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PubMed2002

Shear profiles and localization in simulations of granular materials.

We present results from two-dimensional computer simulations of shearing granular layers, using a discrete element code, and applying a wide range of boundary conditions. We specifically investigate the distribution of shear within the granular layer and find two different modes of localization depending on the applied shear velocity, pressure, and layer thickness: (1) granular layers that develop a persistent shearing boundary region ("fluidlike" behavior) and (2) layers that switch between diffuse deformation and randomly positioned internal shear bands ("solidlike" behavior). The two end-member deformation modes can be found in laboratory experiments performed under low and high confining pressure, respectively. Micromechanical investigation reveals two different statistical distributions of the grain contacts correlating with the two different shearing modes. These results imply that rehological transitions in granular flow modes are linked to quantifiable microtstructural organization.

Journal Article↗

PubMed1981

Development of statistical analysis for single dose bronchodilators.

When measurements developed for the diagnosis of patients are used to detect treatment effects in clinical trials with chronic disease, problems in definition of response and in the statistical distributions of those measurements within patients have to be resolved before the results of clinical studies can be analyzed. An example of this process is shown in the development of the analysis of single-dose bronchodilator trials.

Bronchodilator Agents↗

PubMedDate not supplied

Fluorescence microscopic observation of catalysis by single or few LDH-1 enzyme molecules.

Lactate dehydrogenase (LDH-1) catalyzes the reaction of lactate and nonfluorescent NAD+ to pyruvate, NADH (fluorescence at lambda em = 455 nm, lambda em = 365 nm) and H+. The injection of highly diluted LDH-1 solution into a drop of substrate solution results in the formation of a bubble of enzyme inside the drop of substrate. At the contact surface between the enzyme solution and the substrate, discrete and statistically distributed zones of increasing fluorescence intensity and different size can be observed after enzyme injection. These zones can be interpreted as clouds of NADH around a single or a few enzyme molecules. The kinetics of the NADH formation in every fluorescent zone, and the size of the zone, can be described by a zero order production combined with a diffusion controlled loss of the reaction's product NADH from the reaction zone. From the dilution of the enzyme solution and from statistical analysis one can conclude that only few enzyme molecules in the center of the fluorescent reaction zones catalyze the NADH formation.

Catalysis↗

PubMed1998

Method to assist in the scheduling of add-on surgical cases--upper prediction bounds for surgical case durations based on the log-normal distribution.

BACKGROUND: A problem that operating room (OR) managers face in running an OR suite on the day of surgery is to identify "holes" in the OR schedule in which to assign "add-on" cases. This process necessitates knowing the typical and maximum amounts of time that the case is likely to require. The OR manager may know previous case durations for the particular surgeon performing a particular scheduled procedure. The "upper prediction bound" specifies with a certain probability that the duration of the surgeon's next case will be less than or equal to the bound. METHODS: Prediction bounds were calculated by using methods that (1) do not assume that case durations follow a specific statistical distribution or (2) assume that case durations follow a log-normal distribution. These bounds were tested using durations of 48,847 cases based on 15,574 combinations of scheduled surgeon and procedure. RESULTS: Despite having 3 yr of data, 80 or 90% prediction bounds would not be able to be calculated using the distribution-free method for 35 or 49% of future cases versus 22 or 22% for the log-normal method, respectively. Prediction bounds based on the log-normal distribution overestimated the desired value less often than did the distribution-free method. The chance that the duration of the next case would be less than or equal to its 90% bound based on the log-normal distribution was within 2% of the expected rate. CONCLUSIONS: Prediction bounds classified by scheduled surgeon and procedure can be accurately calculated using a method that assumes that case durations follow a log-normal distribution.

Algorithms↗

PubMed1995

Pol gene quasispecies of human immunodeficiency virus: mutations associated with drug resistance in virus from patients undergoing no drug therapy.

The nucleotide sequences of two pol gene regions (codons 41 to 108 and 181 to 219 of reverse transcriptase) of 60 human immunodeficiency virus type 1 genomes obtained directly from primary lymphocytes from infected individuals are reported. In addition, the mutant spectra of several quasispecies have been sampled by repetitive sequencing of molecular clones representing the same pol genomic regions. Average mutation frequencies ranged from 1.6 x 10(-2) to 3.4 x 10(-2) substitutions per nucleotide for independent samples (relative to their consensus nucleotide sequence) and from 3.6 x 10(-3) to 1.1 x 10(-2) substitutions per nucleotide for individual quasispecies distributions. Several mutations leading to amino acid substitutions related to loss of sensitivity to reverse transcriptase inhibitors have been identified in samples from patients not subjected to antiretroviral therapy. Mutation frequencies in the codons previously identified as involved in resistance to reverse transcriptase inhibitors were very similar to the average mutation frequencies in the pol region analyzed. Thus, the finding of mutations related to drug resistance (even in the absence of positive selection by the corresponding drugs) is the expected consequence of the statistical distribution of mutations along the pol gene. The presence of such critical amino acid replacements in human immunodeficiency virus type 1 populations underscores the importance of viral quasispecies as reservoirs of phenotypic virus variants and has a number of implications for AIDS control.

Amino Acid Sequence↗

PubMed1996

Probabilistic assessment of health risks of methylmercury from burning coal.

This paper describes a probabilistic assessment of neurological risks incurred from consuming fish containing methylmercury (MeHg), focusing on the incremental effects of Hg deposited from local coal combustion. A Monte Carlo model is used to simulate a "worst case" scenario in which a population of 5000 fish eaters in the upper midwestern United States derive the freshwater fish portion of their diet from local waters near a hypothetical large coal-fired power plant. This population is characterized by distributions of body mass, half-life of MeHg, and the ratios of blood to body burden and hair to blood MeHg. Each person's diet consists of varying amounts of tuna fish, freshwater sportfish, and marine fish and shellfish, the MeHg contents of which are characterized by national distribution statistics, as are the consumption rates for marine fish. The consumption rates for freshwater fish are specific to the region. The fish portion size is linked to body mass by a variable correlation. Each meal is assumed to be an independent sample; thus, as metabolic equilibrium is approached, each person's body burden of MeHg tends to approach the value corresponding to the mean MeHg intake for the population. Predictions of MeHg levels in hair by this model compared well with an observed distribution of 1437 women. Two neurological endpoints were examined: adult paresthesia, as related to MeHg body burden, and congenital neurological effects, as associated with average concentrations of MeHg in maternal hair during pregnancy. Two exposure scenarios are considered: a "baseline" in which the source of the mercury in fish is from background atmospheric deposition, and an "impact" scenario, in which local Hg deposition and concentrations in fish are roughly doubled to represent additional deposition from the hypothetical nearby power plant. For both scenarios, the 99th percentile of MeHg body burden was more than an order of magnitude below the lowest level at which increased transient adult paresthesia was experienced in an acute MeHg poisoning incident in Iraq. We thus conclude that neurological risks to adults from MeHg resulting from atmospheric Hg deposition are trivial. Based on three epidemiological studies of congenital neurological risks, we find that fetal effects appear to be more critical and that there is a smaller margin of safety for pregnant consumers of freshwater sportfish. However, the margin of safety is still considerable and may have been diminished by uncertainties in the relationships between maternal hair Hg and the actual fetal exposures.

Adult↗

PubMed1999

Selective assembly of cyclodextrins on poly(ethylene oxide)-poly(propylene oxide) block copolymers.

This paper presents a computational study on the formation of a molecular necklace formed by specific threading of cyclodextrins (CDs) on block copolymers. Structural as well as energetic principles for the selective complexation of alpha- and beta-cyclodextrin with poly(ethylene oxide)-poly(propylene oxide) block copolymers (PEO-PPO) are elucidated considering a diblock copolymer of equimolecular composition (PEO)4-(PPO)4 as guest. A non-statistical distribution of CDs, i.e. alpha-CDs primarily located on the PEO chain and beta-CDs on PPO blocks of the polymer, is based on a variety of structural features and energetic preferences considering both potential as well as solvation energies. This selectivity becomes already obvious considering 1:1 complexes between PEO and PPO monomers and the two CDs, but is increasingly evident when calculating higher order ensembles. Besides the host-guest interaction, docking between CDs themselves is an important, also non-statistical, prerequisite for the self-assembly of highly ordered tubes. The formation of intermolecular hydrogen bonds between adjacent CDs in a tubular aggregate gives an important contribution to the overall stability of the molecular necklace. The net effect, based on the preferential interaction between host and guest as well as between the host molecules themselves, results in the formation of a stable, highly ordered macromolecular, multicomponent aggregate.

Cyclodextrins↗

PubMed1999

Energy distribution of the quantum harmonic oscillator under random time-dependent perturbations.

This paper investigates the evolution of a quantum particle in a harmonic oscillator driven by time-dependent forces. The perturbations are small, but they act long enough so that we can solve the problem in the asymptotic framework corresponding to a perturbation amplitude that tends to zero and a perturbation duration that tends to infinity. We describe the effective evolution equation of the state vector, which reads as a stochastic partial differential equation. We exhibit a closed-form equation for the transition probabilities, which can be interpreted in terms of a jump process. Using standard probability tools, we are then able to compute explicitly the probabilities for observing the different energy eigenstates and give the exact statistical distribution of the energy of the particle.

Journal Article↗

PubMed2002

On the detection of early cochlear damage by otoacoustic emission analysis.

Theoretical considerations and experimental evidence suggest that otoacoustic emission parameters may be used to reveal early cochlear damage, even before it can be diagnosed by standard audiometric techniques. In this work, the statistical distributions of a set of otoacoustic emission parameters chosen as candidates for the early detection of cochlear damage (global and band reproducibility, response level, signal-to-noise ratio, spectral latency, and long-lasting otoacoustic emission presence) were analyzed in a population of 138 ears. These ears have been divided, according to a standard audiometric test, in three classes: (1) ears of nonexposed bilaterally normal subjects, (2) normal ears of subjects with unilateral noise-induced high-frequency hearing loss, and (3) their hearing impaired ears. For all analyzed parameters, a statistically significant difference was found between classes 1 and 2. This difference largely exceeds the difference observed between classes 2 and 3. This fact suggests that the noise exposure, which was responsible for the unilateral hearing loss, also caused subclinical damage in the contralateral, audiometrically normal, ear. This is a clear indication that otoacoustic emission techniques may be able to early detect subclinical damages.

Adolescent↗

PubMed2001

Accumulation of deficits as a proxy measure of aging.

This paper develops a method for appraising health status in elderly people. A frailty index was defined as the proportion of accumulated deficits (symptoms, signs, functional impairments, and laboratory abnormalities). It serves as an individual state variable, reflecting severity of illness and proximity to death. In a representative database of elderly Canadians we found that deficits accumulated at 3% per year, and show a gamma distribution, typical for systems with redundant components that can be used in case of failure of a given subsystem. Of note, the slope of the index is insensitive to the individual nature of the deficits, and serves as an important prognostic factor for life expectancy. The formula for estimating an individual's life span given the frailty index value is presented. For different patterns of cognitive impairments the average within-group index value increases with the severity of the cognitive impairment, and the relative variability of the index is significantly reduced. Finally, the statistical distribution of the frailty index sharply differs between well groups (gamma distribution) and morbid groups (normal distribution). This pattern reflects an increase in uncompensated deficits in impaired organisms, which would lead to illness of various etiologies, and ultimately to increased mortality. The accumulation of deficits is as an example of a macroscopic variable, i.e., one that reflects general properties of aging at the level of the whole organism rather than any given functional deficiency. In consequence, we propose that it may be used as a proxy measure of aging.

Aged↗

PubMed1981

Analysis of the spatial organization of the cell: a statistical method for revealing the non-random location of an organelle.

A method is proposed for testing the randomness of the location of an organelle within a given area of a cell section. The approach chosen is to analyse the distance between this organelle and a specific point considered as a point of reference. The method consists of converting this distance into the ratio of one given area to another and comparing the statistical distribution of the converted values to the uniform distribution. This method has the advantage of being valid in the absence of any restrictive assumptions concerning the heterogeneity in size and/or shape of the collection of sections sampled. Detailed examples are given to illustrate the practical use of the method, and its possible extensions are discussed.

Cell Nucleolus↗

PubMed2001

Diffusion tensor trace mapping in normal adult brain using single-shot EPI technique. A methodological study of the aging brain.

PURPOSE: To quantify age-related changes of the average diffusion coefficient value in normal adult brain using orientation-independent diffusion tensor trace mapping and to address the methodological influences on diffusion quantification. MATERIAL AND METHODS: Fifty-four normal subjects (aged 20-79 years) were studied on a 1.5-T whole-body MR medical unit using a diffusion-weighted single-shot echo-planar imaging technique. Orientation-independent diffusion tensor trace maps were constructed for each subject using diffusion-weighted MR measurements in four different directions using a tetrahedral gradient combination pattern. The global average (including cerebral spinal fluid) and the tissue average of diffusion coefficients in adult brains were determined by analyzing the diffusion coefficient distribution histogram for the entire brain. Methodological influences on the measured diffusion coefficient were also investigated by comparing the results obtained using different experimental settings. RESULTS: Both global and tissue averages of the diffusion coefficient are significantly correlated with age (p<0.03). The global average of the diffusion coefficient increases 3% per decade after the age of 40, whereas the increase in the tissue average of diffusion coefficient is about 1% per decade. Experimental settings for self-diffusion measurements, such as data acquisition methods and number of b-values, can slightly influence the statistical distribution histogram of the diffusion tensor trace and its average value. CONCLUSION: Increased average diffusion coefficient in adult brains with aging are consistent with findings regarding structural changes in the brain that have been associated with aging. The study also demonstrates that it is desirable to use the same experimental parameters for diffusion coefficient quantification when comparing between different subjects and groups of interest.

Adult↗

PubMed1997

Advances in statistical methods to map quantitative trait loci in outbred populations.

Statistical methods to map quantitative trait loci (QTL) in outbred populations are reviewed, extensions and applications to human and plant genetic data are indicated, and areas for further research are identified. Simple and computationally inexpensive methods include (multiple) linear regression of phenotype on marker genotypes and regression of squared phenotypic differences among relative pairs on estimated proportions of identity-by-descent at a locus. These methods are less suited for genetic parameter estimation in outbred populations but allow the determination of test statistic distributions via simulation or data permutation; however, further inferences including confidence intervals of QTL location require the use of Monte Carlo or bootstrap sampling techniques. A method which is intermediate in computational requirements is residual maximum likelihood (REML) with a covariance matrix of random QTL effects conditional on information from multiple linked markers. Testing for the number of QTLs on a chromosome is difficult in a classical framework. The computationally most demanding methods are maximum likelihood and Bayesian analysis, which take account of the distribution of multilocus marker-QTL genotypes on a pedigree and permit investigators to fit different models of variation at the QTL. The Bayesian analysis includes the number of QTLs on a chromosome as an unknown.

Bayes Theorem↗

PubMed1995

The mutational demography of protein C deficiency.

The geographical distribution and prevalence of 256 single base-pair substitutions (105 of them being different) within the coding region of the human protein C (PROC) gene were correlated with their initial likelihoods of generation. A significant positive correlation was observed between these "mutational likelihoods" and the geographical dispersal of the PROC gene lesions within and between 16 different countries. This relationship could be attributed to the fact that, with few exceptions, high dispersal was only exhibited by CG-->TG and CG-->CA transitions, i.e. those substitutions that are known to arise de novo at the highest frequency. The statistical distribution of mutational likelihoods was as predicted on the basis of the PROC cDNA sequence alone, allowing however for the redundancy of the genetic code. These findings suggest (1) that genetic drift and lesion-specific selection have been of relatively minor importance in determining the mutational spectrum observed in the PROC gene and (2) that most multiple reports of particular substitutions in different geographical locations appear to reflect recurrent mutation rather than identity-by-descent.

Blood Coagulation Disorders↗

PubMed2001

Polyhedral boranes and elemental boron: direct structural relations and diverse electronic requirements.

Details of the electronic and structural connections between macropolyhedral boranes and elemental boron are reported. The nature of electron deficiency in the beta-rhombohedral polymorph of boron is analyzed by using a molecular fragments approach with boranes as model systems. The B57H36 molecule constructed from such an approach has three more electrons than mandated by the electron-counting rules (Balakrishnarajan, M. M.; Jemmis, E. D. J. Am. Chem. Soc. 2000, 122, 456. Jemmis, E. D.; Balakrishnarajan, M. M.; Pancharatna, P. D. J. Am Chem. Soc. 2001, 123, 4313-4323.) devised for macropolyhedral boranes. This is also confirmed by electronic structure calculations at the extended Hückel and B3LYP/6-31G levels. The aromaticity of this B57H36(3+) molecule is on par with the most stable B12H12(2-) itself, as revealed by nuclear independent chemical shift calculations. The B57 skeleton can be made electron precise by adopting a nido arrangement by eliminating an atom from the closo skeleton, so that three valence electrons will be removed. The exact site of elimination, governed by thermodynamic factors, necessitates the removal of a boron atom from any of the six symmetrically equivalent B[13] sites in the unit cell. This leads to partial occupancies, which causes disorder in packing, as revealed by X-ray structure studies. The rest of the boron atoms are distributed in icosahedral B12 fragments, whose two-electron deficiency is satisfied by the capping of extra atoms, distributed statistically in the interstitial sites. These results show that the three-dimensional network of the idealized beta-rhombohedral unit cell is not stable, unlike the electron-precise carbon polymorphs such as diamond and graphite. Thus, disorder in the form of partial occupancies, interstitial atoms, alien atoms, etc., is necessary for electron sufficiency and hence for the stability of this polymorphic form. Through these ingenious steps, all components of the unit cell attain electron sufficiency, which explains the high thermodynamic stability of the polymorph. The connection established between boranes and elemental boron in terms of their structure and distribution of electrons has important implications in understanding the structure of boron-rich solids and new strategies to utilize their diverse and technologically important properties.

Journal Article↗

PubMed2000

Learning overcomplete representations.

In an overcomplete basis, the number of basis vectors is greater than the dimensionality of the input, and the representation of an input is not a unique combination of basis vectors. Overcomplete representations have been advocated because they have greater robustness in the presence of noise, can be sparser, and can have greater flexibility in matching structure in the data. Overcomplete codes have also been proposed as a model of some of the response properties of neurons in primary visual cortex. Previous work has focused on finding the best representation of a signal using a fixed overcomplete basis (or dictionary). We present an algorithm for learning an overcomplete basis by viewing it as probabilistic model of the observed data. We show that overcomplete bases can yield a better approximation of the underlying statistical distribution of the data and can thus lead to greater coding efficiency. This can be viewed as a generalization of the technique of independent component analysis and provides a method for Bayesian reconstruction of signals in the presence of noise and for blind source separation when there are more sources than mixtures.

Algorithms↗

PubMed2002

Quantitative study of breast cancer progression: different pathways for various in situ cancers.

The chromatin pattern in nuclei from breast ductal proliferative lesions was quantitatively evaluated with the objective of deriving measures of tumor progression. A total of 110 cases were analyzed. There were 38 cases of normal tissue or benign proliferative lesions, 41 cases of ductal carcinoma in situ (DCIS), and 31 cases of microinfiltrating DCIS and of infiltrating cancer. A total of 9424 nuclei were analyzed. High-resolution images were digitally recorded. For each nucleus, 93 karyometric features descriptive of the spatial and statistical distribution of the nuclear chromatin were computed. Data analysis included establishing a profile of relative deviations of each feature from "normal," called the nuclear signature, and of lesion signatures as well as of trends of lesion progression. Two trends of evolution could be discerned: one from normal to hyperplasia, atypical hyperplasia, and comedo DCIS as representative of high-grade lesions; and the other from normal to hyperplasia to cribriform DCIS, solid DCIS, and infiltrating cancer, representing lower grade lesions. The nuclei in microinfiltrating foci are distinctly different from nuclei in high-grade comedo DCIS. The nuclei in microinfiltrating foci have a statistically significantly lower nuclear abnormality. They may represent outgrowing clones.

Breast↗

PubMed1996

Using neural networks to model conditional multivariate densities.

Neural network outputs are interpreted as parameters of statistical distributions. This allows us to fit conditional distributions in which the parameters depend on the inputs to the network. We exploit this in modeling multivariate data, including the univariate case, in which there may be input-dependent (e.g., time-dependent) correlations between output components. This provides a novel way of modeling conditional correlation that extends existing techniques for determining input-dependent (local) error bars.

Economics↗