bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting protein flexibility through the prediction of local structures
Authors: Bornot Aurélie , Etchebest Catherine , de Brevern Alexandre G. 
Published: November 2010

AbstractProtein structures are valuable tools for understanding protein function. However, protein dynamics is also considered a key element in protein function. Therefore, in addition to structural analysis, fully understanding protein function at the molecular level now requires accounting for flexibility. However, experimental techniques that produce both types of information simultaneously are still limited. Prediction approaches are useful alternative tools for obtaining otherwise unavailable data. It has been shown that protein structure can be described by a limited set of recurring local structures. In this context, we previously established a library composed of 120 overlapping long structural prototypes (LSPs) representing fragments of 11 residues in length and covering all known local protein structures. On the basis of the close sequence‐structure relationship observed in LSPs, we developed a novel prediction method that proposes structural candidates in terms of LSPs along a given sequence. The prediction accuracy rate was high given the number of structural classes. In this study, we use this methodology to predict protein flexibility. We first examine flexibility according to two different descriptors, the B‐factor and root mean square fluctuations from molecular dynamics simulations. We then show the relevance of using both descriptors together. We define three flexibility classes and propose a method based on the LSP prediction method for predicting flexibility along the sequence. The prediction rate reaches 49.6%. This method competes rather efficiently with the most recent, cutting‐edge methods based on true flexibility data learning with sophisticated algorithms. Accordingly, flexibility information should be taken into account in structural prediction assessments. Proteins 2011. © 2010 Wiley‐Liss, Inc.
Salt bridges: Geometrically specific, designable interactions
Authors: Donald Jason E. , Kulp Daniel W. , DeGrado William F. 
Published: November 2010

AbstractSalt bridges occur frequently in proteins, providing conformational specificity and contributing to molecular recognition and catalysis. We present a comprehensive analysis of these interactions in protein structures by surveying a large database of protein structures. Salt bridges between Asp or Glu and His, Arg, or Lys display extremely well‐defined geometric preferences. Several previously observed preferences are confirmed, and others that were previously unrecognized are discovered. Salt bridges are explored for their preferences for different separations in sequence and in space, geometric preferences within proteins and at protein–protein interfaces, co‐operativity in networked salt bridges, inclusion within metal‐binding sites, preference for acidic electrons, apparent conformational side chain entropy reduction on formation, and degree of burial. Salt bridges occur far more frequently between residues at close than distant sequence separations, but, at close distances, there remain strong preferences for salt bridges at specific separations. Specific types of complex salt bridges, involving three or more members, are also discovered. As we observe a strong relationship between the propensity to form a salt bridge and the placement of salt‐bridging residues in protein sequences, we discuss the role that salt bridges might play in kinetically influencing protein folding and thermodynamically stabilizing the native conformation. We also develop a quantitative method to select appropriate crystal structure resolution and B‐factor cutoffs. Detailed knowledge of these geometric and sequence dependences should aid de novo design and prediction algorithms. Proteins 2011. © 2010 Wiley‐Liss, Inc.
Exploring the role of structure and dynamics in the function of chymotrypsin inhibitor 2
Authors: Whitley Matthew J. , Lee Andrew L. 
Published: November 2010

AbstractIncreasing awareness of the possible role of internal dynamics in protein function has led to the development of new methods for experimentally characterizing protein dynamics across multiple time scales, especially using NMR spectroscopy. A few analyses of the conformational dynamics of proteins ranging from nonallosteric single domains to multidomain allosteric enzymes are now available; however, demonstrating a connection between dynamics and function remains difficult on account of the comparative lack of studies examining both changes in dynamics and changes in function in response to the same perturbations. In previous work, we characterized changes in structure and dynamics on the ps–ns time scale resulting from hydrophobic core mutations in chymotrypsin inhibitor 2 and found that there are moderate, persistent global changes in dynamics in the absence of gross structural changes (Whitley et al., Biochemistry 2008;47:8566–8576). Here, we assay those and additional mutants for inhibitory ability toward the serine proteases elastase and chymotrypsin to determine the effects of mutation on function. Results indicate that core mutation has only a subtle effect on CI2 function. Using chemical shifts, we also studied the effect of complex formation on CI2 structure and found that perturbations are greatest at the complex interface but also propagate toward CI2's hydrophobic core. The structure–dynamics–function data set completed here suggests that dynamics plays a limited role in the function of this small model system, although we do observe a correlation between nanosecond‐scale reactive loop motions and inhibitory ability for mutations at one key position in the hydrophobic core. Proteins 2011. © 2010 Wiley‐Liss, Inc.
In silico modeling of pH‐optimum of protein–protein binding
Authors: Mitra Rooplekha C. , Zhang Zhe , Alexov Emil 
Published: November 2010

AbstractProtein–protein association is a pH‐dependent process and thus the binding affinity depends on the local pH. In vivo the association occurs in a particular cellular compartment, where the individual monomers are supposed to meet and form a complex. Since the monomers and the complex exist in the same micro environment, it is plausible that they coevolved toward its properties, in particular, toward the characteristic subcellular pH. Here we show that the pH at which the monomers are most stable (pH‐optimum) or the pH at which stability is almost pH‐independent (pH‐flat) of monomers are correlated with the pH‐optimum of maximal affinity (pH‐optimum of binding) or pH interval at which affinity is almost pH‐independent (pH‐flat of binding) of the complexes made of the corresponding monomers. The analysis of interfacial properties of protein complexes demonstrates that pH‐dependent properties can be roughly estimated using the interface charge alone. In addition, we introduce a parameter beta, proportional to the square root of the absolute product of the net charges of monomers, and show that protein complexes characterized with small or very large beta tend to have neutral pH‐optimum. Further more, protein complexes made of monomers carrying the same polarity net charge at neutral pH have either very low or very high pH‐optimum of binding. These findings are used to propose empirical rule for predicting pH‐optimum of binding provided that the amino acid compositions of the corresponding monomers are available. Proteins 2011. © 2010 Wiley‐Liss, Inc.
Harmonic radar: efficacy at detecting and recovering insects on agricultural host plants
Authors: Boiteau Gilles , Vincent Charles , Meloche François , Leskey Tracy C , Colpitts Bruce G 
Published: November 2010

AbstractBACKGROUND: In pest management research, harmonic radar systems have been largely used to study insect movement across open or vegetation‐poor areas because the microwave signal is attenuated by the high water content of vegetation. This study evaluated whether the efficacy of this technology is sufficient to track insects in vegetative landscapes.RESULTS: Field efficacy data were collected using portable harmonic microwave radar and electronic dipole tags mounted on adults of three economically important pests: Leptinotarsa decemlineata (Say), Diabrotica virginifera virginifera (LeComte) and Conotrachelus nenuphar Herbst. Detection and recovery of tagged Colorado potato beetles, plum curculios and western corn rootworms was high within and among potato plants, moderate within apple trees and high within, but not between, corn plants respectively. The efficacy of the radar depends on the ability of the operator to move around the host, scanning for a signal ‘sightline’ with the tagged insect among plant structures.CONCLUSION: The detection rate of tagged insects by harmonic radar systems is high enough to track the walking path of pests through low row crops such as potato, tall row crops such as corn or tall but well‐separated trees of orchard‐type crops by adapting the scanning procedure to the vegetative architecture. Copyright © 2010 Crown in the right of Canada. Published by JohnWiley & Sons, Ltd
Stokes and anti‐Stokes blue light emissions of thermal‐evaporated silica sub‐micron wires
Authors: Tao Chuanyi , Li Xueming , Feng Wenlin , Yang Jianchun , Li Wulin , Li Yongfu , Yang Wenjing 
Published: November 2010

AbstractBased on the thermal evaporation of silicon monoxide at high temperature, an improved method has been developed for large‐scale synthesis of ultralong amorphous silica sub‐micron wires using polished p‐Si wafers as substrates. The synthesis was done with and without thermite. The morphology and structure of the silica wires was investigated through field‐emission scanning electron microscope equipped with energy dispersive X‐ray spectroscopy, and X‐ray diffractometer. Almost uniform sub‐micron wires with average diameters of 300 nm and length up to hundreds of micrometers were obtained in presence of thermite while sub‐micron wires with many curved segments were obtained in absence of the thermite. Both forms of silica wires emitted blue lights at 478 nm (∼2.6 eV) under excitation at 351 nm (∼3.5 eV), while intense anti‐Stokes blue emissions at 464 nm (∼2.7 eV) were observed under the 694 nm (∼1.8 eV) excitation due to the upconversion effect. This effect is associated with defect centers arising from high oxygen deficiency. The emissions from oxygen deficiency centers might be caused by multistep energy transfer from nonbridging oxygen hole centers to oxygen deficiency centers.
A DEM‐based parallel computing hydrodynamic and transport model
Authors: Zhang Yan Jun , Jha Manoj , Gu Roy , Wensheng Luo , Alin Lei 
Published: November 2010

ABSTRACTThe sudden and accidental water pollution response system (SAWPRS) for Yangtze River in central China required to develop a hydrodynamic and transport model, which is readily available and capable of simulating a large river system within GIS environment. This study facilitates such effort by developing a parallel computing method based on digital elevation model (DEM) using overlapping domain decomposition approach (ODDA) and message passing interface (MPI) protocol. The hydrodynamic and transport model was redesigned using finite volume method for hydrodynamic and transport model dispersion, the SIMPLEC method for solving the flow field, and the pressure weighted interpolating method for the flow field modification. This modelling approach was verified in two experiments using different sets of computer clusters. The model output was evaluated against the measured data collected for the year 1998 for Wanzhou, an upstream river segment of Yangtze River. The relative error was found to be less than 10%. The performance of parallel computation was found excellent as evident from the cost efficiency values greater than 0.81 in both experiments and increased computation speed while increasing the number of computer clusters. Overall, the parallel computing modelling system developed here was found to meet all requirements of SAWPRS. Copyright © 2010 John Wiley & Sons, Ltd.
Improved IPsec performance utilizing transport‐layer‐aware compression architecture
Authors: Li Jung‐Shian , Hsieh Che‐Jen , Chang Chih‐Ying , Chilamkurti Naveen 
Published: November 2010

AbstractWith the rapid growth of applications in Internet communication, the security for transmitting information on public network has become a fundamental issue. The Internet Protocol Security (IPsec) standard is developed by Internet Engineering Task Force (IETF) to provide the security services at the IP layer. IPSec solutions invariably result in a large‐packet size and a long processing time. Accordingly, this paper proposes new compression architecture, designated as Efficient Secure Pipe (ES_PIPE), to improve both the security and the performance of IPv6 networks. In contrast to traditional IPsec compression schemes, ES_PIPE provides a transport‐layer‐aware compression capability for different types of packets (e.g., TCP or UDP/RTP packets). The experimental results show that the proposed scheme reduces 20–30% transmission time compared to IPsec. Furthermore, ES_PIPE scheme yields about 20% improvement in the efficiency of the encryption and decryption processes. Copyright © 2010 John Wiley & Sons, Ltd.
RFID system for public train transportation
Authors: Chen Chin‐Ling , Chong Mei‐Li 
Published: November 2010

ABSTRACTNowadays, the problem of a shortage of energy is becoming more and more serious. This has resulted in the global governments' appeal to people to take public transportation systems as much as possible. But, the public transportation system has a lot of problems that cause people's interest in taking the public transportation system to get lower and lower. For example, many passengers use many kinds of management loopholes to avoid buying tickets. This action forces the companies involved in providing the public transportation system to strengthen manpower for inspecting tickets. Hence, the companies will shift cost to the customers forcing ticket prices higher and higher as well as passengers becoming more frustrated with the increase in inspecting tickets. In this paper, we take the Taiwan Railways Administration (it owns different ticket types and different train types in the same public transportation system) as our implement environment and we use Radio‐Frequency Identification (RFID) methods conforming to EPCglobal Class 1 Generation 2 (C1G2) standards to solve this train‐jumping problem and reduce the manpower cost of the public transportation system companies. And most importantly, our scheme also enhances higher security. Copyright © 2010 John Wiley & Sons, Ltd.
Content based image hashing using companding and gray code
Authors: Yang Lei , Chen Qian , Tian Jun , Wu Dapeng 
Published: November 2010

AbstractEasily processing, storing, and propagating of digital images demand efficient and automatic techniques to identify and verify image contents. Image hashing is such a promising technique to represent and authenticate images without changing the content of images. The new robust image feature we use is the Morlet wavelet coefficients at feature points with thek‐largest local total variations in images. The Morlet wavelet coefficients are pseudo randomly permutated such that image hashes have a small collision rate and are difficult to analyze by attackers. The Morlet wavelet coefficients are further quantized using companding technique and binarily coded using Gray code to form the final hash.Experimental resultsshow the effectiveness and robustness of our method. The proposed image hash could have applications in image authentication and video signature. Copyright © 2010 John Wiley & Sons, Ltd.
Mixture cure model with random effects for the analysis of a multi‐center tonsil cancer study
Authors: Peng Yingwei , Taylor Jeremy M. G. 
Published: November 2010

AbstractCure models for clustered survival data have the potential for broad applicability. In this paper, we consider the mixture cure model with random effects and propose several estimation methods based on Gaussian quadrature, rejection sampling, and importance sampling to obtain the maximum likelihood estimates of the model for clustered survival data with a cure fraction. The methods are flexible to accommodate various correlation structures. A simulation study demonstrates that the maximum likelihood estimates of parameters in the model tend to have smaller biases and variances than the estimates obtained from the existing methods. We apply the model to a study of tonsil cancer patients clustered by treatment centers to investigate the effect of covariates on the cure rate and on the failure time distribution of the uncured patients. The maximum likelihood estimates of the parameters demonstrate strong correlation among the failure times of the uncured patients and weak correlation among cure statuses in the same center. Copyright © 2010 John Wiley & Sons, Ltd.
Improving small‐sample inference in group randomized trials with binary outcomes
Authors: Westgate Philip M. , Braun Thomas M. 
Published: November 2010

AbstractGroup Randomized Trials (GRTs) randomize groups of people to treatment or control arms instead of individually randomizing subjects. When each subject has a binary outcome, over‐dispersed binomial data may result, quantified as an intra‐cluster correlation (ICC). Typically, GRTs have a small number,bin, of independent clusters, each of which can be quite large. Treating the ICC as a nuisance parameter, inference for a treatment effect can be done using quasi‐likelihood with a logistic link. A Wald statistic, which, under standard regularity conditions, has an asymptotic standard normal distribution, can be used to test for a marginal treatment effect. However, we have found in our setting that the Wald statistic may have a variance less than 1, resulting in a test size smaller than its nominal value. This problem is most apparent when marginal probabilities are close to 0 or 1, particularly whennis small and the ICC is not negligible. When the ICC is known, we develop a method for adjusting the estimated standard error appropriately such that the Wald statistic will approximately have a standard normal distribution. We also propose ways to handle non‐nominal test sizes when the ICC is estimated. We demonstrate the utility of our methods through simulation results covering a variety of realistic settings for GRTs. Copyright © 2010 John Wiley & Sons, Ltd.
Bias reduction in conditional logistic regression
Authors: Sun Jenny X. , Sinha Samiran , Wang Suojin , Maiti Tapabrata 
Published: November 2010

AbstractWe employ a general bias preventive approach developed by Firth (Biometrika1993;80:27–38) to reduce the bias of an estimator of the log‐odds ratio parameter in a matched case–control study by solving a modified score equation. We also propose a method to calculate the standard error of the resultant estimator. A closed‐form expression for the estimator of the log‐odds ratio parameter is derived in the case of a dichotomous exposure variable. Finite sample properties of the estimator are investigated via a simulation study. Finally, we apply the method to analyze a matched case–control data from a low birthweight study. Copyright © 2010 John Wiley & Sons, Ltd.
Using latent variable modeling and multiple imputation to calibrate rater bias in diagnosis assessment
Authors: Siddique Juned , Crespi Catherine M. , Gibbons Robert D. , Green Bonnie L. 
Published: November 2010

AbstractWe present an approach that uses latent variable modeling and multiple imputation to correct rater bias when one group of raters tends to be more lenient in assigning a diagnosis than another. Our method assumes that there exists an unobserved moderate category of patient who is assigned a positive diagnosis by one type of rater and a negative diagnosis by the other type. We present a Bayesian random effects censored ordinal probit model that allows us to calibrate the diagnoses across rater types by identifying and multiply imputing ‘case’ or ‘non‐case’ status for patients in the moderate category. A Markov chain Monte Carlo algorithm is presented to estimate the posterior distribution of the model parameters and generate multiple imputations. Our method enables the calibrated diagnosis variable to be used in subsequent analyses while also preserving uncertainty in true diagnosis. We apply our model to diagnoses of posttraumatic stress disorder (PTSD) from a depression study where nurse practitioners were twice as likely as clinical psychologists to diagnose PTSD despite the fact that participants were randomly assigned to either a nurse or a psychologist. Our model appears to balance PTSD rates across raters, provides a good fit to the data, and preserves between‐rater variability. After calibrating the diagnoses of PTSD across rater types, we perform an analysis looking at the effects of comorbid PTSD on changes in depression scores over time. Results are compared with an analysis that uses the original diagnoses and show that calibrating the PTSD diagnoses can yield different inferences. Copyright © 2010 John Wiley & Sons, Ltd.
Multinationals' response to major disasters: how does subsidiary investment vary in response to the type of disaster and the quality of country governance?
Authors: Oh Chang Hoon , Oetzel Jennifer 
Published: November 2010

AbstractWe investigate the response of multinational corporations (MNCs) to major disasters at the subsidiary level. We examine the type and severity of the disaster and whether and how country governance moderates the relationship between exogenous disaster risk and subsidiary investment. We test our hypotheses with a panel dataset of 71 large European MNCs and their subsidiaries (2001–2006) with 31,285 total observations. Findings suggest that the number of a firm's foreign subsidiaries is likely to decrease in response to terrorist attacks or technological disasters but not natural disasters, regardless of the severity of the event. For terrorist activities, MNC subsidiary‐level disinvestment is less likely when the quality of host country governance is higher. Copyright © 2011 John Wiley & Sons, Ltd.
Effect of high hydrostatic pressure on starches: A review
Authors: Pei‐Ling Liu , Xiao‐Song Hu , Qun Shen 
Published: November 2010

AbstractVarious strategies have been employed to enhance starch property, including thermal processing, chemical modification. The application of high hydrostatic pressure (HHP) may be a complementary, synergistic, or an additive starch enhancement technique. While most current applications of HHP are in starch processing, over 25 starches had been investigated by HHP, which can induce gelatinization and modification of some starches. Different starch responds differently to high pressure depending on the pressure range, starch source, pressurization temperature and time, different solvent and starch concentration. We have re‐examined the information on the various factors that influence the HHP‐induced structure, gelatinization, retrogradation, and modification of starches from different plant sources, with an emphasis on the HHP‐induced gelatinization. The compiled evidence of high pressure starch enhancement in this paper indicates that HHP is an effective technology with potential for greater utilization in starch application.