Assignment of the bisulfide bridges in bothropstoxin-I, a Myonecrotic Lys49 PLA2 homolog from bothrops jararacussu snake venom

Bothropstoxin-I (BthTX-I), a Lys49 phospholipase A2 homolog with no apparent catalytic activity, was first isolated from Bothrops jararacussu snake venom and completely sequenced in this laboratory. It is a 121-amino-acid single polypeptide chain, highly myonecrotic, despite its inability to catalyze hydrolysis of egg yolk phospholipids, and has 14 half-cystine residues identified at positions 27, 29, 44, 45, 50, 51, 61, 84, 91, 96, 98, 105, 123, and 131 (numbering according to the conventional alignment including gaps, so that the last residue is Cys 131). In order to access its seven disulfide bridges, two strategies were followed: (1) Sequencing of isolated peptides from (tryptic + SV8) and chymotryptic digests by Edman-dansyl degradation; (2) crystallization of the protein and determination of the crystal structure so that at least two additional disulfide bridges could be identified in the final electron density map. Identification of the disulfide-containing peptides from the enzymatic digests was achieved following the disappearance of the original peptides from the HPLC profile after reduction and carboxymethylation of the digest. Following this procedure, four bridges were initially identified from the tryptic and SV8 digests: Cys50-Cysl31, Cys51-Cys98, Cys61-Cys91, and Cys84-Cys96. From the chymotryptic digest other peptides were isolated either containing some of the above bridges, therefore confirming the results from the tryptic digest, or presenting a new bond between Cys27 and Cys 123. The two remaining bridges were identified as Cys29-Cys45 and Cys44-Cysl05 by determination of the crystal structure, showing that BthTX-I disulfide bonds follow the normal pattern of group II PLA2s. © 2001 Plenum Publishing Corporation.

Problem of assignment cells to switches in a cellular mobile network via beam search method

The problem of assigning cells to switches in a cellular mobile network is an NP-hard optimization problem. So, real size mobile networks could not be solved by using exact methods. The alternative is the use of the heuristic methods, because they allow us to find a good quality solution in a quite satisfactory computational time. This paper proposes a Beam Search method to solve the problem of assignment cell in cellular mobile networks. Some modifications in this algorithm are also presented, which allows its parallel application. Computational results obtained from several tests confirm the effectiveness of this approach to provide good solutions for medium- and large-sized cellular mobile network.

Application of an iterative method and an evolutionary algorithm in fuzzy optimization

This work develops two approaches based on the fuzzy set theory to solve a class of fuzzy mathematical optimization problems with uncertainties in the objective function and in the set of constraints. The first approach is an adaptation of an iterative method that obtains cut levels and later maximizes the membership function of fuzzy decision making using the bound search method. The second one is a metaheuristic approach that adapts a standard genetic algorithm to use fuzzy numbers. Both approaches use a decision criterion called satisfaction level that reaches the best solution in the uncertain environment. Selected examples from the literature are presented to compare and to validate the efficiency of the methods addressed, emphasizing the fuzzy optimization problem in some import-export companies in the south of Spain. © 2012 Brazilian Operations Research Society.

A heuristic algorithm based on multi-assignment procedures for nurse scheduling

This paper tackles a Nurse Scheduling Problem which consists of generating work schedules for a set of nurses while considering their shift preferences and other requirements. The objective is to maximize the satisfaction of nurses' preferences and minimize the violation of soft constraints. This paper presents a new deterministic heuristic algorithm, called MAPA (multi-assignment problem-based algorithm), which is based on successive resolutions of the assignment problem. The algorithm has two phases: a constructive phase and an improvement phase. The constructive phase builds a full schedule by solving successive assignment problems, one for each day in the planning period. The improvement phase uses a couple of procedures that re-solve assignment problems to produce a better schedule. Given the deterministic nature of this algorithm, the same schedule is obtained each time that the algorithm is applied to the same problem instance. The performance of MAPA is benchmarked against published results for almost 250,000 instances from the NSPLib dataset. In most cases, particularly on large instances of the problem, the results produced by MAPA are better when compared to best-known solutions from the literature. The experiments reported here also show that the MAPA algorithm finds more feasible solutions compared with other algorithms in the literature, which suggest that this proposed approach is effective and robust. © 2013 Springer Science+Business Media New York.

A theoretical and experimental study to unequivocal structural assignment of tetrahydroquinoline derivatives

The tetrahydroquinoline derivatives can be easily synthesized through Povarov reaction and have several important biological activities. This work describes a comparative study for the unequivocal assignment of molecular structure of different tetrahydroquinoline derivatives, through a complete analysis of NMR 1D and 2D NMR spectra (1H, 13C, COSY, HSQC, and HMBC), and the correlation this data with theoretical calculations of energy-minimization and chemical shift (δ), employing the theory level of DFT/B3LYP with set of the cc-pVDZ basis. For these derivatives the experimental analyses and the theoretical model adopted were sufficient to obtain a good description of its structures, and these results can be used to assign the structure of various others tetrahydroquinoline derivatives. © 2013 Springer Science+Business Media New York.

Wavelength assignment using a hybrid evolutionary computation to reduce cross-phase modulation

In this paper, we propose a hybrid methodology based on Graph-Coloring and Genetic Algorithm (GA) to solve the Wavelength Assignment (WA) problem in optical networks, impaired by physical layer effects. Our proposal was developed for a static scenario where the physical topology and traffic matrix are known a priori. First, we used fixed shortest-path routing to attend demand requests over the physical topology and the graph-coloring algorithm to minimize the number of necessary wavelengths. Then, we applied the genetic algorithm to solve WA. The GA finds the wavelength activation order on the wavelengths grid with the aim of reducing the Cross-Phase Modulation (XPM) effect; the variance due to the XPM was used as a function of fitness to evaluate the feasibility of the selected WA solution. Its performance is compared with the First-Fit algorithm in two different scenarios, and has shown a reduction in blocking probability up to 37.14% when considered both XPM and residual dispersion effects and up to 71.42% when only considered XPM effect. Moreover, it was possible to reduce by 57.14% the number of wavelengths.

Using Proteomic Strategies for Sequencing and Post-Translational Modifications Assignment of Antigen-5, a Major Allergen from the Venom of the Social Wasp Polybia paulista

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Biological and molecular characterisation of Bidens mosaic virus supports its assignment as a member of a distinct species in the genus Potyvirus

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Synthesis and total 1H- and 13C-NMR assignment of cephem derivatives for use in ADEPT approaches

We report the synthesis and total NMR characterization of 5-thia-1-azabicyclo-[4.2.0]oct-2-ene-2-carboxylic acid-3-[[[(4″- nitrophenoxy)carbonyl]oxy]-methyl]-8-oxo-7-[(2-thienyloxoacetyl)amino] -diphenylmethyl ester-5-dioxide (5), a new cephalosporin derivative. This compound can be used as the carrier of a wide range of drugs containing an amino group. The preparation of the intermediate product, 5-thia-1-azabicyclo[4.2.0] oct-2-ene-2-carboxylic acid-3-[methyl 4-(6-methoxyquinolin-8-ylamino) pentylcarbamate]-8-oxo-7-[(2-thienyloxoacetyl)amino]-diphenylmethyl ester-5-dioxide (6), as well as the synthesis of the antimalarial primaquine prodrug 5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid-3-[methyl 4-(6-methoxyquinolin-8-ylamino)pentylcarbamate]-8-oxo-7-[(2-thienyloxoacetyl) amino]- 5-dioxide (7) are also described, together with their total 1H- and 13C-NMR assignments. © 2008 by MDPI.

Routing and Wavelength Assignment (RWA) with Power Considerations In All- Optical Wavelength-Routed Networks

Routing and wavelength assignment (RWA) is an important problem that arises in wavelength division multiplexed (WDM) optical networks. Previous studies have solved many variations of this problem under the assumption of perfect conditions regarding the power of a signal. In this paper, we investigate this problem while allowing for degradation of routed signals by components such as taps, multiplexers, and fiber links. We assume that optical amplifiers are preplaced. We investigate the problem of routing the maximum number of connections while maintaining proper power levels. The problem is formulated as a mixed-integer nonlinear program and two-phase hybrid solution approaches employing two different heuristics are developed

Assignment of Putative Functions to Membrane "Hypothetical Proteins" from the Trypanosoma cruzi Genome

Protozoan parasites cause thousands of deaths each year in developing countries. The genome projects of these parasites opened a new era in the identification of therapeutic targets. However, the putative function could be predicted for fewer than half of the protein-coding genes. In this work, all Trypanosoma cruzi proteins containing predicted transmembrane spans were processed through an automated computational routine and further analyzed in order to assign the most probable function. The analysis consisted of dissecting the whole predicted protein in different regions. More than 5,000 sequences were processed, and the predicted biological functions were grouped into 19 categories according to the hits obtained after analysis. One focus of interest, due to the scarce information available on trypanosomatids, is the proteins involved in signal-transduction processes. In the present work, we identified 54 proteins belonging to this group, which were individually analyzed. The results show that by means of a simple pipeline it was possible to attribute probable functions to sequences annotated as coding for "hypothetical proteins.'' Also, we successfully identified the majority of candidates participating in the signal-transduction pathways in T. cruzi.

Fuzzy Connectedness Image Segmentation in Graph Cut Formulation: A Linear-Time Algorithm and a Comparative Analysis

A deep theoretical analysis of the graph cut image segmentation framework presented in this paper simultaneously translates into important contributions in several directions. The most important practical contribution of this work is a full theoretical description, and implementation, of a novel powerful segmentation algorithm, GC(max). The output of GC(max) coincides with a version of a segmentation algorithm known as Iterative Relative Fuzzy Connectedness, IRFC. However, GC(max) is considerably faster than the classic IRFC algorithm, which we prove theoretically and show experimentally. Specifically, we prove that, in the worst case scenario, the GC(max) algorithm runs in linear time with respect to the variable M=|C|+|Z|, where |C| is the image scene size and |Z| is the size of the allowable range, Z, of the associated weight/affinity function. For most implementations, Z is identical to the set of allowable image intensity values, and its size can be treated as small with respect to |C|, meaning that O(M)=O(|C|). In such a situation, GC(max) runs in linear time with respect to the image size |C|. We show that the output of GC(max) constitutes a solution of a graph cut energy minimization problem, in which the energy is defined as the a"" (a) norm ayenF (P) ayen(a) of the map F (P) that associates, with every element e from the boundary of an object P, its weight w(e). This formulation brings IRFC algorithms to the realm of the graph cut energy minimizers, with energy functions ayenF (P) ayen (q) for qa[1,a]. Of these, the best known minimization problem is for the energy ayenF (P) ayen(1), which is solved by the classic min-cut/max-flow algorithm, referred to often as the Graph Cut algorithm. We notice that a minimization problem for ayenF (P) ayen (q) , qa[1,a), is identical to that for ayenF (P) ayen(1), when the original weight function w is replaced by w (q) . Thus, any algorithm GC(sum) solving the ayenF (P) ayen(1) minimization problem, solves also one for ayenF (P) ayen (q) with qa[1,a), so just two algorithms, GC(sum) and GC(max), are enough to solve all ayenF (P) ayen (q) -minimization problems. We also show that, for any fixed weight assignment, the solutions of the ayenF (P) ayen (q) -minimization problems converge to a solution of the ayenF (P) ayen(a)-minimization problem (ayenF (P) ayen(a)=lim (q -> a)ayenF (P) ayen (q) is not enough to deduce that). An experimental comparison of the performance of GC(max) and GC(sum) algorithms is included. This concentrates on comparing the actual (as opposed to provable worst scenario) algorithms' running time, as well as the influence of the choice of the seeds on the output.

Simple heuristics for the assembly line worker assignment and balancing problem

We propose simple heuristics for the assembly line worker assignment and balancing problem. This problem typically occurs in assembly lines in sheltered work centers for the disabled. Different from the well-known simple assembly line balancing problem, the task execution times vary according to the assigned worker. We develop a constructive heuristic framework based on task and worker priority rules defining the order in which the tasks and workers should be assigned to the workstations. We present a number of such rules and compare their performance across three possible uses: as a stand-alone method, as an initial solution generator for meta-heuristics, and as a decoder for a hybrid genetic algorithm. Our results show that the heuristics are fast, they obtain good results as a stand-alone method and are efficient when used as a initial solution generator or as a solution decoder within more elaborate approaches.

Detailed H-1 and C-13 NMR structural assignment and relative stereochemistry determination for three new and one known semi-synthetic sesquiterpene lactones

In this work is described a complete H-1 and C-13 NMR analysis for a group of four sesquiterpene lactones, three previously unknown. The unequivocal assignments were achieved by H-1 NMR, C-13{H-1} NMR, gCOSY. gHMQC, gHMBC and NOESY experiments and no ambiguities were left behind. All hydrogen coupling constants were measured, clarifying all hydrogen signals multiplicities. (C) 2011 Elsevier B.V. All rights reserved.