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PubMed2005

Transform and embedded coding techniques for maximum efficiency and random accessibility in 3-D scalable compression.

This study investigates random accessibility and efficiency enhancements in highly scalable video and volumetric compression. With the advent of interactive multimedia technology, random accessibility has emerged as an increasingly important consideration in the design and optimization process. In this paper, we assess the impact that the transform, embedded coding components, and code-block configurations have on the compression efficiency and accessibility of a scalable codestream. We develop performance bounds on techniques which exploit temporal redundancy within the confines of a feed-forward compression system. We also examine their random access properties to argue the significance of motion-adaptive subband transforms. When information-theoretic measures are used to determine the potential benefits of three-dimensional (3-D) context coding, we find that most of the coding gain is attributed to code-block extension, rather than interslice context modeling itself. To gain further insight into the tradeoffs that the coding part has to offer, we run a series of simulations to determine code-block partitioning strategies which maximize reconstruction quality and space-time localization. The LIMAT framework and EBCOT coding paradigm have laid a solid foundation for further progress in the development of highly scalable 3-D compression systems.

Algorithms↗

PubMed2003

Mutual information-based CT-MR brain image registration using generalized partial volume joint histogram estimation.

Mutual information (MI)-based image registration has been found to be quite effective in many medical imaging applications. To determine the MI between two images, the joint histogram of the two images is required. In the literature, linear interpolation and partial volume interpolation (PVI) are often used while estimating the joint histogram for registration purposes. It has been shown that joint histogram estimation through these two interpolation methods may introduce artifacts in the MI registration function that hamper the optimization process and influence the registration accuracy. In this paper, we present a new joint histogram estimation scheme called generalized partial volume estimation (GPVE). It turns out that the PVI method is a special case of the GPVE procedure. We have implemented our algorithm on the clinically obtained brain computed tomography and magnetic resonance image data furnished by Vanderbilt University. Our experimental results show that, by properly choosing the kernel functions, the GPVE algorithm significantly reduces the interpolation-induced artifacts and, in cases that the artifacts clearly affect registration accuracy, the registration accuracy is improved.

Algorithms↗

PubMed2005

On the shaping of the main lobe in wide-band arrays.

This paper describes a method to obtain a wide-band beam pattern whose main lobe has the desired shape and, at the same time, the level of the side lobes is acceptable. The aim is to reproduce a main lobe profile as close as possible to the desired one through the synthesis of the array-weighting window. A typical goal is to obtain, in wide-band conditions, a flat-top shaped beam similar to the ones produced by specific narrow-band windows. To achieve this result, an optimization process based on simulated annealing is developed and applied under different operating conditions, including two wide-band beam pattern definitions and different values of the fractional bandwidth. Although the shape of the resulting main lobe is not as good as the one obtained in narrow-band conditions (the reasons for this drawback are given), it is shown that the adoption of windows synthesized by the proposed method is more suitable than the direct application of narrow-band windows in wide-band conditions. In addition to providing better performances, it is shown that the windows synthesized by the proposed method also result in greater robustness to random perturbations of weight values, which are unavoidable in real systems.

Acoustics↗

PubMedDate not supplied

CartoDraw: a fast algorithm for generating contiguous cartograms.

Cartograms are a well-known technique for showing geography-related statistical information, such as population demographics and epidemiological data. The basic idea is to distort a map by resizing its regions according to a statistical parameter, but in a way that keeps the map recognizable. In this study, we formally define a family of cartogram drawing problems. We show that even simple variants are unsolvable in the general case. Because the feasible variants are NP-complete, heuristics are needed to solve the problem. Previously proposed solutions suffer from problems with the quality of the generated drawings. For a cartogram to be recognizable, it is important to preserve the global shape or outline of the input map, a requirement that has been overlooked in the past. To address this, our objective function for cartogram drawing includes both global and local shape preservation. To measure the degree of shape preservation, we propose a shape similarity function, which is based on a Fourier transformation of the polygons' curvatures. Also, our application is visualization of dynamic data, for which we need an algorithm that recalculates a cartogram in a few seconds. None of the previous algorithms provides adequate performance with an acceptable level of quality for this application. In this paper, we therefore propose an efficient iterative scanline algorithm to reposition edges while preserving local and global shapes. Scanlines may be generated automatically or entered interactively to guide the optimization process more closely. We apply our algorithm to several example data sets and provide a detailed comparison of the two variants of our algorithm and previous approaches.

Algorithms↗

PubMed1986

Monoclonal antibody labeling of mononuclear cell surface antigens in formaldehyde-fixed paraffin-embedded cutaneous tissue.

The influence of the sequential stages of conventional formaldehyde fixation and paraffin embedding of cutaneous tissue on monoclonal antibody labeling of cell surface antigens is described. The effects of variation in fixation time, dehydration, clearing, wax embedding, and enzyme treatment of cutaneous sections were examined. By curtailing fixation time, using cold ethanol dehydration, and limited cold clearing with xylene, immunoreactivity of several important monoclonal antibodies was retained. Wax embedding could be achieved at 58 degrees C for 1 h or by using low-melting-point wax at 42 degrees C for 3 h. Thus was derived an optimal processing procedure which afforded good tissue morphology and allowed reliable reproducible labeling by monoclonal antibodies to cell surface antigens.

Antibodies, Monoclonal↗

PubMed1990

Membrane and cytosolic interleukin-1 alpha and beta in normal human epidermal cells: variability of epitope exposure in immunohistochemistry.

Previous studies have shown that interleukin-1 (IL-1) is present in normal human epidermis. However, with immunohistochemical techniques, epidermal IL-1 immunoreactivity has been found in only a limited number of epidermal cells. In the present study, we show that both IL-1 alpha and beta immunoreactivities can be detected in all epidermal cell layers, provided optimal processing of tissue samples is used. The use of isolated epidermal cells showed that keratinocytes at various stages of maturation display both membrane-associated and cytosolic IL-1 alpha and beta immunoreactivities. After protease treatment of tissue sections, the IL-1 beta immunoreactivity of the granular cell layer was enhanced by some antibodies used, whereas in the other cell layers it was clearly lower. We a) suggest a different cellular localization, processing, and/or binding to subcellular structures of IL-1 during the differentiation process of human keratinocytes and b) outline the technical difficulties in any immunohistologic approach to IL-1 status in diseased skin.

Cell Membrane↗

PubMed2004

Fermentation conditions affecting the bacterial growth and exopolysaccharide production by Streptococcus thermophilus ST 111 in milk-based medium.

AIMS: To study the effect of different fermentation conditions and to model the effect of temperature and pH on different biokinetic parameters of bacterial growth and exopolysaccharides (EPS) production of Streptococcus thermophilus ST 111 in milk-based medium. METHODS AND RESULTS: The influence of temperature and pH was studied through fermentation and modelling. Fermentations under non-pH controlled conditions with S. thermophilus ST 111 indicated that the EPS production was low in milk medium, even if additional nitrogen sources were supplemented. Under pH-controlled conditions, addition of whey protein hydrolysate to the milk medium resulted in a fivefold increase of the EPS production. This medium did not contain polysaccharides interfering with EPS isolation. Primary and secondary modelling of different fermentations revealed an optimum temperature and pH of 40 degrees C and constant pH 6.2, respectively, for growth in milk medium supplemented with whey protein hydrolysate. Maximum EPS production was observed in the range of 32-42 degrees C and constant pH 5.5-6.6. Whereas growth and maximum EPS production were clearly influenced by temperature and pH, the specific EPS production was only affected by stress conditions (T = 49 degrees C). CONCLUSIONS: Addition of whey protein hydrolysate to milk medium resulted in an increased growth and EPS production of S. thermophilus ST 111 under pH-controlled conditions. A modelling approach allowed studying the influence of temperature and pH on the kinetics of both growth and EPS production. SIGNIFICANCE AND IMPACT OF THE STUDY: The use of an appropriate milk-based medium and a combined model of temperature and pH can be of practical importance for the production of yoghurt or other fermented milks as well as for process optimization of the large-scale production of starter strains to be used for their EPS production.

Animals↗

PubMed1990

A new force-field program for the calculation of glycopeptides and its application to a heptacosapeptide-decasaccharide of immunoglobulin G1. Importance of 1-6-glycosidic linkages in carbohydrate.peptide interactions.

Energetically favored conformations of glycopeptide 1 were calculated using the newly developed force-field program, GEGOP (geometry of glycopeptides). The three-dimensional structure of glycopeptide 1, which is part of the Fc fragment of IgG1, has been calculated. 1 contains 27 amino acid residues from Pro291 to Lys317 and a biantennary decasaccharide N-linked to Asn297. The conformations of the peptide and the carbohydrate parts are shown to be mutually dependent. Single glycosyl residues of 1 exhibit interaction energies of up to -31.8 kJ/mol with the peptide portion. Generally, only a few of the glycosyl residues of the oligosaccharide moiety express significant interaction energies with the peptide part. No easy prediction is possible of glycosyl residues which exhibit favorable interaction energies. However, in all of the calculated structures, the glycosyl residues of the 1-6-linked branches show strong attractive forces for the peptide part. 1-6-glycosidically linked branches can adopt a larger number of conformations than other linkages due to their high flexibility which allows more favorable interactions with proteins. We developed the GEGOP program in order to be able to study the preferred conformations of large glycopeptides. The program is based on the GESA (geometry of saccharides) program and utilizes the HSEA (hard sphere exo anomeric) force field for the carbohydrate part and the ECEPP/2 (empirical conformation energy program for peptides) force field [Némethy, G., Pottle, M. S. & Scheraga, H. A. (1983) J. Phys. Chem. 87, 1883-1887] for the peptide part. The GEGOP program allows the simultaneous relaxation of all rotational degrees of freedom of these glycoconjugates during the energy optimization process. Thus, mutual interactions between glycosyl and amino acid residues can be studied in detail.

Carbohydrate Conformation↗

PubMed2006

Computer-based measurement of letter and word acuity.

Determining causes of poor reading ability is an important step in trying to ameliorate reading performance in low-vision patients. One important parameter is word acuity. The principal aim of the current study is to develop a method to reliably measure acuities for isolated lowercase letters and words of differing length that can be used to test low-vision patients. Using isolated stimuli means that testing is relatively free of potential crowding and/or distracting attentional effects from surrounding words, it is unambiguous which stimulus subjects are trying to read and response times can be recorded for each stimulus. Across a series of experiments, subjects with normal vision were asked to read isolated lowercase single letters and lowercase words of 4, 7 and 10 letters, in separate tests. Acuities for uppercase Sloan letters were also measured to provide a reference, as they are commonly used to measure visual acuity. Each test was based upon the design principles and scoring procedures used in the Bailey-Lovie and ETDRS charts. Acuities for uppercase Sloan letters were found to be equivalent whether measured using ETDRS charts or the computer-based method. Measurement of acuities for lowercase single letters and lowercase words of 4, 7 and 10 letters had a reliability that was no worse than acuities for uppercase Sloan letters. Lowercase word acuities were essentially independent of word length. Acuities for single lowercase letters and lowercase words were slightly better than uppercase Sloan letters acuity. Optimal processing of lowercase single letters and 4-, 7- and 10-letter words occurred at character sizes that were at least 0.2-0.40 log MAR above acuity threshold, i.e. between 1.5 and 3 times threshold acuity for that particular stimulus. In general, critical character sizes appear similar across word lengths as progressive increases or decreases in these values were not observed as a function of the number of letters in the stimulus. We conclude that a computer-based method of stimulus presentation can be used to obtain highly repeatable measures of acuity for lowercase single letters and lowercase words in normal vision.

Adult↗

PubMed1994

Development of a radiopaque, autopolymerizing dental acrylic resin.

PURPOSE: Current prosthetic acrylic resins are radiolucent and cannot be imaged using standard radiographic techniques. If accidentally impacted or ingested, delays in localizing or removing the foreign body may be life-threatening. The purpose of this study was to evaluate the influence of an experimental radiopaque additive, triphenyl bismuth (TPB), on polymethyl methacrylate resins formulated for dental use. We also investigated methods to improve TPB-containing resin microbeads and optimize processing variables for specimen fabrication in autopolymerizing resin systems. MATERIALS AND METHODS: Selfcured samples of experimental resins were prepared containing 0% to 27% TPB and were tested according to American National Standards Institute/American Dental Association and International Organization for Standardization performance standards. A control group and two commercial provisional crown and bridge resins were used for comparison. RESULTS: The standard of radiopacity (> or = aluminum radiopacity) is met at TPB levels of > or = 14.5%. The control resin had a greater transverse deflection compared with the TPB-resin groups, but deflection was within standard limits for all resins. Polishability, color stability, and solubility were unaffected by TPB, whereas sorption decreased, although not significantly, at higher TPB levels. Translucency decreased at 27% TPB, and specimens containing 0% to 20% TPB were transparent. A tendency to entrain air bubbles, because of the hydrophobicity of TPB, resulted in increased susceptibility to brittle failure at the higher TPB levels. Solubility slightly exceeded American Dental Association standards for all TPB-resins and the control. All other performance standards were acceptable for resins containing 0% to 20% TPB. CONCLUSIONS: At concentrations that provide a diagnostic level of radiopacity, TPB does not significantly alter required performance and processing properties. Thus, TPB is capable of commercially acceptable performance as a radiopacifying additive for dental acrylics.

Analysis of Variance↗

PubMed2005

Highly sensitive SIV plasma viral load assay: practical considerations, realistic performance expectations, and application to reverse engineering of vaccines for AIDS.

As new assay methods for quantitative reverse transcription-polymerase chain reaction (RT-PCR), such as real time RT-PCR techniques, approach theoretical limits of per reaction sensitivity, further increments in the sensitivity of measurements of viral load can only be achieved by increasing the amount of input RNA per reaction. We describe a robust, convenient, rapid integrated approach for specimen preparation and real time RT-PCR assay for plasma simian immunodeficiency virus (SIV) RNA viral load that provides a threshold sensitivity of 10 copy Eq/ml, and tolerates less than optimally processed specimens. The method provides accurate quantitation of viral load for the SIV virus isolates in common use for non-human primate studies. We demonstrate the utility of the method in sensitively tracking viral load in an animal showing effective control of viral replication to levels below the threshold for quantitation in conventional assays.

AIDS Vaccines↗

PubMed2006

Structure-based optimization of MurF inhibitors.

The D-Ala-D-Ala adding enzyme (MurF) from Streptococcus pneumoniae catalyzes the ATP-dependent formation of the UDP-MurNAc-pentapeptide, a critical component of the bacterial cell wall. MurF is a potential target for antibacterial design because it is unique to bacteria and performs an essential non-redundant function in the bacterial cell. The recent discovery and subsequent cocrystal structure determination of MurF in complex with a new class of inhibitors served as a catalyst to begin a medicinal chemistry program aimed at improving their potency. We report here a multidisciplinary approach to this effort that allowed for rapid generation of cocrystal structures, thereby providing the crystallographic information critical for driving the inhibitor optimization process. This effort resulted in the discovery of low-nanomolar inhibitors of this bacterial enzyme.

Crystallization↗

PubMed1994

Analysis of foreign protein overproduction in recombinant CHO cells. Effect of growth kinetics and cell cycle traverse.

Intracellular foreign protein (beta-galactosidase) expression in recombinant CHO cell lines in continuous culture was analyzed by developing a mathematical model that includes the effects of metabolic burden and cell cycle dependence of intracellular foreign protein expression. This combined growth kinetic and cell cycle model, assuming S- or G1-phase-dependent expression, was stimulated to predict productivity on a single-cell and culture-volume basis in continuous cultures. In the case of S-phase-dependent expression, the intracellular foreign protein level increases monotonically, but in the case of G1-phase-dependent expression it decreases monotonically with increasing dilution rate. Also, the trends of foreign protein concentration in the culture volume differ significantly between S- and G1-dependent expression kinetics. Thus, the cell cycle dependency of foreign protein expression should be included in process optimization concepts and operating strategies of continuous bioreactors.

Animals↗

PubMed2005

What are the relevant parameters for the geometrical optimization of an implantable bioartificial pancreas?

A sphere within a cylinder representing the islet encapsulated in a hollow fiber can model an implantable bioartificial pancreas. Based on a finite element model for insulin response to a glucose load in the presence of various oxygen supplies, the present study aimed at pointing out the major parameters influencing this secretion. The computational results treated with the Taguchi method clearly demonstrated that geometrical parameters (fiber length and islet density) should be precisely optimized for an enhanced insulin response. This requires the collection of more relevant experimental data concerning the islet oxygen consumption. Moreover, the relative errors on glucose consumption or insulin secretion by the islets do not seem to affect the whole optimization process, which should focus on the oxygen supply to islets.

Bioartificial Organs↗

PubMed1998

Performance analysis of a cardiac assist device in counterpulsation.

Performance of a cardiac assist device pumping chamber in counterpulsation was evaluated using numerical simulations of the unsteady, three-dimensional flow inside the chamber and an analytical model of the force required to eject and fill the chamber. The wall shear stress within the device was similarly computed and modeled. The analytical model was scaled to match the numerical results and then used to predict performance at physiological operating conditions. According to these models for a stroke volume of 70 ml, between 0.4 and 1.0 W is required for counterpulsation at a frequency of 1.33 Hz against a restorative spring, depending on the spring constant chosen. The power and the maximum force calculated are within the ranges a trained skeletal muscle is capable of providing. Shear stress predictions show that platelet activation in the absence of surface effects and hemolysis due to high shear are unlikely to occur with this design. Furthermore, vortices that develop in the chamber during filling are predicted to increase blood mixing and provide favorable washing of the chamber walls. A computational-analytical approach such as this may have potential to aid rapid performance evaluation of new devices and streamline the design optimization process.

Counterpulsation↗

PubMed2002

Beyond bixels: generalizing the optimization parameters for intensity modulated radiation therapy.

Intensity modulated radiation therapy (IMRT) treatment planning systems optimize fluence distributions by subdividing the fluence distribution into rectangular bixels. The algorithms typically optimize the fluence intensity directly, often leading to fluence distributions with sharp discontinuities. These discontinuities may yield difficulties in delivery of the fluence distribution, leading to inaccurate dose delivery. We have developed a method for decoupling the bixel intensities from the optimization parameters; either by introducing optimization control points from which the bixel intensities are interpolated or by parametrizing the fluence distribution using basis functions. In either case, the number of optimization search parameters is reduced from the direct bixel optimization method. To illustrate the concept, the technique is applied to two-dimensional idealized head and neck treatment plans. The interpolation algorithms investigated were nearest-neighbor, linear and cubic spline, and radial basis functions serve as the basis function test. The interpolation and basis function optimization techniques were compared against the direct bixel calculation. The number of optimization parameters were significantly reduced relative to the bixel optimization, and this was evident in the reduction of computation time of as much as 58% from the full bixel optimization. The dose distributions obtained using the reduced optimization parameter sets were very similar to the full bixel optimization when examined by dose distributions, statistics, and dose-volume histograms. To evaluate the sensitivity of the fluence calculations to spatial misalignment caused either by delivery errors or patient motion, the doses were recomputed with a 1 mm shift in each beam and compared to the unshifted distributions. Except for the nearest-neighbor algorithm, the reduced optimization parameter dose distributions were generally less sensitive to spatial shifts than the bixel optimization. These results indicate that significant reductions in optimization parameter sets can be accomplished with a negligible reduction in dose distribution quality. The decreased parameters can result in a reduced optimization time, or can be used to allow an improved and consequently more computation-intensive dose calculation for more accurate dose calculations during the optimization process. The basis functions may be generalized to model the accelerator motion for direct computation of the accelerator motion sequence, removing the need for developing an independent leaf sequence step.

Algorithms↗

PubMed2004

Incorporating model parameter uncertainty into inverse treatment planning.

Radiobiological treatment planning depends not only on the accuracy of the models describing the dose-response relation of different tumors and normal tissues but also on the accuracy of tissue specific radiobiological parameters in these models. Whereas the general formalism remains the same, different sets of model parameters lead to different solutions and thus critically determine the final plan. Here we describe an inverse planning formalism with inclusion of model parameter uncertainties. This is made possible by using a statistical analysis-based frameset developed by our group. In this formalism, the uncertainties of model parameters, such as the parameter a that describes tissue-specific effect in the equivalent uniform dose (EUD) model, are expressed by probability density function and are included in the dose optimization process. We found that the final solution strongly depends on distribution functions of the model parameters. Considering that currently available models for computing biological effects of radiation are simplistic, and the clinical data used to derive the models are sparse and of questionable quality, the proposed technique provides us with an effective tool to minimize the effect caused by the uncertainties in a statistical sense. With the incorporation of the uncertainties, the technique has potential for us to maximally utilize the available radiobiology knowledge for better IMRT treatment.

Algorithms↗

PubMed2006

Coronary x-ray angiographic reconstruction and image orientation.

We have developed an interactive geometric method for 3D reconstruction of the coronary arteries using multiple single-plane angiographic views with arbitrary orientations. Epipolar planes and epipolar lines are employed to trace corresponding vessel segments on these views. These points are utilized to reconstruct 3D vessel centerlines. The accuracy of the reconstruction is assessed using: (1) near-intersection distances of the rays that connect x-ray sources with projected points, (2) distances between traced and projected centerlines. These same two measures enter into a fitness function for a genetic search algorithm (GA) employed to orient the angiographic image planes automatically in 3D avoiding local minima in the search for optimized parameters. Furthermore, the GA utilizes traced vessel shapes (as opposed to isolated anchor points) to assist the optimization process. Differences between two-view and multiview reconstructions are evaluated. Vessel radii are measured and used to render the coronary tree in 3D as a surface. Reconstruction fidelity is demonstrated via (1) virtual phantom, (2) real phantom, and (3) patient data sets, the latter two of which utilize the GA. These simulated and measured angiograms illustrate that the vessel center-lines are reconstructed in 3D with accuracy below 1 mm. The reconstruction method is thus accurate compared to typical vessel dimensions of 1-3 mm. The methods presented should enable a combined interpretation of the severity of coronary artery stenoses and the hemodynamic impact on myocardial perfusion in patients with coronary artery disease.

Adult↗