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PubMed2003

Reverse Monte Carlo analysis of extended energy-loss fine structure for disordered structures of tetrahedrally coordinated materials: its applicability.

Capabilities of the reverse Monte Carlo method for characterizing the short-range structural correlations of solids were examined in the analysis of extended energy-loss fine structure (EXELFS). Since this method gives a three-dimensional atomic configuration consistent with the experimental EXELFS spectra, one can extract the statistical distributions of bond lengths, coordination numbers and bond angles of atom species of interest, which have been hard to achieve by conventional EXELFS analysis. The method was applied for the determination of amorphous Si structures and the damaged structure of an electron-irradiated SiC crystal. Advantages and disadvantages of the present method over the precise diffraction intensity measurement are discussed.

Carbon↗

PubMed1993

Bioelectric and anthropometric assessments and reference data in the elderly.

Most studies using bioelectric impedance have estimated the volume of total body water, fat-free mass and on occasion extracellular fluid volume using whole-body resistance and reactance. However, the validity of bioelectric impedance has not been established for the elderly except in small samples of limited age ranges. The estimation of whole-body composition from impedance of body segments may be an alternative method that can be applied to many chair- and bedfast elderly patients. Also, measures of bioelectric impedance at lower and higher frequencies than 50 kHz are reported to differentiate the proportions of intra- and extracellular fluid volumes, and this could also provide important information about fluid quantities and balances in the elderly. Distribution statistics for body measurements for persons 65-85 y of age are available from the national health surveys and large clinical studies but reference data for persons > or = 80 y are sparse. Some reference data may be from groups that are not representative of the elderly because the samples were from cohorts older than elderly persons living today and significant group and racial differences existed among these as children and adults. These differences may have increased interindividual variances among the elderly. Suitable reference data for the present generations of elderly in the United States will be available with the culmination of NHANES III after 1994, but limited reference data for elderly persons up to 90 y of age have been published.(ABSTRACT TRUNCATED AT 250 WORDS)

Aged↗

PubMed2005

Growth, fructan yield, and quality of chicory (Cichorium intybus L.) as related to photosynthetic capacity, harvest time, and water regime.

Fructans are polymers that are widely used in several industrial applications. In the last few years they have received increasing interest because of their positive effects on health. At present, fructans are mostly supplied by chicory, which is only grown and processed in The Netherlands, France, and Belgium. It would therefore be an attractive concept to expand its cultivation to the southern European countries, although water shortage and high temperatures may hinder its growth and yield. So far, few experiments have been carried out on the effects of water, so the present research was focused on the course of growth and fructan quality in rainfed (W(0)) and well-watered (W(1)) conditions. The positive effects of water restoration mostly concerned the above-ground dry weight (ADW), whereas the root dry weight (RDW) was less influenced. No significant differences on RDW were found in 1999, whereas it was 14% higher (P <0.01) in W(1) in 2000. The effect of water was very clear on assimilate allocation: the overall priority at the whole plant scale seemed to be root structures, then storage reserves, and finally ADW. Therefore, the fructan content was higher in W(0), and insignificant differences between W(0) and W(1) were found on fructan yield at the final harvests. The only significant effect of the water regime on fructans was to speed up their storage. The leaf photosynthetic capacity (A) was poorly affected by water availability, whereas it appeared consistently modulated by leaf temperature and leaf nitrogen content. Stomatal conductance appeared to be mostly affected by the soil water content and it was mostly related to A up to about 300 mmol m(-2) s(-1). The fructan chain length (DP) was not affected by water regime. Besides, DP classes showed a normal statistical distribution; skewness and kurtosis significantly changed only when the harvest was very late. Equally, a very late harvest time significantly lowered DP.

Cichorium intybus↗

PubMed2005

Bayes empirical bayes inference of amino acid sites under positive selection.

Codon-based substitution models have been widely used to identify amino acid sites under positive selection in comparative analysis of protein-coding DNA sequences. The nonsynonymous-synonymous substitution rate ratio (d(N)/d(S), denoted omega) is used as a measure of selective pressure at the protein level, with omega > 1 indicating positive selection. Statistical distributions are used to model the variation in omega among sites, allowing a subset of sites to have omega > 1 while the rest of the sequence may be under purifying selection with omega < 1. An empirical Bayes (EB) approach is then used to calculate posterior probabilities that a site comes from the site class with omega > 1. Current implementations, however, use the naive EB (NEB) approach and fail to account for sampling errors in maximum likelihood estimates of model parameters, such as the proportions and omega ratios for the site classes. In small data sets lacking information, this approach may lead to unreliable posterior probability calculations. In this paper, we develop a Bayes empirical Bayes (BEB) approach to the problem, which assigns a prior to the model parameters and integrates over their uncertainties. We compare the new and old methods on real and simulated data sets. The results suggest that in small data sets the new BEB method does not generate false positives as did the old NEB approach, while in large data sets it retains the good power of the NEB approach for inferring positively selected sites.

Alleles↗

PubMed2005

Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds.

We implement a Bayesian Markov chain Monte Carlo algorithm for estimating species divergence times that uses heterogeneous data from multiple gene loci and accommodates multiple fossil calibration nodes. A birth-death process with species sampling is used to specify a prior for divergence times, which allows easy assessment of the effects of that prior on posterior time estimates. We propose a new approach for specifying calibration points on the phylogeny, which allows the use of arbitrary and flexible statistical distributions to describe uncertainties in fossil dates. In particular, we use soft bounds, so that the probability that the true divergence time is outside the bounds is small but nonzero. A strict molecular clock is assumed in the current implementation, although this assumption may be relaxed. We apply our new algorithm to two data sets concerning divergences of several primate species, to examine the effects of the substitution model and of the prior for divergence times on Bayesian time estimation. We also conduct computer simulation to examine the differences between soft and hard bounds. We demonstrate that divergence time estimation is intrinsically hampered by uncertainties in fossil calibrations, and the error in Bayesian time estimates will not go to zero with increased amounts of sequence data. Our analyses of both real and simulated data demonstrate potentially large differences between divergence time estimates obtained using soft versus hard bounds and a general superiority of soft bounds. Our main findings are as follows. (1) When the fossils are consistent with each other and with the molecular data, and the posterior time estimates are well within the prior bounds, soft and hard bounds produce similar results. (2) When the fossils are in conflict with each other or with the molecules, soft and hard bounds behave very differently; soft bounds allow sequence data to correct poor calibrations, while poor hard bounds are impossible to overcome by any amount of data. (3) Soft bounds eliminate the need for "safe" but unrealistically high upper bounds, which may bias posterior time estimates. (4) Soft bounds allow more reliable assessment of estimation errors, while hard bounds generate misleadingly high precisions when fossils and molecules are in conflict.

Animals↗

PubMed1992

Computer methods for locating kinetoplastid cryptogenes.

RNA editing in the mitochondria of kinetoplastid protoza involves the insertion and/or deletion of precise numbers of uridine residues at precise locations in the numbers of uridine residues at precise locations in the transcribed RNA of certain genes. These genes are known as cryptogenes. In this paper we study computational algorithms to search for unknown cryptogenes and for the associated templates for insertion of uridines, gRNA sequences. The pairwise similarity search algorithm of Smith and Waterman (1) is modified to study this problem. The algorithm searches for unknown gRNAs given the cryptogene sequence. The method is tested on 4 known cryptogenes from L.tarentolae which are known to have 7 associated gRNAs. The statistical distribution of the longest gRNA when comparing random sequences is derived. Finally we develop an algorithm to search for cryptogenes using amino acid sequences from related proteins.

Algorithms↗

PubMed2002

Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes.

The nonsynonymous to synonymous substitution rate ratio (omega = d(N)/d(S)) provides a sensitive measure of selective pressure at the protein level, with omega values <1, =1, and >1 indicating purifying selection, neutral evolution, and diversifying selection, respectively. Maximum likelihood models of codon substitution developed recently account for variable selective pressures among amino acid sites by employing a statistical distribution for the omega ratio among sites. Those models, called random-sites models, are suitable when we do not know a priori which sites are under what kind of selective pressure. Sometimes prior information (such as the tertiary structure of the protein) might be available to partition sites in the protein into different classes, which are expected to be under different selective pressures. It is then sensible to use such information in the model. In this paper, we implement maximum likelihood models for prepartitioned data sets, which account for the heterogeneity among site partitions by using different omega parameters for the partitions. The models, referred to as fixed-sites models, are also useful for combined analysis of multiple genes from the same set of species. We apply the models to data sets of the major histocompatibility complex (MHC) class I alleles from human populations and of the abalone sperm lysin genes. Structural information is used to partition sites in MHC into two classes: those in the antigen recognition site (ARS) and those outside. Positive selection is detected in the ARS by the fixed-sites models. Similarly, sites in lysin are classified into the buried and solvent-exposed classes according to the tertiary structure, and positive selection was detected at the solvent-exposed sites. The random-sites models identified a number of sites under positive selection in each data set, confirming and elaborating the results of the fixed-sites models. The analysis demonstrates the utility of the fixed-sites models, as well as the power of previous random-sites models, which do not use the prior information to partition sites.

Alleles↗

PubMed1999

Detecting and characterizing gene conversions between multigene family members.

We used a variety of methods to detect known gene conversions in the actin gene families of five angiosperm species, the beta-globin gene families of two primate species, and the Zfx/Zfy gene families of seven mammalian species. Our goal was to devise a working strategy which would allow the analysis of the members of a multigene family in order to determine whether there had been gene conversions between its members, identify the genes involved in the gene conversions, establish the lengths of the converted regions, and determine the polarities of the gene conversions. We show that three phylogenetic methods and the homoplasy test of Maynard Smith and Smith perform relatively poorly on our data sets because the sequences we analyzed had large levels of multiple substitutions. The method of Sawyer, the compatibility method of Jakobsen and Easteal, the partition matrix method of Jakobsen, Wilson, and Easteal, and the co-double method of Balding, Nichols, and Hunt can be used to identify the genes which have been involved in gene conversions. The co-double method is more powerful than other methods but requires orthologous sequences from related species. Compatibility, phylogenetic, and nucleotide substitution distribution statistics methods can be used to identify the location of the converted region(s). Site-by-site compatibility analyses can also be used to identify the direction of the conversion event(s). Combinations of these methods can therefore be used to establish the presence, locations, and polarities of gene conversions between multigene family members.

Actins↗

PubMed1999

Folding funnels and binding mechanisms.

The long-held views on lock-and-key versus induced fit in binding arose from the notion that a protein exists in a single, most stable conformation, dictated by its sequence. However, in solution proteins exist in a range of conformations, which may be described by statistical mechanical laws and their populations follow statistical distributions. Upon binding, the equilibrium will shift in favor of the bound conformation from the ensemble of conformations around the bottom of the folding funnel. Hence here we extend the implications and the usefulness of the folding funnel concept to explain fundamental binding mechanisms.

Peptides↗

PubMed1990

Tests for the statistical significance of protein sequence similarities in data-bank searches.

A suite of tests to evaluate the statistical significance of protein sequence similarities is developed for use in data bank searches. The tests are based on the Wilbur-Lipman word-search algorithm, and take into account the sequence lengths and compositions, and optionally the weighting of amino acid matches. The method is extended to allow for the existence of a sequence insertion/deletion within the region of similarity. The accuracy of statistical distributions underlying the tests is validated using randomly generated sequences and real sequences selected at random from the data banks. A computer program to perform the tests is briefly described.

Algorithms↗

PubMed2000

Prevalence and characteristics of pressure ulcers. A one-day patient population in a Finnish city.

This article discusses the prevalence and characteristics of pressure ulcers in a one-day patient population in a Finnish city. The data was collected using two questionnaires. Data analysis was based on percentage distributions; statistical significances were tested with the Chi-square test. The measurement identified 186 patients with a total of 300 pressure ulcers. The majority (90%) of these patients were hospitalized and 10% were in outpatient care. The main causes for the development of pressure ulcers were inadequate turning and positioning and the patient's primary illness. Most of the ulcers were grade II. Only a few patients had ulcers that exposed bone. The preventive effort should extend from the nursing unit level, through the organizational level, to the level of society as a whole. It should consist of the identification of people at high risk for pressure ulcers and the provisions of quality care for these people.

Adolescent↗

PubMed2002

Neuroelectric mechanisms applied to low frequency electric and magnetic field exposure guidelines--part I: sinusoidal waveforms.

Electric and magnetic field exposure guidelines are developed from established mechanisms of bioelectric interaction. Such mechanisms involve phenomena of electrostimulation-the functional influence of applied electrical forces on nerve and muscle, and, at quasi-static frequencies, on magneto-dynamic mechanisms. The paper develops criteria of human reactions based on theoretical models with parametric values derived from experimental observations. These basic restrictions on electrostimulation effects are referenced to the induced in situ electric fields. Basic limitations are differentiated for induction in the heart, peripheral nerves, the extremities, and the central nervous system. The paper recommends maximum permissible exposure limits which account for (a) adverse reaction criteria, (b) statistical distribution of reaction thresholds, and (c) acceptability factors. From the basic limitations the paper further develops reference levels which apply to environmental electric or magnetic fields.

Biophysical Phenomena↗

PubMedDate not supplied

Estimating emergency service treatment bed needs.

Estimating the required number of emergency service treatment beds must be sensitive to utilization patterns and strategic operational assumptions. This article describes key issues and illustrates techniques for the analysis of arrival and service times. Seasonal arrival patterns, time of day of arrivals, and common statistical distributions for length of stay are discussed. Alternative modeling approaches to estimate future bed needs are described, including visits/year per treatment space, simple queuing modeling, and detailed computer simulation. Sample estimates of treatment rooms needs are provided for typical arrival rates and lengths of stay. A generalized regression model based on the simulation trials is suggested for cases that fall outside of the illustrated simulation case studies.

Beds↗

PubMedDate not supplied

Survey of automated noninvasive blood pressure monitors.

Automated noninvasive blood pressure (NIBP) monitors, or automated sphygmomanometers, have been increasingly used both inside and outside clinical environments. An extensive survey of such monitors was carried out over the past five years. This survey covers a broad spectrum of monitors including ambulatory monitors, bedside and transport monitors, stress-test monitors, and monitors that are intended for self-measurement. It includes more than 400 models from suppliers in the United States and many other countries. A review of NIBP measurement methods that have been used in automated NIBP monitors is presented in this paper, along with statistical distributions of their use in the surveyed monitors and a list of the suppliers and monitors.

Blood Pressure Determination↗

PubMedDate not supplied

Identification of task-specific rCBF changes in individual subjects: validation and application for PET.

OBJECTIVE: A method for identification and quantitative evaluation of task-specific changes of the regional cerebral blood flow (rCBF) measured with PET in activation studies of individual subjects is presented. The method is based on the statistical distributions of the quantitative and spatial information of regions of interest in rCBF subtraction images. METHODS: For validation, a cylindrical phantom of 20 cm diameter containing six spheres of 10-30 mm in diameter was used. The spheres representing the specific signals were filled with 18F, while one-tenth of this activity concentration was filled into the background compartment of the phantom representing "noise." Of a sequence of dynamically recorded frames, subtraction images with different signal-to-noise ratios were calculated. RESULTS: In these subtraction images, our method allowed us to identify the larger spheres accurately and to quantify the signals. Comparison with t map analysis in averaged subtraction images revealed a high correspondence with the results obtained by our method in individual subtraction images. Based on this phantom validation, the method was applied for mapping of rCBF changes in humans. The rCBF was measured with [15O]butanol in four subjects during unilateral somatosensory discrimination and during rest. CONCLUSION: The method proved to be capable of identifying task-specific rCBF changes in the contralateral motor, premotor, and sensory cortex accurately and with high quantitative and anatomical precision in each subject.

Adult↗

PubMed2002

Intima-media thickness: a new tool for diagnosis and treatment of cardiovascular risk.

Increased intima-media thickness (IMT) is a non-invasive marker of early arterial wall alteration, which is easily assessed in the carotid artery by B-mode ultrasound, and more and more widely used in clinical research. Methods of IMT measurement can be categorized by two approaches: (i) measurement at multiple extracranial carotid sites in near and far walls and (ii) computerized measurement restricted to the far wall of the distal common carotid artery. Because IMT reflects global cardiovascular risk, its normal value might be better defined in terms of increased risk rather than in terms of statistical distribution within a healthy population. The available epidemiological data indicate that increased IMT (at or above 1 mm) represents a risk of myocardial infarction and/or cerebrovascular disease. Close relationships have been shown between: (i) most traditional cardiovascular risk factors; (ii) certain emerging risk factors such as lipoproteins, psychosocial status, plasma viscosity, or hyperhomocysteinemia; and (iii) various cardiovascular or organ damages such as white matter lesion of the brain, left ventricular hypertrophy, microalbuminuria or decreased ankle to brachial systolic pressure index. Thus, IMT gives a comprehensive picture of the alterations caused by multiple risk factors over time on arterial walls. Prospective primary and secondary prevention studies have also shown that increased IMT is a powerful predictor of coronary and cerebrovascular complications (risk ratio from 2 to 6) with a higher predictive value when IMT is measured at multiple extracranial carotid sites than solely in the distal common carotid artery. Therapeutic double-blind trials have shown that lipid-lowering drugs, such as resin and overall statines, and to a lesser extent antihypertensive drugs, such as calcium antagonists, may have a beneficial effect on IMT progression in asymptomatic or in coronary patients. However, methodological standardization of IMT measurement still needs to be implemented before routine measurement of IMT can be proposed in clinical practice as a diagnostic tool for stratifying cardiovascular risk in primary prevention and for aggressive treatment decision. It can be anticipated however, that the presence of increased carotid IMT in one individual with intermediate cardiovascular risk would lead to his classification into the high-risk category and thus influence the aggressiveness of risk factor modifications.

Cardiovascular Diseases↗

PubMed1995

Parallel blood concentrations of second-generation cyclosporine metabolites and bilirubin in liver graft recipients.

Cyclosporine, a cyclic undecapeptide, is currently the major immunosuppressant used after liver transplantation. Since it is unclear whether or not cyclosporine metabolites play a part in toxicity, high concentrations of metabolites should be avoided. The quantification of cyclosporine metabolites requires immunoassays using nonspecific antibodies cross-reacting with metabolites or high-performance liquid chromatography (HPLC) analysis. Since no guidelines are available to date concerning when such additional analysis is required, it was the aim of this study to define biochemical parameters that parallel cyclosporine elimination and indicate whether or not cyclosporine elimination is impaired, requiring quantification of cyclosporine metabolites. One hundred and thirty adult liver graft recipients were included in a prospective study during their first hospital stay. Cyclosporine and 11 metabolites were quantified in blood every second day using radioimmunoassay and HPLC. When the cyclosporine metabolite patterns in trough blood samples of patients with impaired liver function were compared with those of patients with good liver function, concentrations of metabolites AM19 and AM1A were found to be elevated. Serum concentrations of conjugated and total bilirubin were significantly correlated with blood trough concentrations of AM19 and AM1A, while there was no correlation with cyclosporine or its first-generation metabolites. Distribution statistics showed that liver graft patients with impaired cyclosporine elimination had total bilirubin concentrations in serum > 60 mumol/l L. No correlation was found between bile acids and the concentrations of metabolites AM19 and AM1A, suggesting that the ion-coupled transport system is not quantitatively involved in cyclosporine excretion and that bilirubin and cyclosporine metabolites are eliminated by the same transport system through the biliary membrane. It is concluded that bilirubin and cyclosporine metabolite concentrations are strictly parallel and that the total bilirubin concentration in serum may be used as an indicator of impaired cyclosporine elimination.

Administration, Oral↗

PubMed2005

PELD score and posttransplant outcome in pediatric liver transplantation: a retrospective study of 100 recipients.

BACKGROUND: Pediatric End-stage Liver Disease (PELD) score is proposed as an objective tool to prioritize children awaiting liver transplantation (LT), higher PELD being associated with increased pre-LT mortality. This study investigated whether PELD may also impact on post-LT results. METHODS: PELD was retrospectively analyzed in 100 pediatric recipients of a primary LT from living-related (n = 49) or postmortem donors (PMD, n = 51). The main pre-LT diagnosis was biliary atresia (n = 64), hepatic malignancy and fulminant hepatitis cases being excluded. PELD was calculated in all patients at the time of pre-LT assessment. Considering the median delay of 117 days between listing and LT in the PMD subgroup, a second PELD was calculated at the time of LT, allowing the determination of a delta PELD during the waiting period. PMD grafts were allocated using an allocation system taking into account waiting times as well as medical urgency, operative at EuroTransplant. RESULTS: Overall 5-year actuarial patient and graft survivals were 96% and 91%, respectively. PELD at listing (13.3 +/- 9.7) showed a normal statistical distribution. PELD scores at listing and at LT were not found to significantly impact on post-LT outcome (NS). In contrast, higher delta PELD might be associated with lower posttransplant patient survival (p = 0.094). CONCLUSIONS: The results of this retrospective analysis suggest that giving priority to high PELD recipients may not result in worsening post-LT outcome. Accordingly, these data support such "sickest children first" allocation policy, which should contribute to reduce pre-LT mortality without worsening post-LT results and increasing organ waste.

Child↗