bluuebunny/crossref_metadata_2025 huggingface dataset:
Structure of Au40/−1 in the gas phase: A joint geometry relaxed ab initio calculations and vibrationally resolved photoelectron imaging investigation
Authors: Liu Zhiling , Qin Zhengbo , Xie Hua , Cong Ran , Wu Xia , Tang Zichao
Published: September 2013

We have combined photoelectron velocity-map imaging spectroscopy and high-level ab initio calculations to elucidate the geometries of Au40/−1. Well-resolved ground-state electronic transition was observed in the photoelectron spectrum of Au4− at 446 nm, leading to more accurate electron affinity and vibrational frequencies for the ground state of the neutral Au4−. The pure and vibrationally resolved spectra provide definitive experimental evidence for the resolution of the ground-state gold tetramer in the gaseous phase, with the aid of the ab initio calculations and Franck-Condon simulations. The comprehensive comparisons between the experiment and theoretical calculations suggest that the Y-shaped structure is the global minimum for both the neutral and anionic Au4.
The autofocusing system of the IMAT neutron camera
Authors: Finocchiaro V. , Aliotta F. , Tresoldi D. , Ponterio R. C. , Vasi C. S. , Salvato G.
Published: September 2013

In this paper, we present the autofocusing system of the imaging instrument to be used on IMAT, a new neutron-imaging facility under construction at the ISIS (UK) target station 2. We have compared 16 different autofocus algorithms to select the one with the best performance. The algorithms have been evaluated by using both a qualitative analysis and a quantitative one. An overall score has been computed and the “contrast based” algorithm has been selected for the autofocusing system. The adopted setup together with the described autofocusing system makes the camera a user-friendly imaging device allowing the optimization of beam time use.
Electrical properties of solution processed p-SnS nanosheets/n-TiO2 heterojunction assembly
Authors: Umar Ahmad , Akhtar M. S. , Badran R. I. , Abaker M. , Kim S. H. , Al-Hajry A. , Baskoutas S.
Published: September 2013

A heterojunction device was fabricated with solution processed SnS nanosheets (p-type)/TiO2 nanoparticles (n-type) and a top Pt thin layer to form Pt/SnS/TiO2/fluorine doped tin oxide diode assembly. The SnS nanosheets were synthesized by facile hydrothermal process at low-temperature and the detailed morphological characterizations revealed that the SnS nanosheets are uniformly grown in high density. The structural characterizations confirmed the well-crystallinity and purity of the synthesized SnS nanosheets. The fabricated heterostructure device presented considerably improved electrical properties with high current of 0.78 mA at 1 V, reasonable ideality factor of 31 and relatively high effective barrier height of 0.634 eV.
Enhancing the performance of green GaN-based light-emitting diodes with graded superlattice AlGaN/GaN inserting layer
Authors: Kang Junjie , Li Hongjian , Li Zhi , Liu Zhiqiang , Ma Ping , Yi Xiaoyan , Wang Guohong
Published: September 2013

Green InGaN/GaN multiple quantum wells light-emitting diodes with graded superlattice (GSL) AlGaN/GaN inserting layer are investigated numerically and experimentally. Our simulation results indicate that GSL inserting layer can decrease the effective barrier height of holes by 57 meV, which makes holes more easily inject into the quantum wells. The piezoelectric polarization field near the last barrier is suppressed effectively by introducing of the GSL inserting layer. As a result, the efficiency droop radio is improved from 35.8% to 19.4% at current density of 100 A/cm−2.
Ewald summation on a helix: A route to self-consistent charge density-functional based tight-binding objective molecular dynamics
Authors: Nikiforov I. , Hourahine B. , Aradi B. , Frauenheim Th. , Dumitrică T.
Published: September 2013

We explore the generalization to the helical case of the classical Ewald method, the harbinger of all modern self-consistent treatments of waves in crystals, including ab initio electronic structure methods. Ewald-like formulas that do not rely on a unit cell with translational symmetry prove to be numerically tractable and able to provide the crucial component needed for coupling objective molecular dynamics with the self-consistent charge density-functional based tight-binding treatment of the inter-atomic interactions. The robustness of the method in addressing complex hetero-nuclear nano- and bio-systems is demonstrated with illustrative simulations on a helical boron nitride nanotube, a screw dislocated zinc oxide nanowire, and an ideal DNA molecule.
Engineered spin-valve type magnetoresistance in Fe3O4-CoFe2O4 core-shell nanoparticles
Authors: Anil Kumar P. , Ray Sugata , Chakraverty S. , Sarma D. D.
Published: September 2013

Naturally occurring spin-valve-type magnetoresistance (SVMR), recently observed in Sr2FeMoO6 samples, suggests the possibility of decoupling the maximal resistance from the coercivity of the sample. Here we present the evidence that SVMR can be engineered in specifically designed and fabricated core-shell nanoparticle systems, realized here in terms of soft magnetic Fe3O4 as the core and hard magnetic insulator CoFe2O4 as the shell materials. We show that this provides a magnetically switchable tunnel barrier that controls the magnetoresistance of the system, instead of the magnetic properties of the magnetic grain material, Fe3O4, and thus establishing the feasibility of engineered SVMR structures.
Breit interaction effects in relativistic theory of the nuclear spin-rotation tensor
Authors: Aucar I. Agustín , Gómez Sergio S. , Giribet Claudia G. , Ruiz de Azúa Martín C.
Published: September 2013

In this work, relativistic effects on the nuclear spin-rotation (SR) tensor originated in the electron-nucleus and electron-electron Breit interactions are analysed. To this end, four-component numerical calculations were carried out in model systems HX (X=H,F,Cl,Br,I). The electron-nucleus Breit interaction couples the electrons and nuclei dynamics giving rise to a purely relativistic contribution to the SR tensor. Its leading order in 1/c is of the same value as that of relativistic corrections on the usual second order expression of the SR tensor considered in previous work [I. A. Aucar, S. S. Gómez, J. I. Melo, C. G. Giribet, and M. C. Ruiz de Azúa, J. Chem. Phys. 138, 134107 (2013)]10.1063/1.4796461, and therefore it is absolutely necessary to establish its relative importance. For the sake of completeness, the corresponding effect originating in the electron-electron Breit interaction is also considered. It is verified that in all cases these Breit interactions yield only very small corrections to the SR tensors of both the X and H nuclei in the present series of compounds. Results of the present work strongly suggest that in order to achieve experimental accuracy in the theoretical study of the SR tensor both electron-nucleus and electron-electron Breit effects can be safely neglected.
Drive current enhancement in tunnel field-effect transistors by graded heterojunction approach
Authors: Chien Nguyen Dang , Vinh Luu The
Published: September 2013

The heterostructure technique has recently demonstrated an excellent solution to resolve the trade-off between on- and off-state currents in tunnel field-effect transistors (TFETs). This paper shows the weakness of abrupt heterojunctions and explores the physics of drive current enhancement as well as generalizes the proposed graded heterojunction approach in both n-type and p-type TFETs. It is shown that the presence of thermal emission barriers formed by abrupt band offsets is the physical reason of the on-current lowering observed in abrupt heterojunction TFETs. By employing graded heterojunctions in TFETs, the thermal emission barriers for electrons and holes are completely eliminated to narrow the tunnel widths in n-type and p-type TFETs, respectively. With the significant improvement in on-current, this novel approach of graded heterojunctions provides an effective technique for enhancing the drive current in heterostructure-based TFET devices.
Demagnetization factor for a powder of randomly packed spherical particles
Authors: Bjørk R. , Bahl C. R. H.
Published: September 2013

The demagnetization factors for randomly packed spherical particle powders with different porosities, sample aspect ratios, and monodisperse, normal, and log-normal particle size distributions have been calculated using a numerical model. For a relative permeability of 2, comparable to room temperature Gd, the calculated demagnetization factor is close to the theoretical value. The normalized standard deviation of the magnetization in the powder was 6.0%–6.7%. The demagnetization factor decreased significantly, while the standard deviation of the magnetization increased, for increasing relative permeability.
Electromagnetic force on a magnetic dipole inside an annular pipe flow
Authors: Heinicke Christiane , Thess André
Published: September 2013

We present an illuminating example of electromagnetic flow measurement in liquid metals that is easy to analyze yet displays a remarkably good agreement with laboratory experiments. Our system involves a small permanent magnet located inside an annular pipe carrying the flow of a liquid metal. We investigate the Lorentz force acting upon the magnet using a combination of laboratory experiments with liquid metal at room temperature and a simple analytical model. We demonstrate that the measured Lorentz forces are in very good agreement with the predictions of our model over a wide range of geometry parameters. By virtue of its simplicity and close relationship to the well known “creeping magnet” classroom experiment, our system can also serve as an educational tool for introductory courses in liquid metal magnetohydrodynamics.
Decoherence in a pair of long-lived Cooper-pair boxes
Authors: Zaretskey V. , Novikov S. , Suri B. , Kim Z. , Wellstood F. C. , Palmer B. S.
Published: September 2013

We have investigated the decoherence of quantum states in two Al/AlOx/Al Cooper-pair boxes coupled to lumped element superconducting inductor-capacitor resonators. At 25 mK, the first qubit had an energy relaxation time T1 that varied from 30 μs to 200 μs between 4 and 8 GHz and displayed an inverse correlation between T1 and the coupling to the microwave drive line. The Ramsey fringe decay times T2* were in the [200–500] ns range while the spin echo envelope decay times Techo varied from 2.4–3.3 μs, consistent with 1/f charge noise with a high frequency cutoff of 0.2 MHz. A second Cooper-pair box qubit with similar parameters showed T1=4−30 μs between 4 and 7.3 GHz, and that the T1 and the coupling were again inversely correlated. Although the lifetime of the second device was shorter than that of the first device, the dependence on coupling in both devices suggests that further reduction in coupling should lead to improved qubit performance.
Radio frequency sputtered Al:ZnO-Ag transparent conductor: A plasmonic nanostructure with enhanced optical and electrical properties
Authors: Sytchkova Anna , Luisa Grilli Maria , Rinaldi Antonio , Vedraine Sylvain , Torchio Philippe , Piegari Angela , Flory François
Published: September 2013

Optimization of metal-based transparent conductors (MTCs) made of silver and aluminium-doped zinc oxide (AZO) prepared by radio-frequency (r.f.) sputtering has been carried out through tuning of metal film properties. The influence of morphology and related plasmonic features of AZO/Ag/AZO MTCs on their optical and electrical performance is demonstrated and it is shown that the nominal thickness of the silver layer itself is not the most crucial value determining the MTC performance. The MTC performance has been optimized by a search of deposition conditions ensuring fractal-type metal layer formation up to a certain coalescence state that enables full gaining from silver optical properties, including its plasmonic features. For 150 W- and 200 W-deposited silver, MTCs with maximum transmittance as high as 83.6% have been obtained. These coatings have a figure of merit as good as 0.01 Ω−1 and a remarkably wide spectral transparency region: transmittance higher than 70% down to 1200 nm for 200W-samples. Modelling of the MTC coatings is proposed additionally, based on variable angle spectroscopic ellipsometric measurements, which takes into account the variation of the optical properties of silver when deposited in various conditions and embedded in a semiconductor stack.
Resonant tunneling in a topological insulator superlattice
Authors: Li H. , Shao J. M. , Zhang H. B. , Yao Dao-Xin , Yang G. W.
Published: September 2013

The transport properties of the Dirac fermions through the topological insulator superlattice (TISL) have been investigated by means of the transfer matrix method. It was found that the transmission probability of TISL exhibits the strong resonant peaks due to the modulation of SL. It was remarkable that the Dirac fermions perform the perfect transmission at the normal incidence regardless of TISL's parameters and the Fermi energy, even though the linear dispersion is distorted at the high energy. Intriguingly, the perfect transmission occurs in the case of the oblique incidence if the Fermi energy is large enough. The warping effect induces some mini-peaks in the conductance curves, while the conductance oscillates with the delta-function potential strength due to the unique chiral surface states of TI. These findings are useful for developing TISL-based devices.
Atomic dipole moment distribution on a hydrogen-adsorbed Si(111)-(7 × 7) surface observed by noncontact scanning nonlinear dielectric microscopy
Authors: Mizuno Daisuke , Yamasue Kohei , Cho Yasuo
Published: September 2013

Noncontact scanning nonlinear dielectric microscopy (NC-SNDM) can atomically resolve the polarization distribution on material surfaces. We observed a hydrogen-adsorbed Si(111)–(7 × 7) surface using NC-SNDM and found that hydrogen-adsorbed Si adatoms had lower dipole moments than bare Si adatoms. We discuss the charge distribution around a hydrogen-adsorbed Si adatom in terms of its geometry and the electronegativities of hydrogen and silicon. Our model suggests that the charge distribution around a hydrogen-adsorbed adatom is nearly symmetric and it qualitatively explains the experimental results. We thus conclude that the hydrogen-adsorbed Si adatoms are both electrically and chemically passivated.
Transfer and recombination mechanism of carriers in phase-separated InGaN quantum wells
Authors: Sun Hu , Ji Ziwu , Wang Huining , Xiao Hongdi , Qu Shuang , Xu Xiangang , Jin Aizi , Yang Haifang
Published: September 2013

Photoluminescence (PL) properties of InGaN/GaN multiple quantum wells are studied. Two InGaN-related peaks are observed in the full PL spectrum and are assigned to the quasi-quantum dots (QDs) (2.42 eV) and the InGaN matrix (2.66 eV), due to a strong phase separation. As the carriers transfer from the matrix down to the QDs, an increase of the QDs-related PL intensity (ID) accompanied by the decrease of the matrix-related PL intensity (IM) results. A slight increase of the total PL intensity is also observed, and is attributed to the QDs providing deep potential levels to suppress the outflow of carriers toward surrounding nonradiative centers. A piezoelectric field resulting from the high indium content inside the QDs is observed, which is speculated from Coulomb screening effect. Additionally, we find that the sublinear dependence of the ID on excitation power (P) is due to the saturation of the QDs states, while the superlinear dependence of the IM on P is simultaneously attributed to the suppression of the carriers transferring from the matrix to the QDs and the saturation of the nonradiative centers in the matrix.
Microscopic characterization of metal-carbon-hydrogen composites (metal = Li, Mg)
Authors: Isobe Shigehito , Yamada Sumito , Wang Yongming , Hashimoto Naoyuki , Ohnuki Somei , Miyaoka Hiroki , Ichikawa Takayuki , Kojima Yoshitsugu
Published: September 2013

Li-C-H system, which can store about 5.0 mass% of rechargeable H2, has been reported as a promising hydrogen storage system by Ichikawa et al. [Appl. Phys. Lett. 86, 241914 (2005); Mater. Trans. 46, 1757 (2005)]. This system was investigated from the thermodynamic and structural viewpoints. However, hydrogen absorption/desorption mechanism and the state of hydrogen atoms absorbed in the composite have not been clarified yet. In order to find new or better hydrogen storage system, graphite powder and nano-structural graphite ball-milled under H2 and Ar atmosphere were prepared and milled with Li and Mg under Ar atmosphere in this study. Microstructural analysis for those samples by transmission electron microscope revealed that LiC6 and/or LiC12 were formed in Li-C-H system. On the other hand, MgC2 was found in Mg-C-H system ball-milled under H2 atmosphere, but not in the system ball-milled under Ar atmosphere. These results indicated that nano-structure in composites of nano-structural graphite is different from that of alkali (-earth) metal. For these reasons, metal-C-H system can be recognized to be a new family of hydrogen storage materials.
Investigation of anisotropic photonic band gaps in three-dimensional magnetized plasma photonic crystals containing the uniaxial material
Authors: Zhang Hai-Feng , Liu Shao-Bin , Kong Xiang-Kun
Published: September 2013

In this paper, the dispersive properties of three-dimensional (3D) magnetized plasma photonic crystals (MPPCs) composed of anisotropic dielectric (the uniaxial material) spheres immersed in homogeneous magnetized plasma background with face-centered-cubic (fcc) lattices are theoretically investigated by the plane wave expansion method, as the Voigt effects of magnetized plasma are considered. The equations for calculating the anisotropic photonic band gaps (PBGs) in the first irreducible Brillouin zone are theoretically deduced. The anisotropic PBGs and two flatbands regions can be obtained. The effects of the ordinary-refractive index, extraordinary-refractive index, filling factor, plasma frequency, and external magnetic field on the dispersive properties of the 3D MPPCs are investigated in detail, respectively, and some corresponding physical explanations are also given. The numerical results show that the anisotropy can open partial band gaps in 3D MPPCs with fcc lattices and the complete PBGs can be found compared to the conventional 3D MPPCs doped by the isotropic material. The bandwidths of PBGs can be tuned by introducing the magnetized plasma into 3D PCs containing the uniaxial material. It is also shown that the anisotropic PBGs can be manipulated by the ordinary-refractive index, extraordinary-refractive index, filling factor, plasma frequency, and external magnetic field, respectively. The locations of flatbands regions cannot be manipulated by any parameters except for the plasma frequency and external magnetic field. Introducing the uniaxial material can obtain the complete PBGs as the 3D MPPCs with high symmetry and also provides a way to design the tunable devices.
Communication: Long-lived states of nuclear spins in solids
Authors: Turanov A. , Khitrin A. K.
Published: September 2013

We report an observation of extremely long-lived spin states in systems of dipolar-coupled nuclear spins in solids. The “suspended echo” experiment uses a simple stimulated echo pulse sequence and creates non-equilibrium states which live many orders of magnitude longer than the characteristic time of spin-spin dynamics T2. Large amounts of information can be encoded in such long-lived states and subsequently retrieved by an application of a single “reading” pulse.
Age-dependent dissociation of ATP synthase dimers and loss of inner-membrane cristae in mitochondria
Authors: Daum Bertram , Walter Andreas , Horst Angelika , Osiewacz Heinz D. , Kühlbrandt Werner
Published: September 2013

Aging is one of the most fundamental, yet least understood biological processes that affect all forms of eukaryotic life. Mitochondria are intimately involved in aging, but the underlying molecular mechanisms are largely unknown. Electron cryotomography of whole mitochondria from the aging model organism
Podospora anserina
revealed profound age-dependent changes in membrane architecture. With increasing age, the typical cristae disappear and the inner membrane vesiculates. The ATP synthase dimers that form rows at the cristae tips dissociate into monomers in inner-membrane vesicles, and the membrane curvature at the ATP synthase inverts. Dissociation of the ATP synthase dimer may involve the peptidyl prolyl isomerase cyclophilin D. Finally, the outer membrane ruptures near large contact-site complexes, releasing apoptogens into the cytoplasm. Inner-membrane vesiculation and dissociation of ATP synthase dimers would impair the ability of mitochondria to supply the cell with sufficient ATP to maintain essential cellular functions.
Activation and control of p53 tetramerization in individual living cells
Authors: Gaglia Giorgio , Guan Yinghua , Shah Jagesh V. , Lahav Galit
Published: September 2013

Significance

p53 oligomerization has been the topic of many previous studies, mainly due to the connection between mutations in the p53 tetramerization domain and Li–Fraumeni syndrome. However, all previous studies have measured p53 oligomeric state in vitro. We measure the dynamics of p53 oligomerization in living cells using fluorescence correlation spectroscopy and quantify the discrete number of oligomers over time after DNA damage. Our study demonstrates the power of using sensitive analytical tools for acquiring accurate measures of fluctuation correlation in living cells and the use of mathematical models to gain new insights about p53 biology. The approach we used here should be of general utility in studying the quantitative dynamics and function of protein oligomerization in any cellular system.
The rise and fall of trade unionism in Zimbabwe, Part II: 1995–2000
Authors: Yeros Paris
Published: September 2013

This article is the second of a two-part study on the evolution of the Zimbabwe Congress of Trade Unions (ZCTU) in the 1990s. This second part covers the period 1995–2000, when the labour centre adopted a ‘social democratic’ ideology and a strategy of negotiation. This lasted until 1997, when the labour centre resolved to challenge the ruling party's hold on power. The article argues that the labour centre increasingly narrowed its democratisation critique to ‘regime change’, through which it gained a broad array of new allies, but which also terminally weakened its organic basis in the working class.

[L'ascension et la chute du syndicalisme au Zimbabwe, 2e partie: 1995–2000]. Cet article est le second d'une étude en deux parties sur l’évolution du Congrès des syndicats du Zimbabwe (Zimbabwe Congress of Trade Unions, ZCTU) dans les années 90. Cette seconde partie couvre la période 1995–2000, durant laquelle le syndicat adopta une idéologie ‘social démocrate’ et une stratégie de négociation. Cela dura jusqu'en 1997, lorsqu'il décida de défier la mainmise du parti en place sur le pouvoir. Cet article soutient que le syndicat a peu à peu restreint sa critique de la démocratisation au ‘changement de régime’, évolution qui lui a rapporté tout un éventail de nouveaux alliés, mais qui a aussi, au final, affaibli sa base dans la classe ouvrière.

Mots-clés : Afrique ; Zimbabwe ; relations de travail ; syndicalisme ; démocratisation ; développement
Rescuing African bodies: celebrities, consumerism and neoliberal humanitarianism
Authors: Daley Patricia
Published: September 2013

This article examines the role of Western celebrities as part of new networks in the increasing commodification of humanitarianism in Africa. It explores the relationship between celebrities as neoliberal subjectivities and their shaping of ethical consumerism and humanitarian interventions. Using various case studies (Product RED, 50 Cent's SK drink, Save Darfur Campaign [United to End Genocide], Kony2012, Raise Hope for the Congo and the Eastern Congo Initiative), the article considers how celebrities frame humanitarian crises for public consumption, their link to accumulation by dispossession, and their impact on African agency and on international solidarity against corporate exploitation.

[Secourir des corps africains: stars, consumérisme et humanitaire néolibéral.] Cet article examine le rôle de stars occidentales membres de nouveaux réseaux dans la marchandisation croissante de l'humanitaire en Afrique. Il explore les relations entre les stars, êtres néolibéraux, et leur façon d’élaborer un consumérisme éthique et des interventions humanitaires. Utilisant diverses études de cas (Produit rouge Product RED, boisson SK de 50 Cent, campagne pour sauver le Darfour [unis pour mettre fin au génocide], Kony2012, Espoir pour le Congo et l'Initiative pour l'est du Congo), l'article étudie comment les stars formatent les crises humanitaires pour la consommation du public, leur lien à l'accumulation par dépossession et leur impact sur l'agence africaine et la solidarité internationale contre l'exploitation commerciale.

Mots-clés: stars ; humanitaire ; Kony2012 ; marchandisation ; consumérisme
Neoliberal globalisation and evolving local traditional institutions: implications for access to resources in rural northern Ghana
Authors: Yaro Joseph
                      A.
Published: September 2013

The world has become interconnected and interdependent well beyond the economic domains of life and this has consequences for the role of major institutions governing access to resources in rural Africa. Neoliberal globalisation is eroding the moral foundation of rural societies in ways that create unequal access to the resources needed for involvement and inclusion in the market relations of production and social reproduction. Using the case of rural northern Ghana, this article shows how the transformation of local traditional governance and institutions led to processes of accumulation for a few privileged ones while the majority are excluded through dispossession.

[Mondialisation néolibérale et évolution d'institutions traditionnelles locales: impacts pour l'accès aux ressources dans le nord Ghana rural.] Le monde est devenu interconnecté et interdépendant, bien au-delà des questions économiques et cela a des conséquences pour le rôle d'institutions majeures qui gèrent l'accès aux ressources dans l'Afrique rurale. La mondialisation néolibérale érode les fondations morales des sociétés rurales à tel point qu'elle génère des inégalités dans l'accès aux ressources nécessaires pour l'inclusion au marché de la production et de la reproduction sociale. En travaillant sur le cas du nord Ghana rural, cet article montre comment la transformation des modes de gouvernance et institutions locales traditionnelles a conduit à des processus d'accumulation réservés à quelques rares privilégiés tandis que la majorité était spoliée et victime d'exclusion.

Mots-clés : mondialisation néolibérale ; tradition ; institutions locales ; Ghana rural
DrosophilaRic-8 interacts with the Gα12/13subunit, Concertina, during activation of the Folded gastrulation pathway
Authors: Peters Kimberly A. , Rogers Stephen L.
Published: September 2013

Heterotrimeric G proteins, composed of α, β, and γ subunits, are activated by exchange of GDP for GTP on the Gα subunit. Canonically, Gα is stimulated by the guanine-nucleotide exchange factor (GEF) activity of ligand-bound G protein–coupled receptors. However, Gα subunits may also be activated in a noncanonical manner by members of the Ric-8 family, cytoplasmic proteins that also act as GEFs for Gα subunits. We used a signaling pathway active during Drosophila gastrulation as a model system to study Ric-8/Gα interactions. A component of this pathway, the Drosophila Gα12/13subunit, Concertina (Cta), is necessary to trigger actomyosin contractility during gastrulation events. Ric-8 mutants exhibit similar gastrulation defects to Cta mutants. Here we use a novel tissue culture system to study a signaling pathway that controls cytoskeletal rearrangements necessary for cellular morphogenesis. We show that Ric-8 regulates this pathway through physical interaction with Cta and preferentially interacts with inactive Cta and directs its localization within the cell. We also use this system to conduct a structure–function analysis of Ric-8 and identify key residues required for both Cta interaction and cellular contractility.
CD47 plays a critical role in T-cell recruitment by regulation of LFA-1 and VLA-4 integrin adhesive functions
Authors: Azcutia Veronica , Routledge Matthew , Williams Marcie R. , Newton Gail , Frazier William A. , Manica Andrè , Croce Kevin J. , Parkos Charles A. , Schmider Angela B. , Turman Melissa V. , Soberman Roy J. , Luscinskas Francis W.
Published: September 2013

CD47 plays an important but incompletely understood role in the innate and adaptive immune responses. CD47, also called integrin-associated protein, has been demonstrated to associate in cis with β1 and β3 integrins. Here we test the hypothesis that CD47 regulates adhesive functions of T-cell α4β1 (VLA-4) and αLβ2 (LFA-1) in in vivo and in vitro models of inflammation. Intravital microscopy studies reveal that CD47−/−Th1 cells exhibit reduced interactions with wild-type (WT) inflamed cremaster muscle microvessels. Similarly, murine CD47−/−Th1 cells, as compared with WT, showed defects in adhesion and transmigration across tumor necrosis factor-α (TNF-α)–activated murine endothelium and in adhesion to immobilized intercellular adhesion molecule 1 (ICAM-1) and vascular cell adhesion protein 1 (VCAM-1) under flow conditions. Human Jurkat T-cells lacking CD47 also showed reduced adhesion to TNF-α–activated endothelium and ICAM-1 and VCAM-1. In cis interactions between Jurkat T-cell β2 integrins and CD47 were detected by fluorescence lifetime imaging microscopy. Unexpectedly, Jurkat CD47 null cells exhibited a striking defect in β1 and β2 integrin activation in response to Mn2+or Mg2+/ethylene glycol tetraacetic acid treatment. Our results demonstrate that CD47 associates with β2 integrins and is necessary to induce high-affinity conformations of LFA-1 and VLA-4 that recognize their endothelial cell ligands and support leukocyte adhesion and transendothelial migration.
Finding the accelerator and brake in an individual quota fishery: linking ecology, economics, and fleet dynamics of US West Coast trawl fisheries
Authors: Kaplan Isaac C. , Holland Daniel S. , Fulton Elizabeth A.
Published: September 2013

Isaac C. Kaplan, Daniel S. Holland, and Elizabeth A. Fulton. 2014. Finding the accelerator and brake in an individual quota fishery: linking ecology, economics, and fleet dynamics of US West Coast trawl fisheries. – ICES Journal of Marine Science, 71: 308–319. In 2011, the Pacific Fisheries Management Council implemented an individual transferrable quota (ITQ) system for the US West Coast groundfish trawl fleet. Under the ITQ system, each vessel now receives transferrable annual allocations of quota for 29 groundfish species, including target and bycatch species. Here we develop an ecosystem and fleet dynamics model to identify which components of an ITQ system are likely to drive responses in effort, target species catch, bycatch, and overall profitability. In the absence of penalties for discarding over-quota fish, ITQs lead to large increases in fishing effort and bycatch. The penalties fishermen expect for exceeding quota have the largest effect on fleet behaviour, capping effort and total bycatch. Quota prices for target or bycatch species have lesser impacts on fishing dynamics, even up to bycatch quota prices of $50 kg−1. Ports that overlap less with bycatch species can increase effort under individual quotas, while other ports decrease effort. Relative to a prior management system, ITQs with penalties for exceeding quotas lead to increased target species landings and lower bycatch, but with strong variation among species. The model illustrates how alternative fishery management policies affect profitability, sustainability and the ecosystem.
Environmental factors influencing δ13C and δ15N in three Chesapeake Bay fishes
Authors: Davias Lori A. , Kornis Matthew S. , Breitburg Denise L.
Published: September 2013

Stable isotope analysis has become a common tool for mapping trophic relationships, describing foodweb changes, and assessing ecosystem health. Clear interpretation of stable isotopes is facilitated by understanding how environmental factors can affect isotopic values; in estuarine systems, these factors may include salinity, land use, and shoreline habitat. To evaluate these factors, fish were collected from shallow-water habitats next to hardened (bulkhead and riprap) and unhardened (beach and marsh) shorelines within five subestuaries of the Chesapeake Bay that differed in predominant land use and salinity. This study focused on three common mid-Atlantic fish species: mummichog, Fundulus heteroclitus, Atlantic silverside, Menidia menidia, and white perch, Morone americana. Multiple regression analyses pointed to standard length, salinity, % of watershed as developed or crop land, and shoreline habitat type as important predictors for δ15N in all three species and for δ13C in mummichog and white perch. Further analysis controlling for the effects of salinity, land use, and fish size demonstrated that δ13C and δ15N were lower in tissues of fish collected next to marsh compared with hardened or beach habitat. Habitat effects were strongest for mummichog. This study focused on overarching patterns driving stable isotope signatures in fish; however, it also indicated potentially important interactions between nearshore habitat type and land use or salinity that deserve further analysis. Results have implications for the scale of isotope inquiry and give justification for more detailed follow-up studies of foodweb structure along modified and natural shorelines.
Lack of equivalence in the elemental and stable isotope chemistry within the sagittal otolith pair of the summer flounder, Paralichthys dentatus
Authors: Kajajian Antranik , Schaffler Jason J. , Jones Cynthia M.
Published: September 2013

Kajajian, A., Schaffler, J. J., and Jones, C. M. 2014. Lack of equivalence in the elemental and stable isotope chemistry within the sagittal otolith pair of the summer flounder, Paralichthys dentatus. – ICES Journal of Marine Science, 71: 356–364. In fish that are not bilaterally symmetrical, the left and right sagittae are often not symmetrical, exhibiting divergent growth patterns and mass, and may have differences in chemical composition. We investigated this in the asymmetrical summer flounder Paralichthys dentatus, collected from different nursery habitats along the US east coast. Significant differences were detected in otolith mass, δ13C, δ18O, Li:Ca, Mg:Ca, and Sr:Ca, and overall chemical signatures. These results refute the hypothesis of left–right equivalence that is prevalent for bilaterally symmetrical fishes. We tested whether a specific side was better suited for classification. The best models differed between sagittae and resulted in different classification accuracies. The left otolith produced better classification accuracies. Simulated samples of randomized sets of left or right otoliths produced mean accuracies intermediate to classification and were often highly variable. We recommend that future otolith chemistry studies involving bilaterally asymmetrical species test the hypothesis of equivalence within the sagittae before randomly choosing an otolith for chemical analyses.
Pseudocollapse and rebuilding of North Sea mackerel (Scomber scombrus)
Authors: Jansen Teunis
Published: September 2013

Jansen, T. 2014. Pseudocollapse and rebuilding of North Sea mackerel (Scomber scombrus). – ICES Journal of Marine Science, 71: 299–307. The largest observed change in mackerel (Scomber scombrus) abundance in the North Atlantic happened when the so-called “North Sea mackerel” collapsed due to overfishing. Despite protection, it has remained in a depleted state. Central to this interpretation was that the “North Sea mackerel” was considered to be a distinct spawning component. However, a recent study has shown that this is not likely. In the light of this study, a review of the history of mackerel spawning in the North Sea found that the traditional explanation of the collapse did not account for a range of unfavourable environmental changes: high fishing pressure was followed by decreasing temperatures that reduced the spawning migration into the North Sea. This was further supplemented by unfavourable changes in food and wind-induced turbulence. On the population level, this was, therefore, not a local stock collapse, but a southwest shift in spawning distribution combined with a reduction in that portion of the population cline with an affinity for spawning in the northeastern part of the spawning area, including the North Sea. No indication of irreversible genetic or behavioural losses caused by the events was found. The previously unexplained lack of rebuilding of spawning in the North Sea consequently seems related to two environmental factors that have remained unfavourable: (i) zooplankton concentration, and (ii) wind-induced turbulence. Furthermore, the large commercial autumn–winter fishery in the North Sea continues to land unknown quantities of mackerel that have an affinity for spawning in the northeastern part of the spawning area, including the North Sea.
Helq acts in parallel to Fancc to suppress replication-associated genome instability
Authors: Luebben Spencer W. , Kawabata Tsuyoshi , Akre Monica K. , Lee Wai Long , Johnson Charles S. , O’Sullivan M. Gerard , Shima Naoko
Published: September 2013

HELQ is a superfamily 2 DNA helicase found in archaea and metazoans. It has been implicated in processing stalled replication forks and in repairing DNA double-strand breaks and inter-strand crosslinks. Though previous studies have suggested the possibility that HELQ is involved in the Fanconi anemia (FA) pathway, a dominant mechanism for inter-strand crosslink repair in vertebrates, this connection remains elusive. Here, we investigated this question in mice using the Helqgt and Fancc− strains. Compared with Fancc−/− mice lacking FANCC, a component of the FA core complex, Helqgt/gt mice exhibited a mild of form of FA-like phenotypes including hypogonadism and cellular sensitivity to the crosslinker mitomycin C. However, unlike Fancc−/− primary fibroblasts, Helqgt/gt cells had intact FANCD2 mono-ubiquitination and focus formation. Notably, for all traits examined, Helq was non-epistatic with Fancc, as Helqgt/gt;Fancc−/− double mutants displayed significantly worsened phenotypes than either single mutant. Importantly, this was most noticeable for the suppression of spontaneous chromosome instability such as micronuclei and 53BP1 nuclear bodies, known consequences of persistently stalled replication forks. These findings suggest that mammalian HELQ contributes to genome stability in unchallenged conditions through a mechanism distinct from the function of FANCC.
A Salicylic Acid–Induced Lectin-Like Protein Plays a Positive Role in the Effector-Triggered Immunity Response of Arabidopsis thaliana to Pseudomonas syringae Avr-Rpm1
Authors: Armijo Grace , Salinas Paula , Monteoliva Mariela Inés , Seguel Aldo , García Consuelo , Villarroel-Candia Eva , Song Wei , van der Krol Alexander Ronald , Álvarez María Elena , Holuigue Loreto
Published: September 2013

Salicylic acid (SA) is one of the key hormones that orchestrate the pathogen-induced immune response in plants. This response is often characterized by the activation of a local hypersensitive reaction involving programmed cell death, which constrains proliferation of biotrophic pathogens. Here, we report the identification and functional characterization of an SA-induced legume lectin-like protein 1 (SAI-LLP1), which is coded by a gene that belongs to the group of early SA-activated Arabidopsis genes. SAI-LLP1 expression is induced upon inoculation with avirulent strains of Pseudomonas syringae pv. tomato via an SA-dependent mechanism. Constitutive expression of SAI-LLP1 restrains proliferation of P. syringae pv. tomato Avr-Rpm1 and triggers more cell death in inoculated leaves. Cellular and biochemical evidence indicates that SAI-LLP1 is a glycoprotein located primarily at the apoplastic side of the plasma membrane. This work indicates that SAI-LLP1 is involved in resistance to P. syringae pv. tomato Avr-Rpm1 in Arabidopsis, as a component of the SA-mediated defense processes associated with the effector-triggered immunity response.
Sporulation Capacity and Longevity of Puccinia horiana Teliospores in Infected Chrysanthemum Leaves
Authors: Bonde Morris R. , Palmer Cristi L. , Luster Douglas G. , Nester Susan E. , Revell Jason M. , Berner Dana K.
Published: September 2013

Puccinia horiana Henn., a quarantine-significant fungal pathogen and causal agent of chrysanthemum white rust (CWR), was first discovered in the United States in 1977 and later believed to have been eradicated. Recently, however, the disease has sporadically reappeared in the northeastern US. Possible explanations for the reappearance include survival of the pathogen in the local environment, and reintroduction from other locations. To determine the possibility that the pathogen might be overwintering in the field, we undertook the study described here. Results from the study showed that P. horiana teliospores, imbedded in infected leaves, were capable of sporulating 2 weeks after inoculation, and this capacity continued until the leaf became necrotic and desiccated. This is the first report of the extreme susceptibility of P. horiana teliospores to leaf necrosis and desiccation and suggests that field infections following winter are unlikely to originate from teliospores. Teliospore germination on excised leaves was shown to be inhibited by light.

Accepted for publication 3 April 2013. Published 23 August 2013.
Brain transcriptome of the violet-eared waxbillUraeginthus granatinaand recent evolution in the songbird genome
Authors: Balakrishnan Christopher N. , Chapus Charles , Brewer Michael S. , Clayton David F.
Published: September 2013

Songbirds are important models for the study of social behaviour and communication. To complement the recent genome sequencing of the domesticated zebra finch, we sequenced the brain transcriptome of a closely related songbird species, the violet-eared waxbill (Uraeginthus granatina).Both the zebra finch and violet-eared waxbill are members of the family Estrildidae, but differ markedly in their social behaviour. Using Roche 454 RNA sequencing, we generated an assembly and annotation of 11 084 waxbill orthologues of 17 475 zebra finch genes (64%), with an average transcript length of 1555 bp. We also identified 5985 single nucleotide polymorphisms (SNPs) of potential utility for future population genomic studies. Comparing the two species, we found evidence for rapid protein evolution (ω) and low polymorphism of the avian Z sex chromosome, consistent with prior studies of more divergent avian species. An intriguing outlier was putative chromosome 4A, which showed a high density of SNPs and low evolutionary rate relative to other chromosomes. Genome-wideωwas identical in zebra finch and violet-eared waxbill lineages, suggesting a similar demographic history with efficient purifying natural selection. Further comparisons of these and other estrildid finches may provide insights into the evolutionary neurogenomics of social behaviour.
Streptococcus dentisani sp. nov., a novel member of the mitis group
Authors: Camelo-Castillo Anny , Benítez-Páez Alfonso , Belda-Ferre Pedro , Cabrera-Rubio Raúl , Mira Alex
Published: September 2013

Genomic, taxonomic and biochemical studies were performed on two strains of α-haemolytic streptococci that showed them to be clustered with major members of the

Streptococcus mitis

group. These Gram-stain-positive strains were isolated from tooth surfaces of caries-free humans and showed the classical spherical shape of streptococcal species growing in chains. Sequence analysis from concatenated 16S and 23S rRNA gene and sodA genes showed that these strains belonged to the mitis group, but both of them clustered into a new phylogenetic branch. The genomes of these two isolates were sequenced, and whole-genome average nucleotide identity (ANI) demonstrated that these strains significantly differed from any streptococcal species, showing ANI values under 91 % even when compared with the phylogenetically closest species such as

Streptococcus oralis

and

S. mitis

. Biochemically, the two isolates also showed distinct metabolic features relative to closely related species, like α-galactosidase activity. From the results of the present study, the name Streptococcus dentisani sp. nov. is proposed to accommodate these novel strains, which have been deposited in open collections at the Spanish type Culture Collection (CECT) and Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures (DSMZ), being respectively identified as Streptococcus dentisani Str. 7746 ( = CECT 8313 = DSM 27089) and Streptococcus dentisani Str. 7747T ( = CECT 8312T = DSM 27088T).
Chitinophaga polysaccharea sp. nov., an exopolysaccharide-producing bacterium isolated from the rhizoplane of Dioscorea japonica
Authors: Han Song-Ih , Lee Hyo-Jin , Whang Kyung-Sook
Published: September 2013

A novel strain designated MRP-15T, belonging to the class

Sphingobacteriia

(phylum

Bacteroidetes

), was isolated from the rhizoplane of Dioscorea japonica in South Korea and was characterized taxonomically using a polyphasic approach. The strain was found to comprise Gram-stain-negative, aerobic, non-motile, non-spore-forming rods. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain belonged to the genus

Chitinophaga

but was clearly separated from established species of the genus

Chitinophaga

. 16S rRNA gene sequence similarities between strain MRP-15T and type strains of established species of the genus

Chitinophaga

ranged from 90.3 to 97.8 %. Phenotypic and chemotaxonomic data (major menaquinone, MK-7; major fatty acids, iso-C15 : 0 and C16 : 1ω5c) supported the affiliation of strain MRP-15T with the genus

Chitinophaga

. Therefore strain MRP-15T represents a novel species of the genus

Chitinophaga

, for which the name Chitinophaga polysaccharea sp. nov. is proposed. The type strain is MRP-15T ( = KACC 17184T = NCAIMB 02530T).
Identifying multiple causative genes at a single GWAS locus
Authors: Flister Michael J. , Tsaih Shirng-Wern , O'Meara Caitlin C. , Endres Bradley , Hoffman Matthew J. , Geurts Aron M. , Dwinell Melinda R. , Lazar Jozef , Jacob Howard J. , Moreno Carol
Published: September 2013

Genome-wide association studies (GWAS) are useful for nominating candidate genes, but typically are unable to establish disease causality or differentiate between the effects of variants in linkage disequilibrium (LD). Additionally, some GWAS loci might contain multiple causative variants or genes that contribute to the overall disease susceptibility at a single locus. However, the majority of current GWAS lack the statistical power to test whether multiple causative genes underlie the same locus, prompting us to adopt an alternative approach to testing multiple GWAS genes empirically. We used gene targeting in a disease-susceptible rat model of genetic hypertension to test all six genes at the Agtrap-Plod1 locus (Agtrap, Mthfr, Clcn6, Nppa, Nppb, and Plod1) for blood pressure (BP) and renal phenotypes. This revealed that the majority of genes at this locus (five out of six) can impact hypertension by modifying BP and renal phenotypes. Mutations of Nppa, Plod1, and Mthfr increased disease susceptibility, whereas Agtrap and Clcn6 mutations decreased hypertension risk. Reanalysis of the human AGTRAP-PLOD1 locus also implied that disease-associated haplotype blocks with polygenic effects were not only possible, but rather were highly plausible. Combined, these data demonstrate for the first time that multiple modifiers of hypertension can cosegregate at a single GWAS locus.