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PubMedDate not supplied

Refractive correction method for digital charge-coupled device-recorded Scheimpflug photographs by means of ray tracing.

Our purpose is to correct digital CCD-recorded Scheimpflug photographs, imaging both the anterior and posterior corneal surface, the anterior chamber, and the anterior eye lens surface for optical distortions. In a ray-tracing algorithm the imaging of the posterior corneal surface in a given Scheimpflug photograph is corrected by applying Snell's law on parallel incident rays entering through the anterior corneal surface. Once the posterior corneal surface is corrected, the procedure is repeated, again with parallel incident rays entering through both the anterior and now corrected posterior corneal surface, to correct the imaging of the anterior eye lens surface. The refractive indices necessary for Snell's law are taken from Gullstrand's exact schematic eye model. Due to the optical/refractive correction, the digital Scheimpflug photograph decreases in size perpendicular to the direction of the optical axis. As a consequence the curvature radii of both the posterior corneal surface and the anterior lens surface are reduced significantly, as compared to the original digital Scheimpflug photograph. Furthermore, the corneal thickness and the anterior chamber depth are increased. The presented refractive correction method enables us to extract from Scheimpflug photographs the following quantities rather realistically: structure coordinates and curvature radii of both the posterior corneal surface and the anterior lens surface, corneal thickness, and anterior chamber depth. This method can readily be applied to other imaged quantities, such as the posterior eye lens surface, the lens thickness, and the pupillary opening.

Cornea↗

PubMed2006

Properties of correlated neural activity clusters in cat auditory cortex resemble those of neural assemblies.

Spiking activity was recorded from cat auditory cortex using multi-electrode arrays. Cross-correlograms were calculated for spikes recorded on separate microelectrodes. The pair-wise cross-correlation matrix was constructed for the peak values of the correlograms. Hierarchical clustering was performed on the cross-correlation matrix for six stimulus conditions. These were silence, three multi-tone stimulus ensembles with different spectral densities, low-pass amplitude-modulated noise, and Poisson-distributed click trains that each lasted 15 min. The resulting neuron clusters reflect patches in cortex of up to several mm(2) in size that expand and contract in response to different stimuli. Cluster positions and size were very similar for spontaneous activity and multi-tone stimulus-evoked activity but differed between those conditions and the noise and click stimuli. Cluster size was significantly larger in posterior auditory field (PAF) compared with primary auditory cortex (AI), whereas the fraction of common spikes (within a 10-ms window) across all electrode activity participating in a cluster was significantly higher in AI compared with PAF. Clusters crossed area boundaries in <5% of the cases were simultaneous recording were made in AI and PAF. Clusters are therefore similar to but not synonymous with the traditional view of neural assemblies. Common-spike spectrotemporal receptive fields (STRFs) were obtained for common-spike activity and all-spike activity within a cluster. Common-spike STRFs had higher signal-to-noise ratio than all-spike STRFs and showed generally spectral and temporal sharpening. The coincident and noncoincident output of the clusters could potentially act in parallel and may serve different modes of stimulus coding.

Acoustic Stimulation↗

PubMed1981

Oblique-angle tomography: a restructuring algorithm for transaxial tomographic data.

A set of contiguous transaxial tomographic sections obtained with a rotating-camera tomograph represents the full three-dimensional distribution of activity within a volume of the body. Tomographic sections in planes other than the origianl transverse plane can be produced from these data merely by resorting the data appropriately. The paper presents a simple and efficient algorithm for producing tomograms of the heart oriented either at right angles to the long axis of the left ventricle, or parallel to it. Tomograms in these orientations have specific advantages for imaging the heart and avoid some of the limitations seen in comparable tomograms obtained by the seven-pinhole technique.

Heart↗

PubMed1986

Eye-hand-coordination: a model for computing reaction times in a visually guided reach task.

A model is described which provides a simple algorithm to compute the reaction times of saccadic eye movements and reach movements aimed at a single visual target. It is assumed, that the two movements are prepared in parallel and initiated independently unless the preparation of the saccade for some reason takes longer than the preparation of the reach movement. In the latter case the final command to execute the reach movement is synchronized with that to execute the eye movement and therefore the corresponding reaction times are highly correlated in a one-to-one relationship. Random variables are used to predict sets of data that are directly comparable with the experimental results. The algorithm includes the effects of daily practice (learning). The structure of the model and its computational results will be compared with the physiological data from monkey and man.

Algorithms↗

PubMed2006

An algorithm for assembly of ordered restriction maps from single DNA molecules.

The restriction mapping of a massive number of individual DNA molecules by optical mapping enables assembly of physical maps spanning mammalian and plant genomes; however, not through computational means permitting completely de novo assembly. Existing algorithms are not practical for genomes larger than lower eukaryotes due to their high time and space complexity. In many ways, sequence assembly parallels map assembly, so that the overlap-layout-consensus strategy, recently shown effective in assembling very large genomes in feasible time, sheds new light on solving map construction issues associated with single molecule substrates. Accordingly, we report an adaptation of this approach as the formal basis for de novo optical map assembly and demonstrate its computational feasibility for assembly of very large genomes. As such, we discuss assembly results for a series of genomes: human, plant, lower eukaryote and bacterial. Unlike sequence assembly, the optical map assembly problem is actually more complex because restriction maps from single molecules are constructed, manifesting errors stemming from: missing cuts, false cuts, and high variance of estimated fragment sizes; chimeric maps resulting from artifactually merged molecules; and true overlap scores that are "in the noise" or "slightly above the noise." We address these problems, fundamental to many single molecule measurements, by an effective error correction method using global overlap information to eliminate spurious overlaps and chimeric maps that are otherwise difficult to identify.

Algorithms↗

PubMed1993

New approaches with the Chem-1 creatinine determination.

Three modifications of the Chem-1 determination of serum creatinine were tested. Two different algorithms developed for compensating the interference of bilirubin were compared with the current one by analysing bilirubin-enriched albumin solutions and 82 icteric serum samples. A number of known other interfering substances were also tested. The modification involving parallel bichromatic measurement plus bilirubin correction appeared to give the best performance. However, despite the improvements, the determination is not yet completely satisfactory.

Algorithms↗

PubMed1997

An algorithm for the detection of surface-active alpha helices with the potential to anchor proteins at the membrane interface.

MOTIVATION: Surface-active peptides are amphiphilic in nature and have been shown to have the potential to interact at the membrane interface, possibly by lying parallel to the membrane surface. Present methodology for the identification of these helices uses a fixed window size, is based on a two-dimensional sum of hydrophobicity vectors and gives no measure of the statistical significance for any region identified as amphiphilic. Identification of weakly surface-active structures is difficult and here we have attempted to remedy this by introducing an algorithm which considers three-dimensional geometries and variable window size. RESULTS: A new measure of membrane-interactive potential is proposed, called the depth-weighted inserted hydrophobicity (DWIH), which is based on the sequestration of hydrophobic residues within a hydrophobic compartment, such as that produced by a membrane bilayer. A statistical significance for this measure has been derived using Monte Carlo techniques. The algorithm is applied to a set of proteins which are thought to anchor to the membrane via C-terminal amphiphilic alpha helices. The DWIH measure appears to allow the identification of this category of membrane-interactive helices which lie near the boundary of the hydrophobic moment plot and which have previously been hard to classify.

Algorithms↗

PubMed2002

Comparison of analog and digital Fourier transforms in medical image analysis.

The effectiveness and limitations of medical image processing using analog and digital methods are studied. Several types of errors introduced during the image processing are analyzed. For the analog optical Fourier transform, errors are introduced by the vignetting effect and lens aberration. For the digital Fourier transform, errors are introduced by the aliasing effect and the band limit. To compare the results obtained by the two techniques, a set of x-ray images was processed both optically and digitally. The former was achieved by an optical system containing a large Fourier telephoto lens and the latter by a personal computer using a Fourier transform algorithm. The veracity of both the optical and digital Fourier spectra is analyzed. Our results indicate that the optical method has high speed due to parallel processing. High veracity can be achieved in high frequency regions by using an optimal optical system. In comparison, the digital method has the advantages of high processing precision and programmability, but has low processing speed. The comparison of the two different techniques presented in this article can provide a basis for selection of the processing method in different clinical settings. Even with today's fast computers, the optical method is still suitable for many clinical applications. The best choice lies in an analog-digital combination.

Algorithms↗

PubMed2004

Pregnancy-associated changes in genome-wide gene expression profiles in the liver of cow throughout pregnancy.

The objective of the present study was to fabricate and use a bovine liver complementary DNA (cDNA) microarray to profile genome-wide gene expressions in the liver of cow throughout pregnancy. A cDNA library was prepared from liver total RNA collected from cows during estrous cycle and pregnancy, and from fetuses at different stages of pregnancy. The sequenced clones were compiled and annotated by basic local alignment search tool (BLASTn) and spotted onto glass slides. The annotated liver array represented 2675 genes. Of which, 1442 were known genes while 617 sequences had matches with sequences found in expressed sequence tags databases. In addition, 616 unknown sequences were found and these sequences may possibly be identified as candidates for novel bovine genes. For gene expression profiling studies, total RNA from livers of cows slaughtered on days 19, 27-28, 49-58, 150, and 245 of pregnancy (test RNAs) was separately reverse transcribed and labeled with either cyanine 5-fluorescent dye (Cy5) or Cy3. The test samples were individually compared with liver total RNA collected from nonpregnant cycling cows (control RNA) after reverse transcription and labeling with the opposite dye following a two-color hybridization method. After scanning, image acquisition, and normalization, genes that showed either more than 1.5-fold (test/control) induction or repression were selected for further analyses. Hierarchical clustering algorithm showed a clear induction of most liver genes on days 27-28 of pregnancy. Self-organizing maps algorithm identified groups of genes whose differential expression patterns were similar across pregnancy. In conclusion, we described fabrication of a bovine liver cDNA microarray, and demonstrate, for the first time, differential expression patterns of a large number of coregulated liver genes in parallel throughout pregnancy in the bovine.

Algorithms↗

PubMed1997

A focus-of-attention preprocessing scheme for EM-ML PET reconstruction.

The expectation-maximization maximum-likelihood (EM-ML) algorithm belongs to a family of algorithms that compute positron emission tomography (PET) reconstructions by iteratively solving a large linear system of equations. We describe a preprocessing scheme for automatically focusing the attention, and thus the computational resources, on a subset of the equations and unknowns. Experimental work with a CM-5 parallel computer implementation using a simulated phantom as well as real data obtained from an ECAT 921 PET scanner indicates that quite significant savings can be obtained with respect to both time and space requirements of the EM-ML algorithm without compromising the quality of the reconstructed images.

Abdomen↗

PubMed1998

Feasibility study of x-ray diffraction computed tomography for medical imaging.

A feasibility study of soft-tissue imaging based on x-ray wide-angle diffraction contrast has been performed at the medical beamline of the European Synchrotron Radiation Facility (ESRF). The technique employs computed-tomography algorithms to reconstruct from one data set the spatial distribution of several tissues differentiated by their diffraction properties. Radial diffraction profiles are measured in parallel projections from the sample and decomposed into material-selective weighting factors, which form the sinograms for the reconstructions. Attenuation effects--inherent in imaging techniques using scattered radiation--are efficiently corrected for by a ray-tracing method applied to the corresponding absorption image. Images of 7 cm diameter samples composed of fat, bone and muscle were generated at 60 and 80 keV x-ray energy. The highest surface-absorbed dose was 24 mGy, but substantial contrast could still be obtained at 7 mGy, indicating potential applicability in medical imaging. The dominant noise contribution in the images stems from the detection system, pointing to a possible decrease in the surface-absorbed dose for an optimized system of more than a factor of 2.

Adipose Tissue↗

PubMed2006

JCell--a Java-based framework for inferring regulatory networks from time series data.

MOTIVATION: JCell is a Java-based application for reconstructing gene regulatory networks from experimental data. The framework provides several algorithms to identify genetic and metabolic dependencies based on experimental data conjoint with mathematical models to describe and simulate regulatory systems. Owing to the modular structure, researchers can easily implement new methods. JCell is a pure Java application with additional scripting capabilities and thus widely usable, e.g. on parallel or cluster computers. AVAILABILITY: The software is freely available for download at http://www-ra.informatik.uni-tuebingen.de/software/JCell.

Algorithms↗

PubMedDate not supplied

Interactive collision detection for deformable models using streaming AABBs.

We present an interactive and accurate collision detection algorithm for deformable, polygonal objects based on the streaming computational model. Our algorithm can detect all possible pairwise primitive-level intersections between two severely deforming models at highly interactive rates. In our streaming computational model, we consider a set of axis aligned bounding boxes (AABBs) that bound each of the given deformable objects as an input stream and perform massively-parallel pairwise, overlapping tests onto the incoming streams. As a result, we are able to prevent performance stalls in the streaming pipeline that can be caused by expensive indexing mechanism required by bounding volume hierarchy-based streaming algorithms. At runtime, as the underlying models deform over time, we employ a novel, streaming algorithm to update the geometric changes in the AABB streams. Moreover, in order to get only the computed result (i.e., collision results between AABBs) without reading back the entire output streams, we propose a streaming en/decoding strategy that can be performed in a hierarchical fashion. After determining overlapped AABBs, we perform a primitive-level (e.g., triangle) intersection checking on a serial computational model such as CPUs. We implemented the entire pipeline of our algorithm using off-the-shelf graphics processors (GPUs), such as nVIDIA GeForce 7800 GTX, for streaming computations, and Intel Dual Core 3.4G processors for serial computations. We benchmarked our algorithm with different models of varying complexities, ranging from 15K up to 50K triangles, under various deformation motions, and the timings were obtained as 30 approximately 100 FPS depending on the complexity of models and their relative configurations. Finally, we made comparisons with a well-known GPU-based collision detection algorithm, CULLIDE [4] and observed about three times performance improvement over the earlier approach. We also made comparisons with a SW-based AABB culling algorithm [2] and observed about two times improvement.

Algorithms↗

PubMed1998

A harmonic decomposition reconstruction algorithm for spatially varying focal length collimators.

Spatially varying focal length fan-beam collimators can be used in single photon emission computed tomography to improve detection efficiency and to reduce reconstruction artifacts resulting from the truncation of projection data. It has been proven that there exists no convolution backprojection algorithm for this type of collimator, so a complicated interpolation between two nonparallel projection rays is necessary for existing algorithms. The interpolation may generate blurring and artifacts in the reconstructed images. Based on a harmonic decomposition technique and the translation property of Fourier series, a semifrequency resampling technique is proposed to avoid the above mentioned interpolations. By this technique, the harmonic decomposition of projection data for spatially varying focal length fan-beam collimators has the same form as that for parallel-beam collimators in the semifrequency domain (Fourier transform with respect to angular variables only). An alternative version of the inverse Cormack transform is then proposed to reconstruct the images. The derived reconstruction algorithm was implemented in a Pentium II/266 PC computer. Numerical simulations demonstrated its efficiency (3 s for 128 x 128 reconstruction arrays) and its robust performance (compared to the existing algorithms).

Algorithms↗

PubMed2003

Hybrid global optimization algorithms for protein structure prediction: alternating hybrids.

Hybrid global optimization methods attempt to combine the beneficial features of two or more algorithms, and can be powerful methods for solving challenging nonconvex optimization problems. In this paper, novel classes of hybrid global optimization methods, termed alternating hybrids, are introduced for application as a tool in treating the peptide and protein structure prediction problems. In particular, these new optimization methods take the form of hybrids between a deterministic global optimization algorithm, the alphaBB, and a stochastically based method, conformational space annealing (CSA). The alphaBB method, as a theoretically proven global optimization approach, exhibits consistency, as it guarantees convergence to the global minimum for twice-continuously differentiable constrained nonlinear programming problems, but can benefit from computationally related enhancements. On the other hand, the independent CSA algorithm is highly efficient, though the method lacks theoretical guarantees of convergence. Furthermore, both the alphaBB method and the CSA method are found to identify ensembles of low-energy conformers, an important feature for determining the true free energy minimum of the system. The proposed hybrid methods combine the desirable features of efficiency and consistency, thus enabling the accurate prediction of the structures of larger peptides. Computational studies for met-enkephalin and melittin, employing sequential and parallel computing frameworks, demonstrate the promise for these proposed hybrid methods.

Algorithms↗

PubMed2006

Algorithmic computation of knot polynomials of secondary structure elements of proteins.

The classification of protein structures is an important and still outstanding problem. The purpose of this paper is threefold. First, we utilize a relation between the Tutte and homfly polynomial to show that the Alexander-Conway polynomial can be algorithmically computed for a given planar graph. Second, as special cases of planar graphs, we use polymer graphs of protein structures. More precisely, we use three building blocks of the three-dimensional protein structure--alpha-helix, antiparallel beta-sheet, and parallel beta-sheet--and calculate, for their corresponding polymer graphs, the Tutte polynomials analytically by providing recurrence equations for all three secondary structure elements. Third, we present numerical results comparing the results from our analytical calculations with the numerical results of our algorithm-not only to test consistency, but also to demonstrate that all assigned polynomials are unique labels of the secondary structure elements. This paves the way for an automatic classification of protein structures.

Algorithms↗

PubMed2005

Alkylation of cytochrome c by (glutathion-S-yl)-1,4-benzoquinone and iodoacetamide demonstrates compound-dependent site specificity.

The reaction of cytochrome c with the electrophilic compounds (glutathion-S-yl)-1,4-benzoquinone (GSBQ) and iodoacetamide was studied using mass spectrometry. GSBQ is a nephrotoxic quinol-thioether metabolite of benzoquinone, while iodoacetamide is an alkylating agent targeting cysteine thiols. Both chemicals formed covalent adducts with cytochrome c. GSBQ formed adducts with cytochrome c at pH 6 on several histidine and lysine residues. At a pH >7, the initial product rearranged to a disubstituted cyclic quinone species preferentially found at two sites on the protein, Lys25-Lys27 and Lys86-Lys87, via quinol amine linkages. These two sites were previously determined to be the targets of benzoquinone adduct formation [Person et al. (2003) Chem. Res. Toxicol. 16, 598-608]. Cyclic reaction products are preferentially formed at two sites on the protein because of the presence of multiple basic residues in a conformationally flexible region whereas noncyclic products bind to a broad spectrum of available lysine and histidine nucleophiles. Iodoacetamide was a less selective alkylating agent able to form adducts on the majority of the nucleophilic sites of the protein. MS/MS spectra were used to identify signature ions for GSBQ-adducted peptides from the characteristic fragmentation patterns. Neutral losses of the 129 Da gamma-glutamate residue and of the 273 Da glutathione moiety were found in both cysteine thiol- and lysine amine-linked GSBQ adduct MS/MS. Characteristic fragment ions were used in conjunction with the scoring algorithm for spectral analysis to search for adducted species present at low levels in the sample, and the analysis is applicable generally to detection of glutathione conjugates by MS/MS. Parallel analysis using matrix-assisted laser desorption/ionization-MS to compare spectra of control and treated samples allowed identification of peptide adducts formed by direct addition of GSBQ and by the subsequent loss of the glutathione moiety in a pH-dependent cyclization reaction.

Algorithms↗

PubMed2006

Aperture collimation correction and maximum-likelihood image reconstruction for near-field coded aperture imaging of single photon emission computerized tomography.

Coded aperture (CA) imaging originally developed in X-ray astronomy has not been widely used in nuclear medicine due to the decoding complexity of near-field CA images. In this paper, we present a near-field CA imaging technique and image reconstruction method for high sensitivity and high resolution single photon emission computerized tomography (SPECT). Our approach makes three contributions. First, a correction method for the aperture collimation effect is used to eliminate the near-field artifacts without dual acquisitions of mask and anti-mask images. Second, a maximum-likelihood expectation-maximization (MLEM) deconvolution method is used to restore CA images. Finally, a new MLEM-based algorithm is used to partially reconstruct three-dimensional (3-D) objects from a single projection of CA images. Experiments conducted using a dual-head SPECT system equipped with a parallel-hole collimator and a CA module show a tenfold increase in count sensitivity and significant improvement in image resolution with CA collimation as compared to parallel-hole collimation. Experiments conducted using the same dual-head SPECT system equipped with a pinhole collimator show that when the object is closer to the pinhole collimator the CA image resolution is only slightly inferior to the pinhole collimated image. We found that the MLEM deconvolution method provides an inherent nonnegativity constraint on pixel values and remarkably reduces background activities of CA images. The MLEM reconstruction algorithm for CA images is capable of reconstructing 3-D objects from a single projection and can be potentially extended to full 3-D SPECT reconstruction for CA images.

Algorithms↗