Understanding the role of open peer review and dynamic academic articles

We welcome the commentary by L. Egghe (Scientometrics, this issue) stimulating discussion on our recent article “Natural selection of academic papers” (NSAP) (Scientometrics, 85(2):553–559, 2010) that focuses on an important modern issue at the heart of the scientific enterprise—the open and continuous evaluation and evolution of research. We are also grateful to the editor of Scientometrics for giving us the opportunity to respond to some of the arguments by L. Egghe that we believe are inaccurate or require further comment.     

融合2D-PCA及稀疏表示的掌纹识别方法

提出一种基于稀疏表示的掌纹识别方法,该方法借鉴二维主成分分析(PCA)良好的数据压缩属性和较快的特征提取速度,生成掌纹特征图像.二维PCA不仅克服了一维PCA数据维数过大不易计算的缺点,而且保留了原始图像的数据结构,提取的特征能更好的代表原始图像.为了便于稀疏表达,对提取的掌纹特征图像利用一维主成分分析进行二次特征提取,得到训练样本.虽然此处使用了一维PCA,但是由于这是二次特征提取,提取的特征还是保留了原始图像的数据结构,相比单纯的一维PCA,提高了识别率.利用训练样本构造出冗余字典,并采用稀疏表示理论将测试样本表示为字典原子的线性组合,然后根据表示系数的稀疏性与稀疏集中度实现分类识别.由于该方法利用了表达系数的稀疏性,因此减小了算法的时间和空间复杂度.实验表明,针对香港理工大学的MSpalmprints Database,本文方法的识别率较传统方法有明显提高.     

Model checks for parametric regression models

In the paper we deal with the problem of model selection among fixed-design regression models. We establish a new test that indicates whether or not the model fits the data. The test statistic is based on the difference between a parametric estimator for the model variance and a nonparametric difference-based estimator, see Hall et al. (Biometrika 77:521–528, 1990). The weights in the nonparametric estimator depend on n, and they are chosen by solving an optimisation problem in order to obtain a test with high power.     

Finite-temperature Effect in Phase Transition to Superfluidity for Bose–Einstein Condensates in a 1-D Optical Lattice

We experimentally study the phase transition of ⁸⁷Rb Bose–Einstein condensates adiabatically loaded to a combined trap of a 1D optical lattice and a magnetic trap. The phase coherence property of this system is probed by recording the interference pattern of the expanded atomic cloud suddenly released from the combined trap. We show that as the temperature is sufficiently low (below the critical temperature T _C ), an interference pattern has a “peak on a peak” feature which is a true signature of macroscopic superfluid states. The normal gas only contributes to the broad background and three wide peaks in an interference pattern. These observations qualitatively agree with the recent theoretical predictions (Diener et al. in Phys. Rev. Lett. 98:180404, 2007; Kato et al. in Nat. Phys. 4:617, 2008). We also computed both the critical temperature and the interference pattern for a practical combined trap as ours in the tight-binding limit, and the numerical results are consistent with our experimental observations.     

Exploiting group symmetry in truss topology optimization

We consider semidefinite programming (SDP) formulations of certain truss topology optimization problems, where a lower bound is imposed on the fundamental frequency of vibration of the truss structure. These SDP formulations were introduced in Ohsaki et al. (Comp. Meth. Appl. Mech. Eng. 180:203–217, 1999). We show how one may automatically obtain symmetric designs, by eliminating the ‘redundant’ symmetry in the SDP problem formulation. This has the advantage that the original SDP problem is substantially reduced in size for trusses with large symmetry groups.     

A comment to the paper by Waltman et al., Scientometrics, 87, 467–481, 2011

In reaction to a previous critique (Opthof and Leydesdorff, J Informetr 4(3):423–430, 2010), the Center for Science and Technology Studies (CWTS) in Leiden proposed to change their old “crown” indicator in citation analysis into a new one. Waltman (Scientometrics 87:467–481, 2011a) argue that this change does not affect rankings at various aggregated levels. However, CWTS data is not publicly available for testing and criticism. Therefore, we comment by using previously published data of Van Raan (Scientometrics 67(3):491–502, 2006) to address the pivotal issue of how the results of citation analysis correlate with the results of peer review. A quality parameter based on peer review was neither significantly correlated with the two parameters developed by the CWTS in the past citations per paper/mean journal citation score (CPP/JCSm) or CPP/FCSm (citations per paper/mean field citation score) nor with the more recently proposed h-index (Hirsch, Proc Natl Acad Sci USA 102(46):16569–16572, 2005). Given the high correlations between the old and new “crown” indicators, one can expect that the lack of correlation with the peer-review based quality indicator applies equally to the newly developed ones.     

Stability analysis of undrained adiabatic shearing of a rock layer with Cosserat microstructure

Stability of undrained shearing in a classical Cauchy continuum has been first analyzed by Rice (J Geophys Res 80(11):1531–1536, 1975) who showed that instability occurs when the underlying drained deformation becomes unstable (i.e. in the softening regime of the corresponding drained stress-strain curve). However Vardoulakis (Int J Numer Anal Methods Geomech 9:339–414, 1985; Int J Numer Anal Methods Geomech 10:177–190, 1986) has shown that Rice’s linear stability analysis, if performed at the state of maximum deviator, leads to a sharp transition from infinitely stable to infinitely unstable behaviour, which indicates that the solution of the considered initial-value problem does not exist and consequently that the corresponding problem is mathematically ill-posed. Vardoulakis (Géotechnique 46(3):441–456, 1996; Géotechnique 46(3):457–472, 1996) proposed a regularization of the ill-posed problem in the softening regime by resorting to a second grade extension of plasticity theory. In this paper, the kinetics of a granular material is described by a Cosserat continuum as first suggested by Mühlhaus and Vardoulakis (Géotechnique 37:271–283, 1987) and we incorporate the effect of shear heating due to the dissipation of the frictional work. The undrained adiabatic limit is applicable as soon as the slip event is sufficiently rapid and the shear zone broad enough to effectively preclude heat or fluid transfer as it is the case during an earthquake or a landslide. It is shown that shear heating has a destabilizing effect and that instability can occur in the hardening regime if the amount of dilatant strengthening is not sufficient as compared to the effect of thermal pressurization of the pore fluid. It is shown that the linear stability analysis with macro and micro inertia terms leads to the selection of a preferred wave length of the instability mode corresponding to the instability mode with fastest (but finite) growth coefficient.     

Problems with “natural selection of academic papers”

In this short communication we give critical comments on the paper of Perakakis et al. (Scientometrics 85(2):553–559, 2010) on “Natural selection of academic papers”. The criticism mainly focusses on their unbalanced criticism of peer review and their negative evaluation of the link of peer review with commercial publishing.     

A time-discrete model for dynamic fracture based on crack regularization

We propose a discrete time model for dynamic fracture based on crack regularization. The advantages of our approach are threefold: first, our regularization of the crack set has been rigorously shown to converge to the correct sharp-interface energy Ambrosio and Tortorelli (Comm. Pure Appl. Math., 43(8): 999–1036 (1990); Boll. Un. Mat. Ital. B (7), 6(1):105–123, 1992); second, our condition for crack growth, based on Griffith’s criterion, matches that of quasi-static settings Bourdin (Interfaces Free Bound 9(3): 411–430, 2007) where Griffith originally stated his criterion; third, solutions to our model converge, as the time-step tends to zero, to solutions of the correct continuous time model Larsen (Math Models Methods Appl Sci 20:1021–1048, 2010). Furthermore, in implementing this model, we naturally recover several features, such as the elastic wave speed as an upper bound on crack speed, and crack branching for sufficiently rapid boundary displacements. We conclude by comparing our approach to so-called “phase-field” ones. In particular, we explain why phase-field approaches are good for approximating free boundaries, but not the free discontinuity sets that model fracture.     

Comprehensive analysis of LPG‐PCA algorithms in denoising and deblurring of medical images

This article presents the detailed analysis of the local pixel grouping–principle component analysis (LPG‐PCA) algorithm in denoising and deblurring of medical images. Inefficient diagnosis of the medical images containing lot of information is often affected by the noise and artifacts. In order to remove these noises and artifacts, a statistical decorrelation technique, LPG‐PCA is used which is found to be one of the efficient methods, which could be used in improving the performance of medical images. For better preservation of local structures of the image, a pixel and its nearest neighbors are modeled as a vector variable, which leads to the selection of similar intensity characteristics. Denoising method used in this article is done in two stages for improving the denoising performance. The smoothening caused by the denoising process is removed by using LPG‐PCA along with adaptive sparse domain representations in the deblurring process. This involves clustering of data and finding the subdictionary of each cluster using LPG‐PCA. Experimental results show that an average improvement of 2.9 and 5.1 dB is found in the computed tomography and magnetic resonance imaging images using denoising and deblurring process. © 2013 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 23, 157–170, 2013     

About Two-Component Physics of HTSC

We present a first-principles, microscopic calculation of the ground state of cuprates indicating the presence of two groups of charge carriers in these compounds associated with free and localized states. The localized component arises due to a charge density wave instability in the free component. The instability occurs in underdoped cuprates where the attractive Coulomb interaction between dopant impurities and charge carriers becomes strongly over-screened at low carrier densities and divides charge carriers into two orthogonal states. Within this new two-component state a novel quasi-particle entity, a microscopic Coulomb clump (CC), emerges. Our results are completely consistent with the analysis of the Hall effect and the ARPES spectra made earlier by Gorkov and Teitelbaum (GT) (Phys. Rev. Lett., 97:247003, 2006, and J. Phys.: Conf. Ser., 108:012009, 2008) that includes also available neutron scattering, NMR and μSR data. The density of localized component is temperature dependent, which is due to thermal activation of bound holes from Coulomb clumps. The clumps also induce nanoscale superstructures observed in Scanning Tunneling Microscope (STM) experiments (Pan, et al. Nature, 413:282–285, 2001; Dubi, et al. Nature, 449:876–879, 2007; Gomes, et al. Nature, 447:569, 2007; Lee, et al. Nature, 442:546, 2006; McElroy, et al. Science, 309:1048, 2005; Zhu, et al. Phys. Rev. Lett., 97:177001, 2006) and are responsible for the pseudogap and Nernst effect in HTSC. Following GT we stress the importance of these findings for the pseudogap physics. We present a first-principles, microscopic calculation of the ground state of cuprates indicating the presence of two groups of charge carriers in these compounds associated with free and localized states. The localized component arises due to a charge density wave instability in the free component. The instability occurs in underdoped cuprates where the attractive Coulomb interaction between dopant impurities and charge carriers becomes strongly over-screened at low carrier densities and divides charge carriers into two orthogonal states. Within this new two-component state a novel quasi-particle entity, a microscopic Coulomb clump (CC), emerges.     

Influence diagnostics in a general class of beta regression models

In this article, we consider the issue of assessing influence of observations in the general class of beta regression models introduced by Simas et al. (Comput. Stat. Data Anal. 54:348–366, 2010), which is very useful in situations in which the response is restricted to the standard unit interval (0,1). Our results generalize those in Espinheira et al. (Comput. Stat. Data Anal. 52:4417–4431, 2008a; J. Appl. Stat. 35:407–419, 2008b), which only apply to linear beta regression models. We define some residuals, and a Portmanteau test for serial correlation. Further, some influence methods, such as the global, local, and total local influence of an individual and generalized leverage, are discussed. Moreover, we also derive the normal curvatures of local influence under various perturbation schemes. Finally, simulation results and an application to real data show the usefulness of our results.     

Fabrication of Robust Superconducting Granular Aluminium/Palladium Bilayer Microbolometers with Sub-Nanosecond Response

We provide a convenient recipe for fabricating reliable superconducting microbolometers as acoustic phonon detectors with sub-nanosecond response, using image-reversal optical lithography and dc-magnetron sputtering, and our recipe requires no chemical or plasma etching. Our approach solves the traditional problem for granular aluminium bolometers of unreliable (i.e., non-Ohmic) electrical contacts by sequentially sputtering the granular aluminium film and then a palladium capping layer. We use dc calibration data, the method of Danilchenko et al. (Acta Phys. Pol. A 103(4):325, [2003]) and direct nanosecond-pulsed photoexcitation to obtain the microbolometer’s characteristic current, thermal conductance, characteristic relaxation time, and heat capacity. We also demonstrate the use of the deconvolution algorithm of Edwards et al. (J. Phys. E Sci. Instrum. 22:582, [1989]) to obtain the phonon flux in a heat pulse experiment with nanosecond resolution.      

Replies to the comments on “Faber series method for plane problems of an arbitrarily shaped inclusion [1]”

This work presents a brief introduction to the Faber polynomials and Faber series in order to reply to the comments made by Prof. Y. Z. Chen on “Faber series method for plane problems of an arbitrarily shaped inclusion (Luo and Gao in Acta Mech 208:133–145, 2009),” and finally, it is shown that his comments and conclusion are hasty and incorrect.     

Formation of new materials based on cast aluminum alloy

We show the dynamic formation of composite materials using the polycrystalline cast alloy Al + 12% Si as the example. The volume fraction of the synthesized framework (“influence zones”) of the composite material has been estimated to be at a level of 11%. Upon the introduction of lead a material practically insoluble under the experimental conditions was synthesized in the framework. Upon the introduction into the Al + 12% Si cast alloy of silicon carbide particles, we obtained a material with a specific corrosion exceeding by a factor of 5.6 the given index of the source matrix material.[1–7]     

Investigating variability of fatigue indicator parameters of two-phase nickel-based superalloy microstructures

Variability of fatigue properties of Nickel-based superalloys induced by microstructure feature uncertainties is investigated. The microstructure at one material point is described by its grain size and orientation features, as well as the volume fraction of the γ′ phase. Principal component analysis (PCA) is introduced to reduce the dimensionality of the microstructure feature space. PCA and kernel PCA (KPCA) techniques are presented and compared. Reduced representations of input features are mapped to uniform or standard Gaussian distributions through polynomial chaos expansion (PCE) so that the sampling of new microstructure realizations becomes feasible. A crystal plasticity constitutive model is adopted to evaluate fatigue properties of two-phase superalloy microstructures under cyclic loading. The fatigue properties are measured by strain-based fatigue indicator parameters (FIP). Adaptive sparse grid collocation (ASGC) and Monte Carlo (MC) methods are used to establish the relation between microstructure feature uncertainties and the variability of macroscopic properties. Convergence with increasing dimensionality of the reduced surrogate stochastic space is studied. Distributions of FIPs and the convex hulls describing the envelope of these parameters in the presence of microstructure uncertainties are shown.     

Beta autoregressive moving average models

We build upon the class of beta regressions introduced by Ferrari and Cribari-Neto (J. Appl. Stat. 31:799–815, 2004) to propose a dynamic model for continuous random variates that assume values in the standard unit interval (0,1). The proposed βARMA model includes both autoregressive and moving average dynamics, and also includes a set of regressors. We discuss parameter estimation, hypothesis testing, goodness-of-fit assessment and forecasting. In particular, we give closed-form expressions for the score function and for Fisher’s information matrix. An application that uses real data is presented and discussed.     

Subsampling weakly dependent time series and application to extremes

This paper provides extensions of the work on subsampling by Bertail et al. in J. Econ. 120:295–326 (2004) for strongly mixing case to weakly dependent case by application of the results of Doukhan and Louhichi in Stoch. Proc. Appl. 84:313–342 (1999). We investigate properties of smooth and rough subsampling estimators for sampling distributions of converging and extreme statistics when the underlying time series is η- or λ-weakly dependent.     

Pseudo maximum likelihood estimates using ranked set sampling with applications to estimating correlation

Suppose θ is the parameter of interest and λ is the nuisance parameter. When obtaining the maximum likelihood estimator (MLE) of θ in the presence of λ requires intensive computation, the pseudo MLE of θ, based on a pseudo likelihood function, can be used. Gong and Samaniego (Ann. Stat. 9:861–869, 1981) proposed a pseudo MLE (PMLE) based on simple random samples. Ranked set sampling has been applied to the bivariate variables (X,Y) where measuring one of the variables is difficult or costly. In this paper, we obtain the pseudo MLE of the correlation coefficient from a bivariate normal distribution (X,Y) based on ranked set samples, assuming that Y is difficult or more expensive to measure and that the mean and variance of Y are the nuisance parameters. The PMLE is compared with three other estimators of the correlation coefficient. Simulations show that the PMLE is more (less) efficient than other estimators, depending on value of ρ. Testing of soil contamination provides an example of the use of the methods.     

CovSel: Variable selection for highly multivariate and multi-response calibration: Application to IR spectroscopy

Variable selection is of major interest for NIR calibration, either as a feature selection or for the design of multi-wavelength devices. Some dedicated methods have been developed in chemometrics, but a few of them addresses explicitly the case of multi-response calibration. Variable selection for NIR spectroscopy must face two problems: (1) the huge number of variables yields a very large solution space; (2) variables are highly correlated, and if no special attention is paid the model built on the selection may be ill-conditioned. This article presents a new method, CovSel, which tackles these two problems by following this procedure: (1) variable selection step by step on the basis of their global covariance with all the responses; and (2) projection of the data orthogonally to the selected variable. CovSel was applied on three problems: the first one concerns a single response MIR calibration (Brix degree content in apricot), the second one concerns a multi-response NIR calibration (4 main constituents in corn) and the last application concerns the NIR discrimination of 3 wine grape varieties.