Random frog: An efficient reversible jump Markov Chain Monte Carlo-like approach for variable selection with applications to gene selection and disease classification

The identification of disease-relevant genes represents a challenge in microarray-based disease diagnosis where the sample size is often limited. Among established methods, reversible jump Markov Chain Monte Carlo (RJMCMC) methods have proven to be quite promising for variable selection. However, the design and application of an RJMCMC algorithm requires, for example, special criteria for prior distributions. Also, the simulation from joint posterior distributions of models is computationally extensive, and may even be mathematically intractable. These disadvantages may limit the applications of RJMCMC algorithms. Therefore, the development of algorithms that possess the advantages of RJMCMC methods and are also efficient and easy to follow for selecting disease-associated genes is required. Here we report a RJMCMC-like method, called random frog that possesses the advantages of RJMCMC methods and is much easier to implement. Using the colon and the estrogen gene expression datasets, we show that random frog is effective in identifying discriminating genes. The top 2 ranked genes for colon and estrogen are Z50753, U00968, and Y10871_at, Z22536_at, respectively. (The source codes with GNU General Public License Version 2.0 are freely available to non-commercial users at: http://code.google.com/p/randomfrog/.)     

An Expeditious Method Combining Multi-Components Determination and Fingerprinting Based on Ultra Performance Liquid Chromatography-Photo Diode Array-Tandem Mass Spectrometry and Chemometrics: Application for Authentication and Quality Evaluation of Cornus Officinalis Sieb. et Zucc

Selective and efficient analytical methods for authentication and quality evaluation of herbal medicines are significant and necessary. An expeditious method combining multi-components determination and fingerprinting based on ultra-performance liquid chromatography-photo diode array-tandem mass spectrometry (UPLC-PDA -MS/MS) and chemometrics for authentication and quality evaluation of Cornus Officinalis Sieb. et Zucc was developed. Tandem mass spectrometer operating in multiple reaction monitoring (MRM) was used for determination of three characteristic constituents (morroniside, sweroside, and loganin) in C. Officinalis. Meanwhile, UPLC fingerprint of C. Officinalis was established and the data set was submitted for classification to a suite of chemometrics method. Combing main biologically active components content level and chemometrics analysis, the effects of cultivation area, harvesting, and storage time on the quality of C. Officinalis were investigated. The study reveals that multi-components determination coupled with fingerprinting could be applied for authentication and quality evaluation of C. Officinalis which is accurate, efficient, and reliable.     

Effect of conformational rigidity on the glass transition and initial decomposition temperatures of polyimides

The dependence of the glass transition and initial decomposition temperatures of polyperyleneimide and polynaphthylimide on the conformational rigidity was studied by the Monte Carlo, Kuhn segment, and quantum chemical AM1 methods. The corresponding linear plots can be used for estimation of the glass transition and initial decomposition temperatures when experimental determination is difficult.     

Re-Evaluation of the Activity Coefficients of Aqueous Hydrochloric Acid Solutions up to a Molality of 2.0 Using Two-Parameter Hückel and Pitzer Equations. Part I. Results at 25°C

Simple two-parameter Hückel and Pitzer equations were used for the calculation of the activity coefficients of aqueous hydrochloric acid at 25°C up to a molality of 2.0 mol-kg^–1. The data obtained by Harned and Ehlers^(12,13) from galvanic cells without liquid junction were used in the analysis and the parameters obtained were compared to those obtained from all reliable data presented in the literature for HCl at this temperature. A good agreement between the parameters was always observed. The activity coefficients obtained by the new equations were compared to those suggested by Robinson and Stokes,⁽⁸⁾ Hamer and Wu,⁽¹⁾ and Pitzer and Mayorga,⁽⁹⁾ and good agreement was also found. The data from the most important literature data sets for HCl were also predicted using the new activity coefficient equations, and the magnitude of the resulting errors was close to the precision of the measurements, the errors forming an almost random pattern for all data sets.     

Re-Evaluation of the Activity Coefficients of Aqueous Hydrochloric Acid Solutions up to a Molality of 2.0 Using Two-Parameter Hückel and Pitzer Equations. Part II. Results from 0 to 95°C

Simple two-parameter Hückel and Pitzer equations were used for the calculation of the activity coefficients of aqueous hydrochloric acid at temperatures 0–60°C up to a molality of 2.0 mol-kg^–1. The data obtained by Harned and Ehlers^(2,3) on galvanic cells without a liquid junction were used in the parameter estimations of these equations. These data consist of sets of measurements at the temperature intervals of 5°C. It was observed that all estimated parameters follow very simple equations with respect to temperature. They are either constant or depend linearly on the temperature. The values for the activity coefficient parameters calculated by these simple equations are recommended here. The recommended parameter values were tested by predicting the data of Gupta, Hills, and Ives,⁽⁵⁾ consisting of cell measurements from 5 to 45°C and molalities up to 1.0 mol-kg^–1, and the data of Bates and Bower,⁽⁴⁾ which extend to 95°C but measurements were only made on molalities less than about 0.1 mol-kg^–1. The activity coefficients obtained by the new equations were also compared to those calculated by the Pitzer equations with the parameter values determined by Saluja, Pitzer, and Phutela⁽⁶⁾ from calorimetric data. The agreement observed was excellent up to a molality of 1.5 mol-kg^–1 at temperatures from 0 to 60°C.     

The quality of leadership (QL): the EFQM leadership criterion in relation to the 360° feedback evaluation method

The European Foundation for Quality Management (EFQM) integral quality management model covers nine issues: five so-called enabler criteria and four so-called result-oriented criteria. The first enabler criterion concerns leadership and covers all kind of strategic management aspects. However, directly or indirectly, the leadership of the board of directors or its individual members is characterized and scored. An even more explicate technique, originated in a totally different way, is the 360° feedback evaluation method. In this paper both methods are compared and practiced on various individuals. A checklist was developed to facilitate scoring in the EFQM leadership submodel. Both methods, although from a different origin, could be linked easily, covered very similar aspects and gave results that were in excellent agreement with each other. The scoring showed almost identical results, supporting in large the use of the integral EFQM model. Received: 25 May 2002 Accepted: 17 July 2002 Presented at the European Conference on Quality in the Spotlight in Medical Laboratories, 7–9 October 2001, Antwerp, Belgium Correspondence to H. M. J. Goldschmidt     

超支化聚合反应的多尺度模拟

超支化聚合物具有与树枝状大分子相似的物理和化学性质,其具有合成简单、分子量分布宽等突出特点,超支化聚合物分子的结构形成取决于聚合反应过程,本文介绍了超支化聚合反应模拟研究的最新进展.首先介绍了八位置键涨落粗粒化格子模型在超支化聚合反应模拟中的应用,该方法考虑了聚合物分子空间位阻效应、分子内成环和反应点活性等影响因素,从而可以模拟不同类型的超支化聚合反应;为了定量描述单体和聚合物分子结构,研究者进一步发展了杂化多尺度超支化聚合反应模拟方法,该方法通过玻尔兹曼反演迭代方法获取单体和聚合物特异性粗粒化力场,然后通过粗粒化分子动力学方法结合反应性Monte Carlo方法对特异性超支化聚合反应进行定量模拟.多尺度聚合反应模拟不仅可以精确计算超支化聚合物分子量、多分散性指数和支化度等一般性聚合物参数,还可以获取分子成环率、超支化大分子构象等重要分子结构信息,在超支化聚合反应基础研究与预测方面具有重要应用价值.     

A sustainable method of mitigating acid corrosion of mild steel using jackfruit pectin (JP) as green inhibitor: Theoretical and electrochemical studies

This study is attempted to develop a green corrosion inhibitor from a waste material of Jack fruit (Artocarpus heterophyllus). This method is therefore quite valuable to health, environment, and economic point of view. Pectin is isolated from the jackfruit peel waste using 0.05 ?N oxalic acid and used as an inhibitor for mild steel corrosion in acidic environment as it is highly water soluble. 250–1000 ?ppm of pectin was used in this study at a temperature range of 303–323 ?K. The protection efficiency of jack fruit pectin (JP) in 0.5 ?M HCl was evaluated by conventional weight loss and electrochemical techniques. The potentiodynamic polarization results revealed that JP could effectively reduce the corrosion of mild steel in acidic medium at 1000 ?ppm concentration with an inhibition efficiency of 89.75% and corrosion rate of 2.392 mpy. The mixed type behavior of the inhibitor is identified from Tafel polarization studies. Electrochemical impedance spectroscopy (EIS) measurements suggest that the corrosion inhibition process is kinetically controlled. adsorption and kinetic behavior of the inhibitor also have been studied. Surface manifestations were followed using FESEM and AFM techniques. DFT calculations and Monte Carlo simulations were also carried out to corroborate the experimental results with theoretical outputs and succeeded to a great extent.     

Prediction of sound velocity and compressibility via molecular simulation at fixed entropy

A molecular-level simulation route is proposed to compute the isentropic thermodynamic properties in a fluid system by Monte Carlo simulation at fixed entropy. The method involves computation of the pressure response of a system to an infinitesimal change in system density by introduction of a single molecule, while retaining the system volume as well as the absolute molar entropy. The probability for accepting a change in temperature during the Monte Carlo moves was weighted against the argument proposed by Smith et al. [W.R. Smith, M. Lísal, I. Nezbeda, Chem. Phys. Lett. 426 (2006) 436–440]. Application to fluid argon has confirmed superior accuracy for the technique within the gas state to yield results within 1.2% of the measured values for the range of thermodynamic conditions investigated.     

Information content of data and variables and types of weighting in least-squares regression methods

Algorithms are given for evaluating the relative amount of useful information related to a particular parameter which is carried by individual data points and intervals of the variables. The algorithms provide an efficient means of using the information contained in a set of data. Applications to the optimization of weighting in regression methods are described. Several informational and combined informational-statistical types of weighting are studied as a means of improving the accuracy and precision of the parameters obtained by non-linear regression.