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At least 325 records · Page 18Linked to original sources
PubMed2002

Diagnostic potential of Fourier-transform infrared microspectroscopy and advanced computational methods in colon cancer patients.

Colon cancer is the third leading class of cancer causing increased mortality in developed countries. A polyp is one type of lesion observed in a majority of colon cancer patients. Here, we report a microscopic Fourier transform infrared (FTIR) study of normal, adenomatous polyp and malignant cells from biopsies of 24 patients. The goal of our study was to differentiate an adenomatous polyp from a malignant cell using FTIR microspectroscopy and artificial neural network (ANN) analysis. FTIR spectra and biological markers such as phosphate, RNA/DNA derived from spectra, were useful in identifying normal cells from abnormal ones that consisted of adenomatous polyp and malignant cells. However, the biological markers failed to differentiate between adenomatous polyp and malignant cases. By employing a combination of wavelet features and an ANN based classifier, we were able to classify the different cells as normal, adenomatous polyp and cancerous in a given tissue sample. The percentage of success of classification was 89%, 81%, and 83% for normal, adenomatous polyp, and malignant cells, respectively. A comparison of the method proposed with the pathological method is also discussed.

Adenocarcinoma↗
PubMed1994

Computational methods for wide-field reconstruction of transoesophageal echocardiographic images.

Transoesophageal echocardiography imaging is limited by the proximity of the transducer to many cardiovascular structures. The location of the transducer causes these structures to appear near the apex of the backscatter image, and since the angle of the scan cannot exceed 90 degrees, much of the image information appears in a constricted area. We describe a computer-based, wide-field reconstruction technique which pieces together the picture fields from adjacent sector scans to form composite images. This description includes information regarding lessons learned, as well as technical details of the algorithms, in sufficient depth to permit reproduction of the system by interested parties. Significant aspects of wide-field image reconstruction, including computational complexity, image-pair alignment processes, requirements of alignment resolution, and image acquisition techniques, are addressed in depth. We believe that wide-field presentation of echocardiographic backscatter data enhances the utility of the transoesophageal approach, particularly when dealing with posteriorly located cardiovascular lesions.

Adolescent↗
PubMed1999

Assessment of the bioactive conformation of the farnesyltransferase protein binding recognition motif by computational methods.

Ras farnesyltransferase catalyzes the carboxyl-terminal farnesylation of Ras as well as other proteins involved in signal transduction processes. Previous studies demonstrated that its inhibition suppresses the activity of Ras transformed phenotypes in cultured cells, causing tumor regression in animal models. This observation led to the consideration of farnesyltransferase as a target for cancer therapy. In the present work we report the results of a computational study aimed at assessing the bioactive conformation of the peptide Cys-Val-Phe-Met, known to be the minimum peptide sequence that inhibits farnesyltransferase. For this purpose the conformational preferences of four analogs of the peptide were assessed by means of thorough searches of their respective conformational spaces, using a simulated annealing protocol as sampling technique. Specifically, two active analogs: Cys-Val-Tic-Met and Cys-Val-psi(CH2NH)Tic-Met and two inactive analogs: Cys-Val-Tic-psi(CH2NH)Met and Cys-Val-Aic-Met were selected for the present study. Low energy conformations of the four analogs were classified according to their structural motifs. The putative bioactive conformation of the minimum farnesyltransferase recognition motif was assessed by cross-comparison of the different classes of conformations obtained for the two active and the two inactive analogs. The putative bioactive conformation is characterized by two structural motifs: i) a C14 pseudo-ring stabilized by a hydrogen bond between the amino group of Cys1 and the carboxylate group of Met4 and a C11 pseudo-ring involving the residues Cys1 and Tic3. In addition, the thiol group of Cys1 side chain of the bioactive conformation points to the carboxylate moiety of Met4.

Algorithms↗
PubMed2003

Lifetime prediction of all-ceramic bridges by computational methods.

There has been limited use of ceramic materials for all-ceramic posterior bridges. Major reasons are the low strength, the strength scatter, and the time-dependent strength decrease of ceramics due to slow crack growth. The objective of this study was to predict the long-term failure probability and loading capability of all-ceramic bridges (Empress 1, Empress 2, In-Ceram Alumina, and ZrO(2)) by computational techniques. The lifetimes of different bridge model designs were predicted by means of the NASA post-processor CARES. Bridges made of zirconia showed a very high mechanical long-term reliability. Empress I and InCeram Alumina seem to be insufficient as posterior bridge materials based on this prediction. The lifetime of the all-ceramic bridges can be significantly increased by improving the design in the connector area. We conclude that computational techniques can help to judge a ceramic material and a specific ceramic bridge design with respect to mechanical reliability before clinical use.

Aluminum Oxide↗
PubMed2003

Gold finder: a computer method for fast automatic double gold labeling detection, counting, and color overlay in electron microscopic images.

This work presents a computerized method to identify, detect, evaluate, and, by colored overlay, present gold particle pairs in electron microscopy (EM), even in wide-field views. Double gold immunolabeled specimens were analyzed in a LEO 912 electron microscope equipped with a 2k x 2k-pixel slow-scan cooled CCD camera connected to a computer with analySIS 3.1 PRO image processing software. The acquisition of a high-resolution and high-dynamic-range image by the camera allowed correct segmentation of the gold particles, separating them from other cell structures and from the substrate. Particle identification was performed by a classification module designed by us. Based on shape and size, the computer recognized the group of small particles and classified them as either singular or clustered and differentiated these from the single bigger type. The final image shows the particle types separated and colored, and indicates the total number of objects encountered in the specific region of interest. Moreover, a montage tool allowed us to obtain final representative images of large microscopic fields, which on analysis by the Gold Finder module provided information on the distribution and localization of antigens comparable to that provided by the wide-field light microscope images.

Animals↗
PubMed2001

GeneSplicer: a new computational method for splice site prediction.

GeneSplicer is a new, flexible system for detecting splice sites in the genomic DNA of various eukaryotes. The system has been tested successfully using DNA from two reference organisms: the model plant Arabidopsis thaliana and human. It was compared to six programs representing the leading splice site detectors for each of these species: NetPlantGene, NetGene2, HSPL, NNSplice, GENIO and SpliceView. In each case GeneSplicer performed comparably to the best alternative, in terms of both accuracy and computational efficiency.

Algorithms↗
PubMed1983

Computer methods, uremic encephalopathy, and adequacy of dialysis.

It has been recognized for over 30 years that increased renal dysfunction results in increased slow wave activity in the EEG generally prior to the clinical appearance of disabling, dialysis-responsive encephalopathic symptoms of clinical uremia. This paper describes computerized methods that have been used to quantify this slow wave activity and the results of studies that have employed such computerized techniques. Practical information is furnished to guide those who wish to use these methods in their own research and practice. A survey of the limitations and pitfalls inherent in the various techniques is given. A prospectus outlines possible future directions in the field.

Brain Diseases↗
PubMed2005

Computational methods for protein-protein interaction and their application.

Protein-protein interactions play a central role in numerous processes in cell and are one of the main research fields in current functional proteomics. The increase of finished genomic sequences has greatly stimulated the progress for detecting the functions of the genes and their encoded proteins. As complementary ways to the high through-put experimental methods, various methods of bioinformatics have been developed for the study of the protein-protein interaction. These methods range from the sequence homology-based to the genomic-context based. Recently, it tends to integrate the data from different methods to build the protein-protein interaction network, and to predict the protein function from the analysis of the network structure. Efforts are ongoing to improve these methods and to search for novel aspects in genomes that could be exploited for function prediction. This review highlights the recent advances of the bioinformatics methods in protein-protein interaction researches. In the end, the application of the protein-protein interaction has also been discussed.

Computational Biology↗
PubMed2003

Application of spectroscopic and computational methods in the study of the electronic excitations of partially silylated hydroxyquinones.

The silylation of hydroxynaphthoquinones and hydroxyanthraquinones with N-methyl-N-(tert-butyldimethylsilyl)-2,2,2-trifluoroacetamide, in one step reaction, under mild conditions, has led, in nearly quantitative yields, to the isolation of hydrolytically stable partially silylated products (only of the hydroxyl groups), which differ dramatically in color from the starting materials. The spectroscopic investigation of the silylated products in solution as well as the correlation of the observed data with computationally derived results have been carried out within a study aiming at the understanding of the visible maxima shift to either the ultraviolet or near-infrared region of the electromagnetic spectrum, which would imply availability of the silylated products in a variety of related applications.

Computational Biology↗
PubMed2005

Computational methods for the HZETRN code.

Asymptotic expansion has been used to simplify the transport of high charge and energy ions for broad beam applications in the laboratory and space. The solution of the lowest order asymptotic term is then related to a Green's function for energy loss and straggling coupled to nuclear attenuation providing the lowest order term in a rapidly converging Neumann series for which higher order collisions terms are related to the fragmentation events including energy dispersion and downshift. The first and second Neumann corrections were evaluated numerically as a standard for further analytic approximation. The first Neumann correction is accurately evaluated over the saddle point whose width is determined by the energy dispersion and located at the downshifted ion collision energy. Introduction of the first Neumann correction leads to significant simplification of the second correction term allowing application of the mean value theorem and a second saddle point approximation. The regular dependence of the second correction spectral dependence lends hope to simple approximation to higher corrections. At sufficiently high energy nuclear cross-section variations are small allowing non-perturbative methods to all orders and renormalization of the second corrections allow accurate evaluation of the full Neumann series.

Algorithms↗
PubMedDate not supplied

Computational methods for analysis of human breast tumor tissue in optical coherence tomography images.

Optical coherence tomography (OCT) has been demonstrated as a promising means of identifying the boundaries between normal and diseased breast tissue. This capability has yielded promise for the development of OCT techniques for biopsy guidance, surgical margin assessment, and minimally invasive evaluation of disease states. We present methods for the assessment of human breast tissue based on spatial and Fourier-domain analysis. Derived from preliminary OCT data, these methods are aimed at the development of automated diagnostic tools that will aid in the translation of this technology into the clinical environment.

Algorithms↗
PubMed1991

Computational methods for analyzing the structure of cancellous bone in planar sections.

Conventional stereologic methods for expressing the orientation of anisotropic materials are limited to materials assumed to possess orthogonal directions of orientation. In many substances, including cancellous bone, this assumption is unsubstantiated. Presented here are two simple methods for characterizing the orientation of any anisotropic material within a plane. By modeling the substance as a series of lines oriented in particular directions, it is possible to arrive at either a "phase distribution" that expresses the degree of orientation distributed over a range of angles or a series of "primary orientations" that express the degree of orientation at a select number of angles, with an additional measure of the degree of isotropy. This characterization of anisotropy is highly dependent on such parameters as feature size, sample size, test line spacing, and test line width. Given the careful selection of these parameters, the new methods provide simple measures of orientation, which may prove useful in testing Wolff's trajectorial theory of the relationship between mechanical stresses and the orientation of cancellous bone.

Animals↗
PubMed1995

Computational methods for Markov series with large state spaces, with application to AIDS modeling.

AIDS models, and epidemiological models generally, are almost exclusively either differential equations or Markov processes. Of course, the phenomena are fundamentally random, so at best differential equations track the expectation of the process and variability is masked. There are few techniques in the literature for numerical analysis of Markov chains of any size, and so those wishing to analyze stochastic epidemics presently have little alternative to simulation. The contribution of the present paper is to propose numerical techniques capable of finding marginal probabilities of Markov chains having thousands and even millions of states. The ideas are illustrated by application to AIDS models in the literature which formerly had been investigated only through Monte Carlo. This introductory foray has not plumbed the depths of the computational methodology, which yet needs refinement and streamlining that comes through experience. Yet in its primitive form, it is shown herein to be adequate for a computation on the scale of a two-population partition of the San Francisco homosexual epidemic. The closing discussion compares the strengths and weaknesses of the present numerical techniques with the simulation approach to investigation of Markov epidemics.

Acquired Immunodeficiency Syndrome↗
PubMed2001

Numerical models for the simulation of flexible artificial heart valves: part I--computational methods.

A numerical model of the coupled motion of a flexing surface in a high Reynolds number flow is presented for the simulation of flexible polyurethane heart valves in the aortic position. This is achieved by matching a Lagrangian dynamic leaflet model with a panel method based flow solver. The two models are coupled via the time-dependent pressure field using the unsteady Bernoulli equation. Incorporation of sub-cycling in the dynamic model equations and fast pre conditioning techniques in the panel method solver yields efficient convergence and near real-time simulations of valve motion. The generality of dynamic model allows different material properties and/or geometries to be studied easily and interactively. This interactivity is realized by embedding the models within a design environment created using the software IRIS Explorer. Two flow domains are developed, an infinite domain and an internal domain using conformal mapping theory. In addition bending stress on the valve is computed using a simple stress model based on spline and circle equation techniques.

Biomechanical Phenomena↗
PubMed2005

A computational method to predict genetically encoded rare amino acids in proteins.

In several natural settings, the standard genetic code is expanded to incorporate two additional amino acids with distinct functionality, selenocysteine and pyrrolysine. These rare amino acids can be overlooked inadvertently, however, as they arise by recoding at certain stop codons. We report a method for such recoding prediction from genomic data, using read-through similarity evaluation. A survey across a set of microbial genomes identifies almost all the known cases as well as a number of novel candidate proteins.

Amino Acid Sequence↗
PubMed2001

Computational methods for gene annotation: the Arabidopsis genome.

Since the structure of the DNA molecule was identified half a century ago, the complete genome sequence has been determined for 37 prokaryotes and several eukaryotes. With the exponential growth of genetic information, bioinformatics has attempted to predict gene locations and functions in cyberspace prior to experimental confirmation at the bench.

Arabidopsis↗