bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of peptide‐binding sites on protein surfaces: The first step toward the modeling and targeting of peptide‐mediated interactions
Authors: Lavi Assaf , Ngan Chi Ho , Movshovitz‐Attias Dana , Bohnuud Tanggis , Yueh Christine , Beglov Dmitri , Schueler‐Furman Ora , Kozakov Dima 
Published: October 2013

AbstractPeptide‐mediated interactions, in which a short linear motif binds to a globular domain, play major roles in cellular regulation. An accurate structural model of this type of interaction is an excellent starting point for the characterization of the binding specificity of a given peptide‐binding domain. A number of different protocols have recently been proposed for the accurate modeling of peptide‐protein complex structures, given the structure of the protein receptor and the binding site on its surface. When no information about the peptide binding site(s) is a priori available, there is a need for new approaches to locate peptide‐binding sites on the protein surface. While several approaches have been proposed for the general identification of ligand binding sites, peptides show very specific binding characteristics, and therefore, there is a need for robust and accurate approaches that are optimized for the prediction of peptide‐binding sites. Here, we present PeptiMap, a protocol for the accurate mapping of peptide binding sites on protein structures. Our method is based on experimental evidence that peptide‐binding sites also bind small organic molecules of various shapes and polarity. Using an adaptation of ab initio ligand binding site prediction based on fragment mapping (FTmap), we optimize a protocol that specifically takes into account peptide binding site characteristics. In a high‐quality curated set of peptide‐protein complex structures PeptiMap identifies for most the accurate site of peptide binding among the top ranked predictions. We anticipate that this protocol will significantly increase the number of accurate structural models of peptide‐mediated interactions. Proteins 2013; 81:2096–2105. © 2013 Wiley Periodicals, Inc.
Protein docking using case‐based reasoning
Authors: Ghoorah Anisah W. , Devignes Marie‐Dominique , Smaïl‐Tabbone Malika , Ritchie David W. 
Published: October 2013

ABSTRACTProtein docking algorithms aim to calculate the three‐dimensional (3D) structure of a protein complex starting from its unbound components. Although ab initio docking algorithms are improving, there is a growing need to use homology modeling techniques to exploit the rapidly increasing volumes of structural information that now exist. However, most current homology modeling approaches involve finding a pair of complete single‐chain structures in a homologous protein complex to use as a 3D template, despite the fact that protein complexes are often formed from one or more domain–domain interactions (DDIs). To model 3D protein complexes by domain–domain homology, we have developed a case‐based reasoning approach called KBDOCK which systematically identifies and reuses domain family binding sites from our database of nonredundant DDIs. When tested on 54 protein complexes from the Protein Docking Benchmark, our approach provides a near‐perfect way to model single‐domain protein complexes when full‐homology templates are available, and it extends our ability to model more difficult cases when only partial or incomplete templates exist. These promising early results highlight the need for a new and diverse docking benchmark set, specifically designed to assess homology docking approaches. Proteins 2013; 81:2150–2158. © 2013 Wiley Periodicals, Inc.
Role of histidine for charge regulation of unstructured peptides at interfaces and in bulk
Authors: Kurut Anıl , Henriques João , Forsman Jan , Skepö Marie , Lund Mikael 
Published: October 2013

ABSTRACTHistidine‐rich, unstructured peptides adsorb to charged interfaces such as mineral surfaces and microbial cell membranes. At a molecular level, we investigate the adsorption mechanism as a function of pH, salt, and multivalent ions showing that (1) proton charge fluctuations are—in contrast to the majority of proteins—optimal at neutral pH, promoting electrostatic interactions with anionic surfaces through charge regulation and (2) specific zinc(II)‐histidine binding competes with protons and ensures an unusually constant charge distribution over a broad pH interval. In turn, this further enhances surface adsorption. Our analysis is based on atomistic molecular dynamics simulations, coarse grained Metropolis Monte Carlo, and classical polymer density functional theory. This multiscale modeling provides a consistent picture in good agreement with experimental data on Histatin 5, an antimicrobial salivary peptide. Biological function is discussed and we suggest that charge regulation is a significant driving force for the remarkably robust activity of histidine‐rich antimicrobial peptides. Proteins 2014; 82:657–667. © 2013 Wiley Periodicals, Inc.
Comparison of the effect of insecticides on three strains of Tyrophagus putrescentiae (Acari: Astigmata) using an impregnated filter paper test and a growth test
Authors: Stara Jitka , Nesvorna Marta , Hubert Jan 
Published: October 2013

AbstractBACKGROUNDIn this study, we compared the efficacy of insecticides against three strains of Tyrophagus putrescentiae using an impregnated filter paper test and a growth test. We tested the suppressive activity of commercial insecticides and their analytical standards (pirimiphos‐methyl, cypermethrin, deltamethrin, chlorfenapyr, β‐cyfluthrin).METHODSThe strains of T. putrescentiae originated from a laboratory, a field and dog food. The mortality of the mites due to active ingredients and analytical standards was tested using an impregnated filter paper test after 24 h. Lethal doses, LD50, LD95 and LD99 were determined. A growth test was used to observe the suppressive effect of the active ingredients on mites at 21 days after application of the active ingredients to wheat grain. The effective doses ED50, ED95 and ED99 were determined, indicating the concentration at which the population was reduced by 50, 95 and 99% more than control.RESULTSCypermethrin, β‐cyfluthrin and a formulation of deltamethrin with piperonylbutoxide in the pesticide K‐Othrine showed low toxicity to mites. High toxicity was observed for chlorfenapyr (LD50: 0.1–1 µg cm‐2; ED50: 0.11–1.2 µg g‐1) and pirimiphos‐methyl (LD50: 0.01–0.06 µg cm‐2; ED50: 0.2–12 µg g‐1). We did not find significant differences among the compared strains in terms of their sensitivity to highly toxic insecticides.CONCLUSIONThe obtained results showed that a filter paper test is a more sensitive method of identifying differences in pesticide susceptibility among strains, but the efficacy of pesticides against one species should be tested using a growth test. © 2013 Society of Chemical Industry
Assessment of selection and resistance risk for demethylation inhibitor fungicides in Aspergillus fumigatus in agriculture and medicine: a critical review
Authors: Gisi Ulrich 
Published: October 2013

AbstractBACKGROUNDAn increasing number of publications have claimed that demethylation inhibitor (DMI) fungicides are confronted with resistance development in the fungus Aspergillus fumigatus and that the origin of resistant isolates may also be outside the medical area. For resistance risk assessment and sourcing the origin of DMI resistance, the primary exposure events of A. fumigatus with DMI treatments have been analysed case by case, resulting in the pathogen exposure risk (PER).RESULTSThe calculated maximum exposure concentrations (MEC) are highest during medical treatments (human and veterinary), certain fruit and seed treatments and wood preservation, and are much lower for crop protection applications. Most agricultural DMIs are intrinsically ∼ 10–100 times less active than medical DMIs for A. fumigatus control and potential resistance selection. However, imazalil is used in agriculture and veterinary medicine (as enilconazole) expressing strong intrinsic activity against A. fumigatus. The majority of mutations in the target gene, cyp51, of DMI‐resistant isolates are different in A. fumigatus (e.g. TR34/L98H) in comparison with plant pathogens (e.g. A379G, I381V).CONCLUSIONSThe assumed selection risk, ASR (MEC × PER) for resistance evolution to DMIs in A. fumigatus is estimated to be highest for human and veterinary applications. However, environmental origin of DMI‐resistant spores from certain sites cannot be ruled out. © 2013 Society of Chemical Industry
Systematic chemical functionalization of hybrid molecule–surface interfaces
Authors: Caciuc V. , Lennartz M. C. , Atodiresei N. , Tsukamoto S. , Karthäuser S. , Blügel S. 
Published: October 2013

In this article, we briefly overview our experimental and theoretical studies aimed to investigate the electronic structure and the transport properties of several carboxylates chemisorbed on the Cu(110) surface. In particular, we have theoretically explored the possibility to chemically functionalize a carboxylate–Cu(110) system to specifically tune its electronic structure. Experimentally, it could be proven that the transport properties of the carboxylate–Cu(110) interface indeed revealed specific features in the d spectra corresponding to the used functionalization process. Moreover, the d spectra can be used to identify specific adsorption geometries or conformations of carboxylates on Cu(110). Furthermore, transport calculations for molecules with different anchoring groups between two Cu(110) electrodes are also discussed. Schematic view of a STM tip probing a carboxylate molecule chemisorbed on the Cu(110) surface with the corresponding energy level alignment in the case of a zero bias voltage.
Transient thermal response of an individual multiwall carbon nanotube
Authors: Wada Yukiko , Ohshima Yusuke , Arie Takayuki , Akita Seiji 
Published: October 2013

AbstractWe have proposed a method for measuring the transient thermal response of an individual carbon nanotube under Joule heating with pulse current. A transient temperature response with a time constant of about 50 ns was measured. A simplified lumped capacitance model revealed that this fast response corresponds to the small heat capacity of the nanotube. The measured transient response was fairly well reproduced by finite element method analysis using parameters of bulk graphite, which indicates that the bulk graphite parameters are compatible with those of well‐graphitized nanotubes. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Design of new carbon allotropes of fused small fullerenes
Authors: Maruyama Mina , Okada Susumu 
Published: October 2013

AbstractWe have designed novel two‐dimensional (2D) carbon allotropes consisting of the small fullerene C26 using first‐principles total energy calculations based on the density functional theory. We found that the fused C26 polyhedra form a periodic 2D honeycomb covalent net‐work. The initial honeycomb network converted into two different stable structures upon structural optimization.Both phases were found to be energetically stable, and the calculated total energies were found to be 0.6 eV/atom higher than the energy of diamond. The electronic structures of the two fused C26 networks were found to be metals, and one of the structures possesses linear dispersion bands near the Fermi level, owing to the formation of a one‐dimensional fused octagonal sp2 network on the polymeric layer. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
On the possibility of sub 60 mV/decade subthreshold switching in piezoelectric gate barrier transistors
Authors: Jana Raj K. , Snider Gregory L. , Jena Debdeep 
Published: October 2013

AbstractA novel method for the reduction of subthreshold slope below the room‐temperature Boltzmann limit of 60 mV/dec for a field‐effect transistor based on negative differential capacitance is proposed. This effect uses electric field induced electrostriction of a piezoelectric gate barrier of the transistor. The mechanism amplifies the internal surface potential over the applied gate voltage. This internal voltage gain mechanism provides an opportunity for steep subthreshold slope switching below 60 mV/decade of the transistor current. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Thermoelectricity in semiconductor nanowires
Authors: Kim Jungwon , Bahk Je‐Hyeong , Hwang Junphil , Kim Hoon , Park Hwanjoo , Kim Woochul 
Published: October 2013

Abstractmagnified imageIn this paper, we provide a comprehensive review on recent advances in the development of semiconductor nanowires for thermoelectric energy conversion. Semiconductor nanowires can exhibit novel properties in the electron and phonon transport as their diameters approach the characteristic length scales of the material such as the electron wavelength and the phonon mean free path. These size effects in semiconducting nanowires are discussed as a means to enhance the thermoelectric properties of the nanowires over their bulk counterparts. Challenges for the enhancement are also identified. We present recent theoretical and experimental results on various thermoelectric nanowires including Si, Ge, InAs, Bi, Bi–Te and Bi–Sb nanowires. Various characterization techniques for the accurate electrical and thermal measurements of individual nanowires are also covered. Finally, we mention briefly the recent efforts to fabricate thermoelectric devices using nanowire arrays. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Insertion of fullerene layer for bulk heterojunction organic photovoltaic cell fabricated by electrospray deposition method
Authors: Fukuda Takeshi , Takagi Kenji , Liao Yingjie 
Published: October 2013

AbstractAn improved power conversion efficiency (PCE) of bulk heterojunction organic photovoltaic cell (OPV) was achieved by inserting an n‐type [6,6]‐phenyl‐C61‐butyric acid methyl ester (PCBM) layer between the active layer and a metal electrode. The controlled substrate temperature was found to be a useful parameter for the multilayer structure (active layer/ PCBM) by the electrospray deposition method. Under optimized substrate temperature during the PCBM deposition, a multilayer structure could be formed, and the PCE was improved up to 1.94%.magnified image(© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A new continuous high‐gain controller scheme for a class of uncertain nonlinear systems
Authors: Dasdemir Janset , Zergeroglu Erkan 
Published: October 2013

SUMMARYIn this study, we present a new robust continuous controller mechanism for the tracking problem of uncertain nonlinear systems. The proposed strategy is based on a Lyapunov‐type stability argument and only requires the uncertainties of the dynamical system to be the first‐order differentiable to achieve asymptotic practical tracking. For the ease of presentation, the controller formulation is presented on a general, second‐order dynamical system, extension to higher order versions are also possible with a considerably small effort. Simulation studies comparing the performance of the proposed method with the classical Sliding mode and robust integral of the sign of the error controller are presented to illustrate the performance and the feasibility of the proposed strategy. Experimental validation on a two link direct drive robot manipulator are also included to illustrate the implementability of the proposed method. Copyright © 2013 John Wiley & Sons, Ltd.
Model predictive control of directed‐graph constrained systems
Authors: Kobayashi Koichi , Imura Jun‐ichi , Matsushima Hiromichi 
Published: October 2013

SUMMARYThis paper addresses a new type of model predictive control problem for a hybrid system that consists of a continuous‐time linear system and a temporal/spatial directed graph, called a directed‐graph constrained system. Motivated by the obstacle avoidance problem, the problem is newly formulated, where the continuous‐time control input and the waypoints of the state are simultaneously optimized under a temporal/spatial directed graph as well as input/state linear constraints, and a method for efficiently solving this problem is developed. Numerical examples are presented to verify that the proposed approach is effective. Copyright © 2013 John Wiley & Sons, Ltd.
Reachable set estimation for discrete‐time linear systems with time delays
Authors: Lam James , Zhang Baoyong , Chen Yong , Xu Shengyuan 
Published: October 2013

SUMMARYThis paper is concerned with the reachable set estimation problem for discrete‐time linear systems with multiple constant delays and bounded peak inputs. The objective is to check whether there exists a bounded set that contains all the system states under zero initial conditions. First, delay‐dependent conditions for the solvability of the addressed problem are derived by employing a novel Lyapunov–Krasovskii functional. The obtained conditions are expressed in terms of matrix inequalities, which are linear when only one scalar variable is fixed. On the basis of these conditions, an ellipsoid containing the reachable set of the considered system is obtained. An approach for determining the smallest ellipsoid is also provided. Second, the approach and results developed in the first stage are generalized to the case of systems with polytopic parameter uncertainties, and delay‐dependent conditions are given in the form of relaxed matrix inequalities. Finally, two numerical examples are provided to demonstrate the effectiveness of the proposed methods. Copyright © 2013 John Wiley & Sons, Ltd.
A review of climatic controls on δ18O in precipitation over the Tibetan Plateau: Observations and simulations
Authors: Yao Tandong , Masson‐Delmotte Valerie , Gao Jing , Yu Wusheng , Yang Xiaoxin , Risi Camille , Sturm Christophe , Werner Martin , Zhao Huabiao , He You , Ren Wei , Tian Lide , Shi Chunming , Hou Shugui 
Published: October 2013

AbstractThe stable oxygen isotope ratio (δ18O) in precipitation is an integrated tracer of atmospheric processes worldwide. Since the 1990s, an intensive effort has been dedicated to studying precipitation isotopic composition at more than 20 stations in the Tibetan Plateau (TP) located at the convergence of air masses between the westerlies and Indian monsoon. In this paper, we establish a database of precipitation δ18O and use different models to evaluate the climatic controls of precipitation δ18O over the TP. The spatial and temporal patterns of precipitation δ18O and their relationships with temperature and precipitation reveal three distinct domains, respectively associated with the influence of the westerlies (northern TP), Indian monsoon (southern TP), and transition in between. Precipitation δ18O in the monsoon domain experiences an abrupt decrease in May and most depletion in August, attributable to the shifting moisture origin between Bay of Bengal (BOB) and southern Indian Ocean. High‐resolution atmospheric models capture the spatial and temporal patterns of precipitation δ18O and their relationships with moisture transport from the westerlies and Indian monsoon. Only in the westerlies domain are atmospheric models able to represent the relationships between climate and precipitation δ18O. More significant temperature effect exists when either the westerlies or Indian monsoon is the sole dominant atmospheric process. The observed and simulated altitude‐δ18O relationships strongly depend on the season and the domain (Indian monsoon or westerlies). Our results have crucial implications for the interpretation of paleoclimate records and for the application of atmospheric simulations to quantifying paleoclimate and paleo‐elevation changes.
NOVEL AQUATIC ECOSYSTEMS: THE NEW REALITY FOR STREAMS IN CALIFORNIA AND OTHER MEDITERRANEAN CLIMATE REGIONS
Authors: Moyle P. B. 
Published: October 2013

ABSTRACTTemporary streams in California and other Mediterranean climate areas are among the aquatic habitats most altered by human actions and by invasions by alien species. They typically support novel ecosystems, defined as ecosystems dominated by new combinations of organisms in highly altered habitats. Although these new ecosystems have many attributes of the ecosystems they replaced, such as native species, they typically contain many new interactions among species. Managers need to recognize this reality to find ways to direct change towards novel ecosystems with desirable features, including native species. The concept of reconciliation ecology is a practical approach to living with the new reality; it includes actively guiding ecosystem change, as illustrated by Putah Creek, Cosumnes River, Eel River and Six Bit Gulch in California. The first three waterways are all highly altered and managed with varying degrees of success to favour desired aquatic species, whereas Six Bit Gulch experiences such extreme conditions that the original ecosystem is still largely intact. The examples illustrate that most aquatic ecosystems in California are so highly altered that attempting to restore them to an earlier condition or stable state is largely not possible. Where more or less intact systems persist, it is usually because extreme environmental conditions restrict both alien invaders and human use in small watersheds. This pattern appears to be fairly typical of streams in Mediterranean climate areas. Copyright © 2013 John Wiley & Sons, Ltd.
A secure K‐automorphism privacy preserving approach with high data utility in social networks
Authors: Yang Jun , Wang Bin , Yang Xiaochun , Zhang Hongyi , Xiang Guang 
Published: October 2013

ABSTRACTThe prevalence of social networks has raised the concern for individual privacy leakage. Although preserving user privacy in social networks has been studied extensively, there is still a lot of room for improvement in the state of the art techniques. For example, the recently proposed K‐automorphism model can prevent node identity attack by constructing a K‐automorphism graph; however, it ignores preserving the privacy of the edges, resulting in path length leakage and edge leakage in the anonymous graph. Another example is the K‐isomorphism model, which was proposed to improve the K‐automorphism model by transforming the graph of social networks into K disjoined isomorphic subgraphs. However, it cuts off the connection among subgraphs, which impairs the data utility of the released anonymous graph. In this paper, we design a secure and high utility privacy preserving model, called AK‐secure, to prevent node identity attack, path length leakage, and edge leakage effectively. On the basis of the AK‐secure privacy preserving model, we propose a graph anonymous algorithm, which constructs an anonymous graph satisfying the AK‐secure privacy preserving model, minimizing information loss and guaranteeing high data utility. Extensive experiments on real data sets show the security, effectiveness of our AK‐secure privacy preserving model and the high data utility of the released anonymous graph. Copyright © 2013 John Wiley & Sons, Ltd.