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At least 1,567 records · Page 87Linked to original sources

PubMed1999

Predictive medicine: computational techniques in therapeutic decision-making.

The current paradigm for surgery planning for the treatment of cardiovascular disease relies exclusively on diagnostic imaging data to define the present state of the patient, empirical data to evaluate the efficacy of prior treatments for similar patients, and the judgement of the surgeon to decide on a preferred treatment. The individual variability and inherent complexity of human biological systems is such that diagnostic imaging and empirical data alone are insufficient to predict the outcome of a given treatment for an individual patient. We propose a new paradigm of predictive medicine in which the physician utilizes computational tools to construct and evaluate a combined anatomic/physiologic model to predict the outcome of alternative treatment plans for an individual patient. The predictive medicine paradigm is implemented in a software system developed for Simulation-Based Medical Planning. This system provides an integrated set of tools to test hypotheses regarding the effect of alternate treatment plans on blood flow in the cardiovascular system of an individual patient. It combines an Internet-based user interface developed using Java and VRML, image segmentation, geometric solid modeling, automatic finite element mesh generation, computational fluid dynamics, and scientific visualization techniques. This system is applied to the evaluation of alternate, patient-specific treatments for a case of lower extremity occlusive cardiovascular disease.

Arterial Occlusive Diseases↗

PubMed2006

Validation of GATE Monte Carlo simulations of the GE Advance/Discovery LS PET scanners.

The recently developed GATE (GEANT4 application for tomographic emission) Monte Carlo package, designed to simulate positron emission tomography (PET) and single photon emission computed tomography (SPECT) scanners, provides the ability to model and account for the effects of photon noncollinearity, off-axis detector penetration, detector size and response, positron range, photon scatter, and patient motion on the resolution and quality of PET images. The objective of this study is to validate a model within GATE of the General Electric (GE) Advance/Discovery Light Speed (LS) PET scanner. Our three-dimensional PET simulation model of the scanner consists of 12 096 detectors grouped into blocks, which are grouped into modules as per the vendor's specifications. The GATE results are compared to experimental data obtained in accordance with the National Electrical Manufactures Association/Society of Nuclear Medicine (NEMA/SNM), NEMA NU 2-1994, and NEMA NU 2-2001 protocols. The respective phantoms are also accurately modeled thus allowing us to simulate the sensitivity, scatter fraction, count rate performance, and spatial resolution. In-house software was developed to produce and analyze sinograms from the simulated data. With our model of the GE Advance/Discovery LS PET scanner, the ratio of the sensitivities with sources radially offset 0 and 10 cm from the scanner's main axis are reproduced to within 1% of measurements. Similarly, the simulated scatter fraction for the NEMA NU 2-2001 phantom agrees to within less than 3% of measured values (the measured scatter fractions are 44.8% and 40.9 +/- 1.4% and the simulated scatter fraction is 43.5 +/- 0.3%). The simulated count rate curves were made to match the experimental curves by using deadtimes as fit parameters. This resulted in deadtime values of 625 and 332 ns at the Block and Coincidence levels, respectively. The experimental peak true count rate of 139.0 kcps and the peak activity concentration of 21.5 kBq/cc were matched by the simulated results to within 0.5% and 0.1% respectively. The simulated count rate curves also resulted in a peak NECR of 35.2 kcps at 10.8 kBq/cc compared to 37.6 kcps at 10.0 kBq/cc from averaged experimental values. The spatial resolution of the simulated scanner matched the experimental results to within 0.2 mm.

Algorithms↗

PubMed2000

A data fusion environment for multimodal and multi-informational neuronavigation.

OBJECTIVE: Part of the planning and performance of neurosurgery consists of determining target areas, areas to be avoided, landmark areas, and trajectories, all of which are components of the surgical script. Nowadays, neurosurgeons have access to multimodal medical imaging to support the definition of the surgical script. The purpose of this paper is to present a software environment developed by the authors that allows full multimodal and multi-informational planning as well as neuronavigation for epilepsy and tumor surgery. MATERIALS AND METHODS: We have developed a data fusion environment dedicated to neuronavigation around the Surgical Microscope Neuronavigator system (Carl Zeiss, Oberkochen, Germany). This environment includes registration, segmentation, 3D visualization, and interaction-applied tools. It provides the neuronavigation system with the multimodal information involved in the definition of the surgical script: lesional areas, sulci, ventricles segmented from magnetic resonance imaging (MRI), vessels segmented from magnetic resonance angiography (MRA), functional areas from magneto-encephalography (MEG), and functional magnetic resonance imaging (fMRI) for somatosensory, motor, or language activation. These data are considered to be relevant for the performance of the surgical procedure. The definition of each entity results from the same procedure: registration to the anatomical MRI data set (defined as the reference data set), segmentation, fused 3D display, selection of the relevant entities for the surgical step, encoding in 3D surface-based representation, and storage of the 3D surfaces in a file recognized by the neuronavigation software (STP 3.4, Leibinger; Freiburg, Germany). RESULTS: Multimodal neuronavigation is illustrated with two clinical cases for which multimodal information was introduced into the neuronavigation system. Lesional areas were used to define and follow the surgical path, sulci and vessels helped identify the anatomical environment of the surgical field, and, finally, MEG and fMRI functional information helped determine the position of functional high-risk areas. CONCLUSION: In this short evaluation, the ability to access preoperative multi-functional and anatomical data within the neuronavigation system was a valuable support for the surgical procedure.

Adult↗

PubMed2006

Fast, daily linac verification for segmented IMRT using electronic portal imaging.

PURPOSE: Intensity modulated radiotherapy (IMRT) requires dedicated quality assurance (QA). Recently, we have published a method for fast (1-2 min) and accurate linac quality control for dynamic multileaf collimation, using a portal imaging device. This method is in routine use for daily leaf motion verification. The purpose of the present study was to develop an equivalent procedure for QA of IMRT with segmented (static) multileaf collimation (SMLC). MATERIALS AND METHODS: The QA procedure is based on measurements performed during 3- to 8-month periods at Elekta, Siemens and Varian accelerators. On each measurement day, images were acquired for a field consisting of five 3 x 22 cm(2) segments. These 10 monitor unit (MU) segments were delivered in SMLC mode, moving the leaves from left to right. Deviations of realized leaf gap widths from the prescribed width were analysed to study the leaf positioning accuracy. To assess hysteresis in leaf positioning, the sequential delivery of the SMLC segments was also inverted. A static 20 x 20 cm(2) field was delivered with exposures between 1 and 50 MU to study the beam output and beam profile at low exposures. Comparisons with an ionisation chamber were made to verify the EPID dose measurements at low MU. Dedicated software was developed to improve the signal-to-noise ratio and to correct for image distortion. RESULTS AND CONCLUSIONS: The observed long-term leaf gap reproducibility (1 standard deviation) was 0.1 mm for the Varian, and 0.2 mm for the Siemens and the Elekta accelerators. In all cases the hysteresis was negligible. Down to the lowest MU, beam output measurements performed with the EPID agreed within 1+/-1% (1SD) with ionisation chamber measurements. These findings led to a fast (3-4 min) procedure for accurate, daily linac quality control for SMLC.

Calibration↗

PubMed1997

Development of a standard reference material for diesel mutagenicity in the Salmonella plate incorporation assay.

The present study documents the mutagenicity of a new National Institute of Standards and Technology (NIST) standard reference material (SRM) in the Salmonella plate incorporation assay. This study is in response to a previous recommendation by the World Health Organization to develop large batches of new SRMs for biological and chemical research. SRM 1975 is a dichloromethane (DCM) extract of 5.6 kg of filter-collected combustion particulate matter (SRM 2975) from operating forklifts with diesel engines. The mutagenicity and a summary of the related chemical analysis of mutagens in SRM 1975 is presented in this paper, and are available from the NIST. Mutagenicity test conditions were: Salmonella typhimurium TA98, TA100 (standard strains); TA98NR, TA100NR (nitroreductase (NR) gene deficient); and YG1021 and YG1026 (NR gene addition); 10 dose levels in the linear portion of the dose-response curve; duplicate plates per dose; and S9 at 6.4% or 1.1 mg of protein/plate. Four rounds of testing were conducted. Rounds were conducted at least 1 week apart. Slopes (revertants/microg) were calculated by the linear regression rejection model of Bernstein and by the Stead and Krewski models which analyze non-linear data. The GeneTox Manager software package developed at the EPA was used to record the data and calculate the slopes. Results demonstrated: (1) the ranking of slopes without S9 was: YG1021 > TA98 > TA98NR > YG1026 > TA100 > TA100NR in all three statistical models; (2) the mutagenic activity of SRM 1975 was significantly increased by the presence of the NR gene; (3) the slope values for the TA100 series were significantly less than for the TA98 series; (4) in general, the addition of the S9 significantly reduced mutagenic activity; (5) the mutagenic activity of the SRM 1975 was stable over time and variability was low (generally less than 20% in slope values over the 4 rounds); and (6) agreement of the slope values among the three models was excellent due to the linear nature of the data. These data will be useful in ranking other diesel and air samples for mutagenic activity, for quality assurance of data generated in different laboratories, for quality control within a laboratory, and as positive control values for future air and automotive emission studies.

Mutagenicity Tests↗

PubMed2003

[Software for MR image reconstruction from data acquired on an irregular k-space trajectory].

A PC-based software was developed and programmed with VC++6 for reconstructing MR images from the data acquired on an irregular k-space trajectory. It can read clinical MRI raw data and image data, create numerical phantoms, design k-space trajectories, generate k-space data from numerical phantom, calculate weighting functions, reconstruct images, and carry out error analysis for the reconstructed images. It is helpful to the investigations of new k-space trajectories and new reconstruction algorithms.

Algorithms↗

PubMed2002

Performance testing of medical echo/Doppler equipment.

This paper describes the methods applied in a software package developed by the authors for use in a performance testing protocol for medical ultrasound equipment. The history of performance testing of medical ultrasound equipment is briefly reviewed. This paper is confined to the testing of performance of usage aspects, i.e. imaging performance and Doppler velocity estimation performance. Simple test objects are used which have a long life expectancy. The tests performed both in fundamental and in (tissue) harmonic modes when applicable are spatial resolution, contrast sensitivity, and clutter. The concept of a computational observer is used to define the lesion signal-to-noise ratio and the tissue-to-clutter ratio. Further imaging performance features are penetration depth, slice thickness and geometric conformity of display. Pulsed Doppler velocity measurement features tested are: sensitivity, depth and 3D size of the sample volume, velocity measurement, channel separation. The whole performance measurement protocol as well as the quantitative measurements in the digitized images are implemented in software, together with the graphs and data obtained from the measurements.

Blood Flow Velocity↗

PubMed1999

New software applications for interchangeable instrumentation in spinal stereotaxis.

Computer image-guided surgery has been widely accepted because it allows the surgeon to track an instrument through unvisualized critical structures of a patient in real-time, thus minimizing the risk of injury. Current spinal and cranial image-guided surgery is, however, limited by the lack of surgical instruments and software applications that would allow rapid interchange of useful instruments to perform the procedures. Most image-guided systems utilize a single standard probe or a few pre-defined instruments that are not necessarily useful for performing the actual surgical procedure. Present image-guided technology for screw placement in spinal surgery utilizes the standard probe only to confirm the entry point location and view the planned trajectory of the screw. The surgeon then resumes the procedure using standard surgical instruments to drill, tap and place screws without the benefit of image guidance. Our clinical laboratory experience with spinal image-guided surgery indicates that there is potential for error between each of these procedural steps of screw placement. Despite accurately locating an entry point, any deviation in the trajectory during drilling of a pilot hole, tapping or screw placement may result in significant errors in screw placement and potential neurovascular injury. We have developed custom software applications and universal hardware adaptation devices for spinal image-guided surgery that allow the use of standard instruments for intraoperative guidance. Utilizing universal dynamic registration hardware and software, standard surgical instruments are adapted for real-time image guided surgery. An array of light emitting diodes can be attached to essentially any rigid instrument with a definable tip and then calibrated to the system for intraoperative use. Laboratory tests using a cadaveric model indicate a difference in accuracy of less than 1.0 mm between the standard probe and a dynamically registered custom instrument and an absolute mean error of less than 2.0 mm for the image-guided system which is clinically insignificant in most cases. This technology is a significant step forward as it allows the surgeon to use a full array of instruments with image guidance and will ultimately make spinal and intracranial surgery safer and more accurate.

Bone Screws↗

PubMed2003

Quantitative fluorescent speckle microscopy: where it came from and where it is going.

Fluorescent speckle microscopy (FSM) is a technology for analysing the dynamics of macromolecular assemblies. Originally, the effect of random speckle formation was discovered with microtubules. Since then, the method has been expanded to other proteins of the cytoskeleton such as f-actin and microtubule binding proteins. Newly developed, specialized software for analysing speckle movement and photometric fluctuation in the context of polymer transport and turnover has turned FSM into a powerful method for the study of cytoskeletal dynamics in cell migration, division, morphogenesis and neuronal path finding. In all these settings, FSM serves as the quantitative readout to link molecular and genetic interventions to complete maps of the cytoskeleton dynamics and thus can be used for the systematic deciphering of molecular regulation of the cytoskeleton. Fully automated FSM assays can also be applied to live-cell screens for toxins, chemicals, drugs and genes that affect cytoskeletal dynamics. We envision that FSM has the potential to become a core tool in automated, cell-based molecular diagnostics in cases where variations in cytoskeletal dynamics are a sensitive signal for the state of a disease, or the activity of a molecular perturbant. In this paper, we review the origins of FSM, discuss these most recent technical developments and give a glimpse to future directions and potentials of FSM. It is written as a complement to the recent review (Waterman-Storer & Danuser, 2002, Curr. Biol., 12, R633-R640), in which we emphasized the use of FSM in cell biological applications. Here, we focus on the technical aspects of making FSM a quantitative method.

Actins↗

PubMed2003

Pathway studio--the analysis and navigation of molecular networks.

SUMMARY: PathwayAssist is a software application developed for navigation and analysis of biological pathways, gene regulation networks and protein interaction maps. It comes with the built-in natural language processing module MedScan and the comprehensive database describing more than 100 000 events of regulation, interaction and modification between proteins, cell processes and small molecules. AVAILABILITY: PathwayAssist is available for commercial licensing from Ariadne Genomics, Inc. The light version with limited functionality will be available for free for academic users at www.ariadnegenomics.com/downloads/.

Database Management Systems↗

PubMed2001

Spatially modulated illumination microscopy: online visualization of intensity distribution and prediction of nanometer precision of axial distance measurements by computer simulations.

During the last years, measurements considerably beyond the conventional "Abbe-Limit" of optical resolution in far field light microscopy were realized by several light microscopical approaches. Point spread function (PSF) engineering, spectral precision distance microscopy (SPDM), and related methods were used to demonstrate the feasibility of such measurements. SPDM allows the measurement of position and multiple distances between point-like fluorescent objects of different spectral signatures far below the optical resolution criterion as defined by the full width at half maximum of the PSF. Here, we report a software method to obtain online visualization of light distribution in the lateral and axial direction of any object detected in a spatially modulated illumination (SMI) microscope. This strongly facilitates routine application of SMI microscopy. The software was developed using Microsoft Visual C++ running on Windows NT. Furthermore, some aspects of the theoretical limits of the SPDM method were studied by virtual microscopy. For the case of SMI microscopy the precision of axial distance measurements was studied, taking into account photon statistics and image analysis procedures. The results indicate that even under low fluorescence intensity conditions typical for biological structure research, precise distance measurements in the nanometer range can be determined, and that axial distances in the order of 40 nm are detectable with such precision.

Computer Simulation↗

PubMedDate not supplied

Three-dimensional analysis of the proximal femur in patients with slipped capital femoral epiphysis based on computed tomography.

A three-dimensional (3D) analysis based on computed tomography was performed to study the 3D geometry of the proximal femur in cases of slipped capital femoral epiphysis (SCFE). For this purpose, new interactive software was developed to analyze hip joint geometry using 3D models without pelvis tilting and projected errors. Twenty-two patients, 8 girls and 14 boys, with a total of 30 slipped capital femoral epiphyses, were reviewed. In the affected hips, we observed a reduced femoral anteversion of 7.0 degrees (vs. 12.7 degrees) and a reduced femoral shaft neck angle of 134.2 degrees (vs. 141.0 degrees). In response to these results, we suggest that an SCFE is associated with reduced femoral anteversion and a reduced femoral shaft neck angle.

Adolescent↗

PubMed1991

Determination of average heart rate as a sign of the orienting response.

The "O wave" is one component of minute EEG signals recorded from the scalp in response to external stimuli and is one sign of the "orienting response". The orienting response is a fundamental response in which attention is turned to fresh or important sources of information. The orienting response has many signs in the autonomic nervous system including changes in heart rate. Software was developed to track changes in heart rate as an additional sign of the orienting response. Instantaneous heart rate was determined by detecting R waves and calculating the interval between successive R waves. Segments of the instantaneous heart rate, time located to the occurrence of the stimuli, were averaged to produce an average heart rate during the time interval in which the stimuli occurred. Changes in the average heart rate where found to occur in time correspondence to the "O wave" in the EEG signal and thus provide an additional measure of the orienting response.

Attention↗

PubMed1986

Personal computer software for the stereologic evaluation of sympathetic ganglia.

Software was developed on a personal computer for a quantitative study of some ultrastructural aspects of sympathetic ganglia (the neuronal cell body, the surrounding satellite cell layer and the nearby capillaries). A low-cost digitizer, originally designed for teaching, semiprofessional graphics applications and games, was utilized to sample areas and distances on electron micrographs. The processing program derives stereologic parameters from the crude data stored in the memory. Further algorithms then assess the mean thickness and the volume densities of the satellite cell layer, endothelial basal lamina and endothelial layer.

Capillaries↗

PubMedDate not supplied

Computer-based medical system for the computation of blood pressure excess in the diagnosis of hypertension.

A computer-based system for assessing hypertension was designed by combining hardware for automatic, long-term blood pressure (BP) measurement with a set of software modules for computing time-specified tolerance intervals and evaluating measures of BP excess. BP is so variable that the identification and proper definition of hypertension are highly ambiguous when based on single measurements. One first step in dealing with such variability is to replace the constant limits for BP frequently used in the assessment of hypertension by a time-specified reference interval. Once such a threshold is available, a hyperbaric index can be computed by numerical integration as the total area (within one cycle) of any given patient's BP above the threshold. In order to examine the extent of normal physiologic excess, a series of 266 systolic and diastolic BP and heart rate (HR) measurements were automatically monitored every 30 minutes for at least 48 hours from clinically healthy subjects, aged 19 to 25 years. Original data were used to obtain 90% tolerance intervals for each gender separately. The hyperbaric index was then computed for each individual BP profile. The distribution of the maximum hyperbaric index (maximum of the values computed for systolic, mean arterial, and diastolic BP levels shows a highest value of 14.839 mmHg x hr for the men and of 10.229 mmHg x hr for the women. These values represent a testable threshold for assessing hypertension based on the proposed approach. The tolerance intervals obtained from the reference population were also used to compute hyperbaric indices for a series of 175 BP measurements sampled from clinically healthy people, as well as a series of 60 measurements sampled from patients with mild hypertension. Sensitivity and specificity in the diagnosis of hypertension based on the hyperbaric index were both 100%, as opposed to values obtained from computing the BP load, the average of the BP series, or the circadian amplitude, all of which provided a much poorer diagnostic test. The software system developed for automatically establishing time-qualified tolerance limits from a reference population and assessing the extent and timing of BP elevation for a test subject may help to establish a prognosis and diagnosis, with a correspondingly better assessment of health status, to initiate treatment if needed, to time treatment when it is most desirable and least harmful in terms of undesired effects, and to gauge the patient's response to treatment.

Adult↗

PubMed1998

[Detection of recurrent rectal cancer using helical CT with SmartPrep: a new technique for obtaining optimal contrast enhancement].

Seven patients with suspected recurrent rectal cancer underwent Helical CT using SmartPrep. SmartPrep is a software application developed by GE in which the ROI is placed at the desired level of the aorta prior to contrast injection. Using a low-dose continuous scan, the time density curve was obtained instantly, and the optimal timing of scanning was judged from the curve. Four patients who demonstrated intense enhancement at the anastomotic site had local recurrence. No intense enhancement was observed in these areas on conventional delayed CT. Thus, SmartPrep appears to be useful for the accurate diagnosis of recurrent rectal cancer.

Aged↗

PubMed1996

ENZEDUC 1.0: a user-friendly software package for computation of hyperbolic enzyme kinetic data in biochemical education.

ENZEDUC 1.0 is a software package developed in Microsoft QuickBASIC v7.1 for computation of hyperbolic enzyme kinetics. The educational focus of the package is laboratory practical teaching. The program can manage a maximum of 18 substrate concentration values and 72 reaction rate values for each substrate concentration (1296 pairs of values). Samples can also be of unequal sizes. More than one reaction rate value for each substrate concentration can be handled. Real-time screen plots are obtained for the Michaelis-Menten function and the most popular linear transformations. Printer outputs are available. Hardware requirements are minimum 640 Kb RAM, EGA graphics card and 80286 processor.

Algorithms↗

PubMed1986

Fast Inter Library Loans and Statistics, enhanced version 2.0.

F.I.L.L.S. is a library-specific software package developed by librarians for library staff with little or no computer experience. MacNeal Hospital's Health Science Resource Center designed F.I.L.L.S. to allow libraries to save 60 percent of the time devoted to the interlibrary loan function while improving service to users. As a management tool, F.I.L.L.S. creates a dozen (12) preprogrammed reports that provide invaluable information such as Number of Requests for Periodicals, including copyright information; which libraries are borrowed from frequently; and which libraries provide the fastest or slowest service in filling loan requests. The article describes F.I.L.L.S., its capabilities and its limitations in greater detail.

Computers↗