bluuebunny/crossref_metadata_2025 huggingface dataset:
On shock driven jetting of liquid from non-sinusoidal surfaces into a vacuum
Authors: Cherne F. J. , Hammerberg J. E. , Andrews M. J. , Karkhanis V. , Ramaprabhu P.
Published: November 2015

Previous work employed Richtmyer-Meshkov theory to describe the development of spikes and bubbles from shocked sinusoidal surfaces. Here, we discuss the effects of machining different two-dimensional shaped grooves in copper and examine the resulting flow of the material after being shocked into liquid on release. For these simulations, a high performance molecular dynamics code, SPaSM, was used with machined grooves of kh0 = 1 and kh0 = 1/8, where 2h0 is the peak-to-valley height of the perturbation with wavelength λ, and k = 2π/λ. The surface morphologies studied include a Chevron, a Fly-Cut, a Square-Wave, and a Gaussian. We describe extensions to an existing ejecta source model that better captures the mass ejected from these surfaces. We also investigate the same profiles at length scales of order 1 cm for an idealized fluid equation of state using the FLASH continuum hydrodynamics code. Our findings indicate that the resulting mass can be scaled by the missing area of a sinusoidal curve with an effective wavelength, λeff, that has the same missing area. Our extended ejecta mass formula works well for all the shapes considered and captures the corresponding time evolution and total mass.
Crystal structure optimisation using an auxiliary equation of state
Authors: Jackson Adam J. , Skelton Jonathan M. , Hendon Christopher H. , Butler Keith T. , Walsh Aron
Published: November 2015

Standard procedures for local crystal-structure optimisation involve numerous energy and force calculations. It is common to calculate an energy–volume curve, fitting an equation of state around the equilibrium cell volume. This is a computationally intensive process, in particular, for low-symmetry crystal structures where each isochoric optimisation involves energy minimisation over many degrees of freedom. Such procedures can be prohibitive for non-local exchange-correlation functionals or other “beyond” density functional theory electronic structure techniques, particularly where analytical gradients are not available. We present a simple approach for efficient optimisation of crystal structures based on a known equation of state. The equilibrium volume can be predicted from one single-point calculation and refined with successive calculations if required. The approach is validated for PbS, PbTe, ZnS, and ZnTe using nine density functionals and applied to the quaternary semiconductor Cu2ZnSnS4 and the magnetic metal-organic framework HKUST-1.
The effects of grids on the near-field evolution of turbulence in a low-Reynolds number jet
Authors: Senthil Kumar P. , Raghavan V. , Sundararajan T.
Published: November 2015

The near field evolution of a low Reynolds number free jet and associated turbulent fluctuations are investigated experimentally, in the presence of a grid placed at nozzle exit. The jet spreading characteristics without grid are validated first with available data in the literature and the well known features of vortex roll-up and pairing phenomena in the shear layer region are confirmed. The inclusion of a grid at the nozzle exit appears to reduce velocity fluctuations in the near field, but it accelerates the transition to a full-grown turbulent flow field with respect to axial distance, by the introduction of finer scales. Grids also cause mean velocity overshoot in the radial profile by distorting the approach flow in the boundary layer region ahead of the grid. Distinct vortex roll-up and pairing phenomena in the shear layer region could not be observed with grids. However, weak shear mode instabilities originating in the shear layer for 0 ≤ z/D ≤ 3 appear to interact with the potential core, leading to the formation of a “unified shear/preferred mode” instability. These features are dominantly seen for grid-mounted jet flows having large displacement thickness to grid opening ratio. Power spectra indicate a progressive evolution of turbulent flow features with respect to axial distance, starting with the development of inertial sub-range into a −5/3 slope exponent; followed by the establishment of full range of turbulent scales, and the eventual attainment of isotropy. The establishment of inertial sub-range is attributable to vortex-pairing and turbulent fragmentation in free jets and to the introduction of fine scales at the jet inlet in the cases with grids.
Negative terahertz conductivity in remotely doped graphene bilayer heterostructures
Authors: Ryzhii V. , Ryzhii M. , Mitin V. , Shur M. S. , Otsuji T.
Published: November 2015

Injection or optical generation of electrons and holes in graphene bilayers (GBLs) can result in the interband population inversion enabling the terahertz (THz) radiation lasing. The intraband radiative processes compete with the interband transitions. We demonstrate that remote doping enhances the indirect interband generation of photons in the proposed GBL heterostructures. Therefore, such remote doping helps to surpass the intraband (Drude) absorption, and results in large absolute values of the negative dynamic THz conductivity in a wide range of frequencies at elevated (including room) temperatures. The remotely doped GBL heterostructure THz lasers are expected to achieve higher THz gain compared with previously proposed GBL-based THz lasers.
On a simple way to calculate electronic resonances for polyatomic molecules
Authors: Horáček J. , Paidarová I. , Čurík R.
Published: November 2015

We propose a simple method for calculation of low-lying shape electronic resonances of polyatomic molecules. The method introduces a perturbation potential and requires only routine bound-state type calculations in the real domain of energies. Such a calculation is accessible by most of the free or commercial quantum chemistry software. The presented method is based on the analytical continuation in a coupling constant model, but unlike its previous variants, we experience a very stable and robust behavior for higher-order extrapolation functions. Moreover, the present approach is independent of the correlation treatment used in quantum many-electron computations and therefore we are able to apply Coupled Clusters (CCSD-T) level of the correlation model. We demonstrate these properties on determination of the resonance position and width of the 2Πu temporary negative ion state of diacetylene using CCSD-T level of theory.
CAMELOT: A machine learning approach for coarse-grained simulations of aggregation of block-copolymeric protein sequences
Authors: Ruff Kiersten M. , Harmon Tyler S. , Pappu Rohit V.
Published: November 2015

We report the development and deployment of a coarse-graining method that is well suited for computer simulations of aggregation and phase separation of protein sequences with block-copolymeric architectures. Our algorithm, named CAMELOT for Coarse-grained simulations Aided by MachinE Learning Optimization and Training, leverages information from converged all atom simulations that is used to determine a suitable resolution and parameterize the coarse-grained model. To parameterize a system-specific coarse-grained model, we use a combination of Boltzmann inversion, non-linear regression, and a Gaussian process Bayesian optimization approach. The accuracy of the coarse-grained model is demonstrated through direct comparisons to results from all atom simulations. We demonstrate the utility of our coarse-graining approach using the block-copolymeric sequence from the exon 1 encoded sequence of the huntingtin protein. This sequence comprises of 17 residues from the N-terminal end of huntingtin (N17) followed by a polyglutamine (polyQ) tract. Simulations based on the CAMELOT approach are used to show that the adsorption and unfolding of the wild type N17 and its sequence variants on the surface of polyQ tracts engender a patchy colloid like architecture that promotes the formation of linear aggregates. These results provide a plausible explanation for experimental observations, which show that N17 accelerates the formation of linear aggregates in block-copolymeric N17-polyQ sequences. The CAMELOT approach is versatile and is generalizable for simulating the aggregation and phase behavior of a range of block-copolymeric protein sequences.
Electromagnetic diagnostic techniques for hypervelocity projectile detection, velocity measurement, and size characterization: Theoretical concept and first experimental test
Authors: Uhlig W. Casey , Heine Andreas
Published: November 2015

A new measurement technique is suggested to augment the characterization and understanding of hypervelocity projectiles before impact. The electromagnetic technique utilizes magnetic diffusion principles to detect particles, measure velocity, and indicate relative particle dimensions. It is particularly suited for detection of small particles that may be difficult to track utilizing current characterization methods, such as high-speed video or flash radiography but can be readily used for large particle detection, where particle spacing or location is not practical for other measurement systems. In this work, particles down to 2 mm in diameter have been characterized while focusing on confining the detection signal to enable multi-particle characterization with limited particle-to-particle spacing. The focus of the paper is on the theoretical concept and the analysis of its applicability based on analytical and numerical calculation. First proof-of-principle experimental tests serve to further validate the method. Some potential applications are the characterization of particles from a shaped-charge jet after its break-up and investigating debris in impact experiments to test theoretical models for the distribution of particles size, number, and velocity.
A chain-of-states acceleration method for the efficient location of minimum energy paths
Authors: Hernández E. R. , Herrero C. P. , Soler J. M.
Published: November 2015

We describe a robust and efficient chain-of-states method for computing Minimum Energy Paths (MEPs) associated to barrier-crossing events in poly-atomic systems, which we call the acceleration method. The path is parametrized in terms of a continuous variable t ∈ [0, 1] that plays the role of time. In contrast to previous chain-of-states algorithms such as the nudged elastic band or string methods, where the positions of the states in the chain are taken as variational parameters in the search for the MEP, our strategy is to formulate the problem in terms of the second derivatives of the coordinates with respect to t, i.e., the state accelerations. We show this to result in a very simple and efficient method for determining the MEP. We describe the application of the method to a series of test cases, including two low-dimensional problems and the Stone-Wales transformation in C60.
Photodissociation dynamics of HOD via the B̃ (1A1) electronic state
Authors: Su Shu , Wang Hongzhen , Chen Zhichao , Yu Shengrui , Dai Dongxu , Yuan Kaijun , Yang Xueming
Published: November 2015

Photodissociation dynamics of HOD from the B̃ state has been studied using H/D atom Rydberg “tagging” time-of-flight technique. Both the OD + H and OH + D channels have been investigated. Product kinetic energy distributions, internal state distributions of the OD/OH product, as well as the OD/OH quantum state specific angular anisotropy parameters have been determined. Overall, the photodissociation dynamics of HOD via the B̃ state is qualitatively similar to that of the H2O and D2O, with quantitative differences arising probably from the change in masses. At different photolysis energies, similar rovibrational distributions and state-resolved angular distributions have been observed for the OH/OD(X) product, while remarkable differences have been observed in the rovibrational distributions and state-resolved angular distributions of the OH/OD(A) product.
Strong correlation of the electrical properties, up-conversion photoluminescence, and phase structure in Er3+/Yb3+ co-doped (1 − x)K0.5Na0.5NbO3-xLiNbO3 ceramics
Authors: Wang Jia , Luo Laihui , Huang Yinpeng , Li Weiping , Wang Feifei
Published: November 2015

Er3+ and Yb3+ co-doped (1 − x)K0.5Na0.5NbO3-xLiNbO3 (KNN-xLN:Er/Yb, x = 0.04–0.09) ceramics were prepared to investigate their phase structures and piezoelectric, ferroelectric, and up-conversion photoluminescence properties. With increasing LN content, x, KNN-xLN:Er/Yb ceramics at room temperature evolve from the orthorhombic phase to the polymorphic phase and finally to the tetragonal phase. All the ferroelectric and piezoelectric properties and the Ir/Ig ratio of integrated intensities of red and green emission bands reach maximum values within the polymorphic phase transition of the KNN-0.06LN:Er/Yb ceramic. In this work, we find a close correlation between the electrical properties, up-conversion photoluminescence, and phase structure of KNN-xLN:Er/Yb ceramics. This correlation is discussed based on the Judd-Ofelt and crystallographic symmetry theories.
Unraveling irradiation induced grain growth with in situ transmission electron microscopy and coordinated modeling
Authors: Bufford D. C. , Abdeljawad F. F. , Foiles S. M. , Hattar K.
Published: November 2015

Nanostructuring has been proposed as a method to enhance radiation tolerance, but many metallic systems are rejected due to significant concerns regarding long term grain boundary and interface stability. This work utilized recent advancements in transmission electron microscopy (TEM) to quantitatively characterize the grain size, texture, and individual grain boundary character in a nanocrystalline gold model system before and after in situ TEM ion irradiation with 10 MeV Si. The initial experimental measurements were fed into a mesoscale phase field model, which incorporates the role of irradiation-induced thermal events on boundary properties, to directly compare the observed and simulated grain growth with varied parameters. The observed microstructure evolution deviated subtly from previously reported normal grain growth in which some boundaries remained essentially static. In broader terms, the combined experimental and modeling techniques presented herein provide future avenues to enhance quantification and prediction of the thermal, mechanical, or radiation stability of grain boundaries in nanostructured crystalline systems.
Interactions of small platinum clusters with the TiC(001) surface
Authors: Mao Jianjun , Li Shasha , Chu Xingli , Yang Zongxian
Published: November 2015

Density functional theory calculations are used to elucidate the interactions of small platinum clusters (Ptn, n = 1–5) with the TiC(001) surface. The results are analyzed in terms of geometric, energetic, and electronic properties. It is found that a single Pt atom prefers to be adsorbed at the C-top site, while a Pt2 cluster prefers dimerization and a Pt3 cluster forms a linear structure on the TiC(001). As for the Pt4 cluster, the three-dimensional distorted tetrahedral structure and the two-dimensional square structure almost have equal stability. In contrast with the two-dimensional isolated Pt5 cluster, the adsorbed Pt5 cluster prefers a three-dimensional structure on TiC(001). Substantial charge transfer takes place from TiC(001) surface to the adsorbed Ptn clusters, resulting in the negatively charged Ptn clusters. At last, the d-band centers of the absorbed Pt atoms and their implications in the catalytic activity are discussed.
A checkerboard selective absorber with excellent spectral selectivity
Authors: Yang Liu , Mo Lei , Chen Tuo , Forsberg Erik , He Sailing
Published: November 2015

A selective absorber with excellent spectral selectivity is proposed and analyzed. The absorber is based on a germanium (Ge) checkerboard on top of a tantalum (Ta) substrate. At wavelengths shorter than the 1.2 μm cutoff, a very high absorption is achieved due to strong cavity resonances in the Ge nanosquares, and their interactions with adjacent nanocavities and the bottom Ta substrate. At longer wavelengths, absorption is greatly suppressed due to destructive interference between the transparent checkerboard layer and the highly reflective Ta substrate. To better describe the superior selectivity of our configuration, a new figure of merit (FOM) is introduced. We observe a FOM value of 0.88 compared to 0.69 for its planar counterpart. We also conduct a thermal analysis to verify the excellent selectivity of our absorber. A high temperature can be achieved and maintained, promising good potential for applications in solar thermophotovoltaic systems.
Generalised relativistic Ohm's laws, extended gauge transformations, and magnetic linking
Authors: Pegoraro F.
Published: November 2015

Generalisations of the relativistic ideal Ohm's law are presented that include specific dynamical features of the current carrying particles in a plasma. Cases of interest for space and laboratory plasmas are identified where these generalisations allow for the definition of generalised electromagnetic fields that transform under a Lorentz boost in the same way as the real electromagnetic fields and that obey the same set of homogeneous Maxwell's equations.
Photochromism induced nonlinear optical absorption enhancement and ultrafast responses of several dithienylethene compounds
Authors: Wang Yaochuan , Yan Yongli , Liu Dajun , Wang Guiqiu , Pu Shouzhi
Published: November 2015

The nonlinear optical properties and ultrafast dynamics of three dithienylethene photochromic derivatives (i.e., P1, P2, and P3) were investigated by two-photon fluorescence, open-aperture Z-scan, and femtosecond pump-probe experiments. Photoinduced ring-closure and ring-opening phenomena, as well as a photochromism induced nonlinear optical property enhancement, were observed. For both the ring-opening and ring-closure state, the curve exhibited an ultrafast absorption peak approximately 200 fs followed by a fast decay process (i.e., ∼1 ps) and a long decay process that had a duration longer than 5 ps. The ultrafast peak followed by a fast decay process and the long decay process were attributable to a special two-photon absorption process, the formation of a charge separation state, and the relaxation of the charge separation state, respectively. However, the magnitude of the signal under the ring-closure state is approximately fivefold greater than that of the ring-opening state, which is in good agreement with nonlinear optical results. Intramolecular charge transfer processes were observed in the dynamics curves of the P2′ and P3′ isomers with D-π-A and D-π-D structures.
Comparison of line x-ray emission from solid and porous nano-layer coated targets irradiated by double laser pulses
Authors: Fazeli R. , Mahdieh M. H.
Published: November 2015

Enhancement of line x-ray emission from both solid and porous iron targets induced by irradiation of single and double laser pulses is studied numerically. The line emission from laser produced plasma is calculated within the extreme ultra-violet lithography wavelength range of 13.5–13.7 nm. The effects of pre-pulse intensity and delay time between two pulses (pre-pulse and main pulse) are examined. The results show that using double pulses irradiation in the conditions of porous target can reduce the x-ray enhancement. According to the results, the use of both pre-pulse and porous target leads to efficient absorption of the laser energy. Calculations also show that such enhanced laser absorption can ionize atoms of the target material to very high degrees of ionization, leading to decrease of the density of appropriate ions that are responsible for line emission in the selected wavelength region. By increasing the target porosity, x-ray yield was more reduced.
Multidirectional plasma flow measurement by Gundestrup Probe in scrape-off layer of ADITYA tokamak
Authors: Sangwan Deepak , Jha Ratneshwar , Tanna Rakesh L.
Published: November 2015

Multidirectional plasma flow measurements by using Gundestrup Probe in the scrape-off layer of ADITYA tokamak are presented. The ADITYA Gundestrup Probe-head consists of eight plates arranged around the ceramic rod and three pins normal to side plates. Plates are used to measure both parallel and perpendicular flows simultaneously and pins are used to measure plasma density and floating potential. A comparison of direct perpendicular flow measurement and by two other plates of Gundestrup Probe is presented. Possible causes of perpendicular flows are identified and compared with the measured flows. It is observed that the mechanism of the parallel flow and the perpendicular flow is different only at high parallel Mach number. A puff of the working gas is used to study its effect on the perpendicular flows and its reversal with the gas puff is observed.
Colossal magnetoelectric effect induced by parametric amplification
Authors: Wang Yi , Onuta Tiberiu-Dan , Long Christian J. , Geng Yunlong , Takeuchi Ichiro
Published: November 2015

We describe the use of parametric amplification to substantially increase the magnetoelectric (ME) coefficient of multiferroic cantilevers. Parametric amplification has been widely used in sensors and actuators based on optical, electronic, and mechanical resonators to increase transducer gain. In our system, a microfabricated mechanical cantilever with a magnetostrictive layer is driven at its fundamental resonance frequency by an AC magnetic field. The resulting actuation of the cantilever at the resonance frequency is detected by measuring the voltage across a piezoelectric layer in the same cantilever. Concurrently, the spring constant of the cantilever is modulated at twice the resonance frequency by applying an AC voltage across the piezoelectric layer. The spring constant modulation results in parametric amplification of the motion of the cantilever, yielding a gain in the ME coefficient. Using this method, the ME coefficient was amplified from 33 V/(cm Oe) to 2.0 MV/(cm Oe), an increase of over 4 orders of magnitude. This boost in the ME coefficient directly resulted in an enhancement of the magnetic field sensitivity of the device from 6.0 nT/Hz to 1.0 nT/Hz. The enhancement in the ME coefficient and magnetic field sensitivity demonstrated here may be beneficial for a variety actuators and sensors based on resonant multiferroic devices.
In-plane current induced domain wall nucleation and its stochasticity in perpendicular magnetic anisotropy Hall cross structures
Authors: Sethi P. , Murapaka C. , Lim G. J. , Lew W. S.
Published: November 2015

Hall cross structures in magnetic nanowires are commonly used for electrical detection of magnetization reversal in which a domain wall (DW) is conventionally nucleated by a local Oersted field. In this letter, we demonstrate DW nucleation in Co/Ni perpendicular magnetic anisotropy nanowire at the magnetic Hall cross junction. The DWs are nucleated by applying an in-plane pulsed current through the nanowire without the need of a local Oersted field. The change in Hall resistance, detected using anomalous Hall effect, is governed by the magnetic volume switched at the Hall junction, which can be tuned by varying the magnitude of the applied current density and pulse width. The nucleated DWs are driven simultaneously under the spin transfer torque effect when the applied current density is above a threshold. The possibility of multiple DW generation and variation in magnetic volume switched makes nucleation process stochastic in nature. The in-plane current induced stochastic nature of DW generation may find applications in random number generation.
Photo-Hall effect in highly Mg-doped lithium niobate crystals
Authors: Wang Xiaojie , Liu Xiangming , Bo Fang , Chen Shaolin , Chen Jing , Kong Yongfa , Xu Jingjun , Zhang Guoquan
Published: November 2015

We characterized the ultraviolet-light-excited charge carriers in highly Mg-doped lithium niobate crystals using photo-Hall effect. The experimental results confirm that electrons are the dominant photo-excited charge carriers under ultraviolet light (λ=365 nm) illumination, and they transport in an anisotropic way. The photo-Hall mobilities of photo-excited electrons in the crystalline x- and z-axes were measured to be μx = 0.066 m2·V−1·s−1 and μz = 0.14 m2·V−1·s−1, respectively, which are 2–3 orders of magnitude higher than that of thermalized electrons. In addition, we found that the magneto-resistance effect is taking part in the charge transport process, which results in a nonlinear dependence of the photo-Hall current on the external magnetic field in Mg-doped lithium niobate crystals.
A reciprocal theorem for boundary-driven channel flows
Authors: Michelin Sébastien , Lauga Eric
Published: November 2015

In a variety of physical situations, a bulk viscous flow is induced by a distribution of surface velocities, for example, in diffusiophoresis (as a result of chemical gradients) and above carpets of cilia (as a result of biological activity). When such boundary-driven flows are used to pump fluids, the primary quantity of interest is the induced flow rate. In this letter, we propose a method, based on the reciprocal theorem of Stokes flows, to compute the net flow rate for arbitrary flow distribution and periodic pump geometry using solely stress information from a dual Poiseuille-like problem. After deriving the general result, we apply it to straight channels of triangular, elliptic, and rectangular geometries and quantify the relationship between bulk motion and surface forcing.
Mid-infrared electroluminescence from InAs type-I quantum wells grown on InAsP/InP metamorphic buffers
Authors: Jung Daehwan , Yu Lan , Wasserman Daniel , Larry Lee Minjoo
Published: November 2015

We report room-temperature (RT) electroluminescence (EL) from InAs/InAsxP1−x quantum well (QW) light-emitting diodes (LEDs) over a wide wavelength range of 2.50–2.94 μm. We demonstrate the ability to accurately design strained InAs QW emission wavelengths while maintaining low threading dislocation density, coherent QW interfaces, and high EL intensity. Investigation of the optical properties of the LEDs grown on different InAsxP1−x metamorphic buffers showed higher EL intensity and lower thermal quenching for QWs with higher barriers and stronger carrier confinement. Strong RT EL intensity from LEDs with narrow full-width at half-maximum shows future potential for InAs QW mid-infrared laser diodes on InAsP/InP.
Suppressed grain-boundary scattering in atomic layer deposited Nb:TiO2 thin films
Authors: Niemelä Janne-Petteri , Hirose Yasushi , Shigematsu Kei , Sano Masahito , Hasegawa Tetsuya , Karppinen Maarit
Published: November 2015

We have fabricated high-quality thin films of the transparent conducting anatase Nb:TiO2 on glass substrates through atomic layer deposition, and a subsequent reductive heat treatment of the as-deposited amorphous films. Hall-effect measurements and Drude-fitting of the Vis-NIR spectra indicate that for lightly doped films deposited at temperatures around 170 °C, grain boundary scattering becomes negligible and the mobility is predominately limited by phonon-electron scattering inherent to the anatase lattice and by impurities. Simultaneously, such lighter doping leads to reduced plasma absorption, thereby improving material's performance as a transparent conductor.
Low-frequency noise in InAs films bonded on low-k flexible substrates
Authors: Le Son Phuong , Ui Toshimasa , Suzuki Toshi-kazu
Published: November 2015

We have systematically investigated low-frequency noise (LFN) in InAs films with several thicknesses (≃10-100 nm) bonded on low-k flexible substrates (InAs/FS), comparing with that in InAs films epitaxially grown on GaAs(001) substrates (InAs/GaAs). We obtain current LFN spectra exhibiting approximate 1/f characteristics and consequent effective Hooge parameters α depending on the thickness, where we find that α in the InAs/FS is larger than that in the InAs/GaAs. The behavior of α can be attributed to the fluctuation of the electron mobility dominated by surface/interface charge scattering and by thickness fluctuation scattering.
Highly efficient and controllable method to fabricate ultrafine metallic nanostructures
Authors: Cai Hongbing , Zhang Kun , Yu Xinxin , Pan Nan , Tian Yangchao , Luo Yi , Wang Xiaoping
Published: November 2015

We report a highly efficient, controllable and scalable method to fabricate various ultrafine metallic nanostructures in this paper. The method starts with the negative poly-methyl-methacrylate (PMMA) resist pattern with line-width superior to 20 nm, which is obtained from overexposing of the conventionally positive PMMA under a low energy electron beam. The pattern is further shrunk to sub-10 nm line-width through reactive ion etching. Using the patter as a mask, we can fabricate various ultrafine metallic nanostructures with the line-width even less than 10 nm. This ion tailored mask lithography (ITML) method enriches the top-down fabrication strategy and provides potential opportunity for studying quantum effects in a variety of materials.
Radicalising the rangelands: disruptive change or progressive policy?
Authors: Walker Bruce W.
Published: November 2015

Only ~15% of Australians now live outside the cities and the essentially suburban coastal corridor. Those coastal suburbs are home not to the descendants of drovers and Anzacs, but to ambitious migrants from Asia and the Middle–East, with no taste for rural life. Under pressure of globalisation and market economics the narrative of the rangelands has changed and with that the national interest in the rangelands has declined. Increasingly self-interest has over-powered national interest in the rangelands. The traditional narrative relied on mining, pastoralism and tourism and the contest for land and resources between these sectors and Aboriginal interests. The early champions in each of these sectors were revered. Today these sectors are driven more by self-interest and international investors than national interest. Today, there is not the same recognition of the names like Kidman or Flynn or Perkins as in the past. The rangelands are no longer in the hearts and minds of the nation. Rangelands impinge to a degree on national security through the buffer of confidence their vast expanse provides to coastal communities. Rangelands also figure in the national conscience through the complexity of issues around ‘the problem’ of Aboriginal lifestyles as perceived by coastal communities. Yet topics that spark national interest in rangelands are hard to identify unless they relate to share dividends. In this indifferent environment, will the rangelands benefit from grand national-policy initiatives or from increasingly focussed progressive policy? This paper argues for a narrative with a more disruptive and innovative radicalisation of the rangelands to re-ignite national interest and national investment.
Dingo interactions with exotic mesopredators: spatiotemporal dynamics in an Australian arid-zone study
Authors: Schroeder T. , Lewis M. M. , Kilpatrick A. D. , Moseby K. E.
Published: November 2015

Context Apex predators occupy the top level of the trophic cascade and often perform regulatory functions in many ecosystems. Their removal has been shown to increase herbivore and mesopredator populations, and ultimately reduce species diversity. In Australia, it has been proposed that the apex predator, the dingo (Canis dingo), has the potential to act as a biological control agent for two introduced mesopredators, the red fox (Vulpes vulpes) and the feral cat (Felis catus). Understanding the mechanisms of interaction among the three species may assist in determining the effectiveness of the dingo as a control agent and the potential benefits to lower-order species. Aims To test the hypotheses that feral cats and foxes attempt to both temporally avoid dingoes and spatially avoid areas of high dingo use. Methods Static and dynamic interaction methodologies based on global positioning system (GPS) telemetry data were applied to test temporal and spatial interactions between the two mesopredators (n = 15) and a dingo pair (n = 2). The experimental behavioural study was conducted in a 37-km2 fenced enclosure located in arid South Australia. Key results The dynamic interaction analysis detected neither attraction nor avoidance between dingoes and cats or foxes at short temporal scales. There was no suggestion of delayed interactions, indicating that dingoes were not actively hunting mesopredators on the basis of olfactory signalling. However, static interaction analysis suggested that, although broad home ranges of cats and foxes overlapped with dingoes, core home ranges were mutually exclusive. This was despite similar habitat preferences among species. Conclusions We found that avoidance patterns were not apparent when testing interactions at short temporal intervals, but were manifested at larger spatial scales. Results support previous work that suggested that dingoes kill mesopredators opportunistically rather than through active hunting. Implications Core home ranges of dingoes may provide refuge areas for small mammals and reptiles, and ultimately benefit threatened prey species by creating mesopredator-free space. However, the potential high temporal variation in core home-range positioning and small size of mutually exclusive areas suggested that further work is required to determine whether these areas provide meaningful sanctuaries for threatened prey.
Cdc42-dependent actin dynamics controls maturation and secretory activity of dendritic cells
Authors: Schulz Anna M. , Stutte Susanne , Hogl Sebastian , Luckashenak Nancy , Dudziak Diana , Leroy Céline , Forné Ignasi , Imhof Axel , Müller Stephan A. , Brakebusch Cord H. , Lichtenthaler Stefan F. , Brocker Thomas
Published: November 2015

Cell division cycle 42 (Cdc42) is a member of the Rho guanosine triphosphatase family and has pivotal functions in actin organization, cell migration, and proliferation. To further study the molecular mechanisms of dendritic cell (DC) regulation by Cdc42, we used Cdc42-deficient DCs. Cdc42 deficiency renders DCs phenotypically mature as they up-regulate the co-stimulatory molecule CD86 from intracellular storages to the cell surface. Cdc42 knockout DCs also accumulate high amounts of invariant chain–major histocompatibility complex (MHC) class II complexes at the cell surface, which cannot efficiently present peptide antigens (Ag’s) for priming of Ag-specific CD4 T cells. Proteome analyses showed a significant reduction in lysosomal MHC class II–processing proteins, such as cathepsins, which are lost from DCs by enhanced secretion. As these effects on DCs can be mimicked by chemical actin disruption, our results propose that Cdc42 control of actin dynamics keeps DCs in an immature state, and cessation of Cdc42 activity during DC maturation facilitates secretion as well as rapid up-regulation of intracellular molecules to the cell surface.
Bub3–BubR1-dependent sequestration of Cdc20Fizzy at DNA breaks facilitates the correct segregation of broken chromosomes
Authors: Derive Nicolas , Landmann Cedric , Montembault Emilie , Claverie Marie-Charlotte , Pierre-Elies Priscillia , Goutte-Gattat Damien , Founounou Nabila , McCusker Derek , Royou Anne
Published: November 2015

The presence of DNA double-strand breaks during mitosis is particularly challenging for the cell, as it produces broken chromosomes lacking a centromere. This situation can cause genomic instability resulting from improper segregation of the broken fragments into daughter cells. We recently uncovered a process by which broken chromosomes are faithfully transmitted via the BubR1-dependent tethering of the two broken chromosome ends. However, the mechanisms underlying BubR1 recruitment and function on broken chromosomes were largely unknown. We show that BubR1 requires interaction with Bub3 to localize on the broken chromosome fragments and to mediate their proper segregation. We also find that Cdc20, a cofactor of the E3 ubiquitin ligase anaphase-promoting complex/cyclosome (APC/C), accumulates on DNA breaks in a BubR1 KEN box–dependent manner. A biosensor for APC/C activity demonstrates a BubR1-dependent local inhibition of APC/C around the segregating broken chromosome. We therefore propose that the Bub3–BubR1 complex on broken DNA inhibits the APC/C locally via the sequestration of Cdc20, thus promoting proper transmission of broken chromosomes.
Endosomal sorting of Notch receptors through COMMD9-dependent pathways modulates Notch signaling
Authors: Li Haiying , Koo Yeon , Mao Xicheng , Sifuentes-Dominguez Luis , Morris Lindsey L. , Jia Da , Miyata Naoteru , Faulkner Rebecca A. , van Deursen Jan M. , Vooijs Marc , Billadeau Daniel D. , van de Sluis Bart , Cleaver Ondine , Burstein Ezra
Published: November 2015

Notch family members are transmembrane receptors that mediate essential developmental programs. Upon ligand binding, a proteolytic event releases the intracellular domain of Notch, which translocates to the nucleus to regulate gene transcription. In addition, Notch trafficking across the endolysosomal system is critical in its regulation. In this study we report that Notch recycling to the cell surface is dependent on the COMMD–CCDC22–CCDC93 (CCC) complex, a recently identified regulator of endosomal trafficking. Disruption in this system leads to intracellular accumulation of Notch2 and concomitant reduction in Notch signaling. Interestingly, among the 10 copper metabolism MURR1 domain containing (COMMD) family members that can associate with the CCC complex, only COMMD9 and its binding partner, COMMD5, have substantial effects on Notch. Furthermore, Commd9 deletion in mice leads to embryonic lethality and complex cardiovascular alterations that bear hallmarks of Notch deficiency. Altogether, these studies highlight that the CCC complex controls Notch activation by modulating its intracellular trafficking and demonstrate cargo-specific effects for members of the COMMD protein family.
Automatic generation of bioinformatics tools for predicting protein–ligand binding sites
Authors: Komiyama Yusuke , Banno Masaki , Ueki Kokoro , Saad Gul , Shimizu Kentaro
Published: November 2015

Motivation: Predictive tools that model protein–ligand binding on demand are needed to promote ligand research in an innovative drug-design environment. However, it takes considerable time and effort to develop predictive tools that can be applied to individual ligands. An automated production pipeline that can rapidly and efficiently develop user-friendly protein–ligand binding predictive tools would be useful.

Results: We developed a system for automatically generating protein–ligand binding predictions. Implementation of this system in a pipeline of Semantic Web technique-based web tools will allow users to specify a ligand and receive the tool within 0.5–1 day. We demonstrated high prediction accuracy for three machine learning algorithms and eight ligands.

Availability and implementation: The source code and web application are freely available for download at http://utprot.net. They are implemented in Python and supported on Linux.

Contact:  shimizu@bi.a.u-tokyo.ac.jp

Supplementary information:  Supplementary data are available at Bioinformatics online.
De novo identification of replication-timing domains in the human genome by deep learning
Authors: Liu Feng , Ren Chao , Li Hao , Zhou Pingkun , Bo Xiaochen , Shu Wenjie
Published: November 2015

Motivation: The de novo identification of the initiation and termination zones—regions that replicate earlier or later than their upstream and downstream neighbours, respectively—remains a key challenge in DNA replication.

Results: Building on advances in deep learning, we developed a novel hybrid architecture combining a pre-trained, deep neural network and a hidden Markov model (DNN-HMM) for the de novo identification of replication domains using replication timing profiles. Our results demonstrate that DNN-HMM can significantly outperform strong, discriminatively trained Gaussian mixture model–HMM (GMM-HMM) systems and other six reported methods that can be applied to this challenge. We applied our trained DNN-HMM to identify distinct replication domain types, namely the early replication domain (ERD), the down transition zone (DTZ), the late replication domain (LRD) and the up transition zone (UTZ), using newly replicated DNA sequencing (Repli-Seq) data across 15 human cells. A subsequent integrative analysis revealed that these replication domains harbour unique genomic and epigenetic patterns, transcriptional activity and higher-order chromosomal structure. Our findings support the ‘replication-domain’ model, which states (1) that ERDs and LRDs, connected by UTZs and DTZs, are spatially compartmentalized structural and functional units of higher-order chromosomal structure, (2) that the adjacent DTZ-UTZ pairs form chromatin loops and (3) that intra-interactions within ERDs and LRDs tend to be short-range and long-range, respectively. Our model reveals an important chromatin organizational principle of the human genome and represents a critical step towards understanding the mechanisms regulating replication timing.

Availability and implementation: Our DNN-HMM method and three additional algorithms can be freely accessed at https://github.com/wenjiegroup/DNN-HMM. The replication domain regions identified in this study are available in GEO under the accession ID GSE53984.

Contact:  shuwj@bmi.ac.cn or boxc@bmi.ac.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
Comparison of genetic variants in matched samples using thesaurus annotation
Authors: Konopka Tomasz , Nijman Sebastian M.B.
Published: November 2015

Motivation: Calling changes in DNA, e.g. as a result of somatic events in cancer, requires analysis of multiple matched sequenced samples. Events in low-mappability regions of the human genome are difficult to encode in variant call files and have been under-reported as a result. However, they can be described accurately through thesaurus annotation—a technique that links multiple genomic loci together to explicate a single variant.

Results: We here describe software and benchmarks for using thesaurus annotation to detect point changes in DNA from matched samples. In benchmarks on matched normal/tumor samples we show that the technique can recover between five and ten percent more true events than conventional approaches, while strictly limiting false discovery and being fully consistent with popular variant analysis workflows. We also demonstrate the utility of the approach for analysis of de novo mutations in parents/child families.

Availability and implementation: Software performing thesaurus annotation is implemented in java; available in source code on github at GeneticThesaurus (https://github.com/tkonopka/GeneticThesaurus) and as an executable on sourceforge at geneticthesaurus (https://sourceforge.net/projects/geneticthesaurus). Mutation calling is implemented in an R package available on github at RGeneticThesaurus (https://github.com/tkonopka/RGeneticThesaurus).

Supplementary information:  Supplementary data are available at Bioinformatics online.

Contact:  tomasz.konopka@ludwig.ox.ac.uk
Therapeutic antibodies that target inflammatory cytokines in autoimmune diseases
Authors: Lai Yuping , Dong Chen
Published: November 2015

Inflammatory cytokines are key regulators of immune responses. Persistent and excessive production of inflammatory cytokines underscores the development of autoimmune diseases. Therefore, neutralizing inflammatory cytokines or antagonizing their receptor function is considered as a useful therapeutic strategy to treat autoimmune diseases. To achieve the success of such a strategy, understanding of the complex actions of these cytokines and cytokine networks is required. In this review we focus on four inflammatory cytokines—tumor necrosis factor α (TNFα), interleukin-6 (IL-6), IL-23 and IL-17—and dissect how the dysregulation of these cytokines regulates autoimmune diseases. On the basis of pre-clinical and clinical data, we specifically discuss the therapeutic rationale for targeting these cytokines and describe the potential adverse effects.
Influence of Vacuum Mixing on Structural Characteristics and Physical Properties of Noodle Dough
Authors: Liu Rui , Zhang Yingquan , Zhang Bo , Ban Jinfu , Wei Yimin
Published: November 2015

The effects of vacuum mixing on the structural characteristics and physical properties of noodle dough were investigated using three leading Chinese wheat cultivars. Texture profile analysis showed that vacuum mixed doughs when sheeted all gave significantly higher levels of adhesiveness, elasticity, and chewiness than doughs from nonvacuum mixing. The cross section of sheeted dough mixed at 0.06 MPa had a more continuous and compact microstructure with fewer holes and gaps, as well as more even protein distribution at the surface, as evidenced by scanning electron microscopy and Fourier transform infrared microimaging. However, a higher degree of vacuum was detrimental to the developed network for weak dough. Dough mixed at 0.06 MPa had higher glutenin macropolymer content and lower free thiol group concentration compared with nonvacuum mixed doughs, which may largely relate to the improvement of dough texture. The development of the gluten network for weak gluten flour was more sensitive to the degree of vacuum.
Distribution ofAgrobacterium vitisin Grapevines and Its Relevance to Pathogen Elimination
Authors: Johnson Kameka Latoya , Cronin Heather , Reid Cheryl L. , Burr Thomas J.
Published: November 2015

Agrobacterium vitis, the cause of crown gall disease on grapevine, survives internally in vines and can be spread in cuttings for propagation. The possibility of generating pathogen-free vines through tissue culture makes it essential to understand the distribution of the pathogen in grapevines. A highly sensitive magnetic capture hybridization procedure along with real-time polymerase chain reaction were used to measure the distribution of tumorigenic A. vitis in dormant canes and green shoots of grapevines. Tumorigenic A. vitis was distributed from the basal to apical nodal and internodal tissues of canes as well as in nonlignified green shoots. In experiments conducted in 2013, A. vitis was detected in up to 17% of shoot tips and 52% of meristems of greenhouse-grown plants initiated from known A. vitis-contaminated cuttings. A lower frequency of detection was observed from surface-disinfected shoot tips (7%) as compared with nondisinfected tips (37%), suggesting epiphytic survival on green tissues. In 2014, vines propagated from cuttings collected from crown gall-infected vines from a different vineyard yielded lower incidences of A. vitis from shoot tips, and the bacterium was not detected in meristems. Tumorigenic A. vitis was also detected in cuttings of wild grapevines (Vitis riparia) that were collected both adjacent to and far removed from commercial vineyards.
The Relationship Between Insertional Torque and Pullout Strength of Surgical Screws
Authors: Rose Kyle M. , Nelson Carolyn M. , Ogden Alan L. , Morandi Massimo “Max”
Published: November 2015

Objectives:

To investigate the role of maximal insertional torque (T
max) of surgical screws and pullout strength (POS) in human cadaveric tibiae.

Methods:

Self-tapping surgical screws (4.5 mm) were inserted into 9 segments of cadaveric tibial cortical bone, measuring T
max and POS of screws inserted at 50%, 70%, 90%, and 100% T
max. Computed tomography was also performed, allowing calculation of bone mineral density (BMD) in K2HPO4 concentration (mg/mL) and cortical thickness (mm).

Results:

POS measurements were highest and similar in screws inserted at 70% and 90% of the established T
max. Screws inserted at 90% T
max offered a significantly different POS than those inserted at 100% T
max. No significant differences were found between samples in BMD or cortical thickness. No significant correlations were found between cortical thickness or BMD and T
max.

Conclusions:

Surgeons should tighten screws to a torque less than T
max to avoid loss of purchase of the screw and reduced POS.