bluuebunny/crossref_metadata_2025 huggingface dataset:
On natural solutal convection in magnetic fluids
Authors: Ivanov A. S. , Pshenichnikov A. F.
Published: September 2015

An experiment was carried out to investigate natural solutal convection in a magnetic fluid caused by non-homogeneous initial distribution of colloidal particles in a vertical Hele-Shaw cell. For experiment, we used a dilute magnetic fluid of the “magnetite–kerosene–oleic acid” type. The initial distribution of particles was formed by magnetophoresis of the drop-like aggregates and their sedimentation on the surface of the diamagnetic disk located in the center of the cell. Application of the magnetic field on the system led to the onset of the Rayleigh-Taylor instability and formation of descending convective jets. The velocity of the flow at the front of descending jets was measured for different values of cell thickness (up to 0.18 mm) and strength of the magnetic field generating the drop-like aggregates (up to 21 kA/m). The solutal Rayleigh numbers varied in the range Ra = 50–105. It was shown that the intensity of the convective flow characterized by the Reynolds number Re, increases with the Rayleigh number according to the power law: Re = 1.16 × 10−5Ra0.86.
Energy transfer between a passing vortex ring and a flexible plate in an ideal quiescent fluid
Authors: Hu JiaCheng , Porfiri Maurizio , Peterson Sean D.
Published: September 2015

Recent advancements in highly deformable smart materials have lead to increasing interest in small-scale energy harvesting research for powering low consumption electronic devices. One such recent experimental study by Goushcha et al. explored energy harvesting from a passing vortex ring by a cantilevered smart material plate oriented parallel to and offset from the path of the ring in an otherwise quiescent fluid. The present study focuses on modeling this experimental study using potential flow to facilitate optimization of the energy extraction from the passing ring to raise the energy harvesting potential of the device. The problem is modeled in two-dimensions with the vortex ring represented as a pair of counter-rotating free vortices. Vortex pair parameters are determined to match the convection speed of the ring in the experiments, as well as the imposed pressure loading on the plate. The plate is approximated as a Kirchhoff-Love plate and represented as a finite length vortex sheet in the fluid domain. The analytical model matches experimental measurements, including the tip displacement, the integrated force along the entire plate length as a function of vortex ring position, and the pressure along the plate. The potential flow solution is employed in a parametric study of the governing dimensionless parameters in an effort to guide the selection of plate properties for optimal energy harvesting performance. Results of the study indicate an optimal set of plate properties for a given vortex ring configuration, in which the time-scale of vortex advection matches that of the plate vibration.
Theoretical study of the thermodynamic properties, phase transition wave, and phase transition velocity for octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine
Authors: Long Yao , Chen Jun
Published: September 2015

We develop a phonon-electron free energy model to study the thermodynamic properties and phase transitions of δ-octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine. The bulk modulus, thermal expansion coefficient, specific heat, Hugoniot curve, and phase transition curve are calculated in wide temperature and pressure ranges. The results are in agreement with the available experiments at zero pressure, and are reasonable predictions at high pressure for the lack of experiment. Two kinds of phase transition waves are investigated. We find the velocity of shock-induced phase transition wave is between 3400 m/s and 4700 m/s, and the velocity of self-sustaining phase transition wave is between 1300 m/s and 1900 m/s.
Morphological impact on the reaction kinetics of size-selected cobalt oxide nanoparticles
Authors: Bartling Stephan , Pohl Marga-Martina , Meiwes-Broer Karl-Heinz , Barke Ingo
Published: September 2015

Apart from large surface areas, low activation energies are essential for efficient reactions, particularly in heterogeneous catalysis. Here, we show that not only the size of nanoparticles but also their detailed morphology can crucially affect reaction kinetics, as demonstrated for mass-selected, soft-landed, and oxidized cobalt clusters in a 6 nm to 18 nm size range. The method of reflection high-energy electron diffraction is extended to the quantitative determination of particle activation energies which is applied for repeated oxidation and reduction cycles at the same particles. We find unexpectedly small activation barriers for the reduction reaction of the largest particles studied, despite generally increasing barriers for growing sizes. We attribute these observations to the interplay of reaction-specific material transport with a size-dependent inner particle morphology.
Counter-ion specificity explored in abnormal expansion of supra-molecular aggregates in aqueous solution of alkaline metal salts
Authors: Huang Ningdong , Tao Jiaojiao , Wei Shenghui , Chen Mingming , Wei Chengsha , Li Liangbin
Published: September 2015

Ionic effects in aqueous solution of macro-ions showing specificity and unconventional characters, respectively, receive a lot of interests recently; however, the complexity of specific ion effects in unconventional phenomena remains ambiguous. In this study, the effects of univalent ions on aggregation of supra-molecular nano-fibrils with charged carboxylate groups on the surface as a prototype of macro-ions are investigated by Small Angle X-ray Scattering (SAXS) in aqueous solutions of alkaline metal chlorides. It is found that the columnar bundles of charged fibrils are expanded in certain salt concentration range contradicting the conventional screening effects of salts. The degree of expansion is dominated by cations as Na+ induces drastic effects in comparison to rather gentle changes from K+ and Cs+. The specific cations effects observed by SAXS correlate with the pH behavior of the solutions, an indicator of surface charge, or number of carboxylate groups along the supra-molecular fibrils. It is postulated that while Na+ with stronger affinity to carboxylates apparently reduces the surface charge, K+ and Cs+ only weakly interact with carboxylates and induce minor changes, accounting for the cation-sensitive aggregation behavior of fibrils observed by SAXS. By probing the bundling aggregation of charged supra-molecular nano-fibrils in salty water, we provide direct evidence of specific counter-ion effects in unusual expansion caused by univalent salts.
Quantum Newtonian cosmology and the biconfluent Heun functions
Authors: Vieira H. S. , Bezerra V. B.
Published: September 2015

We obtain the exact solution of the Schrödinger equation for a particle (galaxy) moving in a Newtonian universe with a cosmological constant, which is given in terms of the biconfluent Heun functions. The first six Heun polynomials of the biconfluent function are written explicitly. The energy spectrum which resembles the one corresponding to the isotropic harmonic oscillator is also obtained. The wave functions as well as the energy levels codify the role played by the cosmological constant.
Global chaotization of fluid particle trajectories in a sheared two-layer two-vortex flow
Authors: Ryzhov Evgeny A. , Koshel Konstantin V.
Published: September 2015

In a two-layer quasi-geostrophic approximation, we study the irregular dynamics of fluid particles arising due to two interacting point vortices embedded in a deformation flow consisting of shear and rotational components. The two vortices are arranged within the bottom layer, but an emphasis is on the upper-layer fluid particle motion. Vortices moving in one layer induce stirring of passive scalars in the other layer. This is of interest since point vortices induce singular velocity fields in the layer they belong to; however, in the other layer, they induce regular velocity fields that generally result in a change in passive particle stirring. If the vortices are located at stagnation points, there are three different types of the fluid flow. We examine how properties of each flow configuration are modified if the vortices are displaced from the stagnation points and thus circulate in the immediate vicinity of these points. To that end, an analysis of the steady-state configurations is presented with an emphasis on the frequencies of fluid particle oscillations about the elliptic stagnation points. Asymptotic relations for the vortex and fluid particle zero–oscillation frequencies are derived in the vicinity of the corresponding elliptic points. By comparing the frequencies of fluid particles with the ones of the vortices, relations between the parameters that lead to enhanced stirring of fluid particles are established. It is also demonstrated that, if the central critical point is elliptic, then the fluid particle trajectories in its immediate vicinity are mostly stable making it harder for the vortex perturbation to induce stirring. Change in the type of the central point to a hyperbolic one enhances drastically the size of the chaotic dynamics region. Conditions on the type of the central critical point also ensue from the derived asymptotic relations.
Nonadiabatic dynamics in energetic negative fluorine ions scattering from a Si(100) surface
Authors: Chen Lin , Qiu Shunli , Xiong Feifei , Lu Jianjie , Liu Pinyang , Ding Bin , Li Yuan , Cui Ying , Guo Yanling , Chen Ximeng
Published: September 2015

The dependence of the negative-ion fractions on incident energy and angle is reported for 8.5–22.5 keV F− ions scattered from a Si(100) surface at a fixed scattering angle of 38°. The negative-ion fraction increases monotonically with incident velocity for specular scattering. In particular, the variation of the fraction with incident angle is bell shaped for a given incident energy. We interpret this variation using the incident-velocity effect at short distances where the yield of negative ions depends on the number of initial neutrals. It strongly indicates that at short distances, a dynamical equilibrium population is never achieved. This nonadiabatic feature is supported by simple calculations using modified rate equations.
Tuning of interlayer exchange coupling in Ni80Fe20/Ru/Ni80Fe20 nanowires
Authors: Liu X. M. , Lupo P. , Cottam M. G. , Adeyeye A. O.
Published: September 2015

In this work, we demonstrate how the static and dynamic properties of Ni80Fe20/Ru/Ni80Fe20 nanowires can be tuned by varying the Ru spacer layer thickness. Specifically, changing the Ru thickness we have tuned the Ruderman-Kittel-Kasuya-Yosida exchange interaction, and thus the antiferromagnetic (AFM) strength between the Ni80Fe20 layers. We show that there is a strong correlation between the interlayer coupling and features in ferromagnetic resonance (FMR) modes. We found different mode-softening degree of the FMR curves as function of the strength of AFM coupling, together with a clear frequency gap at around zero field. These experimental results are in qualitative agreement with presented micromagnetic simulations that also include biquadratic interface exchange. Understanding these characteristics may offer insights for reconfigurable vertical magnetic logic devices and microwave filters.
Excitons and Davydov splitting in sexithiophene from first-principles many-body Green’s function theory
Authors: Leng Xia , Yin Huabing , Liang Dongmei , Ma Yuchen
Published: September 2015

Organic semiconductors have promising and broad applications in optoelectronics. Understanding their electronic excited states is important to help us control their spectroscopic properties and performance of devices. There have been a large amount of experimental investigations on spectroscopies of organic semiconductors, but theoretical calculation from first principles on this respect is still limited. Here, we use density functional theory (DFT) and many-body Green’s function theory, which includes the GW method and Bethe-Salpeter equation, to study the electronic excited-state properties and spectroscopies of one prototypical organic semiconductor, sexithiophene. The exciton energies of sexithiophene in both the gas and bulk crystalline phases are very sensitive to the exchange-correlation functionals used in DFT for ground-state structure relaxation. We investigated the influence of dynamical screening in the electron-hole interaction on exciton energies, which is found to be very pronounced for triplet excitons and has to be taken into account in first principles calculations. In the sexithiophene single crystal, the energy of the lowest triplet exciton is close to half the energy of the lowest singlet one. While lower-energy singlet and triplet excitons are intramolecular Frenkel excitons, higher-energy excitons are of intermolecular charge-transfer type. The calculated optical absorption spectra and Davydov splitting are in good agreement with experiments.
Quartz enhanced photoacoustic H2S gas sensor based on a fiber-amplifier source and a custom tuning fork with large prong spacing
Authors: Wu Hongpeng , Sampaolo Angelo , Dong Lei , Patimisco Pietro , Liu Xiaoli , Zheng Huadan , Yin Xukun , Ma Weiguang , Zhang Lei , Yin Wangbao , Spagnolo Vincenzo , Jia Suotang , Tittel Frank K.
Published: September 2015

A quartz enhanced photoacoustic spectroscopy (QEPAS) sensor, employing an erbium-doped fiber amplified laser source and a custom quartz tuning fork (QTF) with its two prongs spaced ∼800 μm apart, is reported. The sensor employs an acoustic micro-resonator (AmR) which is assembled in an “on-beam” QEPAS configuration. Both length and vertical position of the AmR are optimized in terms of signal-to-noise ratio, significantly improving the QEPAS detection sensitivity by a factor of ∼40, compared to the case of a sensor using a bare custom QTF. The fiber-amplifier-enhanced QEPAS sensor is applied to H2S trace gas detection, reaching a sensitivity of ∼890 ppb at 1 s integration time, similar to those obtained with a power-enhanced QEPAS sensor equipped with a standard QTF, but with the advantages of easy optical alignment, simple installation, and long-term stability.
Unconventional ballooning structures for toroidal drift waves
Authors: Xie Hua-sheng , Xiao Yong
Published: September 2015

With strong gradients in the pedestal of high confinement mode (H-mode) fusion plasmas, gyrokinetic simulations are carried out for the trapped electron and ion temperature gradient modes. A broad class of unconventional mode structures is found to localize at arbitrary poloidal positions or with multiple peaks. It is found that these unconventional ballooning structures are associated with different eigen states for the most unstable mode. At weak gradient (low confinement mode or L-mode), the most unstable mode is usually in the ground eigen state, which corresponds to a conventional ballooning mode structure peaking in the outboard mid-plane of tokamaks. However, at strong gradient (H-mode), the most unstable mode is usually not the ground eigen state and the ballooning mode structure becomes unconventional. This result implies that the pedestal of H-mode could have better confinement than L-mode.
Anomalous Hall effect engineering via interface modification in Co/Pt multilayers
Authors: Jiang Shao-Long , Chen Xi , Li Xu-Jing , Yang Kang , Zhang Jing-Yan , Yang Guang , Liu Yi-Wei , Lu Jin-Hui , Wang Dong-Wei , Teng Jiao , Yu Guang-Hua
Published: September 2015

An enhanced anomalous Hall effect (AHE) is observed via interface modification in MgO/[Co/Pt]2/Co/MgO multilayers, due to the insertion of a Hf metal layer at the Co/MgO interface. It is shown that the saturation anomalous Hall resistivity is 215% larger than that in the multilayers without Hf insertion. More importantly, thermally stable AHE and perpendicular magnetic anisotropy features are obtained in MgO/[Co/Pt]2/Co/Hf/MgO multilayers. The AHE is improved for sample MgO/[Co/Pt]2/Co/Hf/MgO by annealing, which is attributed to the enhancement of the side jump contribution.
Two-dimensional Dirac signature of germanene
Authors: Zhang L. , Bampoulis P. , van Houselt A. , Zandvliet H. J. W.
Published: September 2015

The structural and electronic properties of germanene coated Ge2Pt clusters have been determined by scanning tunneling microscopy and spectroscopy at room temperature. The interior of the germanene sheet exhibits a buckled honeycomb structure with a lattice constant of 4.3 Å and a buckling of 0.2 Å. The zigzag edges of germanene are reconstructed and display a 4× periodicity. The differential conductivity of the interior of the germanene sheet has a V-shape, which is reminiscent of the density of states of a two-dimensional Dirac system. The minimum of the differential conductivity is located close to the Fermi level and has a non-zero value, which we ascribe to the metallic character of the underlying Ge2Pt substrate. Near the reconstructed germanene zigzag edges the shape of the differential conductivity changes from a V-shape to a more parabolic-like shape, revealing that the reconstructed germanene zigzag edges do not exhibit a pronounced metallic edge state.
A study of the impact of gate metals on the performance of AlGaN/AlN/GaN heterostructure field-effect transistors
Authors: Zhao Jingtao , Lin Zhaojun , Chen Quanyou , Yang Ming , Cui Peng , Lv Yuanjie , Feng Zhihong
Published: September 2015

The fabrication processes of heterostructure field-effect transistors (HFETs) often introduce stresses into the device structures. These stresses can significantly affect the electrical characteristics of the device. We investigated the additional strain induced by the gate metals (in this study, Au, Cu, Fe, Al, and Ni) in AlGaN/AlN/GaN HFETs using the measured capacitance-voltage and current-voltage characteristics. We found that the intensity of the additional strain of the AlGaN barrier layer is greatly affected by the types of gate metals. For those metals that mainly undergo a physical interaction with the AlGaN barrier layer, there is a negative correlation between the intensity of the additional strain and the Young's modulus of the gate metal. Therefore, the gate metal with a larger Young's modulus will be more favorable for weakening polarization Coulomb field scattering and increasing both the carrier mobility and the sheet carrier density in AlGaN/AlN/GaN HFETs.
Strain softening mechanism at meso scale during micro-compression in an ultrafine-grained pure copper
Authors: Xu Jie , Li Jianwei , Shan Debin , Guo Bin
Published: September 2015

Strain softening behavior has been found at meso scale using micro-compression testing in an ultrafine-grained (UFG) pure copper by comparison with the typical strain hardening in conventional coarse-grained (CG) material. Microstructural observations show that grain size remains nearly the same including the fraction of high-angle grain boundaries during micro-compression in UFG pure copper. The Kernel average misorientation(KAM) distribution measured by electron backscatter diffraction (EBSD), as a statistical method, is applied to qualitatively evaluate dislocation density in the interior of the grains. It is suggested that the deformation mechanisms are dominated by grain boundary sliding and grain rotation accompanied by dislocation slip in UFG pure copper, which demonstrates that the strain softening behavior is primarily caused by dislocation annihilation during micro-compression.
Buffer layer between a planar optical concentrator and a solar cell
Authors: Solano Manuel E. , Barber Greg D. , Lakhtakia Akhlesh , Faryad Muhammad , Monk Peter B. , Mallouk Thomas E.
Published: September 2015

The effect of inserting a buffer layer between a periodically multilayered isotropic dielectric (PMLID) material acting as a planar optical concentrator and a photovoltaic solar cell was theoretically investigated. The substitution of the photovoltaic material by a cheaper dielectric material in a large area of the structure could reduce the fabrication costs without significantly reducing the efficiency of the solar cell. Both crystalline silicon (c-Si) and gallium arsenide (GaAs) were considered as the photovoltaic material. We found that the buffer layer can act as an antireflection coating at the interface of the PMLID and the photovoltaic materials, and the structure increases the spectrally averaged electron-hole pair density by 36% for c-Si and 38% for GaAs compared to the structure without buffer layer. Numerical evidence indicates that the optimal structure is robust with respect to small changes in the grating profile.
Crystallization processes of Sb100−xZnx (0 ≤ x ≤ 70) amorphous films for use as phase change memory materials
Authors: Saito Yuta , Sumiya Masashi , Sutou Yuji , Ando Daisuke , Koike Junichi
Published: September 2015

The phase change processes of as-deposited Sb-Zn films were investigated. The as-deposited amorphous SbZn film showed an unusual increase in resistance during heating, which was attributed to crystallization of the metastable SbZn phase. Further heating up to more than 300oC resulted in a structural transformation into the stable SbZn phase accompanied by a drop in resistance as in conventional phase change materials. Even though off-stoichiometric Sb-rich films exhibited crystallization into the metastable phase as well, the precipitation of Sb crystalline grains caused an undesirable drop in resistance at temperatures lower than that of the SbZn film. A memory device using an SbZn film showed typical switching behavior and successfully switched from the amorphous to crystal state and vice versa by the application of an electric pulse. These results revealed that stoichiometric SbZn film is a promising novel phase change material for phase change memory with high thermal stability.
Studies Towards a Concise Enantioselective Synthesis of Roseophilins
Authors: Kerr Daniel J. , Flynn Bernard L.
Published: September 2015

An oxazolidone auxiliary-controlled asymmetric Nazarov reaction has been applied to the synthesis of the cyclopentyl-fused pyrrole core of roseophilins. Additionally, a concise synthetic route to the pyrrole-furan biaryl fragment required in the synthesis of the recently isolated dechlororoseophilin is described. It is anticipated that these two syntheses can be combined in future efforts to provide efficient, convergent access to (+)-dechlororoseophilin.
Termite mounds harness diurnal temperature oscillations for ventilation
Authors: King Hunter , Ocko Samuel , Mahadevan L.
Published: September 2015

Significance

Termite mounds are meter-sized structures built by millimeter-sized insects. These structures provide climate-controlled microhabitats that buffer the organisms from strong environmental fluctuations and allow them to exchange energy, information, and matter with the outside world. By directly measuring the flow inside a mound, we show that diurnal ambient temperature oscillations drive cyclic flows that flush out CO2from the nest and ventilate the mound. This swarm-built architecture demonstrates how work can be derived from the fluctuations of an intensive environmental parameter, and might serve as an inspiration and model for the design of passive, sustainable human architecture.
Toward a trophic theory of species diversity
Authors: Terborgh John W.
Published: September 2015

Efforts to understand the ecological regulation of species diversity via bottom-up approaches have failed to yield a consensus theory. Theories based on the alternative of top-down regulation have fared better. Paine’s discovery of keystone predation demonstrated that the regulation of diversity via top-down forcing could be simple, strong, and direct, yet ecologists have persistently failed to perceive generality in Paine’s result. Removing top predators destabilizes many systems and drives transitions to radically distinct alternative states. These transitions typically involve community reorganization and loss of diversity, implying that top-down forcing is crucial to diversity maintenance. Contrary to the expectations of bottom-up theories, many terrestrial herbivores and mesopredators are capable of sustained order-of-magnitude population increases following release from predation, negating the assumption that populations of primary consumers are resource limited and at or near carrying capacity. Predation
sensu lato
(to include Janzen–Connell mortality agents) has been shown to promote diversity in a wide range of ecosystems, including rocky intertidal shelves, coral reefs, the nearshore ocean, streams, lakes, temperate and tropical forests, and arctic tundra. The compelling variety of these ecosystems suggests that top-down forcing plays a universal role in regulating diversity. This conclusion is further supported by studies showing that the reduction or absence of predation leads to diversity loss and, in the more dramatic cases, to catastrophic regime change. Here, I expand on the thesis that diversity is maintained by the interaction between predation and competition, such that strong top-down forcing reduces competition, allowing coexistence.
Targeted, activity-dependent spinal stimulation produces long-lasting motor recovery in chronic cervical spinal cord injury
Authors: McPherson Jacob G. , Miller Robert R. , Perlmutter Steve I.
Published: September 2015

Significance

This study describes a new strategy for enhancing motor recovery after neurological injury. Using a recurrent neural–computer interface, we attempt to facilitate and direct functionally relevant activity-dependent neural plasticity, the mechanism thought to underlie the benefits of use-dependent physical therapy. We show that this approach can lead to meaningful functional gains that last for weeks after discontinuation of stimulation, a finding that is both unique and highly clinically relevant. Our results suggest that we have leveraged the nervous system’s intrinsic capacity for reorganization and repair to drive true neurological rehabilitation rather than enhancing performance through reanimation or replacement of function. This approach could also be adapted to other impairments, such as locomotion, bowel, bladder or sexual dysfunction, and pain.
Integration of high-content screening and untargeted metabolomics for comprehensive functional annotation of natural product libraries
Authors: Kurita Kenji L. , Glassey Emerson , Linington Roger G.
Published: September 2015

Significance

Compound Activity Mapping provides an alternative approach to natural products drug discovery by integrating high-content biological screening and untargeted metabolomics to directly reveal the identities and biological functions of individual bioactive compounds in complex natural product libraries. This accelerated discovery pipeline addresses many of the issues that have contributed to the decline of natural products research in some areas by improving dereplication and lead prioritization strategies. The detailed structural and functional annotation offered by this tool may help to improve the integration of natural products with modern high-content, high-throughput screening and provide an additional strategy for the discovery of the next generation of natural product-inspired drug leads and chemical probes.
Regional centromeres in the yeast
Candida lusitaniae
lack pericentromeric heterochromatin
Authors: Kapoor Shivali , Zhu Lisha , Froyd Cara , Liu Tao , Rusche Laura N.
Published: September 2015

Significance

Centromeres are the sites where chromosomes attach to microtubules during mitosis, and they are necessary for chromosome segregation. We discovered an unusual type of centromere in the yeast
Candida lusitaniae
, which is an occasional human pathogen. These centromeres are similar to many eukaryotic centromeres in that they are not specified by a particular sequence. However, unlike other centromeres of this type,
C. lusitaniae
centromeres are not flanked by a compact chromatin structure, known as pericentromeric heterochromatin. This finding reveals that, although pericentromeric heterochromatin is generally important for promoting proper centromere function, it is not universally necessary. This unusual centromere structure could contribute to stress-induced errors in chromosome segregation that are observed in
Candida
species.
Protecting group-free, selective cross-coupling of alkyltrifluoroborates with borylated aryl bromides via photoredox/nickel dual catalysis
Authors: Yamashita Yohei , Tellis John C. , Molander Gary A.
Published: September 2015

Significance

Efficient assembly of small-molecule scaffolds is among the most fundamental goals of organic synthesis. Iterative synthesis, wherein predefined building blocks are unified in an “assembly line” fashion using only a small number of reaction types, is an attractive means for achieving this ideal. These methods are particularly well-suited for applications in drug discovery, agrochemistry, and materials science, where rapid generation of structural diversity is a central objective. A strategy is described in which two reactive sites are differentiated by their preferred mode of reactivity (single vs. two electron). This unique platform allows discrimination between the two sites without artificial blocking of reactivity, streamlining the iterative process by removing the need for deprotection or interconversion of functional groups.
Structure of subcomplex Iβ of mammalian respiratory complex I leads to new supernumerary subunit assignments
Authors: Zhu Jiapeng , King Martin S. , Yu Minmin , Klipcan Liron , Leslie Andrew G. W. , Hirst Judy
Published: September 2015

Significance

Mitochondrial complex I (proton-pumping NADH:ubiquinone oxidoreductase) is the largest respiratory chain enzyme. Mammalian complex I contains 45 subunits: the structures of the 14 “core” subunits (which are sufficient for catalysis and conserved from bacteria to humans) were described in the 5-Å resolution structure of
Bos taurus
complex I, but only 14 supernumerary subunits could be located. Here, we exploit new structural information from the membrane domain of mammalian complex I to assign eight further supernumerary subunits. We locate two oxidatively-folded CHCH-domain subunits in the intermembrane space, and reveal a second LYR protein–acyl carrier protein module. Thus, we extend knowledge of how the supernumerary subunits are arranged around the core, and provide insights into their roles in biogenesis and regulation.
Musical expertise is related to altered functional connectivity during audiovisual integration
Authors: Paraskevopoulos Evangelos , Kraneburg Anja , Herholz Sibylle Cornelia , Bamidis Panagiotis D. , Pantev Christo
Published: September 2015

Significance

Multisensory integration engages distributed cortical areas and is thought to emerge from their dynamic interplay. Nevertheless, large-scale cortical networks underpinning audiovisual perception have remained undiscovered. The present study uses magnetoencephalography and a methodological approach to perform whole-brain connectivity analysis and reveals, for the first time to our knowledge, the cortical network related to multisensory perception. The long-term training-related reorganization of this network was investigated by comparing musicians to nonmusicians. Results indicate that nonmusicians rely on processing visual clues for the integration of audiovisual information, whereas musicians use a denser cortical network that relies mostly on the corresponding auditory information. These data provide strong evidence that cortical connectivity is reorganized due to expertise in a relevant cognitive domain, indicating training-related neuroplasticity.
Erosion in southern Tibet shut down at ∼10 Ma due to enhanced rock uplift within the Himalaya
Authors: Tremblay Marissa M. , Fox Matthew , Schmidt Jennifer L. , Tripathy-Lang Alka , Wielicki Matthew M. , Harrison T. Mark , Zeitler Peter K. , Shuster David L.
Published: September 2015

Significance

The Himalaya–Tibet plateau system formed by collision between India and Asia that began ca. 50 Ma and is still ongoing today. Despite being the most studied example of continent–continent collision, the evolution of topography in the Himalaya and Tibetan plateau remains an area of vigorous debate and active research. We present geochemical data on the cooling history of granites from the southern Tibetan plateau, which indicate that exhumation of these granites and therefore erosion rates in this region decreased significantly by ∼10 Ma after ∼5 Ma of rapid erosion. We hypothesize that this change in erosion rate reflects a tectonically imposed shift of the topographic and drainage divides south to their current positions within the Himalaya.
Creation of a histone deacetylase 6 inhibitor and its biological effects
Authors: Lee Ju-Hee , Yao Yuanshan , Mahendran Adaickapillai , Ngo Lang , Venta-Perez Gisela , Choy Megan L. , Breslow Ronald , Marks Paul A.
Published: September 2015

Significance

We discovered an improved hydroxamic acid-based small-molecule N-hydroxy-4-[(N(2-hydroxyethyl)-2-phenylacetamido)methyl)benzamide)] that selectively inhibits histone deacetylase 6 catalytic activity in vivo and in vitro. This can have important anticancer activity.
Magnesium pyrophosphates in enzyme mimics of nucleotide synthases and kinases and in their prebiotic chemistry
Authors: Gopinath Purushothaman , Ramalingam Vijayakumar , Breslow Ronald
Published: September 2015

Significance

Nucleotides are biosynthesized from a ribose pyrophosphate species, with enzymes and magnesium ions as catalysts. Magnesium ions alone can perform this process with synthetic ribose pyrophosphates, by binding to the pyrophosphate groups and linking cyclic nitrogen bases to the ribose. In a kinase mimic ATP transfers the terminal phosphate to receptors catalyzed by magnesium ions, binding to pyrophosphate groups, but magnesium ion at low concentrations inhibits the process, and only at higher concentrations is it a catalyst. This affords great insight into the mechanism of ATP phosphorylation, a fundamental biological process. Our enzyme mimics could well operate on prebiotic earth before enzymes were present. This work strengthens the picture of how important components of life could have been formed prebiotically.
Activation of cyclic GMP-AMP synthase by self-DNA causes autoimmune diseases
Authors: Gao Daxing , Li Tuo , Li Xiao-Dong , Chen Xiang , Li Quan-Zhen , Wight-Carter Mary , Chen Zhijian J.
Published: September 2015

Significance

The immune system detects microbial DNA in the cytosol of infected cells and mounts effective antimicrobial responses, including the production of type-I interferons. However, when self-DNA enters or accumulates in the cytosol, it can cause autoimmune diseases. Mutations of the exonuclease Trex1 in humans have been linked to autoimmune diseases including Aicardi–Goutieres Syndrome (AGS) and systemic lupus erythematosus (SLE). In mice, genetic deletion of Trex1 or the lysosomal nuclease DNaseII leads to lethal autoimmune diseases. Here we show that cyclic GMP-AMP synthase (cGAS) activation by self-DNA is responsible for the lethal autoimmune diseases in these models. These results provide the proof-of-concept that inhibition of cGAS may be an effective therapy for some autoimmune diseases such as AGS and SLE.
Role of water and steric constraints in the kinetics of cavity–ligand unbinding
Authors: Tiwary Pratyush , Mondal Jagannath , Morrone Joseph A. , Berne B. J.
Published: September 2015

Significance

The unbinding of ligand–substrate systems in molecular water is a problem of great theoretical and practical interest. To understand the dynamical nature of the unbinding, it is desirable to use atomistic techniques like molecular dynamics (MD). However, the associated timescales are typically too long for MD to be applicable. In this work, we apply a recent metadynamics scheme that allows the use of MD to get information on thermodynamics and kinetics of systems that are virtually impossible to treat with unbiased MD. We calculate unbinding pathways and timescales, and show that solvent molecules play a crucial role in cooperation with steric effects. The approaches used here demonstrate a broadly applicable methodology for studying ligand unbinding.
Constructing the authority of women through custom: Bulak village, Kyrgyzstan
Authors: Ismailbekova Aksana
Published: September 2015

The traditional authority of Kyrgyz women operates within moral frameworks and through their roles as keepers of hearth and home, and has been recognized by the state for its important role in family life and in society. Women are responsible for the health of future generations, for the quality of children's education, and for safeguarding and passing on moral principles, which contribute to the formation of the traditional Kyrgyz family, and thus to the Kyrgyz nation. Kyrgyz ideas that women are keepers of hearth and home are exactly the ideas that allow women to build authority within the home and family. Not only do Kyrgyz women actually gain a great deal of power in their families over the course of their lives, but also this female power is foundational to the Kyrgyz sense of nation and sovereignty. Thus, what seems to be “domestic” power is, in fact, power with very public connections and effects.
Enzymatic transglycosylation of ginsenoside Rg1 by rice seed α-glucosidase
Authors: Kim Min-Ji , Kim Young-Hoi , Song Geun-Sup , Suzuki Yukio , Kim Myung-Kon
Published: September 2015

Six α-monoglucosyl derivatives of ginsenoside Rg1 (G-Rg1) were synthesized by transglycosylation reaction of rice seed α-glucosidase in the reaction mixture containing maltose as a glucosyl donor and G-Rg1 as an acceptor. Their chemical structures were identified by spectroscopic analysis, and the effects of reaction time, pH, and glycosyl donors on transglycosylation reaction were investigated. The results showed that rice seed α-glucosidase transfers α-glucosyl group from maltose to G-Rg1 by forming either α-1,3 (α-nigerosyl)-, α-1,4 (α-maltosyl)-, or α-1,6 (α-isomaltosyl)-glucosidic linkages in β-glucose moieties linked at the C6- and C20-position of protopanaxatriol (PPT)-type aglycone. The optimum pH range for the transglycosylation reaction was between 5.0 and 6.0. Rice seed α-glucosidase acted on maltose, soluble starch, and PNP α-D-glucopyranoside as glycosyl donors, but not on glucose, sucrose, or trehalose. These α-monoglucosyl derivatives of G-Rg1 were easily hydrolyzed to G-Rg1 by rat small intestinal and liver α-glucosidase in vitro.
The microRNA-212/132 cluster regulates B cell development by targeting Sox4
Authors: Mehta Arnav , Mann Mati , Zhao Jimmy L. , Marinov Georgi K. , Majumdar Devdoot , Garcia-Flores Yvette , Du Xiaomi , Erikci Erdem , Chowdhury Kamal , Baltimore David
Published: September 2015

MicroRNAs have emerged as key regulators of B cell fate decisions and immune function. Deregulation of several microRNAs in B cells leads to the development of autoimmune disease and cancer in mice. We demonstrate that the microRNA-212/132 cluster (miR-212/132) is induced in B cells in response to B cell receptor signaling. Enforced expression of miR-132 results in a block in early B cell development at the prepro–B cell to pro–B cell transition and induces apoptosis in primary bone marrow B cells. Importantly, loss of miR-212/132 results in accelerated B cell recovery after antibody-mediated B cell depletion. We find that Sox4 is a target of miR-132 in B cells. Co-expression of SOX4 with miR-132 rescues the defect in B cell development from overexpression of miR-132 alone, thus suggesting that miR-132 may regulate B lymphopoiesis through Sox4. In addition, we show that the expression of miR-132 can inhibit cancer development in cells that are prone to B cell cancers, such as B cells expressing the c-Myc oncogene. We have thus uncovered miR-132 as a novel contributor to B cell development.
Nonlinear surface waves on the plasma-vacuum interface
Authors: Secchi Paolo
Published: September 2015

In this paper we study the propagation of weakly nonlinear surface waves on a plasma-vacuum interface. In the plasma region we consider the equations of incompressible magnetohydrodynamics, while in vacuum the magnetic and electric fields are governed by the Maxwell equations. A surface wave propagates along the plasma-vacuum interface when it is linearly weakly stable.

Following the approach of Ali and Hunter (2003), we measure the amplitude of the surface wave by the normalized displacement of the interface in a reference frame moving with the linearized phase velocity of the wave, and obtain that it satisfies an asymptotic nonlocal, Hamiltonian evolution equation. We show the local-in-time existence of smooth solutions to the Cauchy problem for the amplitude equation in noncanonical variables, and we derive a blow up criterion.
Surgical Reconstruction for Talocalcaneal Coalitions With Severe Hindfoot Valgus Deformity
Authors: Javier Masquijo Julio , Vazquez Ignacio , Allende Victoria , Lanfranchi Lucas , Torres-Gomez Armando , Dobbs Matthew B.
Published: September 2015

Introduction:

Coalition resection can restore motion, and improve pain in patients with talocalcaneal coalitions (TCCs) and an aligned foot. However, there is some debate regarding appropriate treatment of patients with associated valgus deformity. The purpose of this study was to present the outcomes and complications following surgical reconstruction, with or without coalition resection, in a series of patients with TCC and severe hindfoot valgus.

Methods:

Thirteen consecutive patients (14 feet) were evaluated. Eleven patients were male. Mean age was 14 years. Mean follow-up was 43.8 months. Seven patients (8 feet) underwent simultaneous resection of the coalition and reconstruction, and 6 patients (6 feet) isolated reconstruction. The talar-first metatarsal angle, the talar-horizontal angle, and calcaneal pitch were measured preoperatively and postoperatively. Clinical evaluation was made according to the American Orthopaedic Foot and Ankle Society ankle-hindfoot score.

Results:

All radiographic values improved significantly and were within the normal ranges postoperatively. The average American Orthopaedic Foot and Ankle Society ankle-hindfoot score had improved from 45 to 98 points (P<0.001) in the group of simultaneous resection and reconstruction, and from 60 to 92.3 points (P=0.002) in the group of isolated reconstruction. All patients were asymptomatic at the last follow-up and were satisfied with the procedure.

Discussion:

Surgical reconstruction with or without coalition resection can achieve significant functional and radiographic improvements, and symptoms relief in selected patients with TCCs and severe valgus deformity.

Level of Evidence:

Level IV—therapeutic study.
Association Between Phosphorylated Histone H3 and Oncotype DX Recurrence Scores in Breast Cancer
Authors: Lee Lik Hang , Swanson Paul E. , Tang Patricia A. , Bigras Gilbert , Yang Hua
Published: September 2015

We investigate the association between phosphorylated histone H3 (PhH3) and Oncotype DX recurrence score (RS). All invasive breast carcinoma with RS results from our city between 2007 and 2010 (n=47) were reviewed. Whole-tumor sections were stained for PhH3. Mitotic and PhH3 counts were performed and clinical charts reviewed. PhH3 correlated well with RS (r=0.69, P<0.001). Other correlations were: PhH3 versus mitotic count (r=0.87, P<0.001), PhH3 versus mitotic score (r=0.71, P<0.001), PhH3 versus modified Bloom-Richardson-Elston (MBR) grade (r=0.65, P<0.001), RS versus mitotic count (r=0.62, P<0.001), RS versus mitotic score (r=0.44, P=0.002), and RS versus MBR grade (r=0.49, P=0.001). Significant correlation between PhH3 and RS remained after controlling for mitotic count (r=0.39, P=0.007), mitotic score (r=0.60, P<0.001), MBR grade (r=0.56, P<0.001), and all 3 (r=0.37, P=0.014) by partial correlation. Two patients died of metastasis at 12 and 38 months after diagnosis. One had intermediate RS, and 1 high RS; both were in the top-third of PhH3 count. All other patients are alive and recurrence free. Correlation between PhH3 and RS was statistically significant in our cohort, and remained significant after controlling for traditional measures of proliferation. Given that RS has an established strong relationship with prognosis and therapy responsiveness, PhH3 may thus also be an important prognostic/predictive marker in breast cancer.
Sphingobacterium suaedae sp. nov., isolated from the rhizosphere soil of Suaeda corniculata
Authors: Sun Ji-Quan , Liu Min , Wang Xin-Ying , Xu Lian , Wu Xiao-Lei
Published: September 2015

A Gram-stain-negative, non-motile, non-spore-forming bacterium, designated T47T, was isolated from saline soil of the Suaeda corniculata rhizosphere, located on the bank of Wuliangsuhai Lake, Inner Mongolia, northern China. Strain T47T could grow at 10–40 °C (with 30 °C the optimal temperature), pH 6.0–8.0 (optimal pH 6.0) and in the presence of 0–6.0 % (w/v) NaCl [optimal 0–1.0 % (w/v)]. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain T47T formed a stable clade with Sphingobacterium composti 4M24T, Sphingobacterium bambusae IBFC2009T, Sphingobacterium paludis S37T and Sphingobacterium wenxiniae LQY-18T, with the 16S rRNA gene sequence similarities ranging from 91.9–95.4 %. Its major cellular fatty acids contained iso-C15 : 0 (39.9 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c, 23.0 %), C16 : 0 (12.8 %) and iso-C17 : 0 3-OH (9.9 %). MK7 was the major menaquinone. The G+C content of the genomic DNA was 45.5 mol%. Based on the phenotypic, phylogenetic and genotypic characteristics, strain T47T represents a novel species within the genus Sphingobacterium, for which the name Sphingobacterium suaedae sp. nov. is proposed. The type strain is T47T ( = CGMCC 1.15277T = KCTC 42662T).
Photobacterium galatheae sp. nov., a bioactive bacterium isolated from a mussel in the Solomon Sea
Authors: Machado Henrique , Giubergia Sonia , Mateiu Ramona Valentina , Gram Lone
Published: September 2015

A novel, Gram-negative marine bacterium, S2753T, was isolated from a mussel of the Solomon Sea, Solomon Islands. Analysis of the 16S rRNA gene sequence and whole genome sequence data placed strain S2753T in the genus Photobacterium with the closest relative being Photobacterium halotolerans DSM 18316T (97.7 % 16S rRNA gene similarity). Strain S2753T was able to grow from 15 to 40 °C and in NaCl concentrations of 0.5 to 9 % (w/v). The predominant fatty acids were 16 : 1ω7c/16 : 1ω6c (27.9 %), 16 : 0 (22.1 %) and 18 : 1ω7c/8 : 1ω6c (21.4 %). The genomic DNA G+C mol content was 49.5 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic differences, strain S2753T is considered to represent a novel species of the genus Photobacterium. Furthermore, whole genome sequence analysis comparing S2753T and type-strains of closely related species of the genus Photobacterium also demonstrated that the strain is genomically distinct enough to be considered a novel species. The name Photobacterium galatheae is proposed and the type-strain is S2753T( = LMG 28894T = DSM 100496T).