Highly sensitive histamine-sensitization test for residual activity of pertussis toxin in acellular pertussis vaccine

Histamine-sensitization test method based on histamine-sensitizing death is widely used for controlling residual activity of pertussis toxin in acellular pertussis vaccines. The test method evaluates the residual activity according to the death of mice injected with a test vaccine after histamine challenge and the test result, therefore, depends on the sensitivity of mice. A highly sensitive test method based on change in rectal temperature of mice has been used in Japan for many years but has limited feasibility in other countries. We examined the possibility of a test method using dermal temperature measured by infrared thermometer to reduce animal suffering instead of rectal temperature. The dermal temperature method was shown to be as sensitive as the rectal temperature method. Furthermore, the dermal as well as rectal temperature methods can evaluate the activity of a test vaccine in relative to a reference preparation so as to allow direct comparison of the test results among different laboratories. The activity by means of the dermal temperature method was also found to be well consistent with that by the rectal temperature method.     

基于热消散探针法的植物水分运输的研究进展

液流是分析树木耗水特性、研究树木水分传输机制的重要途径之一,热消散探针法已广泛用于树干液流变化的监测.热消散探针法是目前研究不同时空尺度上植物蒸腾耗水特性较为灵活、可靠、经济的一种方法.但由于物种特性的差异,可能造成试验过程中出现测量值与实际值相比偏低的状况.此外,相当一部分植物依赖树干储存水进行蒸腾,因此木材含水量的...     

The quantitative assay of the clustering activity of the lymphocytosis-promoting factor (pertussis toxin) of Bordetella pertussis on Chinese hamster ovary (CHO) cells

An experimental design and a statistical method for the estimation of the clustering-response activity of lymphocytosis-promoting factor (LPF) in Chinese hamster ovary cells growing in wells on a microplate were investigated. The scoring method introduced by Ipsen was adopted to express the grade of the clustering response rather than the end-point method generally used. The scoring method was validated by statistical analyses. The grade of response varied with the location of the wells on a microplate, and thus the expression of the clustering activity of a test sample in terms of the end-point may be inadequate in terms of accuracy and reproducibility. It was shown that the allocation of test samples to individual wells according to a Latin square design minimized the effect of the location of wells on the clustering response. Under such experimental conditions, a fairly precise and reproducible method for the quantification of the clustering activity was developed.     

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.     

Retinal Vessel Width Measurement at Branchings Using an Improved Electric Field Theory-Based Graph Approach

The retinal vessel width relationship at vessel branch points in fundus images is an important biomarker of retinal and systemic disease. We propose a fully automatic method to measure the vessel widths at branch points in fundus images. The method is a graph-based method, in which a graph construction method based on electric field theory is applied which specifically deals with complex branching patterns. The vessel centerline image is used as the initial segmentation of the graph. Branching points are detected on the vessel centerline image using a set of detection kernels. Crossing points are distinguished from branch points and excluded. The electric field based graph method is applied to construct the graph. This method is inspired by the non-intersecting force lines in an electric field. At last, the method is further improved to give a consistent vessel width measurement for the whole vessel tree. The algorithm was validated on 100 artery branchings and 100 vein branchings selected from 50 fundus images by comparing with vessel width measurements from two human experts.     

Processing of natural language queries to a relational database

MOTIVATION: A new method is developed to query a relational database in natural language (NL). RESULTS: The method, based on a semantic approach, interprets grammatical and lexical units of a natural language into concepts of subject domain, which are given in a conceptual scheme. The conceptual scheme is mapped formally onto the logical scheme. We applied the method to query the FlyEx database in natural language. FlyEx contains information on the expression of segmentation genes in Drosophila melanogaster. The method allows formulation of queries in various natural languages simultaneously, and is adaptive to changes in the knowledge domain and user's views. It provides optimal transformation of queries from natural language to SQL, as well as visualization of information as a hyperscheme. The method does not require specification of all possible language constructions as well as a standard grammar accuracy in formulation of NL queries.     

Nonhomogeneous strain from sparse marker arrays for analysis of transmural myocardial mechanics

BACKGROUND: Knowledge of normal cardiac kinematics is important when attempting to understand the mechanisms that impair the contractile function of the heart during disease. The complex kinematics of the heart can be studied by inserting radiopaque markers in the cardiac wall and study the pumping heart with biplane cineradiography. In order to study the local strain, the bead array was developed where small radiopaque beads are inserted along three columns transmurally in the left ventricle. METHOD: This paper suggests a straightforward method for strain computation, based on polynomial least-squares fitting and tailored for combined marker and bead array analyses. RESULTS: This polynomial method gives small errors for a realistic bead array on an analytical test case. The method delivers an explicit expression of the Lagrangian strain tensor as a polynomial function of the coordinates of material points in the reference configuration. The method suggested in this paper is validated with analytical strains on a deforming cylinder resembling the heart, compared to a previously suggested finite element method, and applied to in vivo ovine data. The errors in the estimated strain components are shown to remain unchanged on an analytical test case when evaluating the effects of one missing bead. In conclusion, the proposed strain computation method is accurate and robust, with errors smaller or comparable to the current gold standard when applied on an analytical test case.     

On-line dialysis and weak cation-exchange enrichment of dialysate : Automated high-performance liquid chromatography of pholcodine in human plasma and whole blood

An automated method for the determination of pholcodine in plasma and whole blood is described. The technique combines dialysis and trace enrichment prior to high-performance liquid chromatography. Dialysis, trace enrichment on a weak cation-exchange column, separation on a cyano column and fluorescence detection was shown to be an extremely selective and sensitive method. The method has been used successfully in the analysis of real samples after administration of pholcodine. The automated method can be used, after minor modification, to determine other basic drugs in whole blood and plasma.     

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.     

分子系统进化关系分析的一种新方法--贝叶斯法在硬蜱属中的应用

距离矩阵邻接法、最大简约法和最大似然法是重建生物系统关系的3种主要方法。普遍认为最大似然法在原理上优于前二种方法，但其计算复杂费时。由于现行计算机的能力尚达不到其要求而实用性差，特别是在处理大数据集样本(即大于25个分类单元)时，用此方法几乎不可能。新近提出的贝叶斯法(Bayesianmethod)既保留了最大似然法的基本原理，又引进了马尔科夫链的蒙特卡洛方法，并使计算时间大大缩短。本文用贝叶斯法对硬蜱属(Ixodes)19个种的线粒体16S rDNA片段进行了系统进化分析。从总体上看，分析结果与现有的基于形态学的分类体系基本吻合。但与现存的假说相反，莱姆病的主要宿主蓖籽硬蜱复合种组并非单系。通过比较贝叶斯法与其它三种方法的结果，我们认为贝叶斯法是一种系统进化分析的好方法，它既能根据分子进化的现有理论和各种模型用概率重建系统进化关系，又克服了最大似然法计算速度慢、不适用于大数据集样本的缺陷。贝叶斯法根据后验概率直观地表示系统进化关系的分析结果，不需要用自引导法进行检验。可以预料，贝叶斯法将会被广泛地应用到系统进化分析上[动物学报49(3)：380—388，2003]。     

Quantification of airborne microorganisms and investigation of their interactions with non-living particles

A fluorescence method was developed for the direct counting of airborne microorganisms and for the examination of their interactions with other aerosol particles. The method is based on a combination of the aerosol sampling technique using a cascade impactor and the selective dyeing of the trapped microorganisms with ethidium bromide. The method enables both the total microorganism concentrations and their counts in clusters to be evaluated. The new method and the cultivation method, enabling the colony-forming units (CFU) to be determined, were compared. Based on the results obtained by the fluorescence technique, a procedure is suggested for the conversion of CFU data to bacteria and yeast concentrations.     

Limb locomotion--speed distribution analysis as a new method for stance phase detection.

The stance phase is used for the determination of many parameters in motion analysis. In this technical note the authors present a new kinematical method for determination of stance phase. From the high-speed video data, the speed distribution of the horizontal motion of the distal limb is calculated. The speed with the maximum occurrence within the motion cycle defines the stance phase, and this speed is used as threshold for beginning and end of the stance phase. In seven horses the results obtained with the presented method were compared to synchronous stance phase determination using a force plate integrated in a hard track. The mean difference between the results was 10.8 ms, equalling 1.44% of mean stance phase duration. As a test, the presented method was applied to a horse trotting on the treadmill, and to a human walking on concrete. This article describes an easy and safe method for stance phase determination in continuous kinematic data and proves the reliability of the method by comparing it to kinetic stance phase detection. This method may be applied in several species and all gaits, on the treadmill and on firm ground.     

Automatic generation of accurate subject-specific bone finite element models to be used in clinical studies

Most of the finite element models of bones used in orthopaedic biomechanics research are based on generic anatomies. However, in many cases it would be useful to generate from CT data a separate finite element model for each subject of a study group. In a recent study a hexahedral mesh generator based on a grid projection algorithm was found very effective in terms of accuracy and automation. However, so far the use of this method has been documented only on data collected in vitro and only for long bones. The present study was aimed at verifying if this method represents a procedure for the generation of finite element models of human bones from data collected in vivo, robust, accurate, automatic and general enough to be used in clinical studies. Robustness, automation and numerical accuracy of the proposed method were assessed on five femoral CT data sets of patients affected by various pathologies. The generality of the method was verified by processing a femur, an ileum, a phalanx, a proximal femur reconstruction, and the micro-CT of a small sample of spongy bone. The method was found robust enough to cope with the variability of the five femurs, producing meshes with a numerical accuracy and a computational weight comparable to those found in vitro. Even when the method was used to process the other bones the levels of mesh conditioning remained within acceptable limits. Thus, it may be concluded that the method presents a generality sufficient to cope with almost any orthopaedic application.     

A hierarchical method for molecular docking using cloud computing

Discovering small molecules that interact with protein targets will be a key part of future drug discovery efforts. Molecular docking of drug-like molecules is likely to be valuable in this field; however, the great number of such molecules makes the potential size of this task enormous. In this paper, a method to screen small molecular databases using cloud computing is proposed. This method is called the hierarchical method for molecular docking and can be completed in a relatively short period of time. In this method, the optimization of molecular docking is divided into two subproblems based on the different effects on the protein–ligand interaction energy. An adaptive genetic algorithm is developed to solve the optimization problem and a new docking program (FlexGAsDock) based on the hierarchical docking method has been developed. The implementation of docking on a cloud computing platform is then discussed. The docking results show that this method can be conveniently used for the efficient molecular design of drugs.     

Evaluation of a scanner-assisted colorimetric MIC method for susceptibility testing of gram-negative fermentative bacteria

We describe the ScanMIC method, a colorimetric MIC method for susceptibility testing of gram-negative fermentative bacteria. The method is a slight modification of the National Committee for Clinical Laboratory Standards (NCCLS) recommended broth microdilution method that uses a redox indicator 2,3,5-triphenyltetrazolium chloride (TTC) to enhance the estimate of bacterial growth inhibition in a microplate and a flatbed scanner to capture the microplate image. In-house software was developed to transform the microplate image into numerical values based on the amount of bacterial growth and to generate the MICs automatically. The choice of indicator was based on its low toxicity and ease of reading by scanner. We compared the ScanMIC method to the NCCLS recommended broth microdilution method with 197 coliform strains against seven antibacterial agents. The interpretative categorical agreement was obtained in 92.4% of the assays, and the agreement for MIC differences (within +/-1 log(2) dilution) was obtained in 96% for ScanMIC versus broth microdilution and 97% for a two-step incubation colorimetric broth microdilution versus the broth microdilution method. The method was found to be labor-saving, not to require any initial investment, and to show reliable results. Thus, the ScanMIC method could be useful for epidemiological surveys that include susceptibility testing of bacteria.     

A point cluster method for in vivo motion analysis: applied to a study of knee kinematics.

A new method for deriving limb segment motion from markers placed on the skin is described. The method provides a basis for determining the artifact associated with nonrigid body movement of points placed on the skin. The method is based on a cluster of points uniformly distributed on the limb segment. Each point is assigned an arbitrary mass. The center of mass and the inertia tensor of this cluster of points are calculated. The eigenvalues and eigenvectors of the inertia tensor are used to define a coordinate system in the cluster as well as to provide a basis for evaluating non-rigid body movement. The eigenvalues of the inertia tensor remain invariant if the segment is behaving as a rigid body, thereby providing a basis for determining variations for nonrigid body movement. The method was tested in a simulation model where systematic and random errors were introduced into a fixed cluster of points. The simulation demonstrated that the error due to nonrigid body movement could be substantially reduced. The method was also evaluated in a group of ten normal subjects during walking. The results for knee rotation and translation obtained from the point cluster method compared favorably to results previously obtained from normal subjects with intra-cortical pins placed into the femur and tibia. The resulting methodology described in this paper provides a unique approach to the measurement of in vivo motion using skin-based marker systems.     

QTL mapping in outbred half-sib families using Bayesian model selection

In this article, we propose a model selection method, the Bayesian composite model space approach, to map quantitative trait loci (QTL) in a half-sib population for continuous and binary traits. In our method, the identity-by-descent-based variance component model is used. To demonstrate the performance of this model, the method was applied to map QTL underlying production traits on BTA6 in a Chinese half-sib dairy cattle population. A total of four QTLs were detected, whereas only one QTL was identified using the traditional least square (LS) method. We also conducted two simulation experiments to validate the efficiency of our method. The results suggest that the proposed method based on a multiple-QTL model is efficient in mapping multiple QTL for an outbred half-sib population and is more powerful than the LS method based on a single-QTL model.     

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 method for estimating the effective number of loci affecting a quantitative character

A likelihood method is introduced that jointly estimates the number of loci and the additive effect of alleles that account for the genetic variance of a normally distributed quantitative character in a randomly mating population. The method assumes that measurements of the character are available from one or both parents and an arbitrary number of full siblings. The method uses the fact, first recognized by Karl Pearson in 1904, that the variance of a character among offspring depends on both the parental phenotypes and on the number of loci. Simulations show that the method performs well provided that data from a sufficient number of families (on the order of thousands) are available. This method assumes that the loci are in Hardy–Weinberg and linkage equilibrium but does not assume anything about the linkage relationships. It performs equally well if all loci are on the same non-recombining chromosome provided they are in linkage equilibrium. The method can be adapted to take account of loci already identified as being associated with the character of interest. In that case, the method estimates the number of loci not already known to affect the character. The method applied to measurements of crown–rump length in 281 family trios in a captive colony of African green monkeys (Chlorocebus aethiopus sabaeus) estimates the number of loci to be 112 and the additive effect to be 0.26 cm. A parametric bootstrap analysis shows that a rough confidence interval has a lower bound of 14 loci.