The double travelling salesman problem with multiple stacks – Formulation and heuristic solution approaches

This paper introduces the double travelling salesman problem with multiple stacks and presents four different metaheuristic approaches to its solution. The double TSP with multiple stacks is concerned with determining the shortest route performing pickups and deliveries in two separated networks (one for pickups and one for deliveries) using only one container. Repacking is not allowed, instead each item can be positioned in one of several rows in the container, such that each row can be considered a LIFO (last in, first out) stack, but no mutual constraints exist between the rows. Two different neighbourhood structures are developed for the problem and used with each of three local search metaheuristics. Additionally some simpler removal and reinsertion operators are used in a Large neighbourhood search framework. Finally some computational results are given along with lower bounds on the objective value.     

Steepest-edge simplex algorithms for linear programming

We present several new steepest-edge simplex algorithms for solving linear programming problems, including variants of both the primal and the dual simplex method. These algorithms differ depending upon the space in which the problem is viewed as residing, and include variants in which this space varies dynamically. We present computational results comparing steepest-edge simplex algorithms and approximate versions of them against simplex algorithms that use standard pivoting rules on truly large-scale realworld linear programs with as many as tens of thousands of rows and columns. These results demonstrate unambiguously the superiority of steepest-edge pivot selection criteria to other pivot selection criteria in the simplex method.The research of this author was supported in part by NSF Grants DMS 85-12277, DMS 91-0619 and CDR 84-21402.     

Isolation of ovine β-lactoglobulin genetic variants by chromatofocusing: Heterogeneity of β-lactoglobulin A

Summary Chromatofocusing was applied to the isolation of ovine -Lactoglubulin (-Lg) genetic variants. Ovine -Lg A and B, which are known to differ only by a single amino-acid substitution, were separated. Moreover, one component differing from A variant in isoelectric point and relative molecular mass has been isolated in samples containing ovine -Lg A. Although elution of -Lgs occurred far from their normal isoelectric points, chromatofocusing is a powerful technique effective for both analytical and preparative scale.     

Hydrolates from lavender (Lavandula angustifolia) – their chemical composition as well as aromatic,antimicrobial and antioxidant properties

It was shown that the method for obtaining hydrolates from lavender (Lavandula angustifolia) influences the content of active compounds and the aromatic, antimicrobial and antioxidant properties of the hydrolates. The content of volatile organic compounds ranged from 9.12 to 97.23 mg/100 mL of hydrolate. Lavender hydrolate variants showed low antimicrobial activity (from 0% to 0.05%). The radical scavenging activity of DPPH was from 3.6 ± 0.5% to 3.8 ± 0.6% and oxygen radical absorbance capacity (ORAC_FL) results were from 0 to 266 μM Trolox equivalent, depending on the hydrolate variant.     

CE-based analysis of hemoglobin and its applications in clinical analysis

This review focuses on the developments and trends in CE including CIEF, CZE, MEKC, two-dimensional conjunction of CIEF-capillary gel electrophoresis, and MEKC-CZE on microfluidic devices coupled to different detection approaches, such as UV absorbance, LIF, MS, and chemiluminescence etc. for performing analysis of hemoglobin (Hb), also with an emphasis on its applications in clinical analysis. Analysis of human Hb is of important clinical sense for numerous hemoglobinopathies associated with the congenital defects and abnormal contents of Hb. The diversiform modes render CE a comprehensive primary clinical tool for Hb analysis, which is rapid, sensitive, high-resolution, and not labor-intensive.     

Rare variants analysis by risk-based variable-threshold method

Genome-wide association studies, as a powerful approach for detecting common variants associated with diseases, have revealed many disease-associated loci. However, the traditional association analysis methods do not have enough power for detecting the effects of rare variants with limited sample size. As a solution to this problem, pooling rare variants by their functions into a composite variant provides an alternative way for identifying susceptible genes. In this paper, we propose a new pooling method to test the variant–disease association and to identify the functional rare variants related with the disease. Variants with smaller and larger risk measures defined as the ratio of allele frequencies between cases and controls are pooled and a chi-square test of the resultant pooled table is calculated. We vary the threshold of pooling over all possible values and use the maximal chi-square as test statistic. The maximal chi-square is in fact the global maximum over all possible poolings. Our approach is similar to the existing variable-threshold method, but we threshold on the risk measure instead of allele frequencies of controls. Simulation results show that our method performs better in both association testing and variant selection.     

Separation of somatropin charge variants by multiple‐injection CZE with Polybrene/chondroitin sulfate A double‐coated capillaries

The performance of dynamic double‐coated fused‐silica capillaries with Polybrene and chondroitin sulfate A has been compared with uncoated fused‐silica capillaries for the determination of recombinant human growth factor (somatropin) charge variants. The separations were carried out under the same electrophoretic conditions as described in the European Pharmacopoeia, i.e. at pH 6.0 and 30°C. The coating significantly reduced the interactions between the proteins and the surface of the fused‐silica capillary. The first five separations performed in a new bare fused‐silica capillary were discarded because of very poor separation performance as a result of protein–surface interactions. There was an approximate twofold increase in the interday migration time precision (%RSD ≤ 6.5%) in the double‐coated capillaries. The method was successfully transferred to a multiple CZE mode where two samples were analyzed in a single electrophoretic run. The average purity of somatropin certified reference standard was 98.0% (%RSD ≤ 0.3%) determined by using uncoated and coated capillaries.     

Cytochrome P450 2C9 polymorphism: Effect of amino acid substitutions on protein flexibility in the presence of tamoxifen

Tamoxifen is a prodrug and cytochrome P450 2C9 (CYP2C9) has a significant role in the formation of a therapeutically more potent metabolite (4-hydroxytamoxifen) than tamoxifen. Since CYP2C9 exhibits genetic polymorphism, it may contribute to different phenotypic drug response. Moreover, it may be misleading if the possibility of heterogeneous clinical observations of pharmacogenetic investigations is ignored. Above all, clinical investigation of all the polymorphic variants is beyond the scope of a pharmacogenetic study. Therefore, in order to understand the genotype-phenotype association, it is aimed to study the interatomic interactions of amino acid substitutions in CYP2C9 variants in the presence of tamoxifen. Computational structural biology approach was adopted to study the effect of amino acid substitutions of polymorphic variants of CYP2C9 R144C (*2), I359 L (*3), D360E (*5), R150H (*8), R335W (*11) and L90 P (*13) on the flexibility of the enzyme in the presence of tamoxifen. The mutations were selected based on previously determined associations on genotype and clinical outcome of drugs.Against the above plane, docking of tamoxifen was performed with the crystal structure representing the wild-type form of the enzyme. The docked conformation of tamoxifen was favourable for 4-hydroxylation with the site of metabolism within 5 Å of oxyferrylheme consistent with the drug metabolism pathway of tamoxifen. Further, the effect of amino acid substitutions CYP2C9 variants on the protein flexibility in the presence of tamoxifen in 4-hydroxy orientation was evaluated by molecular dynamics (MD) simulations.Distinct protein flexibility modulations between variants were observed in F/G segment constituting the substrate access/egress channels, helix B' involved with substrate specificity and helix I associated with the holding of substrates. Root Mean Square Fluctuation analysis of the trajectories of variants exhibited fluctuations in F/G segment, B’ and I helix. Dominant motions in the structure were identified by performing Principal Component Analysis on trajectories and the porcupine plot depicted displaced F/G segment in variants.Thus, the interatomic interaction study of CYP2C9 variants in the presence of tamoxifen predicts the plausible effect of the investigated variants on the therapeutic outcome of tamoxifen. It is presumed that the observations of the study would be meaningful to understand tamoxifen pharmacogenetics.     

Oligomerization Profile of Human Transthyretin Variants with Distinct Amyloidogenicity

One of the molecular hallmarks of amyloidoses is ordered protein aggregation involving the initial formation of soluble protein oligomers that eventually grow into insoluble fibrils. The identification and characterization of molecular species critical for amyloid fibril formation and disease development have been the focus of intense analysis in the literature. Here, using photo-induced cross-linking of unmodified proteins (PICUP), we studied the early stages of oligomerization of human transthyretin (TTR), a plasma protein involved in amyloid diseases (ATTR amyloidosis) with multiple clinical manifestations. Upon comparison, the oligomerization processes of wild-type TTR (TTRwt) and several TTR variants (TTRV30M, TTRL55P, and TTRT119M) clearly show distinct oligomerization kinetics for the amyloidogenic variants but a similar oligomerization mechanism. The oligomerization kinetics of the TTR amyloidogenic variants under analysis showed a good correlation with their amyloidogenic potential, with the most amyloidogenic variants aggregating faster (TTRL55P > TTRV30M > TTRwt). Moreover, the early stage oligomerization mechanism for these variants involves stepwise addition of monomeric units to the growing oligomer. A completely different behavior was observed for the nonamyloidogenic TTRT119M variant, which does not form oligomers in the same acidic conditions and even for longer incubation times. Thorough characterization of the initial steps of TTR oligomerization is critical for better understanding the origin of ATTR cytotoxicity and developing novel therapeutic strategies for the treatment of ATTR amyloidosis.