bluuebunny/crossref_metadata_2025 huggingface dataset:
A finite difference Davidson procedure to sidestep full ab initio hessian calculation: Application to characterization of stationary points and transition state searches
Authors: Sharada Shaama Mallikarjun , Bell Alexis T. , Head-Gordon Martin
Published: May 2014

The cost of calculating nuclear hessians, either analytically or by finite difference methods, during the course of quantum chemical analyses can be prohibitive for systems containing hundreds of atoms. In many applications, though, only a few eigenvalues and eigenvectors, and not the full hessian, are required. For instance, the lowest one or two eigenvalues of the full hessian are sufficient to characterize a stationary point as a minimum or a transition state (TS), respectively. We describe here a method that can eliminate the need for hessian calculations for both the characterization of stationary points as well as searches for saddle points. A finite differences implementation of the Davidson method that uses only first derivatives of the energy to calculate the lowest eigenvalues and eigenvectors of the hessian is discussed. This method can be implemented in conjunction with geometry optimization methods such as partitioned-rational function optimization (P-RFO) to characterize stationary points on the potential energy surface. With equal ease, it can be combined with interpolation methods that determine TS guess structures, such as the freezing string method, to generate approximate hessian matrices in lieu of full hessians as input to P-RFO for TS optimization. This approach is shown to achieve significant cost savings relative to exact hessian calculation when applied to both stationary point characterization as well as TS optimization. The basic reason is that the present approach scales one power of system size lower since the rate of convergence is approximately independent of the size of the system. Therefore, the finite-difference Davidson method is a viable alternative to full hessian calculation for stationary point characterization and TS search particularly when analytical hessians are not available or require substantial computational effort.
Benchmarking the performance of density functional theory and point charge force fields in their description of sI methane hydrate against diffusion Monte Carlo
Authors: Cox Stephen J. , Towler Michael D. , Alfè Dario , Michaelides Angelos
Published: May 2014

High quality reference data from diffusion Monte Carlo calculations are presented for bulk sI methane hydrate, a complex crystal exhibiting both hydrogen-bond and dispersion dominated interactions. The performance of some commonly used exchange-correlation functionals and all-atom point charge force fields is evaluated. Our results show that none of the exchange-correlation functionals tested are sufficient to describe both the energetics and the structure of methane hydrate accurately, while the point charge force fields perform badly in their description of the cohesive energy but fair well for the dissociation energetics. By comparing to ice \documentclass[12pt]{minimal}\begin{document}${\rm I}_{\textrm {h}}$\end{document}Ih, we show that a good prediction of the volume and cohesive energies for the hydrate relies primarily on an accurate description of the hydrogen bonded water framework, but that to correctly predict stability of the hydrate with respect to dissociation to ice \documentclass[12pt]{minimal}\begin{document}${\rm I}_{\textrm {h}}$\end{document}Ih and methane gas, accuracy in the water-methane interaction is also required. Our results highlight the difficulty that density functional theory faces in describing both the hydrogen bonded water framework and the dispersion bound methane.
Deducting the temperature dependence of the structural relaxation time in equilibrium far below the nominal T
g by aging the decoupled conductivity relaxation to equilibrium
Authors: Wojnarowska Z. , Ngai K. L. , Paluch M.
Published: May 2014

Using broadband dielectric spectroscopy we investigate the changes in the conductivity relaxation times τσ observed during the physical aging of the protic ionic conductor carvedilol dihydrogen phosphate (CP). Due to the large decoupling of ion diffusion from host molecule reorientation, the ion conductivity relaxation time τσ(Tage,tage) can be directly measured at temperatures Tage below Tg for exceedingly long aging times tage till τσ(Tage,tage) has reached the equilibrium value $\tau _\sigma ^{eq} ( {T_{age} } )$τσeq(Tage). The dependence of τσ(Tage,tage) on tage is well described by the stretched exponential function, $\tau _\sigma ( {T_{age},t_{age} } ) = A{\rm exp}[ { - ( {\frac{{t_{age} }}{{\tau _{age} ( {T_{age} } )}}} )^\beta } ] + \tau _\sigma ^{eq} ( {T_{age} } )$τσ(Tage,tage)=A exp [−(tageτage(Tage))β]+τσeq(Tage), where β is a constant and τage(Tage) can be taken as the structural α-relaxation time of the equilibrium liquid at T = Tage. The value of $\tau _\sigma ^{eq} ( {T_{age} } )$τσeq(Tage) obtained after 63 days long annealing of CP, deviates from the Vogel-Fulcher-Tammann-Hesse (VFTHσ) dependence of τσ(T) determined from data taken above Tg and extrapolated down to Tage. Concurrently, τage(Tage) also deviates from the Vogel-Fulcher-Tammann-Hesse (VFTHα) dependence. The results help to answer the longstanding question of whether the VFTH dependence of τσ(T) as well as the structural α-relaxation time τα(T) holds or not in the equilibrium liquid state far below Tg.
Energy and exergy analysis of an adiabatic water-LiBr absorption system
Authors: Gutiérrez-Urueta G. , Huicochea A. , Rodríguez-Aumente P. , Rivera W.
Published: May 2014

This paper presents the exergy analysis of a single effect water-LiBr adiabatic absorption facility. A comparison to diabatic (isothermal) absorption systems was carried out, under varying operating parameters in terms of the coefficient of performance and exergy efficiency. The effect of generator, absorption, and evaporator temperatures on these parameters was determined as well as the inclusion of the exergy analysis for individual components. The results obtained allowed for the identification of the parameters that influence the performance of the adiabatic absorption system: where the recirculation ratio RR emerged as an important parameter showing that with increasing RR values the exergy efficiency and coefficient of performance improved and that the irreversibility of absorber and generator was more sensible to RR variations than to other components. Two recirculation configurations were analyzed, and it was verified that there were not significant differences in performance when the presented configuration was modified. The results also showed that the coefficient of performance could be up to 20% higher with adiabatic absorbers than with those systems operating with diabatic absorbers.
Effects of second-order difference-frequency wave forces on a new floating platform for an offshore wind turbine
Authors: Jiawen Li A. , Yougang Tang B. , Yeung C. Ronald W.
Published: May 2014

This paper presents a study on an innovative floating platform for an offshore wind turbine operating at water depth of 50-80 m. The main focus is on hydrodynamic modelling of the floating platform, with emphasis on the computation of second-order difference-frequency wave forces and their effects on the global rigid-body motion response. The time-domain analysis is conducted by coupling the wave analysis software WADAM of Det Norske Veritas and the aerodynamic code FAST of the National Renewable Energy Laboratory, USA, to consider the interaction between the wind turbine and floating platform. The numerical model accounts for aerodynamics, control system of the wind turbine, hydrodynamics, and the mooring dynamics of the platform. Case studies with irregular waves and dynamic wind load are performed. A comparison of the results of different case studies is made to assess the influence of second-order wave forces on the motions of the floating platform.
Effect of CoFe insertion in Co2MnSi/CoFe/n-GaAs junctions on spin injection properties
Authors: Ebina Yuya , Akiho Takafumi , Liu Hong-xi , Yamamoto Masafumi , Uemura Tetsuya
Published: May 2014

The CoFe thickness (tCoFe) dependence of spin injection efficiency was investigated for Co2MnSi/CoFe/n-GaAs junctions. The ΔVNL/I value, which is a measure of spin injection efficiency, strongly depended on tCoFe, where ΔVNL is the amplitude of a nonlocal spin-valve signal, and I is an injection current. Importantly, the maximum value of ΔVNL/I for a Co2MnSi/CoFe/n-GaAs junction was one order of magnitude higher than that for a CoFe/n-GaAs junction, indicating that a Co2MnSi electrode works as a highly polarized spin source. No clear spin signal, on the other hand, was observed for a Co2MnSi/n-GaAs junction due to diffusion of Mn atoms into the GaAs channel. Secondary ion mass spectrometry analysis indicated that the CoFe insertion effectively suppressed the diffusion of Mn into GaAs, resulting in improved spin injection properties compared with those for a Co2MnSi/n-GaAs junction.
A mathematical method for extracting cell secretion rate from affinity biosensors continuously monitoring cell activity
Authors: Gao Yandong , Zhou Qing , Matharu Zimple , Liu Ying , Kwa Timothy , Revzin Alexander
Published: May 2014

Our laboratory has previously developed miniature aptasensors that may be integrated at the site of a small group of cells for continuous detection of cell secreted molecules such as inflammatory cytokine interferon gamma (IFN-γ). In a system such as this, the signal measured at the sensor surfaces is a complex function of transport, reaction, as well as of cellular activity. Herein, we report on the development of a mathematical framework for extracting cell production rates from binding curves generated with affinity biosensors. This framework consisted of a diffusion-reaction model coupled to a root finding algorithm for determining cell production rates values causing convergence of a predetermined criterion. To experimentally validate model predictions, we deployed a microfluidic device with an integrated biosensor for measuring the IFN-γ release from CD4 T cells. We found close agreement between secretion rate observed theoretically and those observed experimentally. After taking into account the differences in sensor geometry and reaction kinetics, the method for cell secretion rate determination described in this paper may be broadly applied to any biosensor continuously measuring cellular activity.
Large enhancement of ferromagnetism by Cr doping in Mn3O4 nanowires
Authors: Li GaoMin , Tang XiaoBing , Lou ShiYun , Zhou ShaoMin
Published: May 2014

The Mn3O4 nanostructures having low temperature Curie point (45 K) disqualify them for most practical applications. In this work, single-crystalline Cr-doped Mn3O4 nanowires with ferromagnetic Curie point at room temperature (305 K) have been investigated. Our experimental results show an increase in effective magnetic moment per gram as Cr3+ replaces Mn3+ and oxygen vacancies, which result in a transition from paramagnetic (Mn3O4) to ferromagnetic. The doped Cr3+ and oxygen vacancies reveal the remarkable ferromagnetic in Mn3−xCrxO4 nanowires may be ascribed to bound magnetic polarons model. Our experimental results suggest these obtained nanowires are promising nanoscale building blocks in spintronic devices.
Vibration-based energy harvesting with stacked piezoelectrets
Authors: Pondrom P. , Hillenbrand J. , Sessler G. M. , Bös J. , Melz T.
Published: May 2014

Vibration-based energy harvesters with multi-layer piezoelectrets (ferroelectrets) are presented. Using a simple setup with nine layers and a seismic mass of 8 g, it is possible to generate a power up to 1.3 µW at 140 Hz with an input acceleration of 1g. With better coupling between seismic mass and piezoelectret, and thus reduced damping, the power output of a single-layer system is increased to 5 µW at 700 Hz. Simulations indicate that for such improved setups with 10-layer stacks, utilizing seismic masses of 80 g, power levels of 0.1 to 1 mW can be expected below 100 Hz.
Assessment of plasma impedance probe for measuring electron density and collision frequency in a plasma with spatial and temporal gradients
Authors: Hopkins Mark A. , King Lyon B.
Published: May 2014

Numerical simulations and experimental measurements were combined to determine the ability of a plasma impedance probe (PIP) to measure plasma density and electron collision frequency in a plasma containing spatial gradients as well as time-varying oscillations in the plasma density. A PIP is sensitive to collision frequency through the width of the parallel resonance in the Re[Z]-vs.-frequency characteristic, while also being sensitive to electron density through the zero-crossing of the Im[Z]-vs.-frequency characteristic at parallel resonance. Simulations of the probe characteristic in a linear plasma gradient indicated that the broadening of Re[Z] due to the spatial gradient obscured the broadening due to electron collision frequency, preventing a quantitative measurement of the absolute collision frequency for gradients considered in this study. Simulation results also showed that the PIP is sensitive to relative changes in electron collision frequency in a spatial density gradient, but a second broadening effect due to time-varying oscillations made collision frequency measurements impossible. The time-varying oscillations had the effect of causing multiple zero-crossings in Im[Z] at parallel resonance. Results of experiments and simulations indicated that the lowest-frequency zero-crossing represented the lowest plasma density in the oscillations and the highest-frequency zero-crossing represented the highest plasma density in the oscillations, thus the PIP probe was found to be an effective tool to measure both the average plasma density as well as the maximum and minimum densities due to temporal oscillations.
Differentiating the role of lithium and oxygen in retaining deuterium on lithiated graphite plasma-facing components
Authors: Taylor C. N. , Allain J. P. , Luitjohan K. E. , Krstic P. S. , Dadras J. , Skinner C. H.
Published: May 2014

Laboratory experiments have been used to investigate the fundamental interactions responsible for deuterium retention in lithiated graphite. Oxygen was found to be present and play a key role in experiments that simulated NSTX lithium conditioning, where the atomic surface concentration can increase to >40% when deuterium retention chemistry is observed. Quantum-classical molecular dynamic simulations elucidated this oxygen-deuterium effect and showed that oxygen retains significantly more deuterium than lithium in a simulated matrix with 20% lithium, 20% oxygen, and 60% carbon. Simulations further show that deuterium retention is even higher when lithium is removed from the matrix. Experiments artificially increased the oxygen content in graphite to ∼16% and then bombarded with deuterium. X-ray photoelectron spectroscopy showed depletion of the oxygen and no enhanced deuterium retention, thus demonstrating that lithium is essential in retaining the oxygen that thereby retains deuterium.
Analytical expressions for spectral composition of band luminescence from silicon solar cells under optical and electrical bias
Authors: Lan Dongchen , Green Martin A.
Published: May 2014

Luminescence imaging, utilizing optical and/or electrical excitation, is now a widely used characterization technique for silicon devices, particularly solar cells. Analytical solutions for the spectral distribution of band luminescence from planar silicon solar cells, including the previously neglected junction depletion region, are reported showing the dependence on wavelengths of optical excitation and emission, exciting voltage and the relevant device material and optical parameters. It is shown that solutions for all combinations of optical and electrical excitation modes under low-level injection can be expressed as superposition of photoluminescence at short circuit and electroluminescence in the dark. Important reciprocal relations between luminescence and its reverse absorption-related process are also discussed as is application of the solutions to textured devices.
High photoresponse inverted ultraviolet photodectectors consisting of iridium phosphor doped into poly(N-vinylcarbazole) polymeric matrix
Authors: Wang Xiao , Huang Jiang , Han Shijiao , Yu Junsheng
Published: May 2014

Highly sensitive inverted polymer ultraviolet (UV) photodectectors were fabricated by doping a phosphorescent material of bis[2-(4-tertbutylphenyl)benzothiazolato-N,C2′] iridium(acetylacetonate) [(t-bt)2Ir(acac)] into poly(N-vinylcarbazole) (PVK) polymeric matrix. Under the UV-260 nm illumination with an intensity of 0.7 mW/cm2, the device achieved a photocurrent of 11.37 mA/cm2 at −3 V, corresponding to a photoresponse of 15.97 A/W, which is 381% higher than the undoped device. Detailed analysis of photoluminescence, charge carrier transportation and film morphologies of PVK polymer active layers were carried out, and the enhanced UV absorption, formation of the triplet excitons and better charge carrier transport are ascribed to the improved photodectector performance.
Tunneling magnetoresistance in Fe3Si/MgO/Fe3Si(001) magnetic tunnel junctions
Authors: Tao L. L. , Liang S. H. , Liu D. P. , Wei H. X. , Wang Jian , Han X. F.
Published: May 2014

We present a theoretical study of the tunneling magnetoresistance (TMR) and spin-polarized transport in Fe3Si/MgO/Fe3Si(001) magnetic tunnel junction (MTJ). It is found that the spin-polarized conductance and bias-dependent TMR ratios are rather sensitive to the structure of Fe3Si electrode. From the symmetry analysis of the band structures, we found that there is no spin-polarized Δ1 symmetry bands crossing the Fermi level for the cubic Fe3Si. In contrast, the tetragonal Fe3Si driven by in-plane strain reveals half-metal nature in terms of Δ1 state. The giant TMR ratios are predicted for both MTJs with cubic and tetragonal Fe3Si electrodes under zero bias. However, the giant TMR ratio resulting from interface resonant transmission for the former decreases rapidly with the bias. For the latter, the giant TMR ratio can maintain up to larger bias due to coherent transmission through the majority-spin Δ1 channel.
Exfoliation of self-assembled 2D organic-inorganic perovskite semiconductors
Authors: Niu Wendy , Eiden Anna , Vijaya Prakash G. , Baumberg Jeremy J.
Published: May 2014

Ultra-thin flakes of 2D organic-inorganic perovskite (C6H9C2H4NH3)2PbI4 are produced using micromechanical exfoliation. Mono- and few-layer areas are identified using optical and atomic force microscopy, with an interlayer spacing of 1.6 nm. Refractive indices extracted from the optical spectra reveal a sample thickness dependence due to the charge transfer between organic and inorganic layers. These measurements demonstrate a clear difference in the exciton properties between “bulk” (>15 layers) and very thin (<8 layer) regions as a result of the structural rearrangement of organic molecules around the inorganic sheets.
A sessile drop setup for the time-resolved synchrotron study of solid-liquid interactions: Application to intermetallic formation in 55%Al-Zn alloys
Authors: Bernier N. , Vaughan G. B. M. , De Bruyn D. , Vitoux H. , De Craene M. , Gleyzolle H. , Gorges B. , Scheers J. , Claessens S.
Published: May 2014

We introduce a dedicated setup for measuring by synchrotron diffraction in-situ crystallographic and chemical information at the solid–liquid interface. This setup mostly consists of a double-heating furnace composed of a resistive heating for the solid surface and an inductive heating to produce a liquid droplet. The available high energy and high flux beams allow the rapid reaction kinetics to be investigated with very good time resolution down to 1 ms. An application of this setup is illustrated for the growth mechanisms of intermetallic phases during the hot-dipping of steel in a 55%Al-Zn bath. Results show that the three η-Al5Fe2, θ-Al13Fe4, and α-Al8Fe2Si phases grow at different times and rates during the dipping process, whereas the face-centered cubic AlFe3 phase is not formed.
Quantitative analysis of anisotropic magnetoresistance in Co2MnZ and Co2FeZ epitaxial thin films: A facile way to investigate spin-polarization in half-metallic Heusler compounds
Authors: Sakuraba Y. , Kokado S. , Hirayama Y. , Furubayashi T. , Sukegawa H. , Li S. , Takahashi Y. K. , Hono K.
Published: May 2014

Anisotropic magnetoresistance (AMR) effect has been systematically investigated in various Heusler compounds Co2MnZ and Co2FeZ (Z = Al, Si, Ge, and Ga) epitaxial films and quantitatively summarized against the total valence electron number NV. It was found that the sign of AMR ratio is negative when NV is between 28.2 and 30.3, and turns positive when NV becomes below 28.2 and above 30.3, indicating that the Fermi level (EF) overlaps with the valence or conduction band edges of half-metallic gap at NV ∼ 28.2 or 30.3, respectively. We also find out that the magnitude of negative AMR ratio gradually increases with shifting of EF away from the gap edges, and there is a clear positive correlation between the magnitude of negative AMR ratio and magnetoresistive output of the giant magnetoresistive devices using the Heusler compounds. This indicates that AMR can be used as a facile way to optimize a composition of half-metallic Heusler compounds having a high spin-polarization at room temperature.
Chirped-pulse manipulated carrier dynamics in low-temperature molecular-beam-epitaxy grown GaAs
Authors: Lee Chao-Kuei , Lin Yuan-Yao , Lin Sung-Hui , Lin Gong-Ru , Pan Ci-Ling
Published: May 2014

Chirped pulse controlled carrier dynamics in low-temperature molecular-beam-epitaxy grown GaAs are investigated by degenerate pump-probe technique. Varying the chirped condition of excited pulse from negative to positive increases the carrier relaxation time so as to modify the dispersion and reshape current pulse in time domain. The spectral dependence of carrier dynamics is analytically derived and explained by Shockley-Read Hall model. This observation enables the new feasibility of controlling carrier dynamics in ultrafast optical devices via the chirped pulse excitations.
Highly efficient greenish-blue platinum-based phosphorescent organic light-emitting diodes on a high triplet energy platform
Authors: Chang Y. L. , Gong S. , Wang X. , White R. , Yang C. , Wang S. , Lu Z. H.
Published: May 2014

We have demonstrated high-efficiency greenish-blue phosphorescent organic light-emitting diodes (PHOLEDs) based on a dimesitylboryl-functionalized C^N chelate Pt(II) phosphor, Pt(m-Bptrz)(t-Bu-pytrz-Me). Using a high triplet energy platform and optimized double emissive zone device architecture results in greenish-blue PHOLEDs that exhibit an external quantum efficiency of 24.0% and a power efficiency of 55.8 lm/W. This record high performance is comparable with that of the state-of-the-art Ir-based sky-blue organic light-emitting diodes.
Social interactions dominate speed control in poising natural flocks near criticality
Authors: Bialek William , Cavagna Andrea , Giardina Irene , Mora Thierry , Pohl Oliver , Silvestri Edmondo , Viale Massimiliano , Walczak Aleksandra M.
Published: May 2014

Significance

The coherent flight of bird flocks is one of nature’s most impressive aerial displays. Beyond the fact that thousands of birds fly, on average, with the same velocity, quantitative observations show that small deviations of individual birds from this average are correlated across the entire flock. By learning minimally structured models from field data, we show that these long-ranged correlations are consistent with local interactions among neighboring birds, but only because the parameters of the flock are tuned to special values, mathematically equivalent to a critical point in statistical mechanics. Being in this critical regime allows information to propagate almost without loss throughout the flock, while keeping the variance of individual velocities small.
Understanding the pharmacological properties of a metabolic PET tracer in prostate cancer
Authors: Viola-Villegas Nerissa Therese , Carlin Sean D. , Ackerstaff Ellen , Sevak Kuntal K. , Divilov Vadim , Serganova Inna , Kruchevsky Natalia , Anderson Michael , Blasberg Ronald G. , Andreev Oleg A. , Engelman Donald M. , Koutcher Jason A. , Reshetnyak Yana K. , Lewis Jason S.
Published: May 2014

Significance

Solid tumors adapt a glycolytic phenotype for their energetic requirements, leading to acidification of the extracellular environment. Targeting this global event is important to gauge the pace of tumor growth and invasiveness, as well as to provide a basis for predicting disease response to pH-dependent chemotherapies. To realize this goal, a noninvasive method is necessary to measure tumor extracellular acidification to meet clinical needs. This study explores the utility of pH (low) insertion peptide, an acidosis-targeting peptide, as a PET-based imaging probe to provide a method for quantifying extracellular pH and its correlation to known acidity markers, such as hypoxia, carbonic anhydrase IX, and lactate dehydrogenase A, within the prostate tumor tissue.
La dislocation dans le français oral d’apprenants suédophones
Authors: Engel Hugues
Published: May 2014

This chapter investigates the use and development of dislocations in oral productions by Swedish learners of French L2. Dislocations are highly frequent in French oral speech and play an essential role in building utterances. L2 users of French must therefore acquire the grammatical means necessary to build this structure as well as the pragmatic principles underlying its use. The study is empirical, and based on a corpus of oral productions from a wide range of non-native speakers (NNS), from beginners studying at university to L2 users who have spent many years in France. The corpus also includes oral productions from a control group of native speakers (NS). The aim is to determine how the different forms and functions of dislocations develop in French L2. Furthermore, the study examines the influence of tasks on the use of dislocations, by analysing two tasks which place very different demands on the informants in terms of cognitive effort, namely interviews and retellings.
Vocabulary aspects of advanced L2 French
Authors: Lundell Fanny Forsberg , Lindqvist Christina
Published: May 2014

In her overview of research on the advanced L2 learner, Bartning (1997) aims at characterizing the advanced learner variety. This characterization is above all based on morphosyntactic traits. The aim of this contribution is to present additional characteristics of the advanced learner as defined by Bartning (1997), as well as to describe even more advanced levels based on recent research concerning spoken L2 French. More specifically, the main issue under investigation is whether two vocabulary measures, viz. lexical richness and lexical formulaic sequences, can be used to distinguish between different advanced levels and thus contribute to the characterization of the advanced learner of French. An additional issue investigated here is whether these two lexical aspects correlate with each other or whether they develop at different rates.
Formulaic and proceduralised language in the initial and advanced stages of learning French
Authors: Towell Richard J.
Published: May 2014

This chapter is based on the model of SLA presented in Approaches to Second Language Acquisition (Towell & Hawkins 1994). It begins by presenting that view in summarised form. It then looks at four sets of empirical data drawn from two longitudinal multiple case studies and interprets the evidence in the light of the particular approach. The first two deal with learners in the initial stages of learning and show how they have to store formulaic knowledge in order to be able to extract syntactic information. The second two deal with advanced learners and show how they have to chunk and proceduralise intermediate knowledge in order to be able to develop both their knowledge and their fluency. The study of the advanced learners shows, however, that they do not become either as knowledgeable or as fluent in the L2 as they are in the L1. An interpretation of that evidence within the model offered suggests that this is because their L2 is based on a multiplicity of knowledge sources and that processing this kind of knowledge is more demanding of the memory systems than acquiring knowledge of and the ability to process the L1.
The acquisition of additive scope particles by Moroccan Arabic L1 learners of French
Authors: Véronique Georges Daniel
Published: May 2014

The study analyzes the acquisition of the additive particles aussi (‘also’), même (‘even’) and encore (‘still’) by five Moroccan Arabic L1 adult learners of French, participants in the ESF project (Perdue 1984). On the basis of a comparison between the French scope particles and their Moroccan Arabic equivalents, it is hypothesised that transfer from L1 plays an indirect role in the acquisition of French scope particles because of major semantic and syntactic differences between the two languages. The study sets out to describe the emergence and use of additive scope particles in a sample of texts spanning circa three years. It is shown that aussi is used quite early in the longitudinal data collected. Même is differently used in various learner varieties and encore is acquired late. The study compares the findings about the acquisition of additive particles in Moroccan Arabic learner varieties with previous work.
Development of object clitics in child L2 French
Authors: Granfeldt Jonas
Published: May 2014

It has been argued that the study of child L2 development can inform different maturational accounts of language acquisition. One such specific proposal was put forward by Meisel (2008), arguing for a cut-off point for monolingual or bilingual first language acquisition — (2)L1 — type of development at 3–4 years. The paper analyses the longitudinal development of object clitics in child L2 French (L1 Swedish) and compares the developmental sequence in child L2 learners (n = 7) with different Ages of onset of Acquisition (AoA) (from 3;0 to 6;5) to the adult L2 sequence that was found in previous studies (Granfeldt & Schlyter 2004). The study also includes age-matched simultaneous bilingual children (n = 3) and monolingual controls (n = 5). The results show that some of the child L2 learners with an AoA over 4 years display structures that are typical of adult L2 acquisition, whereas these structures were not found in the simultaneous bilingual children or in the child second language acquisition (cL2) children with an AoA under 4 years. It is suggested that differences in developmental sequences are due to a combination of AoA and the level of L1 linguistic development at the onset of L2 acquisition.
Scripting radio language amidst language shift in Indonesia
Authors: Manns Howard
Published: May 2014

There is a shift underway in many areas of Indonesia from local, ethnic languages like Javanese, to the national language, Indonesian. Few studies have explored the complexities faced by radio stations targeting the audiences undergoing this shift. This article explores the attitudes influencing the design of radio language at three local radio stations in East Java. Semi-structured interviews, based on extracts of radio language, are conducted with program directors and announcers at these stations. These data are used to outline how radio stations approach the design of radio talk amidst language shift. This paper explains this shift using two overlapping frames of media and language: audience design and mental scripts. Analysis shows both frames to be useful for understanding the design of radio language in East Java. A concluding discussion shows how a multi-dimensional understanding of radio language can provide important information on speech communities in-flux.
A post-mortem on the Malaysian content-based instruction initiative
Authors: Lee Seung Chun
Published: May 2014

This is a post-mortem on Malaysian TeSME (Teaching of Science and Mathematics in English) program based on its comparison with Canadian immersion programs. Malaysia and Canada have some common sociological aspects such as the size of population, the ratio of indigenous people and immigrants, and multilingual contexts. It also has in common various core elements in the set of criteria proposed by Swain and Johnson (1997) to define a prototypical immersion program. Thus, the lessons Canadians have learned from immersion may be seen as significant guiding light for TeSME and other attempts of content-based instruction programs. Canadian immersion has been different from TeSME at least in terms of three core features: overt support exists for the L1; the teachers are bilingual; and the classroom culture is that of the local L1 community. These differences made four issues more prominent: Learning outcome of TeSME; mainstay of TeSME; judicious use of L1; and function of TeSME. Finally some suggestions are proposed: give higher priority to promoting concept development across languages for now; make English classes more effective; promote bilingualism in TeSME; and extend TeSME’s function to understanding and integrating other cultures and languages.
Negotiation of power and solidarity in email
Authors: Nakane Ikuko , Kinoshita Thomson Chihiro , Tokumaru Satoko
Published: May 2014

The issue of e-politeness has been attracting increasing attention in the field of foreign language teaching and learning. This article examines how students of Japanese as a foreign language in Australia negotiated power and solidarity in their email correspondence with ‘facilitators’ in Japan who provided support in essay writing tasks. Their relationships, which were neither completely status-unequal nor status-equal, offer a unique social context for an examination of politeness. The study examines whether and how power and solidarity shifted over the 12 weeks of email exchanges. The results show varying levels of rapport and orientations to politeness developing over time, as well as evidence of students applying implicit input from the facilitators’ email messages. The article also considers the impacts, on the politeness phenomena in the data, of students’ cultural backgrounds and prior exposure to casual Japanese. The findings are discussed in relation to the question of ‘appropriateness’ in fostering foreign language learner ability to negotiate power and solidarity in intercultural communication.
Conjugative pili.
Authors: Christie P. J.
Published: May 2014

This chapter provides an overview of the biogenesis, structure and biological functions of conjugative pili. The discussion will focus mainly on the 2 more extensively characterized pili, F-pili elaborated by the Escherichia coli F plasmid and P-pili produced by E. coli plasmids of the P, N or W incompatibility (Inc) groups and the Agrobacterium tumefaciens VirB/VirD4 T-DNA transfer system.
Pilus biogenesis by the chaperone-usher pathway.
Authors: Phan G. , Waksman G.
Published: May 2014

Gram-negative bacteria display a variety of multi-subunit fibrillar structures on their cell surface called 'pili' or 'fimbriae'. Originally based on the filament morphology and the biogenesis machinery, pili are currently classified into five different families: (i) the curli, (ii) the type IV pili, (iii) the type III secretion system needle, (iv) the type IV secretion system pili, and (v) the chaperone-usher (CU) pili. This chapter reviews the biogenesis machinery of one of the most widespread and important microbial adhesion factor, the chaperone-usher (CU) pili, as well as its structure, function and polymerization. The CU pili are made of different subunits that polymerize to either thin flexible fibres or rigid long filaments. The main function of the CU pili is the adhesion to the host cells, mediated by a specialized pilus subunit, the adhesin, often containing a lectin domain that specifically recognizes the lining sugars of the target tissue, thereby defining the host tropism. Generally clustered under the same promoter, all the necessary components for the CU pili biogenesis are encoded within the same operon and it has been shown that multiple CU pathway clusters may be present within the same genome, extending the range of receptors the same bacterium might be able to adhere to.
Type 1 and P pili of uropathogenic Escherichia coli.
Authors: Russell C. , Mulvey M.
Published: May 2014

In uropathogenic Escherichia coli (UPEC), type 1 pili (T1P) and P pili enable the bacterium to bind to host epithelial cells within the urinary tract, which can lead to a urinary tract infection. This chapter reviews the genetics, structure and functions of UPEC T1P and P pili. It also describes the mechanisms by which T1P and P pili contribute to UPEC pathogenesis and host immune response.
Sortase structure and specificity in streptococci.
Authors: Cozzi R. , Maione D. , Rinaudo D.
Published: May 2014

This chapter reviews currently available data on pilus-specific sortases in streptococci, focusing on their genomic organization, structure, substrate recognition specificity and regulation.
Pili of Streptococcus pyogenes.
Authors: Scott J. R.
Published: May 2014

Streptococcus pyogenes, also called group A streptococcus (GAS), is one of the most common human pathogens. Although different GAS strains encode serologically different types of pili, and their structure and assembly differs, all GAS strains have their proteins necessary for synthesis and assembly of pili encoded in a single locus. Pili are composed of many copies of the backbone protein (the T antigen), linked end-to-end by a sortase family transpeptidase, or pilin polymerase. This chapter reviews the genetic organization of pili, the role of FCT genes in pilus assembly, the biological roles of pili in cell adhesion and biofilm formation, and the regulation of pilus gene expression.
Risks to human health from
Encephalitozoon
and
Enterocytozoon
carried by wild animals.
Authors: Lallo M. A. , Spadacci-Morena D. D.
Published: May 2014

The microsporidia are opportunistic pathogens, obligate intracellular parasites of vertebrates and invertebrates. They have been described in patients with AIDS, transplant recipients, children, travellers, seniors, contact lens wearers and patients with other immunosuppressive conditions. These organisms have long been known to be causative agents of economically important diseases in insects (silkworms and honey bees), fish, birds and mammals (lagomorpha, carnivores, rodents and primates). There are about 1300 species of microsporidia described and of the 14 species of microsporidia currently known to infect humans,
Enterocytozoon bieneusi
and
Encephalitozoon
are the most common causes of human infections and are associated with diarrhoea and systemic disease. The microsporidia that infect human beings, in particular,
Enterocytozoon
and
Encephalitozoon
are found in domestic and wild animals, and for this reason, the animals may be considered as a source of infection for humans. The waterborne, foodborne and zoonotic transmission have been demonstrated by molecular epidemiology. In this review, we present the most relevant epidemiological aspects of microsporidia simultaneously observed in humans and wildlife, in order to understand the risks from microsporidiosis in wild animals to human health.
Alternative technologies for tomato post-harvest quality preservation.
Authors: Pinheiro J. , Gonçalves E. M. , Silva C. L. M.
Published: May 2014

Fresh tomato (
Solanum lycopersicum
) is one of the most consumed fruits and the preservation of its quality and shelf-life extension is a continuous challenge. An understanding of fruit deterioration factors allows the investigation of new approaches to reach this objective. Fruit preservation is achieved by destroying enzymes and micro-organisms, and reducing physiological disorders, using treatments such as chlorinated water (HIPO), ozone, low or high temperatures, ultrasounds, UV-C radiation, modified atmosphere packaging, edible coatings and 1-methylcyclopropene. In this review, a description of action, advantages and disadvantages of each preservation treatment, and corresponding effects on tomato quality and safety are presented. The development of a
green
technology for tomato has advantages for all fresh chain interventions, with direct or indirect impacts on human health.
CDK-dependent phosphorylation of Alp7–Alp14 (TACC–TOG) promotes its nuclear accumulation and spindle microtubule assembly
Authors: Okada Naoyuki , Toda Takashi , Yamamoto Masayuki , Sato Masamitsu
Published: May 2014

As cells transition from interphase to mitosis, the microtubule cytoskeleton is reorganized to form the mitotic spindle. In the closed mitosis of fission yeast, a microtubule-associated protein complex, Alp7–Alp14 (transforming acidic coiled-coil–tumor overexpressed gene), enters the nucleus upon mitotic entry and promotes spindle formation. However, how the complex is controlled to accumulate in the nucleus only during mitosis remains elusive. Here we demonstrate that Alp7–Alp14 is excluded from the nucleus during interphase using the nuclear export signal in Alp14 but is accumulated in the nucleus during mitosis through phosphorylation of Alp7 by the cyclin-dependent kinase (CDK). Five phosphorylation sites reside around the nuclear localization signal of Alp7, and the phosphodeficient alp7-5A mutant fails to accumulate in the nucleus during mitosis and exhibits partial spindle defects. Thus our results reveal one way that CDK regulates spindle assembly at mitotic entry: CDK phosphorylates the Alp7–Alp14 complex to localize it to the nucleus.
ReadXplorer—visualization and analysis of mapped sequences
Authors: Hilker Rolf , Stadermann Kai Bernd , Doppmeier Daniel , Kalinowski Jörn , Stoye Jens , Straube Jasmin , Winnebald Jörn , Goesmann Alexander
Published: May 2014

Motivation: Fast algorithms and well-arranged visualizations are required for the comprehensive analysis of the ever-growing size of genomic and transcriptomic next-generation sequencing data.

Results: ReadXplorer is a software offering straightforward visualization and extensive analysis functions for genomic and transcriptomic DNA sequences mapped on a reference. A unique specialty of ReadXplorer is the quality classification of the read mappings. It is incorporated in all analysis functions and displayed in ReadXplorer's various synchronized data viewers for (i) the reference sequence, its base coverage as (ii) normalizable plot and (iii) histogram, (iv) read alignments and (v) read pairs. ReadXplorer's analysis capability covers RNA secondary structure prediction, single nucleotide polymorphism and deletion–insertion polymorphism detection, genomic feature and general coverage analysis. Especially for RNA-Seq data, it offers differential gene expression analysis, transcription start site and operon detection as well as RPKM value and read count calculations. Furthermore, ReadXplorer can combine or superimpose coverage of different datasets.

Availability and implementation: ReadXplorer is available as open-source software at http://www.readxplorer.org along with a detailed manual.

Contact:  rhilker@mikrobio.med.uni-giessen.de

Supplementary information:  Supplementary Data are available at Bioinformatics online.
Wide-field 12CO (J = 1–0) imaging of the nearby barred galaxy M 83 with NMA and Nobeyema 45 m telescope: Mole cular gas kinematics and star formation along the bar
Authors: Hirota Akihiko , Kuno Nario , Baba Junichi , Egusa Fumi , Habe Asao , Muraoka Kazuyuki , Tanaka Ayako , Nakanishi Hiroyuki , Kawabe Ryohei
Published: May 2014

We present the results of the wide-field 12CO(1–0) observations of the nearby barred galaxy M 83 carried out with the Nobeyama Millimeter Array (NMA). The interferometric data are combined with the data obtained with the Nobeyama 45 m telescope to recover the total flux. The target fields of the observations cover the molecular bar and part of the spiral arms, with a spatial resolution of ∼ 110 pc × 260 pc. By exploiting the resolution and sensitivity to extended CO emission, the impact of the galactic structures on the molecular gas content is investigated in terms of the gas kinematics and the star formation. By inspecting the gas kinematics, the pattern speed of the bar is estimated to be 57.4 ± 2.8 km s−1 kpc−1, which places the corotation radius at about 1.7 times the semi-major radius of the bar. Within the observed field, H ii regions brighter than 1037.6 erg s−1 in Hα luminosity are found to be preferentially located downstream of the CO-emitting regions. Azimuthal angular offsets between molecular gas and star forming (SF) calculated with the angular cross-correlation method confirm the trend. By comparing with a cloud orbit model based on the derived pattern speed, the angular offsets are found to be in accordance with a time delay of about 10 Myr. Finally, to test whether the arm/bar promote star formation efficiency [SFE ≡ Star Formation Rate (SFR)/H2 mass], SFR is derived with the diffuse-background-subtracted Hα and 24 μm images. The arm-to-interarm ratio of the SFE is found to lie in the range of 2 to 5, while it is ∼ 1 if no background removal is performed. The CO–SF offsets and the enhancement of the SFE in the arm/bar found in the inner region of M 83 are in agreement with the predictions of the classical galactic shock model.
Magnetic configurations related to the coronal heating and solar wind generation. I. Twist and expansion profiles of magnetic loops produced by flux emergence
Authors: Lee Hwanhee , Magara Tetsuya
Published: May 2014

The generation of outflows from the Sun known as solar winds is coupled with the heating of the solar corona, and both processes are operated in magnetic structures formed on the Sun. To study the magnetic configuration responsible for these processes, we use three-dimensional magnetohydrodynamic simulations to reproduce magnetic structures via flux emergence and investigate their configurations. We focus on two key quantities characterizing a magnetic configuration: the force-free parameter α and the flux expansion rate fex, the former of which represents how much a magnetic field is twisted while the latter represents how sharply a magnetic field expands. We derive distributions of these quantities in an emerging flux region. Our result shows that an emerging flux region consists of an outer part where a magnetic loop takes a large flux expansion rate but a small value of α at their photospheric footpoints, and an inner part occupied by those loops where a strong electric current flows. We also investigate the expansion profile of a magnetic loop comprising an emerging flux region. The profile is given by an exponential expansion type near the solar surface while it is given by a quadratic expansion type in an outer atmosphere. These detailed magnetic configurations obtained by this study contribute to developing a realistic model for the coronal heating and solar wind generation.