A simple and fast two-locus quality control test to detect false positives due to batch effects in genome-wide association studies

The impact of erroneous genotypes having passed standard quality control (QC) can be severe in genome-wide association studies, genotype imputation, and estimation of heritability and prediction of genetic risk based on single nucleotide polymorphisms (SNP). To detect such genotyping errors, a simple two-locus QC method, based on the difference in test statistic of association between single SNPs and pairs of SNPs, was developed and applied. The proposed approach could detect many problematic SNPs with statistical significance even when standard single SNP QC analyses fail to detect them in real data. Depending on the data set used, the number of erroneous SNPs that were not filtered out by standard single SNP QC but detected by the proposed approach varied from a few hundred to thousands. Using simulated data, it was shown that the proposed method was powerful and performed better than other tested existing methods. The power of the proposed approach to detect erroneous genotypes was approximately 80% for a 3% error rate per SNP. This novel QC approach is easy to implement and computationally efficient, and can lead to a better quality of genotypes for subsequent genotype-phenotype investigations.

Minimizing total weighted tardiness on heterogeneous batch processors with incompatible job families

In this paper, we address a scheduling problem for minimizing total weighted tardiness. The background for the paper is derived from the automobile gear manufacturing process. We consider the bottleneck operation of heat treatment stage of gear manufacturing. Real-life scenarios like unequal release times, incompatible job families, nonidentical job sizes, heterogeneous batch processors, and allowance for job splitting have been considered. We have developed a mathematical model which takes into account dynamic starting conditions. The problem considered in this study is NP-hard in nature, and hence heuristic algorithms have been proposed to address it. For real-life large-size problems, the performance of the proposed heuristic algorithms is evaluated using the method of estimated optimal solution available in literature. Extensive computational analyses reveal that the proposed heuristic algorithms are capable of consistently obtaining near-optimal statistically estimated solutions in very reasonable computational time.

Prediction of Queue Waiting Times for Metascheduling on Parallel Batch Systems

Prediction of queue waiting times of jobs submitted to production parallel batch systems is important to provide overall estimates to users and can also help meta-schedulers make scheduling decisions. In this work, we have developed a framework for predicting ranges of queue waiting times for jobs by employing multi-class classification of similar jobs in history. Our hierarchical prediction strategy first predicts the point wait time of a job using dynamic k-Nearest Neighbor (kNN) method. It then performs a multi-class classification using Support Vector Machines (SVMs) among all the classes of the jobs. The probabilities given by the SVM for the class predicted using k-NN and its neighboring classes are used to provide a set of ranges of predicted wait times with probabilities. We have used these predictions and probabilities in a meta-scheduling strategy that distributes jobs to different queues/sites in a multi-queue/grid environment for minimizing wait times of the jobs. Experiments with different production supercomputer job traces show that our prediction strategies can give correct predictions for about 77-87% of the jobs, and also result in about 12% improved accuracy when compared to the next best existing method. Experiments with our meta-scheduling strategy using different production and synthetic job traces for various system sizes, partitioning schemes and different workloads, show that the meta-scheduling strategy gives much improved performance when compared to existing scheduling policies by reducing the overall average queue waiting times of the jobs by about 47%.

Validation of a method for estimating realized annual fecundity in a multiple spawner, the long-snouted seahorse (Hippocampus guttulatus), using underwater visual census

The long-snouted seahorse (Hippocampus guttulatus) (Cuvier, 1829), was used to validate the pre-dictive accuracy of three progressively realistic models for estimating the realized annual fecundity of asyn-chronous, indeterminate, multiple spawners. Underwater surveys and catch data were used to estimate the duration of the reproductive season, female spawning frequency, male brooding frequency, and batch fecun-dity. The most realistic model, a generalization of the spawning fraction method, produced unbiased estimates of male brooding frequency (mean ±standard deviation [SD]=4.2 ±1.6 broods/year). Mean batch fecundity and realized annual fecundity were 213.9 (±110.9) and 903.6 (±522.4), respectively. However, females prepared significantly more clutches than the number of broods produced by males. Thus, methods that infer spawning frequency from patterns in female egg production may lead to significant overestimates of realized annual fecundity. The spawning fraction method is broadly applicable to many taxa that exhibit parental care and can be applied nondestructively to species for which conservation is a concern.

A method for the preparation of cooked-peeled-frozen prawns

Several consignments of cooked-peeled-frozen prawns exported from India were rejected last year due to high total plate count (TPC) at 30°C. The specified temperature of incubation for TPC in our country is 37°C. Hence the effect of incubation at 30 and 37°C on TPC was studied. It is seen that the count is higher on incubation at 30°C. A method for production of cooked-peeled-frozen prawns conforming to the specification for TPC at 30°C is standardized and is reported. It consists of recooking the cooked-peeled prawns followed by packing and freezing without further contamination. The method minimizes batch to batch or sample to sample variation in TPC.

AN INVESTIGATION OF THE EFFECTS OF SOME PROCESS VARIABLES ON THE MICROENCAPSULATION OF PROPRANOLOL HYDROCHLORIDE BY THE SOLVENT EVAPORATION METHOD

The effects of four process factors: pH, emulsifier (gelatin) concentration, mixing and batch, on the % w/w entrapment of propranolol hydrochloride in ethylcellulose microcapsules prepared by the solvent evaporation process were examined using a factorial design. In this design the minimum % w/w entrapments of propranolol hydrochloride were observed whenever the external aqueous phase contained 1.5% w/v gelatin at pH 6.0 (0.71-0.91% w/w) whereas maximum entrapments occurred whenever the external aqueous phase was composed of 0.5% w/v gelatin at pH 9.0,(8.9-9.1% w/w). The theoretical maximum loading was 50% w/w. Statistical evaluation of the results by analysis of variance showed that emulsifer (gelatin) concentration and pH, but not mixing and batch significantly affected entrapment. An interaction between pH and gelatin concentration was observed in the factorial design which was accredited to the greater effect of gelatin concentration on % w/w entrapment at pH 9.0 than at pH 6.0. Maximum theoretical entrapment was achieved by increasing the pH of the external phase to 12.0. Marked increases in drug entrapment were observed whenever the pH of the external phase exceeded the pK(2) of propranolol hydrochloride. It was concluded that pH, and hence ionisation, was the greatest determinant of entrapment of propranolol hydrochloride into microcapsules prepared by the solvent evaporation process.

Direct electroanalytical determination of fluvastatin in a pharmaceutical dosage form: batch and flow analysis

The reduction of luvastatin (FLV) at a hanging mercury-drop electrode (HMDE) was studied by square-wave adsorptive-stripping voltammetry (SWAdSV). FLV can be accumulated and reduced at the electrode, with a maximum peak current intensity at a potential of approximately 1.26V vs. AgCl=Ag, in an aqueous electrolyte solution of pH 5.25. The method shows linearity between peak current intensity and FLV concentration between 1.0 10 8 and 2.7 10 6 mol L 1. Limits of detection (LOD) and quantification (LOQ) were found to be 9.9 10 9 mol L 1 and 3.3 10 8 mol L 1, respectively. Furthermore, FLV oxidation at a glassy carbon electrode surface was used for its hydrodynamic monitoring by amperometric detection in a flow-injection system. The amperometric signal was linear with FLV concentration over the range 1.0 10 6 to 1.0 10 5 mol L 1, with an LOD of 2.4 10 7 mol L 1 and an LOQ of 8.0 10 7 mol L 1. A sample rate of 50 injections per hour was achieved. Both methods were validated and showed to be precise and accurate, being satisfactorily applied to the determination of FLV in a commercial pharmaceutical.

Application of a novel optimal control algorithm to a benchmark fed-batch fermentation process

A novel algorithm for solving nonlinear discrete time optimal control problems with model-reality differences is presented. The technique uses Dynamic Integrated System Optimisation and Parameter Estimation (DISOPE) which has been designed to achieve the correct optimal solution in spite of deficiencies in the mathematical model employed in the optimisation procedure. A method based on Broyden's ideas is used for approximating some derivative trajectories required. Ways for handling con straints on both manipulated and state variables are described. Further, a method for coping with batch-to- batch dynamic variations in the process, which are common in practice, is introduced. It is shown that the iterative procedure associated with the algorithm naturally suits applications to batch processes. The algorithm is success fully applied to a benchmark problem consisting of the input profile optimisation of a fed-batch fermentation process.

New developments in batch process input profile optimisation

A novel algorithm for solving nonlinear discrete time optimal control problems with model-reality differences is presented. The technique uses dynamic integrated system optimisation and parameter estimation (DISOPE) which achieves the correct optimal solution in spite of deficiencies in the mathematical model employed in the optimisation procedure. A new method for approximating some Jacobian trajectories required by the algorithm is introduced. It is shown that the iterative procedure associated with the algorithm naturally suits applications to batch chemical processes.

Fast batch injection analysis of H(2)O(2) using an array of Pt-modified gold microelectrodes obtained from split electronic chips

A fast and robust analytical method for amperometric determination of hydrogen peroxide (H(2)O(2)) based on batch injection analysis (BIA) on an array of gold microelectrodes modified with platinum is proposed. The gold microelectrode array (n = 14) was obtained from electronic chips developed for surface mounted device technology (SMD), whose size offers advantages to adapt them in batch cells. The effect of the dispensing rate, volume injected, distance between the platinum microelectrodes and the pipette tip, as well as the volume of solution in the cell on the analytical response were evaluated. The method allows the H(2)O(2) amperometric determination in the concentration range from 0.8 mu mol L(-1) to 100 mu mol L(-1). The analytical frequency can attain 300 determinations per hour and the detection limit was estimated in 0.34 mu mol L(-1) (3 sigma). The anodic current peaks obtained after a series of 23 successive injections of 50 mu L of 25 mu mol L(-1) H(2)O(2) showed an RSD < 0.9%. To ensure the good selectivity to detect H(2)O(2), its determination was performed in a differential mode, with selective destruction of the H(2)O(2) with catalase in 10 mmol L(-1) phosphate buffer solution. Practical application of the analytical procedure involved H(2)O(2) determination in rainwater of Sao Paulo City. A comparison of the results obtained by the proposed ampermetric method with another one which combines flow injection analysis (FIA) with spectrophotometric detection showed good agreement. (C) 2011 Elsevier B.V. All rights reserved.

Use of electrochemical impedance spectroscopy for study of CO2 corrosion prevention by batch treatment inhibitor films

Electrochemical impedance spectroscopy (EIS) was used to study and evaluate commercial batch treatment inhibitors which are used for protecting oil wells, gas wells, and pipelines from CO2 corrosion, focusing on the evaluation of inhibitor film persistency. It was found that theformation and deterioration of batch treatment inhibitor films were accompanied by typical impedance spectral changes. During the formation of inhibitor films, electrode impedance showed a rapid increase and the Bode phase angle plots also showed a sudden change. Thus, the formation of inhibitor film was a very fast process. During the deterioration of inhibitor films, electrode impedance showed a gradual decrease and the Bode phase angle plots showed changes which characterised the three stages of the inhibitor film deterioration process. The relationships between EIS and corrosion rate are discussed, including comparisons with weight loss measurements. Based on the experimental findings in the present work, a method is suggested for estimating the persistency of inhibitor films by monitoring the characteristic changes in the Bode phase angle plots and by measuring electrochemical charge transfer resistance at the second and third stages of the inhibitor film deterioration process.

Performance analysis of three advanced controllers for polymerization batch reactor: an experimental investigation

The performances of three advanced non-linear controllers are analyzed for the optimal set point tracking of styrene free radical polymerization (FRP) in batch reactors. The three controllers are the artificial neural network-based MPC (NN-MPC), the artificial fuzzy logic controller (FLC) as well as the generic model controller (GMC). A recently developed hybrid model (Hosen et al., 2011a. Asia-Pac. J. Chem. Eng. 6(2), 274) is utilized in the control study to design and tune the proposed controllers. The optimal minimum temperature profiles are determined using the Hamiltonian maximum principle. Different types of disturbances are introduced and applied to examine the stability of controller performance. The experimental studies revealed that the performance of the NN-MPC is superior to that of FLC and GMC. © 2013 The Institution of Chemical Engineers.

Modeling and simulation of cephalosporin C production in a fed-batch tower-type bioreactor

Immobilized cell utilization in tower-type bioreactor is one of the main alternatives being studied to improve the industrial bioprocess. Other alternatives for the production of beta -lactam antibiotics, such as a cephalosporin C fed-batch p recess in an aerated stirred-tank bioreactor with free cells of Cepha-losporium acremonium or a tower-type bioreactor with immobilized cells of this fungus, have proven to be more efficient than the batch profess. In the fed-batch process, it is possible to minimize the catabolite repression exerted by the rapidly utilization of carbon sources (such as glucose) in the synthesis of antibiotics by utilizing a suitable flow rate of supplementary medium. In this study, several runs for cephalosporin C production, each lasting 200 h, were conducted in a fed-batch tower-type bioreactor using different hydrolyzed sucrose concentrations, For this study's model, modifications were introduced to take into account the influence of supplementary medium flow rate. The balance equations considered the effect of oxygen limitation inside the bioparticles. In the Monod-type rate equations, eel concentrations, substrate concentrations, and dissolved oxygen were included as reactants affecting the bioreaction rate. The set of differential equations was solved by the numerical method, and the values of the parameters were estimated by the classic nonlinear regression method following Marquardt's procedure with a 95% confidence interval. The simulation results showed that the proposed model fit well with the experimental data,and based on the experimental data and the mathematical model an optimal mass flow rate to maximize the bioprocess productivity could be proposed.

Flow-batch analyser for preparation of calibration standard mixtures in simultaneous multicomponent spectrometric analysis

ABSTRACT: The application of multivariate calibration techniques to multicomponent analysis by UV-VIS molecular absorption spectrometry is a powerful tool for simultaneous determination of several chemical species. However, when this methodology is accomplished manually, it is slow and laborious, consumes high amounts of reagents and samples, is susceptible to contaminations and presents a high operational cost. To overcome these drawbacks, a flow-batch analyser is proposed in this work. This analyser was developed for automatic preparation of standard calibration and test (or validation) mixtures. It was applied to the simultaneous determination of Cu²⁺, Mn²⁺ and Zn²⁺ in polyvitaminic and polymineral pharmaceutical formulations, using 4-(2-piridilazo) resorcinol as reagent and a UV-VIS spectrophotometer with a photodiode array detector. The results obtained with the proposed system are in good agreement with those obtained by flame atomic absorption spectrometry, which was employed as reference method. With the proposed analyser, the preparation of calibration and test mixtures can be accomplished about four hours, while the manual procedure requires at least two days. Moreover, it consumes smaller amounts of reagents and samples than the manual procedure. After the preparation of calibration and test mixtures, 60 samples^-1 can be carried out with the proposed flow-batch analyser.

Quantification of terbinafine in pharmaceutical tablets using capillary electrophoresis with contactless conductivity detection and batch injection analysis with amperometric detection

Terbinafine hydrochloride (TerbHCl) is an allylamine derivative with fungicidal action, especially against dermatophytes. Different analytical methods have been reported for quantifying TerbHCl in different samples. These procedures require time-consuming sample preparation or expensive instrumentation. In this paper, electrochemical methods involving capillary electrophoresis with contactless conductivity detection, and amperometry associated with batch injection analysis, are described for the determination of TerbHCl in pharmaceutical products. In the capillary electrophoresis experiments, terbinafine was protonated and analyzed in the cationic form in less than 1 min. A linear range from 1.46 to 36.4 mu g mL(-1) in acetate buffer solution and a detection limit of 0.11 mu g mL(-1) were achieved. In the amperometric studies, terbinafine was oxidized at +0.85 V with high throughput (225 injection h(-1)) and good linear range (10-100 mu mol L-1). It was also possible to determine the antifungal agent using simultaneous conductometric and potentiometric titrations in the presence of 5% ethanol. The electrochemical methods were applied to the quantification of TerbHCl in different tablet samples; the results were comparable with values indicated by the manufacturer and those found using titrimetry according to the Pharmacopoeia. The electrochemical methods are simple, rapid and an appropriate alternative for quantifying this drug in real samples. (C) 2012 Elsevier B.V. All rights reserved.