Gene optimization leads to robust expression of human respiratory syncytial virus nucleoprotein and phosphoprotein in human cells and induction of humoral immunity in mice

Human respiratory syncytial virus (HRSV) is the major pathogen leading to respiratory disease in infants and neonates worldwide. An effective vaccine has not yet been developed against this virus, despite considerable efforts in basic and clinical research. HRSV replication is independent of the nuclear RNA processing constraints, since the virus genes are adapted to the cytoplasmic transcription, a process performed by the viral RNA-dependent RNA polymerase. This study shows that meaningful nuclear RNA polymerase II dependent expression of the HRSV nucleoprotein (N) and phosphoprotein (F) proteins can only be achieved with the optimization of their genes, and that the intracellular localization of N and P proteins changes when they are expressed out of the virus replication context. Immunization tests performed in mice resulted in the induction of humoral immunity using the optimized genes. This result was not observed for the non-optimized genes. In conclusion, optimization is a valuable tool for improving expression of HRSV genes in DNA vaccines. (c) 2009 Elsevier B.V. All rights reserved.

Exact Search Directions for Optimization of Linear and Nonlinear Models Based on Generalized Orthonormal Functions

A novel technique for selecting the poles of orthonormal basis functions (OBF) in Volterra models of any order is presented. It is well-known that the usual large number of parameters required to describe the Volterra kernels can be significantly reduced by representing each kernel using an appropriate basis of orthonormal functions. Such a representation results in the so-called OBF Volterra model, which has a Wiener structure consisting of a linear dynamic generated by the orthonormal basis followed by a nonlinear static mapping given by the Volterra polynomial series. Aiming at optimizing the poles that fully parameterize the orthonormal bases, the exact gradients of the outputs of the orthonormal filters with respect to their poles are computed analytically by using a back-propagation-through-time technique. The expressions relative to the Kautz basis and to generalized orthonormal bases of functions (GOBF) are addressed; the ones related to the Laguerre basis follow straightforwardly as a particular case. The main innovation here is that the dynamic nature of the OBF filters is fully considered in the gradient computations. These gradients provide exact search directions for optimizing the poles of a given orthonormal basis. Such search directions can, in turn, be used as part of an optimization procedure to locate the minimum of a cost-function that takes into account the error of estimation of the system output. The Levenberg-Marquardt algorithm is adopted here as the optimization procedure. Unlike previous related work, the proposed approach relies solely on input-output data measured from the system to be modeled, i.e., no information about the Volterra kernels is required. Examples are presented to illustrate the application of this approach to the modeling of dynamic systems, including a real magnetic levitation system with nonlinear oscillatory behavior.

Multivariant optimization, validation, and application of capillary electrophoresis for simultaneous determination of polyphenols and phenolic acids in Brazilian wines

A method for the simultaneous determination of the stilbene resveratrol, four phenolic acids (syringic, coumaric, caffeic, and gallic acids), and five flavonoids (catechin, rutin, kaempferol, myricetin, and quercetin) in wine by CE was developed and validated. The CE electrolyte composition and instrumental conditions were optimized using 2(7-3) factorial design and response surface analysis, showing sodium tetraborate, MeOH, and their interaction as the most influential variables. The optimal electrophoretic conditions, minimizing the chromatographic resolution statistic values, consisted of 17 mmol/L sodium tetraborate with 20% methanol as electrolyte, constant voltage of 25 kV, hydrodynamic injection at 50 mbar for 3 s, and temperature of 25 degrees C. The R(2) values for linearity varied from 0.994 to 0.999; LOD and LOQ were 0.1 to 0.3 mg/L and 0.4 to 0.8 mg/L, respectively. The RSDs for migration time and peak area obtained from ten consecutive injections were less than 2% and recoveries varied from 97 to 102%. The method was applied to 23 samples of inexpensive Brazilian wines, showing wide compositional variation.

Sequential injection analysis (SIA) and response surface methodology: A versatile small volume approach for optimization of photo-Fenton processes

Optimization of photo-Fenton degradation of copper phthalocyanine blue was achieved by response surface methodology (RSM) constructed with the aid of a sequential injection analysis (SIA) system coupled to a homemade photo-reactor. Highest degradation percentage was obtained at the following conditions [H(2)O(2)]/[phthalocyanine] = 7, [H(2)O(2)]/[FeSO(4)] = 10, pH = 2.5, and stopped flow time in the photo reactor = 30 s. The SIA system was designed to prepare a monosegment containing the reagents and sample, to pump it toward the photo-reactor for the specified time and send the products to a flow-through spectrophotometer for monitoring the color reduction of the dye. Changes in parameters such as reagent molar ratios. residence time and pH were made by modifications in the software commanding the SI system, without the need for physical reconfiguration of reagents around the selection valve. The proposed procedure and system fed the statistical program with degradation data for fast construction of response surface plots. After optimization, 97% of the dye was degraded. (C) 2009 Elsevier B.V. All rights reserved.

Applying sequential injection analysis (SIA) and response surface methodology for optimization of Fenton-based processes

This work presents the use of sequential injection analysis (SIA) and the response surface methodology as a tool for optimization of Fenton-based processes. Alizarin red S dye (C.I. 58005) was used as a model compound for the anthraquinones family. whose pigments have a large use in coatings industry. The following factors were considered: [H(2)O(2)]:[Alizarin] and [H(2)O(2)]:[FeSO(4)] ratios and pH. The SIA system was designed to add reagents to the reactor and to perform on-line sampling of the reaction medium, sending the samples to a flow-through spectrophotometer for monitoring the color reduction of the dye. The proposed system fed the statistical program with degradation data for fast construction of response surface plots. After optimization, 99.7% of the dye was degraded and the TOC content was reduced to 35% of the original value. Low reagents consumption and high sampling throughput were the remarkable features of the SIA system. (C) 2008 Published by Elsevier B.V.

Determination of sorbate and benzoate in beverage samples by capillary electrophoresis - Optimization of the method with inspection of ionic mobilities

The aim of this study was to develop a fast capillary electrophoresis method for the determination of benzoate and sorbate ions in commercial beverages. In the method development the pH and constituents of the background electrolyte were selected using the effective mobility versus pH curves. As the high resolution obtained experimentally for sorbate and benzoate in the studies presented in the literature is not in agreement with that expected from the ionic mobility values published, a procedure to determine these values was carried out. The salicylate ion was used as the internal standard. The background electrolyte was composed of 25 mmol L(-1) tris(hydroxymethyl)aminomethane and 12.5 mmol L(-1) 2-hydroxyisobutyric acid, atpH 8.1.Separation was conducted in a fused-silica capillary(32 cm total length and 8.5 cm effective length, 50 mu m I.D.), with short-end injection configuration and direct UV detection at 200 nm for benzoate and salicylate and 254 nm for sorbate ions. The run time was only 28 s. A few figures of merit of the proposed method include: good linearity (R(2) > 0.999), limit of detection of 0.9 and 0.3 mg L(-1) for benzoate and sorbate, respectively, inter-day precision better than 2.7% (n =9) and recovery in the range 97.9-105%. Beverage samples were prepared by simple dilution with deionized water (1:11, v/v). Concentrations in the range of 197-401 mg L(-1) for benzoate and 28-144 mg L(-1) for sorbate were found in soft drinks and tea. (c) 2008 Elsevier B.V. All rights reserved.

Load balancing solution and evaluation of F5 content switch equipment

The Thesis focused on hardware based Load balancing solution of web traffic through a load balancer F5 content switch. In this project, the implemented scenario for distributing HTTPtraffic load is based on different CPU usages (processing speed) of multiple member servers.Two widely used load balancing algorithms Round Robin (RR) and Ratio model (weighted Round Robin) are implemented through F5 load balancer. For evaluating the performance of F5 content switch, some experimental tests has been taken on implemented scenarios using RR and Ratio model load balancing algorithms. The performance is examined in terms of throughput (bits/sec) and Response time of member servers in a load balancing pool. From these experiments we have observed that Ratio Model load balancing algorithm is most suitable in the environment of load balancing servers with different CPU usages as it allows assigning the weight according to CPU usage both in static and dynamic load balancing of servers.

Production and Delivery (Optimization of production system and reliability)

This thesis is done to solve two issues for Sayid Paper Mill Ltd Pakistan. Section one deals with a practical problem arise in SPM that is cutting a given set of raw paper rolls of known length and width, and a set of product paper rolls of known length (equal to the length of raw paper rolls) and width, practical cutting constraints on a single cutting machine, according to demand orders for all customers. To solve this problem requires to determine an optimal cutting schedule to maximize the overall cutting process profitability while satisfying all demands and cutting constraints. The aim of this part of thesis is to develop a mathematical model which solves this problem.Second section deals with a problem of delivering final product from warehouse to different destinations by finding shortest paths. It is an operational routing problem to decide the daily routes for sending trucks to different destination to deliver their final product. This industrial problem is difficult and includes aspect such as delivery to a single destination and multiple destinations with limited resources. The aim of this part of thesis is to develop a process which helps finding shortest path.

INVENTORY CONTROL SYSTEM : Optimization of production system and reliability

The main idea of this research to solve the problem of inventory management for the paper industry SPM PVT limited. The aim of this research was to find a methodology by which the inventory of raw material could be kept at minimum level by means of buffer stock level.The main objective then lies in finding the minimum level of buffer stock according to daily consumption of raw material, finding the Economic Order Quantity (EOQ) reorders point and how much order will be placed in a year to control the shortage of raw material.In this project, we discuss continuous review model (Deterministic EOQ models) that includes the probabilistic demand directly in the formulation. According to the formula, we see the reorder point and the order up to model. The problem was tackled mathematically as well as simulation modeling was used where mathematically tractable solution was not possible.The simulation modeling was done by Awesim software for developing the simulation network. This simulation network has the ability to predict the buffer stock level based on variable consumption of raw material and lead-time. The data collection for this simulation network is taken from the industrial engineering personnel and the departmental studies of the concerned factory. At the end, we find the optimum level of order quantity, reorder point and order days.

Fine mapping and replication of QTL in outbred chicken advanced intercross lines

Background: Linkage mapping is used to identify genomic regions affecting the expression of complex traits. However, when experimental crosses such as F2 populations or backcrosses are used to map regions containing a Quantitative Trait Locus (QTL), the size of the regions identified remains quite large, i.e. 10 or more Mb. Thus, other experimental strategies are needed to refine the QTL locations. Advanced Intercross Lines (AIL) are produced by repeated intercrossing of F2 animals and successive generations, which decrease linkage disequilibrium in a controlled manner. Although this approach is seen as promising, both to replicate QTL analyses and fine-map QTL, only a few AIL datasets, all originating from inbred founders, have been reported in the literature. Methods: We have produced a nine-generation AIL pedigree (n = 1529) from two outbred chicken lines divergently selected for body weight at eight weeks of age. All animals were weighed at eight weeks of age and genotyped for SNP located in nine genomic regions where significant or suggestive QTL had previously been detected in the F2 population. In parallel, we have developed a novel strategy to analyse the data that uses both genotype and pedigree information of all AIL individuals to replicate the detection of and fine-map QTL affecting juvenile body weight. Results: Five of the nine QTL detected with the original F2 population were confirmed and fine-mapped with the AIL, while for the remaining four, only suggestive evidence of their existence was obtained. All original QTL were confirmed as a single locus, except for one, which split into two linked QTL. Conclusions: Our results indicate that many of the QTL, which are genome-wide significant or suggestive in the analyses of large intercross populations, are true effects that can be replicated and fine-mapped using AIL. Key factors for success are the use of large populations and powerful statistical tools. Moreover, we believe that the statistical methods we have developed to efficiently study outbred AIL populations will increase the number of organisms for which in-depth complex traits can be analyzed.

Heuristic optimization of the p-median problem and population re-distribution

This thesis contributes to the heuristic optimization of the p-median problem and Swedish population redistribution.   The p-median model is the most representative model in the location analysis. When facilities are located to a population geographically distributed in Q demand points, the p-median model systematically considers all the demand points such that each demand point will have an effect on the decision of the location. However, a series of questions arise. How do we measure the distances? Does the number of facilities to be located have a strong impact on the result? What scale of the network is suitable? How good is our solution? We have scrutinized a lot of issues like those. The reason why we are interested in those questions is that there are a lot of uncertainties in the solutions. We cannot guarantee our solution is good enough for making decisions. The technique of heuristic optimization is formulated in the thesis.   Swedish population redistribution is examined by a spatio-temporal covariance model. A descriptive analysis is not always enough to describe the moving effects from the neighbouring population. A correlation or a covariance analysis is more explicit to show the tendencies. Similarly, the optimization technique of the parameter estimation is required and is executed in the frame of statistical modeling. 

Optimization of cable cycles : a trade-off between reliability and cost

This paper elaborates the routing of cable cycle through available routes in a building in order to link a set of devices, in a most reasonable way. Despite of the similarities to other NP-hard routing problems, the only goal is not only to minimize the cost (length of the cycle) but also to increase the reliability of the path (in case of a cable cut) which is assessed by a risk factor. Since there is often a trade-off between the risk and length factors, a criterion for ranking candidates and deciding the most reasonable solution is defined. A set of techniques is proposed to perform an efficient and exact search among candidates. A novel graph is introduced to reduce the search-space, and navigate the search toward feasible and desirable solutions. Moreover, admissible heuristic length estimation helps to early detection of partial cycles which lead to unreasonable solutions. The results show that the method provides solutions which are both technically and financially reasonable. Furthermore, it is proved that the proposed techniques are very efficient in reducing the computational time of the search to a reasonable amount.