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PubMed1977

Convex programs having some linear constraints.

The problem of concern is the minimization of a convex function over a normed space (such as a Hilbert space) subject to the constraints that a number of other convex functions are not positive. As is well known, there is a dual maximization problem involving Lagrange multipliers. Some of the constraint functions are linear, and so the Uzawa, Stoer, and Witzgall form of the Slater constraint qualifications is appropriate. A short elementary proof is given that the infimum of the first problem is equal to the supremum of the second problem.

Journal Article↗
PubMed2004

Pharmacokinetic/pharmacodynamic modelling of GnRH antagonist degarelix: a comparison of the non-linear mixed-effects programs NONMEM and NLME.

In this paper, the two non-linear mixed-effects programs NONMEM and NLME were compared for their use in population pharmacokinetic/pharmacodynamic (PK/PD) modelling. We have described the first-order conditional estimation (FOCE) method as implemented in NONMEM and the alternating algorithm in NLME proposed by Lindstrom and Bates. The two programs were tested using clinical PK/PD data of a new gonadotropin-releasing hormone (GnRH) antagonist degarelix currently being developed for prostate cancer treatment. The pharmacokinetics of intravenous administered degarelix was analysed using a three compartment model while the pharmacodynamics was analysed using a turnover model with a pool compartment. The results indicated that the two algorithms produce consistent parameter estimates. The bias and precision of the two algorithms were further investigated using a parametric bootstrap procedure which showed that NONMEM produced more accurate results than NLME together with the nlmeODE package for this specific study.

Algorithms↗
PubMed1980

A program for non-linear regression analysis to be used on desk-top computers.

A simple program for non-linear regression analysis, based upon the strategy of evolution, is described. It should run on any minicomputer (even on "personal computers') if a BASIC interpreter is available. It can easily be modified for the both the type of function and the "best fitting' condition.

Anti-Bacterial Agents↗
PubMed1997

Optimisation in radiotherapy. II: Programmed and inversion optimisation algorithms.

This is the second article in a three part examination of optimisation in radiotherapy. The previous article established the bases of optimisation in radiotherapy, and the formulation of the optimisation problem. This paper outlines several algorithms that have been used in radiotherapy, for searching for the best irradiation strategy within the full set of possible strategies. Two principle classes of algorithm are considered--those associated with mathematical programming which employ specific search techniques, linear programming-type searches or artificial intelligence--and those which seek to perform a numerical inversion of the optimisation problem, finishing with deterministic iterative inversion.

Algorithms↗
PubMed1997

A software program based on robust linear regression methods for instrumental calibration in biochemical analysis.

A microcomputer program written in GWBASIC for conventional least squares regression (LS) and robust linear regression methods (RRMs) such as single median (SM) and repeated median (RM) is described. The main advantages of RRMs is the ability to detect outliers which can cause an inaccurate estimation of the analyzed samples. It requires MS DOS PC version 3.3 or higher and at least 256 kbyte of RAM. The joint application of RRMs and residuals analysis by the studentized method (STRM) allows a more precise biochemical analysis.

Biochemistry↗
PubMed2004

Computational design of reduced metabolic networks.

Cellular functions are based on thousands of chemical reactions and transport processes, most of them being catalysed and regulated by specific proteins. Systematic gene knockouts have provided evidence that this complex reaction network possesses considerable redundancy, that is, alternative routes exist along which signals and metabolic fluxes may be directed to accomplish an identical output behaviour. This property is of particular importance in cases where parts of the reaction network are transiently or permanently impaired, for example, due to an infection or genetic alterations. Here we present a computational concept to determine enzyme-reduced metabolic networks that are still sufficient to accomplish a given set of cellular functions. Our approach consists of defining an objective function that expresses the compromise that has to be made between successive reduction of the network by omission of enzymes and its decreasing thermodynamic and kinetic feasibility. Optimisation of this objective function results in a linear mixed-integer program. With increasing weight given to the reduction of the number of enzymes, the total flux in the network increases and some of the reactions have to proceed in thermodynamically unfavourable directions. The approach was applied to two metabolic schemes: the energy and redox metabolism of red blood cells and the carbon metabolism of Methylobacterium extorquens. For these two example networks, we determined various variants of reduced networks differing in the number and types of disabled enzymes and disconnected reactions. Using a comprehensive kinetic model of the erythrocyte metabolism, we assess the kinetic feasibility of enzyme-reduced subnetworks. The number of enzymes predicted to be indispensable amounts to 14 (out of 28) for the erythrocyte scheme and 13 (out of 77) for the bacterium scheme, the largest group of enzymes predicted to be simultaneously dispensable amounts to 3 and 37 for these two systems. Our approach might contribute to identifying potential target enzymes for rational drug design, to rationalising gene-expression profiles of metabolic enzymes and to designing synthetic networks with highly specialised metabolic functions.

Computational Biology↗
PubMed1976

A computer program suitable for fitting linear models when the dependent variable is dichotomous, polichotomous or censored survival and non-linear models when the dependent variable is quantitative.

Given a set of measurements of s explanatory variables corresponding to each experimental unit, a computer program, whose methodological background can be found in [2] has been written in FORTRAN IV language in order to perform regression analyses when the dependent variable is: (i) dichotomous; (ii) polichotomous; (iii) censored survival. In the two former the Cox's [6] linear logistic models are used while in the third one it has been resorted to the models suggested by Feigl and Zelen [8]. The statistical estimation procedure is maximum likelihood and among the different algorithms developed to reach this goal, the one published by Van der Voort and Dorpema [3], has been utilized. Furthermore, when the dependent variable is quantitative, the program is suitable to fit any function non-linear in the parameters; the pertinent function and its first and second derivatives must be provided by the user. In the present version, implemented on a Univac 1106 machine, the program fits directly the Gompertz function.

Computers↗
PubMed1984

Non-linear curve-fitting programs for Phadezyme IgE PRIST using a Hewlett-Packard HP-97 and a Texas Instruments TI-59 with a PC-100A printer.

A non-linear curve-fitting program using a modified Hoerl's function on the Hewlett-Packard HP-97 and Texas Instruments TI-59 programmable calculators for the determination of Phadezaym IgE PRIST (IgE) results is described. Excellent correlation between the reference serum concentration and the curve fit concentration results were obtained. The equation used in the curve fit is ln y = A + B ln x + CxD, where A, B, C and an accuracy of fit term R are calculated by the program. The value of D must be specified by the user before the curve fit is performed.

Computers↗
PubMed1988

A mechanistic and kinetic analysis of the interactions of the diastereoisomers of adenosine 3',5'-(cyclic)phosphorothioate with purified cyclic AMP-dependent protein kinase.

The binding affinities of the diastereoisomers of adenosine 3',5'-(cyclic)phosphorothioate, Sp-cAMP[S] and Rp-cAMP[S], for the cyclic AMP- (cAMP-)binding sites on purified and reconstituted pig heart type II cAMP-dependent protein kinase holoenzyme were determined by measuring the ability of these compounds to displace [3H]cAMP from this enzyme. Sp-cAMP[S], a cAMP agonist, displaced 50% of the [3H]cAMP bound to the holoenzyme at a concentration 10-fold higher than that of cAMP; Rp-cAMP[S], a cAMP antagonist, required a 100-fold higher concentration relative to cAMP. Activation of the isolated holoenzyme, determined as phosphotransferase activity, was measured in the presence of the agonist and in the absence and in the presence of increasing concentrations of the antagonist. The results of fitting the activation data to sigmoid curves with a non-linear-regression program and to Hill plots by using a linear-regression program showed that Rp-cAMP[S] had no effect on Vmax, increased the EC50 values for agonist activation and had no effect on the co-operativity of activation (h). A Ki value of 11 microM was determined for Rp-cAMP[S] inhibition of cAMP-induced activation of purified type II cAMP-dependent protein kinase. Electrophoresis of the holoenzyme on polyacrylamide gels under non-denaturing conditions in the presence of saturating concentrations of the diastereoisomers resulted in 100% dissociation of the subunits with Sp-cAMP[S] and 0% dissociation with Rp-cAMP[S]. Sp-cAMP[S], the isomer with an axial exocyclic sulphur atom, binds to the holoenzyme, releases the catalytic subunit and activates the phosphotransferase activity. Rp-cAMP[S], the isomer with an equatorial exocyclic sulphur atom, binds to the holoenzyme but does not result in dissociation, and thus acts as a competitive inhibitor of phosphotransferase activity.

Animals↗
PubMedDate not supplied

A linear semi-infinite programming strategy for constructing optimal wavelet transforms in multivariate calibration problems.

A novel strategy for the optimization of wavelet transforms with respect to the statistics of the data set in multivariate calibration problems is proposed. The optimization follows a linear semi-infinite programming formulation, which does not display local maxima problems and can be reproducibly solved with modest computational effort. After the optimization, a variable selection algorithm is employed to choose a subset of wavelet coefficients with minimal collinearity. The selection allows the building of a calibration model by direct multiple linear regression on the wavelet coefficients. In an illustrative application involving the simultaneous determination of Mn, Mo, Cr, Ni, and Fe in steel samples by ICP-AES, the proposed strategy yielded more accurate predictions than PCR, PLS, and nonoptimized wavelet regression.

Journal Article↗
PubMed1978

BANDSCAN--a computer program for on-line linear scanning of human banded chromosomes.

BANDSCAN, an interactive program for on-line linear scanning of human G-banded chromosomes quantitative analysis is described. This program was written for a Wang 720 C programmable desk calculator associated to the Zeiss scanning photometer MP01. The system can detect up to a maximum of 24 densitometric band peaks found along banded chromosome arms or chromatids, estimate the total arm length and localize bands in terms of their relative positions. The scanning stage under control is always returned to the pre-fixed scanning starting point (centromere) which allows a user to scan the specimen repeatedly at different sensitivities and thus to reject minor bands or suspected chromosome artifacts. This facilitates a better visualization of major bands and chromosome landmarks. A fully formated print-out on band localizations and their relative positions is obtained at the end of each scanning. The possibilities of the application of this program to band mapping of human chromosomes and to the study of small chromosome band aberrations is discussed.

Animals↗
PubMed1993

AMESFIT: a microcomputer program for fitting linear-exponential dose-response models in the Ames Salmonella assay.

The Ames Salmonella/microsome assay remains the most widely used microbial test for genotoxicity. In this article, we describe a microcomputer program developed to fit a linear-exponential dose-response model to Ames assay data for established mutagens. The model includes a linear term to describe the mutagenic effects of the test agent at low to moderate doses and an exponential attenuation factor to accommodate downturns at high doses due to cytotoxicity. Quasi-likelihood methods are used to obtain estimates of the unknown model parameters, thereby avoiding the need to fully specify the distribution of the experimental data. This method of estimation also allows for extra-Poisson variation that is characteristic of counts of mutant colonies of bacteria observed in the Ames assay. The particular linear-exponential model used here was developed for use in the analysis of a recent large-scale collaborative trial using the Ames assay sponsored by the International Programme on Chemical Safety. The use of our program is illustrated using sample data sets taken from that collaborative study.

Dose-Response Relationship, Drug↗
PubMed1999

Successful conversion from a linear accelerator-based program to a Gamma Knife radiosurgery program: the Cleveland Clinic experience.

From August 1989 to January 1997, 307 treatments in 293 patients were performed with a linear accelerator-based (LINAC) stereotactic radiosurgery system. Because of the program s success, the need for a dedicated radiosurgery unit in Ohio and the desire to treat functional disorders, the Cleveland Clinic Health System (CCHS) obtained the first Gamma Knife in the state of Ohio. Based on the previous volume of patients for radiosurgery, it was estimated that 75-100 patients would be treated during the first year of operation. However, during the first calendar year, 214 treatments were performed on 205 patients, which far exceeded expectations. The success of the CCHS Gamma Knife Center can be attributed to an increase in a number of factors. These included marketing efforts, patient awareness, increased use for functional disorders, physician understanding of radiosurgery, use by qualified nonaffiliated radiation oncologists and neurosurgeons, and outpatient delivery (95% with the Gamma Knife vs <5% with the LINAC). With proper planning, education, and awareness, the opening of a Gamma Knife Center can greatly increase the volume of radiosurgery performed when compared with a LINAC-based program.

Brain Neoplasms↗