Sightseeing Around the Single Cosinor

Misuses of the single cosinor analysis are numerous. We give three rules of thumb, providing guidelines as to whether results obtained from this analysis are dubious. This short note avoids mathematical development so as to be comprehensible to the nonspecialist. However, a few endnotes, give some technical comments.     

Chiral aminonaphthol-catalyzed enantioselective carbonyl addition of diethylzinc to aromatic aldehydes high-throughput screened by CD-HPLC analysis

Optically active aminonaphthols derivatives are obtained by condensation of 2-naphthol, substituted benzaldehyde, and (S)-methylbenzylamine under mild conditions, without side products. Their absolute configurations are determined by X-ray crystallographic analysis. The addition of diethylzinc to aromatic aldehydes is considerably accelerated by the presence of a catalytic amount of crystalline to give, after hydrolysis, the corresponding 1-phenylpropanol in good enantiomeric purity, as determined by CD-HPLC analysis as HTPS (high-throughput screening).     

Acceptor reactions of maltodextrins with Leuconostoc mesenteroides B-512FM dextransucrase

The acceptor products of maltose with Leuconostoc mesenteroides B-512FM dextransucrase are panose (6(2)-alpha-D-glucopyranosyl maltose) and a homologous series of 6(2)-isomaltodextrinosyl maltoses. The structures of the acceptor products of dextransucrase with other maltodextrins, maltotriose to maltooctaose (G3-G8), were determined by using the known specificities of alpha-glucosidase and porcine pancreatic alpha-amylase, and by methylation analysis. It has been found that dextransucrase transfers a D-glucopyranosyl residue to C-6 of either the nonreducing end or the reducing end residues of the maltodextrins, G3-G8, forming an alpha(1----6) linkage. When a D-glucose was transferred to the nonreducing residue, the first product was also an acceptor to give the second product, which served as an acceptor to give the third product, etc. to give a homologous series. When D-glucose was transferred to the reducing residue, the first product did not readily serve as an acceptor to give products or it served only as a very poor acceptor to give a small amount of the next homologue. The effectiveness of maltodextrins as acceptors decreased as the size of the maltodextrin chain increased. Maltotriose was 40% as effective as maltose and maltooctaose was only 6% as effective.     

Limitations of methods of determining effective diffusion coefficients in cell immobilization matrices

Various techniques are available for determining the effective diffusivity D(e) of solutes such as glucose in cell immobilization matrices. Nearly all, if not all, are subject to errors and limitations as regards the ranges of temperature, pressure, and/or concentration over which they give reliable results. It is the purpose of this article to compare three of these methods, designated (a) thin disc, (b) cylinder, and (c) beads types, and to show by means of a sensitivity and error analysis of the equation used in each method that the thin-disc and cylindrical techniques give more accurate results of D(e) than does the bead method.     

The preparation of cervical scrape material for automated cytology using gallocyanin chrome-alum stain.

A method is described for preparing cervical scrape specimens for automated analysis on the Cerviscan prescreening system. In order to reduce the cellular clumping found in cervical scrape material, cells are collected in suspension, syringed to disaggregate the cell clumps, and then pipetted onto a glass to give a monolayer of cells. The cells are then stained with gallocyanin chrome-alum to give the required quantitation of nucleic acid content, using a rapid staining procedure. Experimental results are given which show that specimens prepared by this method are more suitable for automated analysis than the conventional Papanicolaou stained preparation.     

The use of generalized linear models and generalized estimating equations in bioarchaeological studies

The current article explores whether the application of generalized linear models (GLM) and generalized estimating equations (GEE) can be used in place of conventional statistical analyses in the study of ordinal data that code an underlying continuous variable, like entheseal changes. The analysis of artificial data and ordinal data expressing entheseal changes in archaeological North African populations gave the following results. Parametric and nonparametric tests give convergent results particularly for P values <0.1, irrespective of whether the underlying variable is normally distributed or not under the condition that the samples involved in the tests exhibit approximately equal sizes. If this prerequisite is valid and provided that the samples are of equal variances, analysis of covariance may be adopted. GLM are not subject to constraints and give results that converge to those obtained from all nonparametric tests. Therefore, they can be used instead of traditional tests as they give the same amount of information as them, but with the advantage of allowing the study of the simultaneous impact of multiple predictors and their interactions and the modeling of the experimental data. However, GLM should be replaced by GEE for the study of bilateral asymmetry and in general when paired samples are tested, because GEE are appropriate for correlated data. Am J Phys Anthropol 153:473–483, 2014. © 2013 Wiley Periodicals, Inc.     

Discriminant analysis. 2. A new index for antitumor activity

The antitumor activities of 17 nitrogen analogs of 1, 4-benzoquinone, expressed in eight different ways, were subjected to discriminant analysis. Different methods of measuring the effectiveness of antitumor agents give different results. Methods based on dose levels such as the optimum dose or the lethal dose appear to be more useful in classifying compounds as antitumor agents than methods based on the maximum antitumor effect. A new index for antitumor activity involving the maximum antitumor effect, the optimum dose, and the therapeutic index, examined by discriminant analysis with substitutive parameters as discriminatory variables, can give valuable information for the design of new antitumor drugs.     

Evaluating real-life high-throughput screening data

High-throughput screening (HTS) is the result of a concerted effort of chemistry, biology, information technology, and engineering. Many factors beyond the biology of the assay influence the quality and outcome of the screening process, yet data analysis and quality control are often focused on the analysis of a limited set of control wells and the calculated values derived from these wells. Taking into account the large number of variables and the amount of data generated, multiple views of the screening data are necessary to guarantee quality and validity of HTS results. This article does not aim to give an exhaustive outlook on HTS data analysis but tries to illustrate the shortfalls of a reductionist approach focused on control wells and give examples for further analysis.     

A Reproducible Colonial Morphology Formed by Individual Pluripotent Embryonal Carcinoma Cells in Culture and Selection of Variants

Embryonal carcinoma cells are stem cells equivalent to those of the early embryo which can be grown in vitro and which under certain conditions can differentiate into many cell types. Events in this differentiation process are numerous and complex, thus a system for the analysis of clonal differentiation is essential. In this paper I report that individual pluripotent embryonal carcinoma cells can each give rise to colonies, in the absence of a feeder layer but in the presence of β-mercaptoethanol, that show a distinctive and reproducible gross morphology. Embryonal carcinoma cell lines can be derived from the stem cells in these colonies. Furthermore, variant cell lines can be derived from those colonies showing an altered gross morphology. These lines when cloned as above give rise to colonies showing a gross colonial morphology different to that of wild-type. These variant lines have been shown to be embryonal carcinoma cell lines. These findings indicate that genetic and cell lineage analysis of embryonal carcinoma cell differentiation might be possible.     

Regime analysis and scale-down: Tools to investigate the performance of bioreactors

Scale-up and optimization of biotechnological processes on a large scale tend to be more methodically approached than the application of rules of thumb, experience, and trial and error. Methods frequently used in chemical engineering are adopted in biochemical engineering and are employed with great effect. A summary is given of methods and rules of thumb used in scaling up chemical processes. A procedure to scale up and optimize bioreactors is presented. It is based on the so-called scale-down approach. Some elements of this procedure, viz. theoretical regime analysis and small-scale investigations, are extensively demonstrated by examples. It is shown that a regime analysis based on characteristic times can give a quick estimation of the performance of bioreactors. Small-scale experiments based on the result of such analysis or on the results of a dimensional analysis can give valuable information for scale-up or optimization fermentation processes.     

龟类外来种的生物入侵隐患及其防治措施

本文在国家林业局“中国龟鳖市场调查”项目的基础上,查阅了相关文献及报道,考察了国内主要的大型龟鳖养殖场及10多个省份的观赏龟类和水产品龟类市场,针对龟类外来种的养殖现状和发展趋势及对生态系统潜在的危害进行了分析,探讨了龟类外来种成为入侵种的成因,并对龟类生物入侵的防治进行了讨论,旨在引起龟鳖行业对生物入侵的重视及防范.     

Approximating subtree distances between phylogenies.

We give a 5-approximation algorithm to the rooted Subtree-Prune-and-Regraft (rSPR) distance between two phylogenies, which was recently shown to be NP-complete. This paper presents the first approximation result for this important tree distance. The algorithm follows a standard format for tree distances. The novel ideas are in the analysis. In the analysis, the cost of the algorithm uses a "cascading" scheme that accounts for possible wrong moves. This accounting is missing from previous analysis of tree distance approximation algorithms. Further, we show how all algorithms of this type can be implemented in linear time and give experimental results.     

Concepts and therapeutic perspectives of proteomics

The present paper aims at clarifying some important aspects of proteomics, i.e. the large scale analysis of proteins. To this purpose, the main types of proteomic analyses are presented, i.e. those aiming at determining expression levels and those aiming at unravelling protein-protein interactions networks. Their performances and limitations are outlined, as well as their potential applications in biomedicine, to give an reasoned view of the current state of the art.     

A general framework for two-stage analysis of genome-wide association studies and its application to case-control studies

Two-stage analyses of genome-wide association studies have been proposed as a means to improving power for designs including family-based association and gene-environment interaction testing. In these analyses, all markers are first screened via a statistic that may not be robust to an underlying assumption, and the markers thus selected are then analyzed in a second stage with a test that is independent from the first stage and is robust to the assumption in question. We give a general formulation of two-stage designs and show how one can use this formulation both to derive existing methods and to improve upon them, opening up a range of possible further applications. We show how using simple regression models in conjunction with external data such as average trait values can improve the power of genome-wide association studies. We focus on case-control studies and show how it is possible to use allele frequencies derived from an external reference to derive a powerful two-stage analysis. An illustration involving the Wellcome Trust Case-Control Consortium data shows several genome-wide-significant associations, subsequently validated, that were not significant in the standard analysis. We give some analytic properties of the methods and discuss some underlying principles.     

16S rRNA序列分析法在大气微生物检测中的应用

随首微生物核糖体数据库的日益完善,１６Ｓ ｒＲＮＡ序列分析技术已应用于海洋、湖泊和土壤等环境微生物多样性的分析,但尚未见其在大气微生物菌群分析中的应用报道。本研究选择５株大气中采集分离的菌株,通过细胞１６Ｓ ｒＲＮＡ通过引物ＰＣＲ扩增其对应序列,直接对ＰＣＲ产物进行测序,分析鉴定其对应细胞的种属,并将该结果同细胞表型鉴定、全自动微生物分析仪以及相色谱分析结果加以比较。结果表明１６Ｓ ｒＲＮＡ序列分     

Analysis of limit-cycle conditions in intercoupled relay oscillators with reference to gastrointestinal modelling

This paper presents an exact analysis of a mutually coupled relay oscillator based on a method orignated by Tsypkin. Limit-cycle frequencies and phases can be determined exactly using this method, unlike other approximate methods based on describing functions and harmonic balance techniques. A new method of exact determination of limit-cycle stability is also shown to give excellent agreement with simulation studies. Different types of intercoupling are shown to give different stability conditions, and these are discussed in relation to gastrointestinal (GI) smooth muscle modelling. GI tract electrical activity has previously been modelled using bidirectionally coupled nonlinear oscillators, and the results of the present analysis of relay oscillators is compared with other studies using van der Pol dynamics.     

APPLICATION OF FUZZY SETS AND NEURAL NETWORKS IN SENSORY ANALYSIS

This paper describes an initial but fundamental attempt to lay some groundwork for a fuzzy-set-based paradigm for sensory analysis and to demonstrate how fuzzy set and neural network techniques may lead to a natural way for sensory data interpretation. Sensory scales are described as fuzzy sets, sensory attributes as fuzzy variables, and sensory responses as sample membership grades. Multi-judge responses are formulated as a fuzzy membership vector or fuzzy histogram of response, which gives an overall panel response free of the unverifiable assumptions implied in conventional approaches. Neural networks are used to provide an effective tool for modeling and analysis of sensory responses in their naturally fuzzy and complex forms. A maximum method of defuzzification is proposed to give a crisp grade of the majority opinion. Two applications in meat quality evaluation are used to demonstrate the use of the paradigm and procedure. It is hoped that this work will bring up some new ideas and generate interest in research on application of fuzzy sets and neural networks in sensory analysis.     

On rethinking allometry: which regression model to use?

Recently the methods of major axis analysis and reduced major axis analysis have frequently been used in allometric studies as a complement to linear regression analysis. This paper gives a comparison, based on some reasonable assumptions, of these three methods. It is shown how the choice of method should depend on (i) which a priori assumptions that are present and (ii) the purpose of the analysis. Neither major axis analysis nor reduced major axis analysis are appropriate for estimating regression lines, but both methods are valuable when estimating a structural relation. Major axis analysis gives consistent estimates of the coefficients when the two error variances are equal, while reduced major axis analysis gives consistent estimates when the relative sizes of the two error variances are equal.None of the methods have universal application. The three methods give rise to the same conclusions only in data-sets with very high correlation coefficients     

Cytogenetic analysis and occupational health in the Czech Republic

This paper summarizes the experiences of the Czech Hygiene Service since the middle 1970s until the present time, using cytogenetic analysis as a biomarker of exposure. We have included a review of all the available scientific literature in Czech as well as in English, and have described the most important milestones in the history of the use of cytogenetic analysis in the Czech Republic. Details on the levels of occupational exposure and the corresponding observed frequencies of aberrant cells are provided. Furthermore, we discuss the interpretation of the cytogenetic findings in the context of occupational health and give several examples when the results of cytogenetic analysis provided the chief argument used to enforce improved working conditions and to establish safer maximum allowable concentrations.     

Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603.

The study of antibody-antigen interactions should greatly benefit from the development of quantitative models for the evaluation of binding free energies in proteins. The present work addresses this challenge by considering the test case of the binding free energies of phosphorylcholine analogs to the murine myeloma protein McPC603. This includes the evaluation of the differential binding energy as well as the absolute binding energies and their corresponding electrostatic contributions. Four different approaches are examined: the Protein Dipoles Langevin Dipoles (PDLD) method, the semi-microscopic PDLD (PDLD/S) method, a free energy perturbation (FEP) method based on an adiabatic charging procedure and a linear response approximation that accelerates the FEP calculation. The PDLD electrostatic calculations are augmented by estimates of the relevant hydrophobic and steric contributions. The determination of the hydrophobic energy involves an approach which considers the modification of the effective surface area of the solute by local field effects. The steric contributions are analyzed in terms of the corresponding reorganization energies. This treatment, which considers the protein as a harmonic system, views the steric forces as the restoring forces for the electrostatic interactions. The FEP method is found to give unreliable results with regular cut-off radii and starts to give quantitative results only in very expensive treatment with very large cut-off radii. The PDLD and PDLD/S methods are much faster than the FEP approach and give reasonable results for both the relative and absolute binding energies. The speed and simplicity of the PDLD/S method make it an effective strategy for interactive docking studies and indeed such an option is incorporated in the program MOLARIS. A component analysis of the different energy contributions of the FEP treatment and a similar PDLD analysis indicate that electrostatic effects provide the largest contribution to the differential binding energy, while the hydrophobic and steric contributions are much smaller. This finding lends further support to the idea that electrostatic interactions play a major role in determining the antigen specificity of McPC603.