Structured minimal-memory inexact quasi-Newton method and secant preconditioners for augmented Lagrangian optimization

Augmented Lagrangian methods for large-scale optimization usually require efficient algorithms for minimization with box constraints. On the other hand, active-set box-constraint methods employ unconstrained optimization algorithms for minimization inside the faces of the box. Several approaches may be employed for computing internal search directions in the large-scale case. In this paper a minimal-memory quasi-Newton approach with secant preconditioners is proposed, taking into account the structure of Augmented Lagrangians that come from the popular Powell-Hestenes-Rockafellar scheme. A combined algorithm, that uses the quasi-Newton formula or a truncated-Newton procedure, depending on the presence of active constraints in the penalty-Lagrangian function, is also suggested. Numerical experiments using the Cute collection are presented.

Improving ultimate convergence of an augmented Lagrangian method

Optimization methods that employ the classical Powell-Hestenes-Rockafellar augmented Lagrangian are useful tools for solving nonlinear programming problems. Their reputation decreased in the last 10 years due to the comparative success of interior-point Newtonian algorithms, which are asymptotically faster. In this research, a combination of both approaches is evaluated. The idea is to produce a competitive method, being more robust and efficient than its `pure` counterparts for critical problems. Moreover, an additional hybrid algorithm is defined, in which the interior-point method is replaced by the Newtonian resolution of a Karush-Kuhn-Tucker (KKT) system identified by the augmented Lagrangian algorithm. The software used in this work is freely available through the Tango Project web page:http://www.ime.usp.br/similar to egbirgin/tango/.

Use of copper and gold electrodes as sensitive elements for fabrication of an electronic tongue: Discrimination of wines and whiskies

A low-cost method is proposed to classify wine and whisky samples using a disposable voltammetric electronic tongue that was fabricated using gold and copper substrates and a pattern recognition technique (Principal Component Analysis). The proposed device was successfully used to discriminate between expensive and cheap whisky samples and to detect adulteration processes using only a copper electrode. For wines, the electronic tongue was composed of copper and gold working electrodes and was able to classify three different brands of wine and to make distinctions regarding the wine type, i.e., dry red, soft red, dry white and soft white brands. Crown Copyright (C) 2011 Published by Elsevier B.V. All rights reserved.

A Gradient-Type Method For Real-Time State Estimation Of Water Distribution Networks

Drinking water distribution networks risk exposure to malicious or accidental contamination. Several levels of responses are conceivable. One of them consists to install a sensor network to monitor the system on real time. Once a contamination has been detected, this is also important to take appropriate counter-measures. In the SMaRT-OnlineWDN project, this relies on modeling to predict both hydraulics and water quality. An online model use makes identification of the contaminant source and simulation of the contaminated area possible. The objective of this paper is to present SMaRT-OnlineWDN experience and research results for hydraulic state estimation with sampling frequency of few minutes. A least squares problem with bound constraints is formulated to adjust demand class coefficient to best fit the observed values at a given time. The criterion is a Huber function to limit the influence of outliers. A Tikhonov regularization is introduced for consideration of prior information on the parameter vector. Then the Levenberg-Marquardt algorithm is applied that use derivative information for limiting the number of iterations. Confidence intervals for the state prediction are also given. The results are presented and discussed on real networks in France and Germany.

Membrane-bound alkaline phosphatase from ectopic mineralization and rat bone marrow cell culture

Cells from rat bone marrow exhibit the proliferation-differentiation sequence of osteoblasts, form mineralized extracellular matrix in vitro and release alkaline phosphatase into the medium. Membrane-bound alkaline phosphatase was obtained by method that is easy to reproduce, simpler and fast when compared with the method used to obtain the enzyme from rat osseous plate. The membrane-bound alkaline phosphatase from cultures of rat bone marrow cells has a MWr of about 120 kDa and specific PNPP activity of 1200 U/tng. The ecto-enzyme is anchored to the plasma membrane by the GPI anchor and can be released by PIPLC (selective treatment) or polidocanol (0.2 mg/mL protein and 1% (w/v) detergent). The apparent optimum pH for PNPP hydrolysis by the enzyme was pH 10. This fraction hydrolyzes ATP (240 U/mg), ADP (350 U/ mg), glucose 1-phosphate (1100 U/mg), glucose 6-phosphate (340 Wing), fructose 6-phosphate (460 U/mg), pyrophosphate (330 U/mg) and (3glycerophosphate (600 U/mg). Cooperative effects were observed for the hydrolysis of PPi and beta-glycerophosphate. PNPPase activity was inhibited by 0.1 mM vanadate (46%), 0.1 mM ZnCl2 (68%), 1 mM levamisole (66%), 1 mM arsenate (44%), 10 mM phosphate (21%) and 1 mM theophylline (72%). We report the biochemical characterization of membrane-bound alkaline phosphatase obtained from rat bone marrow cells cultures, using a method that is simple, rapid and easy to reproduce. Its properties are compared with those of rat osseous plate enzyme and revealed that the alkaline phosphatase obtained has some kinetics and structural behaviors with higher levels of enzymatic activity, facilitating the comprehension of the mineralization process and its function. (c) 2006 Elsevier B.V. All rights reserved.

Three- and Four-Nucleon Bound States in Three Dimensions, Without PW Decomposition

A brief review of a three-dimensional (3D) numerical method to solve few-nucleon bound and scattering states, without the standard partial-wave (PW) decomposition, is presented. The approach is applied to three-and four-nucleon bound states, by considering the solutions of the corresponding Faddeev-Yakubovsky (FY) integral equations in momentum space. Realistic spin-isospin dependent 3D and PW formalism are presented for the alpha particle and the triton binding energies, with numerical results given in both schemes for comparison.

AN IMPROVED ELECTROPHORETIC METHOD FOR THE DETERMINATION OF SERUM MILK PROTEIN VARIANTS IN GYR-HOLSTEIN COWS

Milk serum proteins such as alpha-lactalbumin (ALA) and beta-lactoglobulin (BLG) present biochemical polymorphism which is under the control of codominant autosomal alleles. In the present report, we propose modifications of traditional electrophoretic techniques such as increasing the running gel concentration from 5 to 10% and the addition of 5 M urea to the stacking gel, which permitted the detection of two variants (A and B) at the ALA and BLG loci. About 8 mul of milk serum (6 mg/ml protein) and 10 pl of total fresh milk were applied. Bovine serum albumin (BSA) and immunolactoglobulins (ILG) could also be discriminated. Total fresh milk was as useful as the purified serum milk proteins for the discrimination of ALA and BLG serum milk protein polymorphism by alkaline vertical slab polyacrylamide gel electrophoresis. However, BSA and ILG ran with caseins, which prevented their characterization in this system.

COMPLEX KOHN VARIATIONAL PRINCIPLE FOR 2-NUCLEON BOUND-STATE AND SCATTERING WITH THE TENSOR POTENTIAL

Complex Kohn variational principle is applied to the numerical solution of the fully off-shell Lippmann-Schwinger equation for nucleon-nucleon scattering for various partial waves including the coupled S-3(1), D-3(1), channel. Analytic expressions are obtained for all the integrals in the method for a suitable choice of expansion functions. Calculations with the partial waves S-1(0), P-1(1), D-1(2), and S-3(1)-D-3(1) of the Reid soft core potential show that the method converges faster than other solution schemes not only for the phase shift but also for the off-shell t matrix elements. We also show that it is trivial to modify this variational principle in order to make it suitable for bound-state calculation. The bound-state approach is illustrated for the S-3(1)-D-3(1) channel of the Reid soft-core potential for calculating the deuteron binding, wave function, and the D state asymptotic parameters. (c) 1995 Academic Press, Inc.

Branch and bound algorithm for transmission system expansion planning using a transportation model

A method for optimal transmission network expansion planning is presented. The transmission network is modelled as a transportation network. The problem is solved using hierarchical Benders decomposition in which the problem is decomposed into master and slave subproblems. The master subproblem models the investment decisions and is solved using a branch-and-bound algorithm. The slave subproblem models the network operation and is solved using a specialised linear program. Several alternative implementations of the branch-and-bound algorithm have been rested. Special characteristics of the transmission expansion problem have been taken into consideration in these implementations. The methods have been tested on various test systems available in the literature.

Molecular fingerprinting methods for the discrimination between C-albicans and C-dubliniensis

Opportunistic fungal pathogens are becoming increasingly important causes of both community-acquired and nosocomial infections. The most important fungal pathogens are yeast species belonging to the genus Candida. These species show differences in levels of resistance to antifungal agents and mortality. Consequently, it is important to correctly identify the causative organism to the species level. Identification of Candida dubliniensis in particular remains problematic because of the high degree of phenotypic similarity between this species and Candida albicans. However, as the differences between both are most pronounced at the genetic level, several studies have been conducted in order to provide a specific and rapid identification fingerprinting molecular test. In most candidal infectious, no single DNA fingerprinting technique has evolved as a dominant method, and each method has its advantages, disadvantages and limitations. Moreover, the current challenge of these techniques is to compile standardized patterns in a database for interlaboratory use and future reference. This review provides an overview of most common molecular fingerprinting techniques currently available for discrimination of C. albicans and C. dubliniensis.

Water regulation of actinomycin-D binding to DNA: the interplay among drug affinity, DNA long-range conformation, and hydration

Actiaomycin-D (actD) binds to natural DNA at two different classes of binding sites, weak and strong. The affinity for these sites is highly dependent on DNA se(sequence and solution conditions, and the interaction appears to be purely entropic driven Although the entropic character of this reaction has been attributed to the release of water molecules upon drug to DNA complex formation, the mechanism by which hydration regulates actD binding and discrimination between different classes of binding sites on natural DNA is still unknown. In this work, we investigate the role of hydration on this reaction using the osmotic stress method. We skew that the decrease of solution water activity, due to the addition of sucrose, glycerol ethylene glycol, and betaine, favors drug binding to the strong binding sites on DNA by increasing both the apparent binding affinity Delta G, and the number of DNA base pairs apparently occupied by the bound drug n(bp/actD). These binding parameters vary linearly with the logarithm of the molar fraction of water in solution log(X-w), which indicates the contribution of water binding to the energetic of the reaction. It is demonstrated that the hydration change measured upon binding increases proportionally to the apparent size of the binding site n(bp/uctD). This indicates that n(bp/actD) measured from the Scatchard plod is a measure of the size of the DNA molecule changing conformation due to ligand binding. We also find that the contribution of DNA deformation, gauged by n(bp/act) to the total free energy of binding Delta G, is given by Delta G = Delta G(local) + n(bp/actD) x delta G(DNA), where Delta G(local), = -8020 +/- 51 cal/mol of actD bound and delta G(DNa) = -24.1 +/- 1.7cal/mol of base pair at 25 degrees C. We interpret Delta G(local), as the energetic contribution due to the direct interactions of actD with the actual tetranucleotide binding site, and it n(bp/actB) X delta G(DNA) as that due to change inconformation, induced by binding, of it n(bp/actD) DNA base pairs flanking the local site. This interpretation is supported by the agreement found between the value of delta G(DNA) and the torsional free energy change measured independently. We conclude suggesting an allosteric model for ligand binding to DNA, such that the increase in binding affinity is achieved by increasing the relaxation of the unfavorable free energy of binding storage at the local site through a larger number of DNA base pairs. The new aspect on this model is that the size of the complex is not fixed but determined by solutions conditions, such as water activity, which modulate the energetic barrier to change helix conformation. These results may suggest that long-range allosteric transitions of duplex DNA are involved in the inhibition of RNA synthesis by actD, and more generally, in the regulation of transcription. (C) 2000 John Wiley & Sons, Inc.

CD147 overexpression allows an accurate discrimination of bladder cancer patients' prognosis

Background: Urothelial bladder carcinoma (UBC) is a chemo-sensitive tumour, but the response to treatment is heterogeneous. CD 147 has been associated with chemotherapy resistance. We aimed to define tumours with an aggressive phenotype by the combined analysis of clinicopathological and biological parameters.Methods: 77 patients with T1G3 or muscle-invasive UBC treated by radical cystectomy were studied. Immunohistochemistry was performed to detect CD147, heparanase, CD31 (blood vessels identification) and D2-40 (lymphatic vessels identification) expressions. The immunohistochemical reactions were correlated with the clinicopathological and the outcome parameters. 5-year disease-free survival (DFS) and overall survival (OS) rates were estimated using the Kaplan-Meier method. Multivariate analysis was performed by Cox proportional hazards analysis.Results: The 5-year DFS and OS rates were significantly influenced by the classical clinicopathological parameters, and by the occurrence of lymphovascular invasion. CD 147 and heparanase immunoexpression did not affect patients' outcome. However, patients with pT3/pT4 tumours had a median OS time of 14.7 months (95% CI 7.1-22.3, p = 0.003), which was reduced to 9.2 months (95% CI 1.5-17.0, p = 0.008) if the tumours were CD147 positive. We developed a model of tumour aggressiveness using parameters as stage, grade, lymphovascular invasion and CD147 immunoexpression, which separated a low aggressiveness from a high aggressiveness group, remaining as an independent prognostic factor of DFS (HR 3.746; 95% CI 1.244-11.285; p = 0.019) and OS (HR 3.247; 95% CI 1.015-10.388, p = 0.047).Conclusion: CD 147 overexpression, included in a model of UBC aggressiveness, may help surgeons to identify patients who could benefit from a personalized therapeutic regimen. Additional validation is needed. (C) 2011 Elsevier Ltd. All rights reserved.

Transmission system expansion planning by a branch-and-bound algorithm

A branch and bound (B& B) algorithm using the DC model, to solve the power system transmission expansion planning by incorporating the electrical losses in network modelling problem is presented. This is a mixed integer nonlinear programming (MINLP) problem, and in this approach, the so-called fathoming tests in the B&B algorithm were redefined and a nonlinear programming (NLP) problem is solved in each node of the B& B tree, using an interior-point method. Pseudocosts were used to manage the development of the B&B tree and to decrease its size and the processing time. There is no guarantee of convergence towards global optimisation for the MINLP problem. However, preliminary tests show that the algorithm easily converges towards the best-known solutions or to the optimal solutions for all the tested systems neglecting the electrical losses. When the electrical losses are taken into account, the solution obtained using the Garver system is better than the best one known in the literature.

Branch and bound algorithm for transmission network expansion planning using DC model

This paper presents an algorithm to solve the network transmission system expansion planning problem using the DC model which is a mixed non-linear integer programming problem. The major feature of this work is the use of a Branch-and-Bound (B&B) algorithm to directly solve mixed non-linear integer problems. An efficient interior point method is used to solve the non-linear programming problem at each node of the B&B tree. Tests with several known systems are presented to illustrate the performance of the proposed method. ©2007 IEEE.

Solution of two-body bound state problems with confining potentials

The homogeneous Lippmann-Schwinger integral equation is solved in momentum space by using confining potentials. Since the confining potentials are unbounded at large distances, they lead to a singularity at small momentum. In order to remove the singularity of the kernel of the integral equation, a regularized form of the potentials is used. As an application of the method, the mass spectra of heavy quarkonia, mesons consisting from heavy quark and antiquark (Υ(bb̄), ψ(cc̄)), are calculated for linear and quadratic confining potentials. The results are in good agreement with configuration space and experimental results. © 2010 American Institute of Physics.