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At least 721 records · Page 40Linked to original sources

PubMed2004

Analysis of cerebral microvascular architecture--application to cortical and subcortical vessels in rat brain.

Cerebral vascular morphology, including vascular diameters, lengths and branch points, was measured using quantitative three-dimensional (3D) imaging software developed in our laboratory, where data were collected from cortical and subcortical regions of a rat brain. To compare multiple records of the vascular morphological differences between anatomical regions with unpaired data, a simple analysis of variance (ANOVA) model may not be applicable, or may not be valid without considering correlation and unpaired data. In this paper, we formulate a novel outcome to study vascular morphological differences, discuss proper paired test statistics on unpaired data and apply the proposed methods to study the cerebral vascular morphological differences between cortical and sub-cortical regions in rats (N=6). The total vessel surface was analyzed as a composite of diameter, length and branches of vessels. The extended Fisher permutation test provides the paired test on unpaired data, which is equivalent to a permutation test based on the average of multiple sections; however, the permutation test may not be exact. The repeated measure analysis of variance using Generalized Estimating Equations (GEE) can be used to conduct the paired test on unpaired data as an alternative, when the permutation test is not exact. These new approaches can be applied in the study of treatment effects on changes of vascular morphology under physiological and pathological conditions.

Animals↗

PubMed2004

Use of X-ray computed microtomography for non-invasive determination of wood anatomical characteristics.

Quantitative analysis of wood anatomical characteristics is usually performed using classical microtomy yielding optical micrographs of stained thin sections. It is time-consuming to obtain high quality cross-sections from microtomy, and sections can be damaged. This approach, therefore, is often impractical for those who need quick acquisition of quantitative data on vessel characteristics in wood. This paper reports results of a novel approach using X-ray computed microtomography (microCT) for non-invasive determination of wood anatomy. As a case study, stem wood samples of a 2-year-old beech (Fagus sylvatica L.) and a 3-year-old oak (Quercus robur L.) tree were investigated with this technique, beech being a diffuse-porous and oak a ring-porous tree species. MicroCT allowed non-invasive mapping of 2-D transverse cross-sections of both wood samples with micrometer resolution. Self-developed software 'microCTanalysis' was used for image processing of the 2-D cross-sections in order to automatically determine the inner vessel diameters, the transverse cross-sectional surface area of the vessels, the vessel density and the porosity with computer assistance. Performance of this new software was compared with manual analysis of the same micrographs. The automatically obtained results showed no significant statistical differences compared to the manual measurements. Visual inspection of the microCT slices revealed very good correspondence with the optical micrographs. Statistical analysis confirmed this observation in a more quantitative way, and it was, therefore, argued that anatomical analysis of optical micrographs can be readily substituted by automated use of microCT, and this without loss of accuracy. Furthermore, as an additional application of microCT, the 3-D renderings of the internal microstructure of the xylem vessels for both the beech and the oak sample could be reconstructed, clearly showing the complex nature of vessel networks. It can be concluded that the use of microCT in wood science offers an interesting potential for all those who need quantitative data of wood anatomical characteristics in either the 2-D or the 3-D space.

Fagus↗

PubMed2006

Risk assessment of patient handling with ambulance stretcher systems (ramp/(winch), easi-loader, tail-lift) using biomechanical failure criteria.

The research aims to carry out a detailed analysis of the loads applied by the ambulance workers when loading/unloading ambulance stretchers. The forces required of the ambulance workers for each system are measured using a load cell in a force handle arrangement. The process of loading and unloading is video recorded for all the systems to register the posture of the ambulance workers in different stages of the process. The postures and forces exerted by the ambulance workers are analyzed using biomechanical assessment software to examine if the work loads at any stage of the process are harmful. Kinetic analysis of each stretcher loading system is performed. Comparison of the kinetic analysis and measurements shows very close agreement for most of the cases. The force analysis results are evaluated against derived failure criteria. The evaluation is extended to a biomechanical failure analysis of the ambulance worker's lower back using 3DSSPP software developed at the Centre for Ergonomics at the University of Michigan. The critical tasks of each ambulance worker during the loading and unloading operations for each system are identified. Design recommendations are made to reduce the forces exerted based on loading requirements from the kinetic analysis.

Allied Health Personnel↗

PubMed2005

Lorentz-force-induced motion in conductive media.

This project was designed to assess whether MRI imaging could detect Lorentz-force-induced motion in conductive samples. Experiments were performed by applying alternating voltages across 2% agar and 18% bovine gels placed in the field of a 1.5-T MRI scanner. Motion-sensitized time-gated MRI images that were obtained and analyzed with custom-developed software used in previous studies revealed the production of movement in both agar and gel samples. Motion was most pronounced in the plane vertical to the sample and had the greatest amplitude when the current path was perpendicular to the scanner's magnetic field. These findings are compatible with the vector cross product nature of the Lorentz force and suggest that the imaging of Lorentz-force-induced motion in conductive samples is feasible. Whether this approach can be extended to study electrically active tissues such as the peripheral nerves, brain and heart remains to be seen.

Gels↗

PubMed2004

Optimal source position for irradiation of coronary bifurcations in endovascular brachytherapy with catheter based beta or iridium-192 sources.

BACKGROUND AND PURPOSE: Intracoronary brachytherapy after percutaneous transluminal coronary angioplasty (PTCA) is usually performed with catheter-based treatment techniques in a straight vessel segment. There is a growing interest for treatment of bifurcations, which requires consecutive positioning of the source in main vessel and side branch. MATERIALS AND METHODS: In-house developed software (IC-BT doseplan) is used to explore the optimal positioning of the source in modelled bifurcations with different shape for the source types available in our hospital, i.e. (90)Sr/(90)Y, (32)P and (192)Ir. The results were summarised in look-up tables. The usefulness of these look-up tables was tested on various clinical examples. RESULTS: Tabulated results for the modelled bifurcations yield an estimation of the distance between the sources (gap width) in relation to the geometry and source type: (90)Sr/(90)Y gap range 3-8.5 mm, (32)P gap range 2-7 mm and (192)Ir gap range 3.5-8 mm. The average dose relative to 2 mm from the source axis is: (90)Sr/(90)Y, (mean+/-SD) 120+/-40%; (32)P, 125+/-50% and (192)Ir, 120+/-22%. The look-up tables also provide the coarse location and value of maximum and minimum dose: (90)Sr/(90)Y, 220-60%, (32)P, 230-55% and (192)Ir, 170-85%. It appeared that the look-up tables provide a good approximation of the optimal gap width in the clinical examples. CONCLUSIONS: Tabulated optimal gap widths are very useful for quick estimation of the required gap width for a given bifurcation and source type, in case the prescribed dose in both vessels is the same. In unfavourable geometries there is a risk of local underdosage. Individual treatment planning using a program such as IC-BT doseplan is then recommended.

Angioplasty, Balloon, Coronary↗

PubMed2004

Novel pulsed switched power supply for a fast field cycling NMR spectrometer.

In this paper, we outline the operating principles of a pulsed switched power supply for a fast field-cycling nuclear magnetic resonance spectrometer. The power supply uses a variant of a four-quadrant chopper with a duty cycle that defines the average output current. With this topology only two semiconductors are necessary to drive hundreds of amperes with an output power of several kilowatts. The output current ripple has a well-defined shape that can be reduced to acceptable values by a careful design of the semiconductors' controlling circuits and drivers. A power supply prototype was tested with a home build air-core magnet operating with fields between 0 and 0.21 T. The system is computer controlled using pulse generator and data acquisition PC cards, and specific user-friendly home-developed software. A comparative proton relaxometry study in two well-known liquid crystal compounds 5CB and MBBA was performed to check the reproducibility of the T1 measurements.

Journal Article↗

PubMed2006

Single-trial EEG-fMRI reveals the dynamics of cognitive function.

Two major non-invasive techniques in cognitive neuroscience, electroencephalography (EEG) and functional magnetic resonance imaging (fMRI), have complementary advantages with regard to their spatial and temporal resolution. Recent hardware and software developments have made it feasible to acquire EEG and fMRI data simultaneously. We emphasize the potential of simultaneous EEG and fMRI recordings to pursue new strategies in cognitive neuroimaging. Specifically, we propose that, by exploiting the combined spatiotemporal resolution of the methods, the integration of EEG and fMRI recordings on a single-trial level enables the rich temporal dynamics of information processing to be characterized within spatially well-defined neural networks.

Brain↗

PubMed2004

Acoustic microscopy system: design and preliminary results.

An acoustic microscopy system was designed to perform 2D imaging in the C-plane with a single-element transducer. The ultrasound transducer was fabricated by polishing bulk lithium niobate (LiNbO(3)) to the required thickness (approximately 60 or 45 micro) for the desired operating frequency (55 or 75 MHz). The polished LiNbO(3) was attached to acoustic backing and matching layers. Finally, an epoxy lens was applied and the transducer mounted in a housing. The transducer was mounted in a 3D motorized positioning stage and operated by a high-frequency pulser/receiver. Received echoes were sampled with a 2 GHz ADC card and displayed on a PC using software developed in the Matlab environment. Transducer frequency and bandwidth were measured off a steel plate positioned at the focal length. A penny was scanned initially to confirm expected performance before acquiring data from liver (n=3) and spleen (n=3) specimens. For the first probe, the peak frequency was 54.05 MHz with a -6 dB bandwidth of 6.76 MHz. The axial and lateral resolutions were estimated to be 114 and 188 microm, respectively. For the second probe, the peak frequency was measured to 82 MHz with a -6 dB bandwidth of approximately 23 MHz. The axial and lateral resolutions were estimated to be around 33 and 81 microm, respectively. C-scans of the penny clearly showed detailed structures on front and back, while the capsule and the trabecular structures of the splenic tissues could easily be separated in different layers. In conclusion, an acoustic microscopy system operating at 55-75 MHz has been constructed and the feasibility of obtaining high-resolution images of tissue specimens demonstrated.

Acoustics↗

PubMed2004

Modeling NDT piezoelectric ultrasonic transmitters.

Ultrasonic NDT applications are frequently based on the spike excitation of piezoelectric transducers by means of efficient pulsers which usually include a power switching device (e.g. SCR or MOS-FET) and some rectifier components. In this paper we present an approximate frequency domain electro-acoustic model for pulsed piezoelectric ultrasonic transmitters which, by integrating partial models of the different stages (driving electronics, tuning/matching networks and broadband piezoelectric transducer), allows the computation of the emission transfer function and output force temporal waveform. An approximate frequency domain model is used for the evaluation of the electrical driving pulse from the spike generator. Tuning circuits, interconnecting cable and mechanical impedance matching layers are modeled by means of transmission lines and the classical quadripole approach. The KLM model is used for the piezoelectric transducer. In addition, a PSPICE scheme is used for an alternative simulation of the broadband driving spike, including the accurate evaluation of non-linear driving effects. Several examples illustrate the capabilities of the specifically developed software.

Journal Article↗

PubMed2005

A parametric imaging approach for the segmentation of ultrasound data.

When an ultrasonic examination is performed, a segmentation tool would often be very useful, either for the detection of pathologies, the early diagnosis of cancer or the follow-up of the lesions. Such a tool must be both reliable and accurate. However, because of the relatively reduced quality of ultrasound images due to the speckled texture, the segmentation of ultrasound data is a difficult task. We have previously proposed to tackle the problem using a multiresolution Bayesian region-based algorithm. For computation time purposes, a multiresolution version has been implemented. In order to improve the quality of the segmentation, we propose to perform the segmentation not only from the envelope image but to combine more information about the properties of the tissues in the segmentation process. Several acoustical parameters have thus been computed, either directly from the images or from the radio-frequency (RF) signal. In a previous study, two parametric images were involved in the segmentation process. The parameter represented the integrated backscatter (IBS) and the mean central frequency (MCF), which is a measurement related to the attenuation of ultrasound waves in the media. In this study, parameters representative of the scattering conditions in the tissue are evaluated in the multiparametric segmentation process. They are extracted from the K-distribution (alpha,b) and the Nakagami distribution (m,Omega) and are related to the local density of scatterers (alpha,m), the size of the scatterers (b) and the backscattering properties of the medium (Omega). The acoustical features are calculated locally on a sliding window. This procedure allows to built parametric mapping representing the particular characteristics of the medium. To test the influence of the acoustical parameters in the segmentation process, a set of numerical phantoms has been computed using the Field software developed by J.A. Jensen. Each phantom consists in two regions with two different acoustical properties: the density of scatterers and the scattering amplitude. From both the simulated RF signals and envelope images, the parameters have been computed; their relevance to represent a particular characteristic of the medium is evaluated. The segmentation has been processed for each phantom. The ability of each parameter to improve the segmentation results is validated. A agar-gel phantom has also been created, in order to test the accuracy of the parameters in conditions closer to the in vivo ultrasound imaging. This phantom contains four inclusions with different concentrations of silica. A B&K ultrasound device provides the RF data. The quantification of the segmentation quality is based on the rate of correctly classified pixels and it has been computed for all the parameters either from the field images or the phantom images. The large improvement in the segmentation results obtained reveals that the multiparametric segmentation scheme proposed in this study can be a reliable tool for the processing of noisy ultrasound data.

Mathematics↗

PubMed2006

Numerical simulation of wave propagation in cancellous bone.

Numerical simulation of wave propagation is performed through 31 3D volumes of trabecular bone. These volumes were reconstructed from high synchrotron microtomography experiments and are used as the input geometry in a simulation software developed in our laboratory. The simulation algorithm accounts for propagation into both the saturating fluid and bone but absorption is not taken into account. We show that 3D simulation predicts phenomena observed experimentally in trabecular bones : linear frequency dependence of attenuation, increase of attenuation and speed of sound with the bone volume fraction, negative phase velocity dispersion in most of the specimens, propagation of fast and slow wave depending on the orientation of the trabecular network compared to the direction of propagation of the ultrasound. Moreover, the predicted attenuation is in very close agreement with the experimental one measured on the same specimens. Coupling numerical simulation with real bone architecture therefore provides a powerful tool to investigate the physics of ultrasound propagation in trabecular structures.

Algorithms↗

PubMed2005

Development of a support vector machine-based image analysis system for assessing the thyroid nodule malignancy risk on ultrasound.

An SVM-based image analysis system was developed for assessing the malignancy risk of thyroid nodules. Ultrasound images of 120 cytology confirmed thyroid nodules (78 low-risk and 42 high-risk of malignancy) were manually segmented by a physician using a custom developed software in C++. From each nodule, 40 textural features were automatically calculated and were used with the SVM algorithm in the design of the image analysis system. Highest classification accuracy was 96.7%, misdiagnosing two high-risk and two low-risk thyroid nodules. The proposed system may be of value to physicians as a second opinion tool for avoiding unnecessary invasive procedures.

Algorithms↗

PubMed2005

High throughput sequence analysis reveals hitherto unreported recombination in the genus Norovirus.

Viruses of the Norovirus genus (Caliciviridae family) are a major cause of human gastroenteritis. In some viruses, recombination is an important evolutionary process and therefore we should try to discover the quantity and characteristics of such events in Noroviruses. In order to identify recombination events, multiple sequence alignments were assembled from publicly available strains, and were tested using RAT, a recently developed software tool. Strains identified by RAT as putative recombinants were tested further, using a phylogenetic approach, the LARD software, and a Monte Carlo method, to gain additional support for their status. The identification of two previously described recombinants, WUG1 and Snow Mountain, was made. Furthermore, three instances of hitherto unreported recombination implicating Norovirus strains MD 145-12, Gifu'96 and Saitama U4 were found, with good statistical support for the latter two of these cases. Lordsdale-like viruses were highlighted as major contributors to recombination events during Norovirus evolution. Finally, the relevance of recombinants to the worldwide transmission of Norovirus is discussed.

Caliciviridae Infections↗

PubMed2006

High throughput DNA sequence variant detection by conformation sensitive capillary electrophoresis and automated peak comparison.

We report the development of a heteroduplex-based mutation detection method using multicapillary automated sequencers, known as conformation-sensitive capillary electrophoresis (CSCE). Our optimized CSCE protocol detected 93 of 95 known base substitution sequence variants. Since the optimization of the method, we have analyzed 215 Mb of DNA and identified 3397 unique variants. An analysis of this data set indicates that the sensitivity of CSCE is above 95% in the central 56% of the average PCR product. To fully exploit the mutation detection capacity of this method, we have developed software, canplot, which automatically compares normal and test results to prioritize samples that are most likely to contain variants. Using multiple fluorescent dyes, CSCE has the capacity to screen over 2.2 Mb on one ABI3730 each day. Therefore this technique is suitable for projects where a rapid and sensitive DNA mutation detection system is required.

Algorithms↗

PubMed1987

Evaluation of myocardial perfusion and function by single photon emission computed tomography.

Although planar radionuclide techniques provide accurate, noninvasive measurements of myocardial perfusion and function that are of proven clinical value in the evaluation of the cardiac patient, they are limited by poor object contrast and superimposition of surrounding structures. Due to incomplete angular sampling and significant longitudinal distortion, limited angle tomography did not solve these problems. Single photon emission computed tomography (SPECT) can acquire scintillation information over very small angles of rotation and, thus, improve both object contrast and delineation of overlying or adjacent structures without distortion. The early SPECT systems were cumbersome, dependent on individual user developed software, and had extremely long acquisition and processing time. Improved camera design, new software algorithms, and the use of array processors have simplified and standardized quality control, decreased processing time, and minimized the number of user interventions. New image display formats and quantitative methods of analysis have made interpretation less cumbersome, more reliable and highly reproducible. Cardiac SPECT has been used with thallium-201 and gated blood pool imaging in both research and clinical applications and shown an improvement over planar methods of acquisition.

Algorithms↗

PubMed2002

Acid hydrolysis of silk fibroins and determination of the enrichment of isotopically labeled amino acids using precolumn derivatization and high-performance liquid chromatography-electrospray ionization-mass spectrometry.

Silk fibroins from moth larvae and spiders are composed of highly repetitive Ala- and Gly-rich blocks that determine their structure, properties, and function. To investigate the metabolic integration of isotopically labeled amino acids in the excreted silk, the enrichment of ingested tracers was determined after acid hydrolysis of the fibroins. Thus, spiders and moth larvae were fed with stable isotope tracers such as [1-13C]Ala or [1-13C]Gly and silked. After hydrolysis of the silk proteins, the corresponding amino acids were derivatized with Nalpha-(2,4-dinitro-5-fluorophenyl)-L-alaninamide (Marfey's reagent) and separated by liquid chromatography. The isotopical enrichment of the amino acids was determined by online electrospray mass spectrometry and calculated by newly developed software. Depending on the feeding protocol, enrichments of up to 58% in Gly and 31% in Ala were found in the investigated silks. The highly enriched silk fibroins are suitable for further structural investigation such as solid-state nuclear magnetic resonance.

Acetic Acid↗

PubMed2003

Fluorescent in situ sequencing on polymerase colonies.

Integration of DNA isolation, amplification, and sequencing can be achieved by the use of polymerase colonies (polonies) and cycles of fluorescent dNTP incorporation. In this paper, we present four advances that bring us closer to sequencing genomes cost-effectively using the polony technology. First, a polymerase trapping technique enables efficient nucleotide extension by DNA polymerase in a polyacrylamide matrix and eliminates loss of enzyme during sequencing cycles. Next, we present two novel types of reversibly dye-labeled nucleotide analogues, show that DNA polymerase can incorporate these analogues, and demonstrate that the dyes can be removed by thiol reduction or light exposure. Using these nucleotides, we have sequenced multiple polonies in parallel. In addition, we have found that a high density of polonies can be achieved with minimal overlap between adjacent polonies by limiting the concentration of free primer in the polony amplification reactions. Finally, we have developed software for automated image alignment and sequence calling.

DNA-Directed DNA Polymerase↗

PubMed2000

Helmet accommodation analysis using 3D laser scanning.

A method used to determine the probable population accommodation of a helmet sizing system is described. The method involves the use of 3D laser scanning, as a means of measuring helmet standoff distance (distance between the inside of the helmet and the skull), and the selection of a representative sample of test subjects. The laser scanner and the software developed to calculate standoff distance proved to be an excellent tool for the assessment of helmet fit. The main advantages include ease of use and visualization of problem areas. This 3D-analysis method gives designers objective evidence of the need for design changes as well as an idea of what these changes should be. A comparison was made between standoff distance results obtained from the scanner and those obtained using a physical measurement method (a probe). Although discrepancies were found between the two, sources of errors intrinsic to both methods make it difficult to determine which of the two methods yielded the truest standoff distance. Analysis of the comparison data shows laser scanning to be slightly more conservative than the probe method for standoff distance purposes, i.e. erring on the side of safety.

Cephalometry↗