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PubMed2004

Generalized parallel-perspective stereo mosaics from airborne video.

In this paper, we present a new method for automatically and efficiently generating stereoscopic mosaics by seamless registration of images collected by a video camera mounted on an airborne platform. Using a parallel-perspective representation, a pair of geometrically registered stereo mosaics can be precisely constructed under quite general motion. A novel parallel ray interpolation for stereo mosaicing (PRISM) approach is proposed to make stereo mosaics seamless in the presence of obvious motion parallax and for rather arbitrary scenes. Parallel-perspective stereo mosaics generated with the PRISM method have better depth resolution than perspective stereo due to the adaptive baseline geometry. Moreover, unlike previous results showing that parallel-perspective stereo has a constant depth error, we conclude that the depth estimation error of stereo mosaics is in fact a linear function of the absolute depths of a scene. Experimental results on long video sequences are given.

Aircraft↗
PubMed2003

Aquaporin gene expression and regulation in the ovine fetal lung.

Fetal lung development is dependent upon secretion of liquid into the future airways which must be cleared at birth to establish air-breathing. Aquaporins (AQP) 1, 3, 4 and 5 are membranous water channel proteins that are present in the lung after birth in rodents, with little expression before birth. Our aim was to describe the changes in AQP1, 3, 4 and 5 expression and protein levels in the fetal lung of a long-gestation species (sheep) and in response to physiological factors known to alter fetal lung liquid dynamics. Both mRNA and high protein levels were detected for AQP1, 3, 4 and 5 by day 100 (term is ~150 days in ovine fetuses). A cortisol infusion (120-131 days) significantly (P < 0.05) increased AQP1 (0.9 +/- 0.2 (n = 4) vs.1.8 +/- 0.3 (n = 5)) and AQP5 (8.8 +/- 0.6 vs. 14.1 +/- 1.2) mRNA levels in fetal lung (measured by real-time PCR). Ten days of tracheal obstruction significantly (P < 0.05) decreased AQP5 mRNA levels (6.1 +/- 0.9 (n = 5) vs. 2.7 +/- 0.3 (n = 5)). Immunohistochemistry was used to show that protein levels changed in parallel with the mRNA changes. These findings suggest that AQPs could be involved in lung liquid production and reabsorption during fetal development in long-gestation species.

Aging↗
PubMedDate not supplied

Multiple regression and vector analyses of laser in situ keratomileusis for myopia and astigmatism.

PURPOSE: To construct a quantitative model relating refractive results to laser settings and other factors. METHODS: A prospective clinical trial was performed, including 14 surgeons and 523 eyes of 278 patients who desired correction of myopia from -1.00 to -16.00 D (mean, -6.20 D) and astigmatism up to 6.00 D (mean, 1.10 D). Myopia and astigmatism were corrected by laser in situ keratomileusis (LASIK) with sequential spherical and cylindrical ablations using a 5.5-mm ablation zone and a transition zone to 7.0 mm. The Nidek EC-5000 excimer laser and the Chiron Automated Corneal Shaper were used. RESULTS: Surgically induced refractive changes 3 months after surgery were measured. Spherical ablation by LASIK produced a 19% greater refractive change than that predicted by the Nidek PRK algorithm. The laser setting needed to achieve each 1.00 D of cylinder correction induced 1.30 D change in spherical equivalent refraction (0.80 D more than expected). Patient age and nonlinear effects had small but statistically significant influences on refractive outcome. Sex, left/right eye, and surgeon were not significant factors. Residual variations in spherical equivalent refraction included a 0.50-D constant plus 9% of the predicted spherical equivlanet change. Residual variations in the parallel and orthogonal components of cylinder correction were, respectively, 28% and 13% of the predicted cylinder change plus a 0.30-D constant component. The standard deviation of axis alignment error for cylinder ablation was 3.7 degrees. CONCLUSIONS: Cylindrical ablation produced a spherical change that was larger than expected. To compensate for this, spherical ablation should be reduced in eyes with astigmatism. Variability in the correction of astigmatism was proportionally larger than that for spherical correction and was primarily due to magnitude rather than axis error.

Adult↗
PubMed1995

Evaluation of SPECT quantification of radiopharmaceutical distribution in canine myocardium.

UNLABELLED: This study evaluates the quantitative accuracy of SPECT for in vivo distributions of 99mTc radiopharmaceuticals using fanbeam (FB) and parallel-beam (PB) collimators and compares uniform and nonuniform attenuation correction methods in terms of quantitative accuracy. METHODS: SPECT quantification of canine myocardial radioactivity was performed followed by well counter measurements of extracted myocardial tissue samples. Transmission scans using a line source and an FB collimator were performed to generate nonuniform attenuation maps of the canine thorax. Emission scans with two energy windows were acquired. Images were reconstructed using a filtered backprojection algorithm, with a dual-window scatter subtraction combined with either no attenuation compensation or single iteration Chang attenuation compensation based on an uniform attenuation map (mu = 0.152 cm-1) or the nonuniform transmission map. RESULTS: The measured mean counts from the SPECT images were converted to radionuclide concentrations (MBq/g) using a standard source calibration and were compared with those obtained using the well counter. CONCLUSION: The experimental results demonstrate that, compared with well counter values, the in vivo distributions of 99mTc were most accurately determined in FB and PB SPECT reconstructions with nonuniform attenuation compensation, under-estimated without attenuation compensation and overestimated with uniform attenuation compensation.

Animals↗
PubMed1996

Detection of non-topological motifs in protein structures.

We present an efficient technique for the comparison of protein structures. The algorithm uses a vector representation of the secondary structure elements and searches for spatial configurations of secondary structure elements in proteins. In such recurring protein folds, the order of the secondary structure elements in the protein chains is disregarded. The method is based on the geometric hashing paradigm and implements approaches originating in computer vision. It represents and matches the secondary structure element vectors in a 3-D translation and rotation invariant manner. The matching of a pair of proteins takes on average under 3 s on a Silicon Graphics Indigo2 workstation, allowing extensive all-against-all comparisons of the data set of non-redundant protein structures. Here we have carried out such a comparison for a data set of over 500 protein molecules. The detection of recurring topological and non-topological, secondary structure element order-independent protein folds may provide further insight into evolution. Moreover, as these recurring folding units are likely to be conformationally favourable, the availability of a data set of such topological motifs can serve as a rich input for threading routines. Below, we describe this rapid technique and the results it has obtained. While some of the obtained matches conserve the order of the secondary structure elements, others are entirely order independent. As an example, we focus on the results obtained for Che Y, a signal transduction protein, and on the profilin-beta-actin complex. The Che Y molecule is composed of a five-stranded, parallel beta-sheet flanked by five helices. Here we show its similarity with the Escherichia coli elongation factor, with L-arabinose binding protein, with haloalkane dehalogenase and with adenylate kinase. The profilin-beta-actin contains an antiparallel beta-pleated sheet with alpha-helical termini. Its similarities to lipase, fructose disphosphatase and beta-lactamase are displayed.

Algorithms↗
PubMed1999

An algorithm for evaluating human cytotoxic T lymphocyte responses to candidate AIDS vaccines.

Development of an effective vaccine against HIV-1 will likely require the induction of a broad array of immune responses, including virus-specific CTLs and neutralizing antibodies. One promising vaccine approach involves live recombinant canarypox (CP)-based vectors (ALVAC) containing multiple HIV-1 genes. In phase I clinical trials in HIV-1-seronegative volunteers, the cumulative rate of detection of HIV-1-specific CTLs has been as high as 60-70%. In the present study, the factors associated with CTL responsiveness were evaluated in a subset of vaccinees immunized with a CP vector expressing portions of the gag, pro, and env genes of HIV-1 (ALVAC-HIV). CTL responses were detected in one of seven examined. While the responding individual had both CD4+ and CD8+ CTLs directed at multiple HIV-1 antigens, this response was not detectable 1 year after the last vaccination. In-depth characterization of "CTL nonresponders" showed that nonresponsiveness was not associated with defects in antigen processing or presentation. A generalized defect in CTL responsiveness was ruled out by parallel assays to detect CMV-specific CTLs from these same volunteers. Furthermore, HIV-1-specific memory CTLs were not detectable by peptide stimulation or by a novel technique for flow cytometric visualization of Gag epitope-specific T lymphocytes while HIV-1-seropositive donors frequently had 0.1-3% of CD8+ cells stain positively for this epitope (SLYNTVATL). Taken together, these results suggest that the lack of detectable HIV-1 CTLs in these volunteers was not due to classic MHC-linked nonresponsiveness.

AIDS Vaccines↗
PubMed2005

Modeling and optimization of high-sensitivity, low-volume microfluidic-based surface immunoassays.

Microfluidics are emerging as a promising technology for miniaturizing biological assays for applications in diagnostics and research in life sciences because they enable the parallel analysis of multiple analytes with economy of samples and in short time. We have previously developed microfluidic networks for surface immunoassays where antibodies that are immobilized on one wall of a microchannel capture analytes flowing in the microchannel. This technology is capable of detecting analytes with picomolar sensitivity and from sub-microliter volume of sample within 45 min. This paper presents the theoretical modeling of these immunoassays where a finite difference algorithm is applied to delineate the role of the transport of analyte molecules in the microchannel (convection and diffusion), the kinetics of binding between the analyte and the capture antibodies, and the surface density of the capture antibody on the assay. The model shows that assays can be greatly optimized by varying the flow velocity of the solution of analyte in the microchannels. The model also shows how much the analyte-antibody binding constant and the surface density of the capture antibodies influence the performance of the assay. We then derive strategies to optimize assays toward maximal sensitivity, minimal sample volume requirement or fast performance, which we think will allow further development of microfluidic networks for immunoassay applications.

Antigen-Antibody Complex↗
PubMed2005

Hepatobiliary disposition of liposomal amphotericin B in the isolated perfused rat liver.

The hepatic distribution, biliary excretion, and mass balance of liposomal amphotericin B (L-AmB) were investigated in recirculated isolated perfused rat liver. The results were compared with those from the conventional AmB formulation, amphotericin B deoxycholate (D-AmB). L-AmB was introduced as a bolus into the perfusate reservoir, at doses of 1000, 4000, and 8000 mug, to achieve therapeutically relevant concentrations. AmB concentrations in perfusate, ultrafiltrate, bile, and liver homogenate over 120 min were measured using a validated high-performance liquid chromatography assay. AmB hepatic disposition in isolated perfused rat liver after L-AmB bolus was characterized by a higher recovery in perfusate (81.7 +/- 9.4%, n = 13) and a significant decrease in hepatic distribution (5.9 +/- 2.4% at low dose, 2.4 +/- 0.9% at medium dose, and 1.9 +/- 0.7% at high dose) compared with D-AmB (32.2 +/- 4.5% in perfusate, 52.1 +/- 8.2% in liver at the dose of 198 microg). Tissue-to-perfusate partition coefficient of L-AmB calculated at 120 min decreased dramatically with the dose and was approximately 100-fold less than that achieved with D-AmB at the high dose (0.17 +/- 0.11 in L-AmB versus 15.82 +/- 6.43 in D-AmB). AmB displayed negligible biliary excretion, representing <0.1% of the dose administered with L-AmB. Hepatic uptake clearance of L-AmB (CL(H,uptake)) decreased with the increase in perfusate area under the curve at each dose. The relationship between perfusate area under the curve and CL(H,uptake) was described by a parallel hepatic uptake clearance model. In conclusion, liposomal encapsulation significantly alters the hepatobiliary disposition of AmB; the ability of liposomes to sequester AmB and the dose-dependent hepatic uptake clearance may account for dose-form-dependent differences in AmB pharmacokinetics.

Algorithms↗
PubMed2002

In vitro, pharmacokinetic, and pharmacodynamic interactions of ketoconazole and midazolam in the rat.

Interactions of midazolam and ketoconazole were studied in vivo and in vitro in rats. Ketoconazole (total dose of 15 mg/kg intraperitoneally) reduced clearance of intravenous midazolam (5 mg/kg) from 79 to 55 ml/min/kg (p < 0.05) and clearance of intragastric midazolam (15 mg/kg) from 1051 to 237 ml/min/kg (p < 0.05), increasing absolute bioavailability from 0.11 to 0.36 (p < 0.05). Presystemic extraction occurred mainly across the liver as opposed to the gastrointestinal tract mucosa. Midazolam increased electroencephalographic (EEG) amplitude in the beta-frequency range. Ketoconazole shifted the concentration-EEG effect relationship rightward (increase in EC(50)), probably because ketoconazole is a neutral benzodiazepine receptor ligand. Ketoconazole competitively inhibited midazolam hydroxylation by rat liver and intestinal microsomes in vitro, with nanomolar K(i) values. At a total serum ketoconazole of 2 microg/ml (3.76 microM) in vivo, the predicted reduction in clearance of intragastric midazolam by ketoconazole (to 6% of control) was slightly greater than the observed reduction in vivo (to 15% of control). However, unbound serum ketoconazole greatly underpredicted the observed clearance reduction. Although the in vitro and in vivo characteristics of midazolam in rats incompletely parallel those in humans, the experimental model can be used to assess aspects of drug interactions having potential clinical importance.

Algorithms↗
PubMed2006

Genetic Parallel Programming: design and implementation.

This paper presents a novel Genetic Parallel Programming (GPP) paradigm for evolving parallel programs running on a Multi-Arithmetic-Logic-Unit (Multi-ALU) Processor (MAP). The MAP is a Multiple Instruction-streams, Multiple Data-streams (MIMD), general-purpose register machine that can be implemented on modern Very Large-Scale Integrated Circuits (VLSIs) in order to evaluate genetic programs at high speed. For human programmers, writing parallel programs is more difficult than writing sequential programs. However, experimental results show that GPP evolves parallel programs with less computational effort than that of their sequential counterparts. It creates a new approach to evolving a feasible problem solution in parallel program form and then serializes it into a sequential program if required. The effectiveness and efficiency of GPP are investigated using a suite of 14 well-studied benchmark problems. Experimental results show that GPP speeds up evolution substantially.

Algorithms↗
PubMed2004

Improved parametric imaging of scatterer size estimates using angular compounding.

The feasibility of estimating and imaging scatterer size using backscattered ultrasound signals and spectral analysis techniques was demonstrated previously. In many cases, size estimation, although computationally intensive, has proven to be useful for monitoring, diagnosing, and studying disease. However, a difficulty that is encountered in imaging scatterer size is the large estimator variance caused by statistical fluctuations in echo signals from random media. This paper presents an approach for reducing these statistical uncertainties. Multiple scatterer size estimates are generated for each image pixel using data acquired from several different directions. These estimates are subsequently compounded to yield a single estimate that has a reduced variance. In this feasibility study, compounding was achieved by translating a sectored-array transducer in a direction parallel to the acquired image plane. Angular compounding improved the signal-to-noise ratio (SNR) in scatterer size images. The improvement is proportional to the square root of the effective number of statistically independent views available for each image pixel.

Algorithms↗
PubMed1994

The cardiofocal collimator: a variable-focus collimator for cardiac SPECT.

Investigators in nuclear medicine have long been in search of a practical method to increase the number of detected events in cardiac SPECT. A clinically practical method requires a simple data acquisition protocol, clinically acceptable reconstruction times, artifact levels near or below visual threshold, and the use of currently available cameras and computers. Towards this end, we have developed the Cardiofocal collimator, a variable-focus collimator for cardiac SPECT that increases the number of detected events from the heart by more than a factor of two compared to that of a parallel-hole collimator with equivalent resolution. In both the transverse and axial dimensions, the focusing is strongest at the centre of the collimator, and gradually relaxes to nearly parallel-hole collimation at the edge of the collimator. The variable-focus concept provides an increase in the number of counts from organs imaged near the centre of the collimator, where the heart will spend most of the time during a cardiac SPECT study, while adequately sampling enough of the background activity distribution to prevent truncation artifacts in the reconstructed images. Images are reconstructed in clinically acceptable times using a filtered backprojection reconstruction algorithm. The algorithm supports both full-scan (360 degrees) and short-scan (180 degrees plus the fan angle) acquisitions. The results of simulations and phantom studies are included to demonstrate the performance of the Cardiofocal collimator.

Algorithms↗
PubMed2001

Automated identification of Fos expression.

The concentration of Fos, a protein encoded by the immediate-early gene c-fos, provides a measure of synaptic activity that may not parallel the electrical activity of neurons. Such a measure is important for the difficult problem of identifying dynamic properties of neuronal circuitries activated by a variety of stimuli and behaviours. We employ two-stage statistical pattern recognition to identify cellular nuclei that express Fos in two-dimensional sections of rat forebrain after administration of antipsychotic drugs. In stage one, we distinguish dark-stained candidate nuclei from image background by a thresholding algorithm and record size and shape measurements of these objects. In stage two, we compare performance of linear and quadratic discriminants, nearest-neighbour and artificial neural network classifiers that employ functions of these measurements to label candidate objects as either Fos nuclei, two touching Fos nuclei or irrelevant background material. New images of neighbouring brain tissue serve as test sets to assess generalizability of the best derived classification rule, as determined by lowest cross-validation misclassification rate. Three experts, two internal and one external, compare manual and automated results for accuracy assessment. Analyses of a subset of images on two separate occasions provide quantitative measures of inter- and intra-expert consistency. We conclude that our automated procedure yields results that compare favourably with those of the experts and thus has potential to remove much of the tedium, subjectivity and irreproducibility of current Fos identification methods in digital microscopy.

Journal Article↗
PubMed2004

Finite helical axes of motion are a useful tool to describe the three-dimensional in vitro kinematics of the intact, injured and stabilised spine.

The finite helical-axes method can be used to describe the three-dimensional in vitro kinematics of the spine. However, this method still suffers from large stochastic calculation errors and poorly conceived visualisation techniques. The aim of the present study, therefore, was to improve the currently used finite helical axes description, by use of a less error-prone calculation algorithm and a new visualisation technique, and to apply this improved method to the study of the three-dimensional in vitro kinematics of the spine. Three-dimensional, continuous motion data of spinal motion segments were used to calculate the position and orientation of the finite helical axes (FHAs). The axes were then projected on plane antero-posterior, lateral and axial radiographs in order to depict the relation to the anatomy of each individual specimen. A hinge joint was used to estimate the measurement error of data collection and axes calculation. In an exemplary in vitro experiment, this method was used to demonstrate the ability of a prosthetic disc nucleus to restore the three-dimensional motion pattern of lumbar motion segments. In the validation experiment with the hinge joint, the calculated FHAs were lying within +/-2.5 mm of the actual joint axis and were inclined relative to this axis at up to +/-1.5 degrees . In the exemplary in vitro experiment, the position and orientation of the FHAs of the intact specimens were subject to large inter-individual differences in all loading directions. Nucleotomy of the lumbar segments caused the axes to spread out, indicating complex coupled motions. The implantation of the prosthetic disc nucleus, for the most part, more than reversed this effect: the axes became oriented almost parallel to each other. The experiments showed that the present improved description of finite helical axes is a valid and useful tool to characterise the three-dimensional in vitro kinematics of the intact, injured and stabilised spine. The main advantage of this new method is the comprehensive visualisation of joint function with respect to the individual anatomy.

Algorithms↗
PubMed2003

A QM-MM interface between CHARMM and TURBOMOLE: implementation and application to systems in bulk phase and biologically active systems.

The implementation of a hybrid QM-MM approach combining ab initio and density functional methods of TURBOMOLE with the molecular mechanics program package CHARMM is described. An interface has been created to allow data exchange between the two applications. With this method the efficient multiprocessor capabilities of TURBOMOLE can be utilized with CHARMM running as a single processor application. Therefore, features of nonparallel running code in CHARMM like the TRAVEL module for locating saddle points or VIBRAN for the calculation of second derivatives can be exploited by running the CPU intensive QM calculations in parallel. To test the methodology, several small systems are studied with both Hartree-Fock and density functional methods and varying QM-MM boundaries. Also, the computationally efficient RI-J method has been examined for use in QM-MM applications. A B(12) cofactor containing cobalt has been studied, to examine systems with a large QM region and transition metals. All tested methods perform satisfactory in comparison with pure quantum calculations. Additionally, algorithms for the characterization of saddle points have been tested for their potential use in QM-MM problems. The TRAVEL module of CHARMM has been applied to the Menshutkin reaction in the condensed phase, and a saddle point was located. This saddle point was verified by calculation of a steepest descent path connecting educt, transition state, and product, and by calculation of vibrational modes.

Cobamides↗
PubMed2005

XMVB: a program for ab initio nonorthogonal valence bond computations.

An ab initio nonorthogonal valence bond program, called XMVB, is described in this article. The XMVB package uses Heitler-London-Slater-Pauling (HLSP) functions as state functions, and calculations can be performed with either all independent state functions for a molecule or preferably a few selected important state functions. Both our proposed paired-permanent-determinant approach and conventional Slater determinant expansion algorithm are implemented for the evaluation of the Hamiltonian and overlap matrix elements among VB functions. XMVB contains the capabilities of valence bond self-consistent field (VBSCF), breathing orbital valence bond (BOVB), and valence bond configuration interaction (VBCI) computations. The VB orbitals, used to construct VB functions, can be defined flexibly in the calculations depending on particular applications and focused problems, and they may be strictly localized, delocalized, or bonded-distorted (semidelocalized). The parallel version of XMVB based on MPI (Message Passing Interface) is also available.

Journal Article↗
PubMed2006

A novel registration method for interval change detection between two chest X-ray images with different rotation angles.

RATIONALE AND OBJECTIVES: Registration is an important process to detect interval changes between two chest x-ray images. However, the conventional registration methods suffer from misregistration because of the difference in rotation angles of human body around an axis parallel to the x-ray films, such as anteroposterior inclination. Such difference causes permutation of the shadows between the two images, which makes registration difficult. This article proposes a novel registration method in cases where two chest x-ray images have different rotation angles. MATERIALS AND METHODS: Twelve x-ray images taken from a chest phantom and four chest photofluorograms of two patients were used to evaluate the performance. First, the proposed algorithm estimates the rotation angles of the body from the pair of two x-ray images based on the function describing the relationship between a point in the current image and that in the previous image, which is derived from a three-dimensional rotational model of the body. Then it aligns two images according to the function. RESULTS: From the results of estimating rotation angles, it was found that proposed method can estimate the angles with an error of less than 1 degrees. Then two physicians evaluated the subtraction images and confirmed that this approach makes it possible to detect the interval changes accurately even if there are permutations of shadows in the x-ray image. CONCLUSIONS: The proposed method is superior to the conventional one when two chest x-ray images have different rotation angles.

Algorithms↗
PubMed2006

Ultrasonic pulse waves in cancellous bone analyzed by finite-difference time-domain methods.

The trabecular frame of cancellous bone has a high degree of porosity, anisotropy and inhomogeneity. The propagation of ultrasonic waves in cancellous bone is significantly affected by the trabecular structure. In this paper, two two-dimensional finite-difference time-domain (FDTD) methods, which were the popular viscoelastic FDTD method for a viscoelastic medium and Biot's FDTD method for a fluid-saturated porous medium, have been applied to numerically analyze the ultrasonic pulse waves propagating through bovine cancellous bone in the directions parallel and perpendicular to the trabecular alignment. The Biot's fast and slow longitudinal waves, which were identified in previous experiments for the propagation parallel to the trabecular orientation, could be analyzed using Biot's FDTD method rather than the viscoelastic FDTD method. For the single wave propagation in the perpendicular direction, on the other hand, the viscoelastic FDTD result was found to be in more good agreement with the experimental result.

Algorithms↗