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At least 1,333 records · Page 74Linked to original sources
PubMed2002

PCNA and Ki-67 in central nervous system tumors: correlation with the histological type and grade.

Determination of proteins in the control of proliferation in normal cells helps a better understanding of cellular transformation and proliferation mechanisms. Measurement of proliferative activity is important in determining the tumor grade, recurrence span and malignancy. Proliferating cell nuclear antigen (PCNA) and Ki-67 are two of the nuclear markers used to demonstrate the proliferative phase of the cell cycle. In the present study, 63 central nervous system (CNS) tumors of various histologic types, diagnosed in Cukurova University Medical Faculty. Department of Pathology and graded according to WHO grading system were examined for PCNA and Ki-67 monoclonal antibodies using immunohistochemistry. Results were analyzed with statistical methods. Distribution of PCNA and Ki-67 LI (labeling index) values were determined for different tumor types. The highest PCNA and Ki-67 LI values were detected in medulloblastoma, malignant meningioma, primitive neuroectodermal tumor (PNET) and glioblastoma (GBM) groups, while pilocytic astrocytoma, meningioma, craniopharyngioma and oligodendroglioma showed the lowest values. In such tumors, the correlation between the increasing grade and PCNA and Ki-67 LI values were statistically significant. A correlation between the clinical outcome and Ki-67 and PCNA LI values was also detected. Conclusively, both markers can be used to evaluate the tumor grade and to asses the possibility of recurrence and malignancy in CNS tumors.

Astrocytoma↗
PubMed2003

On methods of spatial analysis for genotyped individuals.

Spatial autocorrelation methods have commonly been applied to individual-based spatial genetic studies, although their properties and the relations among the statistics have not been carefully examined. This paper first introduces a reformulation of widely used spatial statistics using point processes. When Moran's I statistics are applied to allele frequencies within an individual, the frequencies are no longer continuous variables but have only three discrete values and specific interpretations of Moran's I statistics and the number of alleles in common (NAC) can be expressed as the weighted sum of join-count statistics. The distributions of minor genotypes are amplified in Moran's I depending on the allele frequency in the population, while NAC uses a constant weighting system. Under the point process framework, spatial analysis can be conducted on the common theoretical base, from individual locations to genetic distributions of different levels, (for example, genotype and allele). The methodology is demonstrated by application to field data for molecular ecological studies of Fagus crenata population dynamics.

Biological Evolution↗
PubMed2003

Distance distributions and electron-density characteristics of protein models.

The analytical expression for the distribution of an interatomic distance resulting from a known error-free distance and a Gaussian perturbation of the atomic coordinates is presented. This is used to estimate the coordinate error on the basis of known geometric features of protein models via the nearest-neighbour or the radial distance distribution. A simple relation is presented that describes the dependence of the map correlation on the positional error of the protein model, the resolution of the X-ray data and the overall atomic displacement parameter. The distribution of geometrical features and the relation between the map correlation and the positional error can be used in assisting the decision-making process during automated model-building procedures.

Crystallography, X-Ray↗
PubMed2003

Formula-based approach of statistical tests for peri-stimulus time histograms.

We introduce formula-based approaches for statistical tests regarding peri-stimulus time histograms (PSTHs) in cases when a conditioning stimulus was triggered by a motor-unit discharge with a constant delay time. The individual bin test and the cumulative sum test have recently been reported as methods for the quantitative analysis of PSTHs in the evaluation of human neural projections. These tests calculate confidence intervals using simulated point processes on the discharge of a motor unit, but require a significant amount of calculation time for the point process simulation. In order to overcome such a disadvantage in practical use, we provide a statistical formulization of the two above-mentioned tests using a combination theory. In general, the time required for calculating confidence intervals using these formula-based approaches was 2-13 times faster than when using the previous approaches. Unlike the previous ones, these formula-based approaches do not need to judge that a simulation process converges to the substationary state, and calculate an ideal distribution of statistical noise on the histogram, thereby providing high accuracy. We conclude that the formula-based approaches increase reliability and are sufficiently sophisticated for practical use.

Action Potentials↗
PubMed1995

Non-random distribution of spontaneous chromosome aberrations in two Bloom Syndrome patients.

The distribution of breakpoints involved in spontaneous chromosome aberrations (CA) was analyzed in lymphocytes from a family with Bloom's Syndrome (BS) and 9 healthy individuals. Standard and G-banded metaphases from each individual were analyzed to allow the identification of the breakpoints involved in spontaneously occurring chromosome aberrations. A total of 85 breakpoints in BS patients, 17 in their parents and 35 in controls, could be exactly localized to specific chromosome bands. Breakpoint distribution was statistically analyzed considering the formula proposed by Brøgger (1977), showing a non-random pattern in BS patients. Thirteen bands non-randomly involved in spontaneous CA (p < 0.005) were recognized in BS, located at 1p36, 1q21, 1q32, 2q33, 3p24, 3p14, 3q27, 5q31, 6p21, 7q22, 9q13, 11q13, and 17q23. Only 1 band (1q21) was significantly implicated in both parents (p < 0.005), while controls showed a random distribution. BS non-random bands were correlated with the chromosomal location of fragile sites, oncogenes, and breakpoints involved in cancer rearrangements. A significant correlation with the location of fragile sites and cancer-breakpoints (p < 0.005), particularly with acute myeloid leukemia and malignant lymphomas rearrangements was found. These findings demonstrate that constitutional chromosome instability in BS might involve specific points, such as fragile sites and cancer breakpoints, suggesting an association with the increased incidence of cancer.

Acute Disease↗
PubMed2001

An explicit representation of the Luria-Delbrück distribution.

The probability distribution of the number of mutant cells in a growing single-cell population is presented in explicit form. We use a discrete model for mutation and population growth which in the limit of large cell numbers and small mutation rates reduces to certain classical models of the Luria-Delbrück distribution. Our results hold for arbitrarily large values of the mutation rate and for cell populations of arbitrary size. We discuss the influence of cell death on fluctuation experiments and investigate a version of our model that accounts for the possibility that both daughter cells of a non-mutant cell might be mutants. An algorithm is presented for the quick calculation of the distribution. Then, we focus on the derivation of two essentially different limit laws, the first of which applies if the population size tends to infinity while the mutation rate tends to zero such that the product of mutation rate times population size converges. The second limit law emerges after a suitable rescaling of the distribution of non-mutant cells in the population and applies if the product of mutation rate times population size tends to infinity. We discuss the distribution of mutation events for arbitrary values of the mutation rate and cell populations of arbitrary size, and, finally, consider limit laws for this distribution with respect to the behavior of the product of mutation rate times population size. Thus, the present paper substantially extends results due to Lea and Coulson (1949), Bartlett (1955), Stewart et al. (1990), and others.

Algorithms↗
PubMed2003

The distribution of viral blips observed in HIV-1 infected patients treated with combination antiretroviral therapy.

Human immunodeficiency virus type 1 (HIV-1) infected patients treated with combination antiretroviral therapy frequently have the level of HIV-1 RNA detectable in plasma driven below the lower limit of detection of current assays, 50 copies ml(-1). Patients may continue to exhibit viral loads (VLs) below the assay limit for years, yet on some occasions the VL may be above the limit of detection. Whether these 'blips' in VL are simply assay errors or are indicative of intermittent episodes of increased viral replication is of great clinical concern. By analyzing the occurrence of viral blips in 123 treated HIV-infected patients, we show that patients do not share a common probability distribution of blip amplitude and thus reject the hypothesis that blips are solely due to assay variation.

Antiretroviral Therapy, Highly Active↗
PubMed2002

Distribution of monthly deaths, solar (SA) and geomagnetic (GMA) activity: their interrelationship in the last decade of the second millennium: the Lithuanian study 1990-1999.

Thirty percent of cardiovascular deaths cannot be explained by known risk factors. In this study, we sought links between 1) circannual rhythmicity, solar activity (SA) - sunspot number, solar radioflux and geomagnetic activity (GMA) - Ap., Cp., Am. with monthly number of deaths looking for environmental influence on mortality at the end of the second millennium. The Lithuanian national death data from for 120 consecutive months according to the IDC (1990 - 1999, n = 424925 deaths) was studied: 157189 from IHD (72144 male, 85045 female), 50228 from stroke (19062 male, 31166 female), 33722 from accidents (26193 male, 7529 female), 10655 from road accidents (8127 male, 2528 female) and 14810 from suicide (12137 male, 2673 female), 217508 - non cardiovascular (134308 male, 83200 female). Monthly death numbers (total, < 65y, 65-74, > 74y old for IHD and Stroke, and by gender) were compared with time of year, SA and GMA indices obtained from the National Geophysical Data and National Space Services Center, USA. Circannual rhythmicity indices, Pearson correlation coefficients and their probabilities were obtained and analyzed. The interrelationships of deaths from IHD and stroke and some other pathologies were also studied. In addition a multivariate linear regression analysis was done in order to evaluate the influence of time (month), Solar (S.A.) and Geomagnetic (GMA) activity on the temporal distribution of deaths. The total IHD monthly death number was significantly linked with GMA indices (r = 0.2-0.24, p = 0.03-0.075), but not with SA. IHD correlated with SA (r = 0.25-0.27, p = 0.006-0.0026), only in the 74 year age group. p = 0.0001) In the 65-74 age group, there was an inverse relationship with SA (r = -0.46-0.44) and no significant relationship to GMA. The IHD death number was correlated with GMA only in the < 65 and > 74 year age group (r = 0.30-0.36, p = 0.001-0.001). 2) Stroke-related deaths showed an inverse correlation with SA and GMA only for the 65-74y age group (r = -0.5, p = 0.0001 - SA, r = -0.4, p = 0.0001- GMA) and with GMA at age < 65 only for males (r = 0.20-0.25, p = 0.03-0.04). 3) Both IHD and stroke were strongly circannual rhythmic with acrophase at month 1.27 (IHD) and 1.32 (stroke) - first half of February, (p = 0.0001). 4) The IHD / stroke death ratio was correlated both with SA and GMA (r = 0.35, p 0.0001 - SA, r = 0.40-0.44, p = 0.0001 - GMA). 5) There was a strong inverse monthly deaths correlation between IHD and suicide (n = 14,810, r = -0.53, p = 0.0001). Stroke and suicide were also related, but to a much weaker extent (r = -0.217, p = 0.017). Accidents were inverse related to S.A. (r = -0.286, p = 0.0015), but not to GMA. Road Accidents - with both S.A. (r = 0.427, p < 0.0001) and GMA (r = 0.258, p = 0.004); with acrophases in October for road and November for other fatal accidents. Non cardiovascular deaths were annually rhythmic only for female - acrophase in early February, and for both gender inverse related to S.A. (r = -0.57, p < 0.0001) but not with GMA. Suicide victims had their acrophase in July (p < 0.0001) and were inverse related to S.A. (r = -0.6, p < 0.0001) and GMA (r = -0.27, p = 0.002). At the onset of the third millennium, the temporal distribution of deaths is still related to environmental physical activity. Those links differ for each of the pathologies, and by age and gender.

Aged↗
PubMed1999

Detecting outliers in non-redundant diffraction data.

Outliers are observations which are very unlikely to be correct, as judged by independent observations or other prior information. Such unexpected observations are treated, effectively, as being more informative about possible models, so they can seriously impede the course of structure determination and refinement. The best way to detect and eliminate outliers is to collect highly redundant data, but it is not always possible to make multiple measurements of every reflection. For non-redundant data, the prior expectation given either by a Wilson distribution of intensities or model-based structure-factor probability distributions can be used to detect outliers. This captures mostly the excessively strong reflections, which dominate the features of electron-density maps or, even more so, Patterson maps. The outlier rejection tests have been implemented in a program, Outliar.

Research Design↗
PubMed2006

Distribution of postpartum amenorrhea in rural Bangladeshi women.

Previous studies of postpartum amenorrhea (PPA) demonstrated distinct subgroups of women with short and long durations of amenorrhea. This phenomenon was attributed to cases where breastfeeding is absent because of pregnancy loss or infant death, or confusion of postpartum bleeding with resumption of menses. We explored these ideas using data from an 11-month prospective study in Bangladesh in which 858 women provided twice-weekly interviews and urine specimens for up to 9 months; 300 women were observed while experiencing PPA. The resulting exact, interval-censored, or right-censored durations were used to estimate parameters of two-component mixture models. A mixture of two Weibull distributions provided the best fit to the observations. The long-duration subgroup made up 84% (+/- 4% SE) of the population, with a mean duration of 457 (+/- 31) days. The short-duration subgroup had a mean duration of 94 (+/- 17) days. Three covariates were associated with the duration of PPA: women whose husbands had high-wage employment had a greater probability of falling in the short-duration subgroup; women in the long-duration subgroup whose husbands seasonally migrated had shorter periods of PPA within the subgroup; and mothers in the short-duration subgroup who gave birth during the monsoon season experienced a shortened duration of PPA within the subgroup. We conclude that the bimodal distribution of PPA reflects biological or behavioral heterogeneity rather than shortcomings of data collection.

Adolescent↗
PubMed2004

A model explaining the size distribution of gene and protein families.

This article deals with the theoretical size distribution of gene and protein families in complete genomes. A simple evolutionary model for the development of such families in which genes in a family are formed or selected against independently and at random, and in which new families are formed by the random splitting of existing families, is used to derive the resulting size distribution. Mathematically this turns out to be the distribution of the state of a homogeneous birth-and-death process after an exponentially distributed time, which it is shown will under certain conditions exhibit the power-law behaviour observed for gene and protein family sizes.

Algorithms↗
PubMed2006

On the distribution of saliency.

Detecting salient structures is a basic task in perceptual organization. Saliency algorithms typically mark edge-points with some saliency measure, which grows with the length and smoothness of the curve on which these edge-points lie. Here, we propose a modified saliency estimation mechanism that is based on probabilistically specified grouping cues and on curve length distributions. In this framework, the Shashua and Ullman saliency mechanism may be interpreted as a process for detecting the curve with maximal expected length. Generalized types of saliency naturally follow. We propose several specific generalizations (e.g., gray-level-based saliency) and rigorously derive the limitations on generalized saliency types. We then carry out a probabilistic analysis of expected length saliencies. Using ergodicity and asymptotic analysis, we derive the saliency distributions associated with the main curves and with the rest of the image. We then extend this analysis to finite-length curves. Using the derived distributions, we derive the optimal threshold on the saliency for discriminating between figure and background and bound the saliency-based figure-from-ground performance.

Algorithms↗
PubMed2002

Classification of oral clefts by affection site and laterality: a genotype-phenotype correlation study.

OBJECTIVES: The aim of this study was to classify the phenotypes found in a series of patients with non-syndromic cleft lip (CL) with or without cleft palate (CP) and isolated cleft palate. Additionally, the frequency distribution of cases belonging to families linked to markers on chromosomes 6 and 2 within these phenotypic patterns were estimated. DESIGN: A retrospective examination of all the available affected cases collected in Italy. SETTING AND SAMPLE POPULATION: Ninety-seven affected subjects aged 5-18 years belonging to 38 families were considered. Patterns were identified by variance of the cleft (lip, primary palate, secondary palate) and stratified according to the side of occurrence (right, left, or bilateral). Latent class analysis was used as main statistical tool for carrying out the results. RESULTS: Three homogenous classes were identified (P < 0.0001) by means of latent class analysis. Individuals were assigned to the most suited class. All three variables (lip, primary and secondary cleft palate) generated a specific class. Optimal findings were reported in cases having 'any isolated cleft lip' (class 1); 'secondary CP with or without bilateral/right primary cleft palate + bilateral/right cleft lip' (class 2); and 'left primary cleft palate + left/bilateral cleft lip with or without secondary CP' (class 3). Correspondence to the evidence of linkage to chromosome 6 showed that 9 of 10 cases presenting with 'right primary CP + right CL with secondary cleft palate' (class 2) belonged to a linked family. The same combination, but occurring on the left side (class 3), revealed that only three of nine cases belong to families linked to chromosome 6 (P-value = 0.02). The two patterns (right and left) never occurred in the same family. Three reliable groups were identified based on laterality and the presence of a cleft. A single right sided pattern displayed a statistically different distribution of linkage to chromosome 6 when compared with the homologous left side. CONCLUSION: Non-syndromic CL with/without CP can be classified according to laterality that can be under genetic control.

Adolescent↗
PubMed2003

Statistical thermodynamics of internal rotation in a hindering potential of mean force obtained from computer simulations.

A method of statistical estimation is applied to the problem of one-dimensional internal rotation in a hindering potential of mean force. The hindering potential, which may have a completely general shape, is expanded in a Fourier series, the coefficients of which are estimated by fitting an appropriate statistical-mechanical distribution to the random variable of internal rotation angle. The function of reduced moment of inertia of an internal rotation is averaged over the thermodynamic ensemble of atomic configurations of the molecule obtained in stochastic simulations. When quantum effects are not important, an accurate estimate of the absolute internal rotation entropy of a molecule with a single rotatable bond is obtained. When there is more than one rotatable bond, the "marginal" statistical-mechanical properties corresponding to a given internal rotational degree of freedom are reduced. The method is illustrated using Monte Carlo simulations of two public health relevant halocarbon molecules, each having a single internal-rotation degree of freedom, and a molecular dynamics simulation of an immunologically relevant polypeptide, in which several dihedral angles are analyzed.

Algorithms↗
PubMed2006

Thermophoretic depletion follows Boltzmann distribution.

Thermophoresis, also termed thermal diffusion or the Soret effect, moves particles along temperature gradients. For particles in liquids, the effect lacks a theoretical explanation. We present experimental results at moderate thermal gradients: (i) Thermophoretic depletion of 200 nm polystyrene spheres in water follows an exponential distribution over 2 orders of magnitude in concentration; (ii) Soret coefficients scale linearly with the sphere's surface area. Based on the experiments, it is argued that local thermodynamic equilibrium is a good starting point to describe thermophoresis.

Diffusion↗
PubMed2004

A method for modeling noise in medical images.

We have developed a method to study the statistical properties of the noise found in various medical images. The method is specifically designed for types of noise with uncorrelated fluctuations. Such signal fluctuations generally originate in the physical processes of imaging rather than in the tissue textures. Various types of noise (e.g., photon, electronics, and quantization) often contribute to degrade medical images; the overall noise is generally assumed to be additive with a zero-mean, constant-variance Gaussian distribution. However, statistical analysis suggests that the noise variance could be better modeled by a nonlinear function of the image intensity depending on external parameters related to the image acquisition protocol. We present a method to extract the relationship between an image intensity and the noise variance and to evaluate the corresponding parameters. The method was applied successfully to magnetic resonance images with different acquisition sequences and to several types of X-ray images.

Algorithms↗
PubMed2006

Reverse mapping of normal tissue complication probabilities onto dose volume histogram space: the problem of randomness of the dose volume histogram sampling.

A very important issue in contemporary inverse treatment radiotherapy planning is the specification of proper dose-volume constraints limiting the treatment planning algorithm from delivering high doses to the normal tissue surrounding the tumor. Recently we have proposed a method called reverse mapping of normal tissue complication probabilities (NTCP) onto dose-volume histogram (DVH) space, which allows the calculation of appropriate biologically based dose-volume constraints to be used in the inverse treatment planning. The method of reverse mapping requires random sampling from the functional space of all monotonically decreasing functions in the unit square. We develop, in this paper, a random function generator for the purpose of the reverse mapping. Since the proposed generator is based on the theory of random walk, it is therefore designated in this work, as a random walk DVH generator. It is theoretically determined that the distribution of the number of monotonically decreasing functions passing through a point in the dose volume histogram space follows the hypergeometric distribution. The proposed random walk DVH generator thus simulates, in a random fashion, trajectories of monotonically decreasing functions (finite series) that are situated in the unit square [0, 1] X [1,0] using the hypergeometric distribution. The DVH generator is an important tool in the study of reverse NTCP mapping for the calculation of biologically based dose-volume constraints for inverse treatment planning.

Computer Simulation↗