bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular dynamics calculation of rotational diffusion coefficient of a carbon nanotube in fluid
Authors: Cao Bing-Yang , Dong Ruo-Yu
Published: January 2014

Rotational diffusion processes are correlated with nanoparticle visualization and manipulation techniques, widely used in nanocomposites, nanofluids, bioscience, and so on. However, a systematical methodology of deriving this diffusivity is still lacking. In the current work, three molecular dynamics (MD) schemes, including equilibrium (Green-Kubo formula and Einstein relation) and nonequilibrium (Einstein–Smoluchowski relation) methods, are developed to calculate the rotational diffusion coefficient, taking a single rigid carbon nanotube in fluid argon as a case. We can conclude that the three methods produce same results on the basis of plenty of data with variation of the calculation parameters (tube length, diameter, fluid temperature, density, and viscosity), indicative of the validity and accuracy of the MD simulations. However, these results have a non-negligible deviation from the theoretical predictions of Tirado et al. [J. Chem. Phys. 81, 2047 (1984)], which may come from several unrevealed factors of the theory. The three MD methods proposed in this paper can also be applied to other situations of calculating rotational diffusion coefficient.
Strain relaxation of GaAs/Ge crystals on patterned Si substrates
Authors: Taboada A. G. , Kreiliger T. , Falub C. V. , Isa F. , Salvalaglio M. , Wewior L. , Fuster D. , Richter M. , Uccelli E. , Niedermann P. , Neels A. , Mancarella F. , Alén B. , Miglio L. , Dommann A. , Isella G. , von Känel H.
Published: January 2014

We report on the mask-less integration of GaAs crystals several microns in size on patterned Si substrates by metal organic vapor phase epitaxy. The lattice parameter mismatch is bridged by first growing 2-μm-tall intermediate Ge mesas on 8-μm-tall Si pillars by low-energy plasma enhanced chemical vapor deposition. We investigate the morphological evolution of the GaAs crystals towards full pyramids exhibiting energetically stable {111} facets with decreasing Si pillar size. The release of the strain induced by the mismatch of thermal expansion coefficients in the GaAs crystals has been studied by X-ray diffraction and photoluminescence measurements. The strain release mechanism is discussed within the framework of linear elasticity theory by Finite Element Method simulations, based on realistic geometries extracted from scanning electron microscopy images.
Comment on “On the quantum theory of molecules” [J. Chem. Phys. 137, 22A544 (2012)]
Authors: Sutcliffe Brian T. , Woolley R. Guy
Published: January 2014

In our previous paper [B. T. Sutcliffe and R. G. Woolley, J. Chem. Phys. 137, 22A544 (2012)] we argued that the Born-Oppenheimer approximation could not be based on an exact transformation of the molecular Schrödinger equation. In this Comment we suggest that the fundamental reason for the approximate nature of the Born-Oppenheimer model is the lack of a complete set of functions for the electronic space, and the need to describe the continuous spectrum using spectral projection.
Communication: Fully alignment-specified O2 chemisorption on vicinal Si(100)
Authors: Kurahashi Mitsunori , Yamauchi Yasushi
Published: January 2014

A fully alignment-resolved O2 sticking experiment on a single domain Si(100)-(2×1) surface is presented. This provides the first experimental evidence that the reactivity of O2 depends on both the polar and azimuthal angles of the molecular axis relative to a surface. It has been found that, in case of side-on collision, an O2 molecule perpendicular to the dimer on Si(100) is about 40% more reactive than that parallel to the dimer. Comparison of the O2 sticking on flat and vicinal Si(100) surfaces indicates that barrierless dissociation channels exist at the double layer step.
Exchange interaction in hexagonal MnRhP from first-principles studies
Authors: Liu X. B. , Zhang Qiming , Yue M. , Altounian Z. , Ping Liu J.
Published: January 2014

Electronic structure and magnetic properties for MnRhP have been studied from a first-principles density functional calculation. The calculated lattice constants, a = 6.228 Å and c = 3.571 Å, are in good agreement with the experimental values of a = 6.223 Å and c = 3.585 Å. The calculated moment of Mn is 3.1 μB/atom, resulting in a total moment of 3.0 μB/atom due to small moments induced at Rh and P sites. The magnetic moment of Mn decreases with unit cell size. The exchange interactions are dominated by positive Mn-Mn exchange coupling (JMn−Mn), implying a stable ferromagnetic ordering in Mn sublattice. In particular, JMn−Mn shows a maximum value (1.5 mRy) at the the optimized unit cell size. The structural distortion or unit cell size change will affect JMn−Mn, which is intimately related to the magneto-elastic and magneto-caloric effect.
Current-induced switching of magnetic tunnel junctions: Effects of field-like spin-transfer torque, pinned-layer magnetization orientation, and temperature
Authors: Tiwari R. K. , Jhon M. H. , Ng N. , Srolovitz D. J. , Gan C. K.
Published: January 2014

We study current-induced switching in magnetic tunnel junctions in the presence of a field-like spin-transfer torque and titled pinned-layer magnetization in the high current limit at finite temperature. We consider both the Slonczewski and field-like torques with coefficients aJ and bJ, respectively. At finite temperatures, σ=bJ/aJ=±1 leads to a smaller mean switching time compared that with σ=0. The reduction of switching time in the presence of the field-like term is due to the alignment effect (for σ>0) and the initial torque effect.
Improved light extraction with nano-particles offering directional radiation diagrams
Authors: Jouanin A. , Hugonin J. P. , Besbes M. , Lalanne P.
Published: January 2014

We propose a unique approach for light extraction, using engineered nano-particles to efficiently decouple the light guided in transverse-magnetic guided modes into free-space radiation modes that leak out normally to the thin-film stacks. The underlying mechanism takes advantage of a small electric field variation at the nano-particle scale and induces a “polarization conversion,” which renders the induced dipole moment perpendicular to the polarization of the incident light. Our analysis is supported by 2D fully vectorial computational results. Potential applications for light emitting or photovoltaic devices are outlined.
The spin Hall angle and spin diffusion length of Pd measured by spin pumping and microwave photoresistance
Authors: Tao X. D. , Feng Z. , Miao B. F. , Sun L. , You B. , Wu D. , Du J. , Zhang W. , Ding H. F.
Published: January 2014

We present the experimental study of the spin Hall angle (SHA) and spin diffusion length of Pd with the spin pumping and microwave photoresistance effects. The Py/Pd bilayer stripes are excited with an out-of-plane microwave magnetic field. The pure spin current is thus pumped and transforms into charge current via the inverse spin Hall effect (ISHE) in Pd layer, yielding an ISHE voltage. The ISHE voltage can be distinguished from the unwanted signal caused by the anisotropic magnetoresistance according to their different symmetries. Together with Pd thickness dependent measurements of in and out-of-plane precessing angles and effective spin mixing conductance, the SHA and spin-diffusion length of Pd are quantified as 0.0056 ± 0.0007 and 7.3 ± 0.7 nm, respectively.
Strength and equation of state of NaCl from radial x-ray diffraction
Authors: Xiong Lun , Bai Ligang , Liu Jing
Published: January 2014

The strength and equation of state of NaCl were determined under nonhydrostatic compression up to 27 GPa using an energy-dispersive radial x-ray diffraction technique in a diamond-anvil cell using the lattice strain theory. Together with estimation of the high-pressure shear modulus, it is suggested that NaCl could support a maximum differential stress of 0.980 GPa at 22.6 GPa under uniaxial compression. The differential stress rapidly drops at 27.2 GPa due to the phase transition from B1 phase to B2 phase for NaCl. The hydrostatic compression data of B1 phase yield a bulk modulus K0 = 25.6(8) GPa and its pressure derivative K0′ = 5.16(20) using Pt pressure scale. In addition, a comparative study of the observed pressures from Pt scale and ruby-fluorescence scale shows that the ruby-fluorescence pressures may reflect the lower stress state under nonhydrostatic compression compared with hydrostatic compression.
Phenomenological study of barrier imperfection and interfacial scattering on MgO based tunnel junctions
Authors: Chen B. J. , Tan S. G.
Published: January 2014

We investigate the barrier imperfection and interfacial scattering effects on resistance-area product (RA) and tunneling magnetoresistance (TMR) of magnesium oxide (MgO) based magnetic tunneling junction (MTJ). We assume that barrier imperfection reduces the band gap of MgO; thus, it affects both TMR and RA values. The lattice mismatch between MgO and magnetic electrodes leads to interface scattering which reduces TMR. As an application, the MTJ two-state resistance variations due to the process variations are also discussed in the paper.
Positional-dependent luminescence property of β-SiAlON:Eu2+ phosphor particle
Authors: Zhang Chenning , Uchikoshi Tetsuo , Liu Lihong , Dierre Benjamin , Sakka Yoshio , Hirosaki Naoto
Published: January 2014

The relationship between the luminescence property and particle faces of the β-SiAlON:Eu2+ phosphors was investigated by performing the cathodoluminescence (CL) measurements on the tip and side faces of the rod-like phosphor particles. It was found a positional dependence of the CL intensity on the particle faces, that is, the side face possessed higher CL intensity than the tip face, probably due to uneven distribution of the Eu2+ sites in the β-SiAlON host particles: the Eu2+ ions more intensively concentrated at the side face of the particle, particularly at the central area of the side face, than at the tip face.
Improved lateral photovoltaic effect of Ti and carbon films by interface modification with single-walled carbon nanotubes
Authors: Lu Jing , Wang Hui
Published: January 2014

An efficiently improved lateral photovoltaic effect (LPE) has been successfully observed in Ti/Si and amorphous carbon (a-C) film/Si structures by introducing single-walled carbon nanotubes (SWNTs) as modifying interface instead of native SiO2 layer grown on Si substrate. The largest lateral photovoltage (LPV) position sensitivity achieved is 67.02 mV/mm for the Ti/Si system and 2.23 mV/mm for the a-C/Si system. This corresponds to an improvement of 40% for the Ti/Si system and 2600% for the a-C/Si system. Besides, the SWNTs modified interface also induced a well-marked shift of optimal film thickness in both materials. An additional novel phenomenon is that the directly observed LPV is much larger in SWNTs/Si system compared to the improved a-C/SWNTs/Si structure. A mechanism based on the change of interface states is given to interpret these results, which not only suggests a new common modulation method for LPE, but also a new potential application of SWNTs for photo-electronic device.
Short-range correlations control the G/K and Poisson ratios of amorphous solids and metallic glasses
Authors: Zaccone Alessio , Terentjev Eugene M.
Published: January 2014

The bulk modulus of many amorphous materials, such as metallic glasses, behaves nearly in agreement with the assumption of affine deformation, namely that the atoms are displaced just by the amount prescribed by the applied strain. In contrast, the shear modulus behaves as for nonaffine deformations, with additional displacements due to the structural disorder which induce a marked material softening to shear. The consequence is an anomalously large ratio of the bulk modulus to the shear modulus for disordered materials characterized by dense atomic packing, but not for random networks with point atoms. We explain this phenomenon with a microscopic derivation of the elastic moduli of amorphous solids accounting for the interplay of nonaffinity and short-range particle correlations due to excluded volume. Short-range order is responsible for a reduction of the nonaffinity which is much stronger under compression, where the geometric coupling between nonaffinity and the deformation field is strong, whilst under shear this coupling is weak. Predictions of the Poisson ratio based on this model allow us to rationalize the trends as a function of coordination and atomic packing observed with many amorphous materials.
Application of a Della Torre-Oti-Kadar stress-dependent Preisach model through a numerical model
Authors: Burgy C. D. , ElBidweihy H. , Della Torre E.
Published: January 2014

Many magnetomechanical models fit the data sets, they were originally developed from very well but are not transportable to different data sets or geometries. In order to test the portability of a previously developed Della Torre-Oti-Kadar (DOK) stress-dependent Preisach model for high strength steels, a numerical model was implemented to replicate data taken on a non-trivial geometry made of the same material. The data used for comparison were measured previously by the National Institute of Standards and Technology on a toroidal-like sample which allowed for the simultaneous application of longitudinal stresses and transverse magnetic fields. The geometry was modeled in a finite element modeling package and coupled with a DOK model via material parameters. A coupling framework was developed and B-H loops were modeled and compared to the NIST data available with some agreement. In the future, this modeling approach will be extended to incorporate more complex field and stress interactions and applied to additional data sets as available.
Transition Metal-Free Synthesis of Pinacol Arylboronate: Regioselective Boronation of 1,3-Disubstituted Benzenes
Authors: Wang Yan , Wang Le , Chen Ling-Yan , Bhadury Pinaki S. , Sun Zhihua
Published: January 2014

The regioselective synthesis of pinacol arylboronate has been achieved from 1,3-disubstituted benzene through directed ortho-metallation (DoM)–borylation sequence. A wide range of substituents and borylating reagents were investigated. In situ lithiation and subsequent boronation predominantly occurred at the ortho-position to afford the desired products in moderate yields.
Current status of HIV treatment in Asia and the Pacific region
Authors: Phuphuakrat Angsana , Kiertiburanakul Sasisopin , Sungkanuparph Somnuek
Published: January 2014

Asia and the Pacific represent a diverse group of nations facing HIV epidemic profiles of differing severity. Compared to other parts of the world, the burden of HIV disease is high in this region because of its large populations. At the end of 2011, 5 million people were living with HIV in Asia and the Pacific. This accounted for 15% of people living with HIV worldwide. The prevalence of people living with HIV, as well as access to HIV treatment and care, varies widely between countries. Differences between high-income economies and the rest of the continent are remarkable. Many high-income countries provide antiretroviral therapy (ART) to their citizens. Middle- and low-income countries have rapid ART scale-up and are dependent on international funding. This may compromise the sustainability of ART availability. In addition, lack of access to second- and third-line therapy remains a problem in many countries. The global goal of achieving universal access to ART by 2015 requires mainly low- and middle-income countries to be targeted. Regional policy should be developed in order to identify new infections in key populations, to start earlier treatment, to retain patients in care and to maintain funding.
A general approach to site-specific antibody drug conjugates
Authors: Tian Feng , Lu Yingchun , Manibusan Anthony , Sellers Aaron , Tran Hon , Sun Ying , Phuong Trung , Barnett Richard , Hehli Brad , Song Frank , DeGuzman Michael J. , Ensari Semsi , Pinkstaff Jason K. , Sullivan Lorraine M. , Biroc Sandra L. , Cho Ho , Schultz Peter G. , DiJoseph John , Dougher Maureen , Ma Dangshe , Dushin Russell , Leal Mauricio , Tchistiakova Lioudmila , Feyfant Eric , Gerber Hans-Peter , Sapra Puja
Published: January 2014

Significance

Here we demonstrate the ability to genetically incorporate nonnative amino acids into proteins in mammalian cells using both transient and stable platform expression systems that provide yields and fidelities compatible with commercial applications. To illustrate the utility of this methodology we have generated chemically homogeneous antibody drug conjugates (NDCs) with precise control over the site and stoichiometry of drug conjugation. In rodent xenograft models these NDCs display improved properties, including half-life, efficacy and safety, relative to conventional heterogeneous ADCs. These advances allow the generation of therapeutic antibody drug conjugates with medicinal chemistry like control over structure, which should greatly facilitate the optimization of their pharmacological activities.
Searching for missing heritability: Designing rare variant association studies
Authors: Zuk Or , Schaffner Stephen F. , Samocha Kaitlin , Do Ron , Hechter Eliana , Kathiresan Sekar , Daly Mark J. , Neale Benjamin M. , Sunyaev Shamil R. , Lander Eric S.
Published: January 2014

Significance

Discovering the genetic basis of common diseases, such as diabetes, heart disease, and schizophrenia, is a key goal in biomedicine. Genomic studies have revealed thousands of common genetic variants underlying disease, but these variants explain only a portion of the heritability. Rare variants are also likely to play an important role, but few examples are known thus far, and initial discovery efforts with small sample sizes have had only limited success. In this paper, we describe an analytical framework for the design of rare variant association studies of disease. It provides guidance with respect to sample size, as well as the roles of selection, disruptive and missense alleles, gene-specific allele frequency thresholds, isolated populations, gene sets, and coding vs. noncoding regions.
The essence of light
Authors: Tomei Renato
Published: January 2014

‘The Essence of Light in Translation’ takes the move from George Steiner’s After Babel and his observations on the word ‘Light’. Scope of the present contribution envisages to highlight the awareness of the dynamics of ‘otherness’ and diachronic variation by examining the one key-word (Light) as it is thematized and foregrounded in sacred texts across cultures, with a focus on English and varieties of English. The comparative approach here focuses on parallel texts and intertexts to propose a different ‘vision’ of a major theme, where conceptual and semantic variation accounts for the choice of one specific theme, i.e. spiritual illumination, revelation, and the resulting creation and ‘trans-creation’ of the same theme in translation.
The challenges of translating English compounds into Arabic
Authors: Amer Walid M. , Menacere Karim
Published: January 2014

This paper examines the main challenges of translating English compounds into Arabic. Compounding is linguistically a common process across many languages where compounds are frequently formed. In English compounding is highly creative and innovative, and often used as a means of introducing new phrases or coining new words into the lexicon. In contrast, Arabic is less resourceful. Arabic does not possess similar multiword expressions as an integral linguistic mechanism that merges language items to form a unit of language that can be broken down into single words and display idiosyncratic features. (Sag et al. 2002). As the English text-writer and the Arabic translator use their respective languages from different mental pictures and from disparate thought processes, each operates from a different worldview, so transferring English compounds often leads to loss of meaning. Understanding and interpreting compounds has been a long-standing area of interest in Indo-European language research but remains under-researched in Arabic. This paper contributes to the debate on how to deal with English compounds in Arabic.
“Let’s live like Galicians”
Authors: Screti Francesco
Published: January 2014

This project consists of the multidisciplinary analysis of the persuasive strategies used in a regional TV commercial to promote GADIS, a Galician (Spain) supermarket chain. The video, which provoked an overwhelmingly positive reaction within Galician society, strategically appeals nationalistic feelings in order to achieve specific commercial objectives. In this commercial GADIS presents itself as a company that defends local attributes (Galician, Galicians, and ‘Galicianness’) against foreign ones. The speaker, by playing off positive stereotypical features of Galicia and inverting negative ones, builds and conveys a positive image of Galicia which is intended to make Galicians proud of their Galicianness. In order to make the advertisements more acceptable, GADIS praises the Galicians through the use of humor and irony, which serves to mitigate the nationalism presented.
The biomechanics of race walking: Literature overview and new insights
Authors: Pavei Gaspare , Cazzola Dario , La Torre Antonio , Minetti Alberto E.
Published: January 2014

This review aims to provide both researchers and coaches with a comprehensive overview of race walking biomechanics and to point out new viable route for future analyses. The examined literature has been divided into three categories according to the method of analysis: kinematics, ground reaction forces and joint power/efficiency. From an overall view, race walking athletes seem to adhere to the ‘straightened knee’ rule, but at race speed they do not observe the ‘no‐flight time’ rule. The coach‐oriented analysis highlights that stride length (SL) is more important than stride frequency (SF) for increasing speed and it is mainly obtained by ankle and hip joint power. Moreover, kinematic differences (SF, SL and flight time) between male and female athletes were shown. Also, we found that the maximal speed prediction according to dynamic similarity theory with walking (Froude number) is not applicable as the 3D trajectory of the body centre of mass does not follow an arc of circumference as in walking. The analysed literature shows some shortcomings: (1) the data collection is often unreliable because of the mixture of gender and performance level and (2) the analysis has sometimes been performed on a limited number of strides and speeds. These limitations lead to a scattered and incomplete gait description and a biased application of the results. The research strategy adopted so far is promising but further rigorous analyses need to be approached to obtain a fully comprehensive picture of race walking and to provide coaches with consistent results and reference values.
The Impact of Aerators on Water Contamination by Emerging Gram-Negative Opportunists in At-Risk Hospital Departments
Authors: Cristina Maria Luisa , Spagnolo Anna Maria , Casini Beatrice , Baggiani Angelo , Giudice Pietro Del , Brusaferro Silvio , Poscia Andrea , Moscato Umberto , Perdelli Fernanda , Orlando Paolo
Published: January 2014

Objective.

Our aim was to evaluate the impact of aerators on water microbiological contamination in at-risk hospital departments, with a view to quantifying the possible risk of patient exposure to waterborne microorganisms.

Design.

We analyzed the microbiological and chemical-physical characteristics of hot and cold water in some critical hospital departments.

Setting.

Two hospitals in northern Italy.

Methods.

We took 304 water samples over a 1-year period, at 3-month intervals, from taps used by healthcare personnel for handwashing, surgical washing, and the washing of medical equipment. We analyzed heterotrophic plate counts (HPCs) at 36°C and 22°C, nonfastidious gram-negative bacteria (GNB-NE), andLegionella pneumophila.

Results.

The percentages of positivity and mean values of HPCs at 22°C, HPCs at 36°C, and GNB-NE loads were significantly higher at outlet points than in the plumbing system. In particular, GNB-NE positivity was higher at outlet points than in the plumbing system in both the cold water (31.58% vs 6.58% of samples were positive) and hot water (21.05% vs 3.95%) supplies. Our results also revealed contamination byL. pneumophilaboth in the plumbing system and at outlet points, with percentages of positive samples varying according to the serogroup examined (serogroups 1 and 2-14). The mean concentrations displayed statistically significant (P< .001) differences between the outlet points (27,382.89 ± 42,245.33 colony-forming units [cfu]/L) and the plumbing system (19,461.84 ± 29,982.11 cfu/L).

Conclusions.

These results reveal a high level of contamination of aerators by various species of gram-negative opportunists that are potentially very dangerous for immunocompromised patients and, therefore, the need to improve the management of these devices.
Non-commutative Hodge structures: Towards matching categorical and geometric examples
Authors: Shklyarov D.
Published: January 2014

The subject of the present work is the de Rham part of non-commutative Hodge structures on the periodic cyclic homology of differential graded algebras and categories. We discuss explicit formulas for the corresponding connection on the periodic cyclic homology viewed as a bundle over the punctured formal disk. Our main result says that for the category of matrix factorizations of a polynomial the formulas reproduce, up to a certain shift, a well-known connection on the associated twisted de Rham cohomology which plays a central role in the geometric approach to the Hodge theory of isolated singularities.
Incentivizing Safety and Discrimination: Employment Risks under Workmen’s Compensation in the Early Twentieth Century United States
Authors: Holdren Nate
Published: January 2014

This article takes criticisms of employment discrimination in the aftermath of the creation of workmen’s compensation legislation as a point of entry for arguing that compensation laws created new incentives for employment discrimination. Compensation laws turned the costs of employees’ workplace accidents into a risk that many employers sought to manage by screening job applicants in a manner analogous to how insurance companies screened policy applicants. While numerous critics blamed insurers for discrimination, I argue that the problem was lack of insurance. The less that companies pooled their compensation risks via insurance, the greater the incentives for employers to stop employing people they would have previously been willing to hire.
Generic management procedures for data-poor fisheries: forecasting with few data
Authors: Geromont H. F. , Butterworth D. S.
Published: January 2014

The majority of fish stocks worldwide are not managed quantitatively as they lack sufficient data, particularly a direct index of abundance, on which to base an assessment. Often these stocks are relatively “low value”, which renders dedicated scientific management too costly, and a generic solution is therefore desirable. A management procedure (MP) approach is suggested where simple harvest control rules are simulation tested to check robustness to uncertainties. The aim of this analysis is to test some very simple “off-the-shelf” MPs that could be applied to groups of data-poor stocks which share similar key characteristics in terms of status and demographic parameters. For this initial investigation, a selection of empirical MPs is simulation tested over a wide range of operating models (OMs) representing resources of medium productivity classified as severely depleted, to ascertain how well these different MPs perform. While the data-moderate MPs (based on an index of abundance) perform somewhat better than the data-limited ones (which lack such input) as would be expected, the latter nevertheless perform surprisingly well across wide ranges of uncertainty. These simple MPs could well provide the basis to develop candidate MPs to manage data-limited stocks, ensuring if not optimal, at least relatively stable sustainable future catches.
Hierarchical reverberation mapping
Authors: Brewer Brendon J. , Elliott Tom M.
Published: January 2014

Reverberation mapping (RM) is an important technique in studies of active galactic nuclei (AGN). The key idea of RM is to measure the time lag τ between variations in the continuum emission from the accretion disc and subsequent response of the broad-line region (BLR). The measurement of τ is typically used to estimate the physical size of the BLR and is combined with other measurements to estimate the black hole mass MBH. A major difficulty with RM campaigns is the large amount of data needed to measure τ. Recently, Fine et al. introduced a new approach to RM where the BLR light curve is sparsely sampled, but this is counteracted by observing a large sample of AGN, rather than a single system. The results are combined to infer properties of the sample of AGN. In this Letter, we implement this method using a hierarchical Bayesian model and contrast this with the results from the previous stacked cross-correlation technique. We find that our inferences are more precise and allow for more straightforward interpretation than the stacked cross-correlation results.
A successful search for hidden Barbarians in the Watsonia asteroid family
Authors: Cellino A. , Bagnulo S. , Tanga P. , Novaković B. , Delbò M.
Published: January 2014

Barbarians, so named after the prototype of this class (234) Barbara, are a rare class of asteroids exhibiting anomalous polarimetric properties. Their very distinctive feature is that they show negative polarization at relatively large phase angles, where all ‘normal’ asteroids show positive polarization. The origin of the Barbarian phenomenon is unclear, but it seems to be correlated with the presence of anomalous abundances of spinel, a mineral usually associated with the so-called calcium–aluminium-rich inclusions (CAIs) on meteorites. Since CAIs are samples of the oldest solid matter identified in our Solar system, Barbarians are very interesting targets for investigations. Inspired by the fact that some of the few known Barbarians are members of, or very close to, the dynamical family of Watsonia, we have checked whether this family is a major repository of Barbarians, in order to obtain some hints about their possible collisional origin. We have measured the linear polarization of a sample of nine asteroids which are members of the Watsonia family within the phase-angle range 17°–21°. We found that seven of them exhibit the peculiar Barbarian polarization signature, and we conclude that the Watsonia family is a repository of Barbarian asteroids. The new Barbarians identified in our analysis will be important to confirm the possible link between the Barbarian phenomenon and the presence of spinel on the surface.
Dicer-related helicase 3 forms an obligate dimer for recognizing 22G-RNA
Authors: Fitzgerald Megan E. , Vela Adriana , Pyle Anna Marie
Published: January 2014

Dicer is a specialized nuclease that produces RNA molecules of specific lengths for use in gene silencing pathways. Dicer relies on the correct measurement of RNA target duplexes to generate products of specific lengths. It is thought that Dicer uses its multidomain architecture to calibrate RNA product length. However, this measurement model is derived from structural information from a protozoan Dicer, and does not account for the helicase domain present in higher organisms. The Caenorhabditis elegans Dicer-related helicase 3 (DRH-3) is an ortholog of the Dicer and RIG-I family of double-strand RNA activated ATPases essential for secondary siRNA production. We find that DRH-3 specifies 22 bp RNAs by dimerization of the helicase domain, a process mediated by ATPase activity and the N-terminal domain. This mechanism for RNA length discrimination by a Dicer family protein suggests an alternative model for RNA length measurement by Dicer, with implications for recognition of siRNA and miRNA targets.
NS1′ protein expression facilitates production of Japanese encephalitis virus in avian cells and embryonated chicken eggs
Authors: Takamatsu Yuki , Okamoto Kenta , Dinh Duc Tuan , Yu Fuxun , Hayasaka Daisuke , Uchida Leo , Nabeshima Takeshi , Buerano Corazon C. , Morita Kouichi
Published: January 2014

Japanese encephalitis virus (JEV), which belongs to the genusFlavivirusof the familyFlaviviridae, is a leading cause of meningo-encephalitis in Asian countries. The flavivirus non-structural protein 1 (NS1) plays a role in virus replication and in the elicitation of an immune response. The NS1′ protein found among the members of the JEV subgroup is an extended form of NS1 and is generated by a −1 ribosomal frameshift. This protein is known to be involved in viral pathogenicity; however, its specific function is still unknown. Here, we describe an investigation of the molecular function of NS1′ protein through the production of JEV NS1′-expressing and -non-expressing clones and their infection of avian and mammalian cells. Efficient NS1′ protein expression was observed in avian cells and was found to facilitate JEV production in both avian cultured cells and embryonated chicken eggs. NS1′ protein was observed to co-localize with NS5 protein and resulted in increased viral RNA levels in avian cells. These findings clearly indicate that NS1′ enhances the production of JEV in avian cells and may facilitate the amplification/maintenance role of birds in the virus transmission cycle in nature.
How and where to look for tRNAs in Metazoan mitochondrial genomes, and what you might find when you get there
Authors: Morrison David A.
Published: January 2014

The ability to locate and annotate mitochondrial genes is an important practical issue, given the rapidly increasing number of mitogenomes appearing in the public databases. Unfortunately, tRNA genes in Metazoan mitochondria have proved to be problematic because they often vary in number (genes missing or duplicated) and also in the secondary structure of the transcribed tRNAs (T or D arms missing). I have performed a series of comparative analyses of the tRNA genes of a broad range of Metazoan mitogenomes in order to address this issue. I conclude that no single computer program is necessarily capable of finding all of the tRNA genes in any given mitogenome, and that use of both the ARWEN and DOGMA programs is sometimes necessary because they produce complementary false negatives. There are apparently a very large number of erroneous annotations in the databased mitogenome sequences, including missed genes, wrongly annotated locations, false complements, and inconsistent criteria for assigning the 5′ and 3′ boundaries; and I have listed many of these. The extent of overlap between genes is often greatly exaggerated due to inconsistent annotations, although notable overlaps involving tRNAs are apparently real. Finally, three novel hypotheses were examined and found to have support from the comparative analyses: (1) some organisms have mitogenomic locations that simultaneously code for multiple tRNAs; (2) some organisms have mitogenomic locations that simultaneously code for tRNAs and proteins (but not rRNAs); and (3) one group of nematodes has several genes that code for tRNAs lacking both the D and T arms.
The shrinking human protein coding complement: are there now fewer than 20,000 genes?
Authors: Ezkurdia Iakes , Juan David , Rodriguez Jose Manuel , Frankish Adam , Diekhans Mark , Harrow Jennifer , Vazquez Jesus , Valencia Alfonso , Tress Michael L.
Published: January 2014

Determining the full complement of protein-coding genes is a key goal of genome annotation. The most powerful approach for confirming protein coding potential is the detection of cellular protein expression through peptide mass spectrometry experiments. Here we map the peptides detected in 7 large-scale proteomics studies to almost 60% of the protein coding genes in the GENCODE annotation the human genome. We find that conservation across vertebrate species and the age of the gene family are key indicators of whether a peptide will be detected in proteomics experiments. We find peptides for most highly conserved genes and for practically all genes that evolved before bilateria. At the same time there is almost no evidence of protein expression for genes that have appeared since primates, or for genes that do not have any protein-like features or cross-species conservation. We identify 19 non-protein-like features such as weak conservation, no protein features or ambiguous annotations in major databases that are indicators of low peptide detection rates. We use these features to describe a set of 2,001 genes that are potentially non-coding, and show that many of these genes behave more like non-coding genes than protein-coding genes. We detect peptides for just 3% of these genes. We suggest that many of these 2,001 genes do not code for proteins under normal circumstances and that they should not be included in the human protein coding gene catalogue. These potential non-coding genes will be revised as part of the ongoing human genome annotation effort.
AMPK agonist AICAR improves cognition and motor coordination in young and aged mice
Authors: Kobilo Tali , Guerrieri Davide , Zhang Yongqing , Collica Sarah C. , Becker Kevin G. , van Praag Henriette
Published: January 2014

Normal aging can result in a decline of memory and muscle function. Exercise may prevent or delay these changes. However, aging-associated frailty can preclude physical activity. In young sedentary animals, pharmacological activation of AMP-activated protein kinase (AMPK), a transcriptional regulator important for muscle physiology, enhanced spatial memory function, and endurance. In the present study we investigated effects of AMPK agonist 5-aminoimidazole-4-carboxamide riboside (AICAR) on memory and motor function in young (5- to 7-wk-old) and aged (23-mo-old) female C57Bl/6 mice, and in young (4- to 6-wk-old) transgenic mice with muscle-specific mutated AMPK α2-subunit (AMPK-DN). Mice were injected with AICAR (500 mg/kg) for 3–14 d. Two weeks thereafter animals were tested in the Morris water maze, rotarod, and open field. Improved water maze performance and motor function were observed, albeit at longer duration of administration, in aged (14-d AICAR) than in young (3-d AICAR) mice. In the AMPK-DN mice, the compound did not enhance behavior, providing support for a muscle-mediated mechanism. In addition, microarray analysis of muscle and hippocampal tissue derived from aged mice treated with AICAR revealed changes in gene expression in both tissues, which correlated with behavioral effects in a dose-dependent manner. Pronounced up-regulation of mitochondrial genes in muscle was observed. In the hippocampus, genes relevant to neuronal development and plasticity were enriched. Altogether, endurance-related factors may mediate both muscle and brain health in aging, and could play a role in new therapeutic interventions.
Antagonistic Regulation of Growth and Immunity by the Arabidopsis Basic Helix-Loop-Helix Transcription Factor HOMOLOG OF BRASSINOSTEROID ENHANCED EXPRESSION2 INTERACTING WITH INCREASED LEAF INCLINATION1 BINDING bHLH1
Authors: Malinovsky Frederikke Gro , Batoux Martine , Schwessinger Benjamin , Youn Ji Hyun , Stransfeld Lena , Win Joe , Kim Seong-Ki , Zipfel Cyril
Published: January 2014

Plants need to finely balance resources allocated to growth and immunity to achieve optimal fitness. A tradeoff between pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and brassinosteroid (BR)-mediated growth was recently reported, but more information about the underlying mechanisms is needed. Here, we identify the basic helix-loop-helix (bHLH) transcription factor HOMOLOG OF BRASSINOSTEROID ENHANCED EXPRESSION2 INTERACTING WITH IBH1 (HBI1) as a negative regulator of PTI signaling in Arabidopsis (Arabidopsis thaliana). HBI1 expression is down-regulated in response to different PAMPs. HBI1 overexpression leads to reduced PAMP-triggered responses. This inhibition correlates with reduced steady-state expression of immune marker genes, leading to increased susceptibility to the bacterium Pseudomonas syringae. Overexpression of the HBI1-related bHLHs BRASSINOSTEROID ENHANCED EXPRESSION2 (BEE2) and CRYPTOCHROME-INTERACTING bHLH (CIB1) partially inhibits immunity, indicating that BEE2 and CIB1 may act redundantly with HBI1. In contrast to its expression pattern upon PAMP treatment, HBI1 expression is enhanced by BR treatment. Also, HBI1-overexpressing plants are hyperresponsive to BR and more resistant to the BR biosynthetic inhibitor brassinazole. HBI1 is nucleus localized, and a mutation in a conserved leucine residue within the first helix of the protein interaction domain impairs its function in BR signaling. Interestingly, HBI1 interacts with several inhibitory atypical bHLHs, which likely keep HBI1 under negative control. Hence, HBI1 is a positive regulator of BR-triggered responses, and the negative effect of PTI is likely due to the antagonism between BR and PTI signaling. This study identifies a novel component involved in the complex tradeoff between innate immunity and BR-regulated growth.
Cytokinin Antagonizes Abscisic Acid-Mediated Inhibition of Cotyledon Greening by Promoting the Degradation of ABSCISIC ACID INSENSITIVE5 Protein in Arabidopsis
Authors: Guan Chunmei , Wang Xingchun , Feng Jian , Hong Sulei , Liang Yan , Ren Bo , Zuo Jianru
Published: January 2014

In higher plants, seed germination is followed by postgerminative growth. One of the key developmental events during postgerminative growth is cotyledon greening, which enables a seedling to establish photosynthetic capacity. The plant phytohormone abscisic acid (ABA) plays a vital role by inhibiting seed germination and postgerminative growth in response to dynamically changing internal and environmental cues. It has been shown that ABSCISIC ACID INSENSITIVE5 (ABI5), a basic leucine zipper transcription factor, is an important factor in the regulation of the ABA-mediated inhibitory effect on seed germination and postgerminative growth. Conversely, the phytohormone cytokinin has been proposed to promote seed germination by antagonizing the ABA-mediated inhibitory effect. However, the underpinning molecular mechanism of cytokinin-repressed ABA signaling is largely unknown. Here, we show that cytokinin specifically antagonizes ABA-mediated inhibition of cotyledon greening with minimal effects on seed germination in Arabidopsis (Arabidopsis thaliana). We found that the cytokinin-antagonized ABA effect is dependent on a functional cytokinin signaling pathway, mainly involved in the cytokinin receptor gene CYTOKININ RESPONSE1/ARABIDOPSIS HISTIDINE KINASE4, downstream histidine phosphotransfer protein genes AHP2, AHP3, and AHP5, and a type B response regulator gene, ARR12, which genetically acts upstream of ABI5 to regulate cotyledon greening. Cytokinin has no apparent effect on the transcription of ABI5. However, cytokinin efficiently promotes the proteasomal degradation of ABI5 in a cytokinin signaling-dependent manner. These results define a genetic pathway through which cytokinin specifically induces the degradation of ABI5 protein, thereby antagonizing ABA-mediated inhibition of postgerminative growth.
Novel Application of Diffusion Soldering*
Authors: Jacobson D.M. , Sangha S.P.S
Published: January 2014

The comparatively new process of diffusion soldering combines the
merits of Soldering and diffusion bonding. It is tolerant to surfaces that are not perfectly flat while, at flat
while, at the same time, it is capable of producing large‐area joints that are void free, a normal failing of
conventional soldering. Diffusion soldering processes have been successfully developed, based copper,
silver and gold. The metallurgical principles behind the design of these processes are explained and
prospective applications of each of the diffusion soldering systems are described. These range from the
attachment of heat‐sinks to silicon power devices, to jewellery and the fabrication of semiconductor
packaging.
Cutaneous lymphoma in Japan: A nationwide study of 1733 patients
Authors: Hamada Toshihisa , Iwatsuki Keiji
Published: January 2014

Types of cutaneous lymphoma (CL) and their incidences may vary among geographic areas or ethnic groups. The present study aimed to investigate the incidences of various CL in Japan, using epidemiological data from a nationwide registration system for CL. Between 2007 and 2011, 1733 new patients with CL were registered from over 600 dermatological institutes in Japan. The 1733 patients registered included 1485 (85.7%) patients with mature T‐ and natural killer (NK)‐cell neoplasms, 224 (12.9%) with B‐cell neoplasms and 24 (1.4%) with blastic plasmacytoid dendritic cell neoplasm. Mycosis fungoides (MF) is the most common CL subtype in the present study (750 patients, 43.3%). The proportion of MF patients with early‐stage disease was 73%, similar to that of previous studies from other cohorts. The incidence rates of adult T‐cell leukemia/lymphoma and extranodal NK/T‐cell lymphoma, nasal type were 16.7% and 2.0%, respectively, which may account for the higher incidence of mature T‐ and NK‐cell neoplasms in Japan, as compared with that in the USA and Europe. A male predominance was observed in most types of CL, except for several CL subtypes such as subcutaneous panniculitis‐like T‐cell lymphoma.
Immunological milieu in mycosis fungoides and Sézary syndrome
Authors: Miyagaki Tomomitsu , Sugaya Makoto
Published: January 2014

Tumor genesis and development are driven by a combination of intrinsic events such as oncogene activation and tumor‐suppressor gene inactivation, and extrinsic events that are dependent on the interaction with the stroma. Different types of growth factors, cytokines and chemokines secreted by the surrounding stromal cells are thought to play key roles in solid tumor progression. Accumulating evidence indicates that the immunological milieu plays an essential role in tumor development, not only in solid tumors, but also in hematopoietic malignancies. Understanding the interactions between tumor cells and microenvironment in mycosis fungoides (MF) and Sézary syndrome (SS) could provide a basis for the development of new treatments for these diseases that are sometimes resistant to current therapies. This article focuses on the wide variety of cell types and immunological milieus, affecting the characteristic features of MF and SS, such as skin‐homing of tumor cells, T‐helper type 2‐dominant tumor microenvironment, accumulation of dermal dendritic cells, epidermal hyperplasia, angiogenesis and pruritus.
Depsipeptide and roxithromycin induce apoptosis of lymphoma cells by blocking extracellular signal‐regulated kinase activation
Authors: Morimura Sohshi , Sugaya Makoto , Kai Hiromichi , Miyagaki Tomomitsu , Asano Yoshihide , Tada Yayoi , Kadono Takafumi , Murakami Takashi , Sato Sinichi
Published: January 2014

Depsipeptide (FK228), a histone deacetylase inhibitor, was recently approved for use in cutaneous T‐cell lymphoma. Roxithromycin (RXM) is a macrolide antibiotic that can induce apoptosis of some T‐cell lines. In this study, we investigated whether combination of FK228 and RXM had a synergistic inhibitory effect on cell survival of various lymphoma cells and which signaling pathway was affected by the drugs in the presence or absence of chemokines, which were reported to inhibit apoptosis of some tumor cells. FK228 and RXM additively decreased the number of HUT‐78, Ki‐JK and EL‐4 lymphoma cells at doses over 50 nmol/L and 50 μmol/L, respectively. These drugs inhibited phosphorylation of Akt and extracellular signal‐regulated kinase (ERK) of EL‐4 cells in a dose‐dependent manner. Significant association between ERK phosphorylation and cell number or annexin V+ cells suggested that the ERK pathway may be critical for survival of EL‐4 cells. Combination of 10 or 50 nmol/L of FK228 and 10 μmol/L of RXM decreased cell number of HUT78 and EL‐4 compared to a single use of each drug. Our in vitro study suggested that combination of FK228 and RXM may be helpful for enhancing tumor killing effects. Although further study is necessary, this combination may be applicable to patients with cutaneous T‐cell lymphoma in the future.