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PubMed1980

The random character of protein evolution and its effects on the reliability of phylogenetic information deduced from amino acid sequences and compositions.

Because evolution occurs by random events, the actual number of substitutions that occur in any period is not exactly equal to the number expected from the mean rate of substitution, but is statistically distributed about it. In consequence, even if rates of evolution are constant in different lineages, 'trees' deduced from descendant protein sequences contain random errors. When there are fewer than about eight differences between the sequences of the most distantly related pair from a set of proteins, this random effect is very large. It can then render trivial the statistical disadvantage inherent in using a crude measure of protein difference, such as amino acid composition or immunological cross-reactivity, in preference to a measure based the sequences of the most distantly related pair from a set of proteins, this random effect is very large. It can then render trivial the statistical disadvantage inherent in using a crude measure of protein difference, such as amino acid composition or immunological cross-reactivity, in preference to a measure based the sequences of the most distantly related pair from a set of proteins, this random effect is very large. It can then render trivial the statistical disadvantage inherent in using a crude measure of protein difference, such as amino acid composition or immunological cross-reactivity, in preference to a measure based on amino acid sequence. In some cases, such as classification of mammals on the basis of cytochrome c structure, it appears to make little difference to the reliability of the results whether the sequences of the protein concerned are known or not. It may also be possible to obtain more reliable phylogenetic information from composition measurements on several kinds of protein than one could obtain from sequence measurements on a single kind of protein.

Amino Acid Sequence↗

PubMed1990

The distribution of physical, chemical and conformational properties in signal and nascent peptides.

Signal peptides play a major role in an as-yet-undefined way in the translocation of proteins across membranes. The sequential arrangement of the chemical, physical and conformational properties of the signal and nascent amino acid sequences of the translocated proteins has been compiled and analysed in the present study. The sequence data of 126 signal peptides of length between 18 and 21 residues form the basis of this study. The statistical distribution of the following properties was studied hydrophobicity, Mr, bulkiness, chromatographic index and preference for adopting alpha-helical, beta-sheet and turn structures. The contribution of each property to the sequence arrangement was derived. A hydrophobic core sequence was found in all signal peptides investigated. The structural arrangement of the cleavage site was also clearly revealed by this study. Most of the physical properties of the individual sequences correlated (correlation coefficient approximately 0.4) very well with the average distribution. The preferred occupancy of amino acid residues in the signal and nascent sequences was also calculated and correlated with their property distribution. The periodic behaviour of the signal and nascent chains was revealed by calculating their hydrophobic moments for various repetitive conformations. A graphical analysis of average hydrophobic moments versus average hydrophobicity of peptides revealed the transmembrane characteristics of signal peptides and globular characteristics of the nascent peptides.

Amino Acid Sequence↗

PubMed1980

[Effects of molecular parameters of galacturonan substrate on the activity of a polygalacturonase from tomatoes].

The activity of a major form of the tomato polygalacturonase (EC 3.2.1.15) depends of the origin of the galacturonan substrates (apple, citrus) as well as upon the molecular mass, the degree of esterification and the distribution of the ester methoxyl groups. Optimal substrates are citrus pectic acids with a degree of esterification < 1% and a molecular mass corresponding to a viscosity number [eta] = 90 ml/g galacturonan. In the [eta] range from 16 to 474 ml/g, the Km values decrease to constant amount of 15.6 mM galacturonic acid units, which corresponds to 0.27% galacturonan. In a statistical distribution of the ester methoxyl groups, the activity reaches zero in the range of the degree of esterification from 80 to 90%. Enzymatically de-esterified pectins with a degree of esterification < 32% and a block-like distribution of the ester methoxyl groups behave as comparable pectic acids. In summary, there is a good agreement between these enzymesubstrate interactions and those of endopolygalacturonases from Aspergillus spec. Differentiations manifested themselves only in the transition range between macromolecular galacturonan substrates and oligomeric substrates below the established critical molecular mass.

Glycoside Hydrolases↗

PubMed1998

Predicting the distribution of synaptic strengths and cell firing correlations in a self-organizing, sequence prediction model.

This article investigates the synaptic weight distribution of a self-supervised, sparse, and randomly connected recurrent network inspired by hippocampal region CA3. This network solves nontrivial sequence prediction problems by creating, on a neuron-by-neuron basis, special patterns of cell firing called local context units. These specialized patterns of cell firing--possibly an analog of hippocampal place cells--allow accurate prediction of the statistical distribution of synaptic weights, and this distribution is not at all gaussian. Aside from the majority of synapses that are, at least functionally, lost due to synaptic depression, the distribution is approximately uniform. Unexpectedly, this result is relatively independent of the input environment, and the uniform distribution of synaptic weights can be approximately parameterized based solely on the average activity level. Next, the results are generalized to other cell firing types (frequency codes and stochastic firing) and place cell-like firing distributions. Finally, we note that our predictions concerning the synaptic strength distribution can be extended to the distribution of correlated cell firings. Recent published neurophysiological results are consistent with this extension.

Electrophysiology↗

PubMed1972

Statistical analysis of the bioassay of continuous carcinogens.

In an experiment consisting of the continuous constant application of various carcinogenic regimens to a pure strain of experimental animals for a long period, the cancer incidence rates so caused may be studied and compared by the fit of an appropriate class of statistical distributions. In this paper we show that a Weibull distribution in which the age-specific cancer incidence rate rises as a power of time since first risk is more appropriate than a lognormal distribution. If the Weibull family of distributions is used, more information can be extracted from the data, and differences of toxicity between various regimens will not bias the comparison of their carcinogenic forces.

Animals↗

PubMed1986

[Statistical patterns of the anomalous staining of 5-bromodeoxyuridine-substituted chromosomes].

Five large chromosome segments showing sometimes an abnormal staining were found in the genome of Chinese hamster (clone 237). Three types of abnormal staining were recorded. After one round of replication in the presence of BrdUrd these segments showed a hetero-staining, whereas after two rounds of replication the same segments showed iso-dark or iso-light staining. Pulse labeling with 3H-thymidine showed that all these segments were the late-replicating ones. The labeling proceeded according to all-or-none principle; in a given cell all five segments showed either presence or absence of the label. On the contrary, the abnormal staining was statistically distributed among these segments. These results are in disagreement with the current view that the abnormal staining is associated with asymmetrical distribution of thymine among two strands of DNA duplex. The above regularities are considered as an argument for the two-stranded model of chromosome.

Animals↗

PubMed1997

NMR analysis of main-chain conformational preferences in an unfolded fibronectin-binding protein.

A 130-residue fragment of the Staphylococcus aureus fibronectin-binding protein has been found to exist in a highly unfolded conformation at neutral pH. Measurement of experimental NMR 3JHNalpha coupling constants provides evidence for individual residues having distinct main-chain conformational preferences that are dependent both on the amino acid concerned and on neighbouring residues in the sequence. Analysis shows that these variations in the populations of individual residues can be explained in detail in terms of statistical distributions of conformational states derived from the protein data base. In particular, when the preceding residue has a beta-branched or aromatic side-chain, a significant increase occurs in the population of the less sterically restricted b region of phi,psi space. The results indicate that the local structure of the fibronectin binding protein in solution, under conditions where it displays full activity, approximates very closely to a statistical random coil structure. This may be an important feature in the biological role of this and other polypeptides involved in protein-protein interactions.

Adhesins, Bacterial↗

PubMed1984

Estimation of cumulative exposures to ethylene oxide associated with hospital sterilizer operation.

The statistical distribution of exposures to ethylene oxide was estimated for a task involving transfer of materials from a hospital sterilizer. The exposure data are consistent with either a normal or log-normal distribution. It is shown how the single-task distribution and the number of task repetitions can be used to determine the minimum differences in task repetitions necessary to distinguish for epidemiological purposes between worker groups on the basis of cumulative exposure.

Environmental Exposure↗

PubMed1998

Evaluation of bioequivalence of highly variable drugs using clinical trial simulations. II: Comparison of single and multiple-dose trials using AUC and Cmax.

PURPOSE: Evaluating of the effects of high intrasubject variability in clearance (CL) and volume of distribution (V), on 90% confidence intervals (CIs) for AUC (Area Under the concentration Curve) in single and multiple-dose bioequivalence studies. The main methodology was Monte Carlo simulation, and we also used deterministic simulation, and examination of clinical trials. The results are compared with those previously observed for Cmax (maximum concentration.) METHODS: The time course of drug concentration in plasma was simulated using a one-compartment model with log-normal statistical distributions of intersubject and intrasubject variabilities in the pharmacokinetic parameters. Both immediate-release and prolonged-release products were simulated using several levels of intrasubject variability in single-dose and multiple-dose studies. Simulations of 2000 clinical bioequivalence trials per condition (138 conditions) with 30 subjects in each crossover trial were carried out. Simulated data were compared with data from actual bioequivalence trials. RESULTS: The current simulations for AUC show similar probabilities of failure for single-dose and multiple-dose bioequivalence studies, even with differences in the rate of absorption or fraction absorbed. AUC values from prolonged-release scenario studies are more sensitive to changes in the first order absorption rate constant ka, and to variability in CL and V than AUC from studies of immediate-release studies. CONCLUSIONS: We showed that multiple-dose designs for highly variable drugs do not always reduce intrasubject variability in either AUC or Cmax, although the behavior of AUC differs from Cmax. Single dose AUC to the last quantifiable concentration was more reliable than either single dose AUC extrapolated to infinity, or multiple dose AUC during a steady-state interval. Multiple-dose designs may not be the best solution for assessing bioequivalence of highly variable drugs.

Area Under Curve↗

PubMed1994

A statistical analysis of side-chain conformations in proteins: comparison with ECEPP predictions.

A comparison of the statistical distributions of side-chain conformations of 17 amino acids (Gly, Ala, and Pro excluded), observed in 63 nonhomologous globular proteins (covering 10,832 residues), is made with similar distributions calculated from the low-energy conformational states for the same amino acids (blocked with acetyl and N-methylamide groups at the N- and C-termini, respectively) obtained by Vásquez et al. [(1983), Macromolecules 16, 1043-1049] using the ECEPP/2 force field. Those residues (i) with linear side chains (Arg, Lys, Met, Cys, Ser), or those that are unbranched through the gamma-carbon atom (Glu, Gln) show good agreement, whereas (ii) those with side chains that are branched at C beta or C gamma show poor agreement with ECEPP calculations. A possible explanation for this is shown to be the greater tendency for side-chain atoms in class (ii) to interact with the backbone and/or adjacent side chains. Accordingly, ECEPP/3 calculations, carried out after elongating the backbone chain of the model peptide unit (by adding three Ala residues on each side of the central residue, and then blocking the termini as before), result in distributions that are often closer to the observed side-chain distributions. The implications of these results for the relative importance of short-range versus long-range interactions in determining protein structure are discussed.

Amino Acids↗

PubMed1987

The galactose-specific receptor system in rat liver during development.

The number and distribution of galactose-specific binding sites were investigated in rat liver cells during perinatal development. Ligand binding to hepatocytes, macrophages and endothelial cells was followed with in vitro and in situ experiments by electron microscopy, using lactosylated bovine serum albumin adsorbed onto 5 nm colloidal gold particles as ligand. Binding capacity, starting at a late stage of fetal development, is very low both on the hepatocyte and on the macrophage surface, which show single particles statistically distributed. By contrast, bound particles are absent from fetal endothelial cells, which also lack the typical coated regions. In vivo, experiments at 37 degrees C show that endocytosis occurs to some extent in prenatal life. These results indicate that the expression of galactose-specific receptors' activity on the different liver cell types follows different developmental patterns, which are independently modulated.

Animals↗

PubMed1989

Marked regional heterogeneity in blood flow within a single skeletal muscle at rest and during exercise hyperaemia in the rabbit.

In 1985 both Pendergast et al. and Piiper et al. described a major regional heterogeneity in blood flow within single skeletal muscles both at rest and during exercise. Based on the microsphere method they described large variations in blood flow between muscle samples as large as 1 g each. The aims of the present study were: (1) To test this notion of regional heterogeneity in microsphere deposition within single skeletal muscles both at rest and during exercise. (2) To compare the distribution of microspheres with other blood flow tracers. (3) To test whether or not any heterogeneity was due to vasomotion in small arteries or arterioles. Microspheres were infused into anaesthetized rabbits over either 10, 30 or 120 s, or 10 min. Exercise was mimicked by tetanic contractions obtained by electrical stimulation of the motor nerves. Three hindleg muscles were divided into samples of 0.25 g each. Regional heterogeneity was expressed as the coefficient of variation corrected for statistical distribution of microspheres (CVc). The CVc at rest was about 0.34. The CVc was unaffected by the various infusion periods and did not change during exercise. Simultaneous infusions of microspheres and 86Rb+ or antipyrine gave high correlations between the two blood flow tracers, with all r values exceeding 0.83 (n = 18). We conclude that the microsphere method provides reliable estimates for regional blood flow within single skeletal muscles. The distribution of blood flow was markedly heterogeneous both at rest and during exercise. The heterogeneity in blood flow was apparently not a result of vasomotion.

Animals↗

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↗

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↗