bluuebunny/crossref_metadata_2025 huggingface dataset:
Hot-electron refluxing enhanced relativistic transparency of overdense plasmas
Authors: Yu Yong , Li Xiao-Ya , Chen Zi-Yu , Wang Jia-Xiang , Shen Bai-Fei , Zhu Wen-Jun
Published: March 2017

A new phenomenon of an enhanced relativistic transparency of overdense plasmas by the influence of hot-electron refluxing has been discovered via particle-in-cell simulations. When a p-polarized laser pulse, with intensity below the self-induced-transparency (SIT) threshold, obliquely irradiates a thin overdense plasma, the initially opaque plasma becomes transparent after a time interval that is linearly dependent on the thickness of the plasma. This phenomenon can be interpreted as a consequence of hot-electron refluxing, which reduces the effective electron density by longitudinal heating. When the laser intensity is higher than the SIT threshold, the penetration velocity of the laser in the plasma is enhanced when the refluxing is present.
Maximally symmetric stabilizer MUBs in even prime-power dimensions
Authors: Carmeli Claudio , Schultz Jussi , Toigo Alessandro
Published: March 2017

One way to construct a maximal set of mutually unbiased bases (MUBs) in a prime-power dimensional Hilbert space is by means of finite phase-space methods. MUBs obtained in this way are covariant with respect to some subgroup of the group of all affine symplectic phase-space transformations. However, this construction is not canonical: as a consequence, many different choices of covariance subgroups are possible. In particular, when the Hilbert space is 2n dimensional, it is known that covariance with respect to the full group of affine symplectic phase-space transformations can never be achieved. Here we show that in this case there exist two essentially different choices of maximal subgroups admitting covariant MUBs. For both of them, we explicitly construct a family of 2n covariant MUBs. We thus prove that, contrary to the odd dimensional case, maximally covariant MUBs are very far from being unique in even prime-power dimensions.
Equilibrium and dynamic pleating of a crystalline bonded network
Authors: Ganguly Saswati , Nath Parswa , Horbach Jürgen , Sollich Peter , Karmakar Smarajit , Sengupta Surajit
Published: March 2017

We describe a phase transition that gives rise to structurally non-trivial states in a two-dimensional ordered network of particles connected by harmonic bonds. Monte Carlo simulations reveal that the network supports, apart from the homogeneous phase, a number of heterogeneous “pleated” phases, which can be stabilised by an external field. This field is conjugate to a global collective variable quantifying “non-affineness,” i.e., the deviation of local particle displacements from local affine deformation. In the pleated phase, stress is localised in ordered rows of pleats and eliminated from the rest of the lattice. The kinetics of the phase transition is unobservably slow in molecular dynamics simulation near coexistence, due to very large free energy barriers. When the external field is increased further to lower these barriers, the network exhibits rich dynamic behaviour: it transforms into a metastable phase with the stress now localised in a disordered arrangement of pleats. The pattern of pleats shows ageing dynamics and slow relaxation to equilibrium. Our predictions may be checked by experiments on tethered colloidal solids in dynamic laser traps.
Solvent fluctuations around solvophobic, solvophilic, and patchy nanostructures and the accompanying solvent mediated interactions
Authors: Chacko Blesson , Evans Robert , Archer Andrew J.
Published: March 2017

Using classical density functional theory (DFT), we calculate the density profile ρ(𝐫) and local compressibility χ(𝐫) of a simple liquid solvent in which a pair of blocks with (microscopic) rectangular cross section are immersed. We consider blocks that are solvophobic, solvophilic and also ones that have both solvophobic and solvophilic patches. Large values of χ(𝐫) correspond to regions in space where the liquid density is fluctuating most strongly. We seek to elucidate how enhanced density fluctuations correlate with the solvent mediated force between the blocks, as the distance between the blocks and the chemical potential of the liquid reservoir vary. For sufficiently solvophobic blocks, at small block separations and small deviations from bulk gas-liquid coexistence, we observe a strongly attractive (near constant) force, stemming from capillary evaporation to form a low density gas-like intrusion between the blocks. The accompanying χ(𝐫) exhibits a structure which reflects the incipient gas-liquid interfaces that develop. We argue that our model system provides a means to understanding the basic physics of solvent mediated interactions between nanostructures, and between objects such as proteins in water that possess hydrophobic and hydrophilic patches.
Quantum behavior of water nano-confined in beryl
Authors: Finkelstein Y. , Moreh R. , Shang S. L. , Wang Y. , Liu Z. K.
Published: March 2017

The proton mean kinetic energy, Ke(H), of water confined in nanocavities of beryl (Be3Al2Si6O18) at 5 K was obtained by simulating the partial vibrational density of states from density functional theory based first-principles calculations. The result, Ke(H) = 104.4 meV, is in remarkable agreement with the 5 K deep inelastic neutron scattering (DINS) measured value of 105 meV. This is in fact the first successful calculation that reproduces an anomalous DINS value regarding Ke(H) in nano-confined water. The calculation indicates that the vibrational states of the proton of the nano-confined water molecule distribute much differently than in ordinary H2O phases, most probably due to coupling with lattice modes of the hosting beryl nano-cage. These findings may be viewed as a promising step towards the resolution of the DINS controversial measurements on other H2O nano-confining systems, e.g., H2O confined in single and double walled carbon nanotubes.
Fluid-structure interaction of a rolling restrained body of revolution at high angles of attack
Authors: Degani D. , Ishay M. , Gottlieb O.
Published: March 2017

The current work investigates numerically rolling instabilities of a free-to-roll slender rigid-body of revolution placed in a wind tunnel at a high angle of attack. The resistance to the roll moment is represented by a linear torsion spring and equivalent linear damping representing friction in the bearings of a simulated wind tunnel model. The body is subjected to a three-dimensional, compressible, laminar flow. The full Navier-Stokes equations are solved using the second-order implicit finite difference Beam-Warming scheme, adapted to a curvilinear coordinate system, whereas the coupled structural second order equation of motion for roll is solved by a fourth-order Runge-Kutta method. The body consists of a 3.5-diameter tangent ogive forebody with a 7.0-diameter long cylindrical afterbody extending aft of the nose-body junction to x/D = 10.5. We describe in detail the investigation of three angles of attack 20°, 40°, and 65°, at a Reynolds number of 30 000 (based on body diameter) and a Mach number of 0.2. Three distinct configurations are investigated as follows: a fixed body, a free-to-roll body with a weak torsion spring, and a free-to-roll body with a strong torsion spring. For each angle of attack the free-to-roll configuration portrays a distinct and different behavior pattern, including bi-stable limit-cycle oscillations. The bifurcation structure incorporates both large and small amplitude periodic roll oscillations where the latter lose their periodicity with increasing stiffness of the restraining spring culminating with distinct quasiperiodic oscillations. We note that removal of an applied upstream disturbance for a restrained body does not change the magnitude or complexity of the oscillations or of the flow patterns along the body. Depending on structure characteristics and flow conditions even a small rolling moment coefficient at the relatively low angle of attack of 20° may lead to large amplitude resonant roll oscillations.
Adaptive microfluidic gradient generator for quantitative chemotaxis experiments
Authors: Anielski Alexander , Pfannes Eva K. B. , Beta Carsten
Published: March 2017

Chemotactic motion in a chemical gradient is an essential cellular function that controls many processes in the living world. For a better understanding and more detailed modelling of the underlying mechanisms of chemotaxis, quantitative investigations in controlled environments are needed. We developed a setup that allows us to separately address the dependencies of the chemotactic motion on the average background concentration and on the gradient steepness of the chemoattractant. In particular, both the background concentration and the gradient steepness can be kept constant at the position of the cell while it moves along in the gradient direction. This is achieved by generating a well-defined chemoattractant gradient using flow photolysis. In this approach, the chemoattractant is released by a light-induced reaction from a caged precursor in a microfluidic flow chamber upstream of the cell. The flow photolysis approach is combined with an automated real-time cell tracker that determines changes in the cell position and triggers movement of the microscope stage such that the cell motion is compensated and the cell remains at the same position in the gradient profile. The gradient profile can be either determined experimentally using a caged fluorescent dye or may be alternatively determined by numerical solutions of the corresponding physical model. To demonstrate the function of this adaptive microfluidic gradient generator, we compare the chemotactic motion of Dictyostelium discoideum cells in a static gradient and in a gradient that adapts to the position of the moving cell.
A new efficient method for the calculation of interior eigenpairs and its application to vibrational structure problems
Authors: Petrenko Taras , Rauhut Guntram
Published: March 2017

Vibrational configuration interaction theory is a common method for calculating vibrational levels and associated IR and Raman spectra of small and medium-sized molecules. When combined with appropriate configuration selection procedures, the method allows the treatment of configuration spaces with up to 1010 configurations. In general, this approach pursues the construction of the eigenstates with significant contributions of physically relevant configurations. The corresponding eigenfunctions are evaluated in the subspace of selected configurations. However, it can easily reach the dimension which is not tractable for conventional eigenvalue solvers. Although Davidson and Lanczos methods are the methods of choice for calculating exterior eigenvalues, they usually fall into stagnation when applied to interior states. The latter are commonly treated by the Jacobi-Davidson method. This approach in conjunction with matrix factorization for solving the correction equation (CE) is prohibitive for larger problems, and it has limited efficiency if the solution of the CE is based on Krylov’s subspace algorithms. We propose an iterative subspace method that targets the eigenvectors with significant contributions to a given reference vector and is based on the optimality condition for the residual norm corresponding to the error in the solution vector. The subspace extraction and expansion are modified according to these principles which allow very efficient calculation of interior vibrational states with a strong multireference character in different vibrational structure problems. The convergence behavior of the method and its performance in comparison with the aforementioned algorithms are investigated in a set of benchmark calculations.
Electrically pumped all photonic crystal 2nd order DFB lasers arrays emitting at 2.3 μm
Authors: Adelin B. , Gauthier-Lafaye O. , Dubreuil P. , Lecestre A. , Rouillard Y. , Bahriz M. , Boissier G. , Vicet A. , Monmayrant A.
Published: March 2017

Single-mode, widely tunable laser diodes in the mid-infrared range are highly interesting for demanding spectroscopic applications involving multi-species discrimination. We report on an alternative approach using single frequency laser arrays. Single-mode laser arrays were fabricated using all-photonic-crystal electrically pumped distributed feedback cavities on GaSb. The fabricated lasers exhibit thresholds in the 3.2 kA/cm2 range in a continuous wave regime at room temperature. The maximum output power reaches 1 mW and single mode operation with a side-mode suppression ratio of 30 dB is demonstrated. These lasers were used to perform tunable diode laser absorption spectroscopy of several gases in standard gas cells. Continuous spectral coverage of a 40 nm band using 10 lasers seems an achievable goal using laser arrays with PhC lattice constant variations of 1 nm from laser to laser.
Weakly parametrized Jastrow ansatz for a strongly correlated Bose system
Authors: Lutsyshyn Yaroslav
Published: March 2017

We consider the Jastrow pair-product wavefunction for strongly correlated Bose systems, in our case liquid helium-4. An ansatz is proposed for the pair factors which consist of a numeric solution to a modified and parametrized pair scattering equation. We consider a number of such simple one-variable parametrizations. Additionally, we allow for a parametrizeable cutoff of the pair factors and for the addition of a long-range phonon tail. This approach results in many-body wavefunctions that have between just one and three variational parameters. Calculation of observables is carried with the variational Monte Carlo method. We find that such a simple parametrization is sufficient to produce results that are comparable in quality to the best available two-body factors for helium. For the two-parameter wavefunction, we find variational energies of −6.04 K per particle for a system of one thousand particles. It is also shown that short-range two-body correlations are reproduced in good detail by the two- and three-parameter functions.
Regenerating time series from ordinal networks
Authors: McCullough Michael , Sakellariou Konstantinos , Stemler Thomas , Small Michael
Published: March 2017

Recently proposed ordinal networks not only afford novel methods of nonlinear time series analysis but also constitute stochastic approximations of the deterministic flow time series from which the network models are constructed. In this paper, we construct ordinal networks from discrete sampled continuous chaotic time series and then regenerate new time series by taking random walks on the ordinal network. We then investigate the extent to which the dynamics of the original time series are encoded in the ordinal networks and retained through the process of regenerating new time series by using several distinct quantitative approaches. First, we use recurrence quantification analysis on traditional recurrence plots and order recurrence plots to compare the temporal structure of the original time series with random walk surrogate time series. Second, we estimate the largest Lyapunov exponent from the original time series and investigate the extent to which this invariant measure can be estimated from the surrogate time series. Finally, estimates of correlation dimension are computed to compare the topological properties of the original and surrogate time series dynamics. Our findings show that ordinal networks constructed from univariate time series data constitute stochastic models which approximate important dynamical properties of the original systems.
Observation of the Korteweg-de Vries soliton in molecular dynamics simulations of a dusty plasma medium
Authors: Kumar Sandeep , Tiwari Sanat Kumar , Das Amita
Published: March 2017

The excitation and evolution of Korteweg-de Vries (KdV) solitons in a dusty plasma medium are studied using Molecular Dynamics (MD) simulations. The dusty plasma medium is modelled as a collection of dust particles interacting through Yukawa potential, which takes into account dust charge screening due to the lighter electron and ion species. The collective response of such screened dust particles to an applied electric field impulse is studied here. An excitation of a perturbed positive density pulse propagating in one direction along with a train of negative perturbed rarefactive density oscillations in the opposite direction is observed. These observations are in accordance with evolution governed by the KdV equation. Detailed studies of (a) amplitude vs. width variation of the observed pulse, (b) the emergence of intact separate pulses with an associated phase shift after collisional interaction amidst them, etc., conclusively qualify the positive pulses observed in the simulations as KdV solitons. It is also observed that by increasing the strength of the electric field impulse, multiple solitonic structures get excited. The excitations of the multiple solitons are similar to the experimental observations reported recently by Boruah et al. [Phys. Plasmas 23, 093704 (2016)] for dusty plasmas. The role of coupling parameter has also been investigated here, which shows that with increasing coupling parameter, the amplitude of the solitonic pulse increases whereas its width decreases.
Design and application of a novel high precision and low cost electronic tachogenerator for sensor-based brushless direct current motor drivers
Authors: Ozgenel Mehmet Cihat , Bal Gungor , Uygun Durmus
Published: March 2017

This study presents a precise speed control method for Brushless Direct Current (BLDC) Motors using an electronic tachogenerator (ETg) instead of an electro-mechanical tachogenerator. Most commonly used three-phase BLDC motors have three position sensors for rotor position data to provide commutation among stator windings. Aforementioned position sensors are usually Hall-effect sensors delivering binary-high and binary-low data as long as the motor rotates. These binary sets from three Hall-effect sensors can be used as an analogue rotor speed signal for closed loop applications. Each position sensor signal is apart from 120 electrical degrees. By using an electronic circuitry, a combination of position sensor signals is converted to the analogue signal providing an input to a PI speed controller. To implement this, a frequency to voltage converter has been used in this study. Then, the analogue speed signal has been evaluated as rotor speed data in comparison with the reference speed. So, an ETg system has been successfully achieved in place of an electro-mechanical tachogenerator for BLDC motor speed control. The proposed ETg has been tested under various speed conditions on an experimental setup. Employed tests and obtained results show that the proposed low-cost speed feedback sub-system can be effectively used in BLDC motor drive systems. Through the proved method and designed sub-system, a new motor controller chip with a speed feedback capability has been aimed.
Piezoelectrically and triboelectrically hybridized self-powered sensor with applications to smart window and human motion detection
Authors: Fuh Yiin-Kuen , Li Shan-Chien , Chen Chun-Yu
Published: March 2017

In this paper, we demonstrate a hybrid generator, derived from the concurrent adoption of piezoelectric and triboelectric mechanisms in one press-and-release cycle, called a Hybridized Self-Powered sensor (HSPS). A new integration of print circuit board (PCB) technology-based piezoelectric generator (PG) concurrently adopted the direct-write, near-field electrospun polyvinylidene fluoride (PVDF) nano/micro-fibers as piezoelectric source materials. On the other hand, triboelectric nanogenerators have the advantages of a high output performance with a simple structure which is also concurrently combined with the PG. The working mechanism of the HSPS includes the PCB-based substrate mounted with parallel aligned piezoelectric PVDF fibers in planar configuration which first bended and generated the electric potential via the effect of piezoelectricity. In what follows, the deformation of a cylindrical rolled-up piezoelectric structure is exercised, and finally, the triboelectric contact of Cu and PTFE layers is physically rubbed against each other with a separation to induce the triboelectric potential. This hybridized generator with a double domed shape design simultaneously combines piezoelectric output and triboelectric output and offers a built-in spacer with automatically spring back capability, which produces a peak output voltage of 100 V, a current of 4 μA, and a maximum power output of 450 nW. A self-powered smart window system was experimentally driven through finger-induced strain of HSPS, showing the optical properties with reversibly tunable transmittances. This research is a substantial advancement in the field of piezoelectric PVDF fibers integration toward the practical application of the whole self-powered system.
Elucidating the DEP phenomena using a volumetric polarization approach with consideration of the electric double layer
Authors: Zhao Yu , Brcka Jozef , Faguet Jacques , Zhang Guigen
Published: March 2017

Dielectrophoretic (DEP) phenomena have been explored to great success for various applications like particle sorting and separation. To elucidate the underlying mechanism and quantify the DEP force experienced by particles, the point-dipole and Maxwell Stress Tensor (MST) methods are commonly used. However, both methods exhibit their own limitations. For example, the point-dipole method is unable to fully capture the essence of particle-particle interactions and the MST method is not suitable for particles of non-homogeneous property. Moreover, both methods fare poorly when it comes to explaining DEP phenomena such as the dependence of crossover frequency on medium conductivity. To address these limitations, the authors have developed a new method, termed volumetric-integration method, with the aid of computational implementation, to reexamine the DEP phenomena, elucidate the governing mechanism, and quantify the DEP force. The effect of an electric double layer (EDL) on particles' crossover behavior is dealt with through consideration of the EDL structure along with surface ionic/molecular adsorption, unlike in other methods, where the EDL is accounted for through simply assigning a surface conductance value to the particles. For validation, by comparing with literature experimental data, the authors show that the new method can quantify the DEP force on not only homogeneous particles but also non-homogeneous ones, and predict particle-particle interactions fairly accurately. Moreover, the authors also show that the predicted dependence of crossover frequency on medium conductivity and particle size agrees very well with experimental measurements.
Superamphiphobic miniature boat fabricated by laser micromachining
Authors: Yin Kai , Dong Xinran , Zhang Fan , Wang Cong , Duan Ji'an
Published: March 2017

We fabricated a superamphiphobic miniature boat with marked drag reduction and excellent loading capacity using femtosecond laser direct writing technology. The as-prepared superamphiphobic surface of the boat exhibited apparent contact angles larger than 150° toward both water and oil. Miniature boats with the superamphiphobic surface slid effortlessly on both water and oil-polluted water surfaces, with an increase in sliding distance by up to 52% and load increase of up to 27% compared with those of a boat with an untreated surface. A potential mechanism that explains the excellent performance of the superamphiphobic miniature boat was also discussed. This work provides a simple and economically viable strategy to obtain advanced surfaces for use in microfluidics and marine engineering.
Circuit simulation and physical implementation for a memristor-based colpitts oscillator
Authors: Deng Hongmin , Wang Dongping
Published: March 2017

This paper implements two kinds of memristor-based colpitts oscillators, namely, the circuit where the memristor is added into the feedback network of the oscillator in parallel and series, respectively. First, a MULTISIM simulation circuit for the memristive colpitts oscillator is built, where an emulator constructed by some off-the-shelf components is utilized to replace the memristor. Then the physical system is implemented in terms of the MULTISIM simulation circuit. Circuit simulation and experimental study show that this memristive colpitts oscillator can exhibit periodic, quasi-periodic, and chaotic behaviors with certain parameter’s variances. Besides, in a sense, the circuit is robust with circuit parameters and device types.
Concentric artificial impedance surface for directional sound beamforming
Authors: Song Kyungjun , Anzan-Uz-Zaman Md. , Kwak Jun-Hyuk , Jung Joo-Yun , Kim Jedo , Hur Shin
Published: March 2017

Utilizing acoustic metasurfaces consisting of subwavelength resonant textures, we design an artificial impedance surface by creating a new boundary condition. We demonstrate a circular artificial impedance surface with surface impedance modulation for directional sound beamforming in three-dimensional space. This artificial impedance surface is implemented by revolving two-dimensional Helmholtz resonators with varying internal coiled path. Physically, the textured surface has inductive surface impedance on its inner circular patterns and capacitive surface impedance on its outer circular patterns. Directional receive beamforming can be achieved using an omnidirectional microphone located at the focal point formed by the gradient-impeding surface. In addition, the uniaxial surface impedance patterning inside the circular aperture can be used for steering the direction of the main lobe of the radiation pattern.
Tropical seaweed beds as important habitats for juvenile fish
Authors: Tano S. A. , Eggertsen M. , Wikström S. A. , Berkström C. , Buriyo A. S. , Halling C.
Published: March 2017

Seaweed beds within tropical seascapes have received little attention as potential fish habitat, despite other vegetated habitats, such as seagrass meadows and mangroves, commonly being recognised as important nurseries for numerous fish species. In addition, studies of vegetated habitats rarely investigate fish assemblages across different macrophyte communities. Therefore, the aim of the present study was to investigate the role of tropical seaweed beds as fish habitat, particularly for juvenile fish, by comparing their fish assemblages with those of closely situated seagrass beds. Fish assemblages were assessed by visual census in belt transects, where fish were identified and their length estimated, and habitat variables were estimated for each transect. The abundance of juvenile fish in seaweed beds was twice as high as that in seagrass meadows, whereas there was no difference in total, subadult or adult fish abundance. In addition, the abundance of commercially important and coral reef-associated juveniles was higher in seaweed beds, as was fish species richness. Fish assemblages differed between habitats, with siganids being more common in seagrass meadows and juvenile Labridae and Serranidae more common in seaweed beds. These results highlight that tropical seaweed beds are important juvenile fish habitats and underscore the need to widen the view of the shallow tropical seascape.
Life history aspects of carp (Pisces : Cyprinidae) in a dam lake ecosystem: current status and future needs
Authors: Ablak Gurbuz Ozlem
Published: March 2017

An increase in aquaculture production may have positive effects on both food resources and a country’s economy. Carp (Cyprinus carpio L.) is the most common cyprinid species in Turkey and accounts for approximately one-fifth of total inland water aquaculture production. However, carp production in Turkey has decreased in recent years. Changes in carp population of Hirfanli Dam were compared with previous studies in similar and different habitats worldwide. The population structure, growth and reproduction of carp were investigated. The length–weight relationships for the carp population of Hirfanli Dam indicated negative allometric growth in males and females, but the condition factor was greater for these carp than carp elsewhere. Asymptotic length and the growth coefficient were 89.42cm and 0.071year–1. Fecundity was positively correlated with fork length, total weight, gonad weight and age. The carp population of Hirfanli Dam evaluated in the present study appeared to have a lower fecundity and smaller egg diameter compared with other carp populations.
Experimental comparison of two quantum computing architectures
Authors: Linke Norbert M. , Maslov Dmitri , Roetteler Martin , Debnath Shantanu , Figgatt Caroline , Landsman Kevin A. , Wright Kenneth , Monroe Christopher
Published: March 2017

Significance

Quantum computers are an emerging technology promising to be vastly more powerful at solving certain problems than any conventional computer. These devices are now moving out of the laboratory and becoming generally programmable. This allows identical quantum tasks or algorithms to be implemented on radically different technologies to inform further development and scaling. We run a series of algorithms on the two leading platforms: trapped atomic ions and superconducting circuits. Whereas the superconducting system offers faster gate clock speeds and a solid-state platform, the ion-trap system features superior qubits and reconfigurable connections. The performance of these systems is seen to reflect the topology of connections in the base hardware, supporting the idea that quantum computer applications and hardware should be codesigned.
Comprehensive and quantitative mapping of RNA–protein interactions across a transcribed eukaryotic genome
Authors: She Richard , Chakravarty Anupam K. , Layton Curtis J. , Chircus Lauren M. , Andreasson Johan O. L. , Damaraju Nandita , McMahon Peter L. , Buenrostro Jason D. , Jarosz Daniel F. , Greenleaf William J.
Published: March 2017

Significance

High-throughput sequencing has transformed modern biology, but its repertoire is currently confined to reading DNA molecules. Here, we report hardware and software adaptations that allow the very methods that enabled the genomic sequencing revolution to be applied to fluorescence-based biochemical assays, on a massive scale. We demonstrate the unique value of this approach by finding previously unknown features of an ancient developmental regulator, Vts1 (Smaug in metazoans), despite its extensive study with previously available techniques. Our work couples transcriptome-wide measurements of binding affinity, sequence, and structural determinants of binding, and phenotypic outcomes to provide a comprehensive portrait of Vts1 function. Our technology is easily extensible to other RNA-binding proteins involved in disease and development, and facilitates diverse applications in systems biochemistry.
CRISPR-Cas9–guided oncogenic chromosomal translocations with conditional fusion protein expression in human mesenchymal cells
Authors: Vanoli Fabio , Tomishima Mark , Feng Weiran , Lamribet Khadija , Babin Loelia , Brunet Erika , Jasin Maria
Published: March 2017

Significance

Fusion genes resulting from recurrent chromosomal translocations are associated with several tumor types. Cell lines carrying translocations represent important models to study the oncogenic properties of fusion proteins and develop therapeutic strategies. The desmoplastic small round cell tumor is a rare sarcoma characterized by translocation between the
EWSR1
and
WT1
genes, resulting in expression of the
EWSR1–WT1
fusion. A paucity of isogenic cell lines expressing the fusion protein has hindered our understanding of mechanisms associated with tumor development. Here we develop a strategy using CRISPR-Cas9 genome editing to select cells harboring the
EWSR1–WT1
translocation with conditional fusion protein expression. This system provides a flexible tool that can be adapted to any translocation or rearrangement in cell lines.
Ab initio solution of macromolecular crystal structures without direct methods
Authors: McCoy Airlie J. , Oeffner Robert D. , Wrobel Antoni G. , Ojala Juha R. M. , Tryggvason Karl , Lohkamp Bernhard , Read Randy J.
Published: March 2017

Significance

It is now possible to make an accurate prediction of whether or not a molecular replacement solution of a macromolecular crystal structure will succeed, given the quality of the model, its size, and the resolution of the diffraction data. This understanding allows the development of powerful structure-solution strategies, and leads to the unexpected finding that, with data to sufficiently high resolution, fragments as small as single atoms can be placed as the basis for ab initio structure solutions.
Bull Trout Movements Match the Life History of Sockeye Salmon: Consumers Can Exploit Seasonally Distinct Resource Pulses
Authors: Furey N. B. , Hinch S. G.
Published: March 2017

Resource pulses provide consumers with opportunities to feed at high rates. The spawning and die‐off of semelparous Pacific salmon provide consumers with feeding opportunities that contribute substantially to annual energy budgets. The life history of Pacific salmon also includes the downstream migration of smolts, which could provide similar opportunities for consumers to exploit. We tracked seasonal movements of adult Bull Trout Salvelinus confluentus in and out of the Chilko Lake–River outlet in interior British Columbia, which is characterized by a large Sockeye Salmon Oncorhynchus nerka population. Use of the outlet, lake, and river habitats were compared with the timing of out‐migrations of Sockeye Salmon smolt and the spawning events of Sockeye Salmon, Chinook Salmon O. tshawytscha, and Coho Salmon O. kisutch. Bull Trout activity and residency in the outlet increased during the spring Sockeye Salmon smolt out‐migration, and 40% of Bull Trout were found to return to the outlet in successive years. During Sockeye Salmon spawning, Bull Trout residency was increased in the river where most Sockeye Salmon spawning occurs. Therefore, Bull Trout may exploit both life history events, although direct consumption of eggs was not observed. Spawning by Chinook Salmon and Coho Salmon in the river did not appear to attract Bull Trout; Bull Trout residency increased in the lake (where spawning does not occur) during these times. Bull Trout residency in the lake also increased when outlet water temperatures were >16°C, and thus the lake may provide thermal refuge when river temperatures are above optima for this coldwater char. This research demonstrates that movements of aquatic consumers can depend upon smolt out‐migrations, and such movements can allow exploitation of multiple pulses that are seasonally distinct. These results also highlight the ecological significance of Pacific salmon for consumers in freshwater systems.

Received August 18, 2016; accepted January 11, 2017 Published online March 21, 2017
Spanish version of the Objectified Body Consciousness Scale (OBCS): results from two samples of female university students / Versión española de la Objectified Body Consciousness Scale (OBCS): resultados correspondientes a dos muestras de estudiantes universitarias
Authors: Moya-Garófano Alba , Megías Jesús L. , Rodríguez-Bailón Rosa , Moya Miguel
Published: March 2017

Self-objectification happens when people internalize a view of themselves as an object or collection of body parts. Two studies were conducted to validate the Spanish version of the Objectified Body Consciousness Scale (OBCS). This scale assesses self-objectification through three components: body surveillance, body shame and appearance control beliefs in women. In Study 1 and Study 2, 218 and 201 female undergraduate students, respectively, responded to the Spanish version of this scale and other related measures. In Study 2, they also reported on their emotions after being exposed to an objectifying scenario. The three subscales of the Spanish version of the OBCS showed acceptable indices of internal consistency (ranging between α = .68 to .84), and the confirmatory factor analysis showed a three-factor solution to be the most appropriate. Adequate convergent validity was found with respect to the Self-Objectification Questionnaire (SOQ) and other variables such as self-esteem, other-directedness, hostile sexism and enjoyment of sexualization. These findings suggest that the Spanish version of the OBCS is a satisfactory measure of college women’s self-objectification.
3D technology of Sony Bloggie has no advantage in decision‐making of tennis serve direction: A randomized placebo‐controlled study
Authors: Liu Sicong , Ritchie Jason , Sáenz‐Moncaleano Camilo , Ward Savanna K. , Paulsen Cody , Klein Tyler , Gutierrez Oscar , Tenenbaum Gershon
Published: March 2017

This study aimed at exploring whether 3D technology enhances tennis decision‐making under the conceptual framework of human performance model. A 3 (skill‐level: varsity, club, recreational) × 3 (experimental condition: placebo, weak 3D [W3D], strong 3D [S3D]) between‐participant design was used. Allocated to experimental conditions by a skill‐level stratified randomization, 105 tennis players judged tennis serve direction from video scenarios and rated their perceptions of enjoyment, flow, and presence during task performance. Results showed that varsity players made more accurate decisions than less skilled ones. Additionally, applying 3D technology to typical video displays reduced tennis players’ decision‐making accuracy, although wearing the 3D glasses led to a placebo effect that shortened the decision‐making reaction time. The unexpected negative effect of 3D technology on decision‐making was possibly due to participants being more familiar to W3D than to S3D, and relatedly, a suboptimal task‐technology match. Future directions for advancing this area of research are offered.

Highlights

3D technology augments binocular depth cues to tradition video displays, and thus results in the attainment of more authentic visual representation. This process enhances task fidelity in researching perceptual‐cognitive skills in sports.

The paper clarified both conceptual and methodological difficulties in testing 3D technology in sports settings. Namely, the nomenclature of video footage (with/without 3D technology) and the possible placebo effect (arising from wearing glasses of 3D technology) merit researchers' attention.

Participants varying in level of domain‐specific expertise were randomized into viewing conditions using a placebo‐controlled design. Measurement consisted of both participants' subjective experience (i.e., presence, flow, and enjoyment) and objective performance (i.e., accuracy and reaction time) in a decision‐making task.

Findings revealed that wearing glasses of 3D technology resulted in a placebo effect that shortened participants' reaction times in decision‐making. Moreover, participants' decision‐making accuracy decreased when viewing video scenarios using 3D technology. The findings generated meaningful implications regarding applying 3D technology to sports research.
Peripersonal versus extrapersonal visual scene information for egocentric direction and position perception
Authors: Nakashima Ryoichi , Kumada Takatsune
Published: March 2017

When perceiving the visual environment, people simultaneously perceive their own direction and position in the environment (i.e., egocentric spatial perception). This study investigated what visual information in a scene is necessary for egocentric spatial perceptions. In two perception tasks (the egocentric direction and position perception tasks), observers viewed two static road images presented sequentially. In Experiment 1, the critical manipulation involved an occluded region in the road image, an extrapersonal region (far-occlusion) and a peripersonal region (near-occlusion). Egocentric direction perception was worse in the far-occlusion condition than in the no-occlusion condition, and egocentric position perceptions were worse in the far- and near-occlusion conditions than in the no-occlusion condition. In Experiment 2, we conducted the same tasks manipulating the observers’ gaze location in a scene—an extrapersonal region (far-gaze), a peripersonal region (near-gaze) and the intermediate region between the former two (middle-gaze). Egocentric direction perception performance was the best in the far-gaze condition, and egocentric position perception performances were not different among gaze location conditions. These results suggest that egocentric direction perception is based on fine visual information about the extrapersonal region in a road landscape, and egocentric position perception is based on information about the entire visual scene.
Item-method directed forgetting and working memory capacity: A hierarchical multinomial modeling approach
Authors: Marevic Ivan , Arnold Nina R , Rummel Jan
Published: March 2017

Intentional forgetting of information that has recently been encoded is regarded an active and adaptive process and is widely studied using the item-method or the list-method directed forgetting (DF) paradigm. In the present research, we tested whether inter-individual differences in working-memory capacity (WMC), that have been identified as a relevant predictor of DF within the list method, are also related to stronger DF effects within the item method. Furthermore, we investigated relationships between WMC and item-method DF at different processing stages by applying the multinomial storage–retrieval model hierarchically to our data. Results showed that individuals with high WMC are better able to store to-be-remembered information than individuals with low WMC, whereas WMC was not related to retrieval of to-be-remembered information or to either storage or retrieval of to-be-forgotten information. Implications for theoretical accounts of item-method DF are discussed.
Autonomous TNF is critical for in vivo monocyte survival in steady state and inflammation
Authors: Wolf Yochai , Shemer Anat , Polonsky Michal , Gross Mor , Mildner Alexander , Yona Simon , David Eyal , Kim Ki-Wook , Goldmann Tobias , Amit Ido , Heikenwalder Mathias , Nedospasov Sergei , Prinz Marco , Friedman Nir , Jung Steffen
Published: March 2017

Monocytes are circulating mononuclear phagocytes, poised to extravasate to sites of inflammation and differentiate into monocyte-derived macrophages and dendritic cells. Tumor necrosis factor (TNF) and its receptors are up-regulated during monopoiesis and expressed by circulating monocytes, as well as effector monocytes infiltrating certain sites of inflammation, such as the spinal cord, during experimental autoimmune encephalomyelitis (EAE). In this study, using competitive in vitro and in vivo assays, we show that monocytes deficient for TNF or TNF receptors are outcompeted by their wild-type counterpart. Moreover, monocyte-autonomous TNF is critical for the function of these cells, as TNF ablation in monocytes/macrophages, but not in microglia, delayed the onset of EAE in challenged animals and was associated with reduced acute spinal cord infiltration of Ly6Chi effector monocytes. Collectively, our data reveal a previously unappreciated critical cell-autonomous role of TNF on monocytes for their survival, maintenance, and function.
Asymptotic behavior of positively curved steady Ricci solitons
Authors: Deng Yuxing , Zhu Xiaohua
Published: March 2017

In this paper, we analyze the asymptotic behavior of

κ
\kappa

-noncollapsed and positively curved steady Ricci solitons and prove that any

n
n

-dimensional

κ
\kappa

-noncollapsed steady Kähler–Ricci soliton with nonnegative sectional curvature must be flat.
Invited Commentary: Selection Bias Without Colliders
Authors: Hernán Miguel A.
Published: March 2017

In causal analyses, conditioning on a collider generally results in selection bias. Conditioning on a prognostic factor that is independent of the exposure—and therefore is not a collider—can also result in selection bias when 1) the exposure has a non-null effect on the outcome and 2) the association between the noncollider and the outcome is heterogenous across levels of the exposure. This result was empirically demonstrated by Greenland in 1977 (Am J Epidemiol. 1977;106(3):184–187).
biMM: efficient estimation of genetic variances and covariances for cohorts with high-dimensional phenotype measurements
Authors: Pirinen Matti , Benner Christian , Marttinen Pekka , Järvelin Marjo-Riitta , Rivas Manuel A , Ripatti Samuli
Published: March 2017

Genetic research utilizes a decomposition of trait variances and covariances into genetic and environmental parts. Our software package biMM is a computationally efficient implementation of a bivariate linear mixed model for settings where hundreds of traits have been measured on partially overlapping sets of individuals.

Availability and Implementation

Implementation in R freely available at www.iki.fi/mpirinen.

Supplementary information

Supplementary data are available at Bioinformatics online.
The bio-economic effects of artificial reefs: mixed evidence from Shandong, China
Authors: Sun Peng , Liu Xiaozi , Tang Yanli , Cheng Wenzhi , Sun Runlong , Wang Xinxin , Wan Rong , Heino Mikko
Published: March 2017

Artificial reefs are used to protect coastal habitats and rebuild fisheries. This engineering approach to fisheries management has gained popularity in many coastal areas, including China. In Shandong province alone, over USD 50 million were invested in artificial reefs during 2005–2013. Have artificial reefs achieved their biological and economic objectives? We compared reef and control sites in terms of catch and value per unit effort and average body length across species, based on surveys carried out during 2012–2013. We found that in aggregate, with all fish and invertebrates combined, artificial reefs did not improve the overall catches or revenues. Instead, seasonal fluctuations were prominent. However, when we allow for species-specific differences and focus on the common fish species, we find that an artificial reef can increase the catch and value per unit effort on average by approximately 40% compared to the control sites. The difference between these contrasting results occurs because some of the dominant species that comprise the bulk of the catches did not benefit from the reef, while many of the less dominant ones did so. This underlines the importance of being specific about what is meant by “benefiting fisheries” when evaluating artificial reefs, as well as when the objectives of reef projects are formulated in the first place. The positive effects of artificial reefs can be caused by the reefs themselves and by their influence on fishing patterns. Our study was not designed to separate these effects but we suggest that in Shandong, restrictions on fishing access may have been as important as the presence of the reef itself.