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At least 829 records · Page 46Linked to original sources
PubMed1986

[Identification of the nucleotide sequences specific for the 5'-flanking regions of the genes regulated by glucocorticoids by a computer analysis method].

Nucleotide sequences of 5'-flanking regions of 11 glucocorticoid-regulated genes and 14 genes non-regulated by these hormones were studied using context computer analysis. Consensus TGTTCT, previously found in DNA fragments protected by glucocorticoid-receptor complexes from DNAase I digestion, was shown to be nonspecific for glucocorticoid-regulated genes. However, the analysis of sequences flanking the TGTTCT consensus has revealed that only glucocorticoid-regulated genes contain four regularly distributed cytosine residues, one of them belonging to TGTTCT consensus. Three of cytosine residues are separated by 8-10 bp, which provides their close neighbourhood at one side of DNA double helix; the fourth extreme cytosine residue is located 6 bp from the nearest one and therefore, the complementary guanine residue is adjacent to the consensus in DNA helix. It is suggested that the consensus itself and two flanking cytosine and one guanine residues form a specific site for the interaction with glucocorticoid-receptor complex.

Animals↗
PubMed2002

Computationally inexpensive methods for intra-cardiac atrial bipolar electrogram compression.

AIM: This paper reports studies of mathematical algorithms for intra-cardiac atrial bipolar electrogram compression suitable with implementation on implantable devices. PATIENTS AND METHODS: Bipolar intra-cardiac electrograms (IEGMs) of high right atrium were obtained from 20 patients who underwent electrophysiological studies for arrhythmias. Four thousand seven hundred and eighty-two seconds of IEGM were collected and divided into three rhythm groups: sinus rhythm (SR), atrial fibrillation (AF) and atrial flutter (AFL). Since mathematical algorithms suitable for use with implantable devices demand low computational cost, we employed piecemeal linear approximation methods (ZOP--Zero Order Prediction and SAPA--Scan Along Polygonal Approximation), and beat detection method (Peak) both or which need small numbers of operations to perform electrogram compression. Compression ratio (CR) and percent root mean square difference (PRD) were used to compare the three methods, with statistical analyses performed using paired t-test. RESULTS AND CONCLUSION: The best performance was obtained using the Peak method which reaches an average CR of 10.6 in the case of SR group, 2.8 for AF, and 3.6 for AFL groups, respectively, while PRD lies below 2% for SR and AFL groups and 6% for the AF group. Results show that, for bipolar electrograms, the Peak method reaches statistically significant better performance (P<0.001) in all cases except for Peak vs SAPA applied to AF (P=0.2). The number of operations necessary to compress the data indicate that time consumption can be reduced to be suitable for real time compression in implantable devices. The Peak method, which was assumed to receive the instant of occurrence of each recognized beat, from the hardware of the device, requires fewer operations than ZOP and SAPA. Increasing the length of electrograms recorded in pacemakers will enhance the amount of information provided by the implantable device, allowing more detailed characterization of the intra-cardiac activity and leading to new perspectives in arrhythmia diagnosis and therapy.

Adult↗
PubMed1986

[A rapid computer-assisted method for the determination of urea in dairy products: skim milk powder from various sources].

The enzymatic determination of urea in spray-dried skim milk powders was transferred to a computer aided photometric analysing system. Sample preparation is optimal using ultrafiltration, but the direct use of a milk sample is also possible with this system. The precision including sample preparation as coefficient of variation was about 0.69%, the standard deviation of the assay was 0.115-0.135 at an average content of 5.4-5.5 mg urea per 100 ml skim milk. The method was tested on 147 spray-dried skim milk powders, which were of varying origin and collected at different times of the year (Jan.-Oct.). In this way a representative survey for the urea content of a great number of skim milk powders was possible. It was also shown, that the urea content is highly affected by season. It is very constant from February to May (0.25-0.26%), and rises from June to October up to nearly 0.32%.

Animals↗
PubMed2000

Characteristics of the quenching of 9-aminoacridine fluorescence by liposomes made from plant lipids.

Several laboratories have determined the surface charge density of membranes utilizing methods based on vesicle-induced quenching of the fluorescence of 9-aminoacridine and its relief by other cations. However, the computational methods by which surface charge density were calculated have not been verified in a model system. In this study, the quenching of 9-aminoacridine fluorescence by liposomes made from varying amounts of digalactosyldiacylglyceride and phosphatidic acid and relief of quenching by salts was examined. Quenching of 9-aminoacridine fluorescence increased with increasing amounts of phosphatidic acid added, independent of the composition of the added liposomes. In certain instances, the computational methods did not yield the surface charge density of the liposomes expected from their composition. However, when the effects of background ionic strength on surface potential were considered, there was a positive correlation between expected and calculated values. Therefore, the data support the contention that changes in the fluorescence of 9-aminoacridine can be used to calculate surface charge density of membranes.

Aminacrine↗
PubMed2006

Conformational changes in protein loops and helices induced by post-translational phosphorylation.

Post-translational phosphorylation is a ubiquitous mechanism for modulating protein activity and protein-protein interactions. In this work, we examine how phosphorylation can modulate the conformation of a protein by changing the energy landscape. We present a molecular mechanics method in which we phosphorylate proteins in silico and then predict how the conformation of the protein will change in response to phosphorylation. We apply this method to a test set comprised of proteins with both phosphorylated and non-phosphorylated crystal structures, and demonstrate that it is possible to predict localized phosphorylation-induced conformational changes, or the absence of conformational changes, with near-atomic accuracy in most cases. Examples of proteins used for testing our methods include kinases and prokaryotic response regulators. Through a detailed case study of cyclin-dependent kinase 2, we also illustrate how the computational methods can be used to provide new understanding of how phosphorylation drives conformational change, why substituting Glu or Asp for a phosphorylated amino acid does not always mimic the effects of phosphorylation, and how a phosphatase can "capture" a phosphorylated amino acid. This work illustrates how computational methods can be used to elucidate principles and mechanisms of post-translational phosphorylation, which can ultimately help to bridge the gap between the number of known sites of phosphorylation and the number of structures of phosphorylated proteins.

Algorithms↗
PubMed1994

[Evaluation of 3 calculation methods to compute the PER, PFR, TPER, TPFR with equilibrium radioisotopic angiocardiography].

The author wanted to test 3 FITS to compute the peak ejection rate, the time of the peak ejection rate, the peak filling rate, the time of the peak filling rate from the left ventricle volume curve computed by means of the multigated radio nuclide angiography; the aim of the test was to ascertain the differences between the 3 methods and the differences between them for medical applications. 25 patients were tested and they were divided as follows: 5 cases of hypertension, 2 cases of obesity, 9 cases of alimentary diabetes, 3 cases of coronary heart disease, 6 cases with other diseases. The investigated FITS were: 1) the FIT that computes the derivative curve of the volume curve; 2) the FIT that computes the derivative equation of the volume curve and that interpolates it to a polynomial; 3) the FIT of Fourier. A discriminant analysis was performed and the following observations were made: according to a significant probability P < 0.05, FIT 1 classified 40% of the cases, FIT 2 classified 48% of the cases, FIT 3 classified 64% of the cases. A Box's M test was performed and was significant for FIT 3 and FIT 2 but not for FIT 1. In conclusion the test of the 3 FITS showed that FIT 3 is a better discriminant between the diverse diseases.

Gated Blood-Pool Imaging↗
PubMed2006

On statistical analysis of forensic DNA: theory, methods and computer programs.

Statistics plays an important role in evaluating the evidential weight of forensic DNA. In this paper, general statistical principles for forensic DNA analysis are presented. We introduce the theory and methods for the statistical assessment in kinship determination and DNA mixture evaluation. In particular, analytical formulas for testing for biological relationship among three individuals and for assessing the DNA mixture evidence in the case of multiple subdivided ethnic groups are developed. Two user-friendly computer programs are demonstrated to exhibit their wide applicability in tackling with complex kinship/paternity and mixture problems. The EasyDNA program can solve a complicated paternity case in 1 min.

DNA↗
PubMed1993

Methods for computer assisted analysis of lymphoid cell shape and motility, including Fourier analysis of cell outlines.

Locomotion of lymphocytes and other leukocytes is an essential feature of the immune system, and therefore the evaluation of the locomotor behaviour of a lymphocyte population is part of its functional analysis. Paradoxically, the locomotor status of leukocytes is usually assessed on the basis of static information, by counting the number of spherical versus non-spherical cells. In this paper we describe two methods for the measurement of shape changes in microscopic images of lymphoid cells. First we computed a simple shape change factor, coined incongruence factor, based on the degree of non-overlap of the contours of the cell at the beginning and at the end of a 1 min time interval. Second we have used Fourier analysis of the cell outline: a function describing the undulations of the cell outline is broken down into sinusoidal 'waves' of increasing frequency, each with its corresponding amplitude. The amplitude values for the first ten frequencies produced a satisfactory mathematical description of lymphoid cell shapes, and the change of these amplitudes over a 1 minute time interval produced a quantitative description of the shape alterations of the cells. We have used five approaches to evaluate the shape and shape changes in the following populations of mouse lymphoma cells: a constitutively low-motile T lymphoma cell line (BW5147), a high-motile hybridoma (BW-O-Li1) either on plastic or on a precultured fibroblast-like monolayer, BW-O-Li1 cells after penetration through the monolayer, and BW-O-Li1 cells after treatment with cytochalasin B. We compare the results from direct visual evaluation of cell shape, from computer assisted assessment of sphericity and from Fourier analysis of cell shape at one moment, with the two methods for quantitative shape change analysis. All approaches revealed a clear distinction between spherical low-motile populations, and non-spherical high-motile cells. Moreover, the incongruence factor proved to be a reliable single parameter of active cell deformation. In addition, the Fourier analysis of cell outlines produced useful measures of static shape and of dynamic shape change, at any user-defined level of accuracy.

Animals↗
PubMed2002

Three-dimensional volume measurement of the lateral ventricles in preterm and term infants: evaluation of a standardised computer-assisted method in vivo.

BACKGROUND: Assessment of ventricular size still represents a challenge for two-dimensional cranial sonography. OBJECTIVE: Three-dimensional (3D) volume acquisition and volume quantification are easily accomplished by an automatic scanning system without additional examination time. The development of a computer-assisted ultrasonic device will offer new perspectives for the quantification of ventricular volume. MATERIALS AND METHODS: In total, 250 healthy neonates between 27 and 41 weeks' gestation and infants up to 6 months of age without neurological pathology were examined with 3D cranial ultrasound (US). The volume of both lateral ventricles and the third ventricle were separately quantified and summated for the calculation of ventricular volume. The correlation between body weight (BW), head circumference (HC), gestational age (GA) and ventricular volume was statistically analysed. RESULTS: There was a statistically significant correlation between GA, BW, HC and ventricular volume. Normal values for premature and mature infants were established. CONCLUSIONS: 3D US appears to be an accurate imaging modality for the exact calculation of ventricular volume and should, therefore, be incorporated into the cranial sonographic assessment of ventricular size in infants.

Body Weight↗
PubMed2003

Prediction of promiscuous and high-affinity mutated MHC binders.

The identification of peptides in an antigenic sequence that can bind with high affinity to a wide range of MHC alleles is one of the challenges in subunit vaccine design. The mutation of natural peptides is an alternative to obtaining peptides that can bind to a wide range of MHC alleles with high affinity. A large number of experiments are typically necessary to identify mutations that define high-affinity binding peptides. Therefore there is a need to develop a computational method for detecting amino acid mutations in a peptide for making it high-affinity or promiscuous MHC binders. This report describes a high-throughput computer driven solution for the identification of promiscuous and high-affinity mutated binders of 47 MHC class I alleles by introducing mutations in an antigenic sequence. The method implements quantitative matrices for creating optimal mutations in an antigenic sequence. It has two major options: (i) prediction of promiscuous MHC binders and (ii) prediction of high-affinity binders. In case of prediction of promiscuous binders, the server allows a user to select (i) permissible mutations in a peptide; (ii) MHC alleles to whom it should bind; and (iii) positions at which mutation is allowed. In the case of prediction of high-affinity binders, the server allows users to specify the positions that should be conserved in the native protein. In both cases, the method computes the type of mutations and position of mutations in 9-mer peptides required to have the desired results. The web server MMBPred is available at www.imtech.res.in/raghava/mmbpred/.

Algorithms↗
PubMed1989

Estimation of quantal dose response of drugs by the Spearman-Karber method: a computer program written in BASIC.

Quantal-dose response is an important concept in pharmacology and toxicology. The best known variables are the median effective dose and the median lethal dose. These are measured according to the frequency of dichotomous response of the subjects being studied. The Spearman-Karber method is a simple and convenient algorithm to evaluate these indices. A highly portable computer program in BASIC language is also included for the convenience of computation.

Algorithms↗
PubMed2005

Neural network-based prediction of mutation-induced protein stability changes in Staphylococcal nuclease at 20 residue positions.

Protein-based therapeutics are playing an increasingly important role in the treatment of diseases, including diabetes and cancer. The viability of these treatments, however, are highly dependent on the stability of the therapeutic, since stability affects both the shelf life of the therapeutic as well as its active life in the body. Stability engineering can, therefore, be used to increase the effectiveness of protein-based therapeutics. Computational methods of protein stability prediction have been under development for about a decade, but complex molecular interactions make stability prediction difficult and computationally intensive. A rapid computational method of protein stability prediction is developed using feed-forward neural networks and used to predict mutation-induced stability changes in Staphylococcal nuclease. The input to the neural network consisted of sequences of evolutionarily based amino acid similarity scores that were obtained through the comparison of the amino acids in a mutation containing sequence to their positional counterparts in the baseline wild-type amino acid sequence. A training set was created which consisted of similarity score sequences, for which the stabilities of the corresponding amino acid sequences were known, paired with the relative stabilities of the sequences to that of the baseline. Back-propagation of error was used to train the network to output accurate relative stability scores for the sequences in the training set. Neural network-based relative stability predictions for 55 sequences containing mutation combinations not found in the training set had an accuracy of 92.8%.

Amino Acid Sequence↗
PubMed2000

An interspike interval method for computing phase locking from neural firing.

Inner hair cells (IHCs) transform the mechanical movements of the basilar membrane into electrical impulses. The impulse coding of the IHCs is the main information carrier in the auditory process and is the basis for improvements of cochlea implants as well as for low rate, high-quality speech processing and compression. This paper shows how to compute the speech signal from the neural firing based on the analysis of the interspike interval histogram. This new approach solves problems that other standard analysis methods do not solve sufficiently well.

Action Potentials↗