Using enhanced development tools offered by analytical Quality by Design to support switching of a quality control method

Quality by Design (QbD) principles play an increasingly important role in the pharmaceutical industry. Here, we used an analytical QbD (AQbD) approach to develop a capillary electrophoresis sodium dodecyl sulfate under reducing conditions (rCE-SDS), with the aim of replacing SDS-polyacrylamide gel electrophoresis (SDS-PAGE) as release and stability test method for a commercialized monoclonal antibody product. Method development started with defining analytical method performance requirements as part of an analytical target profile, followed by a systematic risk assessment of method input parameters and their relation to defined method outputs. Based on this, design of experiments studies were performed to identify a method operable design region (MODR). The MODR could be leveraged to improve method robustness. In a bridging study, it was demonstrated that the rCE-SDS method is more sensitive than the legacy SDS-PAGE method, and a conversion factor could be established to compensate for an off-set due to the higher sensitivity, without losing the correlation to the historical data acquired with the former method. Overall, systematic application of analytical Quality by Design principles for designing and developing a new analytical method helped to elucidate the complex dependency of method outputs on its input parameters. The link of the method to product quality attributes and the definition of method performance requirements were found to be most relevant for derisking the analytical method switch, regarding impact on the control strategy.     

Comparative studies of polyethylene glycol-modified liposomes prepared using different PEG-modification methods

To address the issue of excess polyethylene glycol (PEG)-lipid degradation observed when PEG-modified liposomes are prepared using the pH-gradient method, a concept using a novel PEG-modification method, called the post-modification method, was proposed and evaluated. To assess the proof concept, a preservation-stability study and a pharmacokinetic study were performed that compared the conventional PEG-modification method, called the pre-modification method, with the post-modification method. The results show that PEG-lipid degradation could be markedly inhibited in the post-modification method. Furthermore, the post-modification method could be used without any manufacturing process difficulties, especially with high PEG-lipid content. In addition, a higher blood circulation capability was observed in the post-modification method. Through comparative studies, it was found that the post-modification method was advantageous compared to the pre-modification method. In conclusion, the post-modification method has the potential to be a novel PEG-modification method that can achieve a higher preservation stability of PEG-lipid, a greater ease of manufacturing, and a higher blood circulation capability, especially in the manufacturing of pH-gradient liposomal products.     

A new semiparametric estimation method for accelerated hazard model

The accelerated hazard model has been proposed for more than a decade. However, its application is still very limited, partly due to the complexity of the existing semiparametric estimation method. We propose a new semiparametric estimation method based on a kernel-smoothed approximation to the limit of a profile likelihood function of the model. The method leads to smooth estimating equations and is easy to use. The estimates from the method are proved to be consistent and asymptotically normal. Our numerical study shows that the new method is more efficient than the existing method. The proposed method is employed to reanalyze the data from a brain tumor treatment study.     

Analysis of exponential decay curves: a three-step scheme for computing exponents

A study of four techniques is examined to determine which method has the greater overall utility. An iterative least-squares error minimization method provides the greatest accuracy, while a linear algebraic method is accurate only for two-exponential data with small error. Consequently, a three-method sequential identification scheme is devised utilizing a graphical method, a transform method, and an iterative method. This scheme is successfully applied to physiological data containing three and four exponents.     

啮齿动物的巢区面积估算法

巢区(Home range)是动物在其巢附近进行取食、生殖、育幼等日常活动的区域(Burt 1940)。标志流放法是应用最广的调查啮齿动物巢区的方法,尤其是按方格式布笼。但对同一野外调查结果,由于估算方法不同,巢区估算值相差很大,并且至今尚无学者提出一致公认的估算法。1980年5-10月,我们在青海省门源县的高寒草甸生态系统定位站调查根田鼠的巢区,按多种估算法对同一批实际调查结果估计了巢区面积,并对结果进行了分析比较,检查其特点和优缺点,并提出修正平均值法,作为我们今后讨论根田鼠巢区动态的基础。 对方格式布笼的调查结果进行巢区的估算方法,基本上分二大类,图形法和概率性模型法。图形法是按照捕点分布划出巢区,并直接求出巢区面积,如最小面积法,包括或不包括周边地带法,最大距离法和复合散布图法。     

Condition Number Estimation of Preconditioned Matrices

The present paper introduces a condition number estimation method for preconditioned matrices. The newly developed method provides reasonable results, while the conventional method which is based on the Lanczos connection gives meaningless results. The Lanczos connection based method provides the condition numbers of coefficient matrices of systems of linear equations with information obtained through the preconditioned conjugate gradient method. Estimating the condition number of preconditioned matrices is sometimes important when describing the effectiveness of new preconditionerers or selecting adequate preconditioners. Operating a preconditioner on a coefficient matrix is the simplest method of estimation. However, this is not possible for large-scale computing, especially if computation is performed on distributed memory parallel computers. This is because, the preconditioned matrices become dense, even if the original matrices are sparse. Although the Lanczos connection method can be used to calculate the condition number of preconditioned matrices, it is not considered to be applicable to large-scale problems because of its weakness with respect to numerical errors. Therefore, we have developed a robust and parallelizable method based on Hager’s method. The feasibility studies are curried out for the diagonal scaling preconditioner and the SSOR preconditioner with a diagonal matrix, a tri-daigonal matrix and Pei’s matrix. As a result, the Lanczos connection method contains around 10% error in the results even with a simple problem. On the other hand, the new method contains negligible errors. In addition, the newly developed method returns reasonable solutions when the Lanczos connection method fails with Pei’s matrix, and matrices generated with the finite element method.     

Method for rapid screening of pesticide mineralization in soil

A method has been developed for the analysis of (14)CO(2) evolution from the mineralization of (14)C-labelled organic compounds in soil samples. The new method is less space demanding and substantially cuts down laborious manual work compared to the traditional incubation bottle method used. Furthermore, the use of scintillation cocktail is largely reduced with the new method. In the new method, (14)CO(2) is trapped in filter paper held in the lid of a 20 ml glass vial by surface tension. The trapping solution used is Ca(OH)(2), which fixates CO(2) in the filter paper and the analysis of trapped (14)CO(2) is done using the Cyclone trade mark Storage Phosphor system. The lids are placed in a 32 well holder and exposed to a phosphor screen prior to scanning in a Cyclone trade mark scanner. The new filter method has been tested and compared to results obtained using the traditional method. The results show good agreement but due to a smaller capacity for CO(2) with the filter method compared to the traditional method, the interval between sampling has to be shorter using the filter method when the CO(2) development is high. The detection limits for the filter method is higher compared to the traditional method. With the filter method, the level of radioactivity has to exceed 300 dpm before detection is possible, while the same limit for the traditional method is around 30 dpm. On the other hand, the gas trapping faster and the efficiency is higher with the filter method.     

Comparative Study of Responses to Neomycins B and C by Microbiological and Gas-Liquid Chromatographic Assay Methods

The relative responses of neomycins B and C have been determined by a microbiological agar-diffusion method, a turbidimetric method, and by a recently developed gas-liquid-chromatographic (GLC) method capable of separating the neomycin isomers. The ratios of response of neomycin C to neomycin B by the individual methods were as follows: agar-diffusion method, 1:3; turbidimetric method, 1:2.5; and GLC method, 1:1. When neomycin C is assumed to have 35% biological activity of neomycin B, the calculated drug contents of neomycin sulfate powders obtained by the GLC method correlated well with values obtained by the microbiological agar-diffusion assay method.     

Potential of the pseudo-inverse method as a constrained static optimization for musculo-tendon forces prediction

Inverse dynamics combined with a constrained static optimization analysis has often been proposed to solve the muscular redundancy problem. Typically, the optimization problem consists in a cost function to be minimized and some equality and inequality constraints to be fulfilled. Penalty-based and Lagrange multipliers methods are common optimization methods for the equality constraints management. More recently, the pseudo-inverse method has been introduced in the field of biomechanics. The purpose of this paper is to evaluate the ability and the efficiency of this new method to solve the muscular redundancy problem, by comparing respectively the musculo-tendon forces prediction and its cost-effectiveness against common optimization methods. Since algorithm efficiency and equality constraints fulfillment highly belong to the optimization method, a two-phase procedure is proposed in order to identify and compare the complexity of the cost function, the number of iterations needed to find a solution and the computational time of the penalty-based method, the Lagrange multipliers method and pseudo-inverse method. Using a 2D knee musculo-skeletal model in an isometric context, the study of the cost functions isovalue curves shows that the solution space is 2D with the penalty-based method, 3D with the Lagrange multipliers method and 1D with the pseudo-inverse method. The minimal cost function area (defined as the area corresponding to 5% over the minimal cost) obtained for the pseudo-inverse method is very limited and along the solution space line, whereas the minimal cost function area obtained for other methods are larger or more complex. Moreover, when using a 3D lower limb musculo-skeletal model during a gait cycle simulation, the pseudo-inverse method provides the lowest number of iterations while Lagrange multipliers and pseudo-inverse method have almost the same computational time. The pseudo-inverse method, by providing a better suited cost function and an efficient computational framework, seems to be adapted to the muscular redundancy problem resolution in case of linear equality constraints. Moreover, by reducing the solution space, this method could be a unique opportunity to introduce optimization methods for a posteriori articulation of preference in order to provide a palette of solutions rather than a unique solution based on a lot of hypotheses.     

Simple preparation method of PCR fragments for automated DNA sequencing

In an effort to find a simple and inexpensive purification method of polymerase chain reaction (PCR) reaction before cycle sequencing reaction, we compared a commercial system with a precipitation protocol performed in our laboratory. We found that, particularly with small PCR products, our method works with greater success than the method compared. Our precipitation method may be used on a larger PCR fragment before cycle sequencing reaction as well. Furthermore, it has the advantage of being simple as the well-known dilution method; in contrast to the dilution method, the precipitation method removes excess primers as well as possible primer dimers.     

Genotyping and annotation of Affymetrix SNP arrays

In this paper we develop a new method for genotyping Affymetrix single nucleotide polymorphism (SNP) array. The method is based on (i) using multiple arrays at the same time to determine the genotypes and (ii) a model that relates intensities of individual SNPs to each other. The latter point allows us to annotate SNPs that have poor performance, either because of poor experimental conditions or because for one of the alleles the probes do not behave in a dose–response manner. Generally, our method agrees well with a method developed by Affymetrix. When both methods make a call they agree in 99.25% (using standard settings) of the cases, using a sample of 113 Affymetrix 10k SNP arrays. In the majority of cases where the two methods disagree, our method makes a genotype call, whereas the method by Affymetrix makes a no call, i.e. the genotype of the SNP is not determined. By visualization it is indicated that our method is likely to be correct in majority of these cases. In addition, we demonstrate that our method produces more SNPs that are in concordance with Hardy–Weinberg equilibrium than the method by Affymetrix. Finally, we have validated our method on HapMap data and shown that the performance of our method is comparable to other methods.     

Analysis of qPCR data by converting exponentially related Ct values into linearly related X0 values

A common method for calculating results from qPCR experiments is the comparative Ct method, also called the 2(-ΔΔCt) method. However, several assumptions are included in the 2(-ΔΔCt) method and standard statistical analyses are not directly applicable. Here, we describe a different method, the X(0) method, for result calculations and statistical analysis from qPCR experiments. The X(0) method differs from the 2(-ΔΔCt) method by introducing a conversion of the exponentially related Ct values into linearly related X(0) values, which represent the amount of starting material in a qPCR experiment. Results calculated by the X(0) method are illustrated for qPCR experiments with technical and biological replicates, including procedures to calculate standard deviations. Incorporation of primer efficiencies in calculations by the X(0) method is also described. Altogether, the X(0) method constitutes a very simple and accurate alternative to the 2(-ΔΔCt) method for result calculations from qPCR data.     

Validation of a questionnaire method for estimating extent of menstrual blood loss in young adult women.

The objective of this study was to validate two indirect methods for estimating the extent of menstrual blood loss against a reference method to determine which method would be most appropriate for use in a population of young adult women. Thirty-two women aged 18 to 29 years (mean +/- SD; 22.4 +/- 2.8) were recruited by poster in Dunedin (New Zealand). Data are presented for 29 women. A recall method and a record method for estimating extent of menstrual loss were validated against a weighed reference method. Spearman rank correlation coefficients between blood loss assessed by Weighed Menstrual Loss and Menstrual Record was rs = 0.47 (p = 0.012), and between Weighed Menstrual Loss and Menstrual Recall, was rs = 0.61 (p = 0.001). The Record method correctly classified 66% of participants into the same tertile, grossly misclassifying 14%. The Recall method correctly classified 59% of participants, grossly misclassifying 7%. Reference method menstrual loss calculated for surrogate categories demonstrated a significant difference between the second and third tertiles for the Record method, and between the first and third tertiles for the Recall method. The Menstrual Recall method can differentiate between low and high levels of menstrual blood loss in young adult women, is quick to complete and analyse, and has a low participant burden.     

Comparison of genomic DNA extraction techniques from whole blood samples: a time,cost and quality evaluation study

Genomic DNA obtained from patient whole blood samples is a key element for genomic research. Advantages and disadvantages, in terms of time-efficiency, cost-effectiveness and laboratory requirements, of procedures available to isolate nucleic acids need to be considered before choosing any particular method. These characteristics have not been fully evaluated for some laboratory techniques, such as the salting out method for DNA extraction, which has been excluded from comparison in different studies published to date. We compared three different protocols (a traditional salting out method, a modified salting out method and a commercially available kit method) to determine the most cost-effective and time-efficient method to extract DNA. We extracted genomic DNA from whole blood samples obtained from breast cancer patient volunteers and compared the results of the product obtained in terms of quantity (concentration of DNA extracted and DNA obtained per ml of blood used) and quality (260/280 ratio and polymerase chain reaction product amplification) of the obtained yield. On average, all three methods showed no statistically significant differences between the final result, but when we accounted for time and cost derived for each method, they showed very significant differences. The modified salting out method resulted in a seven- and twofold reduction in cost compared to the commercial kit and traditional salting out method, respectively and reduced time from 3 days to 1 hour compared to the traditional salting out method. This highlights a modified salting out method as a suitable choice to be used in laboratories and research centres, particularly when dealing with a large number of samples.     

A Monte Carlo sampling method of amino acid sequences adaptable to given main-chain atoms in the proteins

We have developed a computational method of protein design to detect amino acid sequences that are adaptable to given main-chain coordinates of a protein. In this method, the selection of amino acid types employs a Metropolis Monte Carlo method with a scoring function in conjunction with the approximation of free energies computed from 3D structures. To compute the scoring function, a side-chain prediction using another Metropolis Monte Carlo method was performed to select structurally suitable side-chain conformations from a side-chain library. In total, two layers of Monte Carlo procedures were performed, first to select amino acid types (1st layer Monte Carlo) and then to predict side-chain conformations (2nd layers Monte Carlo). We applied this method to sequence design for the entire sequence on the SH3 domain, Protein G, and BPTI. The predicted sequences were similar to those of the wild-type proteins. We compared the results of the predictions with and without the 2nd layer Monte Carlo method. The results revealed that the two-layer Monte Carlo method produced better sequence similarity to the wild-type proteins than the one-layer method. Finally, we applied this method to neuraminidase of influenza virus. The results were consistent with the sequences identified from the isolated viruses.     

Genotyping of single nucleotide polymorphism using model-based clustering

MOTIVATION: Single nucleotide polymorphisms have been investigated as biological markers and the representative high-throughput genotyping method is a combination of the Invader assay and a statistical clustering method. A typical statistical clustering method is the k-means method, but it often fails because of the lack of flexibility. An alternative fast and reliable method is therefore desirable. RESULTS: This paper proposes a model-based clustering method using a normal mixture model and a well-conceived penalized likelihood. The proposed method can judge unclear genotypings to be re-examined and also work well even when the number of clusters is unknown. Some results are illustrated and then satisfactory genotypings are shown. Even when the conventional maximum likelihood method and the typical k-means clustering method failed, the proposed method succeeded.     

广西金丝桃属植物有效成分金丝桃素的含量测定研究

采用 UV-VIS法和 HPLC法检测了广西产金丝桃属植物及其提取物中有效成分金丝桃素的含量 ,建立了 HPLC测定金丝桃素的新方法 ,该法有良好的重现性及精密度。     

A method for characterizing ultrasonically-derived follicular data in heifers

A method was developed for ultrasonically characterizing follicular waves in heifers without the necessity of maintaining day-to-day identities of individual follicles (nonidentity method). Results were compared to a method in which the identities of individual follicles were maintained from day to day (identity method). Data collected daily during 5 estrous cycles were processed by each method, independently, by different operators. The nonidentity method involved grouping and then profiling follicles in order of decreasing diameters without regard to day-to-day identities. The profiling scheme distinguished between follicles of the left versus the right ovary. The dominant and subordinate follicles were readily distinguishable in the nonidentity profiles. When successive dominant follicles developed in the opposite ovary, the follicles were profiled directly. When two successive dominant follicles developed on the same ovary, size information was obscured for a few days where the profiles for each follicle crossed, but continuity of the profiles on each side of the area of ambiguity was maintained. The nonidentity method seemed equivalent to the identity method in determining characteristics of the dominant follicle (e.g., maximal diameter, growth rate, regression rate). Day of emergence of a wave and day of divergence in diameters between dominant and subordinate follicles were readily determined by inspection of the nonidentity profiles. A greater number of subordinate follicles per wave was detected by the nonidentity method due to the inability to individually identify all detected follicles by the identity method. Regression of follicles from a previous wave into the subordinate follicles of a succeeding wave was apparent by either method. The nonidentity method seemed suitable for most needs, was less tedious, and required less skill than the identity method.     

A simple graphic method for reconstructing phylogenetic trees from molecular data

A simple graphic method is proposed for reconstructing phylogenetic trees from molecular data. This method is similar to the unweighted pair-group method with arithmetic mean, but the process of computation of average distances and reconstruction of new matrices, required in the latter method, is eliminated from this new method, so that one can reconstruct a phylogenetic tree without using a computer, unless the number of operational taxonomic units is very large. Furthermore, this method allows a phylogenetic tree to have multifurcating branches whenever there is ambiguity with bifurcation.     

Path reconstruction as a tool for actin filament speed determination in the in vitro motility assay.

The in vitro motility assay is used to measure speed of actin filaments moving over a glass surface coated with heavy meromyosin. In this paper a new method, the path reconstruction method, is presented to evaluate observed speeds. The method is compared with the commonly used centroid method, in which the centroids of the filaments are followed from frame to frame. Instead, in the path reconstruction method speed is evaluated from determination of perimeters of the filaments in each frame and by reconstruction of the traversed paths of the filaments over a number of frames. Biases in the determination of speed occurring in the centroid method due to curvature of paths and to video noise and Brownian motion are eliminated in the path reconstruction method, allowing measurement over a range of frame rates from 5 to 25 per second. The path reconstruction method leads to a clear separation of motile and nonmotile filaments provided that filaments are analyzed over at least 10 successive frames and allows easier separation of uniform and nonuniform sliding behavior.