Biomedical subjects

J M Roos

Publications and source records attributed to J M Roos.

10 recordsLinked to original sources

PubMed1999

Maximum likelihood estimation in calibrating a stereo camera setup.

Motion and deformation of the cardiac wall may be measured by following the positions of implanted radiopaque markers in three dimensions, using two x-ray cameras simultaneously. Regularly, calibration of the position measurement system is obtained by registration of the images of a calibration object, containing 10-20 radiopaque markers at known positions. Unfortunately, an accidental change of the position of a camera after calibration requires complete recalibration. Alternatively, redundant information in the measured image positions of stereo pairs can be used for calibration. Thus, a separate calibration procedure can be avoided. In the current study a model is developed that describes the geometry of the camera setup by five dimensionless parameters. Maximum Likelihood (ML) estimates of these parameters were obtained in an error analysis. It is shown that the ML estimates can be found by application of a nonlinear least squares procedure. Compared to the standard unweighted least squares procedure, the ML method resulted in more accurate estimates without noticeable bias. The accuracy of the ML method was investigated in relation to the object aperture. The reconstruction problem appeared well conditioned as long as the object aperture is larger than 0.1 rad. The angle between the two viewing directions appeared to be the parameter that was most likely to cause major inaccuracies in the reconstruction of the 3-D positions of the markers. Hence, attempts to improve the robustness of the method should primarily focus on reduction of the error in this parameter.

Biomechanical Phenomena↗

PubMed1997

Tracking markers with missing data by lower rank approximation.

Motion and deformation of an object may be quantified by following attached markers in video or cine frame sequences. When recording cardiac motion by video (256 x 256 pixels, 50 Hz), generally no more than approximately 20 markers can be followed due to difficulties in proper identification of marker images. In the present study we developed the lower rank (LR) tracking method which can automatically follow considerably more than 20 markers. The performance of the method was evaluated in computer simulations of naturally moving myocardial markers observed in a sequence of 60 video frames. White noise was added to the marker coordinates. Realistic loss of data due to detection failure was simulated by deleting a generated marker image when the distance to another marker image was below a given minimum value. In a test, realistic values were substituted for the noise level sigma (0.5 pixel) and the minimum marker distance dm (4 pixels). For numbers of markers ranging from 50 to 100, 95-90% of the detected marker images was correctly tracked. Less than 0.7% was part of a false track, i.e. a track containing images of different markers. Under less favourable conditions (sigma = 1 pixel; dm = 8 pixels) the method was robust: for 75 markers with 40% of the marker images missing, still 70% of the detected images was correctly tracked, while the fraction in false tracks did not increase. The LR tracking method appears reliable for automatic tracking of large amounts of moving markers in a sequence of video or cine frames.

Algorithms↗

PubMed1993

Extrapolation of incomplete marker tracks by lower rank approximation.

Motion and deformation of an object such as the heart may be measured by tracking optical or radiopaque markers. In the experimental situation markers may fail to be detected due to occlusion or lack of contrast. As a result a continuous marker track is observed in separated parts, which often cannot be directly identified as corresponding to one marker. This paper presents a method of extrapolating a partly known track by using information provided by the known track part and the available complete tracks of other markers. The extrapolations are obtained by iteratively fitting a lower rank matrix to the set of noisy, incomplete marker tracks. The performance is evaluated with computer-simulated data and data obtained in an animal experiment. In both cases 43% of the available complete tracks were made incomplete by removal of track parts varying in length from 3% up to 44%. For the simulated data comparison of the extrapolations with true signal values results in a root mean square (RMS) error about equal to the noise level. For the animal experiment, when comparing the extrapolations with the measured values, in images of 256 x 256 pixels, the RMS error was found to be +/- 0.5 pixel, which is quite small relative to the total excursion of a marker (20 pixels). Estimation of the missing data by applying BMDPAM (BMDP Statistical Software Inc.) to the same data results in RMS errors which are about twice as high.

Algorithms↗

PubMed1993

Recombinant-expressed virus-like particle pseudotypes as an approach to vaccine development.

Coinfection of a cell with two different types of enveloped virus can result in the generation of infectious virus particle pseudotypes having the internal proteins of one virus and the envelope proteins of the other virus. Vaccinia virus recombinants expressing either non-infectious virus-like particles of simian immunodeficiency virus (SIV) or the gD2 glycoprotein of herpes simplex virus were used to coinfect cells to determine if virus-like particle pseudotypes would be formed. Sucrose gradient sedimentation analysis and immunoprecipitation with a monoclonal antibody provided independent evidence of virus-like particle pseudotype formation. Preparations of such particles were immunogenic in mice. Recombinant-expressed virus-like particles thus represent a novel vaccine approach to presenting envelope glycoprotein antigens in a non-infectious state that mimics natural infection.

Animals↗

PubMed1993

Host range selection of vaccinia recombinants containing insertions of foreign genes into non-coding sequences.

A simple yet powerful selection system was developed for the insertion of foreign genes in vaccinia virus. The selection system utilizes the vaccinia virus K1L (29K) host range gene which is located in HindIII M. This gene is necessary for growth in RK-13 cells but not in BSC40 or CV-1 cells. A vaccinia mutant (vAbT33) unable to grow on RK-13 cells was constructed having sequences at the 3' end of the K1L gene and the adjacent M2L gene deleted and replaced with the beta-galactosidase gene regulated by the BamHI F (F7L) promoter. A recombination plasmid containing the hepatitis B surface (HBs) antigen gene regulated by the M2L promoter and the complete sequence of the K1L gene was used to insert the HBs gene into vAbT33. The M2L negative K1L positive recombinant was easily isolated in two rounds of plaque purification by plating the virus on RK-13 cell monolayers. The K1L gene selection system allows the isolation of recombinants arising at frequencies as low as 1/100,000. It was noted that recombinants containing vaccinia sequence duplications (promoters) resulted in intragenomic recombinations that eliminated all sequences between the duplications. A second recombination plasmid was constructed that allowed insertion into the vaccinia genome without the loss of vaccinia coding sequences. This was achieved by insertion of the pseudorabies virus GIII gene regulated by the vaccinia H5R (40K) promoter between the translation and transcription stop signals at the 3' end of the K1L gene. The K1L gene transcription stop signal thus became the stop signal for the inserted GIII gene and an upstream transcription stop signal present in the H5R promoter fragment provided the stop signal for the K1L gene. This manipulation of the vaccinia genome had no effect on the accumulation or 5' end of the M2L gene transcripts. Although the insertion lengthened the 3' end and lowered the accumulation of K1L transcripts it altered neither the virulence nor the immunogenicity of the recombinant.

Base Sequence↗

PubMed1992

An interactive computer program for randomization analysis of response curves with facilities for multiple comparisons.

An interactive Fortran program, MUCRA, is presented. The program can perform randomization analysis of a completely randomized or randomized-blocks design extended to growth and response curves. A single-step Scheffé-type procedure as well as the Peritz's closed step-down procedure have been implemented which control the familywise type I error-rate. In general, MUCRA is suitable as a computer tool for a distribution-free analysis of variance with repeated measures. The use of MUCRA is demonstrated by analyzing the effects oxprenolol and atenolol have on exercise heart rate. Oxprenolol is a non-selective beta-blocker with moderate intrinsic sympathomimetic activity (ISA), given by the Oros delivery system. Atenolol is a beta 1-selective blocker without ISA. A randomized placebo-controlled crossover design was used to compare the effects of the beta 1-blockers on heart rate during a progressive maximal exercise test on a bicycle ergometer. Application of the Scheffé-type procedure showed that the two drugs significantly (alpha = .05) reduce the heart rate during the exercise test at the three prechosen times (2, 5, and 24 hr) after intake. The reduction from atenolol is more pronounced than from oxprenolol Oros at 2 and 5 hr.

Adult↗

PubMed1992

par-4, a gene required for cytoplasmic localization and determination of specific cell types in Caenorhabditis elegans embryogenesis.

Specification of some cell fates in the early Caenorhabditis elegans embryo is mediated by cytoplasmic localization under control of the maternal genome. Using nine newly isolated mutations, and two existing mutations, we have analyzed the role of the maternally expressed gene par-4 in cytoplasmic localization. We recovered seven new par-4 alleles in screens for maternal effect lethal mutations that result in failure to differentiate intestinal cells. Two additional par-4 mutations were identified in noncomplementation screens using strains with a high frequency of transposon mobility. All 11 mutations cause defects early in development of embryos produced by homozygous mutant mothers. Analysis with a deficiency in the region indicates that it33 is a strong loss-of-function mutation. par-4(it33) terminal stage embryos contain many cells, but show no morphogenesis, and are lacking intestinal cells. Temperature shifts with the it57ts allele suggest that the critical period for both intestinal differentiation and embryo viability begins during oogenesis, about 1.5 hr before fertilization, and ends before the four-cell stage. We propose that the primary function of the par-4 gene is to act as part of a maternally encoded system for cytoplasmic localization in the first cell cycle, with par-4 playing a particularly important role in the determination of intestine. Analysis of a par-4; par-2 double mutant suggests that par-4 and par-2 gene products interact in this system.

Animals↗

PubMed1992

Molecular attenuation of vaccinia virus: mutant generation and animal characterization.

These studies demonstrated that the inbred BALB/c mouse strain can be optimized for the assessment of vaccinia virus virulence, growth, and spread from the site of inoculation and immune protection from a lethal vaccinia virus challenge. The studies established that manipulation of the vaccinia virus genome generated mutants exhibiting a wide range of attenuated phenotypes. The nine NYCBH vaccinia virus mutants had intracranial 50% lethal doses that ranged from 2 to greater than 7 log10 units. The decreased neurovirulence was due to decreased replication in brain tissue. Three mutants had a decreased ability to disseminate to the lungs, brains, livers, and spleens of mice after intranasal infection. One mutant had a decreased transmission from mice infected by tail scarification to naive cage mates. Although the mutants, with one exception, grew to wild-type titers in cell culture, they showed a growth potential on the scarified skin of mice that was dramatically different from that of the wild-type virus. Consequently, all of the mutants had significantly compromised immunogenicities at low virus immunization doses compared with that of the wild-type virus. Conversely, at high immunization doses most mutants could induce an immune response similar to that of the wild-type virus. Three Wyeth vaccine strain mutants were also studied. Whereas the thymidine kinase, ribonucleotide reductase, and hemagglutinin mutants had a reduced virulence (50% lethal dose), only the thymidine kinase mutant retained its immunogenicity.

Administration, Intranasal↗

PubMed1990

Molecular analysis of zyg-11, a maternal-effect gene required for early embryogenesis of Caenorhabditis elegans.

The product of the maternally acting gene zyg-11 is required for early embryogenesis of Caenorhabditis elegans. One-cell embryos that lack a functional zyg-11 gene product exhibit an arrest of meiosis at metaphase II, a delay in the formation of pronuclei, unusually vigorous movements of cytoplasm, the formation of multiple pronuclei, incorrect segregation of P granules, and incorrect placement of the first cleavage furrow. We have isolated and sequenced a molecular clone of zyg-11, and shown that microinjection of the cloned DNA can rescue zyg-11 mutations. A transcriptional analysis shows that transcription of the gene is not limited to the female germ-line, despite the strict maternal-effect phenotype of zyg-11 mutations.

Amino Acid Sequence↗

PubMed1990

Noise reduction in estimating cardiac deformation from marker tracks.

Deformation of the cardiac wall is measured by using optical or radiopaque markers attached to the wall. When digitized images are used, the accuracy of the measurement of a marker position is limited by pixel resolution and the size of the marker. The spatial accuracy is improved by singular value decomposition (SVD) filtering. This filtering procedure is based on the assumption that displacements of markers are mutually related because they are embedded in a common continuum. In a computer stimulation with 48 markers in 51 video frames, the accuracy of the measurement of a marker position improved from 0.14 to 0.045 (SD) pixel. In an open-chest animal experiment, with markers on the surface of the heart, the deformation patterns were extracted more clearly using SVD filtering, while mutually related high-frequency components were not suppressed. In a 50-frame sequence of 256 X 256 video images of a 45 mm X 35 mm deforming surface with 50 markers of 8 pixels in diameter, the marker position resolution improves from 0.1 to 0.03 (SD) pixel (6 microns). Strain is determined with an accuracy of 0.002 over a distance of 30 pixels (6 mm).

Animals↗