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At least 199 records · Page 11Linked to original sources
PubMed1984

A mathematical overview of a computer simulation model of maternity histories with illustrative examples.

A mathematical overview of a stochastic computer simulation model of maternity histories is provided. Various components of human reproduction are accommodated in the model through distributions of waiting times among live births. Included in these components are distributions of age at first marriage in a cohort of women, waiting times to pregnancy for fecundable women, and the lengths of infecundable periods following live births. Probabilities that pregnancies end in either a live birth, induced abortion, or some other type of outcome are also included. Elements of renewal theory and semi-Markov processes in discrete time were the basic mathematical concepts used in the construction of the model. A brief description of an interactive software package called MATHIST, which may be used to implement the model on a computer, is also included. Four illustrative computer runs with MATHIST, pertinent to the operation of family planning programmes in Africa, are also described and discussed.

Adult↗
PubMed1983

On-line digitizing: useful mathematical techniques.

A mathematical and computational approach to some of the common problems found in writing digitizing programs for cephalometric analysis is described. The paper is aimed at those with access to a microcomputer and digitizer, some knowledge of the BASIC computer language and simple mathematics but little experience of writing digitizing programs.

Cephalometry↗
PubMed1996

Computational study of packing a collagen-like molecule: quasi-hexagonal vs "Smith" collagen microfibril model.

The lateral packing of a collagen-like molecule, CH3CO-(Gly-L-Pro-L-Pro)4-NHCH3, has been examined by energy minimization with the ECEPP/3 force field. Two current packing models, the Smith collagen microfibril twisted equilateral pentagonal model and the quasi-hexagonal packing model, have been extensively investigated. In treating the Smith microfibril model, energy minimization was carried out on various conformations including those with the symmetry of equivalent packing, i.e., in which the triple helices were arranged equivalently with respect to each other. Both models are based on the experimental observation of the characteristic axial periodicity, D = 67 nm, of light and dark bands, indicating that, if any superstructure exists, it should consist of five triple helices. The quasi-hexagonal packing structure is found to be energetically more favorable than the Smith microfibril model by as much as 31.2 kcal/mol of five triple helices. This is because the quasi-hexagonal packing geometry provides more nonbonded interaction possibilities between triple helices than does the Smith microfibril geometry. Our results are consistent with recent x-ray studies with synthetic collagen-like molecules and rat tail tendon, in which the data were interpreted as being consistent with either a quasi-hexagonal or a square-triangular structure.

Animals↗
PubMed1998

Biological computation.

It is argued that biological systems can be viewed as special computing devices. This view emerges from considerations of how information is stored in and retrieved from the genes. Genes can only specify the properties of the proteins they code for, and any integrative properties of the system must be 'computed' by their interactions. This provides a framework for analysis by simulation and sets practical bounds on what can be achieved by reductionist models.

Computational Biology↗
PubMed1993

Comparison of conformational characteristics in structurally similar protein pairs.

Although it is known that three-dimensional structure is well conserved during the evolutionary development of proteins, there have been few studies that consider other parameters apart from divergence of the main-chain coordinates. In this study, we align the structures of 90 pairs of homologous proteins having sequence identities ranging from 5 to 100%. Their structures are compared as a function of sequence identity, including not only consideration of C alpha coordinates but also accessibility, Ooi numbers, secondary structure, and side-chain angles. We discuss how these properties change as the sequences become less similar. This will be of practical use in homology modeling, especially for modeling very distantly related or analogous proteins. We also consider how the average size and number of insertions and deletions vary as sequences diverge. This study presents further quantitative evidence that structure is remarkably well conserved in detail, as well as at the topological level, even when the sequences do not show similarity that is significant statistically.

Algorithms↗
PubMed1991

Proline in alpha-helix: stability and conformation studied by dynamics simulation.

Free-energy simulations have been used to estimate the change in the conformational stability of short polyalanine alpha-helices when one of the alanines is replaced by a proline residue. For substituting proline in the middle of the helix the change in free energy of folding (delta delta G degrees) was calculated as 14 kJ/mol (3.4 kcal/mol), in excellent agreement with the one available experimental value. The helix containing proline was found to be strongly kinked; the free energy for reducing the angle of the kink from 40 degrees to 15 degrees was calculated, and found to be small. A tendency to alternate hydrogen bonding schemes was observed in the proline-containing helix. These observations for the oligopeptide agree well with the observation of a range of kink angles (18-35 degrees) and variety of hydrogen bonding schemes, in the rare instances where proline occurs in helices in globular proteins. For substituting proline at the N-terminus of the helix the change in free energy of folding (delta delta G degrees) was calculated as -4 kJ/mol in the first helical position (N1) and +6 kJ/mol in the second helical position (N2). The observed frequent occurrence of proline in position N1 in alpha-helices in proteins therefore has its origin in stability differences of secondary structure. The conclusion reached here that proline may be a better helix former in position N1 than (even) alanine, and thus be a helix initiator may be testable experimentally by measurements of fraction helical conformation of individual residues in oligopeptides of appropriate sequence. The relevance of these results in regards to the frequent occurrence of proline-containing helices in certain membrane proteins is discussed.

Alanine↗
PubMed1993

Resolving power: a quantitative measure of electrophoretic resolution.

Resolving power is a quantitative measure of the ability of an electrophoretic system to separate DNA (and other) molecules of similar size. It is a dimensionless quantity, and hence facilitates comparison of the performance of electrophoretic systems that operate very differently. Resolving power can be determined as a function of molecular length from experimental data consisting of a series of completely resolved bands on a gel or blot; closely spaced bands are not required. We discuss factors such as the mass of DNA in a particular band and the spatial resolution of the system used to image the distribution of DNA on a gel or blot that, while not an intrinsic part of the electrophoretic system, may influence the observed resolving power. We derive an empirical global dispersion function that applies both to images of gels obtained after a fixed time of electrophoresis of all the samples and to images obtained as each species reaches a detector located at a fixed distance from the starting well. We use this dispersion function to show that the improvement in resolving power produced by extending the time or distance of electrophoresis in a static, uniform electric field asymptotically approaches a limiting value that is a function of the length of the DNA. When plotted as a function of molecular length, this limiting value defines an envelope that characterizes the intrinsic limits of performance of a particular electrophoretic system (e.g., electric field strength, gel type and concentration, buffer, temperature). Comparing the resolving power of static field agarose gel electrophoresis as routinely practiced for separating DNA molecules from 10(3) to 10(5) bp long with other electrophoretic schemes suggests that significant improvements should be achievable.

Bacteriophage T7↗
PubMed1997

Absorption lineshapes in two-dimensional electron spin resonance and the effects of slow motions in complex fluids.

A methodology for obtaining pure absorption two-dimensional electron spin resonance spectra is presented for the case of large inhomogeneous broadening and/or slow motions. For slow motions, the spectra consist of "complex Lorentzians" superimposed with complex weighting factors, presenting a challenge to obtaining absorption spectra. It is shown how absorption-type spectra can be recovered for the two-pulse COSY and SECSY experiments in such cases. For three-pulse 2D ELDOR experiments, absorption lineshapes can be obtained for the autopeaks, whereas the cross peaks would be of mixed-mode character, in general. However, for practical cases the dispersive components in the cross peaks will be relatively small. Theoretical and experimental absorption spectra are provided to illustrate the method and to show the improved resolution obtained from absorption lineshapes. In particular, the variation in linewidths across a SECSY spectrum, which is a key component in elucidating motional dynamics, is clearly rendered in the pure absorption mode. A convenient method for introducing the necessary phase corrections for the slow-motional spectra is also provided.

Absorption↗
PubMed1995

A landscape parametric profile approach for rat brain image analysis.

This paper develops the use of the landscape parametric profile as a descriptive and interpretative method of analyzing metabolic activity data obtained by neuroimaging techniques such as 2-deoxyglucose autoradiography. The method is suggested as an initial survey-type approach that can be used to map regional activity throughout the coronal planes of a rat brain and to compare relative differences in the patterns of activity between different brains. Images are acquired using preexisting image analysis software and then transformed to landscape parametric profiles derived from each matrix array. The image profile analysis tasks are done using commercially available software for matrix computations such as MATLAB. An effective way of interpreting activity differences between brains is presented by plotting the results from a randomized blocks ANOVA significance test combined with the average profiles of different subjects within the same experimental group. The method greatly reduces the computational burden associated with image averaging and statistical comparison of brains from different subjects while preserving the richness in topographic metabolic information. One significant advantage of the method is that it results in figures that are readily depicted and interpretable in black and white.

Analysis of Variance↗
PubMed1998

A voxel-based analysis of cerebral perfusion in dementia and depression of old age.

Thirty-nine elderly depressed patients as well as 15 demented patients with Alzheimer's disease and 11 healthy volunteers were imaged at rest with a high resolution single-slice 12-detector head scanner (SME-Neuro 900) and the cerebral perfusion marker 99mTc-Exametazime (HM-PAO). Statistical parametric maps were computed to compare early- and late-onset depressed, Alzheimer patients and healthy volunteers and to examine associations between regional perfusion and clinical and MRI variables. Patients with late-onset depression showed reductions in temporal lobe perfusion compared with early-onset depression and controls. Alzheimer patients had the expected reduced perfusion in temporoparietal and prefontal cortex, as well as basal ganglia, compared with healthy controls. Compared with depressed patients, they showed a relative reduction in temporoparietal cortex, only. This difference was more pronounced between Alzheimer patients and early onset, compared to late-onset patients with depression. Periventricular white matter changes on MRI were associated with temporal lobe reductions of tracer uptake in depression. In the Alzheimer group, deep white matter MRI changes were associated with frontal perfusion deficits. Our results support a vulnerability hypothesis, which predicts that patients with late-onset depression will show more brain changes than patients with an early onset of their illness. Statistical parametric mapping in patients with organic psychiatric brain syndromes is feasible and promising as a clinical and research method.

Aged↗
PubMed1993

The short tail-fiber of bacteriophage T4: molecular structure and a mechanism for its conformational transition.

Electron microscopy, image processing and computational sequence analysis were used to investigate the structure of the short tail-fiber of bacteriophage T4. This molecule, an oligomer of gp12, is an adhesin that binds the virion irreversibly to the bacterial surface. Short tail-fibers were isolated from mutant-infected cells in which gp12 is synthesized and assembled correctly, but not incorporated into virions. Visualized in negative stain, these filamentous molecules are approximately 38 nm in total length, with an arrowhead-shaped head (approximately 10 nm long by 6 nm wide), a 24-nm shaft of uniform width (approximately 3.8 nm), and a small, seemingly flexible, tail. The primary sequence contains a domain consisting of tandem quasi-repeats, each about 40 residues long, extending from approximately residue 50 to residue 320. Molecular mass analyses by scanning transmission electron microscopy confirm that the molecule is a trimer. The masses of the head, shaft, and tail domains are consistent with (trimers of) the carboxy-terminus, the repeat region, and the amino-terminus, respectively. When short tail-fibers are visualized extending from baseplates, their heads are distal, i.e., detached, implying that it is the tail that remains in contact with the baseplate. Analysis of the molecules' curvature properties detects three hinge-sites: these suggest how the short tail-fiber may be initially accommodated in a compact conformation in the "hexagon" state of the baseplate, from which it converts to the extended conformation when the baseplate switches into its "star" state.

Amino Acid Sequence↗
PubMed1989

A parallel implementation of the ALOPEX process.

Optimization techniques have found many applications in science, engineering, and industry. In all applications, the best value of a "cost function" is sought in a well-defined domain; this cost function in general depends on many parameters. An iterative optimization technique has been developed (ALOPEX) that uses feedback in order to optimize the response of a system. The cost function for this process is problem dependent and therefore quite flexible. The method has been applied successfully to different optimization problems such as pattern recognition, receptive field studies in the visual system of animals, curve fitting, etc. We present two special purpose hardware implementations for ALOPEX. The first method takes time O(logN + logm) and uses O(mN2) processing elements. The second method takes O(logN + m) time and uses O(N2) processing elements. Our basic architecture is a binary tree with N2 leaves (equal to the length of the vectors) and therefore had depth O(logN). Different implications of the two approaches will be discussed including similarities with the biological visual process.

Algorithms↗
PubMed1990

Estimation and inference in pharmacokinetic models: the effectiveness of model reformulation and resampling methods for functions of parameters.

It is well known that high parameter estimate correlations and asymptotic variance estimates can cause estimation and inference problems in the analysis of pharmacokinetic models. In this paper we show that analysis of three important functions of pharmacokinetic parameters, the half-life, mean residence time, and the area under the curve, can sometimes be greatly improved by reformulating the model to address collinearity and by using the bootstrap to form confidence intervals. The resultant estimators can be more accurate than the original ones, and resultant confidence intervals can be narrower. Of the three measures, the half-life estimator is much better behaved than the estimators of mean residence time and area under the curve under collinearity, suggesting that it (or measures like it) should be used more often.

Analysis of Variance↗