Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Mathematical Computing”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 667 records · Page 37Linked to original sources

Simulation of diauxic production of cephalosporin C by Cephalosporium acremonium: lag model for fed-batch fermentation.

We extend a previously reported model (Chu, W.B.; Constantinides, A. Biotechnol. Bioeng. 1988, 32, 277-288) for the batch fermentation of cephalosporin C under the diauxic growth of Cephalosporium acremonium on glucose and sucrose to a fed-batch system. For this purpose, a novel lag model is proposed for diauxie, which has two functional forms, each embodying the dependence of lag on total cell mass and secondary substrate concentration. This lag model is applicable for batch simulations for arbitrary initial glucose and sucrose concentrations. We used the previously reported batch data to perform locally optimized fed-batch simulations. When applied to fed-batch fermentations, multiple lag times were accounted for. These studies showed that fed-batch fermentations (under the restriction that cell mass concentration did not exceed 25 g/L) could be more productive than simple batch runs. A representative result for a glucose-pulse fed-batch run at optimal cephalosporin production is a productivity of 4.22 mg of cephalosporin C/(L.h) and a yield of 9.25 mg of cephalosporin C/g of total sugar used.

Acremonium↗

Diffusion modeling of percutaneous absorption kinetics. 1. Effects of flow rate, receptor sampling rate, and viable epidermal resistance for a constant donor concentration.

A diffusion model for the percutaneous absorption of a solute through the skin is developed for the specific case of a constant donor concentration with a finite removal rate from the receptor due to either perfusion rate or sampling. The model has been developed to include a viable epidermal resistance and a donor-stratum corneum interfacial resistance. Numerical inversion of the Laplace domain solutions were used for simulations of solute flux and cumulative amount absorbed and to model specific examples of percutaneous absorption. Limits of the Laplace domain solutions were used to define the steady-state flux, lag time, and receptor concentration. Steady-state approximations obtained from the solutions were used to relate the steady-state flux and the effective permeability coefficient to the viable epidermis resistance, a donor-stratum corneum interfacial resistance, receptor removal rate, and partitioning between the receptor and donor phases. The lag time was shown to be dependent on these parameters and on the volume of the receptor phase. It is concluded that curvilinear cumulative amount and flux-time profiles are dependent on the processes affecting percutaneous absorption, the shapes of the profiles reflecting the processes most determining transport.

Computer Simulation↗

Two computational primitives for algorithmic self-assembly: copying and counting.

Copying and counting are useful primitive operations for computation and construction. We have made DNA crystals that copy and crystals that count as they grow. For counting, 16 oligonucleotides assemble into four DNA Wang tiles that subsequently crystallize on a polymeric nucleating scaffold strand, arranging themselves in a binary counting pattern that could serve as a template for a molecular electronic demultiplexing circuit. Although the yield of counting crystals is low, and per-tile error rates in such crystals is roughly 10%, this work demonstrates the potential of algorithmic self-assembly to create complex nanoscale patterns of technological interest. A subset of the tiles for counting form information-bearing DNA tubes that copy bit strings from layer to layer along their length.

Algorithms↗

Principal component method for assessing structural heterogeneity across multiple alignment media.

The recent availability of residual dipolar coupling measurements in a variety of different alignment media raises the question to what extent biomolecular structure and dynamics are differentially affected by their presence. A computational method is presented that allows the sensitive assessment of such changes using dipolar couplings measured in six or more alignment media. The method is based on a principal component analysis of the covariance matrix of the dipolar couplings. It does not require a priori structural or dynamic information nor knowledge of the alignment tensors and their orientations. In the absence of experimental errors, the covariance matrix has at most five nonzero eigenvalues if the structure and dynamics of the biomolecule is the same in all media. In contrast, differential structural and dynamic changes lead to additional nonzero eigenvalues. Characteristic features of the eigenvalue distribution in the absence and presence of noise are discussed using dipolar coupling data calculated from conformational ensembles taken from a molecular dynamics trajectory of native ubiquitin.

Computational Biology↗

Teaching Bayesian reasoning in less than two hours.

The authors present and test a new method of teaching Bayesian reasoning, something about which previous teaching studies reported little success. Based on G. Gigerenzer and U. Hoffrage's (1995) ecological framework, the authors wrote a computerized tutorial program to train people to construct frequency representations (representation training) rather than to insert probabilities into Bayes's rule (rule training). Bayesian computations are simpler to perform with natural frequencies than with probabilities, and there are evolutionary reasons for assuming that cognitive algorithms have been developed to deal with natural frequencies. In 2 studies, the authors compared representation training with rule training; the criteria were an immediate learning effect, transfer to new problems, and long-term temporal stability. Rule training was as good in transfer as representation training, but representation training had a higher immediate learning effect and greater temporal stability.

Algorithms↗

Theory of covariance nuclear magnetic resonance spectroscopy.

Covariance nuclear magnetic resonance (NMR) spectroscopy provides an effective way for establishing nuclear spin connectivities in molecular systems. The method, which identifies correlated spin dynamics in terms of covariances between 1D spectra, benefits from a high spectral resolution along the indirect dimension without requiring apodization and Fourier transformation along this dimension. The theoretical treatment of covariance NMR spectroscopy is given for NOESY and TOCSY experiments. It is shown that for a large class of 2D NMR experiments the covariance spectrum and the 2D Fourier transform spectrum can be related to each other by means of Parseval's theorem. A general procedure is presented for the construction of a symmetric spectrum with improved resolution along the indirect frequency domain as compared to the 2D FT spectrum.

Computer Simulation↗

Population-response model for vibrotactile spatial summation.

A computational model based on previous physiological and psychophysical data is presented for the human Pacinian (P) psychophysical channel. The model can predict the probability of detection in simple psychophysical tasks, and hence psychometric functions and thresholds. The model simulates stimulating variable and fixed glabrous skin sites with different-sized contactors and includes spatial variation of monkey P-fiber sensitivities. Therefore, it is especially suitable for studying spatial summation, i.e. the improvement of threshold with increasing contactor area. Selective contributions of neural integration (n.i.) and probability summation (p.s.) are also incorporated into the model. Model predictions are compared to psychophysical results of Gescheider et al. (2005). The performance of the model regarding the effects of contactor size is very good. In addition to predicting approximately 3 dB improvement of thresholds when the contactor area is doubled, the model also reveals nonlinear contributions of p.s. and n.i. Furthermore, the model asserts that thresholds are largely governed by neural integration when small contactors are used. These and other findings discussed in the article show that the presented model is a helpful tool for formulating testable hypotheses. Although the model can also simulate some temporal summation effects, simulation results do not conform well to previous data on temporal response properties. Thus, the model needs to be refined in that respect.

Cell Count↗

A sequential trial of pain killers in arthritis: issues of multiple comparisons with control and of interval-censored survival data.

A large clinical comparison of pain killers used in the treatment of arthritis was conducted using a sequential design. The trial presented two major challenges: there were three treatments to be compared, and patients were assessed annually for up to 7 years. Treatment comparisons were made by selecting appropriate pairwise comparisons, to which standard theory could be applied. Rules concerning actions to take in the event of each stopping criterion being reached were evaluated by simulation. The annual assessments were used to create an interval-censored survival time: the year during which "disease progression" first occurred.

Analgesics↗

Biological evaluation of d2, an algorithm for high-performance sequence comparison.

A number of algorithms exist for searching sequence databases for biologically significant similarities based on the primary sequence similarity of aligned sequences. We have determined the biological sensitivity and selectivity of d2, a high-performance comparison algorithm that rapidly determines the relative dissimilarity of large datasets of genetic sequences. d2 uses sequence-word multiplicity as a simple measure of dissimilarity. It is not constrained by the comparison of direct sequence alignments and so can use word contexts to yield new information on relationships. It is extremely efficient, comparing a query of length 884 bases (INS1ECLAC) with 19,540,603 bases of the bacterial division of GenBank (release 76.0) in 51.77 CPU seconds on a Cray Y/MP-48 supercomputer. It is unique in that subsequences (words) of biological interest can be weighted to improve the sensitivity and selectivity of a search over existing methods. We have determined the ability of d2 to detect biologically significant matches between a query and large datasets of DNA sequences while varying parameters such as word-length and window size. We have also determined the distribution of dissimilarity scores within eukaryotic and prokaryotic divisions of GenBank. We have optimized parameters of the d2 program using Cray hardware and present an analysis of the sensitivity and selectivity of the algorithm. A theoretical analysis of the expectation for scores is presented. This work demonstrates that d2 is a unique, sensitive, and selective method of rapid sequence comparison that can detect novel sequence relationships which remain undetected by alternate methodologies.

Algorithms↗

BIOESTIM: software for automatic design of estimators in bioprocess engineering.

This paper describes BIOESTIM, a software package devoted to on-line estimation in bioprocess engineering. BIOESTIM enables bioengineers automatically to design state and parameter estimators from a minimal knowledge of the process kinetics. Such estimators allow development of software sensors capable of coping with the lack of reliable instrumentation suited to real-time monitoring. The estimator building procedure through BIOESTIM starts up from a dynamical material balance model of the bioprocess. This model, supplied by the user, is next completed by other information with no requirement for numerical values: the user has only to specify available measurements, coupled reactions and the known yield coefficients. On the base of this knowledge, BIOESTIM proceeds to symbolic algebraic manipulations on the model in order to study estimation possibilities and check identifiability of yield coefficients. When the design of an estimator is possible, the corresponding equations are automatically generated. Moreover, these estimators are stored in a user-specified file which is automatically interfaced with a specialized simulation software including data treatment and numerical integration packages. Thus, the user can simulate the estimator performances under various operational conditions using available experimental measurements. A typical example dealing with microbial growth and biosynthesis reactions is given in order to illustrate the main functional capabilities of BIOESTIM. BIOESTIM has been designed and written in a modular fashion. The module dealing with estimators design makes use of symbolic computation; it is written in Mathematica and runs on every computer on which this language is available.

Algorithms↗

Limits of homology detection by pairwise sequence comparison.

MOTIVATION: Noise in database searches resulting from random sequence similarities increases as the databases expand rapidly. The noise problems are not a technical shortcoming of the database search programs, but a logical consequence of the idea of homology searches. The effect can be observed in simulation experiments. RESULTS: We have investigated noise levels in pairwise alignment based database searches. The noise levels of 38 releases of the SwissProt database, display perfect logarithmic growth with the total length of the databases. Clustering of real biological sequences reduces noise levels, but the effect is marginal.

Computer Simulation↗

A simple add-on algorithm to extend one-dimensional finite difference diffusion calculations to include charge coupling.

The importance of interionic charge coupling in chemical and biological diffusion problems is discussed, and the Nernst-Planck (ionic) and Onsager-Fuoss (neutral component) methods are considered. A novel single pass charge-coupling algorithm 'Q-COUPLE' is proposed, which should be usable as a separate add-on subroutine with many one-dimensional finite difference diffusion calculations. Its mode of operation is explained with the help of elementary electrostatics and by reference to listings in BASIC. The algorithm is being applied in a finite difference model of diffusion-with-reaction in dental plaque, with 12 ions or ionizable molecules diffusing and interacting with fixed charges. It is shown to be invariant with respect to the direction of sweep, and in the simple case of coupled diffusion of a single polyvalent electrolyte is found to compare well with the analytical solution. Advantages and limitations of the proposal are discussed.

Algorithms↗

The coalescent process with selfing.

A method of estimating the selfing rate using DNA sequence data was recently proposed by Milligan. Unfortunately, a number of errors make interpretation of his results problematic. In the present paper we first show how the usual coalescent process can be adapted to models that include selfing, and then use this result to find moment estimators as well as the likelihood surface for the selfing rate, s, and the scaled mutation rate, theta. We conclude that, regardless of the method used, large sample sizes are necessary to estimate s with any degree of certainty, and that the estimate is always highly sensitive to recent changes in the true value.

Computer Simulation↗

Protein secondary structure prediction using logic-based machine learning.

Many attempts have been made to solve the problem of predicting protein secondary structure from the primary sequence but the best performance results are still disappointing. In this paper, the use of a machine learning algorithm which allows relational descriptions is shown to lead to improved performance. The Inductive Logic Programming computer program, Golem, was applied to learning secondary structure prediction rules for alpha/alpha domain type proteins. The input to the program consisted of 12 non-homologous proteins (1612 residues) of known structure, together with a background knowledge describing the chemical and physical properties of the residues. Golem learned a small set of rules that predict which residues are part of the alpha-helices--based on their positional relationships and chemical and physical properties. The rules were tested on four independent non-homologous proteins (416 residues) giving an accuracy of 81% (+/- 2%). This is an improvement, on identical data, over the previously reported result of 73% by King and Sternberg (1990, J. Mol. Biol., 216, 441-457) using the machine learning program PROMIS, and of 72% using the standard Garnier-Osguthorpe-Robson method. The best previously reported result in the literature for the alpha/alpha domain type is 76%, achieved using a neural net approach. Machine learning also has the advantage over neural network and statistical methods in producing more understandable results.

Amino Acid Sequence↗

Hydration of amino acid side chains: dependence on secondary structure.

Energy calculations have been used to study the hydration sites around the polar groups of serine, threonine and tyrosine side chains. These hydration sites depend not only on the hybridization of the polar group but also on the local secondary structure, the chi 1 side chain torsion angle and the position of the hydroxyl hydrogen atom. For tyrosine side chains, two solvent sites are found approximately in the plane of the ring. Even for serine and threonine side chains only two minimum energy sites are found in general of which one is in an expected position within hydrogen bonding of the hydroxyl hydrogen atom (unless this is blocked from interaction with solvent molecules by, for example, Oi-4 or Oi-3. The position of the second of these sites depends not only on the position of the hydroxyl oxygen but also on neighbouring main chain atoms to which it can also hydrogen bond. There is good agreement with the solvent distributions obtained from crystallographic data.

Amino Acids↗

Theoretical analyses on the role of Mg2+ ions in ribozyme reactions.

To elucidate the role of the Mg2+ ion in ribozyme reactions, we carried out ab initio molecular orbital investigations on dianionic trimethoxyphosphorane A and its Mg2+ complex (overall a neutral molecule) as a model system for the reaction center of Tetrahymena-type ribozyme. Although dianionic oxyphosphorane A concentrates its negative charges on the equatorial phosphoryl oxygens, the coordination of the Mg2+ ion between these two oxygens is unlikely. Geometry optimizations of the complex and the electrostatic potential of A both suggest that Mg2+ coordination preferably occurs in the region between the axial oxygen and the equatorial phosphoryl oxygen. The considerations of electrostatic potential rationalize the geometries of carboxylate-metal and phosphate-metal interactions extracted from the Cambridge Structural Database as well. Consequently, the Mg2+ ion at the active site of Tetrahymena-type ribozyme most likely lies in the regions between the axial and equatorial oxygens. The axial-equatorial coordinations of Mg2+ ions conceivably increase the electronegativities of the axial oxygens and facilitate cleavage of the phosphodiester bond located at the junction of the intron and the exon. It is thus likely that the Mg2+ ions play the key role in the phosphodiester cleavage reactions mediated by ribozymes.

Animals↗

Quantification of osseous facial dysmorphology in untreated unilateral coronal synostosis.

Unilateral coronal synostosis results in dysmorphology of the midface in addition to well-characterized cranial and orbital deformities. Because most American infants with this problem have undergone cranio-orbital surgery within their first year of life for the past 25 years, a paucity of data exist regarding the natural history of untreated unilateral coronal synostosis. In an attempt to remedy this void, an international search was conducted to identify computed tomography data sets of living individuals with untreated unilateral coronal synostosis; data were obtained from two European centers and one center in the United States. Results limited to the study of the midface are presented here. Digital data from high-resolution head computed tomography scans of 11 living, white individuals with untreated unilateral coronal synostosis were obtained from three craniofacial centers (in Denmark, The Netherlands, and the United States). Image volumes were constructed from each scan using ANALYZE biomedical imaging software. Fourteen pairs of three-dimensional distances were calculated on the ipsilateral (the side of the synostosis) and the contralateral (the side opposite to the synostosis) hemifaces using 11 osseous landmarks. The resulting measurements were expressed as a ratio of the ipsilateral: contralateral sides. Descriptive statistics were derived for the untreated unilateral coronal synostosis population and compared with analogous measurements performed on dried skulls. Age at computed tomography ranged from 1.1 to 21.1 years (mean, 6.6 years; median, 4.1 years). Twelve of the 14 measured distances differed by greater than 5 percent on the ipsilateral side, and all but one of these measurements were decreased on the ipsilateral side when compared with contralateral values. The results of this study support the following conclusions: (1) There are discrete and measurable differences in the facial morphology between patients with untreated unilateral coronal synostosis and normal skulls. (2) Intercenter and international collaboration can provide a sufficient number of individuals with rare craniofacial anomalies to quantitatively determine group characteristics. (3) Quantitative documentation of rare anomaly natural history is necessary for quantitative outcome assessment of treated patients.

Adolescent↗