bluuebunny/crossref_metadata_2025 huggingface dataset:
Energy‐efficient transmission for decode‐and‐forward dual‐hop networks with asymmetric traffic demands
Authors: Li Chunguo , Wang Jue , Sun Fan , Cioffi John M. , Zheng Fu‐Chun , Yang Luxi
Published: August 2015

Two‐way relaying systems efficiently accomplish transmissions in both directions within dual‐hop, hence, two time slots can be saved compared with one‐way relaying. However, the conventional two‐way relaying protocol requires the assumption of symmetric traffic demands, that is, each transmitter node has to act as a receiver in latter slot. This assumption restricts applying two‐way relay to general and practical scenarios. In this study, the authors release this unpractical constraint by assuming that the transmitter in slot 1 and receiver in slot 2 can be any nodes, which are not necessarily being the same. For this scenario, a novel transmission protocol exploiting the overhearing link to suppress the interference caused by asymmetric traffic, denoted as overhearing transmission, is proposed. With the overhearing transmission protocol, and in the light of green communications, the precoding matrices at the decode‐and‐forward multi‐antenna relay are optimised to improve energy efficiency in both uplink and downlink (DL) transmission directions, where the objective is to minimise the transmit power at the relay while guaranteeing a target transmission rate. The authors transform the original non‐convex problem to an equivalent form, which can be readily solved by typical semi‐definite relaxation approaches. An efficient algorithm is further proposed to implement the precoding design in practice. Simulation results show that the proposed algorithm is able to minimise the power consumption at the relay, with the minimum rate constraints of both the uplink and DL transmissions being satisfied.
Classification of two‐degree‐of‐freedom underactuated mechanical systems
Authors: Maalouf Divine , Moog Claude H. , Aoustin Yannick , Li Shunjie
Published: August 2015

A new classification for two‐degree‐of‐freedom mechanical systems is introduced, based on structural control properties. The largest feedback linearisable subsystem with internal stability is considered for such systems. The classification is depending on the closed‐loop system that can be achieved under the constraint of internal stability. It is shown that the generalised conjugate momenta corresponding to each degree of freedom play a crucial role for the considered mechanical systems.
Constrained adaptive tracking and command shaped vibration control of flexible hypersonic vehicles
Authors: Su Xiaofeng , Jia Yingmin
Published: August 2015

This study presents a new approach, which integrates the input shaping technique and the constrained adaptive backstepping control method, for constrained adaptive tracking and elastic vibration control of flexible hypersonic vehicles. Specifically, the input shaper as a feedforward part is implemented outside the feedback loop, which can achieve vibration suppression for flexible dynamics; whereas for the feedback loop, the vehicle model is decomposed into functional subsystems, and the decentralised approach is used. Then, by introducing the command filter and the auxiliary system, constrained adaptive control law is formulated to make the closed‐loop system follow the shaped reference trajectory and attenuate the elastic vibration in the presence of parameter uncertainties, external disturbances and input saturation constraints. An attractive feature of this proposed control algorithm is that all signals of closed‐loop system are uniformly ultimately bounded and the tracking error converges to a residual set which can be made sufficiently small by properly designing control parameters. Moreover, by applying the shaped commands, flexible dynamics with less elastic deformation and vibration can be achieved without destroying the closed‐loop performance. Simulation results are provided to verify the effectiveness of the proposed control method.
State‐constrained robust stabilisation for a class of high‐order switched non‐linear systems
Authors: Niu Ben , Xiang Zhengrong
Published: August 2015

This study deals with the problem of robust stabilisation for a class of state‐constrained high‐order uncertain switched non‐linear systems in lower triangular form. Bounded state‐feedback controllers are designed to assure that asymptotic stabilisation is achieved in a domain without violation of the state constraint, and all closed‐loop signals are bounded, when an appropriate requirement on the initial condition is imposed. Simulation results are provided to show the efficiency of the developed method.
ℒ2 neuro‐adaptive tracking control of uncertain port‐controlled Hamiltonian systems
Authors: Qureshi Aminuddin , El Ferik Sami , Lewis Frank L.
Published: August 2015

This study presents a practical method of neural network (NN) adaptive tracking control of uncertain port‐controlled Hamiltonian (PCH) systems. NN is used to compensate for parametric uncertainties and unlike the previous studies, the dynamics of the NN tuning law is driven by both the position as well as the velocity errors owing to the introduction of the information preserving filtering of the Hamiltonian gradient. In addition, the proposed controller achieves the ℒ2 disturbance attenuation objectives as well as preserves the PCH structure of the system in closed loop. Simulation examples demonstrate the efficacy of the proposed approach.
An analytical evaluation of the quality factor QZ for dominant spherical modes
Authors: Jelinek Lukas , Capek Miloslav , Hazdra Pavel , Eichler Jan
Published: August 2015

This study describes an analytical evaluation of the quality factor QZ in a separable system in which the vector potential is known. The proposed method uses a potential definition of active and reactive power, implicitly avoiding infinite entire space integration and extraction of radiation energy. As a result, all the used quantities are finite, and the calculated QZ is always non‐negative function of frequency. The theory is presented on the canonical example of the currents flowing on a spherical shell. The QZ for the dominant spherical transverse magnetic and transverse electric modes and their linear combination are found in closed forms, including both internal and external energies. The proposed analytical method and its results are compared with previously published limits of the quality factor Q.
Unidirectional bowtie array antenna with incision gap for digital video broadcasting‐T2 base station
Authors: Luadang Bancha , Phongcharoenpanich Chuwong
Published: August 2015

This study presents a unidirectional bowtie array antenna with incision gap for a digital video broadcasting‐T2 base station application. The antenna element consists of a bowtie radiator with incision gap on top of a square reflector. The element achieves a bandwidth of 82.35% for |S11| of <−10 dB, covering a frequency range of 450–1080 MHz. The antenna array comprises of four identical antenna elements mounted vertically to form an antenna array. The simulated and measured results of the antenna array show a good impedance matching for |S11| of <−10 dB along a frequency range of 450–1014 MHz (77.05%). The measured gains are 13.4–16.1 dBi along an operating frequency of 470–862 MHz with the narrow half‐power beamwidth in the vertical plane of ∼15° ± 5° and the half‐power beamwidth in the horizontal plane of ∼60° ± 5° for a frequency range of 470–666 MHz and 90.5° for 862 MHz. The radiation pattern is degraded at the frequency higher than 950 MHz.
Continuous wave Cs diode pumped alkali laser pumped by single emitter narrowband laser diode
Authors: Zhdanov B. V. , Venus G. , Smirnov V. , Glebov L. , Knize R. J.
Published: August 2015

This paper presents results of cooperative efforts on development of a continuous wave Cs diode pumped alkali laser with moderate output power, which can be considered as a prototype of the commercial device. The developed system operates at 895 nm with output power about 4 W and slope efficiency 28%. Measured turn on time of this system from the standby mode is about a minute.
Structural stability, vibrational, and bonding properties of potassium 1, 1′-dinitroamino-5, 5′-bistetrazolate: An emerging green primary explosive
Authors: Yedukondalu N. , Vaitheeswaran G.
Published: August 2015

Potassium 1,1′-dinitroamino-5,5′-bistetrazolate (K2DNABT) is a nitrogen rich (50.3% by weight, K2C2N12O4) green primary explosive with high performance characteristics, namely, velocity of detonation (D = 8.33 km/s), detonation pressure (P = 31.7 GPa), and fast initiating power to replace existing toxic primaries. In the present work, we report density functional theory (DFT) calculations on structural, equation of state, vibrational spectra, electronic structure, and absorption spectra of K2DNABT. We have discussed the influence of weak dispersive interactions on structural and vibrational properties through the DFT-D2 method. We find anisotropic compressibility behavior (b<a<c) from pressure dependent structural properties. The predicted equilibrium bulk modulus reveals that K2DNABT is softer than toxic lead azide and harder than the most sensitive cyanuric triazide. A complete assignment of all the vibrational modes has been made and compared with the available experimental results. The calculated zone center IR and Raman frequencies show a blue-shift which leads to a hardening of the lattice upon compression. In addition, we have also calculated the electronic structure and absorption spectra using recently developed Tran Blaha-modified Becke Johnson potential. It is found that K2DNABT is a direct band gap insulator with a band gap of 3.87 eV and the top of the valence band is mainly dominated by 2p-states of oxygen and nitrogen atoms. K2DNABT exhibits mixed ionic (between potassium and tetrazolate ions) and covalent character within tetrazolate molecule. The presence of ionic bonding suggests that the investigated compound is relatively stable and insensitive than covalent primaries. From the calculated absorption spectra, the material is found to decompose under ultra-violet light irradiation.
Thermodynamic precursors, liquid-liquid transitions, dynamic and topological anomalies in densified liquid germania
Authors: Pacaud F. , Micoulaut M.
Published: August 2015

The thermodynamic, dynamic, structural, and rigidity properties of densified liquid germania (GeO2) have been investigated using classical molecular dynamics simulation. We construct from a thermodynamic framework an analytical equation of state for the liquid allowing the possible detection of thermodynamic precursors (extrema of the derivatives of the free energy), which usually indicate the possibility of a liquid-liquid transition. It is found that for the present germania system, such precursors and the possible underlying liquid-liquid transition are hidden by the slowing down of the dynamics with decreasing temperature. In this respect, germania behaves quite differently when compared to parent tetrahedral systems such as silica or water. We then detect a diffusivity anomaly (a maximum of diffusion with changing density/volume) that is strongly correlated with changes in coordinated species, and the softening of bond-bending (BB) topological constraints that decrease the liquid rigidity and enhance transport. The diffusivity anomaly is finally substantiated from a Rosenfeld-type scaling law linked to the pair correlation entropy, and to structural relaxation.
Design and application of permanent magnet flux sources for mechanical testing of magnetoactive elastomers at variable field directions
Authors: Hiptmair F. , Major Z. , Haßlacher R. , Hild S.
Published: August 2015

Magnetoactive elastomers (MAEs) are a class of smart materials whose mechanical properties can be rapidly and reversibly changed by an external magnetic field. Due to this tunability, they are useable for actuators or in active vibration control applications. An extensive magnetomechanical characterization is necessary for MAE material development and requires experiments under cyclic loading in uniform but variable magnetic fields. MAE testing apparatus typically rely on fields of adjustable strength, but fixed (transverse) direction, often provided by electromagnets. In this work, two permanent magnet flux sources were developed as an add-on for a modular test stand, to allow for mechanical testing in uniform fields of variable direction. MAE specimens, based on a silicone matrix with isotropic and anisotropic carbonyl iron particle distributions, were subjected to dynamic mechanical analysis under different field and loading configurations. The magneto-induced increase of stiffness and energy dissipation was determined by the change of the hysteresis loop area and dynamic modulus values. A distinct influence of the composite microstructure and the loading state was observed. Due to the very soft and flexible matrix used for preparing the MAE samples, the material stiffness and damping behavior could be varied over a wide range via the applied field direction and intensity.
Homogeneous SPC/E water nucleation in large molecular dynamics simulations
Authors: Angélil Raymond , Diemand Jürg , Tanaka Kyoko K. , Tanaka Hidekazu
Published: August 2015

We perform direct large molecular dynamics simulations of homogeneous SPC/E water nucleation, using up to ∼ 4 ⋅ 106 molecules. Our large system sizes allow us to measure extremely low and accurate nucleation rates, down to ∼ 1019 cm−3 s−1, helping close the gap between experimentally measured rates ∼ 1017 cm−3 s−1. We are also able to precisely measure size distributions, sticking efficiencies, cluster temperatures, and cluster internal densities. We introduce a new functional form to implement the Yasuoka-Matsumoto nucleation rate measurement technique (threshold method). Comparison to nucleation models shows that classical nucleation theory over-estimates nucleation rates by a few orders of magnitude. The semi-phenomenological nucleation model does better, under-predicting rates by at worst a factor of 24. Unlike what has been observed in Lennard-Jones simulations, post-critical clusters have temperatures consistent with the run average temperature. Also, we observe that post-critical clusters have densities very slightly higher, ∼ 5%, than bulk liquid. We re-calibrate a Hale-type J vs. S scaling relation using both experimental and simulation data, finding remarkable consistency in over 30 orders of magnitude in the nucleation rate range and 180 K in the temperature range.
Interactions between water and 1-butyl-1-methylpyrrolidinium ionic liquids
Authors: Fadeeva Tatiana A. , Husson Pascale , DeVine Jessalyn A. , Costa Gomes Margarida F. , Greenbaum Steven G. , Castner Edward W.
Published: August 2015

We report experimental results on the diffusivity of water in two ionic liquids obtained using the pulsed-gradient spin-echo NMR method. Both ionic liquids have the same cation, 1-butyl-1-methylpyrrolidinium, but different trifluoromethyl-containing anions. One has a strongly hydrophobic anion, bis(trifluoromethylsulfonyl)amide, while the second has a hydrophilic anion, trifluoromethylsulfonate. Transport of water in these ionic liquids is much faster than would be predicted from hydrodynamic laws, indicating that the neutral water molecules experience a very different friction than the anions and cations at the molecular level. Temperature-dependent viscosities, conductivities, and densities are reported as a function of water concentration to further analyze the properties of the ionic liquid-water mixtures. These results on the properties of water in ionic liquids should be of interest to researchers in diverse areas ranging from separations, solubilizing biomass and energy technologies.
Acoustic travel time gauges for in-situ determination of pressure and temperature in multi-anvil apparatus
Authors: Wang Xuebing , Chen Ting , Qi Xintong , Zou Yongtao , Kung Jennifer , Yu Tony , Wang Yanbin , Liebermann Robert C. , Li Baosheng
Published: August 2015

In this study, we developed a new method for in-situ pressure determination in multi-anvil, high-pressure apparatus using an acoustic travel time approach within the framework of acoustoelasticity. The ultrasonic travel times of polycrystalline Al2O3 were calibrated against NaCl pressure scale up to 15 GPa and 900 °C in a Kawai-type double-stage multi-anvil apparatus in conjunction with synchrotron X-radiation, thereby providing a convenient and reliable gauge for pressure determination at ambient and high temperatures. The pressures derived from this new travel time method are in excellent agreement with those from the fixed-point methods. Application of this new pressure gauge in an offline experiment revealed a remarkable agreement of the densities of coesite with those from the previous single crystal compression studies under hydrostatic conditions, thus providing strong validation for the current travel time pressure scale. The travel time approach not only can be used for continuous in-situ pressure determination at room temperature, high temperatures, during compression and decompression, but also bears a unique capability that none of the previous scales can deliver, i.e., simultaneous pressure and temperature determination with a high accuracy (±0.16 GPa in pressure and ±17 °C in temperature). Therefore, the new in-situ Al2O3 pressure gauge is expected to enable new and expanded opportunities for offline laboratory studies of solid and liquid materials under high pressure and high temperature in multi-anvil apparatus.
An improved model to estimate trapping parameters in polymeric materials and its application on normal and aged low-density polyethylenes
Authors: Liu Ning , He Miao , Alghamdi Hisham , Chen George , Fu Mingli , Li Ruihai , Hou Shuai
Published: August 2015

Trapping parameters can be considered as one of the important attributes to describe polymeric materials. In the present paper, a more accurate charge dynamics model has been developed, which takes account of charge dynamics in both volts-on and off stage into simulation. By fitting with measured charge data with the highest R-square value, trapping parameters together with injection barrier of both normal and aged low-density polyethylene samples were estimated using the improved model. The results show that, after long-term ageing process, the injection barriers of both electrons and holes is lowered, overall trap depth is shallower, and trap density becomes much greater. Additionally, the changes in parameters for electrons are more sensitive than those of holes after ageing.
On Yangian covariance of the triple product system with the rational R-matrix
Authors: Jia Xiao-Yu , Yao Shao-Kui , Wu Ke , Zhao Wei-Zhong
Published: August 2015

The triple product system associated with a rational R-matrix is investigated. We prove that there is the Yangian covariant structure for this triple product system. We present a 3-coalgebraic of the Yangian Y(sl2) associated with the triple system. Moreover, we discuss a 3-Hopf algebraic structure of the Yangian Y(sl2).
Study of resistive switching and magnetism modulation in the Pt/CoFe2O4/Nb:SrTiO3 heterostructures
Authors: Wang Qiangwen , Zhu Yongdan , Liu Xiaolian , Zhao Meng , Wei Maocai , Zhang Feng , Zhang Yuan , Sun Beilei , Li Meiya
Published: August 2015

CoFe2O4 (CFO) thin films are epitaxially grown on Nb doped (001) SrTiO3 (NSTO) single-crystal substrates by pulsed laser deposition to form Pt/CFO/NSTO heterostructures. These heterostructures exhibit typical bipolar resistive switching effect with maximum switching ratio of 5 × 104, multi-level resistance states, excellent retention, and anti-fatigue properties. When the resistance states of the heterostructures are switched between low resistance state and high resistance state upon applying bias voltages, the saturation magnetization of the CFO films shows corresponding changes associated with the resistive switching. These close correlations between the resistive switching and the magnetization can be attributed to the electrons filling into and releasing from the defect energy levels introduced by oxygen vacancies in the CFO film. These results show potential application in the multi-functional magnetoelectric sensor and non-volatile multi-level resistive switching memory.
Passive and active plasma deceleration for the compact disposal of electron beams
Authors: Bonatto A. , Schroeder C. B. , Vay J.-L. , Geddes C. G. R. , Benedetti C. , Esarey E. , Leemans W. P.
Published: August 2015

Plasma-based decelerating schemes are investigated as compact alternatives for the disposal of high-energy beams (beam dumps). Analytical solutions for the energy loss of electron beams propagating in passive and active (laser-driven) schemes are derived. These solutions, along with numerical modeling, are used to investigate the evolution of the electron distribution, including energy chirp and total beam energy. In the active beam dump scheme, a laser-driver allows a more homogeneous beam energy extraction and drastically reduces the energy chirp observed in the passive scheme. These concepts could benefit applications requiring overall compactness, such as transportable light sources, or facilities operating at high beam power.
Real-time observation of phonon-polariton dynamics in ferroelectric LiNbO3 in time-frequency space
Authors: Ikegaya Yuki , Sakaibara Hiroyuki , Minami Yasuo , Katayama Ikufumi , Takeda Jun
Published: August 2015

We demonstrate the real-time observation of phonon-polariton propagation in ferroelectric LiNbO3 using a single-shot spectroscopic setup that employs an echelon mirror. The echelon mirror provides a spatially encoded time delay for the probe pulse; therefore, the ultrafast transient behavior of materials can be detected on a single-shot basis. Using optical Kerr gate apparatus, forward and backward propagating E-mode phonon-polaritons were simultaneously induced via an impulsive stimulated Raman scattering process, and subsequently, their dynamics were readily mapped in time-frequency space using heterodyne detection. The two phonon-polaritons appeared on opposite sides of the central probe wavelength and were symmetrically imaged against the ordinary and extraordinary probe lights. By taking into account coupling of the lowest E-mode phonon-polariton to a low-frequency relaxational mode, not only the phonon-polariton dispersion but also the wavevector dependence of the damping rate was unveiled and quantitatively evaluated.
Locomotion of chemically powered autonomous nanowire motors
Authors: Wang Lin , Li Longqiu , Li Tianlong , Zhang Guangyu , Sun Qian
Published: August 2015

Physical insights on the hydrodynamics and locomotion of self-propelled nanowire motor under nonequilibrium steady state are investigated using finite element method in accordance with hybrid molecular dynamics/multiparticle collision dynamics and rigid body dynamics. Nanowire motor is discretized into finite segments, and forces of solvent molecule acting on the motor are assumed to be the sum of forces acting on all segments of the motor. We show that the locomotion of nanowire motor is mainly determined by the imbalance forces acting on the catalytic and noncatalytic segments. The average velocity along the axis increases significantly as a function of time prior to reaching equilibrium. The length of nanowire motor shows negligible effect on the velocity of the motor. Preliminary experimental results are provided to validate the current model.
Winter grazing can reduce wildfire size, intensity and behaviour in a shrub-grassland
Authors: Davies Kirk W. , Boyd Chad S. , Bates Jon D. , Hulet April
Published: August 2015

An increase in mega-fires and wildfires is a global issue that is expected to become worse with climate change. Fuel treatments are often recommended to moderate behaviour and decrease severity of wildfires; however, the extensive nature of rangelands limits the use of many treatments. Dormant-season grazing has been suggested as a rangeland fuel treatment, but its effects on fire characteristics are generally unknown. We investigated the influence of dormant-season (winter) grazing by cattle (Bos taurus) on fuel characteristics, fire behaviour and area burned in Wyoming big sagebrush (Artemisia tridentata subsp. wyomingensis) shrub-grassland communities in south-eastern Oregon, USA. Winter grazing was applied for 5 years before burning and compared with ungrazed areas. Winter grazing decreased fine fuels and increased fine fuel moisture, which reduced flame height and depth, rate of spread and area burned. Winter-grazed areas also had lower maximum temperature and heat loading during fires than ungrazed areas, and thereby decreased risk of fire-induced mortality of important herbaceous functional groups. These results suggest that winter grazing may be a fuel management treatment that can be applied across vast shrub-grasslands to decrease wildfire risk and fire intensity to mediate climate change effects on wildfire activity.
Results of a large-scale randomized behavior change intervention on road safety in Kenya
Authors: Habyarimana James , Jack William
Published: August 2015

Significance

Road accidents kill 1.3 million people each year, most in the developing world. Evocative messages inside Kenyan matatus, or mini-buses, that promote passenger agency and legitimize complaints against dangerous driving are found to reduce average maximum speeds and average moving speeds by 1–2 km/h and insurance claims by between one-quarter and one-third. The cost-effectiveness of the most impactful stickers is between $10 and $45 per disability-adjusted life-year saved.
Antibodies targeting human IL1RAP (IL1R3) show therapeutic effects in xenograft models of acute myeloid leukemia
Authors: Ågerstam Helena , Karlsson Christine , Hansen Nils , Sandén Carl , Askmyr Maria , von Palffy Sofia , Högberg Carl , Rissler Marianne , Wunderlich Mark , Juliusson Gunnar , Richter Johan , Sjöström Kjell , Bhatia Ravi , Mulloy James C. , Järås Marcus , Fioretos Thoas
Published: August 2015

Significance

Acute myeloid leukemia (AML) is a hematologic malignancy with poor survival. Current treatment with chemotherapy does not target the leukemic cells specifically and is associated with severe side effects. Here we demonstrate that antibodies directed at the cell surface molecule IL-1 receptor accessory protein (IL1RAP), expressed on immature AML cells, show strong antileukemic effects in mice transplanted with human AML cells and that the mechanism behind the cell killing is through recruitment of effector cells. Using antibodies against IL1RAP also capable of blocking IL-1 signaling, we show that the proliferation of human AML cells can be inhibited, providing a second mode of action of IL1RAP antibodies. These results provide critical evidence in support of a rapid clinical development of an antibody-based anti-IL1RAP therapy in AML.
Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data
Authors: Yang Laurence , Tan Justin , O’Brien Edward J. , Monk Jonathan M. , Kim Donghyuk , Li Howard J. , Charusanti Pep , Ebrahim Ali , Lloyd Colton J. , Yurkovich James T. , Du Bin , Dräger Andreas , Thomas Alex , Sun Yuekai , Saunders Michael A. , Palsson Bernhard O.
Published: August 2015

Significance

Defining a core functional proteome supporting the living process has importance for both developing fundamental understanding of cell functions and for synthetic biology applications. Comparative genomics has been the primary approach to achieve such a definition. Here, we use genome-scale models to define a core proteome that computationally supports basic cellular function. This core proteome for metabolism and protein expression, defined through systems biology methods, is validated and characterized by using multiple disparate data types.
Quantifying the impact of weak, strong, and super ties in scientific careers
Authors: Petersen Alexander Michael
Published: August 2015

Significance

A scientist will encounter many potential collaborators throughout his/her career. As such, the choice to start or terminate a collaboration can be an important strategic consideration with long-term implications. While previous studies have focused primarily on aggregate cross-sectional collaboration patterns, here we analyze the collaboration network from a researcher’s local perspective along his/her career. Our longitudinal approach reveals that scientific collaboration is characterized by a high turnover rate juxtaposed with surprisingly frequent “life partners.” We show that these extremely strong collaborations have a significant positive impact on productivity and citations—the apostle effect—representing the advantage of “super” social ties characterized by trust, conviction, and commitment.
The amino acid sensor GCN2 inhibits inflammatory responses to apoptotic cells promoting tolerance and suppressing systemic autoimmunity
Authors: Ravishankar Buvana , Liu Haiyun , Shinde Rahul , Chaudhary Kapil , Xiao Wei , Bradley Jillian , Koritzinsky Marianne , Madaio Michael P. , McGaha Tracy L.
Published: August 2015

Significance

Metabolic stress potently modifies immunity. Recently our laboratory identified the stress kinase GCN2 as a key modulator of macrophage responses to toll-like receptor ligands; however, the role of myeloid GCN2 signals in sterile inflammation and homeostatic tolerance is not known. In this study, we tested the requirement of GCN2 for tolerance to apoptotic cells and prevention of autoimmunity in a model of lupus. Our results show that GCN2 in myeloid cells is a critical effector of apoptotic cell-driven tolerance required for regulatory cytokine production and prevention of inflammatory immunity. Moreover, the data indicate that targeting GCN2 is an effective approach to preventing autoimmunity, providing a rationale for developing tools to manipulate GCN2 function in inflammatory immune disease.
Continuous evolutionary change in Plio-Pleistocene mammals of eastern Africa
Authors: Bibi Faysal , Kiessling Wolfgang
Published: August 2015

Significance

Many have argued that major developments in mammalian (including human) evolution were timed with large and sudden changes to Earth’s climate. Our new analyses of the eastern African Plio-Pleistocene mammalian fossil record indicate that most species originations and extinctions took place continuously and gradually. This means that evolution was not clustered in short intervals, nor were sudden global climatic changes the main cause of species extinction in the past. Global climate may have influenced longer-term (million year) evolutionary trends, but local environmental changes and species interactions were more important at shorter (100,000 y) time scales.
Adaptive aneuploidy protects against thiol peroxidase deficiency by increasing respiration via key mitochondrial proteins
Authors: Kaya Alaattin , Gerashchenko Maxim V. , Seim Inge , Labarre Jean , Toledano Michel B. , Gladyshev Vadim N.
Published: August 2015

Significance

Aneuploidy, a condition of abnormal chromosomal content, can support adaptive mechanisms in response to environmental cues but comes at the expense of decreased proliferation and dysfunction of cellular processes. Here we show that the gain of an extra copy of chromosome XI in yeast is an adaptive mechanism to deal with oxidative stress under conditions of antioxidant deficiency. We narrowed down the effect of adaptive aneuploidy to two genes on chromosome XI, which supported increased mitochondrial abundance and respiration, which in turn provided reducing equivalents for hydroperoxide removal. Forced expression of these genes eliminated aneuploidy, improved cell growth, and was sufficient for protection against oxidative stress. Thus, aneuploidy can adaptively reprogram cellular metabolism, protecting against oxidative stress by upregulating respiration.
Geometry and mechanics of two-dimensional defects in amorphous materials
Authors: Moshe Michael , Levin Ido , Aharoni Hillel , Kupferman Raz , Sharon Eran
Published: August 2015

Significance

Modeling defects, or localized strain carriers, are a central challenge in the formulation of elasto-plastic theory of amorphous solids. Whereas in crystalline solids defects are identified as local deviations from the crystal order, it is not clear how, or even if, equivalent intrinsic entities can be defined in amorphous solids. This work presents a new way of defining and describing localized intrinsic geometrical defects in amorphous solids and for computing the stresses within defected bodies. The methods and results that are presented here can be integrated into phenomenological theories of plasticity and can be applied to biomechanical problems that involve strain localization.
Thermophilization of adult and juvenile tree communities in the northern tropical Andes
Authors: Duque Alvaro , Stevenson Pablo R. , Feeley Kenneth J.
Published: August 2015

Significance

Understanding how species respond to climate change is crucial to the development of effective conservation strategies. We found directional and systematic changes in the composition of both adult and juvenile tree species in tropical north Andean forests at rates consistent with concurrent temperature increases, supporting the hypothesis of upward species migrations resulting from global warming. Our results indicate that compositional shifts occur primarily via range retractions. This suggests elevated risk for species extinctions and local biodiversity loss with ongoing warming. Other environmental filters, such as species-soil adaptations, as well as anthropogenic disturbances (e.g., habitat loss and hunting) may limit future species migrations and decrease the ability of forest communities and their constituent species to respond to climate change.
Single methylation of 23S rRNA triggers late steps of 50S ribosomal subunit assembly
Authors: Arai Taiga , Ishiguro Kensuke , Kimura Satoshi , Sakaguchi Yuriko , Suzuki Takeo , Suzuki Tsutomu
Published: August 2015

Significance

Ribosome biogenesis requires a number of assembly factors. However, the exact mechanism of this process remains largely unknown. We could successfully reconstitute the 50S subunit from the 45S precursor by a 2′-
O
-methylation of U2552 (Um2552) mediated by rRNA methyltransferase RlmE, in the presence of the wash fraction from crude ribosomes. To our knowledge, this experiment is the first demonstration of enzymatic formation of a ribosomal subunit in vitro from its precursor via the action of an assembly factor. Mechanistic studies revealed that RlmE-mediated Um2552 formation promotes interdomain interactions of 23S rRNA, in concert with the incorporation of L36, triggering late steps of 50S subunit assembly. RlmE and Um2552 are conserved in other organisms, including human, indicating the functional importance of this process in ribosome biogenesis.
Comanaging fresh produce for nature conservation and food safety
Authors: Karp Daniel S. , Gennet Sasha , Kilonzo Christopher , Partyka Melissa , Chaumont Nicolas , Atwill Edward R. , Kremen Claire
Published: August 2015

Significance

Fresh produce has become the primary cause of foodborne illness in the United States. A widespread concern that wildlife vector foodborne pathogens onto fresh produce fields has led to strong pressure on farmers to clear noncrop vegetation surrounding their farm fields. We combined three large datasets to demonstrate that pathogen prevalence in fresh produce is rapidly increasing, that pathogens are more common on farms closer to land suitable for livestock grazing, and that vegetation clearing is associated with increased pathogen prevalence over time. These findings contradict widespread food safety reforms that champion vegetation clearing as a pathogen mitigation strategy. More generally, our work indicates that achieving food safety and nature conservation goals in produce-growing landscapes is possible.
Disease-associated mutation in
SRSF2
misregulates splicing by altering RNA-binding affinities
Authors: Zhang Jian , Lieu Yen K. , Ali Abdullah M. , Penson Alex , Reggio Kathryn S. , Rabadan Raul , Raza Azra , Mukherjee Siddhartha , Manley James L.
Published: August 2015

Significance

Mutations in genes encoding proteins that function in splicing of mRNA precursors occur frequently in myelodysplastic syndromes (MDS) and certain leukemias. However, the mechanism by which the mutated splicing factors function has begun to be elucidated only recently. Here we use genome-editing techniques to introduce a common MDS mutation in the gene Serine/arginine-rich splicing factor 2 (
SRSF2
), which encodes an RNA-binding splicing regulator, in cultured blood cells. We show that splicing of several hundred transcripts, including some with possible relevance to disease, is altered. We further show that mutant SRSF2 is sufficient to induce these changes and does so by binding to RNA sequence elements in the misregulated mRNAs with altered specificity.
Stationary States and Modulational Instability of Coupled Two-Component Bose–Einstein Condensates in a Ring Trap*
Authors: Deng Hai-Ming , Zhong Hong-Hua , Huang Jia-Hao , Dai Hui , Yao Min , Huang Xiao-Yi
Published: August 2015

We investigate modulational instability (MI) of a coupled two-component Bose–Einstein condensates in a rotating ring trap. The excitation spectrum and the MI condition of the system are presented analytically. We find that the coupling between the two components strongly modifies the MI condition, and the MI condition is phase-dependent. Furthermore, we discuss the effect of MI on both density excitation and spin excitation. If the inter- and intra-component interaction strengths are all equal, the MI causes density excitation but not spin excitation, and if the inter- and intra-component interaction strengths are different, the MI causes both density excitation and spin excitation. Our results provide a promising approach for controlling the stability and excitation of a rotating two-component Bose–Einstein condensates by modulating its coupling strength and interaction strength.
The Effect of Spin-Orbit Coupling and Spin-Spin Coupling of Compact Binaries on Chaos*
Authors: Wang Hong , Huang Guo-Qing
Published: August 2015

There are spin-orbit interaction and spin-spin interaction in a generic post-Newtonian Lagrangian formulation of comparable mass spinning compact binaries. The spin-orbit coupling or the spin-spin coupling plays a quite important role in changing the evolution of the system and may sometime cause chaotic behavior. How do the two types of couplings exert together any influences on chaos in this formulation? To answer it, we simply take the Lagrangian formulation of a special binary system, including the Newtonian term and the leading-order spin-orbit and spin-spin couplings. The key to this question can be found from a Hamiltonian formulation that is completely identical to the Lagrangian formulation. If the Lagrangian does not include the spin-spin coupling, its equivalent Hamiltonian has an additional term (i.e. the next-order spin-spin coupling) as well as those terms of the Lagrangian. The spin-spin coupling rather than the spin-orbit coupling makes the Hamiltonian typically nonintegrable and probably chaotic when two objects spin. When the leading-order spin-spin coupling is also added to the Lagrangian, it still appears in the Hamiltonian. In this sense, the total Hamiltonian contains the leading-order spin-spin coupling and the next-order spin-spin coupling, which have different signs. Therefore, the chaos resulting from the spin-spin interaction in the Legrangian formulations is somewhat weakened by the spin-orbit coupling.
Critical Behaviors and Universality Classes of Percolation Phase Transitions on Two-Dimensional Square Lattice*
Authors: Zhu Yong , Yang Zi-Qing , Zhang Xin , Chen Xiao-Song
Published: August 2015

We have investigated both site and bond percolation on two-dimensional lattice under the random rule and the product rule respectively. With the random rule, sites or bonds are added randomly into the lattice. From two candidates picked randomly, the site or bond with the smaller size product of two connected clusters is added when the product rule is taken. Not only the size of the largest cluster but also its size jump are studied to characterize the universality class of percolation. The finite-size scaling forms of giant cluster size and size jump are proposed and used to determine the critical exponents of percolation from Monte Carlo data. It is found that the critical exponents of both size and size jump in random site percolation are equal to that in random bond percolation. With the random rule, site and bond percolation belong to the same universality class. We obtain the critical exponents of the site percolation under the product rule, which are different from that of both random percolation and the bond percolation under the product rule. The universality class of site percolation differs different from that of bond percolation when the product rule is used.
Vizardous: interactive analysis of microbial populations with single cell resolution
Authors: Helfrich Stefan , Azzouzi Charaf E. , Probst Christopher , Seiffarth Johannes , Grünberger Alexander , Wiechert Wolfgang , Kohlheyer Dietrich , Nöh Katharina
Published: August 2015

Motivation: Single cell time-lapse microscopy is a powerful method for investigating heterogeneous cell behavior. Advances in microfluidic lab-on-a-chip technologies and live-cell imaging render the parallel observation of the development of individual cells in hundreds of populations possible. While image analysis tools are available for cell detection and tracking, biologists are still confronted with the challenge of exploring and evaluating this data.

Results: We present the software tool Vizardous that assists scientists with explorative analysis and interpretation tasks of single cell data in an interactive, configurable and visual way. With Vizardous, lineage tree drawings can be augmented with various, time-resolved cellular characteristics. Associated statistical moments bridge the gap between single cell and the population-average level.

Availability and implementation: The software, including documentation and examples, is available as executable Java archive as well as in source form at https://github.com/modsim/vizardous.

Contact:  k.noeh@fz-juelich.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Neuropathic Allodynia Involves Spinal Neurexin-1β-dependent Neuroligin-1/Postsynaptic Density-95/NR2B Cascade in Rats
Authors: Lin Tzer-Bin , Lai Cheng-Yuan , Hsieh Ming-Chun , Jiang Jian-Lin , Cheng Jen-Kun , Chau Yat-Pang , Ruan Ting , Chen Gin-Den , Peng Hsien-Yu
Published: August 2015

AbstractAbstract

It was shown that the association of N-methyl-d-aspartate receptor NR2B subunits and postsynaptic density-95 scaffolding protein was enhanced in spinal cord dorsal horn neurons after nerve ligation in rats. The disruption of neurexin-1β–neuroligin-1 interaction reduced allodynia and NR2B–postsynaptic density-95 interactions in nerveligated rats.

Background:

Neuroligin-1 (NL1) forms a complex with the presynaptic neurexin-1β (Nrx1b), regulating clustering of N-methyl-d-aspartate receptors with postsynaptic density-95 (PSD-95) to underlie learning-/memory-associated plasticity. Pain-related spinal neuroplasticity shares several common features with learning-/memory-associated plasticity. The authors thereby investigated the potential involvement of NL1-related mechanism in spinal nerve ligation (SNL)–associated allodynia.

Methods:

In 626 adult male Sprague–Dawley rats, the withdrawal threshold and NL1, PSD-95, phosphorylated NR2B (pNR2B) expressions, interactions, and locations in dorsal horn (L4 to L5) were compared between the sham operation and SNL groups. A recombinant Nrx1b Fc chimera (Nrx1b Fc, 10 μg, 10 μl, i.t., bolus), antisense small-interfering RNA targeting to NL1 (10 μg, 10 μl, i.t., daily for 4 days), or NR2B antagonist (Ro 25-6981; 1 μM, 10 μl, i.t., bolus) were administered to SNL animals to elucidate possible cascades involved.

Results:

SNL-induced allodynia failed to affect NL1 or PSD-95 expression. However, pNR2B expression (mean ± SD from 13.1 ± 2.87 to 23.1 ± 2.52, n = 6) and coexpression of NL1–PSD-95, pNR2B–PSD-95, and NL1-total NR2B were enhanced by SNL (from 10.7 ± 2.27 to 22.2 ± 3.94, 11.5 ± 2.15 to 23.8 ± 3.32, and 8.9 ± 1.83 to 14.9 ± 2.27 at day 7, n = 6). Furthermore, neuron-localized pNR2B PSD-95–pNR2B double-labeled and NL1/PSD-95/pNR2B triple-labeled immunofluorescence in the ipsilateral dorsal horn was all prevented by Nrx1b Fc and NL1-targeted small-interfering RNA designed to block and prevent NL1 expression. Without affecting NL1–PSD-95 coupling, Ro 25-6981 decreased the SNL-induced PSD-95–pNR2B coprecipitation (from 18.7 ± 1.80 to 14.7 ± 2.36 at day 7, n = 6).

Conclusion:

SNL-induced allodynia, which is mediated by the spinal NL1/PSD-95/pNR2B cascade, can be prevented by blockade of transsynaptic Nrx1b–NL1 interactions.
‘Bigger data’ on scale-dependent effects of invasive species on biodiversity cannot overcome confounded analyses: a comment on Stohlgren & Rejmánek (2014)
Authors: Chase Jonathan M. , Powell Kristin I. , Knight Tiffany M.
Published: August 2015

A recent study by Stohlgren & Rejmánek (SR: Stohlgren TJ, Rejmánek M. 2014
Biol. Lett.
10. (
doi:10.1098/rsbl.2013.0939
)) purported to test the generality of a recent finding of scale-dependent effects of invasive plants on native diversity; dominant invasive plants decreased the intercept and increased the slope of the species–area relationship. SR (2014) find little correlation between invasive species cover and the slopes and intercepts of SARs across a diversity of sites. We show that the analyses of SR (2014) are inappropriate because of confounding causality.
Anion homeostasis is important for non-lytic release of BK polyomavirus from infected cells
Authors: Evans Gareth L. , Caller Laura G. , Foster Victoria , Crump Colin M.
Published: August 2015

BK polyomavirus (BKPyV) is a member of a family of potentially oncogenic viruses, whose reactivation can cause severe pathological conditions in transplant patients, leading to graft rejection. As with many non-enveloped viruses, it is assumed that virus release occurs through lysis of the host cell. We now show the first evidence for a non-lytic release pathway for BKPyV and that this pathway can be blocked by the anion channel inhibitor DIDS. Our data show a dose-dependent effect of DIDS on the release of BKPyV virions. We also observed an accumulation of viral capsids in large LAMP-1-positive acidic organelles within the cytoplasm of cells upon DIDS treatment, suggesting potential late endosome or lysosome-related compartments are involved in non-lytic BKPyV release. These data highlight a novel mechanism by which polyomaviruses can be released from infected cells in an active and non-lytic manner, and that anion homeostasis regulation is important in this pathway.
Regularity of free boundaries a heuristic retro
Authors: Caffarelli Luis A. , Shahgholian Henrik
Published: August 2015

This survey concerns regularity theory of a few free boundary problems that have been developed in the past half a century. Our intention is to bring up different ideas and techniques that constitute the fundamentals of the theory. We shall discuss four different problems, where approaches are somewhat different in each case. Nevertheless, these problems can be divided into two groups: (i) obstacle and thin obstacle problem; (ii) minimal surfaces, and cavitation flow of a perfect fluid. In each case, we shall only discuss the methodology and approaches, giving basic ideas and tools that have been specifically designed and tailored for that particular problem. The survey is kept at a heuristic level with mainly geometric interpretation of the techniques and situations in hand.