[The ascertainment of the need for institutional care for children with Strabismus and Amblyopia by the Monte Carlo method on the computer].
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Amblyopia↗
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Results for “Monte Carlo Method”
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[Determination of the need for strabological hospital beds using the Monte Carlo method].
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Adolescent↗
Linkage analysis of a complex pedigree with severe bipolar disorder, using a Markov chain Monte Carlo method.
Recently developed algorithms permit nonparametric linkage analysis of large, complex pedigrees with multiple inbreeding loops. We have used one such algorithm, implemented in the package SimWalk2, to reanalyze previously published genome-screen data from a Costa Rican kindred segregating for severe bipolar disorder. Our results are consistent with previous linkage findings on chromosome 18 and suggest a new locus on chromosome 5 that was not identified using traditional linkage analysis.
Algorithms↗
Calculation of the characteristic ratio of randomly coiled poly(L-proline).
Allowing for rotation about the Calpha-C' bond (i.e., variation of psi) and for some degree of freedom about the peptide bond (i.e., small variations of omega), the characteristic ratios, (R2)o/nl2, of the form I (cis) and form II (trans) poly(L-proline) chain have been calculated by a Monte Carlo method in which the conformational energies were used as weighting factors. The Monte Carlo method enabled short-range interactions (beyond those involved in a single residue) to be taken into account. The effect of the presence of a small amount of one form (say cis in a trans-rich chain) on (R2)o/nl2 was also investigated. The results for the trans-rich form are in good agreement with values observed experimentally in solvents in which the poly(L-proline) chain is predominantly in form II; the presence of a small amount of cis residues reduces the characteristic ratio of the trans-rich form of poly(L-proline) significantly.
Dipeptides↗
Estimating effective population size from samples of sequences: a bootstrap Monte Carlo integration method.
We would like to use maximum likelihood to estimate parameters such as the effective population size N(e) or, if we do not know mutation rates, the product 4N(e) mu of mutation rate per site and effective population size. To compute the likelihood for a sample of unrecombined nucleotide sequences taken from a random-mating population it is necessary to sum over all genealogies that could have led to the sequences, computing for each one the probability that it would have yielded the sequences, and weighting each one by its prior probability. The genealogies vary in tree topology and in branch lengths. Although the likelihood and the prior are straightforward to compute, the summation over all genealogies seems at first sight hopelessly difficult. This paper reports that it is possible to carry out a Monte Carlo integration to evaluate the likelihoods approximately. The method uses bootstrap sampling of sites to create data sets for each of which a maximum likelihood tree is estimated. The resulting trees are assumed to be sampled from a distribution whose height is proportional to the likelihood surface for the full data. That it will be so is dependent on a theorem which is not proven, but seems likely to be true if the sequences are not short. One can use the resulting estimated likelihood curve to make a maximum likelihood estimate of the parameter of interest, N(e) or of 4N(e) mu. The method requires at least 100 times the computational effort required for estimation of a phylogeny by maximum likelihood, but is practical on today's work stations. The method does not at present have any way of dealing with recombination.
Base Sequence↗
Calculation of likelihood ratio y/x in diagnosis of paternity using computer methods.
A new computational method using a Monte Carlo technique is described for the calculation of plausibility of paternity in blood group systems. In this study gene frequencies of a blood group system are simulated by the range of the seven digit random numbers. By using a Monte Carlo method, four random numbers are generated and converted into paternal and maternal genotypes. Then the genotype of the child is determined according to the law of inheritance, and finally genotypes of the father, mother and child are converted into phenotypes. Repeating this process more than one hundred thousand times, the phenotypic frequencies of child-mother-father combinations (trio) and the likelihood ratio of paternity in any blood group system are calculated for all phenotypic combinations of the trios. This method is much easier than methods reported previously, and is sufficiently accurate.
Blood Group Antigens↗
Three tests for randomness of attack of social groups during an epidemic.
It is suggested that investigation of the attack of social units can be more illuminating of an epidemic process than the usual study of secondary attack rates of individuals. Three tests for detecting non-random differences in the occurrence of a disease between two groups of social units are presented. In each method the number of units attacked (X) in one of two groups of units is considered, rather than the number of individuals attacked. The tests are: (a) to use the Monte Carlo method, computer simulation of the epidemic process, to obtain an empirical distribution to which the observed value of X is compared; (b) to obtain the exact distribution of X; (c) to standardize X and compare it to the standard normal distribution. The three approaches are compared using data obtained from an epidemic of variola minor in two schools and the differences between the results are trivial. However, for large samples the only feasible approach is the Monte Carlo method.
Brazil↗
Dose distributions and mean doses in cylindrical cavities of bone marrow on X-ray irradiation.
Dose distributions as well as mean doses to cylindrical cavities of bone marrow on X-ray irradiation have been calculated using (a) Monte Carlo method and (b) a simplified straight line approximation method. The results are compared with earlier published ones. Point doses differ appreciably from the earlier results by as much as 40 percent at some points, whereas mean doses agree to within 10 percent for all the three methods.
Bone Marrow↗
Computer simulation of the solvent structure around biological macromolecules.
The structure and energetics of the solvent, both ordered and disordered, in a small peptide crystal and in the triclinic lysozyme crystal have been simulated using the Monte Carlo method. The results are in good agreement with the experimental data and provide insight into the role of solvent structure around biological macromolecules in solution.
Chemical Phenomena↗
Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions.
A lattice model of proteins is introduced. "A protein molecule" is a chain of nown-intersecting units of a given length on the two-dimensional square lattice. The copolymeric character of protein molecules is incorporated into the model in the form of specificities of inter-unit interactions. This model proved most effective for studying the statistical mechanical characteristics of protein folding, unfolding and fluctuations. The specificities of inter-unit interactions are shown to be the primary factors responsible for the all-or-none type transition from native to denatured states of globular proteins. The model has been studied by the Monte Carlo method of Metropolis et al., which is now shown applied to approximately simulating a kinetic process. In the strong limit of the specificity of the inter-unit interaction the native conformation was reached in this method by starting from an extended conformation. The possible generalization and application of this method for finding the native conformation of proteins form their amino sequence are discussed.
Amino Acid Sequence↗
Statistical mechanics of supercoils and the torsional stiffness of the DNA double helix.
The distribution of closed unknotted polymer chains over the writhing number is calculated by the Monte-Carlo method. For circular duplex DNA the variance of the distribution equals approximately half the observed variance of equilibrium distribution over the linking number. The balance which arises from fluctuations in DNA twisting makes it possible to estimate the torsional stiffness of the double helix.
DNA, Superhelical↗
The dose in water surrounding point isotropic gamma-ray emitters.
A Monte Carlo method has been used to calculate the dose distribution around point gamma-ray emitters in water. Five gamma-ray emitting radionuclide, 60Co, 137Cs, 192Ir, 198Au and 226Ra, which are commonly used in radiotherapy interstitial implants have been considered. The results are in substantial agreement with those derived using a combination of experimental and theoretical data.
Gamma Rays↗
Baseline correction in a two-way randomized blocks design.
Randomized blocks designs are used in clinical psychopharmacology research to test the hypothesis that relative effectiveness of different drug treatments depends on the type of patient being treated. Monte Carlo methods were used to evaluate the adequacies of different approaches to statistical control over baseline differences in such a design with special concern for the treatments x blocks interaction effect. Given the usual assumptions, analysis of covariance (ANCOVA) was shown to provide adequate baseline correction with consequent unbiased tests for the treatments x blocks interaction, as well as the main effect for the randomized treatments. Tests relying on simple pre-post difference scores and percentage change scores evidenced seriously conservative or nonconservative bias in the test for treatments x blocks interaction effect, a bias that depended on the direction of the corresponding interaction effect observed in the baseline measurements alone. This is discussed as a serious matter because the interaction effect in a randomized blocks design is a common basis for the claim of specific indications of drug treatments for particular types of patients.
Humans↗
A method for detecting distant evolutionary relationships between protein or nucleic acid sequences in the presence of deletions or insertions.
A method for detecting homology between two protein or nucleic acid sequences which require insertions or deletions for optimum alignment has been devised for use with a computer. Sequences are assessed for possible relationship by Monte Carlo methods involving comparisons between the alignment of the real sequences and alignments of randomly scrambled sequences of the same composition as the real sequences, each alignment having the optimum number of gaps. As each gap is successively introduced into a comparison (real or random) a maximum score is determined from the similarity of the aligned residues. From the distribution of the maximum alignment scores of randomly scrambled sequences having the same number of gaps, the percentage of random comparisons having higher scores is determined, and the smallest of these percentage levels for each pair of sequences (real or random) indicates the optimum alignment. The fraction of the comparisons of random sequences having percentage levels at their optimum alignment below that of the real sequence comparison at its optimum estimates the probability that such an alignment might have arisen by chance. Related sequences are detected since their optimum alignment score, by virtue of a contribution from ancestral homology in addition to optimised random considerations, occupies a more extreme position in the appropriate frequency distribution of score than do the majority of optimum scores of randomly scrambled sequences in their appropriate distributions. Application of this 'optimum match' method of sequence comparison shows that the sensitivity of the 'maximum match' method of Needleman and Wunsch (1970) decreases quite dramatically with sequence comparisons which require only a few gaps for a reasonable alignment, or when sequences differ greatly in length. The 'maximum match' method as applied by Barker and Dayhoff (1972) has the additional disadvantage that deletions which have occurred in the longer of two homologous protein sequences further decrease the sensitivity of detection of relationship. The 'constrained match' method of Sankoff and Cedergren (1973) is seen to be misleading since large increments in the alignment score from added gaps do not necessarily result in a high total alignment score required to demonstrate sequence homology.
Amino Acid Sequence↗
Calculated dose factors for the radiosensitive tissues in bone irradiated by surface-deposited radionuclides.
The method of calculating dose factors for the haemopoitic marrow and endosteal tissues in human trabecular bone, used by Whitwell and Spiers for volume-seeking radionuclides, has been developed for the case of radionuclides which are deposited as very thin layers on bone surfaces. The Monte Carlo method is again used, but modifications to the computer program are made to allow for a surface rather than a volume source of particle emission. The principal change is the introduction of a surface-orientation factor which is shown to have a value of approximately 2, varying slightly with bone structure. Result are given for beta-emitting radionuclides ranging from 171Tm (E (E beta=0.025 MeV) to 90Y(E beta = 0.93MeV), and also for the alpha-emitter 239Pu. It is shown that where the particle ranges are short compared with the dimensions of the bone structures the dose factors for the surface seekers are much greater than those for the volume seekers. For long range particles the dose factors for surface and volume-seeking radionuclides converge. Comparisons are given relating the dose factors calculated in this paper on the basis of measured bone structures to those of other workers based on single plane geometry.
Animals↗
[Separation of the effects of transmutation and radiation after incorporation of radionuclides into DNA (author's transl)].
Among the various methods for studying the relative effects of transmutation and radiation of incorporated nuclides, simulation of beta radiation by external gamma exposure is of practical importance. Self-irradiation and mutual irradiation of the labeled cells cannot be neglected in any case. Furthermore, additional hypothetical and experimental problems may arise from using either external beta radiation or different isotopes of an element. By means of external gamma irradiation on the other hand, this being equivalent to the internal beta radiation from a microdosimetrical point of view, the radiation effect of the nuclide alone can be observed without any modification of other experimental parameters. To determine such equivalent gamma radiation for labeled cell nuclei of Vicia faba roots, the authors applied the Monte Carlo Method to the beta spectra of 32-P, 3-H, 14-C and 131-J, to the energy-dependent LET and to different cell diameters. The existence of secondary particle equilibrium inside the nuclei during gamma exposure was assumed. For certain radionuclides and cell sizes it is possible to calculate gamma spectra which induce energy spectra in the nuclei similar to those caused by the beta particles originating in the nuclear DNA.
Carbon Radioisotopes↗
Binding of brevetoxins and ciguatoxin to the voltage-sensitive sodium channel and conformational analysis of brevetoxin B.
The marine toxins known generically as brevetoxins, as well as their structural relative ciguatoxin, are known as polyether ladder toxins, and bind uniquely to site 5 of the voltage-sensitive sodium channel. Rat brain synaptosome binding data show similarities in binding affinity for brevetoxins having the same structural (ladder) backbone, but different affinities between brevetoxins having different backbones. Ciguatoxin has a different backbone from the brevetoxins, but binds even more strongly to the same site. Could the flexibility of the backbone be related to their relative toxicities? As part of an effort to identify the common pharmacophore for the toxins, Monte Carlo methods were used to generate conformational models of the polyether ladder toxin brevetoxin B (PbTx-2) which shows significant flexibility at the juncture of the two 7-membered rings.
Animals↗
A statistical approach to the calculation of conformation of proteins. 1. Theory.
A quantitative theory is presented for calculating the folding of a polymer, especially as applied to the renaturation of globular proteins. The theory applies to both thermodynamically and kinetically determined processes, so that not only can the equilibrium result be calculated but also the time course of folding. Since it is not automatically assumed that the folding will result in a single "native" conformation, it is possible to conclude that the polymer will exist as a random coil under appropriate conditions. A Monte Carlo method for applications is discussed in detail, and a very simple example is presented.
Chemical Phenomena↗