bluuebunny/crossref_metadata_2025_split huggingface dataset:
Robust polarity specification operates above a threshold of microtubule dynamicity
Authors: Thadani Rahul , Huang Daniel , Oliferenko Snezhana 
Published: May 2011

AbstractMicrotubule arrays effect cell polarisation by directing cellular cues for cortical remodelling and growth. Their function depends crucially on the intrinsic dynamic properties of constituent microtubules. Microtubule dynamicity is restricted to a certain range within the confines of a cellular geometry. Thus it is of great interest to determine whether rescaling of dynamic properties of microtubules has consequences for cell polarity. We constructed fission yeast strains exhibiting depressed microtubule dynamics by mutating the β‐tubulin gene, nda3. This interfered with efficient accumulation of a polarity factor Tea1 at cell tips. Interestingly, the polarity machinery in the mutant cells was highly susceptible to perturbations. Simulations of growth zone formation followed by imaging of actin distribution showed a significantly delayed onset of bipolar growth. We propose that there exists a threshold of microtubule dynamicity that allows robust cellular polarisation. © 2011 Wiley‐Liss, Inc.
Employing graphics processing unit technology, alternating direction implicit method and domain decomposition to speed up the numerical diffusion solver for the biomedical engineering research
Authors: Jiang Beini , Struthers Allan , Sun Zhe , Feng Zhuo , Zhao Xuqian , Zhao Kaiyong , Dai Weizhong , Zhou Xiaobo , Berens Michael E. , Zhang Le 
Published: May 2011

AbstractDiffusion of biological compounds, including nutrients, oxygen, and chemoattractants, is a common component of biomedical engineering models. Conventional numerical schemes, such as alternating direction implicit (ADI) for diffusion, are frequently the computational bottleneck. Our study employs graphics processing unit (GPU) technology to accelerate the diffusion model simulation. We tailor, implement, analyze, and test several parallel ADI algorithms on the highly parallel computational and data architecture of the GPU. Our study confirms that the proposed algorithms provide fast, high‐quality simulation results suitable for inclusion in numerous bioengineering simulations. Copyright © 2011 John Wiley & Sons, Ltd.
Laminar‐to‐turbulent fluid–nanoparticle dynamics simulations: Model comparisons and nanoparticle‐deposition applications
Authors: Zhang Zhe , Kleinstreuer Clement 
Published: May 2011

SUMMARYRelying on benchmark experimental data sets for flow in conduits with local constrictions, LES and three widely used RANS turbulence models, i.e. the low Reynolds number (LRN) k‐ω model, standard k‐ω model and shear stress transport (SST) transition model, were compared and evaluated to gain new physical insight and provide useful turbulence modeling information. These two geometric test cases may represent stenosed arteries and a segment of the human upper airways where the velocity fields undergo all flow regimes, i.e. from laminar, via transitional, to fully turbulent.The comparison study revealed that the standard k‐ω models amplify the flow instabilities after the constrictions, and hence fail to capture the laminar flow behavior at relatively LRNs. The overall performances of LES, the LRN k‐ω model and SST transition model do not have measurable differences in predicting laminar flows and transition to turbulent flow, while the SST transition model may give a better prediction of turbulence kinetic energy profiles in some cases. Clearly, LES can provide instantaneous velocity fluctuations, which may be significant for turbulent micron particle transport/deposition in the respiratory tract. However, it requires 100‐fold more computational time than RANS turbulence models. The use of different turbulence models has a minor effect on nanoparticle deposition in human upper airways when the inspiratory flow rate is low, say, Q = 10L/min. The relative difference for deposition fraction (DF) of nanoparticles with dp>10nm is measurable at a medium inhalation flow rate (say, Q = 30L/min) when employing different turbulence models. However, the absolute difference in DFs is within 0.5% for all‐sized nanoparticles (i.e. 1nm⩽dp⩽50nm) because the DF in the oral airway is very low (say, <1.5%) when 10 nm and 10 L/min.The modeling and simulation information provided are most useful for computational fluid–particle dynamics practitioners to obtain accurate lung deposition concentrations of inhaled toxic or therapeutic nanoparticles. The physical insight provided sheds additional light on the laminar‐to‐turbulent airflow and nanoparticle transport/deposition in locally constricted conduits. Copyright © 2011 John Wiley & Sons, Ltd.
Universality and extremal aging for dynamics of spin glasses on subexponential time scales
Authors: Ben Arous Gérard , Gün Onur 
Published: May 2011

AbstractWe consider random hopping time (RHT) dynamics of the Sherrington‐Kirkpatrick (SK) model and p‐spin models of spin glasses. For any of these models and for any inverse temperature β > 0 we prove that, on time scales that are subexponential in the dimension, the properly scaled clock process (time‐change process) of the dynamics converges to an extremal process. Moreover, on these time scales, the system exhibits aging‐like behavior, which we call extremal aging. In other words, the dynamics of these models ages as the random energy model (REM) does. Hence, by extension, this confirms Bouchaud's REM‐like trap model as a universal aging mechanism for a wide range of systems that, for the first time, includes the SK model. © 2011 Wiley Periodicals, Inc.
Critical behavior of nonintersecting Brownian motions at a tacnode
Authors: Delvaux Steven , Kuijlaars Arno B. J. , Zhang Lun 
Published: May 2011

AbstractWe study a model of n one‐dimensional, nonintersecting Brownian motions with two prescribed starting points at time t = 0 and two prescribed ending points at time t = 1 in a critical regime where the paths fill two tangent ellipses in the time‐space plane as n → ∞. The limiting mean density for the positions of the Brownian paths at the time of tangency consists of two touching semicircles, possibly of different sizes. We show that in an appropriate double scaling limit, there is a new family of limiting determinantal point processes with integrable correlation kernels that are expressed in terms of a new Riemann‐Hilbert problem of size 4 × 4. We prove solvability of the Riemann‐Hilbert problem and establish a remarkable connection with the Hastings‐McLeod solution of the Painlevé II equation. We show that this Painlevé II transcendent also appears in the critical limits of the recurrence coefficients of the multiple Hermite polynomials that are associated with the nonintersecting Brownian motions. Universality suggests that the new limiting kernels apply to more general situations whenever a limiting mean density vanishes according to two touching square roots, which represents a new universality class. © 2011 Wiley Periodicals, Inc
Towards automated HPC scheduler configuration tuning
Authors: Krishnamurthy Diwakar , Alemzadeh Mehrnoush , Moussavi Mahmood 
Published: May 2011

AbstractHigh performance computing (HPC) systems allow researchers and businesses to harness large amounts of computing power needed for solving complex problems. In such systems a job scheduler prioritizes the execution of jobs belonging to users of the system in a manner that allows the system to satisfy performance objectives for various groups of users while simultaneously making efficient use of available resources. Typically, system administrators have the responsibility of manually configuring or tuning the job scheduler such that the performance objectives of user groups as well as system‐level performance objectives are met. Modern job schedulers used in production systems are quite complex. Through detailed trace‐driven simulations, we show that manually tuning the configuration of production schedulers in an environment characterized by multiple performance objectives is very challenging and may not be feasible. To alleviate this problem, this paper describes a toolset that can help a system administrator to automatically configure a scheduler such that the performance objectives for various classes of users in the system as well as other system‐level performance objectives can be satisfied. A unique aspect of this work that differentiates it from the existing work on scheduler tuning is that it has been implemented to work with a widely used production scheduler. Furthermore, in contrast to the existing work it considers the challenging real‐world problem of delivering different levels of performance to different classes of users. System administrators can exploit the toolset to react quickly to changes in performance objectives and workload conditions. Case studies using synthetic and real HPC workloads demonstrate the effectiveness of the technique. Copyright © 2011 John Wiley & Sons, Ltd.
DHTrust: a robust and distributed reputation system for trusted peer‐to‐peer networks
Authors: Xue Weilian , Liu Yaqiong , Li Keqiu , Chi Zhongxian , Min Geyong , Qu Wenyu 
Published: May 2011

SUMMARYThe anonymity and dynamic character of a Peer‐to‐Peer (P2P) network makes it an ideal medium for selfish and vicious action. In order to solve this problem, P2P reputation systems are proposed to evaluate the trustworthiness of peers and to prevent the selfish, dishonest, and malicious peers' behaviors, which collects local reputation scores and aggregates them into the global reputation. In this paper we propose a DHT (Distributed Hash Table) trust overlay network (DHTON) to model the network structure and the storage of reputation information. We also design a robust and distributing reputation system, DHTrust, which takes full advantage of the DHT to distribute local reputation to trade‐off the damage of fake reputation information by genuine reputation information. By using the trust evaluation towards two reputation scores, we can also distinguish and evaluate the fundamental behaviors of peers in the P2P network, i.e. providing service and issuing reputation scores. To adapt to the dynamic P2P networks, we take dynamic node mechanism into account. Our scheme can assure convergence effectiveness and robustness, when nodes enter or leave the system. We conduct extensive simulations to evaluate the performance of DHTrust. The results show that our system makes significant improvement in convergence speed and aggregation accuracy. Moreover, it is robust to malicious peers. Copyright © 2011 John Wiley & Sons, Ltd.
Asynchronous event handling and Safety Critical Java
Authors: Wellings Andy , Kim MinSeong 
Published: May 2011

SUMMARYOver the last few years, the Java Community Process (under the auspices of Java Specification Request 302) has been developing a subset of Java augmented by the Real‐Time Specification for Java (RTSJ) for use in safety critical systems. The concurrency model supported by Safety Critical Java (SCJ) relies almost exclusively on an event‐based model rather than on a thread‐based model. This paper reviews the advantages and disadvantages of the two models and gives the pragmatic reasons that SCJ has adopted the former model. It describes the SCJ approach and gives a simple example of how it can be used, illustrating the difference in style between the RTSJ and SCJ code. The paper then considers the compatibility of the SCJ model with the RTSJ. It argues that by basing the SCJ classes on the RTSJ's BoundAsyncEvent class, some inconsistencies exist between the SCJ and the RTSJ models. Furthermore, some of the optimizations that are possible when mapping handlers to server threads are inhibited, even though the programming restrictions necessary for these optimizations are imposed by the SCJ specification. A revised model is presented that has a slightly more complicated API but is more consistent with the RTSJ and allows the optimizations. However, there is a resulting increase in the necessary run‐time support, particularly for multiprocessor implementations. Copyright © 2011 John Wiley & Sons, Ltd.
Scalability and locality of extrapolation methods on large parallel systems
Authors: Korch Matthias , Rauber Thomas , Scholtes Carsten 
Published: May 2011

AbstractTime‐dependent processes can often be modeled by systems of ordinary differential equations (ODEs). Solving such a system for a detailed model can be highly computationally intensive. We investigate explicit extrapolation methods for solving such systems efficiently on current highly parallel supercomputer systems with shared‐or distributed‐memory architecture. We analyze and compare the scalability of several parallelization variants, some of them using multiple levels of parallelization. For a large class of ODE systems, data access costs are reduced considerably by exploiting the special structure of the ODE system. Furthermore, by employing a pipeline‐like loop structure, the locality of memory references is increased for such systems resulting in a better utilization of the cache hierarchy. Runtime experiments show that the optimized implementations can deliver a high scalability. Copyright © 2011 John Wiley & Sons, Ltd.
Self‐adaptive clock frequency recovery based on buffer control
Authors: Lu Yueming , Ji Yuefeng 
Published: May 2011

SUMMARYWith high‐speed packet networks and packet transport networks (PTNs) beginning to support transmissions of high‐speed time division multiplex and multiplexer (TDM) and 3G services, the clock recovery in packet networks becomes significant and challengeable. This paper proposes a self‐adaptive clock frequency recovery based on buffer control to support the clock recovery in packet networks. It includes an estimation part and an amend part, estimates clock frequencies using the dynamic moving average algorithm, amends clock frequencies according to feedbacks, and balances stability, convergence, and system faults. Simulations show that the method has the ability of self‐adaption, avoids the buffer overflow and underflow, and achieves better accuracy, less packet delay, as well as better convergence ability. Copyright © 2011 John Wiley & Sons, Ltd.
Clustering‐based power‐controlled routing for mobile wireless sensor networks
Authors: Khan Atta ur Rehman , Madani Sajjad A. , Hayat Khizar , Khan Samee Ullah 
Published: May 2011

SUMMARYThis paper presents two new routing protocols for mobile sensor networks, viz. power‐controlled routing (PCR) and its enhanced version, i.e. Enhanced Power‐Controlled Routing (EPCR). In both the protocols, fixed transmission power is employed in the clustering phase but when ordinary nodes are about to send their data to their respective cluster‐heads, they change their transmission power according to their distance from their cluster‐head. While in PCR, the nodes are associated with the cluster‐head on the basis of weight, in EPCR it is done on the basis of distance. In addition to the protocols, we are suggesting a packet loss recovery mechanism for the PCR and EPCR. Both protocols work well for both mobile and static networks and are designed to achieve high network lifetime, high packet delivery ratio, and high network throughput. These protocols are extensively simulated using mass mobility model, with different speeds and different number of nodes to evaluate their performance. Simulation results show that both PCR and EPCR are successful in achieving their objectives by using variable transmission powers and smart clustering. Copyright © 2011 John Wiley & Sons, Ltd.
Myocyte proliferation in the developing heart
Authors: Sedmera David , Thompson Robert P. 
Published: May 2011

AbstractRegulation of organ growth is critical during embryogenesis. At the cellular level, mechanisms controlling the size of individual embryonic organs include cell proliferation, differentiation, migration, and attrition through cell death. All these mechanisms play a role in cardiac morphogenesis, but experimental studies have shown that the major determinant of cardiac size during prenatal development is myocyte proliferation. As this proliferative capacity becomes severely restricted after birth, the number of cell divisions that occur during embryogenesis limits the growth potential of the postnatal heart. We summarize here current knowledge concerning regional control of myocyte proliferation as related to cardiac morphogenesis and dysmorphogenesis. There are significant spatial and temporal differences in rates of cell division, peaking during the preseptation period and then gradually decreasing toward birth. Analysis of regional rates of proliferation helps to explain the mechanics of ventricular septation, chamber morphogenesis, and the development of the cardiac conduction system. Proliferation rates are influenced by hemodynamic loading, and transduced by autocrine and paracrine signaling by means of growth factors. Understanding the biological response of the developing heart to such factors and physical forces will further our progress in engineering artificial myocardial tissues for heart repair and designing optimal treatment strategies for congenital heart disease. Developmental Dynamics 240:1322–1334, 2011. © 2011 Wiley‐Liss, Inc.
Epigenetics in C. elegans: Facts and challenges
Authors: Wenzel Dirk , Palladino Francesca , Jedrusik‐Bode Monika 
Published: May 2011

AbstractEpigenetics is defined as the study of heritable changes in gene expression that are not accompanied by changes in the DNA sequence. Epigenetic mechanisms include histone post‐translational modifications, histone variant incorporation, non‐coding RNAs, and nucleosome remodeling and exchange. In addition, the functional compartmentalization of the nucleus also contributes to epigenetic regulation of gene expression. Studies on the molecular mechanisms underlying epigenetic phenomena and their biological function have relied on various model systems, including yeast, plants, flies, and cultured mammalian cells. Here we will expose the reader to the current understanding of epigenetic regulation in the roundworm C. elegans. We will review recent models of nuclear organization and its impact on gene expression, the biological role of enzymes modifying core histones, and the function of chromatin‐associated factors, with special emphasis on Polycomb (PcG) and Trithorax (Trx‐G) group proteins. We will discuss how the C. elegans model has provided novel insight into mechanisms of epigenetic regulation as well as suggest directions for future research. genesis 49:647–661, 2011. © 2011 Wiley‐Liss, Inc
Combination of lentivector immunization and low‐dose chemotherapy or PD‐1/PD‐L1 blocking primes self‐reactive T cells and induces anti‐tumor immunity
Authors: Sierro Sophie R. , Donda Alena , Perret Rachel , Guillaume Philippe , Yagita Hideo , Levy Frédéric , Romero Pedro 
Published: May 2011

AbstractIn the last two decades, anti‐cancer vaccines have yielded disappointing clinical results despite the fact that high numbers of self/tumor‐specific T cells can be elicited in immunized patients. Understanding the reasons behind this lack of efficacy is critical in order to design better treatment regimes. Recombinant lentivectors (rLVs) have been successfully used to induce antigen‐specific T cells to foreign or mutated tumor antigens. Here, we show that rLV expressing a murine nonmutated self/tumor antigen efficiently primes large numbers of self/tumor‐specific CD8+ T cells. In spite of the large number of tumor‐specific T cells, however, no anti‐tumor activity could be measured in a therapeutic setting, in mice vaccinated with rLV. Accumulating evidence shows that, in the presence of malignancies, inhibition of T‐cell activity may predominate overstimulation. Analysis of tumor‐infiltrating lymphocytes revealed that specific anti‐tumor CD8+ T cells fail to produce cytokines and express high levels of inhibitory receptors such as programmed death (PD)‐1. Association of active immunization with chemotherapy or antibodies that block inhibitory pathways often leads to better anti‐tumor effects. We show here that combining rLV vaccination with either cyclophosphamide or PD‐1 and PD‐L1 blocking antibodies enhances rLV vaccination efficacy and improves anti‐tumor immunity.
Intramolecular Butenolide Allene Photocycloadditions and Ensuing Retro‐Ene Reactions of Some Photoadducts
Authors: Lutteke Ginger , Kleinnijenhuis Roel A. , Jacobs Ivo , Wrigstedt Pauli J. , Correia Ana C. A. , Nieuwenhuizen Rowan , Buu Hue B. T. , Goubitz Kees , Peschar René , van Maarseveen Jan H. , Hiemstra Henk 
Published: May 2011

AbstractThis report describes intramolecular [2+2] photocycloadditions of several butenolides with an allenylmethyl substituent at the 5‐position. These photosubstrates were prepared from 2‐(silyloxy)furans through silver‐mediated reactions with allenylmethyl bromides. Two cases were studied where the lactone was replaced by an N‐Boc‐lactam. Irradiations of the photosubstrates were carried out with 300 nm UV‐light in acetonitrile/acetone mixtures. Crossed cycloadducts were produced in good yields via cycloaddition of the heterocyclic double bond with the allene internal double bond. The products were γ‐lactones (γ‐lactams) containing the strained 5‐methylenebicyclo[2.1.1]hexane skeleton. In some cases the products were unstable due to remarkably facile retro‐ene reactions (1,5‐hydrogen shifts) leading to unique α,β‐unsaturated γ‐lactone derivatives. These reactions occurred only with well‐oriented C–H bonds so that strain‐releasing four‐membered ring opening could take place. This retro‐ene reaction was studied in detail for more highly substituted derivatives in order to establish its relevance in connection with the instability of the natural terpenoid solanoeclepin A, the hatching agent of potato cyst nematodes. To this end, the methylenecyclobutane moiety in one of the cycloadducts was converted into a bicyclo[2.1.1]hexan‐5‐one (cyclobutanone) substructure.
Copper‐Catalyzed Aerobic Oxidative Cyclization of Hydrazones to Pyrazolidinones
Authors: Dos Santos Aurélie , El Kaïm Laurent , Grimaud Laurence , Ronsseray Caroline 
Published: May 2011

AbstractN‐Aryl hydrazones participate, under copper catalysis, in a [3+2] cycloaddition/aerobic oxidation cascade reaction to form pyrazolidinones. The starting hydrazones were prepared by three‐component coupling of allylic amines, acyl chlorides, and aryl diazonium salts.
Theoretical Investigation of Electrochemical Signal from Nanoscale Systems
Authors: Liang Shuai , Dong Xiandui 
Published: May 2011

AbstractIn this paper, we report a theoretical study exploring the stochastic signal from electrochemical detection toward the nanometer scale systems. By using a discrete simulation as well as a statistical theory, this work investigates the distribution of the capturing times for redox molecules that released at a given distance from an electrode. We find that the capturing times tend to distribute over a wider range with a larger distance between the molecule’s source and the electrode, and thus the corresponding electrochemical signal would be somewhat less repeatable.
Pathways of Electrochemical Oxidation of Indolic Compounds
Authors: Enache Teodor Adrian , Oliveira‐Brett Ana Maria 
Published: May 2011

AbstractThe electrochemical behaviour of indole and a group of indole‐containing compounds with a substituent at the C3 position, indol‐3‐acetamide (IAM), tryptamine, gramine, indole acetic acid (IAA), indole propionic acid (IPA), indole butyric acid (IBA) and tryptophan, was investigated at a glassy carbon electrode, in order to determine their oxidation pathways. Indole undergoes one irreversible pH dependent oxidation, whereas the oxidation process of indole derivatives was more complex, a two step, the oxidation at C2 position on the pyrrole ring followed by the hydroxylation at the C7 position of the benzene moiety of indoles, irreversible pH dependent oxidation.