bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of high-dose hydrogen implantation on defect formation and dopant diffusion in silver implanted ZnO crystals
Authors: Yaqoob Faisal , Huang Mengbing
Published: July 2016

This work reports on the effects of a deep high-dose hydrogen ion implant on damage accumulation, defect retention, and silver diffusion in silver implanted ZnO crystals. Single-crystal ZnO samples were implanted with Ag ions in a region ∼150 nm within the surface, and some of these samples were additionally implanted with hydrogen ions to a dose of 2 × 1016 cm−2, close to the depth ∼250 nm. Rutherford backscattering/ion channeling measurements show that crystal damage caused by Ag ion implantation and the amount of defects retained in the near surface region following post-implantation annealing were found to diminish in the case with the H implantation. On the other hand, the additional H ion implantation resulted in a reduction of substitutional Ag atoms upon post-implantation annealing. Furthermore, the presence of H also modified the diffusion properties of Ag atoms in ZnO. We discuss these findings in the context of the effects of nano-cavities on formation and annihilation of point defects as well as on impurity diffusion and trapping in ZnO crystals.
Contributed Review: Quartz force sensing probes for micro-applications
Authors: Abrahamians Jean-Ochin , Pham Van Laurent , Régnier Stéphane
Published: July 2016

As self-sensing and self-exciting probes, quartz sensors present many advantages over silicon cantilevers for microscopy, micro-robotics, and other micro-applications. Their development and use is further bolstered by the fact that they can be manufactured from common quartz components. This paper therefore reviews applications of the increasingly popular quartz tuning fork probes as force sensors in the literature and examines the options for higher-frequency quartz probes using the other available types of flexional, thickness-shear or length-extensional resonators.
Mapping of spin wave propagation in a one-dimensional magnonic crystal
Authors: Ordóñez-Romero César L. , Lazcano-Ortiz Zorayda , Drozdovskii Andrey , Kalinikos Boris , Aguilar-Huerta Melisa , Domínguez-Juárez J. L. , Lopez-Maldonado Guillermo , Qureshi Naser , Kolokoltsev Oleg , Monsivais Guillermo
Published: July 2016

The formation and evolution of spin wave band gaps in the transmission spectrum of a magnonic crystal have been studied. A time and space resolved magneto inductive probing system has been used to map the spin wave propagation and evolution in a geometrically structured yttrium iron garnet film. Experiments have been carried out using (1) a chemically etched magnonic crystal supporting the propagation of magnetostatic surface spin waves, (2) a short microwave pulsed excitation of the spin waves, and (3) direct spin wave detection using a movable magneto inductive probe connected to a synchronized fast oscilloscope. The results show that the periodic structure not only modifies the spectra of the transmitted spin waves but also influences the distribution of the spin wave energy inside the magnonic crystal as a function of the position and the transmitted frequency. These results comprise an experimental confirmation of Bloch′s theorem in a spin wave system and demonstrate good agreement with theoretical observations in analogue phononic and photonic systems. Theoretical prediction of the structured transmission spectra is achieved using a simple model based on microwave transmission lines theory. Here, a spin wave system illustrates in detail the evolution of a much more general physical concept: the band gap.
Nucleation pressure threshold in acoustic droplet vaporization
Authors: Miles Christopher J. , Doering Charles R. , Kripfgans Oliver D.
Published: July 2016

We combine classical nucleation theory with superharmonic focusing to predict necessary pressures to induce nucleation in acoustic droplet vaporization. We show that linear acoustics is a valid approximation to leading order when particle displacements in the sound field are small relative to the radius of the droplet. This is done by perturbation analysis of an axisymmetric compressible inviscid flow about a droplet with small surface perturbations relative to the mean radius subjected to an incoming ultrasonic wave. The necessary nucleation pressure threshold inside the droplet is calculated to be −9.33 ± 0.30 MPa for typical experimental parameters by employing results from classical homogeneous nucleation theory. As a result, we are able to predict if a given incident pressure waveform will induce nucleation.
Analysis of the static magnetic field-dependent optical transmission of Ni nanorod colloidal suspensions
Authors: Krämer Florian , Gratz Micha , Tschöpe Andreas
Published: July 2016

The magnetic field-dependent optical transmission of dilute Ni nanorod aqueous suspensions was investigated. A series of four samples of nanorods were synthesized using the AAO template method and processed to stable colloids. The distributions of their length and diameter were characterized by analysis of TEM images and revealed average diameters of ∼25 nm and different lengths in the range of 60 nm–1100 nm. The collinear magnetic and optical anisotropy was studied by static field-dependent transmission measurements of linearly polarized light parallel and perpendicular to the magnetic field direction. The experimental results were modelled assuming the field-dependent orientation distribution function of a superparamagnetic ensemble for the uniaxial ferromagnetic nanorods in liquid dispersion and extinction cross sections for longitudinal and transversal optical polarization derived from different approaches, including the electrostatic approximation and the separation of variables method, both applied to spheroidal particles, as well as finite element method simulations of spheroids and capped cylindrical particles. The extinction cross sections were compared to reveal the differences associated with the approximations of homogeneous polarization and/or particle shape. The consequences of these approximations for the quantitative analysis of magnetic field-dependent optical transmission measurements were investigated and a reliable protocol derived. Furthermore, the changes in optical cross sections induced by electromagnetic interaction between two nanorods in parallel end-to-end and side-by-side configuration as a function of their separation were studied.
Radiation forces and torque on a rigid elliptical cylinder in acoustical plane progressive and (quasi)standing waves with arbitrary incidence
Authors: Mitri F. G.
Published: July 2016

This paper presents two key contributions; the first concerns the development of analytical expressions for the axial and transverse acoustic radiation forces exerted on a 2D rigid elliptical cylinder placed in the field of plane progressive, quasi-standing, or standing waves with arbitrary incidence. The second emphasis is on the acoustic radiation torque per length. The rigid elliptical cylinder case is important to be considered as a first-order approximation of the behavior of a cylindrical fluid column trapped in air because of the significant acoustic impedance mismatch at the particle boundary. Based on the rigorous partial-wave series expansion method in cylindrical coordinates, non-dimensional acoustic radiation force and torque functions are derived and defined in terms of the scattering coefficients of the elliptic cylinder. A coupled system of linear equations is obtained after applying the Neumann boundary condition for an immovable surface in a non-viscous fluid and solved numerically by matrix inversion after performing a single numerical integration procedure. Computational results for the non-dimensional force components and torque, showing the transition from the progressive to the (equi-amplitude) standing wave behavior, are performed with particular emphasis on the aspect ratio a/b, where a and b are the semi-axes of the ellipse, the dimensionless size parameter, as well as the angle of incidence ranging from end-on to broadside incidence. The results show that the elliptical geometry has a direct influence on the radiation force and torque, so that the standard theory for circular cylinders (at normal incidence) leads to significant miscalculations when the cylinder cross section becomes non-circular. Moreover, the elliptical cylinder experiences, in addition to the acoustic radiation force, a radiation torque that vanishes for the circular cylinder case. The application of the formalism presented here may be extended to other 2D surfaces of arbitrary shape, such as Chebyshev cylindrical particles with a small deformation, stadiums (with oval shape), or other non-circular geometries.
Colossal magnetodielectric effect and spin flop in magnetoelectric Co4Nb2O9 crystal
Authors: Yin L. H. , Zou Y. M. , Yang J. , Dai J. M. , Song W. H. , Zhu X. B. , Sun Y. P.
Published: July 2016

We have investigated the detailed magnetic, magnetoelectric (ME), magnetodielectric (MD) and thermal expansion properties in Co4Nb2O9 crystal. A magnetic-field-induced spin flop was observed below antiferromagnetic (AFM) transition temperature TN. Dielectric constant at applied magnetic field nearly diverges around the AFM transition, giving rise to a colossal MD effect as high as ∼138% around TN. Theoretical analysis of the ME and MD data revealed a major contribution of critical spin fluctuation to the colossal MD effect in Co4Nb2O9. These results suggest that linear ME materials with large ME coupling might be potentially used to realize large MD effect for future application.
Influence of scattering and interference effects on the low-temperature magnetotransport of Cu2ZnSnS4 single crystals
Authors: Lähderanta E. , Guc M. , Shakhov M. A. , Arushanov E. , Lisunov K. G.
Published: July 2016

Activated resistivity, ρ(T), and positive magnetoresistance (MR) are observed in Cu2ZnSnS4 single crystals within the temperature interval between T ∼ 2 and 300 K in pulsed magnetic fields of B up to 20 T. Between T ∼ 50 and 150 K, the charge transfer is described by the Mott variable-range hopping (VRH) transport over localized states of the defect acceptor band with width W ∼ 12–25 meV. Up to the highest applied fields, MR follows the law ln ρ(B) ∝ B2 pertinent to the VRH conduction at λ ≫ a, where λ is the magnetic length and a is the localization radius. The joint analysis of the MR and ρ(T) data yielded a series of microscopic parameters, including the values of a ≈ 22–45 Å, depending on the proximity of a sample to the metal-insulator transition. However, below T ∼ 3–4 K the Shklovskii-Efros VRH conduction is observed. Here, the behavior of MR changes drastically, exhibiting a sharp contraction of the quadratic MR region and transformation of the MR law into those of ln ρ (B) ∝ B2/3 or ∝ B3/4 when B is increased. In addition, such behavior of MR is accompanied by a dramatic increase of the localization radius a ≈ 50–170 Å. Both anomalies above are explained quantitatively by the same reason, connected to the constructive interference of different paths arising from multiple scattering of hopping carriers at low temperatures. In particular, the low-temperature values of the localization radius, evaluated in frames of the theory of interference phenomena in the VRH conduction, exhibit a reasonable agreement with the experimental data.
Design and experiment study of compact circular-rectangular waveguide mode converter
Authors: Zhao Xuhao , Yuan Chengwei , Zhang Qiang , Zhao Lishan
Published: July 2016

A compact mode converter that transforms TM01 circular waveguide mode to TE10 rectangular waveguide mode is investigated. It consists of a circular waveguide with a short circuit terminal and a rectangular waveguide which is perpendicular to the circular waveguide. Simulation results show that conversion efficiency of the mode converter is about 99.8% at central frequency of 1.75 GHz, and the total return loss is approximately −30 dB. The experimental results are well consistent with the computer simulation, which demonstrates the feasibility and high power handling capacity of the mode converter.
Single laser pulse compression via strongly coupled stimulated Brillouin scattering in plasma
Authors: Peng H. , Wu Z. H. , Zuo Y. L. , Zhang Z. M. , Zhou K. N. , Su J. Q.
Published: July 2016

Laser amplification in plasma, including stimulated Raman scattering amplification and strongly coupled stimulated Brillouin scattering (sc-SBS) amplification, is very promising to generate ultrahigh-power and ultrashort laser pulses. But both are quite complex in experiments: at least three different laser pulses must be prepared; temporal delay and spatial overlap of these three pulses are difficult. We propose a single pulse compression scheme based on sc-SBS in plasma. Only one moderately long laser is applied, the front part of which ionizes the gas to produced plasma, and gets reflected by a plasma mirror at the end of the gas channel. The reflected front quickly depletes the remaining part of the laser by sc-SBS in the self-similar regime. The output laser is much stronger and shorter. This scheme is at first considered theoretically, then validated by using 1D PIC simulations.
Tracking the density evolution in counter-propagating shock waves using imaging X-ray scattering
Authors: Zastrau U. , Gamboa E. J. , Kraus D. , Benage J. F. , Drake R. P. , Efthimion P. , Falk K. , Falcone R. W. , Fletcher L. B. , Galtier E. , Gauthier M. , Granados E. , Hastings J. B. , Heimann P. , Hill K. , Keiter P. A. , Lu J. , MacDonald M. J. , Montgomery D. S. , Nagler B. , Pablant N. , Schropp A. , Tobias B. , Gericke D. O. , Glenzer S. H. , Lee H. J.
Published: July 2016

We present results from time-resolved X-ray imaging and inelastic scattering on collective excitations. These data are then employed to infer the mass density evolution within laser-driven shock waves. In our experiments, thin carbon foils are first strongly compressed and then driven into a dense state by counter-propagating shock waves. The different measurements agree that the graphite sample is about twofold compressed when the shock waves collide, and a sharp increase in forward scattering indicates disassembly of the sample 1 ns thereafter. We can benchmark hydrodynamics simulations of colliding shock waves by the X-ray scattering methods employed.
Revisiting radiative deep-level transitions in CuGaSe2 by photoluminescence
Authors: Spindler Conrad , Regesch David , Siebentritt Susanne
Published: July 2016

Recent defect calculations suggest that the open circuit voltage of CuGaSe2 solar cells can be limited by deep intrinsic electron traps by GaCu antisites and their complexes with Cu-vacancies. To gain experimental evidence, two radiative defect transitions at 1.10 eV and 1.24 eV are characterized by steady-state photoluminescence on epitaxial-grown CuGaSe2 thin films. Cu-rich samples are studied, since they show highest crystal quality, exciton luminescence, and no potential fluctuations. Variations of the laser intensity and temperature dependent measurements suggest that emission occurs from two deep donor-like levels into the same shallow acceptor. At 10 K, power-law exponents of 1 (low excitation regime) and 1/2 (high excitation regime) are observed identically for both transitions. The theory and a fitting function for the double power law is derived. It is concluded that the acceptor becomes saturated by excess carriers which changes the exponent of all transitions. Activation energies determined from the temperature quenching depend on the excitation level and show unexpected values of 600 meV and higher. The thermal activation of non-radiative processes can explain the distortion of the ionization energies. Both the deep levels play a major role as radiative and non-radiative recombination centers for electrons and can be detrimental for photovoltaic applications.
Superluminescent light emitting diodes on naturally survived InGaN/GaN lateral nanowires
Authors: Banerjee D. , Sankaranarayanan S. , Khachariya D. , Nadar M. B. , Ganguly S. , Saha D.
Published: July 2016

We demonstrate a method for nanowire formation by natural selection during wet anisotropic chemical etching in boiling phosphoric acid. Nanowires of sub-10 nm lateral dimensions and lengths of 700 nm or more are naturally formed during the wet etching due to the convergence of the nearby crystallographic hexagonal etch pits. These nanowires are site controlled when formed in augmentation with dry etching. Temperature and power dependent photoluminescence characterizations confirm excitonic transitions up to room temperature. The exciton confinement is enhanced by using two-dimensional confinement whereby enforcing greater overlap of the electron-hole wave-functions. The surviving nanowires have less defects and a small temperature variation of the output electroluminescent light. We have observed superluminescent behaviour of the light emitting diodes formed on these nanowires. There is no observable efficiency roll off for current densities up to 400 A/cm2.
Effect of NiO inserted layer on spin-Hall magnetoresistance in Pt/NiO/YIG heterostructures
Authors: Shang T. , Zhan Q. F. , Yang H. L. , Zuo Z. H. , Xie Y. L. , Liu L. P. , Zhang S. L. , Zhang Y. , Li H. H. , Wang B. M. , Wu Y. H. , Zhang S. , Li Run-Wei
Published: July 2016

We investigate spin-current transport with an antiferromagnetic insulator NiO thin layer by means of the spin-Hall magnetoresistance (SMR) over a wide range of temperature in Pt/NiO/Y3Fe5O12 (Pt/NiO/YIG) heterostructures. The SMR signal is comparable to that without the NiO layer as long as the temperature is near or above the blocking temperature of the NiO, indicating that the magnetic fluctuation of the insulating NiO is essential for transmitting the spin current from the Pt to YIG layer. On the other hand, the SMR signal becomes negligibly small at low temperature, and both conventional anisotropic magnetoresistance and the anomalous Hall resistance are extremely small at any temperature, implying that the insertion of the NiO has completely suppressed the Pt magnetization induced by the YIG magnetic proximity effect (MPE). The dual roles of the thin NiO layer are, to suppress the magnetic interaction or MPE between Pt and YIG, and to maintain efficient spin current transmission at high temperature.
Crossover from disordered to core-shell structures of nano-oxide Y2O3 dispersed particles in Fe
Authors: Higgins M. P. , Lu C. Y. , Lu Z. , Shao L. , Wang L. M. , Gao F.
Published: July 2016

Molecular dynamic simulations of Y2O3 in bcc Fe and transmission electron microscopy (TEM) observations were used to understand the structure of Y2O3 nano-clusters in an oxide dispersion strengthened steel matrix. The study showed that Y2O3 nano-clusters below 2 nm were completely disordered. Y2O3 nano-clusters above 2 nm, however, form a core-shell structure, with a shell thickness of 0.5–0.7 nm that is independent of nano-cluster size. Y2O3 nano-clusters were surrounded by off-lattice Fe atoms, further increasing the stability of these nano-clusters. TEM was used to corroborate our simulation results and showed a crossover from a disordered nano-cluster to a core-shell structure.
Metastable phase transformation and hcp-
ω
transformation pathways in Ti and Zr under high hydrostatic pressures
Authors: Gao Lei , Ding Xiangdong , Lookman Turab , Sun Jun , Salje E. K. H.
Published: July 2016

The energy landscape of Zr at high hydrostatic pressure suggests that its transformation behavior is strongly pressure dependent. This is in contrast to the known transition mechanism in Ti, which is essentially independent of hydrostatic pressure. Generalized solid-state nudged elastic band calculations at constant pressure shows that α-Zr transforms like Ti only at the lowest pressure inside the stability field of ω-phase. Different pathways apply at higher pressures where the energy landscape contains several high barriers so that metastable states are expected, including the appearance of a transient bcc phase at ca. 23 GPa. The global driving force for the hcp-ω transition increases strongly with increasing pressure and reaches 23.7 meV/atom at 23 GPa. Much of this energy relates to the excess volume of the hcp phase compared with its ω phase.
Study on aggregation and electric properties in the micro-region of functionalized dithieno[2, 3-b: 3′, 2′-d]thiophene (DTT) oligomers
Authors: Jiang Xiaohong , Huang Xiaowei , Zhang Jiajia , Lu Zhijuan , Wang Hua , Du Zuliang
Published: July 2016

Three kinds of 2,5,-diphenyl-dithienol[2, 3-b: 3′, 2′-d]thiophene (DP-DTT), 2,5,-distyryl-dithienol[2, 3-b: 3′, 2′-d]thiophene (DEP-DTT) and 2,5,-thienyl-dithienol[2, 3-b: 3′, 2′-d]thiophene (DET-DTT) micro-region structure and electronic properties were studied. Thin films of these functionalized DTT oligomers were prepared in a one-step drop-casting deposition onto highly oriented pyrolytic graphite substrates. The surface structure of these films was characterized by atomic force microscopy (AFM). Conducting probe atomic force microscope (C-AFM) and Kelvin probe force microscope (KFM) were both used to characterize the electronic transport behavior and surface potential distribution. The substituents of DTT oligomers can greatly affect their aggregation and the hopping conductance mechanism was used to explain the Au-DTTs-HOPG junctions. KFM investigation revealed that these oligomers with different substituents have different highest occupied molecular orbital energy levels. The corresponding theoretical analysis reveals similar result to KFM characterization. The I-V results indicated that the aggregates of molecules were the dominating factor to their micro-region electrical transport.
Adherence to, and acceptability of, Listerine® mouthwash as a potential preventive intervention for pharyngeal gonorrhoea among men who have sex with men in Australia: a longitudinal study
Authors: Cornelisse Vincent J. , Fairley Christopher K. , Walker Sandra , Young Tameka , Lee David , Chen Marcus Y. , Bradshaw Catriona S. , Chow Eric P. F.
Published: July 2016

We investigated whether men who have sex with men (MSM) would use mouthwash daily to prevent pharyngeal gonorrhoea. Ten MSM attending the Melbourne Sexual Health Centre were asked to use a Listerine® alcohol-containing mouthwash daily for 14 days in August 2015. Mouthwash was used at least once daily for 133 of 140 person-days (95% of days; 95% confidence interval 90–98%). All 10 men were willing to use mouthwash on a daily basis, and nine men were willing to use mouthwash after oral sex. This study showed that daily use of mouthwash is an acceptable intervention to prevent pharyngeal gonorrhoea in MSM.
Epigenetic regulation of
Kcna3
-encoding Kv1.3 potassium channel by cereblon contributes to regulation of CD4
+
T-cell activation
Authors: Kang Jung-Ah , Park Sang-Heon , Jeong Sang Phil , Han Min-Hee , Lee Cho-Rong , Lee Kwang Min , Kim Namhee , Song Mi-Ryoung , Choi Murim , Ye Michael , Jung Guhung , Lee Won-Woo , Eom Soo Hyun , Park Chul-Seung , Park Sung-Gyoo
Published: July 2016

Significance

In resting T cells, CRBN normally represses expression of the Kv1.3 potassium channel by regulating histone modifications to prevent hyperactivation of T cells. It does this by controlling recruitment of EZH1 to the potassium channel region of the Kcna3 gene (or locus). However, lack of CRBN causes up-regulation of Kv1.3 expression, which in turn increases potassium flux, thereby triggering increased calcium flux during T-cell activation.
Deubiquitinase Usp8 regulates α-synuclein clearance and modifies its toxicity in Lewy body disease
Authors: Alexopoulou Zoi , Lang Johannes , Perrett Rebecca M. , Elschami Myriam , Hurry Madeleine E. D. , Kim Hyoung Tae , Mazaraki Dimitra , Szabo Aron , Kessler Benedikt M. , Goldberg Alfred Lewis , Ansorge Olaf , Fulga Tudor A. , Tofaris George K.
Published: July 2016

Significance

A cardinal feature of Parkinson’s disease pathology is the aggregation of α-synuclein in ubiquitin-positive inclusions termed Lewy bodies, yet the composition of ubiquitin conjugates in these inclusions and their role in α-synuclein pathobiology remain unclear. Here we demonstrate that α-synuclein inclusions contain K63-linked ubiquitin chains, which are strikingly reduced in dopaminergic neurons. In these neurons, the deubiquitinase Usp8 is present in Lewy bodies, and its content is related inversely to the extent of K63-linked ubiquitination. Our mechanistic studies in vitro and in flies indicate that Usp8 interacts with and deconjugates K63-linked ubiquitin chains on α-synuclein, prolonging its half-life and increasing its toxicity. Thus, Usp8 appears to be a critical factor determining α-synuclein levels that could be targeted for therapies.
Hydrogen isotopes in individual amino acids reflect differentiated pools of hydrogen from food and water in
Escherichia coli
Authors: Fogel Marilyn L. , Griffin Patrick L. , Newsome Seth D.
Published: July 2016

Significance

Hydrogen isotope (δ
2
H) values of bulk tissues have become valuable tracers for studying migration and movement patterns in animals, but the biochemical mechanism for how hydrogen is incorporated into heterotrophic organisms is not well understood. We grew
Escherichia coli
as a model organism on two different substrates, and then measured δ
2
H values of individual amino acids (AAs) in cellular material. The δ
2
H values of AAs were highly variable within a simple microbial culture. Using isotopic fractionation models, we show that AA δ
2
H provide tracers of an organism’s environmental (e.g., drinking) water, as well as its food, information of prime interest to ecologists. The work is also of significance to microbial physiologists studying metabolic pathways in microbes from extreme environments.
Hhip
haploinsufficiency sensitizes mice to age-related emphysema
Authors: Lao Taotao , Jiang Zhiqiang , Yun Jeong , Qiu Weiliang , Guo Feng , Huang Chunfang , Mancini John Dominic , Gupta Kushagra , Laucho-Contreras Maria E. , Naing Zun Zar Chi , Zhang Li , Perrella Mark A. , Owen Caroline A. , Silverman Edwin K. , Zhou Xiaobo
Published: July 2016

Significance

Genome-wide association studies (GWAS) have been very successful in discovering genetic loci associated with complex traits. However, only few studies applied murine models to investigate how GWAS genes contribute to human lung diseases. Motivated by GWAS linking Hedgehog interacting protein (
HHIP
) to emphysema and impairments in lung function, this study demonstrated that
Hhip
+/−
mice developed spontaneous emphysema and lung function impairment over time. Moreover, emphysema, associated with increased oxidative stress in
Hhip
+/−
lungs, was prevented by treating the mice with the antioxidant,
N
-acetyl cysteine (NAC). This post-GWAS functional study connects aging-related diseases, molecular mechanisms, and potential therapy in a genetic haploinsufficient murine model, which may lead to improvements in understanding pathophysiologic concepts of alveolar loss related to aging.
N-terminal domain of complexin independently activates calcium-triggered fusion
Authors: Lai Ying , Choi Ucheor B. , Zhang Yunxiang , Zhao Minglei , Pfuetzner Richard A. , Wang Austin L. , Diao Jiajie , Brunger Axel T.
Published: July 2016

Significance

Synaptic neurotransmitter release is an essential process for communication between neurons. Neurotransmitter release occurs upon an action potential, resulting in a local Ca
2+
-concentration increase in the presynaptic terminal that triggers synaptic vesicle membrane fusion with the plasma membrane. Synaptic vesicle fusion is orchestrated by neuronal soluble
N
-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs), synaptotagmin, complexin, and other factors. Here, we found that the complexin N-terminal domain binds to membranes and that it can be substituted with the fusion peptide of influenza virus hemagglutinin, resulting in similar activation of Ca
2+
-triggered fusion as wild-type complexin in a reconstituted vesicle fusion system. We conclude that similar fusion elements and principles are used in different contexts of biological membrane fusion.
Engineering of complex protein sialylation in plants
Authors: Kallolimath Somanath , Castilho Alexandra , Strasser Richard , Grünwald-Gruber Clemens , Altmann Friedrich , Strubl Sebastian , Galuska Christina Elisabeth , Zlatina Kristina , Galuska Sebastian Peter , Werner Stefan , Thiesler Hauke , Werneburg Sebastian , Hildebrandt Herbert , Gerardy-Schahn Rita , Steinkellner Herta
Published: July 2016

Significance

Sialic acid (Sia) residues are essential monosaccharides in mammals and confer multiple biological functions. Their precise generation is important for both structure–function studies and biotechnological applications. We describe a unique technology that enables the controlled generation of protein sialylation in
Nicotiana benthamiana
. The plant engineering approach relies on a combination of endogenous glycan deconstruction and the introduction of human sialylation capabilities. An arrangement of transgenic and transient expression modules resulted in the targeted synthesis of Sia structures in three different linkage types, reaching a polymerization degree exceeding 40 residues (polySia). Importantly, the obtained functional activities of polySia point to novel biotherapeutic applications. Our results highlight the exceptional flexibility of the plant-based expression platform for engineering complex posttranslational protein modifications.
Discovery of a sesamin-metabolizing microorganism and a new enzyme
Authors: Kumano Takuto , Fujiki Etsuko , Hashimoto Yoshiteru , Kobayashi Michihiko
Published: July 2016

Significance

Lignans, including sesamin, are produced by a wide variety of plants, but the microbial degradation of lignan has not been identified biochemically. Here, we show that
Sinomonas
sp. no. 22 can catabolize sesamin as a sole-carbon source. We identified the sesamin-converting enzyme, SesA, from strain
Sinomonas
sp. no. 22. SesA catalyzed methylene group transfer from sesamin to tetrahydrofolate (THF). The resulting 5,10-CH
2
-THF might find use as a C1-donor for bioprocesses. SesA gene homologs were found in the genomes of both Gram-positive and Gram-negative bacteria, suggesting that sesamin (lignan) utilization is a widespread, but still unrecognized, function in environments where lignans are produced and degraded.
The conceptual structure of reflexivity in The Anglo-Saxon Chronicle, Manuscript E
Authors: Góralczyk Iwona , Łozinska-Bastek Joanna
Published: July 2016

The chapter views OE reflexive patterns with plain pronouns through the prism of the current cognitive linguistic research on Modern English reflexives in Kemmer (1993) and Talmy (2000). Under both approaches reflexivity is a conceptual relation, yet while Kemmer focuses on canonical reflexive situation types and the semantic roles of event participants, Talmy speaks of the actional content of a situation and personation, which, by and large, translate into the focus on the nature of the verb in the reflexive event. The analysis points out how the prototypical and less prototypical situation types in OE differ from their modern counterparts and lists Modern English cognates or equivalents of verbs that pattern with reflexives in The Anglo-Saxon Chronicle.
Headedness of coordinate compounds in Polish and English
Authors: Cetnarowska Bozena
Published: July 2016

This chapter investigates Polish Noun+Noun combinations and their English equivalents, which can be regarded as appositional or copulative compounds in the terminology employed by Spencer (1991), or Olsen (2004), and as coordinate compounds in the typology proposed by Bisetto and Scalise (2005), e.g. poeta tłumacz (poet translator), piosenkarz-tekściarz (singer-songwriter), kierowca-kobieta (woman driver). They are contrasted with attributive compounds (cf. Bisetto & Scalise 2005), such as pisarz-widmo (ghost writer) and kobieta-guma (lit. woman-rubber/ a female contortionist). The discussion weighs which element should be identified as the head in those compounds (cf. Scalise and Fábregas 2010), when their semantic interpretation, inflectional properties and reversibility are considered.
Does detail matter? The effect of visual detail in line drawings on task execution
Authors: Alexander Kerstin , Schubert Andreas , Meng Michael
Published: July 2016

User manuals often include stylized line drawings to enable accurate and efficient task execution. This study reports the results of an empirical test which aimed at answering the question whether the amount of visual detail in such line drawings affects users’ performance. Results indicate that manuals containing illustrations with optimal amount of detail from a graphic designer’s point of view lead to significantly faster task execution compared to illustrations with the amount of detail beyond or below that level. Age was not a factor here, which suggests that optimizing the amount of detail in line drawings supports younger and older users alike.
Metacommutation as a Group Action on the Projective Line Over 𝔽_{𝕡}
Authors: Forsyth Adam , Gurev Jacob , Shrima Shakthi
Published: July 2016

Cohn and Kumar showed the quadratic character of

q
q

modulo

p
p

gives the sign of the permutation of Hurwitz primes of norm

p
p

induced by the Hurwitz primes of norm

q
q

under metacommutation. We demonstrate that these permutations are equivalent to those induced by the right standard action of

PGL
2

⁡
(

F

p

)

\operatorname {PGL}_2 (\mathbb {F}_p)

on

P

1

(

F

p

)

\mathbb {P}^1 (\mathbb {F}_p)

. This equivalence provides simpler proofs of the results of Cohn and Kumar and characterizes the cycle structure of the aforementioned permutations. Our methods are general enough to extend to all orders over the quaternions with a division algorithm for primes of a given norm

p
p

.
Current developments in the treatment of early-stage classical Hodgkin lymphoma
Authors: Borchmann Sven , von Tresckow Bastian , Engert Andreas
Published: July 2016

Purpose of review

After presenting the current treatment recommendations for early-stage Hodgkin lymphoma, we give an overview on recently published clinical trials in this setting. Furthermore, the potential influence of current trials on the treatment of early-stage Hodgkin lymphoma and integration of newly emerging drugs into treatment protocols will be discussed.

Recent findings

Trials attempting treatment de-escalation and omission of radiotherapy on the basis of early interim PET-scans have been disappointing so far, but results of some large trials employing this strategy are still awaited. In contrast, a more defensive strategy of starting treatment with less aggressive doxorubicine, bleomycin, vinblastine, dacarbazine (ABVD) chemotherapy and intensifying treatment in early interim PET-positive patients has shown encouraging results. New drugs such as brentuximab vedotin and immune checkpoint inhibitors have shown promising results in relapsed and refractory Hodgkin lymphoma. Clinical trials of brentuximab vedotin in early-stage Hodgkin lymphoma have been initiated. Additionally, biomarker-based treatment de-escalation might be a possible route for future improvements.

The challenge for future clinical research in early-stage Hodgkin lymphoma is to continue to cure the majority of patients with first-line treatment while reducing long-term toxicity. New strategies to achieve that goal are currently being developed and will further refine treatment of early-stage Hodgkin lymphoma.
Evidence for functional and non-functional classes of peptides translated from long non-coding RNAs
Authors: Ruiz-Orera Jorge , Verdaguer-Grau Pol , Villanueva-Cañas José Luis , Messeguer Xavier , Albà M Mar
Published: July 2016

There is accumulating evidence that some genes have originatedde novofrom previously non-coding genomic sequences. However, the processes underlyingde novogene birth are still enigmatic. In particular, the appearance of a new functional protein seems highly improbable unless there is already a pool of neutrally evolving peptides that can at some point acquire new functions. Here we show for the first time that such peptides do not only exist but that they are prevalent among the translation products of mouse genes that lack homologues in rat and human. The data suggests that the translation of these peptides is due to the chance occurrence of open reading frames with a favorable codon composition. Our approach combines ribosome profiling experiments, proteomics data and non-synonymous and synonymous nucleotide polymorphism analysis. We propose that effectively neutral processes involving the expression of thousands of transcripts all the way down to proteins provide a basis forde novogene evolution.
Colocalization of GWAS and eQTL Signals Detects Target Genes
Authors: Hormozdiari Farhad , van de Bunt Martijn , Segrè Ayellet V. , Li Xiao , Joo Jong Wha J , Bilow Michael , Sul Jae Hoon , Sankararaman Sriram , Pasaniuc Bogdan , Eskin Eleazar
Published: July 2016

The vast majority of genome-wide association studies (GWAS) risk loci fall in non-coding regions of the genome. One possible hypothesis is that these GWAS risk loci alter the individual’s disease risk through their effect on gene expression in different tissues. In order to understand the mechanisms driving a GWAS risk locus, it is helpful to determine which gene is affected in specific tissue types. For example, the relevant gene and tissue may play a role in the disease mechanism if the same variant responsible for a GWAS locus also affects gene expression. Identifying whether or not the same variant is causal in both GWAS and eQTL studies is challenging due to the uncertainty induced by linkage disequilibrium (LD) and the fact that some loci harbor multiple causal variants. However, current methods that address this problem assume that each locus contains a single causal variant. In this paper, we present a new method, eCAVIAR, that is capable of accounting for LD while computing the quantity we refer to as the colocalization posterior probability (CLPP). The CLPP is the probability that the same variant is responsible for both the GWAS and eQTL signal. eCAVIAR has several key advantages. First, our method can account for more than one causal variant in any loci. Second, it can leverage summary statistics without accessing the individual genotype data. We use both simulated and real datasets to demonstrate the utility of our method. Utilizing publicly available eQTL data on 45 different tissues, we demonstrate that computing CLPP can prioritize likely relevant tissues and target genes for a set of Glucose and Insulin-related traits loci. eCAVIAR is available athttp://genetics.cs.ucla.edu/caviar/
Short Tandem Repeat stutter_model_inferred from direct measurement of in vitro stutter noise
Authors: Raz Ofir , Biezuner Tamir , Spiro Adam , Amir Shiran , Milo Lilach , Titelman Alon , Onn Amos , Chapal-Ilani Noa , Tao Liming , Marx Tzipy , Feige Uriel , Shapiro Ehud
Published: July 2016

Short tandem repeats (STRs) are polymorphic genomic loci valuable for various applications such as research, diagnostics and forensics. However, their polymorphic nature also introduces noise duringin vitroamplification, making them difficult to analyze. Although it is possible to overcome stutter noise by using amplification-free library preparation, such protocols are presently incompatible with single cell analysis and with targeted-enrichment protocols. To address this challenge, we have designed a method for direct measurement ofin vitronoise. Using a synthetic STR sequencing library, we have calibrated a Markov model for the prediction of stutter patterns at any amplification cycle. By employing this model, we have managed to genotype accurately cases of severe amplification bias, and biallelic STR signals, and validated our model for several high-fidelity PCR enzymes. Finally, we compared this model in the context of a naïve STR genotyping strategy against the state-of-the-art on a benchmark of single cells, demonstrating superior accuracy.
mTAIL-seq reveals dynamic poly(A) tail regulation in oocyte-to-embryo development
Authors: Lim Jaechul , Lee Mihye , Son Ahyeon , Chang Hyeshik , Kim V. Narry
Published: July 2016

Eukaryotic mRNAs are subject to multiple types of tailing that critically influence mRNA stability and translatability. To investigate RNA tails at the genomic scale, we previously developed TAIL-seq, but its low sensitivity precluded its application to biological materials of minute quantity. In this study, we report a new version of TAIL-seq (mRNA TAIL-seq [mTAIL-seq]) with enhanced sequencing depth for mRNAs (by ∼1000-fold compared with the previous version). The improved method allows us to investigate the regulation of poly(A) tails in Drosophila oocytes and embryos. We found that maternal mRNAs are polyadenylated mainly during late oogenesis, prior to fertilization, and that further modulation occurs upon egg activation. Wispy, a noncanonical poly(A) polymerase, adenylates the vast majority of maternal mRNAs, with a few intriguing exceptions such as ribosomal protein transcripts. By comparing mTAIL-seq data with ribosome profiling data, we found a strong coupling between poly(A) tail length and translational efficiency during egg activation. Our data suggest that regulation of poly(A) tails in oocytes shapes the translatomic landscape of embryos, thereby directing the onset of animal development. By virtue of the high sensitivity, low cost, technical robustness, and broad accessibility, mTAIL-seq will be a potent tool to improve our understanding of mRNA tailing in diverse biological systems.
Free-electron laser multiplex driven by a superconducting linear accelerator
Authors: Plath Tim , Amstutz Philipp , Bödewadt Jörn , Brenner Günter , Ekanayake Nagitha , Faatz Bart , Hacker Kirsten , Honkavaara Katja , Lazzarino Leslie Lamberto , Lechner Christoph , Maltezopoulos Theophilos , Scholz Matthias , Schreiber Siegfried , Vogt Mathias , Zemella Johann , Laarmann Tim
Published: July 2016

Free-electron lasers (FELs) generate femtosecond XUV and X-ray pulses at peak powers in the gigawatt range. The FEL user facility FLASH at DESY (Hamburg, Germany) is driven by a superconducting linear accelerator with up to 8000 pulses per second. Since 2014, two parallel undulator beamlines, FLASH1 and FLASH2, have been in operation. In addition to the main undulator, the FLASH1 beamline is equipped with an undulator section, sFLASH, dedicated to research and development of fully coherent extreme ultraviolet photon pulses using external seed lasers. In this contribution, the first simultaneous lasing of the three FELs at 13.4 nm, 20 nm and 38.8 nm is presented.
The Munich Compact Light Source: initial performance measures
Authors: Eggl Elena , Dierolf Martin , Achterhold Klaus , Jud Christoph , Günther Benedikt , Braig Eva , Gleich Bernhard , Pfeiffer Franz
Published: July 2016

While large-scale synchrotron sources provide a highly brilliant monochromatic X-ray beam, these X-ray sources are expensive in terms of installation and maintenance, and require large amounts of space due to the size of storage rings for GeV electrons. On the other hand, laboratory X-ray tube sources can easily be implemented in laboratories or hospitals with comparatively little cost, but their performance features a lower brilliance and a polychromatic spectrum creates problems with beam hardening artifacts for imaging experiments. Over the last decade, compact synchrotron sources based on inverse Compton scattering have evolved as one of the most promising types of laboratory-scale X-ray sources: they provide a performance and brilliance that lie in between those of large-scale synchrotron sources and X-ray tube sources, with significantly reduced financial and spatial requirements. These sources produce X-rays through the collision of relativistic electrons with infrared laser photons. In this study, an analysis of the performance, such as X-ray flux, source size and spectra, of the first commercially sold compact light source, the Munich Compact Light Source, is presented.
Crystal structure of (1S,3R,8R,9R)-2,2-dichloro-3,7,7-trimethyl-10-methylenetricyclo[6.4.0.01,3]dodecan-9-ol
Authors: Benzalim Ahmed , Auhmani Aziz , Bimoussa Abdoullah , Ait Itto My Youssef , Daran Jean-Claude , Auhmani Abdelwahed
Published: July 2016

The title compound, C16H24Cl2O, was synthesized by treating (1S,3R,8S,9R,10S)-2,2-dichloro-3,7,7,10-tetramethyl-9,10-epoxytricyclo[6.4.0.01,3]dodecane with a concentrated solution of hydrobromic acid. It is built up from three fused rings: a cycloheptane ring, a cyclohexyl ring bearing alkene and hydroxy substituents, and a cyclopropane ring bearing two chlorine atoms. The asymmetric unit contains two molecules linked by an O—H...O hydrogen bond. In the crystal, further O—H...O hydrogen bonds build up anR44(8) cyclic tetramer. One of the molecules presents disorder that affects the seven-membered ring. In both molecules, the six-membered rings display a chair conformation, whereas the seven-membered rings display conformations intermediate between boat and twist-boat for the non-disordered molecule and either a chair or boat and twist-boat for the disordered molecule owing to the disorder. The absolute configuration for both molecules is 1S,3R,8R,9Rand was deduced from the chemical pathway and further confirmed by the X-ray structural analysis.
Crystal structure ofcatena-poly[[aquabis(4-cyanobenzoato-κO)copper(II)]-μ-N,N-diethylnicotinamide-κ2N1:O]
Authors: Akduran Nurcan , Necefoğlu Hacali , Aydoğdu Ömer , Hökelek Tuncer
Published: July 2016

The asymmetric unit of the title polymeric compound, [Cu(C8H4NO2)2(C10H14N2O)(H2O)]n, contains one CuIIatom, one coordinating water molecule, two 4-cyanobenzoate (CB) ligands and one coordinatingN,N-diethylnicotinamide (DENA) molecule. The DENA ligand acts as a bis-monodentate ligand, while the CB anions are monodentate. Two O atoms of the CB ligands, one O atom of the water molecule and the pyridine N atom of the DENA ligand form a slightly distorted square-planar arrangement around the CuIIatom which is completed to a square-pyramidal coordination by the apically placed O atom of the DENA ligand, with a Cu—O distance of 2.4303 (15) Å. In the two CB anions, the carboxylate groups are twisted relative to the attached benzene rings by 2.19 (12) and 3.87 (15)°, while the benzene rings are oriented at a dihedral angle of 5.52 (8)°. The DENA ligands bridge adjacent Cu2+ions, forming polymeric coordination chains running along thebaxis. In the crystal, strong water–carboxylate O—H...O hydrogen bonds link adjacent chains into layers parallel to (10-1) and weak C—H...O hydrogen bonds further stabilize the crystal structure. The cyano group C and N atoms of one of the CB ligands are disordered over two sets of sites with equal occupancies.
(4E)-1-Decyl-4-(2-oxopropylidene)-2,3,4,5-tetrahydro-1H-1,5-benzodiazepin-2-one
Authors: Sebhaoui Jihad , Zang Ondo Cherryl Mirabelle , El Bakri Youness , Essassi El Mokhtar , Mague Joel T.
Published: July 2016

The title compound, C22H32N2O2, forms bilayers with then-decyl chains in extended conformation oriented towards the interior of the bilayer structure. Weak C—H...O interactions help to stabilize the exterior surfaces. The conformation of the seven-membered ring has been analysed.