In defence of the correlation coefficient

The relationship between calibrated range, residual standard deviation and correlation coefficient r is discussed. It is shown that in typical chemical calibration applications with appropriately distributed calibration points (particularly, with range comparable to mean and with approximately even or with ‘successive dilution’ spacing), the linear correlation coefficient has valid application as a routine criterion for acceptable fit if used with due care.

The correlation coefficient attacks again

The use of the correlation coefficient for testing the linearity of calibration curves is performed according to the ANOVA checking of the lack-of-fit. The procedure is illustrated from a case study.Papers published in this section do not necessarily reflect the opinion of the Editors,the Editorial Board and the Publisher. Apart from exceptional circumstances, they are not submitted to the usual referee procedure and go essentially unaltered.     

CAMWI: Detecting protein complexes using weighted clustering coefficient and weighted density

Detection of protein complexes is very important to understand the principles of cellular organization and function. Recently, large protein–protein interactions (PPIs) networks have become available using high-throughput experimental techniques. These networks make it possible to develop computational methods for protein complex detection. Most of the current methods rely on the assumption that protein complex as a module has dense structure. However complexes have core-attachment structure and proteins in a complex core share a high degree of functional similarity, so it expects that a core has high weighted density. In this paper we present a Core-Attachment based method for protein complex detection from Weighted PPI Interactions using clustering coefficient and weighted density. Experimental results show that the proposed method, CAMWI improves the accuracy of protein complex detection.     

The antiparallel electron correlation coefficient and Coulomb hole structure

Based on the charge density functional theory, a simple method is proposed to calculate the antiparallel electron correlation coefficient, correlation charge, and correlation energy. In contrast to the result stated in the literature, our analysis reveals that the Coulomb hole has a fine structure. To our knowledge, this is the first time it has been proven that the electrons obey the curve correlation law in an intermediate separation range but the electrons obey the linear correlation law in small and large separation ranges. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 74: 1–6, 1999     

Quantitative analysis of infrared absorption coefficient of spider silk fibers

Spider silk has a high degree of crystallinity comprising nanocrystals which are interlinked by amorphous regions containing pre-strained spidroin chains. Both, crystal volume fraction and crystal size were shown to be critical for the macroscopic mechanical properties of silk. In this study, for the first time, quantitative results were obtained from absorption IR spectra. Two main difficulties must be overcome: the cylindrical sample geometry and the absence of suitable reference spectra. We show that it is possible to get reproducible absorption coefficient spectra from dense parallel fiber grids immersed in a refractive index matching liquid. Comparison with model polypeptides yields the nanocrystal volume fraction that is close to the crystallinity values given by solid-state NMR or X-ray scattering.     

Determination of thermal expansion coefficient of a monofilament polyamide fiber using digital image correlation

Coiled polymer actuators are a type of artificial muscles that are a promising development in the field of smart materials. The coefficient of thermal expansion of monofilament polyamide fibers is a crucial parameter for understanding the actuation of coiled fibers. The main purpose of this work is to develop a new methodology for estimating the coefficient of thermal expansion and the transition temperature of monofilament polymer fibers. In the experimental procedure, axial deformations of monofilament polyamide fiber samples were induced by temperature variations using a controlled thermal system. These deformations were determined from images of polyamide samples using the digital image correlation method. Two different approaches based on distinct temperature conditions were conducted. An alternative model with three parameters, including the coefficient of thermal expansion, was introduced to describe the thermal-mechanical behavior of monofilament polyamide fibers. Moreover, polyamide samples were also characterized using four conventional methodologies. Results indicated that the coefficient of thermal expansion changed of a modest negative value to a large negative value and this transition occurred around the glass transition temperature of the polyamide. The thermal expansion curves demonstrate good repeatability and all estimated parameters were in accordance with literature, indicating that the proposed approach can be suitable for the proposed study. This investigation may help in understanding of the intrinsic thermal-mechanical behavior of polymeric monofilaments employed as actuators.     

紫外圆二色光谱预测蛋白质结构的研究方法

介绍了蛋白质紫外圆二色性(CD)产生的原理及其与蛋白质结构的关系。评述了用远紫外CD预测蛋白质二级结构的方法原理、参考蛋白、拟合算法和拟合程序,以及方法存在的问题。近紫外CD与蛋白质的三级结构密切相关,近紫外蛋白质CD反映芳香氨基酸残基、二硫键等微环境的变化,表征着丰富的蛋白质三级结构的信息。     

1H and 13C NMR assignments for two anthraquinones and two xanthones from the mangrove fungus (ZSUH-36)

We report the unambiguous assignments of the (1)H and (13)C NMR spectra of one new natural product, namely, 6,8-di-O-methyl versiconol (1) together with one known anthraquinone aversin (2) and two xanthones 5-methoxysterigmatocystin (3) and sterigmatocystin (4). These compounds were all isolated from the mangrove endophytic fungus ZSUH-36 from the South China Sea. 1D and 2D NMR experiments including COSY, HMQC and HMBC were used to elucidate the structures. Variations in the (1)H NMR spectrum of 6,8-di-O-methyl versiconol (1) were also observed in the temperature range 25-75 degrees C. In addition, the plausible biogenetic path from 1 to 2 is discussed.     

RNA secondary structure prediction using a self‐consistent mean field approach

We propose a method for predicting RNA base pairing which imposes no restrictions on the order of base pairs, allows for pseudoknots and runs in O(mN²) time for N base pairs and m iterations. It employs a self‐consistent mean field method in which all base pairs are possible, but with each iteration, the most energetically favored base pairs become more likely as long as they are consistent with their neighbors. Performance was compared against three other programs using three test sets. Sensitivity varied from 20% to 74% and specificity from 44% to 77% and generally, the method predicts too many base pairs leading to good sensitivity and worse specificity. The predicted structures have excellent energies suggesting that, algorithmically, the method performs well, but the classic literature energy models may not be appropriate when pseudoknots are permitted. Website and source code for the simulations are available at http://cardigan.zbh.uni‐hamburg.de/～rnascmf . © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Electron correlation effects in cobalt fluorides CoFn

The molecular cobalt fluorides CoF₂, CoF₃ and CoF₄ are studied and compared by employing different basis sets as well as Quantum Information Theory (QIT) to investigate their correlation effects. These prototypical monomers may be systematically extended in size yielding a novel quasi 1-dimensional, strongly correlated model system consisting of cobalt atoms bridged by oxygen atoms and fluorine termination on both ends. Accurate correlation energies are obtained using Full Configuration Interaction (FCI) and Full Configuration Interaction Quantum Monte Carlo (FCIQMC) calculations and the results are compared to Coupled Cluster and Density Matrix Renormalization Group (DMRG) energies. The analysis indicates the cobalt atom requires a larger number of one-electron basis functions than fluorine and the use of localized molecular orbitals may facilitate calculations for the extended systems.     

RNA Aptamers That Reversibly Bind Photoresponsive Azobenzene‐Containing Peptides

Modulation of biological networks assembled by diverse interactions among biologically active molecules has provided a platform for innovative biotechnologies. Here, we report RNA aptamers that bind to a photoresponsive peptide (KRAzR; Lys‐Arg‐azobenzene‐Arg) containing azobenzene chromophore, which can change its structure by photoirradiation. Aptamers were identified after 10 cycles of an in vitro selection procedure starting with a DNA library containing a 70 nt random region. Surface plasmon resonance (SPR) analysis demonstrated that interactions between aptamers and KRAzR were fully controlled by appropriate photoirradiation to the SPR sensor chip. Upon irradiation of 360 nm on the KRAzR‐immobilized surface, the binding of each aptamer to the surface was significantly decreased. Subsequent photoirradiation of the same surface with 430 nm restored the aptamer binding to the surface. We also observed that direct photoirradiation of the aptamer–peptide complex on a gold surface actively promoted dissociation of the complex. Furthermore, a doped reselection method was applied to acquire structural and sequence information of aptamer 66. From a data analysis of the conserved region and the mutation frequency, we were able to select a plausible secondary structure among three candidates predicted by computational folding simulation.     

On a four-dimensional representation of RNA secondary structures

We propose a 4-D representation of RNA secondary structures. The four-dimensional representation resolves structures’ degeneracy and avoids loss of information and the limitation that different structures correspond the same plot set (or presentation). The RNA pseudoknpts also can be represented as four-dimensional representations. Based on this representation, we outline an approach to compute the similarities between six RNA secondary structures for illustrating the utility of our approach.     

Structure and two-dimensional correlation infrared spectroscopy study of two isomeric forms of the octamolybdate cluster

Two isomeric forms of the octamolybdate cluster, (NH₄)₂(Hbpy)₂[Mo₈O₂₆](bpy)₃1 (bpy=bipydine), and [Cu₂(imi)₄]₂[Mo₈O₂₆] 2 (imi=imidazole), were synthesized by hydrothermal method and characterized by X-ray single analysis, one-dimensional (1D) infrared spectroscopy and two-dimensional (2D) correlation infrared spectroscopy under thermal perturbation. In compound 1, the [Mo₈O₂₆] units are β-structure, and octamolybdate anion is ζ-structure in compound 2. The 2D IR correlation spectroscopy study indicates that the intensity changes of MoO band are more sensitive to the temperature variation than that of the Mo-O bond. The μ-Mo-O bond and framework vibrations in compound 1 are more sensitive to the temperature variation than that for compound 2. As the vibrations of μ-Mo-O bond accompanied by the transfer of an oxygen atom, the catalysis ability of compound 1 may be higher than that of compound 2.     

RNA secondary structure alignment based on an extended binary coding method

Recently, we proposed a three‐dimensional cube representation of RNA secondary structure. An efficient method for mutation analysis has been proposed based on the introduced representation. According to the proposed three‐dimensional cube representations, we will introduce an extended binary coding method for RNA secondary structure alignment by converting the structure alignment to sequence alignment. Using our method, the result of structure alignment can be obtained quickly. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Determination of Protein Concentration from CD Spectrum

Abstract

Protein concentration can be determined from its circular dichroism(CD) spectrum and from programs that calculate protein secondary structure content from CD. The method established was successfully applied to lysozyme and a de novo designed peptide with a standard error of about 5%, which is comparable to concentrations determined from an estimated extinction coefficient. This procedure is widely applicable in protein and peptide samples.     

Linearity of calibration curves: use and misuse of the correlation coefficient

The correlation coefficient is commonly used to evaluate the degree of linear association between two variables. However, it can be shown that a correlation coefficient very close to one might also be obtained for a clear curved relationship. Other statistical tests, like the Lack-of-fit and Mandel’s fitting test thus appear more suitable for the validation of the linear calibration model. A number of cadmium calibration curves from atomic absorption spectroscopy were assessed for their linearity. All the investigated calibration curves were characterized by a high correlation coefficient (r >0.997) and low quality coefficient (QC <5%), but the straight-line model was systematically rejected at the 95% confidence level on the basis of the Lack-of-fit and Mandel’s fitting test. Furthermore, significantly different results were achieved between a linear regression model (LRM) and a quadratic regression (QRM) model in forecasting values for mid-scale calibration standards. The results obtained with the QRM did not differ significantly from the theoretically expected value, while those obtained with the LRM were systematically biased. It was concluded that a straight-line model with a high correlation coefficient, but with a lack-of-fit, yields significantly less accurate results than its curvilinear alternative. Received: 15 January 2002 Accepted: 18 April 2002     

1H and 13C NMR assignments for two oxaphenalenones bacillosporin C and D from the mangrove endophytic fungus SBE-14

The complete (1)H and (13)C NMR assignments are reported for the novel natural product Bacillosporin D together with the known compound Bacillosporin C. These compounds containing seven rings were isolated from the mangrove endophytic fungus SBE-14 from the South China Sea. 1D and 2D NMR experiments, including COSY, HMQC and HMBC were used to the determination of the structures and NMR assignments. It is proposed that 1 was biogenetically produced by transforming 2. Transforming a lactone to an anhydride is unusual in nature.     

Electrolyte-UNIQUAC-NRF model for the correlation of the mean activity coefficient of electrolyte solutions

The new electrolyte-UNIQUAC-NRF excess Gibbs function is obtained for calculation of the activity coefficient of the binary electrolyte solutions. The excess Gibbs energy of the model consists of the Pitzer–Debye–Hückel equation, describing the long-range electrostatic contribution and the electrolyte-UNIQUAC-NRF model to account for the short-range contributions. With two adjustable parameters per electrolyte, the new model is applied to correlation of the mean activity coefficients of more than 130 binary aqueous electrolyte solutions at 25 °C. Also the binary parameters, obtaining from regression of mean activity data, are used for prediction of osmotic coefficient data for the same electrolytes. The results are compared with various local composition models such as the electrolyte-NRTL, electrolyte NRF-Wilson, electrolyte-NRTL-NRF, N-Wilson-NRF models. The comparison of the results with experiment demonstrates that the new model can correlate the experimental activity coefficient data and predict the osmotic coefficient data of binary electrolytes accurately.     

Correlation of mean ionic activity coefficient using a two-parameters model

In this study, a two-parameters model is presented based on the solvation phenomena. Using this model, the mean ionic activity coefficients of 146 salts and activity coefficients of individual ions of some 1 : 1 and 1 : 2 salts have been correlated successfully. The results of the present model have been compared with the Khoshkbarchi–Vera model and three-characteristic parameter correlation model of Lin and Lee model. These comparisons show that the present model predicts the mean ionic activity coefficient better than others.