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PubMed2003

Molecular computing revisited: a Moore's Law?

Moore's Law states that the processing power of microchips doubles every one to two years. This observation might apply to the nascent field of molecular computing, in which biomolecules carry out logical operations. Incorporation of new technologies that improve sensitivity and throughput has increased the complexity of problems that can be addressed. It is an ultimate goal for molecular computers to use the full potential of massive parallelism.

Algorithms↗
PubMed1989

The clinical utility of renal concentrating capacity in polycystic kidney disease.

We studied 177 adult nonazotemic subjects with autosomal dominant polycystic kidney disease (ADPKD) and 123 unaffected family members (NADPKD). In order to assess the factors influencing renal concentrating capacity maximal urinary osmolality (UOsm) after overnight water deprivation and vasopressin was measured. UOsm was reduced in ADPKD (680 +/- 14) compared to NADPKD subjects (812 +/- 13 mOsm/kg). A greater severity of the architectural abnormality as assessed by cyst number and size and remaining volume of normal parenchyma was associated with a greater impairment of renal concentrating capacity. The concentrating defect was present in the youngest ADPKD subjects and the rate of decline of concentrating capacity with age in ADPKD paralleled that in NADPKD subjects. Based on the initial 135 subjects studied, we developed an algorithm for diagnostic screening for ADPKD utilizing blood pressure, serum creatinine and UOsm designed to maximize sensitivity. When applied to a subsequent population of 165 adults, 121 with ADPKD and 44 unaffected relatives, this algorithm would have spared 20% of unaffected subjects from the cost of ultrasound while failing to detect less than 2% of affected subjects. This simple protocol thus offers a rapid and inexpensive way to screen for ADPKD.

Adult↗
PubMed2005

Universal method for computation of electrostatic potentials.

A computational approach to determine electrostatic interaction and gravitational potentials by performing direct numerical integration is presented. The potential is expanded using finite-element functions of arbitrary order. The method does not involve any solutions of systems of linear equations. The potential is instead obtained as a sum of differential contributions. Thus, no boundary conditions for the potential are needed. It is computationally efficient and well suited for parallel computers, since the innermost loops constitute matrix multiplications and the outer ones can be used as parallel indices. Without using prescreening or other computational tricks to speed up the calculation, the algorithm scales as N4/3 where N denotes the grid size.

Journal Article↗
PubMed1982

Neural networks and physical systems with emergent collective computational abilities.

Computational properties of use of biological organisms or to the construction of computers can emerge as collective properties of systems having a large number of simple equivalent components (or neurons). The physical meaning of content-addressable memory is described by an appropriate phase space flow of the state of a system. A model of such a system is given, based on aspects of neurobiology but readily adapted to integrated circuits. The collective properties of this model produce a content-addressable memory which correctly yields an entire memory from any subpart of sufficient size. The algorithm for the time evolution of the state of the system is based on asynchronous parallel processing. Additional emergent collective properties include some capacity for generalization, familiarity recognition, categorization, error correction, and time sequence retention. The collective properties are only weakly sensitive to details of the modeling or the failure of individual devices.

Animals↗
PubMed2006

Detecting and overcoming hemihedral twinning during the MIR structure determination of Rna1p.

The structure of Rna1p was originally solved to 2.7 A resolution by MIRAS from crystals with partial hemihedral twinning in space group I4(1) [Hillig et al. (1999), Mol. Cell, 3, 781-791] by finding a low-twinned native crystal (twin fraction alpha=0.06) and after twin correction of all data sets. Rna1p crystals have now been used to examine how far twinning and twin correction affect MIR phasing with a higher resolution but highly twinned native data set. Even high hemihedral twinning [alphanative=0.39, alphaderivative=0.24] would not have hindered heavy-atom site identification of strong derivatives using difference Patterson maps. However, a weaker derivative could have been missed and refinement would have stalled at high R values had twinning not been identified and accounted for. Twin correction improved both site identification, experimental phasing statistics and MIR map quality. Different strategies were tested for refinement against twinned data. Using uncorrected twinned data and TWIN-CNS, Rna1p has now been refined to 2.2 A resolution (final twinned R and Rfree were 0.165 and 0.218, respectively). The increased resolution enabled release of the NCS restraints and allowed new conclusions to be drawn on the flexibility of the two molecules in the asymmetric unit. In the case of Rna1p, twinned crystal growth was possible owing to the presence of a twofold NCS axis almost parallel to the twin operator.

Algorithms↗
PubMed2000

Reconstruction of two- and three-dimensional images from synthetic-collimator data.

A novel SPECT collimation method, termed the synthetic collimator, is proposed. The synthetic collimator employs a multiple-pinhole aperture and a high-resolution detector. The problem of multiplexing, normally associated with multiple pinholes, is reduced by obtaining projections at a number of pinhole-detector distances. Projections with little multiplexing are collected at small pinhole-detector distances and high-resolution projections are collected at greater pinhole-detector distances. These projections are then reconstructed using the ML-EM algorithm. It is demonstrated through computer simulations that the synthetic collimator has superior resolution properties to a high-resolution parallel-beam (HRPB) collimator and a specially built ultra-high-resolution parallel-beam (UHRPB) collimator designed for our 0.38-mm pixel CdZnTe detectors. It is also shown that reconstructing images in three dimensions is superior to reconstructing them in two dimensions. The advantages of a high-resolution synthetic collimator over the parallel-hole collimators are apparently reduced in the presence of statistical noise. However, a high-sensitivity synthetic collimator was designed which again shows superior properties to the parallel-hole collimators. Finally, it is demonstrated that, for the cases studied, high-resolution detectors are necessary for the proper functionality of the synthetic collimator.

Algorithms↗
PubMed2005

On using prototype reduction schemes and classifier fusion strategies to optimize kernel-based nonlinear subspace methods.

In Kernel-based Nonlinear Subspace (KNS) methods, the length of the projections onto the principal component directions in the feature space, is computed using a kernel matrix, K, whose dimension is equivalent to the number of sample data points. Clearly this is problematic, especially, for large data sets. In this paper, we solve this problem by subdividing the data into smaller subsets, and utilizing a Prototype Reduction Scheme (PRS) as a preprocessing module, to yield more refined representative prototypes. Thereafter, a Classifier Fusion Strategy (CFS) is invoked as a postprocessing module, to combine the individual KNS classification results to derive a consensus decision. Essentially, the PRS is used to yield computational advantage, and the CFS, in turn, is used to compensate for the decreased efficiency caused by the data set division. Our experimental results demonstrate that the proposed mechanism significantly reduces the prototype extraction time as well as the computation time without sacrificing the classification accuracy. The results especially demonstrate a significant computational advantage for large data sets within a parallel processing philosophy.

Algorithms↗
PubMedDate not supplied

High-dimensional visual analytics: interactive exploration guided by pairwise views of point distributions.

We introduce a method for organizing multivariate displays and for guiding interactive exploration through high-dimensional data. The method is based on nine characterizations of the 2D distributions of orthogonal pairwise projections on a set of points in multidimensional Euclidean space. These characterizations include such measures as density, skewness, shape, outliers, and texture. Statistical analysis of these measures leads to ways for 1) organizing 2D scatterplots of points for coherent viewing, 2) locating unusual (outlying) marginal 2D distributions of points for anomaly detection, and 3) sorting multivariate displays based on high-dimensional data, such as trees, parallel coordinates, and glyphs.

Algorithms↗
PubMed2004

Beam collimation with polycapillary x-ray optics for high contrast high resolution monochromatic imaging.

Monochromatic imaging can provide better contrast and resolution than conventional broadband radiography. In broadband systems, low energy photons do not contribute to the image, but are merely absorbed, while high energy photons produce scattering that degrades the image. By tuning to the optimal energy, one can eliminate undesirable lower and higher energies. Monochromatization is achieved by diffraction from a single crystal. A crystal oriented to diffract at a particular energy, in this case the characteristic line energy, diffracts only those photons within a narrow range of angles. The resultant beam from a divergent source is nearly parallel, but not very intense. To increase the intensity, collimation was performed with polycapillary x-ray optics, which can collect radiation from a divergent source and redirect it into a quasi parallel beam. Contrast and resolution measurements were performed with diffracting crystals with both high and low angular acceptance. Testing was first done at 8 keV with an intense copper rotating anode x-ray source, then 17.5 keV measurements were made with a low power molybdenum source. At 8 keV, subject contrast was a factor of five higher than for the polychromatic case. At 17.5 keV, monochromatic contrast was two times greater than the conventional polychromatic contrast. The subject contrasts measured at both energies were in good agreement with theory. An additional factor of two increase in contrast, for a total gain of four, is expected at 17.5 keV from the removal of scatter. Scatter might be simply removed using an air gap, which does not degrade resolution with a parallel beam.

Algorithms↗
PubMed2004

Design of a high-throughput assay for alternative splicing using polymerase colonies.

We propose an assay to detect and quantify alternative splicing simultaneously for numerous genes in a pool of cellular mRNA. The assay exploits polymerase colonies, a recently developed method for sampling and amplifying large numbers of individual transcript molecules into discrete spots on a gel. The proposed assay combines the advantages of microarrays for transcript quantitation with the sensitivity and precision of methods based on counting single transcript molecules. Given a collection of spots s(i), each containing an unknown splice variant of some known gene G(i), we design a series of hybridizations to short oligonucleotide probes to determine in parallel which exons of G(i) are present in every spot s(i). We give algorithms to minimize the cost of such designs.

Alternative Splicing↗
PubMed2004

Optical computed-tomographic microscope for three-dimensional quantitative histology.

A novel optical computed-tomographic microscope has been developed allowing quantitative three-dimensional (3D) imaging and analysis of fixed pathological material. Rather than a conventional two-dimensional (2D) image, the instrument produces a 3D representation of fixed absorption-stained material, from which quantitative histopathological features can be measured more accurately. The accurate quantification of these features is critically important in disease diagnosis and the clinical classification of cancer. The system consists of two high NA objective lenses, a light source, a digital spatial light modulator (DMD, by Texas Instrument), an x-y stage, and a CCD detector. The DMD, positioned at the back pupil-plane of the illumination objective, is employed to illuminate the specimen with parallel rays at any desired angle. The system uses a modification of the convolution backprojection algorithm for reconstruction. In contrast to fluorescent images acquired by a confocal microscope, this instrument produces 3D images of absorption stained material. Microscopic 3D volume reconstructions of absorption-stained cells have been demonstrated. Reconstructed 3D images of individual cells and tissue can be cut virtually with the distance between the axial slices less than 0.5 microm.

Algorithms↗
PubMed2002

Computational reconstruction of images from holograms.

The equations to reconstruct an image plane from a hologram are developed. This development is carried out for planes parallel to the hologram, which allows fast computation through the use of fast Fourier transforms. Algorithms for a digital computer are developed so images can be reconstructed, both with and without the Fresnel approximation, from a digitized hologram without the need for three-dimensional optical reconstruction equipment. Examples of holographically recorded images of marine micro-organisms are shown. A computational method for counting the number of micro-organisms in the holographically recorded volume is developed, and an example is provided.

Journal Article↗
PubMed2005

Optimized stereo reconstruction of free-form space curves based on a nonuniform rational B-spline model.

Analytical reconstruction of 3D curves from their stereo images is an important issue in computer vision. We present an optimization framework for such a problem based on a nonuniform rational B-spline (NURBS) curve model that converts reconstruction of a 3D curve into reconstruction of control points and weights of a NURBS representation of the curve, accordingly bypassing the error-prone point-to-point correspondence matching. Perspective invariance of NURBS curves and constraints deduced on stereo NURBS curves are employed to formulate the 3D curve reconstruction problem into a constrained nonlinear optimization. A parallel rectification technique is then adopted to simplify the constraints, and the Levenberg-Marquardt algorithm is applied to search for the optimal solution of the simplified problem. The results from our experiments show that the proposed framework works stably in the presence of different data samplings, randomly posed noise, and partial loss of data and is potentially suitable for real scenes.

Algorithms↗
PubMed2003

Two-dimensional correlation analysis in application to a kinetic model of parallel reactions.

By applying generalized two-dimensional (2D) correlation analysis as reported by Noda, we have systematically studied a kinetic model of parallel reactions. Given the related rate constants and absorption coefficients, the correlation between reactant and products are analyzed. The reactant-reactant, reactant-product, and product-product pairs are found to be synchronously correlated, and their intensities increase with increase of the rate constant and the absorption coefficient. On the other hand, only the reactant-product pairs show in the asynchronous spectra. Their intensities also depend proportionally on the rate constant and the absorption coefficient. The influence of signal-to-noise ratio (S/N) and overlapped spectra are further discussed. The resulting synchronous and asynchronous correlation spectra for the kinetic model appear to be weakly influenced by poor quality of the signal when the reference spectrum is set at zero. The ratio of asynchronous to synchronous correlation intensity yields a coherence spectrum. This spectrum remains a constant intensity for all the correlated peaks, being free from the influence of rate constant and absorption coefficient as well as being weakly disturbed by a small S/N ratio. It also provides a way to evaluate the extent of spectral overlap between two peaks. The coherence spectrum is useful to characterize the type of parallel reactions.

Algorithms↗
PubMed2002

[Effectiveness of endovideosurgical technology in diagnosis and treatment of patient with hemoblastoses].

Results of using endovideosurgical technology for diagnosis and treatment of hematological diseases in 123 patients are described. It was shown that laparoscopy is highly effective parallel with ultrasound examination and tomography in a complex diagnostic program. Using the developed diagnostic algorithm was shown to be very expedient for making primary diagnosis, recurrent diseases and control of the effectiveness of chemotherapy. Endovideosurgical interventions were shown to be less invasive and safe in hematological patients. Laparoscopy is an alternative to diagnostic laparotomy which is often used in this group of patients.

Adult↗
PubMed1997

Dynamic three-dimensional echocardiography: a new era in ultrasound technology.

The use of noninvasive methods to visualise the heart has had an extraordinary development over the last decade, with echocardiography demonstrating a particularly fast growth. Despite its unquestionable role in the diagnosis of heart disease and in the management of cardiac patients, it does have some limitations, both in the morphological visualisation, as well as in the functional assessment of the heart, such as blood flow, quantification of intracardiac volumes, etc. The recent development of dynamic three-dimensional (3D) echocardiography from two dimensional images has opened new perspectives in the study of cardiac pathophysiology. There are basically two methods of displaying three dimensional data sets: (1) a two-dimensional display from individual selected cut planes (any-plane echocardiography) or from parallel short axis cuts; (2) a volume rendered technique: from any defined cut plane, different algorithms are applied to represent the information in space. There are several potential clinical applications of 3D such as the measurement and serial follow-up of left ventricular volumes; in valvular heart disease (the abnormalities can be delineated more precisely and in greater detail than conventional imaging, including a detailed definition of mitral apparatus in mitral stenosis), in mitral valve prolapse both leaflets can be seen from the left atrial view and in endocarditis it can aid in deciding when and how to intervene; in complex congenital heart disease, such as reconstruction of double outlet right ventricle, left-sided obstructive and regurgitant lesions and subaortic obstructive cases, in atrial and ventricular septal defects, displaying size, geometry and relationships to other structures; another expression of cardiac disorders are blood flow disturbances (visualisation of flows in 3D could allow a better qualitative and quantitative assessment of their size and severity; the pictures so far generated allow a good perception of the size and shape of mitral, aortic and tricuspid regurgitation jets, by examining them from a new perspective, it also has the potential to display the flow convergence zone and quantify the regurgitant volume). Recent studies have clearly demonstrated the feasibility of performing three-dimensional imaging in a variety of cardiac diseases, but continued development of ultrasound technology must be made to improve better image resolution. The prolonged acquisition time is the most important limiting factor that currently restricts the routine use of 3D echocardiography. The development of faster computers will shorten the time needed for image acquisition, postprocessing, and data analysis, contributing to the goal of easy access and wide use. With improvements in computer technology and production of interactive software, 3D echocardiography will provide a dynamic view of the surgical anatomy of the heart. Thus, the three-dimensional reconstruction concept has the potential to and diagnostic assessment of cardiac pathology in every facet.

Cardiovascular Diseases↗
PubMed2002

A parallel mixture of SVMs for very large scale problems.

Support vector machines (SVMs) are the state-of-the-art models for many classification problems, but they suffer from the complexity of their training algorithm, which is at least quadratic with respect to the number of examples. Hence, it is hopeless to try to solve real-life problems having more than a few hundred thousand examples with SVMs. This article proposes a new mixture of SVMs that can be easily implemented in parallel and where each SVM is trained on a small subset of the whole data set. Experiments on a large benchmark data set (Forest) yielded significant time improvement (time complexity appears empirically to locally grow linearly with the number of examples). In addition, and surprisingly, a significant improvement in generalization was observed.

Algorithms↗