleotide and protein sequences encoded by mitochondrial genomes, selected RNA secondary structures of mitochondria-encoded molecules, genetic maps of completely sequenced genomes, taxonomic information for all species whose sequences are present in the database and organismal descriptions of key protistan eukaryotes. All of these data have been integrated and organized in a formal database structure to allow sophisticated biological queries using terms that are inherent in biological concepts. Most importantly, data have been validated, completed, corrected and standardized, a prerequisite of meaningful analysis. In addition, where critical data are lacking, such as genetic maps and RNA secondary structures, they are generated by the GOBASE team and collaborators, and added to the database. The database is implemented in a relational database management system, but features an object-oriented view of the biological data through a Web/Genera-generated World Wide Web interface. Finally, we have developed software for database curation (i.e. data updates, validation and correction), which will be described in some detail in this paper.

Animals↗
PubMed2004

GeneOrder3.0: software for comparing the order of genes in pairs of small bacterial genomes.

BACKGROUND: An increasing number of whole viral and bacterial genomes are being sequenced and deposited in public databases. In parallel to the mounting interest in whole genomes, the number of whole genome analyses software tools is also increasing. GeneOrder was originally developed to provide an analysis of genes between two genomes, allowing visualization of gene order and synteny comparisons of any small genomes. It was originally developed for comparing virus, mitochondrion and chloroplast genomes. This is now extended to small bacterial genomes of sizes less than 2 Mb. RESULTS: GeneOrder3.0 has been developed and validated successfully on several small bacterial genomes (ca. 580 kb to 1.83 Mb) archived in the NCBI GenBank database. It is an updated web-based "on-the-fly" computational tool allowing gene order and synteny comparisons of any two small bacterial genomes. Analyses of several bacterial genomes show that a large amount of gene and genome re-arrangement occurs, as seen with earlier DNA software tools. This can be displayed at the protein level using GeneOrder3.0. Whole genome alignments of genes are presented in both a table and a dot plot. This allows the detection of evolutionary more distant relationships since protein sequences are more conserved than DNA sequences. CONCLUSIONS: GeneOrder3.0 allows researchers to perform comparative analysis of gene order and synteny in genomes of sizes up to 2 Mb "on-the-fly." AVAILABILITY: http://binf.gmu.edu/genometools.html and http://pasteur.atcc.org:8050/GeneOrder3.0.

Chromosome Mapping↗
PubMed2002

Placing long-term and acute radiation effects in a common framework.

No method presently exists for placing long-term risks from low-level radiation doses and acute radiation sickness (ARS) from high-level doses within a common framework useful for the military commander. This article proposes such a method. The Defense Threat Reduction Agency and its predecessor agencies pioneered the quantitative description of the impact of ARS on human performance capability and military unit effectiveness. One product of these efforts is the Radiation-Induced Performance Decrement (RIPD) software. RIPD software includes physiologically based models of ARS valid for both chronic and one-time radiation exposure. One key element of placing ARS and low-level radiation effects in a common framework is finding independent and dependent variables that have a common meaning for both. This paper examines the use of cumulative probability of effect vs. dose and time after exposure for establishing a common framework. The physiologically based models of upper gastrointestinal distress and fatigability and weakness from the RIPD software support this approach.

Humans↗
PubMed2005

Development and validation of a computed tomography-based methodology to measure carpal kinematics.

Motion of the wrist bones is complicated and difficult to measure. Noninvasive measurement of carpal kinematics using medical images has become popular This technique is difficult and most investigators employ custom software. The objective of this paper is to describe a validated methodology for measuring carpal kinematics from computed tomography (CT) scans using commercial software. Four cadaveric wrists were CT imaged in neutral, full flexion, and full extension. A registration block was attached to the distal radius and used to align the data sets from each position. From the CT data, triangulated surface models of the radius, lunate, and capitate bones were generated using commercial software. The surface models from each wrist position were read into engineering design software that was used to calculate the centroid (position) and principal mass moments of inertia (orientation) of (1) the capitate and lunate relative to the fixed radius and (2) the capitate relative to the lunate. These data were used to calculate the helical axis kinematics for the motions from neutral to extension and neutral to flexion. The kinematics were plotted in three dimensions using a data visualization software package. The accuracy of the method was quantified in a separate set of experiments in which an isolated capitate bone was subjected to two different known rotation/translation motions for ten trials each. For comparison to in vivo techniques, the error in distal radius surface matching was determined using the block technique as a gold standard. The motion that the lunate and capitate underwent was half that of the overall wrist flexion-extension range of motion. Individually, the capitate relative to the lunate and the lunate relative to the radius generally flexed or extended about 30 deg, while the entire wrist (capitate relative to radius) typically flexed or extended about 60 deg. Helical axis translations were small, ranging from 0.6 mm to 1.8 mm across all motions. The accuracy of the method was found to be within 1.4 mm and 0.5 deg (95% confidence intervals). The mean error in distal radius surface matching was 2.4 mm and 1.2 deg compared to the use of a registration block. Carpal kinematics measured using the described methodology were accurate, reproducible, and similar to findings of previous investigators. The use of commercially available software should broaden the access of researchers interested in measuring carpal kinematics using medical imaging.

Adult↗
PubMed2004

The value of SCORAD and beyond. Towards a standardized evaluation of severity?

The clinical scoring systems of atopic dermatitis were analysed and compared. Some biological parameters that can correlate with the clinical score were also reviewed. After the definition of the disease based on validated clinical criteria, the second necessity was the availability of reliable severity scores to allow clinicians to verify the course of the disease and the efficacy of treatments. After many proposals, the SCORAD (SCORing Atopic Dermatitis), that required more than three years of work, was the first one that was validated. SCORAD is freely available from an internet site and can be easily calculated using dedicated software. EASI (Eczema Area and Severity Index) score has also been validated but it has been modified twice. Simpler systems include SASSAD (Six Area, Six Sign Atopic Dermatitis) and TIS score (Three-Item Severity score). In parallel, biological parameters were investigated. Eosinophil cationic protein, circulating basophils, major basic protein, soluble E-selectin, antistaphylococcal enterotoxin B, immunoglobulin E titres and macrophage-derived chemokine, can correlate significantly with the clinical score. The clinicians will not benefit directly from laboratory techniques and will employ clinical scores.

Dermatitis, Atopic↗
PubMed2004

3D-catFISH: a system for automated quantitative three-dimensional compartmental analysis of temporal gene transcription activity imaged by fluorescence in situ hybridization.

Fluorescence in situ hybridization (FISH) of neural activity-regulated, immediate-early gene (IEG) expression provides a method of functional brain imaging with cellular resolution. This enables the identification, in one brain, of which specific principal neurons were active during each of two distinct behavioral epochs. The unprecedented potential of this differential method for large-scale analysis of functional neural circuits is limited, however, by the time-intensive nature of manual image analysis. A comprehensive software tool for processing three-dimensional, multi-spectral confocal image stacks is described which supports the automation of this analysis. Nuclei counterstained with conventional DNA dyes and FISH signals indicating the sub-cellular distribution of specific, IEG RNA species are imaged using different spectral channels. The DNA channel data are segmented into individual nuclei by a three-dimensional multi-step algorithm that corrects for depth-dependent attenuation, non-isotropic voxels, and imaging noise. Intra-nuclear and cytoplasmic FISH signals are associated spatially with the nuclear segmentation results to generate a detailed tabular/database and graphic representation. Here we present a comprehensive validation of data generated by the automated software against manual quantification by human experts on hippocampal and parietal cortical regions (96.5% concordance with multi-expert consensus). The high degree of reliability and accuracy suggests that the software will generalize well to multiple brain areas and eventually to large-scale brain analysis.

Algorithms↗
PubMed2000

A biokinetic model for lead metabolism with a view to its extension to pregnancy and lactation; (1). Further validation of the original model for non-pregnant adults.

A published biokinetic model that describes the absorption, transfer between organs and excretion of lead (Pb) in humans has been established using commercially available simulation software. Recent in vivo data have been used to validate further the model in adults, particularly for non-pregnant females. The validation data centre on: (a) the prediction of blood Pb concentrations due to changes in atmospheric and dietary Pb levels over the last 25 years; (b) the non-linear relationship between Pb in whole blood and that in blood plasma which can be transferred to other organs; and (c) the accumulation of Pb in bone which may be re-mobilised later in time of calcium stress. This work underpins our alteration of the model to encompass pregnancy and lactation so that the build-up of Pb in the developing foetus and breast-fed infant can be estimated from any number of current and historical maternal exposure scenarios.

Adolescent↗
PubMed2000

From digital image processing of colour Doppler M-mode maps to noninvasive evaluation of the left ventricular diastolic function: a dedicated software package.

Noninvasive estimation of diastolic pressure gradients has recently been validated using the space-temporal velocity distribution available from colour Doppler M-mode (CDM). However, the methods currently applied for analysing CDM patterns of left ventricular (LV) filling have limitations, such as lack of automation, subjective variability and limited use of digital velocity map. For this reason, we have developed software able to acquire and process the CDM maps; thus, providing an easily interpretable graphical and numerical display. The pressure field is obtained by approximating the derivatives with centred finite differences via the incompressible Navier-Stokes equations. After digital filtering of the noise and the removal of the colour black spots, the velocity field is utilised to compute the pressure gradient field and the pressure values by spatial integration. It is concluded that automatic quantification of colour CDM patterns is feasible and will be a strategic tool in the investigation of one of the most intriguing topics in cardiology.

Blood Flow Velocity↗
PubMed2003

Axial and peripheral eye length measured with optical low coherence reflectometry.

An optical low-coherence reflectometer (OLCR device) is described that allows the precise and noncontact measurement of eye length. The device measures eye length both on-axis and off-axis, thus enabling the determination of eye shape, an ocular parameter thought to be important in the development of refractive error. It is essential for several applications in ophthalmology and vision science. This improved OLCR device operates using a single-beam interferometer with a beam deflection mechanism that allows the precise measurement of eye length along the visual axis and within 15 deg horizontally and vertically from the fovea. The validity of this instrument and its revised software is evaluated by measuring the reproducibility of axial length results in an adult eye and an artificial eye, and by correlating axial eye length measured in a group of ten adult eyes with axial eye length obtained with A-scan ultrasound in the same eyes. The precision obtained with adult subjects is compared with that obtained with children.

Adult↗
PubMed2000

PSG-EXPERT. An expert system for the diagnosis of sleep disorders.

This paper describes PSG-EXPERT, an expert system in the domain of sleep disorders exploring polysomnographic data. The developed software tool is addressed from two points of view: (1)--as an integrated environment for the development of diagnosis-oriented expert systems; (2)--as an auxiliary diagnosis tool in the particular domain of sleep disorders. Developed over a Windows platform, this software tool extends one of the most popular shells--CLIPS (C Language Integrated Production System) with the following features: backward chaining engine; graph-based explanation facilities; knowledge editor including a fuzzy fact editor and a rules editor, with facts-rules integrity checking; belief revision mechanism; built-in case generator and validation module. It therefore provides graphical support for knowledge acquisition, edition, explanation and validation. From an application domain point of view, PSG-Expert is an auxiliary diagnosis system for sleep disorders based on polysomnographic data, that aims at assisting the medical expert in his diagnosis task by providing automatic analysis of polysomnographic data, summarising the results of this analysis in terms of a report of major findings and possible diagnosis consistent with the polysomnographic data. Sleep disorders classification follows the International Classification of Sleep Disorders. Major features of the system include: browsing on patients data records; structured navigation on Sleep Disorders descriptions according to ASDA definitions; internet links to related pages; diagnosis consistent with polysomnographic data; graphical user-interface including graph-based explanatory facilities; uncertainty modelling and belief revision; production of reports; connection to remote databases.

Computer Systems↗