bluuebunny/crossref_metadata_2025 huggingface dataset:
Mode coupling theory analysis of electrolyte solutions: Time dependent diffusion, intermediate scattering function, and ion solvation dynamics
Authors: Roy Susmita , Yashonath Subramanian , Bagchi Biman
Published: March 2015

A self-consistent mode coupling theory (MCT) with microscopic inputs of equilibrium pair correlation functions is developed to analyze electrolyte dynamics. We apply the theory to calculate concentration dependence of (i) time dependent ion diffusion, (ii) intermediate scattering function of the constituent ions, and (iii) ion solvation dynamics in electrolyte solution. Brownian dynamics with implicit water molecules and molecular dynamics method with explicit water are used to check the theoretical predictions. The time dependence of ionic self-diffusion coefficient and the corresponding intermediate scattering function evaluated from our MCT approach show quantitative agreement with early experimental and present Brownian dynamic simulation results. With increasing concentration, the dispersion of electrolyte friction is found to occur at increasingly higher frequency, due to the faster relaxation of the ion atmosphere. The wave number dependence of intermediate scattering function, F(k, t), exhibits markedly different relaxation dynamics at different length scales. At small wave numbers, we find the emergence of a step-like relaxation, indicating the presence of both fast and slow time scales in the system. Such behavior allows an intriguing analogy with temperature dependent relaxation dynamics of supercooled liquids. We find that solvation dynamics of a tagged ion exhibits a power law decay at long times—the decay can also be fitted to a stretched exponential form. The emergence of the power law in solvation dynamics has been tested by carrying out long Brownian dynamics simulations with varying ionic concentrations. The solvation time correlation and ion-ion intermediate scattering function indeed exhibit highly interesting, non-trivial dynamical behavior at intermediate to longer times that require further experimental and theoretical studies.
Finite-dimensional representations of difference operators and the identification of remarkable matrices
Authors: Calogero Francesco
Published: March 2015

Two square matrices of (arbitrary) order N are introduced. They are defined in terms of N arbitrary numbers zn, and of an arbitrary additional parameter (a respectively q), and provide finite-dimensional representations of the two operators acting on a function f(z) as follows: [f(z + a) − f(z)]/a respectively [f(qz) − f(z)]/[(q − 1) z]. These representations are exact—in a sense explained in the paper—when the function f(z) is a polynomial in z of degree less than N. This formalism allows to transform difference equations valid in the space of polynomials of degree less than N into corresponding matrix-vector equations. As an application of this technique, several remarkable square matrices of order N are identified, which feature explicitly N arbitrary numbers zn, or the N zeros of polynomials belonging to the Askey and q-Askey schemes. Several of these findings have a Diophantine character.
Implementation of EPICS based vacuum control system for variable energy cyclotron centre, Kolkata
Authors: Roy Anindya , Bhole R. B. , Nandy Partha P. , Yadav R. C. , Pal Sarbajit , Roy Amitava
Published: March 2015

The vacuum system of the Room Temperature (K = 130) Cyclotron of Variable Energy Cyclotron Centre is comprised of vacuum systems of main machine and Beam Transport System. The vacuum control system is upgraded to a PLC based Automated system from the initial relay based Manual system. The supervisory control of the vacuum system is implemented in Experimental Physics and Industrial Control System (EPICS). An EPICS embedded ARM based vacuum gauge controller is developed to mitigate the requirement of vendor specific gauge controller for gauges and also for seamless integration of the gauge controllers with the control system. A set of MS-Windows ActiveX components with embedded EPICS Channel Access interface are developed to build operator interfaces with less complex programming and to incorporate typical Windows feature, e.g., user authentication, file handling, better fonts, colors, mouse actions etc. into the operator interfaces. The control parameters, monitoring parameters, and system interlocks of the system are archived in MySQL based EPICS MySQL Archiver developed indigenously. In this paper, we describe the architecture, the implementation details, and the performance of the system.
The evolutionary design of condensers
Authors: Bejan A. , Lee J. , Lorente S. , Kim Y.
Published: March 2015

Condensers are flow architectures needed to provide high rates of condensation (or cooling) per unit volume, in enclosures with fixed volume. Their design has not changed from configurations consisting of the banks of horizontal tubes. In this paper, we outline a free path to evolving the design by exploring new features of flow configuration: flattened tubes, multiple tube sizes, arrays of flattened tubes, vertical tubes with turbulent film flow, forced convection condensation instead of gravity driven condensation, and the optimal length of a horizontal tube, i.e., the number of tubes in a column aligned with vapor cross flow. We show that the condensation density can be increased sizably by varying freely and without bias the morphology of the flow system: the shapes and arrangement of the cooled surfaces on which condensation occurs. The evolution of technology is described in terms of the special time direction of the useful (purposeful) changes in the configuration (shapes, arrangements) of surfaces on which flow/condensation occurs. This explains what “evolution” means. It is an important step for physics, not just technology.
Dynamical disease: Challenges for nonlinear dynamics and medicine
Authors: Glass Leon
Published: March 2015

Dynamical disease refers to illnesses that are associated with striking changes in the dynamics of some bodily function. There is a large literature in mathematics and physics which proposes mathematical models for the physiological systems and carries out analyses of the properties of these models using nonlinear dynamics concepts involving analyses of the stability and bifurcations of attractors. This paper discusses how these concepts can be applied to medicine.
Flag flutter in inviscid channel flow
Authors: Alben Silas
Published: March 2015

Using nonlinear vortex-sheet simulations, we determine the region in parameter space in which a straight flag in a channel-bounded inviscid flow is unstable to flapping motions. We find that for heavier flags, greater confinement increases the size of the region of instability. For lighter flags, confinement has little influence. We then compute the stability boundaries analytically for an infinite flag and find similar results. For the finite flag, we also consider the effect of channel walls on the large-amplitude periodic flapping dynamics. We find that multiple flapping states are possible but rare at a given set of parameters, when periodic flapping occurs. As the channel walls approach the flag, its flapping amplitude decreases roughly in proportion to the near-wall distance, for both symmetric and asymmetric channels. Meanwhile, its dominant flapping frequency and mean number of deflection extrema (or “wavenumber”) increase in a nearly stepwise fashion. That is, they remain nearly unchanged over a wide range of channel spacing, but when the channel spacing is decreased below a certain value, they undergo sharp increases corresponding to a higher flapping mode.
Effects of the internal friction and the solvent quality on the dynamics of a polymer chain closure
Authors: Yu Wancheng , Luo Kaifu
Published: March 2015

Using 3D Langevin dynamics simulations, we investigate the effects of the internal friction and the solvent quality on the dynamics of a polymer chain closure. We show that the chain closure in good solvents is a purely diffusive process. By extrapolation to zero solvent viscosity, we find that the internal friction of a chain plays a non-ignorable role in the dynamics of the chain closure. When the solvent quality changes from good to poor, the mean closure time τc decreases by about 1 order of magnitude for the chain length 20 ≤ N ≤ 100. Furthermore, τc has a minimum as a function of the solvent quality. With increasing the chain length N, the minimum of τc occurs at a better solvent. Finally, the single exponential distributions of the closure time in poor solvents suggest that the negative excluded volume of segments does not alter the nearly Poisson statistical characteristics of the process of the chain closure.
Electrical characterization and analysis of the degradation of electrode Schottky barriers in BaTiO3 dielectric materials due to hydrogen exposure
Authors: Heidary Damoon Sohrabi Baba , Qu Weiguo , Randall Clive A.
Published: March 2015

Hydrogen gas creates a highly damaging environment that degrades electrical properties in oxide based dielectrics and piezoelectrics. In this study, the degradation resistivity due to hydrogen gas in a barium titanate X7R dielectric is designed and processed for base metal electrode capacitors. The present paper is devoted to I-V measurements and the loss of resistivity in the electrode Schottky barriers. The DC degradation and asymmetries noted in I-V forward and reverse biasing conditions were assumed to be hydrogen ion interstitials, locally creating donor substitutions. Thermionic and field emission conductivity mechanisms are applied to model the I-V data; the conductivity is controlled by the Schottky barrier heights and hydrogen ions localizing at the interfaces. Finally, a mechanism was proposed for resistivity degradation due to exposure to hydrogen gas. The proposed mechanism predicts the degradation should be reversible, and its validity was examined by recovery tests.
Control of a three-dimensional magnetic force generated from a magnetic navigation system to precisely manipulate the locomotion of a magnetic microrobot
Authors: Nam J. K. , Jeon S. M. , Lee W. S. , Jang G. H.
Published: March 2015

We propose a method to generate a three-dimensional (3D) magnetic force to manipulate a magnetic microrobot in various environments by using a magnetic navigation system. The proposed method is based on the control of the magnetic force with respect to the change in the magnetization direction of the microrobot and an external magnetic flux gradient. We derived the nonlinear constraint equations which can determine the required direction of the uniform magnetic fields and magnetic gradients to generate the 3D magnetic force of a microrobot. The solutions of the equations were calculated using a geometrical analysis of the equations without any singular point. The proposed methodology was verified on 3D planar environments considering gravitational force, and we also conducted an experiment in a 3D water-filled tubular environment to verify the possibility of the clinical application in human blood vessels.
The creation of large-volume, gradient-free warm dense matter with an x-ray free-electron laser
Authors: Lévy A. , Audebert P. , Shepherd R. , Dunn J. , Cammarata M. , Ciricosta O. , Deneuville F. , Dorchies F. , Fajardo M. , Fourment C. , Fritz D. , Fuchs J. , Gaudin J. , Gauthier M. , Graf A. , Lee H. J. , Lemke H. , Nagler B. , Park J. , Peyrusse O. , Steel A. B. , Vinko S. M. , Wark J. S. , Williams G. O. , Zhu D. , Lee R. W.
Published: March 2015

The efficiency and uniformity of heating induced by hard x-ray free-electron laser pulse is investigated for 0.5 μm silver foils using the X-ray Pump Probe instrument at the Linac Coherent Light Source facility. Intense 8.9 keV x-ray pulses of 60 fs duration deposit energy predominantly via inner-shell ionization to create a non-equilibrium Ag solid density plasma. The x-ray pulses are focused to 14 × 17 μm2 by means of beryllium lenses and by varying the total beam energy, the energy deposition is varied over a range of irradiances from 4.4 to 6.5 × 1015 W/cm2. Two time-and-space resolved interferometers simultaneously probed the expansion of the front and rear sample surfaces and find evidence of a nearly symmetric expansion pointing to the uniformity of energy deposition over the full target thickness. The experimental results are compared with two different hydrodynamic simulations of the sample expansion. The agreement between experimental and theoretical results yields an estimate of the temperature evolution as a function of x-ray irradiance that varies from 8 to 10 eV for the x-ray irradiances studied.
Enhancement of electron energy during vacuum laser acceleration in an inhomogeneous magnetic field
Authors: Saberi H. , Maraghechi B.
Published: March 2015

In this paper, the effect of a stationary inhomogeneous magnetic field on the electron acceleration by a high intensity Gaussian laser pulse is investigated. A focused TEM (0,0) laser mode with linear polarization in the transverse x-direction that propagates along the z-axis is considered. The magnetic field is assumed to be stationary in time, but varies longitudinally in space. A linear spatial profile for the magnetic field is adopted. In other words, the axial magnetic field increases linearly in the z-direction up to an optimum point zm and then becomes constant with magnitude equal to that at zm. Three-dimensional single-particle simulations are performed to find the energy and trajectory of the electron. The electron rotates around and stays near the z-axis. It is shown that with a proper choice of the magnetic field parameters, the electron will be trapped at the focus of the laser pulse. Because of the cyclotron resonance, the electron receives enough energy from the laser fields to be accelerated to relativistic energies. Using numerical simulations, the criteria for optimum regime of the acceleration mechanism is found. With the optimized parameters, an electron initially at rest located at the origin achieves final energy of γ=802. The dynamics of a distribution of off-axis electrons are also investigated in which shows that high energy electrons with small energy and spatial spread can be obtained.
A new closeness centrality measure via effective distance in complex networks
Authors: Du Yuxian , Gao Cai , Chen Xin , Hu Yong , Sadiq Rehan , Deng Yong
Published: March 2015

Closeness centrality (CC) measure, as a well-known global measure, is widely applied in many complex networks. However, the classical CC presents many problems for flow networks since these networks are directed and weighted. To address these issues, we propose an effective distance based closeness centrality (EDCC), which uses effective distance to replace conventional geographic distance and binary distance obtained by Dijkstra's shortest path algorithm. The proposed EDCC considers not only the global structure of the network but also the local information of nodes. And it can be well applied in directed or undirected, weighted or unweighted networks. Susceptible-Infected model is utilized to evaluate the performance by using the spreading rate and the number of infected nodes. Numerical examples simulated on four real networks are given to show the effectiveness of the proposed EDCC.
Continental erosion and the Cenozoic rise of marine diatoms
Authors: Cermeño Pedro , Falkowski Paul G. , Romero Oscar E. , Schaller Morgan F. , Vallina Sergio M.
Published: March 2015

Significance

Diatoms are silica-precipitating microalgae responsible for roughly one-fifth of global primary production. The mechanisms that led these microorganisms to become one of the most prominent primary producers on Earth remain unclear. We explore the linkage between the erosion of continental silicates and the ecological success of marine diatoms over the last 40 My. We show that the diversification and geographic expansion of diatoms coincide with periods of increased continental weathering fluxes and silicic acid input to the oceans. On geological time scales, the ocean’s biologically driven sequestration of organic carbon (the biological pump) is proportional to the input flux of inorganic nutrients to the oceans. Our results suggest that the strength and efficiency of the biological pump increased over geological time.
Biochemical characterization of a
Naegleria
TET-like oxygenase and its application in single molecule sequencing of 5-methylcytosine
Authors: Pais June E. , Dai Nan , Tamanaha Esta , Vaisvila Romualdas , Fomenkov Alexey I. , Bitinaite Jurate , Sun Zhiyi , Guan Shengxi , Corrêa Ivan R. , Noren Christopher J. , Cheng Xiaodong , Roberts Richard J. , Zheng Yu , Saleh Lana
Published: March 2015

Significance

The discovery that 5-methylcytosine (
5m
C) can be iteratively oxidized by mammalian ten-eleven translocation (TET) proteins marks a breakthrough in the field of epigenetics. To better understand the evolutionary and functional linkage of TET family members, we characterized NgTET1 from the protist
Naegleria gruberi
, which bears homology to both TET and base J-binding protein, a thymidine hydroxylase in trypanosomes. We show that NgTET1 performs iterative oxidation of both
5m
C and thymidine (T) (minor activity) on various DNA forms, and that these activities can be modulated by mutagenesis. We also present evidence for the effect of sequence context on both
5m
C- and T-oxygenase activities. Finally, we show the utility of NgTET1 at direct methylome profiling using single-molecule, real-time sequencing.
Modulation of orthogonal body waves enables high maneuverability in sidewinding locomotion
Authors: Astley Henry C. , Gong Chaohui , Dai Jin , Travers Matthew , Serrano Miguel M. , Vela Patricio A. , Choset Howie , Mendelson Joseph R. , Hu David L. , Goldman Daniel I.
Published: March 2015

Significance

We examined the turning behavior of snakes performing sidewinding locomotion using a hypothesized two-wave control template. Sidewinders achieved exceptional maneuverability using two types of turns, shallow differential turns and sharp reversal turns, which we hypothesized are controlled by modulating horizontal wave amplitude and vertical wave phase offset, respectively. We tested these hypothesized control schemes using a modular snake robot capable of sidewinding, resulting in similar behaviors, and explored two-wave parameter space, resulting in discovery of a third turning mechanism that is not seen in snakes. Thus, we show that complex behaviors such as turning while sidewinding can emerge from independent modulations of each of the two waves comprising this control template, underscoring the utility of robots to test biological hypotheses.
TRAPPII regulates exocytic Golgi exit by mediating nucleotide exchange on the Ypt31 ortholog RabE
RAB11
Authors: Pinar Mario , Arst Herbert N. , Pantazopoulou Areti , Tagua Víctor G. , de los Ríos Vivian , Rodríguez-Salarichs Javier , Díaz J. Fernando , Peñalva Miguel A.
Published: March 2015

Significance

Ypt1 and Ypt31/32 RAB GTPases regulate traffic across the Golgi. Both are activated by TRAPP, an oligomeric GEF. Three TRAPP versions share the same core subunits. TRAPPI and TRAPPIII activate Ypt1. The third, TRAPPII, composed of TRAPPI plus specific subunits, appears to act specifically on Ypt31, but this role has been disputed. By combining the resolving power of fungal genetics with biochemical assays, we establish that the physiological target of TRAPPII is RabE, the
Aspergillus
Ypt31 ortholog. However, our data suggest that TRAPPII contains independent binding sites for RabE and RabO (Ypt1), possibly explaining its relative lack of discrimination in vitro. TRAPPII arrives at Golgi cisternae preceding their dissipation into carriers, determining the Golgi–to–post-Golgi transition through RabE recruitment.
Structural and kinetic analysis of protein-aggregate strains in vivo using binary epitope mapping
Authors: Bergh Johan , Zetterström Per , Andersen Peter M. , Brännström Thomas , Graffmo Karin S. , Jonsson P. Andreas , Lang Lisa , Danielsson Jens , Oliveberg Mikael , Marklund Stefan L.
Published: March 2015

Significance

The levels of aggregated specific proteins in the CNS in neurodegenerative diseases are minute, hampering analysis of structure and growth kinetics. Here we describe a generally applicable method based on binary epitope mapping. It was applied to analysis of superoxide dismutase aggregation in amyotrophic lateral sclerosis model mice. Two different strains of aggregates with different structures, physical stabilities, and growth kinetics were readily distinguished. Moreover, they were different from superoxide dismutase aggregates formed in vitro under a variety of conditions, revealing a key role of the CNS in shaping the aggregation process.
Using wavelength and slope to infer the historical origin of semiarid vegetation bands
Authors: Sherratt Jonathan A.
Published: March 2015

Significance

Self-organized vegetation patterns are a characteristic feature of semiarid regions. On gentle slopes banded patterns (stripes) are typical, and their wavelength is probably the most accessible statistic for patterned vegetation. Recent data show that on steeper slopes wavelengths are usually shorter, contradicting previous predictions of mathematical models. I resolve this “contradiction” by a detailed theoretical study of pattern generation. Moreover I show that the wavelength–slope relationship has a wholly unexpected predictive power, enabling one to infer whether the patterns arose from degradation of uniform vegetation or colonization of bare ground. When combined with climate records, this gives valuable insights into the historical origin of the patterns.
Tunable molecular orientation and elevated thermal stability of vapor-deposited organic semiconductors
Authors: Dalal Shakeel S. , Walters Diane M. , Lyubimov Ivan , de Pablo Juan J. , Ediger M. D.
Published: March 2015

Significance

Glasses are solids that lack the regular order of crystals. Organic glasses, when produced by deposition from the vapor, can exhibit high levels of molecular orientation that improve performance of devices such as organic light-emitting diodes. We show here that molecular orientation in such glasses is primarily controlled by the substrate temperature during deposition, suggesting that the performance of almost any device based upon amorphous organic materials might be systematically optimized by this route. We explain molecular orientation in the glass in terms of the orientation present near the surface of the corresponding liquid. The highly oriented glasses formed here also exhibit high density and improved thermal stability. These features will likely further enhance the performance of organic electronics devices.
β-Arrestin–biased signaling mediates memory reconsolidation
Authors: Liu Xing , Ma Li , Li Hao Hong , Huang Bing , Li You Xing , Tao Ye Zheng , Ma Lan
Published: March 2015

Significance

β-Adrenergic receptors (β-ARs) are hormone and neurotransmitter receptors. The data we present in this paper challenge the assumption that memory reconsolidation is governed by the traditional β-AR/G protein signaling pathway. We found that memory reconsolidation is mediated by a β-arrestin–dependent β-adrenergic signaling pathway. Our experiments demonstrate that upon memory retrieval, a β1-AR/β-arrestin2/ERK pathway is activated in distinct brain areas, stimulating de novo protein synthesis and inducing postretrieval memory restabilization. Moreover, memory reconsolidation can be disrupted by propranolol, but not biased β-blockers such as carvedilol and alprenolol. Our study thus demonstrates that memory reconsolidation is mediated by a β-arrestin–biased β-adrenergic signaling pathway and reveals the therapeutic potential for β-arrestin–biased ligands in the treatment of memory-related disorders.
SWI/SNF chromatin-remodeling complexes function in noncoding RNA-dependent assembly of nuclear bodies
Authors: Kawaguchi Tetsuya , Tanigawa Akie , Naganuma Takao , Ohkawa Yasuyuki , Souquere Sylvie , Pierron Gerard , Hirose Tetsuro
Published: March 2015

Significance

The postgenomic era has seen the identification of numerous long noncoding RNA (lncRNAs) in mammalian cells; however, their biological functions remain largely unknown. Nuclear paraspeckle assembly transcript 1 (NEAT1) is an lncRNA that participates in the construction of the massive ribonucleoprotein subnuclear complex, the paraspeckle. Paraspeckle formation proceeds in conjunction with NEAT1 biogenesis and the assembly of >40 proteins. Here, we demonstrate that SWItch/Sucrose NonFermentable (SWI/SNF) chromatin-remodeling complexes play an essential role in organizing the protein–protein interaction network of paraspeckles in a manner that does not require their canonical remodeling activity. We also show that SWI/SNF complexes are required for the assembly of the Satellite III lncRNA-dependent nuclear stress body. These data suggest the presence of a common pathway for the assembly of lncRNA-dependent nuclear bodies in mammalian cells.
Mitochondrial ATP synthase is dispensable in blood-stage
Plasmodium berghei
rodent malaria but essential in the mosquito phase
Authors: Sturm Angelika , Mollard Vanessa , Cozijnsen Anton , Goodman Christopher D. , McFadden Geoffrey I.
Published: March 2015

Mitochondrial ATP synthase is driven by chemiosmotic oxidation of pyruvate derived from glycolysis. Blood-stage malaria parasites eschew chemiosmosis, instead relying almost solely on glycolysis for their ATP generation, which begs the question of whether mitochondrial ATP synthase is necessary during the blood stage of the parasite life cycle. We knocked out the mitochondrial ATP synthase β subunit gene in the rodent malaria parasite,
Plasmodium berghei
, ablating the protein that converts ADP to ATP. Disruption of the β subunit gene of the ATP synthase only marginally reduced asexual blood-stage parasite growth but completely blocked mouse-to-mouse transmission via
Anopheles stephensi
mosquitoes. Parasites lacking the β subunit gene of the ATP synthase generated viable gametes that fuse and form ookinetes but cannot progress beyond this stage. Ookinetes lacking the β subunit gene of the ATP synthase had normal motility but were not viable in the mosquito midgut and never made oocysts or sporozoites, thereby abrogating transmission to naive mice via mosquito bite. We crossed the self-infertile ATP synthase β subunit knockout parasites with a male-deficient, self-infertile strain of
P. berghei
, which restored fertility and production of oocysts and sporozoites, which demonstrates that mitochondrial ATP synthase is essential for ongoing viability through the female, mitochondrion-carrying line of sexual reproduction in
P. berghei
malaria. Perturbation of ATP synthase completely blocks transmission to the mosquito vector and could potentially be targeted for disease control.
A new regime of nanoscale thermal transport: Collective diffusion increases dissipation efficiency
Authors: Hoogeboom-Pot Kathleen M. , Hernandez-Charpak Jorge N. , Gu Xiaokun , Frazer Travis D. , Anderson Erik H. , Chao Weilun , Falcone Roger W. , Yang Ronggui , Murnane Margaret M. , Kapteyn Henry C. , Nardi Damiano
Published: March 2015

Significance

A complete description of nanoscale thermal transport is a fundamental problem that has defied understanding for many decades. Here, we uncover a surprising new regime of nanoscale thermal transport where, counterintuitively, nanoscale heat sources cool more quickly when placed close together than when they are widely separated. This increased cooling efficiency is possible when the separation between nanoscale heat sources is comparable to the average mean free paths of the dominant heat-carrying phonons. This finding suggests new approaches for addressing the significant challenge of thermal management in nanosystems, with design implications for integrated circuits, thermoelectric devices, nanoparticle-mediated thermal therapies, and nanoenhanced photovoltaics for improving clean-energy technologies.
DNA-mediated engineering of multicomponent enzyme crystals
Authors: Brodin Jeffrey D. , Auyeung Evelyn , Mirkin Chad A.
Published: March 2015

Significance

Due to their unique structures and diverse catalytic functionalities, proteins represent a nearly limitless set of precursors for constructing functional supramolecular materials. However, programming the assembly of even a single protein into ordered superlattices is a difficult task, and a generalizable strategy for coassembling multiple proteins with distinct surface chemistries, or proteins and inorganic nanoparticles, does not currently exist. Here, we use the high-fidelity interactions characteristic of DNA–DNA “bonds” to direct the assembly of two proteins into six unique superlattices composed of either a single protein, multiple proteins, or proteins and gold nanoparticles. Significantly, the DNA-functionalized proteins retain their native catalytic functionalities both in the solution and crystalline states.
Structure of the paramyxovirus parainfluenza virus 5 nucleoprotein–RNA complex
Authors: Alayyoubi Maher , Leser George P. , Kors Christopher A. , Lamb Robert A.
Published: March 2015

Significance

Paramyxoviruses, the cause of many important human and animal diseases, constitute a large family of enveloped negative-stranded RNA viruses including parainfluenza virus 5 (PIV5). The virion RNA is associated with ∼2,600 protomers of N-protein in the form of a helical ribonucleoprotein (RNP) (nucleocapsid). The RNP serves as the template for the viral polymerase in vivo. When expressed, N forms a 13 member N-ring that resembles the building block of the RNP. We have determined the atomic structure of the N-ring from PIV5 with 78 bound RNA residues. Precisely, six nucleotides of RNA are associated with each N protomer. Modeling PIV5-N in an “open conformation” in the ring structure indicates how transcription/replication could occur with minimal changes to the nucleocapsid structure.
Dynamin 2-dependent endocytosis sustains T-cell receptor signaling and drives metabolic reprogramming in T lymphocytes
Authors: Willinger Tim , Staron Matthew , Ferguson Shawn M. , De Camilli Pietro , Flavell Richard A.
Published: March 2015

Significance

Signals through the T-cell receptor (TCR) activate T lymphocytes and promote protective immunity. Antigen binding to the TCR triggers both signaling through the receptor and its internalization from the cell surface. Continuous TCR signaling is required for T-lymphocyte proliferation, yet how signaling is maintained for many hours despite TCR internalization is unknown. In this report we show that genetically blocking TCR internalization inhibits T-lymphocyte proliferation. TCR internalization was required for sustained signaling and the activation of key pathways that promote T-lymphocyte metabolism. Together these results may have implications for T-lymphocyte–based immunotherapies.
Introducing relational work in Facebook and discussion boards
Authors: Locher Miriam A. , Bolander Brook , Höhn Nicole
Published: March 2015

This paper functions as the introduction to the special issue on ‘relational work in Facebook and discussion boards’. We position our research endeavors within interpersonal pragmatics (see Locher and Graham 2010), by reviewing literature on politeness, impoliteness and relational work in the context of computer-mediated communication. Foregrounding the relational aspect of language, we are particularly interested in establishing the connections between politeness, face and linguistic identity construction. We then position the four papers that form this special issue within this field of research. Two papers contribute to the study of relational work on discussion boards (Kleinke and Boes; Haugh, Chang and Kádár) and two deal with practices on Facebook (Theodoropoulou; Bolander and Locher).
The Marburg Corpus of Intermediate Learner English (MILE)
Authors: Kreyer Rolf
Published: March 2015

Over the last few decades, corpus linguistic research and methodology have
had a huge impact on the foreign language classroom, mainly as reference tools
but also by introducing new ways of (data-driven) learning into the classroom.
A fairly recent trend is the use of corpus-linguistic methods for the study of the
development of learner language, which has led to the compilation of a fairly
large number of learner corpora. Among other things, this has opened up new
avenues for language testing and assessment, e.g. in the context of the Common
European Framework of Reference for Languages (CEFR). However, although
learner corpora seem to lend themselves easily to such purposes, the role they
have actually played so far is rather minor in comparison to the huge influence
on other aspects of foreign language teaching (at least with regard to German
learners of English). The present chapter explores possible reasons and introduces
the Marburg Corpus of Intermediate Learner English (MILE) as a potential
resource for learner language analysis and for corpus-informed, -based and
-driven contributions to language testing and assessment.
Avalingua
Authors: Gamallo Otero Pablo , Garcia Marcos , del Río Iria , González López Isaac
Published: March 2015

The objective of this article is to present an automatic tool for detecting and
classifying grammatical errors in written language as well as to describe the
evaluation protocol we have carried out to measure its performance on learner
corpora. The tool was designed to detect and analyse the linguistic errors found
in text essays, assess the writing proficiency, and propose solutions with the aim
of improving the linguistic skills of students. It makes use of natural language
processing and knowledge-rich linguistic resources. So far, the tool has been
implemented for the Galician language. The system has been evaluated on two
learner corpora reaching 91% precision and 65% recall (76% F-score) for the
task of detecting different types of grammatical errors, including spelling, lexical
and syntactic ones.
First steps in assigning proficiency to texts in a learner corpus of computer-mediated communication
Authors: Marchand Tim , Akutsu Sumie
Published: March 2015

This chapter presents a new method for assigning proficiency levels to texts in a
learner corpus of computer-mediated communication (CMC). The CMC comes
from learner comments on news articles that form part of an English language
course for university students in Japan. The rationale for using the CMC discourse
as the basis of a learner corpus will be discussed, followed by a justification
of using a text-centred approach of assigning proficiency. The use of binary
decision trees to account for the complexity, accuracy and fluency evident in
the texts will be described, followed by a snapshot of the results from using the
method so far. The chapter concludes with the suggestion that while some of the
details may need refining, in principle the method could be of use in categorizing
the proficiency of texts in other learner corpora.
Genomics in rugby union: A review and future prospects
Authors: Heffernan Shane M. , Kilduff Liam P. , Day Stephen H. , Pitsiladis Yannis P. , Williams Alun G.
Published: March 2015

This article introduces some aspects of sports genomics in a rugby union context, considers the rugby‐specific genetic data in the published literature and outlines the next research steps required if the potential applications of genetic technology in rugby union, also identified here, are to become possible. A substantial proportion of the inter‐individual variation for many traits related to rugby performance, including strength, short‐term muscle power, VO2 max, injury susceptibility and the likelihood of being an elite athlete is inherited and can be investigated using molecular genetic techniques. In sports genomics, significant efforts have been made in recent years to develop large DNA biobanks of elite athletes for detailed exploration of the heritable bases of those traits. However, little effort has been devoted to the study of rugby athletes, and most of the little research that has focused on rugby was conducted with small cohorts of non‐elite players. With steadily growing knowledge of the molecular mechanisms underpinning complex performance traits and the aetiology of injury, investigating sports genomics in the context of rugby is now a viable proposition and a worthwhile endeavour. The RugbyGene project we describe briefly in this article is a multi‐institutional research collaboration in rugby union that will perform molecular genetic analyses of varying complexity. Genetic tests could become useful tools for rugby practitioners in the future and provide complementary and additional information to that provided by the non‐genetic tests currently used.
Neural correlates of early-closure garden-path processing: Effects of prosody and plausibility
Authors: den Ouden Dirk-Bart , Dickey Michael Walsh , Anderson Catherine , Christianson Kiel
Published: March 2015

Functional magnetic resonance imaging (fMRI) was used to investigate neural correlates of early-closure garden-path sentence processing and use of extrasyntactic information to resolve temporary syntactic ambiguities. Sixteen participants performed an auditory picture verification task on sentences presented with natural versus flat intonation. Stimuli included sentences in which the garden-path interpretation was plausible, implausible because of a late pragmatic cue, or implausible because of a semantic mismatch between an optionally transitive verb and the following noun. Natural sentence intonation was correlated with left-hemisphere temporal activation, but also with activation that suggests the allocation of more resources to interpretation when natural prosody is provided. Garden-path processing was associated with upregulation in bilateral inferior parietal and right-hemisphere dorsolateral prefrontal and inferior frontal cortex, while differences between the strength and type of plausibility cues were also reflected in activation patterns. Region of interest (ROI) analyses in regions associated with complex syntactic processing are consistent with a role for posterior temporal cortex supporting access to verb argument structure. Furthermore, ROI analyses within left-hemisphere inferior frontal gyrus suggest a division of labour, with the anterior–ventral part primarily involved in syntactic–semantic mismatch detection, the central part supporting structural reanalysis, and the posterior–dorsal part showing a general structural complexity effect.
Altering attentional control settings causes persistent biases of visual attention
Authors: Knight Helen C. , Smith Daniel T. , Knight David C. , Ellison Amanda
Published: March 2015

Attentional control settings have an important role in guiding visual behaviour. Previous work within cognitive psychology has found that the deployment of general attentional control settings can be modulated by training. However, research has not yet established whether long-term modifications of one particular type of attentional control setting can be induced. To address this, we investigated persistent alterations to feature search mode, also known as an attentional bias, towards an arbitrary stimulus in healthy participants. Subjects were biased towards the colour green by an information sheet. Attentional bias was assessed using a change detection task. After an interval of either 1 or 2 weeks, participants were then retested on the same change detection task, tested on a different change detection task where colour was irrelevant, or were biased towards an alternative colour. One experiment included trials in which the distractor stimuli (but never the target stimuli) were green. The key finding was that green stimuli in the second task attracted attention, despite this impairing task performance. Furthermore, inducing a second attentional bias did not override the initial bias toward green objects. The attentional bias also persisted for at least two weeks. It is argued that this persistent attentional bias is mediated by a chronic change to participants’ attentional control settings, which is aided by long-term representations involving contextual cueing. We speculate that similar changes to attentional control settings and continuous cueing may relate to attentional biases observed in psychopathologies. Targeting these biases may be a productive approach to treatment.
The suffix priming effect: Further evidence for an early morpho-orthographic segmentation process independent of its semantic content
Authors: Lázaro Miguel , Illera Víctor , Sainz Javier
Published: March 2015

This work presents the results of a masked lexical decision experiment in which we explore the morphological parsing of Spanish suffixed or pseudosuffixed words through the suffix priming effect. Priming the bases or pseudobases with their suffixed or pseudosuffixed forms is the standard process in experiments aimed at understanding the processes underlying morphological parsing in visual word recognition with masked priming lexical decision (e.g., darkness–DARK; corner–CORN). We, however, compare the effect of suffix priming on the lexical decision of suffixed ( ero–JORNALERO) and pseudosuffixed words ( ero–CORDERO), as well as the effect of orthographic priming on nonsuffixed words ( eba–PRUEBA). The results show that in the case of suffixed and pseudosuffixed words, related primes ( ero–JORNALERO; ero–CORDERO) significantly accelerated response latencies in comparison to unrelated primes ( ista–JORNALERO; ura–CORDERO), while for simple words there was no facilitation from the orthographically related prime in comparison to the unrelated prime ( eba–PRUEBA; afo–PRUEBA). These results are consistent with the so-called morpho-orthographic segmentation process in the course of visual word recognition, which might also be independent of orthographic and purely semantic factors. Our results also support the view that morphological parsing takes place regardless of whether a stem is present in a word. These results complement findings from studies dealing with CORNER- and BROTHEL-like stimuli.
Rapid Communication: Personality and attention: Levels of neuroticism and extraversion can predict attentional performance during a change detection task
Authors: Hahn Sowon , Buttaccio Daniel R. , Hahn Jungwon , Lee Taehun
Published: March 2015

The present study demonstrates that levels of extraversion and neuroticism can predict attentional performance during a change detection task. After completing a change detection task built on the flicker paradigm, participants were assessed for personality traits using the Revised Eysenck Personality Questionnaire (EPQ–R). Multiple regression analyses revealed that higher levels of extraversion predict increased change detection accuracies, while higher levels of neuroticism predict decreased change detection accuracies. In addition, neurotic individuals exhibited decreased sensitivity A′ and increased fixation dwell times. Hierarchical regression analyses further revealed that eye movement measures mediate the relationship between neuroticism and change detection accuracies. Based on the current results, we propose that neuroticism is associated with decreased attentional control over the visual field, presumably due to decreased attentional disengagement. Extraversion can predict increased attentional performance, but the effect is smaller than the relationship between neuroticism and attention.
miR-501-3p mediates the activity-dependent regulation of the expression of AMPA receptor subunit GluA1
Authors: Hu Zhonghua , Zhao Jun , Hu Tianyi , Luo Yan , Zhu Jun , Li Zheng
Published: March 2015

The number of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs) in synapses determines synaptic strength. AMPAR expression can be regulated locally in dendrites by synaptic activity. The mechanisms of activity-dependent local regulation of AMPAR expression, however, remain unclear. Here, we tested whether microRNAs (miRNAs) are involved in N-methyl-d-aspartate (NMDA) receptor (NMDAR)–dependent AMPAR expression. We used the 3′ untranslated region of Gria1, which encodes the AMPA receptor subunit GluA1, to pull down miRNAs binding to it and analyzed these miRNAs using next-generation deep sequencing. Among the identified miRNAs, miR-501-3p is also a computationally predicted Gria1-targeting miRNA. We confirmed that miR-501-3p targets Gria1 and regulates its expression under physiological conditions. The expression of miR-501-3p and GluA1, moreover, is inversely correlated during postnatal brain development. miR-501-3p expression is up-regulated locally in dendrites through the NMDAR subunit GluN2A, and this regulation is required for NMDA-induced suppression of GluA1 expression and long-lasting remodeling of dendritic spines. These findings elucidate a miRNA-mediated mechanism for activity-dependent, local regulation of AMPAR expression in dendrites.
WISp39 binds phosphorylated Coronin 1B to regulate Arp2/3 localization and Cofilin-dependent motility
Authors: Howell Michael , Brickner Howard , Delorme-Walker Violaine D. , Choi Justin , Saffin Jean-Michel , Miller Daniel , Panopoulos Andreas , DerMardirossian Céline , Fotedar Arun , Margolis Robert L. , Fotedar Rati
Published: March 2015

We previously identified Waf1 Cip1 stabilizing protein 39 (WISp39) as a binding partner for heat shock protein 90 (Hsp90). We now report that WISp39 has an essential function in the control of directed cell migration, which requires WISp39 interaction with Hsp90. WISp39 knockdown (KD) resulted in the loss of directional motility of mammalian cells and profound changes in cell morphology, including the loss of a single leading edge. WISp39 binds Coronin 1B, known to regulate the Arp2/3 complex and Cofilin at the leading edge. WISp39 preferentially interacts with phosphorylated Coronin 1B, allowing it to complex with Slingshot phosphatase (SSH) to dephosphorylate and activate Cofilin. WISp39 also regulates Arp2/3 complex localization at the leading edge. WISp39 KD-induced morphological changes could be rescued by overexpression of Coronin 1B together with a constitutively active Cofilin mutant. We conclude that WISp39 associates with Hsp90, Coronin 1B, and SSH to regulate Cofilin activation and Arp2/3 complex localization at the leading edge.
YB-1 regulates stress granule formation and tumor progression by translationally activating G3BP1
Authors: Somasekharan Syam Prakash , El-Naggar Amal , Leprivier Gabriel , Cheng Hongwei , Hajee Shamil , Grunewald Thomas G.P. , Zhang Fan , Ng Tony , Delattre Olivier , Evdokimova Valentina , Wang Yuzhuo , Gleave Martin , Sorensen Poul H.
Published: March 2015

Under cell stress, global protein synthesis is inhibited to preserve energy. One mechanism is to sequester and silence mRNAs in ribonucleoprotein complexes known as stress granules (SGs), which contain translationally silent mRNAs, preinitiation factors, and RNA-binding proteins. Y-box binding protein 1 (YB-1) localizes to SGs, but its role in SG biology is unknown. We now report that YB-1 directly binds to and translationally activates the 5′ untranslated region (UTR) of G3BP1 mRNAs, thereby controlling the availability of the G3BP1 SG nucleator for SG assembly. YB-1 inactivation in human sarcoma cells dramatically reduces G3BP1 and SG formation in vitro. YB-1 and G3BP1 expression are highly correlated in human sarcomas, and elevated G3BP1 expression correlates with poor survival. Finally, G3BP1 down-regulation in sarcoma xenografts prevents in vivo SG formation and tumor invasion, and completely blocks lung metastasis in mouse models. Together, these findings demonstrate a critical role for YB-1 in SG formation through translational activation of G3BP1, and highlight novel functions for SGs in tumor progression.