bluuebunny/crossref_metadata_2025 huggingface dataset:
Electric Breakdown in Liquids: Faster Ignition Using Less Energy
Authors: Yan Ting‐Ting , Zhong Xiao‐Xia , Rider Amanda E. , Ostrikov Kostya (Ken)
Published: April 2013

The formation of vapor layers around an electrode immersed in a conducting liquid prior to generation of a plasma discharge is studied using numerical simulations. This study quantifies and explains the effects of the electrode geometry and applied voltage pulses, as well as the electrical and thermal properties of the liquids on the temporal dynamics of the pre‐breakdown conditions in the vapor layer. This model agrees well with experimental data, in particular, the time needed to reach the electrical breakdown threshold. Because the time needed for discharge ignition can be accurately predicted from the model, the parameters such as the pulse shape, voltage, and electrode configuration can be optimized under different liquid conditions, which facilitates a faster and more energy‐efficient plasma generation.

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Sequence determinants of protein folding rates: Positive correlation between contact energy and contact range indicates selection for fast folding
Authors: Bastolla Ugo , Bruscolini Pierpaolo , Velasco José Luis
Published: April 2013

In comparison with intense investigation of the structural determinants of protein folding rates, the sequence features favoring fast folding have received little attention. Here, we investigate this subject using simple models of protein folding and a statistical analysis of the Protein Data Bank (PDB). The mean‐field model by Plotkin and coworkers predicts that the folding rate is accelerated by stronger‐than‐average interactions at short distance along the sequence. We confirmed this prediction using the Finkelstein model of protein folding, which accounts for realistic features of polymer entropy. We then tested this prediction on the PDB. We found that native interactions are strongest at contact range l = 8. However, since short range contacts tend to be exposed and they are frequently formed in misfolded structures, selection for folding stability tends to make them less attractive, that is, stability and kinetics may have contrasting requirements. Using a recently proposed model, we predicted the relationship between contact range and contact energy based on buriedness and contact frequency. Deviations from this prediction induce a positive correlation between contact range and contact energy, that is, short range contacts are stronger than expected, for 2/3 of the proteins. This correlation increases with the absolute contact order (ACO), as expected if proteins that tend to fold slowly due to large ACO are subject to stronger selection for sequence features favoring fast folding. Our results suggest that the selective pressure for fast folding is detectable only for one third of the proteins in the PDB, in particular those with large contact order. Proteins 2012; © 2012 Wiley Periodicals, Inc.
Structural and biochemical characterization of native and recombinant single insulin‐like growth factor‐binding domain protein (SIBD‐1) from the Central American Hunting Spider Cupiennius salei (Ctenidae)
Authors: Trachsel Christian , Widmer Christine , Kämpfer Urs , Bühr Claudia , Baumann Tommy , Kuhn‐Nentwig Lucia , Schürch Stefan , Schaller Johann , Baumann Ulrich
Published: April 2013

Cupiennius salei single insulin‐like growth factor binding domain protein (SIBD‐1) is an 8.6 kDa Cys‐, Pro‐, and Gly‐rich protein, discovered in the hemocytes of the Central American hunting spider Cupiennius salei. SIBD‐1 exhibits high sequence similarity to the N‐terminal domain of the insulin‐like growth factor‐binding protein superfamily and has been reported to play an important role in the spider's immune system. Here, the recombinant expression and the elucidation of the three‐dimensional structure of recombinant SIBD‐1 and the characterization of the sugar moiety at Thr2 of native SIBD‐1 is described in detail. Proteins 2012; © 2012 Wiley Periodicals, Inc.
Detection of protein complexes using a protein ranking algorithm
Authors: Zaki Nazar , Berengueres Jose , Efimov Dmitry
Published: April 2013

Detecting protein complexes from protein‐protein interaction (PPI) network is becoming a difficult challenge in computational biology. There is ample evidence that many disease mechanisms involve protein complexes, and being able to predict these complexes is important to the characterization of the relevant disease for diagnostic and treatment purposes. This article introduces a novel method for detecting protein complexes from PPI by using a protein ranking algorithm (ProRank). ProRank quantifies the importance of each protein based on the interaction structure and the evolutionarily relationships between proteins in the network. A novel way of identifying essential proteins which are known for their critical role in mediating cellular processes and constructing protein complexes is proposed and analyzed. We evaluate the performance of ProRank using two PPI networks on two reference sets of protein complexes created from Munich Information Center for Protein Sequence, containing 81 and 162 known complexes, respectively. We compare the performance of ProRank to some of the well known protein complex prediction methods (ClusterONE, CMC, CFinder, MCL, MCode and Core) in terms of precision and recall. We show that ProRank predicts more complexes correctly at a competitive level of precision and recall. The level of the accuracy achieved using ProRank in comparison to other recent methods for detecting protein complexes is a strong argument in favor of the proposed method. Proteins 2012;. © 2012 Wiley Periodicals, Inc.
Event detection and sub‐state discovery from biomolecular simulations using higher‐order statistics: Application to enzyme adenylate kinase
Authors: Ramanathan Arvind , Savol Andrej J. , Agarwal Pratul K. , Chennubhotla Chakra S.
Published: April 2013

Biomolecular simulations at millisecond and longer time‐scales can provide vital insights into functional mechanisms. Because post‐simulation analyses of such large trajectory datasets can be a limiting factor in obtaining biological insights, there is an emerging need to identify key dynamical events and relating these events to the biological function online, that is, as simulations are progressing. Recently, we have introduced a novel computational technique, quasi‐anharmonic analysis (QAA) (Ramanathan et al., PLoS One 2011;6:e15827), for partitioning the conformational landscape into a hierarchy of functionally relevant sub‐states. The unique capabilities of QAA are enabled by exploiting anharmonicity in the form of fourth‐order statistics for characterizing atomic fluctuations. In this article, we extend QAA for analyzing long time‐scale simulations online. In particular, we present HOST4MD—a higher‐order statistical toolbox for molecular dynamics simulations, which (1) identifies key dynamical events as simulations are in progress, (2) explores potential sub‐states, and (3) identifies conformational transitions that enable the protein to access those sub‐states. We demonstrate HOST4MD on microsecond timescale simulations of the enzyme adenylate kinase in its apo state. HOST4MD identifies several conformational events in these simulations, revealing how the intrinsic coupling between the three subdomains (LID, CORE, and NMP) changes during the simulations. Further, it also identifies an inherent asymmetry in the opening/closing of the two binding sites. We anticipate that HOST4MD will provide a powerful and extensible framework for detecting biophysically relevant conformational coordinates from long time‐scale simulations. Proteins 2012. © 2012 Wiley Periodicals, Inc.
Observer‐based linear parameter‐varying control with guaranteed ‐gain and ‐type performance objectives
Authors: Köroğlu Hakan
Published: April 2013

Synthesis of an observer‐based linear parameter‐varying controller is considered for a general linear parameter‐varying plant. The parameter vector and its derivative are both assumed to take values in known bounded domains, whereas only the parameter vector is assumed to be measurable during online operation. The synthesis problem is considered for ‐gain and ‐type performance objectives. Potentially conservative parameter‐dependent linear matrix inequality conditions are derived for the solvability of these two problems. To facilitate the reduction of conservatism, the conditions are expressed in a way to have bilinear dependence on an arbitrary positive scalar. In addition to employing a suitable relaxation scheme to reduce these conditions into finitely many constraints, a line search hence needs to be performed over the positive scalar to obtain the best achievable performance with an observer‐based controller. The online implementation of the observer‐based controller is relatively simpler if compared with a controller of unrestricted structure. Moreover, the observer‐based controller will have no dependence on the parameter derivatives irrespective of the choices of the design variables. Copyright © 2013 John Wiley & Sons, Ltd.
The Road for Nanomaterials Industry: A Review of Carbon Nanotube Production, Post‐Treatment, and Bulk Applications for Composites and Energy Storage
Authors: Zhang Qiang , Huang Jia‐Qi , Qian Wei‐Zhong , Zhang Ying‐Ying , Wei Fei
Published: April 2013

The innovation on the low dimensional nanomaterials brings the rapid growth of nano community. Developing the controllable production and commercial applications of nanomaterials for sustainable society is highly concerned. Herein, carbon nanotubes (CNTs) with sp2 carbon bonding, excellent mechanical, electrical, thermal, as well as transport properties are selected as model nanomaterials to demonstrate the road of nanomaterials towards industry. The engineering principles of the mass production and recent progress in the area of CNT purification and dispersion are described, as well as its bulk application for nanocomposites and energy storage. The environmental, health, and safety considerations of CNTs, and recent progress in CNT commercialization are also included. With the effort from the CNT industry during the past 10 years, the price of multi‐walled CNTs have decreased from 45 000 to 100 $ kg−1 and the productivity increased to several hundred tons per year for commercial applications in Li ion battery and nanocomposites. When the prices of CNTs decrease to 10 $ kg−1, their applications as composites and conductive fillers at a million ton scale can be anticipated, replacing conventional carbon black fillers. Compared with traditional bulk chemicals, the controllable synthesis and applicationsof CNTs on a million ton scale are still far from being achieved due to the challenges in production, purification, dispersion, and commercial application. The basic knowledge of growth mechanisms, efficient and controllable routes for CNT production, the environmental and safety issues, and the commercialization models are still inadequate. The gap between the basic scientific research and industrial development should be bridged by multidisciplinary research for the rapid growth of CNT nano‐industry.
Localization & exact holography
Authors: Dabholkar Atish , Gomes João , Murthy Sameer
Published: April 2013

Abstract

We consider the AdS
2
/CFT
1 holographic correspondence near the horizon of big four-dimensional black holes preserving four supersymmetries in toroidally compactified Type-II string theory. The boundary partition function of CFT
1 is given by the known quantum degeneracies of these black holes. The bulk partition function is given by a functional integral over string fields in AdS
2. Using recent results on localization we reduce the infinite-dimensional functional integral to a finite number of ordinary integrals over a space of localizing instantons. Under reasonable assumptions about the relevant terms in the effective action, these integrals can be evaluated exactly to obtain a bulk partition function. It precisely reproduces all terms in the exact Rademacher expansion of the boundary partition function as nontrivial functions of charges except for the Kloosterman sum which can in principle follow from an analysis of phases in the background of orbifolded instantons. Our results can be regarded as a step towards proving ‘exact holography’ in that the bulk and boundary partition functions computed independently agree for finite charges. Since the bulk partition function defines the quantum entropy of the black hole, our results enable the evaluation of perturbative as well as nonperturbative quantum corrections to the Bekenstein-Hawking-Wald entropy of these black holes.
Physical Properties of Aqueous Solutions of Pectin Containing Sunflower Wax
Authors: Baümler Erica R. , Carelli Amalia A. , Martini Silvana
Published: April 2013

The aim of this study is to investigate the physical properties of aqueous solutions of pectin (PA) containing sunflower wax (SFW), which are used as a basis for producing edible films. The stability and the rheological and microstructural characteristics of SFW/PA mixtures were evaluated. SFW/PA mixtures formed oil‐in‐water emulsions that were milky and opaque in appearance and were stable towards phase separation. Polarized micrographs revealed the presence of wax crystals, whose size decreased as pectin concentration increased. The rheological behavior of the aqueous solutions of pectin containing different amounts of SFW were best described by the generalized power law model of Herschel–Bulkley (H–B), which gave the best fit in all the range of shear rate values. Apparent viscosities and yield stress were determined using this model, and both properties increased with increasing pectin content. The apparent viscosity values were between 0.0095 and 0.1031 Pa s. SFW addition resulted in a small decrease in viscosity for emulsions formulated with 1 and 2 % PA, but the opposite effect was observed for emulsions formulated with 3 % PA. In addition, shear stress values were higher for emulsions with higher PA content, but were not affected by SFW addition.
A case of empty follicle syndrome who conceived after aspiration of an endometrial cyst
Authors: Tanaka Rieko , Murase Mariko , Aizawa Yoshino , Segino Miwa , Ishidera Yumi , Kitagawa Masakazu , Katayama Kayo , Takashima Kunitomo , Yumura Yasushi , Yoshida Hiroshi , Sakakibara Hideya , Hirahara Fumiki
Published: April 2013

Empty follicle syndrome (EFS) has been defined as a condition where no oocytes can be retrieved for in vitro fertilization (IVF) even though ultrasound findings and estradiol (E2) levels suggest the presence of potential follicles. The EFS is a rare condition with an incidence of 0.5–7 % of women undergoing IVF treatments. Although there are many hypotheses as to the cause of EFS, including advanced ovarian age, drug‐related problems, and dysfunctional folliculogenesis, its cause remains unknown. A 37‐year‐old woman with endometriosis and a 5‐year history of primary infertility underwent IVF treatment for 4 cycles. No oocytes were retrieved in 2 cycles and no fertilized eggs were obtained in the other 2 cycles. We assumed that endometriosis adversely affected folliculogenesis and fertilization. Aspiration of an endometrial cyst in the right ovary and subsequent administration of oral contraceptives resulted in successful folliculogenesis and fertilization. Thereafter, she conceived and delivered a 2,662 g female infant at 38 weeks of gestation. Here, we report a case of EFS who conceived in the 5th IVF cycle after aspiration of an endometrial cyst. We assumed that endometriosis might have been involved in the dysfunction of folliculogenesis and EFS.
Dynamical network biomarkers for identifying critical transitions and their driving networks of biologic processes
Authors: Liu Rui , Aihara Kazuyuki , Chen Luonan
Published: April 2013

Non‐smooth or even abrupt state changes exist during many biological processes, e.g., cell differentiation processes, proliferation processes, or even disease deterioration processes. Such dynamics generally signals the emergence of critical transition phenomena, which result in drastic changes of system states or eventually qualitative changes of phenotypes. Hence, it is of great importance to detect such transitions and further reveal their molecular mechanisms at network level. Here, we review the recent advances on dynamical network biomarkers (DNBs) as well as the related theoretical foundation, which can identify not only early signals of the critical transitions but also their leading networks, which drive the whole system to initiate such transitions. In order to demonstrate the effectiveness of this novel approach, examples of complex diseases are also provided to detect pre‐disease stage, for which traditional methods or biomarkers failed.
Sinking inside the box
Authors: Pritchard David
Published: April 2013

Convection in a closed porous domain is a temporally and spatially complex flow which evolves over long time scales as the driving buoyancy contrasts are eliminated by mixing. In a contribution that combines numerical, experimental and asymptotic approaches, Hewitt, Neufeld & Lister (J. Fluid Mech., vol. 719, 2013, pp. 551–586) demonstrate that the essential dynamics can be captured by simple ‘box’ models, both when the buoyancy supply is imposed at the upper boundary and when the domain contains a moving interface between different fluids. This work provides insights into the dynamics and viability of schemes for the geological sequestration of CO2.
Fatty acid desaturase 2 (FADS2) insertion/deletion polymorphism impact on muscle fatty acid profile in European grayling (Thymallus thymallus)
Authors: Renaville Bénédicte , Tulli Francesca , Bruno Massimiliano , Tibaldi Emilio , Messina Maria
Published: April 2013

An insertion (In)/deletion (Del) polymorphism in the fatty acid desaturase 2 (FADS2) gene, which codes for Δ6-desaturase, was for the first time observed in fish. The polymorphism is located in the seventh intron ofFADS2and the insertion consists of eleven repeats of CTGT (44 bp) with an allelic frequency, for the insertion, of 39 %. The polymorphism was associated with a modulation in Δ6-desaturase activity as significant effects on the ratio of EPA or DHA to their precursors were found (P< 0·001). A different distribution of SFA, MUFA and PUFA among the In/In, In/Del and Del/Del groups was also detected in fish fillet. The results suggest that genetic selection for this marker might improve the ability of European grayling to utilise dietaryn-3 long-chain PUFA precursors, as Δ6-desaturase is the rate-limiting enzyme in the production of EPA and DHA from α-linolenic acid.
Nutritional risk, functional status and mortality in newly institutionalised elderly
Authors: Cereda Emanuele , Pedrolli Carlo , Zagami Annunciata , Vanotti Alfredo , Piffer Silvano , Faliva Milena , Rondanelli Mariangela , Caccialanza Riccardo
Published: April 2013

Previous studies have reported a close relationship between nutritional and functional domains, but evidence in long-term care residents is still limited. We evaluated the relationship between nutritional risk and functional status and the association of these two domains with mortality in newly institutionalised elderly. In the present multi-centric prospective cohort study, involving 346 long-term care resident elderly, nutritional risk and functional status were determined upon admission by the Geriatric Nutritional Risk Index (GNRI) and the Barthel Index (BI), respectively. The prevalence of high (GNRI < 92) and low (GNRI 92–98) nutritional risk were 36·1 and 30·6 %, respectively. At multivariable linear regression, functional status was independently associated with age (P= 0·045), arm muscle area (P= 0·048), the number of co-morbidities (P= 0·027) and mainly with the GNRI (P< 0·001). During a median follow-up of 4·7 years (25th–75th percentile 3·7–6·2), 230 (66·5 %) subjects died. In the risk analysis, based on the variables collected at baseline, both high (hazard ratio (HR) 1·86, 95 % CI 1·32, 2·63;P< 0·001) and low nutritional risk (HR 1·52, 95 % CI 1·08, 2·14;P= 0·016) were associated with all-cause mortality. Participants at high nutritional risk (GNRI < 92) also showed an increased rate of cardiovascular mortality (HR 1·93, 95 % CI 1·28, 2·91;P< 0·001). No association with outcome was found for the BI. Upon admission, nutritional risk was an independent predictor of functional status and mortality in institutionalised elderly. Present data support the concept that the nutritional domain is more relevant than functional status to the outcome of newly institutionalised elderly.
On the Diversity and Influence of the Eusebian Alliance: The Case of Theodore of Heraclea
Authors: CRAWFORD MATTHEW R.
Published: April 2013

This article offers, for the first time in English, a reconstruction of the career of Theodore of Heraclea, a leading figure in the Eusebian alliance from the early 330s until the mid-350s. It also provides an overview of Theodore's literary remains and suggests that the anti-Marcellan tone of his surviving fragments is in keeping with the other documents that emanated from the Eusebian alliance during this period, especially those from the Council of Serdica (343) and the Council of Sirmium (351). Finally, it is suggested that the diversity of ways in which Theodore was received by later patristic authors illustrates that the polarising categories of ‘Arian’ and ‘Nicene’ are insufficiently nuanced to describe Theodore's actual theological concerns.
Three-dimensional and nonlinear analysis of efficiency enhancement in the E × B drifting electron laser with a prebunched electron beam and a planar wiggler
Authors: MARAGHECHI B. , JOKAR M. , BAHMAN F. JAFARI , NAEIMABADI A.
Published: April 2013

A nonlinear simulation of the E × B drifting electron laser (DEL) and the free-electron laser (FEL), in three dimensions, is presented for a prebunched electron beam to study efficiency enhancement. For the planar wiggler with flat pole faces, prebunching considerably shortens the saturation length, which favors the DEL compared to the FEL. Operation of the DEL with the planar wiggler with parabolic pole faces was not found to be possible due to the modulation of the E × B drift by the wiggler. However, simulation results of the FEL with this type of wiggler are reported.
Set of wires to simulate tokamaks with poloidal divertor
Authors: KROETZ T. , MARTINS CAROLINE G. L. , ROBERTO M. , CALDAS I. L.
Published: April 2013

Simple wire models have been proposed to simulate magnetic configurations in tokamaks. Here we consider electric currents in five parallel infinite wires to obtain double-null magnetic surfaces with specific choices of magnetic axis positions, triangularity, and elongation. As an example, we choose the position and the electric current of each wire to obtain magnetic surfaces similar to those expected in the tokamak international thermonuclear experimental reactor. Moreover, we also integrate the perturbed field line differential equation to simulate chaotic layers near the hyperbolic points and deposition patterns at the divertor plate observed in tokamaks. To simulate that, we add to the model a perturbing error field, due to asymmetries in the tokamak coils, and introduce a random collisional term to the field line mapping to reproduce escape pattern alterations due to particle collisions.
Text and formula in the Milanese cantus
Authors: HORNBY EMMA
Published: April 2013

This analytical article aims to establish the melodic grammar of thein directumMilanese cantus. Deviations from the generic norms might be experienced in performance as emphasising the words with which they appear. Certain texts (particularly ‘domin-’) are often associated with melodic shapes found elsewhere in the genre on the same words, regardless of what one might expect to encounter formally. Chants that share similar liturgical functions, or which appear in close liturgical proximity, often share melodic material and formal strategies. Building on and responding to Bailey'sThe Ambrosian Cantus(1987), the present article seeks to appreciate the cantus melodies as they have been preserved, rather than using them as a lens through which to seek a putative (and entirely rationally structured) lost ancestor.
Antisense regulation by transposon‐derived RNAs in the hyperthermophilic archaeon Sulfolobus solfataricus
Authors: Märtens Birgit , Manoharadas Salim , Hasenöhrl David , Manica Andrea , Bläsi Udo
Published: April 2013

We report the first example of antisense RNA regulation in a hyperthermophilic archaeon. In Sulfolobus solfataricus, the transposon‐derived paralogous RNAs, RNA‐2571–4, show extended complementarity to the 3′ UTR of the 1183 mRNA, encoding a putative phosphate transporter. Phosphate limitation results in decreased RNA‐2571 and increased 1183 mRNA levels. Correspondingly, the 1183 mRNA is faster degraded in vitro upon duplex formation with RNA‐2571. Insertion of the 1183 3′ UTR downstream of the lacS gene results in strongly reduced lacS mRNA levels in transformed cells, indicating that antisense regulation can function in trans.
Mast cells: from lipid droplets to lipid mediators
Authors: Dichlberger Andrea , Kovanen Petri T. , Schneider Wolfgang J.
Published: April 2013

LDs (lipid droplets) are metabolically highly active intracellular organelles. The lipid and protein profiles of LDs are cell-type-specific, and they undergo dynamic variation upon changes in the physiological state of a cell. It is well known that the main function of the LDs in adipocytes is to ensure energy supply and to maintain lipid homoeostasis in the body. In contrast, LDs in inflammatory cells have been implicated in eicosanoid biosynthesis, particularly under inflammatory conditions, thereby enabling them to regulate immune responses. Human mast cells are potent effector cells of the innate immune system, and the triacylglycerol (triglyceride) stores of their cytoplasmic LDs have been shown to contain large amounts of arachidonic acid, the main precursor of pro-inflammatory eicosanoids. In the present review, we discuss the current knowledge about the formation and function of LDs in inflammatory cells with specific emphasis on arachidonic acid and eicosanoid metabolism. On the basis of findings reported previously and our new observations, we propose a model in which lipolysis of LD-triacylglycerols provides arachidonic acid for lipid mediator generation in human mast cells.
DC‐free codes with complex‐valued signalling constellations
Authors: Jamieson Craig , Fair Ivan
Published: April 2013

The use of spectral shaping constrained codes is commonplace in baseband digital communication systems. In this study, the authors consider the use of constrained codes in bandpass systems through the design of DC‐free codes for the complex baseband representations of commonly used signalling constellations including quaternary phase shift keying, eight‐phase shift keying and sixteen quadrature amplitude modulation. The authors construct DC‐free codes for these signalling alphabets and present their spectral performance. They show that, similar to DC‐free codes for baseband systems, the variance of the running digital sum remains a good indicator of spectral performance and that Justesen's relationship between the sum variance and cut‐off frequency holds.
Space–time coding scheme for time–frequency asynchronous two‐way relay networks
Authors: Zhang Weile , Yin Qinye
Published: April 2013

In this study, the authors develop a distributed space–time coding scheme for a two‐way relay network that contains multiple distributed relay nodes. Both the time and frequency asynchronous nature of the distributed system are considered in the design. Distributed convolutional coding is employed to handle multiple timing errors in the networks. The authors prove that under perfect frequency synchronisation, the proposed scheme can achieve both spatial and multipath diversity by linear receivers, such as linear zero‐forcing or minimum mean‐square‐error receiver, thus providing a low decoding complexity. The authors further find that frequency asynchronism has little effect on the designed scheme and show that the diversity can still be achieved almost surely (in the measured theoretic sense) under both time and frequency asynchronous scenarios. The authors also provide numerical results to corroborate the proposed studies.
Mapping magnetic fields of Fe3O4 nanosphere assemblies by electron holography
Authors: He Kai , Ma Fei-Xiang , Xu Cheng-Yan , Cumings John
Published: April 2013

Crystalline Fe3O4 nanospheres with averaged diameters of 150 nm have been synthesized by a facile solvothermal method and characterized using transmission electron microscopy and electron holography. The nanospheres can self-assemble into either chain-like or ring-like shapes with sizes of a few micrometers, where large magnetic moments are found for individual particles at the remanent state and lead to strong fringing field in vicinity of the assemblies. Magnetic dipolar moments can be aligned both within and out of the sample plane, with a typical length scale on the order of 500 nm.
A semiclassical study of cis-trans isomerization in HONO using an interpolating moving least-squares potential
Authors: Pham Phong , Guo Yin
Published: April 2013

The interpolating moving least-squares (IMLS) approach for constructing potential energy surfaces has been developed and employed in standard classical trajectory simulations in the past few years. We extend the approach to the tunneling regime by combining the IMLS fitting method and the semiclassical scheme that incorporates tunneling into classical trajectory calculations. Dynamics of cis-trans isomerization in nitrous acid (HONO) is studied as a test case to investigate various aspects of the approach such as the strategy for growing the surface, the basis set employed, the scaling of the IMLS fits, and the accuracy of the surface required for obtaining converged rate coefficients. The validity of the approach is demonstrated through comparison with other semiclassical and quantum mechanical studies on HONO.
Effective impact ionization threshold and piecewise linear approximation for impact ionization coefficients in a theory of superfast ionizing fronts in semiconductors
Authors: Minarsky Andrey , Rodin Pavel
Published: April 2013

We focus on theoretical description of superfast ionizing fronts in semiconductor p+−n−n+ structures and argue that in the context of this problem, Townsend's type field dependence of impact ionization coefficients α(E)=α0 exp[(−E0/E)m] can be well approximated by a threshold piecewise linear dependence α(E)=α0′(E−Eb)Θ(E−Eb), where Θ(x) is the unit step function. The possibility of such approximation explains the threshold square dependence υf∼(Em−Eb)2 of the front velocity υf on the maximum electric field Em that the theory of TRAPATT-like ionizing fronts predicts even for threshold-free Townsend's approximation. We suggest a procedure for finding the best-fit parameters of the piecewise linear dependence and determine the values Eb≈0.21 E0, α0′≈0.46α0/E0 for the power m=1 and Eb≈0.5 E0, α0′≈0.7α0/E0 for the power m=2.
Indirect to direct bandgap transition under uniaxial strain in layered ZnO
Authors: Rakshit Bipul , Mahadevan Priya
Published: April 2013

The electronic structure of the α-boron-nitride phase of ZnO has been studied using hybrid functionals as well as local density approximation with Hubbard U (LDA + U) calculations. An indirect bandgap of 3.54 eV has been found in hybrid functional calculations, which transforms to a direct bandgap under uniaxial strain in the c-direction. This behavior also explains the observation of a direct bandgap at the monolayer limit. Similar trends are obtained from LDA + U calculations, and a U value of 8 eV is required to get agreement with experiment for the position of the Zn d-states. Hybrid functional calculations are found to underestimate the position of the Zn d-states in the valence band.
Terahertz full horn-antenna characterization
Authors: Armand D. , Taniguchi H. , Kadoya Y. , Tanaka T. , Tanaka K.
Published: April 2013

We present result of broad-band terahertz (THz) transmission through a couple of horn antennas. Efficiency is high leading to a strong enhancement of THz field at horn-antenna waist (50 × 200 μm2). The device provides an easier and stronger way to couple energy into monomode waveguide than the traditional usage of lens. The dispersion of the pulse is in quite good agreement with a modified rectangular waveguide model, and the phase center as well as the divergence of the field in the E- and H-planes also well predicted by horn antenna theory.
Optimization of ultra-soft CoZrTa/SiO2/CoZrTa trilayer elements for integrated inductor structures
Authors: Cheng Cheng , Davies Ryan , Sturcken Noah , Shepard Kenneth , Bailey William E.
Published: April 2013

We show the optimization of magnetic properties of ferromagnetic (FM)/SiO2/FM trilayer structures as potential candidates for the magnetic core in toroidal integrated inductors, with FM materials Co91.5Zr4.0Ta4.5 (CZT) and Ni80Fe20 (Py). In the single-layer parent films, we found a monotonic reduction of easy-axis coercivity (Hc down to 0.17 Oe in CZT, 0.4 Oe in Py) with increasing dc magnetron sputtering voltage. In the trilayer rectangular structures, with induced easy-axis in the short lateral dimension, we found proof of dipolar coupling between the two FM layers from BH loop measurements in the CZT system, showing linear response with minimal hysteresis loss when the external field is applied in the long axis. Py elements did not show this optimized property. Further investigation of domain configurations using scanning transmission x-ray microscopy suggests an insufficient induced anisotropy in Py compared with the shape anisotropy to realize the antiparallel-coupled state.
Towards optical hyperdoping of binary oxide semiconductors
Authors: Schneider A. , Sebald K. , Dev A. , Frank K. , Rosenauer A. , Voss T.
Published: April 2013

Surface structuring with ultrashort laser pulses is of high interest as a scalable doping technique as well as for surface nanostructuring applications. By depositing a layer of antimony before the irradiation of ZnO, we were able to incorporate a large quantity of Sb atoms into the single crystalline region of the laser modified surface for potential p-type doping. We have studied the incorporation of antimony and the material properties of laser-induced periodic surface structures (LIPSS) on c-plane ZnO upon femtosecond laser processing at two different peak fluences. We observe high spatial frequency LIPSS with structure periods from 200–370 nm and low spatial frequency LIPSS with periods of 600–700 nm. At a fluence of 0.8 J/cm2, close the ablation threshold of ZnO, the LIPSS are single crystalline except for a few nanometers of amorphous material. At a peak laser fluence of 3.1 J/cm2, they consist of polycrystalline and single crystalline ZnO areas. However, the polycrystalline part dominates with a thickness of about 500 nm.
Critical behavior and the universal curve for magnetocaloric effect in textured Mn5Ge3−xAlx ribbons
Authors: Zheng T. F. , Shi Y. G. , Fan J. Y. , Shi D. N. , Tang S. L. , Lv L. Y. , Zhong W.
Published: April 2013

Mn5Ge3−xAlx ribbons with x=0,0.5, and 1 were prepared by single roller melt-spinning method. Textured structures were observed in these ribbons as a result of fast cooling, with highly ordered columnar grains perpendicular to the surface. The magnetocaloric effect and critical behavior were investigated by dc magnetization measurement. Curie temperatures decrease from 297 K to 283 K as the Al content increases, and the peak entropy changes also decrease from 4.92 J/kg K to 3.0 J/kg K under an external magnetic field change of 3 T. Critical exponents were obtained by modified Arrott plots technique, Kouvel-Fisher method, and critical isothermal analysis. Similar values of exponents of β∼0.37, γ∼1, and δ∼3.8 were obtained for all of the compositions. Moreover, rescaled entropy data for all compositions collapse into a universal curve, revealing universal behavior for the magnetocaloric effect in this series of compounds.
Low temperature dielectric relaxation and charged defects in ferroelectric thin films
Authors: Artemenko A. , Payan S. , Rousseau A. , Levasseur D. , Arveux E. , Guegan G. , Maglione M.
Published: April 2013

We report a dielectric relaxation in BaTiO3-based ferroelectric thin films of different composition and with several growth modes: sputtering (with and without magnetron) and sol-gel. The relaxation was observed at cryogenic temperatures (T < 100 K) for frequencies from 100 Hz up to 10 MHz. This relaxationactivation energy is always lower than 200 meV and is very similar to the relaxation that we reported in the parent bulk perovskites. Based on our Electron Paramagnetic Resonance(EPR) investigation, we ascribe this dielectric relaxation to the hopping of electrons among Ti3+-V(O) charged defects. Being dependent on the growth process and on the amount of oxygen vacancies, this relaxation can be a useful probe of defects in actual integrated capacitors with no need for specific shaping.
Morphological and molecular evidence supports the recognition of a new subspecies of the critically endangered Pityrodia scabra (Lamiaceae)
Authors: Shepherd Kelly A. , Perkins Andrew , Collins Joel , Byrne Margaret , Thiele Kevin R.
Published: April 2013

Taxonomic delineation of closely related taxa can be difficult, particularly in regions such as southern Western Australia where a highly diverse flora exhibits complex patterns of subtle morphological variation and genetic structuring and where some taxa have highly disjunct populations. A combined approach utilising highly variable, non-coding chloroplast gene regions and morphological data is used here to help delimit cryptic taxa in the rare Western Australian species Pityrodia scabra A.S.George. The species comprises disjunct populations over 400 km of the Western Australian wheatbelt from near Wyalkatchem, Southern Cross and Lake Lefroy. Morphological features such as leaf phyllotaxy, calyx size and indumentum vary among the populations and provide some evidence for cryptic taxa. Phylogenetic analyses based on cpDNA psbA–trnH and psbD–trnT and nuclear external transcribed spacer (ETS) sequences revealed genetic distinctiveness between the Wyalkatchem (type) population and the Southern Cross and Lake Lefroy populations. This evidence, when used in conjunction with the morphological differences, provides support for the recognition of the new subspecies described herein as Pityrodia scabra subsp. dendrotricha K.A.Sheph. subsp. nov. This new subspecies is of conservation concern because it is currently known only from a few, isolated populations; the typical subspecies remains Critically Endangered because it comprises one extant population. A description of both subspecies, a key and images are provided.
Dynamic interpretation of maternal inputs by the
Drosophila
segmentation gene network
Authors: Liu Feng , Morrison Alexander H. , Gregor Thomas
Published: April 2013

Patterning of body parts in multicellular organisms relies on the interpretation of transcription factor (TF) concentrations by genetic networks. To determine the extent by which absolute TF concentration dictates gene expression and morphogenesis programs that ultimately lead to patterns in
Drosophila
embryos, we manipulate maternally supplied patterning determinants and measure readout concentration at the position of various developmental markers. When we increase the overall amount of the maternal TF Bicoid (Bcd) fivefold, Bcd concentrations in cells at positions of the cephalic furrow, an early morphological marker, differ by a factor of 2. This finding apparently contradicts the traditional threshold-dependent readout model, which predicts that the Bcd concentrations at these positions should be identical. In contrast, Bcd concentration at target gene expression boundaries is nearly unchanged early in development but adjusts dynamically toward the same twofold change as development progresses. Thus, the
Drosophila
segmentation gene network responds faithfully to Bcd concentration during early development, in agreement with the threshold model, but subsequently partially adapts in response to altered Bcd dosage, driving segmentation patterns toward their WT positions. This dynamic response requires other maternal regulators, such as Torso and Nanos, suggesting that integration of maternal input information is not achieved through molecular interactions at the time of readout but through the subsequent collective interplay of the network.
Raspberries.
Authors: Hummer K. , Hall H. K.
Published: April 2013

The history, classification and distribution, red raspberries (Rubus idaeus), raspberry life cycle, black raspberries, purple raspberries, yellow raspberries, species native to Europe, UK, Middle East, Asia, Oceania, North America are discussed.
Site selection.
Authors: Hall H. K. , Sobey T.
Published: April 2013

This chapter focuses on the importance of soil, topography, exposure and layout, climate and elevation in raspberry production. The importance of access of suppliers of industry and horticultural products and services used in the growth and production of raspberries, transport, labour, packing sheds, processing plants and markets are also discussed.
Cultivar development and selection.
Authors: Weber C.
Published: April 2013

The origin-regional adaptations, breeding programs, and breeding goals of raspberry production are discussed.
Baking Characteristics of Chiffon Cake as Influenced by Microbial Transglutaminase
Authors: Wang Feng , Huang Weining , Rayas‐Duarte Patricia , Wang Hongzi , Zou Qibo
Published: April 2013

Protein modification via covalent bonds by using microbial transglutaminase (TGase) has generated many processing functionality improvements in specific food ingredients. In this study, TGase was added into different cake portions (foam and yolk batter) at levels of 0, 0.5, and 1.0% (w/w, total protein weight basis). The treatment of 0.5% TGase in the yolk batter portion significantly (P ≤ 0.05) increased its emulsion activity. The addition of 1.0% TGase in the yolk batter portion significantly increased both foam stability and emulsion activity of cake batter, whereas the addition in the foam portion only increased the emulsion activity of cake batter significantly (P ≤ 0.05). As the addition of TGase, in foam or in the yolk batter portion, rose from 0 to 1.0%, the specific volume of chiffon cake increased. Cakes with 1.0% TGase in the foam portion had the maximum specific volume, 7.078 mL/g, and the softest texture. SDS‐PAGE was used to analyze the modifications of TGase to the protein fractions from different cake portions. The effect of TGase on protein fractions from the yolk batter portion was more evident than that on protein fractions from the foam portion. However, there was no significant difference between the protein fractions of cake batters with the same level of TGase in the foam and yolk portions, which suggested that the main substrates of TGase were yolk protein and wheat protein, instead of egg white protein.
Peroxysomal Carnitine Acetyl Transferase Influences Host Colonization Capacity in Sclerotinia sclerotiorum
Authors: Liberti D. , Rollins J. A. , Dobinson K. F.
Published: April 2013

In lower eukaryotes, the glyoxylate cycle allows cells to utilize two-carbon compounds when simple sugars are not available. In filamentous fungi, glyoxylate metabolism is coupled with β-oxidation of fatty acids, and both are localized to ubiquitous eukaryotic organelles called peroxisomes. Acetyl coenzyme A (acetyl-CoA) produced during β-oxidation is transported via the cytosol into mitochondria for further metabolism. A peroxisomal-specific pathway for acetyl-CoA transport requiring peroxisomal carnitine acetyl transferase (CAT) activity has been identified in Magnaporthe grisea peroxisomes. Here, we report that a Sclerotinia sclerotiorum ortholog of the M. grisea peroxisomal CAT-encoding gene Pth2 (herein designated Ss-pth2) is required for virulence-associated host colonization. Null (ss-pth2) mutants, obtained by in vitro transposon mutagenesis, failed to utilize fatty acids, acetate, or glycerol as sole carbon sources for growth. Gene expression analysis of these mutants showed altered levels of transcript accumulation for glyoxylate cycle enzymes. Ss-pth2 disruption also affected sclerotial, apothecial, and appressorial development and morphology, as well as oxalic acid accumulation when cultured with acetate or oleic acid as sole carbon nutrient sources. Although mutants were able to penetrate and initially colonize host tissue, subsequent colonization was impaired. Genetic complementation with the wild-type Ss-pth2 restored wild-type virulence phenotypes. These findings suggest an essential role in S. sclerotiorum for the peroxisomal metabolic pathways for oxalic acid synthesis and host colonization.
The Prevalence of theCitrus tristeza virusTrifoliate Resistance Breaking Genotype Among Puerto Rican Isolates
Authors: Roy Avijit , Choudhary Nandlal , Hartung John S. , Brlansky R. H.
Published: April 2013

Citrus tristeza virus (CTV) isolates have been grouped into six genotypes: T3, T30, T36, VT, B165, and resistance breaking (RB) based on symptoms, host range, and genomic sequence data. The RB genotype has recently been identified with the novel property of replicating in trifoliate orange trees, a resistant host for the other five genotypes. Puerto Rican CTV isolate B301 caused mild vein clearing symptoms in Mexican lime but did not induce seedling yellows or stem pitting reactions in appropriate indicator Citrus spp., which are typical host reactions of the isolate T30. The isolate B301 was not detected by the genotype specific primer (GSP), which identifies the CTV-T3, -T30, -T36, -VT, and B165 genotypes. A primer pair for reverse transcription polymerase chain reaction (RT-PCR) amplification of the CTV-RB genotype was designed from the heat shock protein (p65) region based on the complete genomic sequences of trifoliate RB isolates from New Zealand available in the GenBank databases. The amplicon sequence from isolate B301 was 98% identical to that of the other trifoliate RB isolates. In addition, B301 was successfully inoculated into ‘Carrizo citrange’ (a trifoliate hybrid) but did not induce any symptoms. Furthermore, the complete genome sequence of B301 followed by the phylogenetic analysis revealed that the isolate is part of the RB clade with other CTV-RB isolates from New Zealand and Hawaii. Additional CTV isolates obtained from Puerto Rico were tested with the RB-GSP and confirmed the presence of trifoliate RB isolates in mixed infection with known CTV genotypes. Although this is the first report of a CTV trifoliate RB genotype from Puerto Rico, this genotype was present there prior to 1992.