bluuebunny/crossref_metadata_2025 huggingface dataset:
Study of the operating parameters of a helicon plasma discharge source using PIC-MCC simulation technique
Authors: Jaafarian Rokhsare , Ganjovi Alireza , Etaati Gholamreza
Published: January 2018

In this work, a Particle in Cell-Monte Carlo Collision simulation technique is used to study the operating parameters of a typical helicon plasma source. These parameters mainly include the gas pressure, externally applied static magnetic field, the length and radius of the helicon antenna, and the frequency and voltage amplitude of the applied RF power on the helicon antenna. It is shown that, while the strong radial gradient of the formed plasma density in the proximity of the plasma surface is substantially proportional to the energy absorption from the existing Trivelpiece-Gould (TG) modes, the observed high electron temperature in the helicon source at lower static magnetic fields is significant evidence for the energy absorption from the helicon modes. Furthermore, it is found that, at higher gas pressures, both the plasma electron density and temperature are reduced. Besides, it is shown that, at higher static magnetic fields, owing to the enhancement of the energy absorption by the plasma charged species, the plasma electron density is linearly increased. Moreover, it is seen that, at the higher spatial dimensions of the antenna, both the plasma electron density and temperature are reduced. Additionally, while, for the applied frequencies of 13.56 MHz and 27.12 MHz on the helicon antenna, the TG modes appear, for the applied frequency of 18.12 MHz on the helicon antenna, the existence of helicon modes is proved. Moreover, by increasing the applied voltage amplitude on the antenna, the generation of mono-energetic electrons is more probable.
The detrimental effect of spontaneous emission in quantum free electron lasers: A discrete Wigner model
Authors: Fares H. , Piovella N. , Robb G. R. M.
Published: January 2018

We study the spontaneous emission in high-gain free-electron lasers operating in the quantum regime and its detrimental effect on coherent emission. A quantum model describing the coherent and spontaneous emission in free electron lasers has been recently proposed and investigated [G. R. M. Robb and R. Bonifacio, Phys. Plasmas 19, 073101 (2012)]. The model is based on a Wigner distribution describing the electron beam dynamics, coupled to Maxwell equations for the emitted radiation field. Here, we rephrase the model in a more rigorous way, considering a discrete Wigner distribution defined for a periodic space coordinate for which the electron momentum is discrete. From its numerical solution, we find good agreement with the approximate continuous model. In the quantum regime of the free-electron laser, we obtain a simple density matrix equation for two momentum states, where the role of the spontaneous emission has a clear interpretation in terms of coherence decay and population transfer.
Material-based figure of merit for caloric materials
Authors: Griffith L. D. , Mudryk Y. , Slaughter J. , Pecharsky V. K.
Published: January 2018

The efficient use of reversible thermal effects in magnetocaloric, electrocaloric, and elastocaloric materials is a promising avenue that can lead to a substantially increased efficiency of refrigeration and heat pumping devices, most importantly, those used in household and commercial cooling applications near ambient temperature. A proliferation in caloric material research has resulted in a wide array of materials where only the isothermal change in entropy in response to a handful of different field strengths over a limited range of temperatures has been evaluated and reported. Given the abundance of such data, there is a clear need for a simple and reliable figure of merit enabling fast screening and down-selection to justify further detailed characterization of those material systems that hold the greatest promise. Based on the analysis of several well-known materials that exhibit vastly different magnetocaloric effects, the Temperature averaged Entropy Change is introduced as a suitable early indicator of the material's utility for magnetocaloric cooling applications, and its adoption by the caloric community is recommended.
Seeded growth of boron arsenide single crystals with high thermal conductivity
Authors: Tian Fei , Song Bai , Lv Bing , Sun Jingying , Huyan Shuyuan , Wu Qi , Mao Jun , Ni Yizhou , Ding Zhiwei , Huberman Samuel , Liu Te-Huan , Chen Gang , Chen Shuo , Chu Ching-Wu , Ren Zhifeng
Published: January 2018

Materials with high thermal conductivities are crucial to effectively cooling high-power-density electronic and optoelectronic devices. Recently, zinc-blende boron arsenide (BAs) has been predicted to have a very high thermal conductivity of over 2000 W m−1 K−1 at room temperature by first-principles calculations, rendering it a close competitor for diamond which holds the highest thermal conductivity among bulk materials. Experimental demonstration, however, has proved extremely challenging, especially in the preparation of large high quality single crystals. Although BAs crystals have been previously grown by chemical vapor transport (CVT), the growth process relies on spontaneous nucleation and results in small crystals with multiple grains and various defects. Here, we report a controllable CVT synthesis of large single BAs crystals (400–600 μm) by using carefully selected tiny BAs single crystals as seeds. We have obtained BAs single crystals with a thermal conductivity of 351 ± 21 W m−1 K−1 at room temperature, which is almost twice as conductive as previously reported BAs crystals. Further improvement along this direction is very likely.
High-performance gap-closing vibrational energy harvesting using electret-polarized dielectric oscillators
Authors: Feng Yue , Yu Zejie , Han Yanhui
Published: January 2018

In conventional gap-closing electret-biased electrostatic energy harvesting (EEEH) schemes, electrets with a very low ratio of electret thickness to permittivity are in great demand to allow the attainment of high power output. However, in practice, pursuing such a low ratio introduces unwanted burdens on the electret stability and therefore the reliability of the EEEH devices. In this paper, we propose a dielectric-oscillator-based electrostatic EH (DEEH) scheme as an alternative approach to harvesting electret-biased electrostatic energy. This approach permits the fabrication of an electret-free closed EH circuit. The DEEH architecture directly collects the electrical energy exclusively through the oscillating dielectric body and thus completely circumvents the restrictions imposed by the electret parameters (thickness and permittivity) on power generation. Significantly, without considering the electret thickness and permittivity, both theoretical analysis and experiments have verified the effectiveness of this DEEH strategy, and a high figure of merit (on the order of 10−8 mW cm−2 V−2 Hz−1) was achieved for low-frequency movements.
A droplet-based passive force sensor for remote tactile sensing applications
Authors: Nie Baoqing , Yao Ting , Zhang Yiqiu , Liu Jian , Chen Xinjian
Published: January 2018

A droplet-based flexible wireless force sensor has been developed for remote tactile-sensing applications. By integration of a droplet-based capacitive sensing unit and two circular planar coils, this inductor-capacitor (LC) passive sensor offers a platform for the mechanical force detection in a wireless transmitting mode. Under external loads, the membrane surface of the sensor deforms the underlying elastic droplet uniformly, introducing a capacitance response in tens of picofarads. The LC circuit transduces the applied force into corresponding variations of its resonance frequency, which is detected by an external electromagnetic coupling coil. Specifically, the liquid droplet features a mechanosensitive plasticity, which results in an increased device sensitivity as high as 2.72 MHz N−1. The high dielectric property of the droplet endows our sensor with high tolerance for noise and large capacitance values (20–40 pF), the highest value in the literature for the LC passive devices in comparable dimensions. It achieves excellent reproducibility under periodical loads ranging from 0 to 1.56 N and temperature fluctuations ranging from 10 °C to 55 °C. As an interesting conceptual demonstration, the flexible device has been configured into a fingertip-amounted setting in a highly compact package (of 11 mm × 11 mm × 0.25 mm) for remote contact force sensing in the table tennis game.
Spatially resolved single crystal x-ray spectropolarimetry of wire array z-pinch plasmas
Authors: Wallace M. S. , Haque S. , Neill P. , Pereira N. R. , Presura R.
Published: January 2018

A recently developed single-crystal x-ray spectropolarimeter has been used to record paired sets of polarization-dependent and axially resolved x-ray spectra emitted by wire array z-pinches. In this measurement, two internal planes inside a suitable crystal diffract the x-rays into two perpendicular directions that are normal to each other, thereby separating incident x-rays into their linearly polarized components. This paper gives considerations for fielding the instrument on extended sources. Results from extended sources are difficult to interpret because generally the incident x-rays are not separated properly by the crystal. This difficulty is mitigated by using a series of collimating slits to select incident x-rays that propagate in a plane of symmetry between the polarization-splitting planes. The resulting instrument and some of the spatially resolved polarized x-ray spectra recorded for a 1-MA aluminum wire array z-pinch at the Nevada Terawatt Facility at the University of Nevada, Reno will be presented.
Manipulation of electron transport in graphene by nanopatterned electrostatic potential on an electret
Authors: Wang Xiaowei , Wang Rui , Wang Shengnan , Zhang Dongdong , Jiang Xingbin , Cheng Zhihai , Qiu Xiaohui
Published: January 2018

The electron transport characteristics of graphene can be finely tuned using local electrostatic fields. Here, we use a scanning probe technique to construct a statically charged electret gate that enables in-situ fabrication of graphene devices with precisely designed potential landscapes, including p-type and n-type unipolar graphene transistors and p-n junctions. Electron dynamic simulation suggests that electron beam collimation and focusing in graphene can be achieved via periodic charge lines and concentric charge circles. This approach to spatially manipulating carrier density distribution may offer an efficient way to investigate the novel electronic properties of graphene and other low-dimensional materials.
A low energy ion beam facility for mass spectrometer calibration: First results
Authors: Meyer Stefan , Tulej Marek , Wurz Peter
Published: January 2018

The exploration of habitable environments around the gas giants in the Solar System is of major interest in upcoming planetary missions. Exactly this theme is addressed by the Jupiter Icy Moons Explorer (JUICE) mission of the European Space Agency (ESA), which will characterise Ganymede, Europa, and Callisto as planetary objects and potential habitats. The NIM, Neutral gas and Ion Mass spectrometer, is part of the PEP experiment and will be used to measure the chemical composition of the exospheres of the icy Jovian moons. We designed and developed a calibration facility (SATANS, Supersonic cATion and ANion Source), especially for use with the NIM instrument. In a first step, we established a low energy ion beam for positive ions in the range of 0.01–30 eV. Then we conducted beam velocity calibrations with a velocity uncertainty <5%, which provided exact settings and formulas for the cation beam velocity of different gas mixtures in the range of 1–15 km/s. In addition, first results are obtained by using the NIM prototype for direct ion beam measurements under realistic JUICE mission conditions, i.e., for velocities from 1 up to 7 km/s and even more.
Nonlinear modeling of stratified shear instabilities, wave breaking, and wave-topography interactions using vortex method
Authors: Bhardwaj Divyanshu , Guha Anirban
Published: January 2018

Theoretical studies on linear shear instabilities often use simple velocity and density profiles (e.g., constant, piecewise) for obtaining good qualitative and quantitative predictions of the initial disturbances. Furthermore, such simple profiles provide a minimal model for obtaining a mechanistic understanding of otherwise elusive shear instabilities. However, except a few specific cases, the efficacy of simple profiles has remained limited to the linear stability paradigm. In this work, we have proposed a general framework that can simulate the fully nonlinear evolution of a variety of stratified shear instabilities as well as wave-wave and wave-topography interaction problems having simple piecewise constant and/or linear profiles. To this effect, we have modified the classical vortex method by extending the Birkhoff-Rott equation to multiple interfaces and, furthermore, have incorporated background shear across a density interface. The latter is more subtle and originates from the understanding that Bernoulli’s equation is not just limited to irrotational flows but can be modified to make it applicable for piecewise linear velocity profiles. We have solved diverse problems that can be essentially reduced to the multiple interacting interfaces paradigm, e.g., spilling and plunging breakers, stratified shear instabilities like Holmboe and Taylor-Caulfield, jet flows, and even wave-topography interaction problems like Bragg resonance. Free-slip boundary being a vortex sheet, its effect can also be effectively captured using vortex method. We found that the minimal models capture key nonlinear features, e.g., wave breaking features like cusp formation and roll-ups, which are observed in experiments and/or extensive simulations with smooth, realistic profiles.
Plasma CVD of hydrogenated boron-carbon thin films from triethylboron
Authors: Imam Mewlude , Höglund Carina , Schmidt Susann , Hall-Wilton Richard , Birch Jens , Pedersen Henrik
Published: January 2018

Low-temperature chemical vapor deposition (CVD) of B—C thin films is of importance for neutron voltaics and semiconductor technology. The highly reactive trialkylboranes, with alkyl groups of 1-4 carbon atoms, are a class of precursors that have been less explored for low-temperature CVD of B—C films. Herein, we demonstrate plasma CVD of B—C thin films using triethylboron (TEB) as a single source precursor in an Ar plasma. We show that the film density and B/C ratio increases with increasing plasma power, reaching a density of 2.20 g/cm3 and B/C = 1.7. This is attributed to a more intense energetic bombardment during deposition and more complete dissociation of the TEB molecule in the plasma at higher plasma power. The hydrogen content in the films ranges between 14 and 20 at. %. Optical emission spectroscopy of the plasma shows that BH, CH, C2, and H are the optically active plasma species from TEB. We suggest a plasma chemical model based on β-hydrogen elimination of C2H4 to form BH3, in which BH3 and C2H4 are then dehydrogenated to form BH and C2H2. Furthermore, C2H2 decomposes in the plasma to produce C2 and CH, which together with BH and possibly BH3−x(C2H5)x are the film forming species.
Ordered defects in Fe1−xS generate additional magnetic anisotropy symmetries
Authors: Koulialias D. , Charilaou M. , Schäublin R. , Mensing C. , Weidler P. G. , Löffler J. F. , Gehring A. U.
Published: January 2018

Non-stoichiometric monoclinic 4C pyrrhotite (Fe7S8), a ferrimagnetic monosulfide that has been intensively used as a remanence carrier to infer the magnetization of the Earth's crust and extraterrestrial materials, exhibits a characteristic low-temperature transition accompanied by complex modifications in anisotropy and magnetization. We demonstrate that the magnetic rotational symmetry of the 4C pyrrhotite is critically affected by the order of the defective Fe-sites, and this in turn is a key to decipher the physics behind the low-temperature transition. Our torque experiments and numerical simulations show an emergent four-fold rotational symmetry in the c-plane of the 4C pyrrhotite at T < 30 K. This symmetry breaking associated with the transition is caused by the competitive interaction of two inherently hexagonal systems generated by two groups of Fe-sites with different local anisotropy fields that stem from the vacancy arrangement in the 4C stacking sequence, and it is triggered by changes in the spin orbit coupling due to the overlap of Fe-Fe electron orbitals at low-temperature. This mechanism provides a new explanation for the magnetic transition in 4C pyrrhotite at low temperature and could also cast light on non-trivial magnetic phenomena in defective systems.
Elastic precursor wave decay in shock-compressed aluminum over a wide range of temperature
Authors: Austin Ryan A.
Published: January 2018

The effect of temperature on the dynamic flow behavior of aluminum is considered in the context of precursor wave decay measurements and simulations. In this regard, a dislocation-based model of high-rate metal plasticity is brought into agreement with previous measurements of evolving wave profiles at 300 to 933 K, wherein the amplification of the precursor structure with temperature arises naturally from the dislocation mechanics treatment. The model suggests that the kinetics of inelastic flow and stress relaxation are governed primarily by phonon scattering and radiative damping (sound wave emission from dislocation cores), both of which intensify with temperature. The manifestation of these drag effects is linked to low dislocation density ahead of the precursor wave and the high mobility of dislocations in the face-centered cubic lattice. Simulations performed using other typical models of shock wave plasticity do not reproduce the observed temperature-dependence of elastic/plastic wave structure.
An atomistic fingerprint algorithm for learning ab initio molecular force fields
Authors: Tang Yu-Hang , Zhang Dongkun , Karniadakis George Em
Published: January 2018

Molecular fingerprints, i.e., feature vectors describing atomistic neighborhood configurations, is an important abstraction and a key ingredient for data-driven modeling of potential energy surface and interatomic force. In this paper, we present the density-encoded canonically aligned fingerprint algorithm, which is robust and efficient, for fitting per-atom scalar and vector quantities. The fingerprint is essentially a continuous density field formed through the superimposition of smoothing kernels centered on the atoms. Rotational invariance of the fingerprint is achieved by aligning, for each fingerprint instance, the neighboring atoms onto a local canonical coordinate frame computed from a kernel minisum optimization procedure. We show that this approach is superior over principal components analysis-based methods especially when the atomistic neighborhood is sparse and/or contains symmetry. We propose that the “distance” between the density fields be measured using a volume integral of their pointwise difference. This can be efficiently computed using optimal quadrature rules, which only require discrete sampling at a small number of grid points. We also experiment on the choice of weight functions for constructing the density fields and characterize their performance for fitting interatomic potentials. The applicability of the fingerprint is demonstrated through a set of benchmark problems.
The Bloch equation with terms induced by an electric field
Authors: Garbacz Piotr
Published: January 2018

The Bloch equation of the nuclear magnetization of spin-1/2 nuclei in molecules, which have permanent electric dipole moments μe that are placed simultaneously in a magnetic field B and an electric field E, is derived. It is shown that if the principal components of the nuclear magnetic shielding tensor σ and the dipole moment μe are known, then the measurement of the transverse component to the magnetic field B of the nuclear magnetization, which is induced by the application of the electric field oscillating at the half of the spin precession frequency, allows determining the orientation of the dipole moment μe with respect to the principal axis system of the symmetric part of the tensor σ. Four-component relativistic density functional theory computations, which have been performed for several molecules containing heavy nuclei, i.e., 207Pb, 205Tl, 199Hg, 195Pt, and 125Te, indicate that coefficients of the relaxation matrix perturbed by the electric field E are in favorable cases of the order of 1000 pm2 V−2 T−2. Therefore, the spin dynamics is perturbed at experimentally observable levels for the strengths of electric and magnetic fields E = 5 kV/mm and B = 10 T, respectively.
Vertical leakage induced current degradation and relevant traps with large lattice relaxation in AlGaN/GaN heterostructures on Si
Authors: Hu Anqi , Yang Xuelin , Cheng Jianpeng , Song Chunyan , Zhang Jie , Feng Yuxia , Ji Panfeng , Xu Fujun , Zhang Yan , Yang Zhijian , Tang Ning , Ge Weikun , Wang Xinqiang , Hu Zonghai , Guo Xia , Shen Bo
Published: January 2018

We present a mechanism for the vertical leakage induced current degradation with identification of the properties of the relevant traps in AlGaN/GaN heterostructures on Si. The extent of the current degradation is determined by back-gating sweep measurements in double directions at different sweep rates and temperatures. It is found that the current degradation is only observed at relatively slow sweep rates and high temperatures. Time dependent back-gating measurements further suggest that the current degradation process is related to traps with long time constants. By comparing with the measurement results of samples on sapphire substrates, we confirm that the current degradation is caused by vertical leakage in heterostructures on Si. On the basis of the vertical leakage induced current degradation mechanism and in conjunction with the long-time degradation process, we measure both the trapping and detrapping processes of the relevant trap states to identify their properties. We find that there is a 0.6 eV capture barrier and a 0.67 eV emission barrier for the trap states, indicating that the trap states are of large lattice relaxation.
Pressure, temperature, and thickness dependence of transmittance in a 1D superconductor-semiconductor photonic crystal
Authors: Herrera Alan Y. , Calero J. M. , Porras-Montenegro N.
Published: January 2018

Using the transfer matrix method, we study the transmittance of 1D photonic crystals made of alternated layers of a semiconductor (GaAs) and a high-Tc superconductor (HgBa2Ca2Cu3O8+δ) under the effects of temperature, applied hydrostatic pressure, and thickness of the layers. The frequency-dependent dispersion formula according to the two-fluid model was adopted to describe the optical response of the superconducting system. We found that increasing the superconductor (semiconductor) layer thickness results in a shift to higher (lower) values of the transmittance cutoff frequency. Additionally, this cutoff frequency is shifted to lower values with the temperature increase. Furthermore, we found that the width of the photonic bandgaps varies with the applied pressure. The most notorious variation is presented near the 17 THz region, where a new gap appears with the increase in pressure. We hope this work may be taken into consideration for the development of new perspectives in the design of new optical devices.
High-performance axicon lenses based on high-contrast, multilayer gratings
Authors: Doshay Sage , Sell David , Yang Jianji , Yang Rui , Fan Jonathan A.
Published: January 2018

Axicon lenses are versatile optical elements that can convert Gaussian beams to Bessel-like beams. In this letter, we demonstrate that axicons operating with high efficiencies and at large angles can be produced using high-contrast, multilayer gratings made from silicon. Efficient beam deflection of incident monochromatic light is enabled by higher-order optical modes in the silicon structure. Compared to diffractive devices made from low-contrast materials such as silicon dioxide, our multilayer devices have a relatively low spatial profile, reducing shadowing effects and enabling high efficiencies at large deflection angles. In addition, the feature sizes of these structures are relatively large, making the fabrication of near-infrared devices accessible with conventional optical lithography. Experimental lenses with deflection angles as large as 40° display field profiles that agree well with theory. Our concept can be used to design optical elements that produce higher-order Bessel-like beams, and the combination of high-contrast materials with multilayer architectures will more generally enable new classes of diffractive photonic structures.
Asperomagnetic order in diluted magnetic semiconductor (Ba,Na)(Zn,Mn)2As2
Authors: Gu Gangxu , Zhao Guoqiang , Lin Chaojing , Li Yongqing , Jin Changqing , Xiang Gang
Published: January 2018

We report an investigation of magnetic ordering in (Ba,Na)(Zn,Mn)2As2 (BNZMA) single crystals, a type of II-II-V magnetic semiconductor based on BaZn2As2, with a combination of magnetic, electron transport, and spin polarization measurements. At temperatures above 90 K, the susceptibility is found to follow the Curie-Weiss law with a Curie-Weiss temperature of 16 K. At low temperatures, both the dc and ac susceptibilities exhibit spin-glass-like features and the electron spin polarization is determined to be 48 ± 8% using Andreev reflection spectroscopy. Our experimental results suggest that the ground state of BNZMA has an asperomagnetic order, an intermediate regime between a ferromagnet and a canonical spin glass. Such a partially spin polarized glassy phase can be attributed to the competition between the short range antiferromagnetic superexchange interaction and the long range ferromagnetic/antiferromagnetic exchange interactions mediated by high-density holes.
From elemental tellurium to Ge2Sb2Te5 melts: High temperature dynamic and relaxation properties in relationship with the possible fragile to strong transition
Authors: Flores-Ruiz H. , Micoulaut M.
Published: January 2018

We investigate the dynamic properties of Ge–Sb–Te phase change melts using first principles molecular dynamics with a special emphasis on the effect of tellurium composition on melt dynamics. From structural models and trajectories established previously [H. Flores-Ruiz et al., Phys. Rev. B 92, 134205 (2015)], we calculate the diffusion coefficients for the different species, the activation energies for diffusion, the Van Hove correlation, and the intermediate scattering functions able to substantiate the dynamics and relaxation behavior of the liquids as a function of temperature and composition that is also compared to experiment whenever possible. We find that the diffusion is mostly Arrhenius-like and that the addition of Ge/Sb atoms leads to a global decrease of the jump probability and to an increase in activated dynamics for diffusion. Relaxation behavior is analyzed and used in order to evaluate the possibility of a fragile to strong transition that is evidenced from the calculated high fragility (M = 129) of Ge2Sb2Te5 at high temperatures.
Infrared emission of a freestanding plasmonic membrane
Authors: Monshat Hosein , Liu Longju , McClelland John , Biswas Rana , Lu Meng
Published: January 2018

This paper reports a free-standing plasmonic membrane as a thermal emitter in the near- and mid-infrared regions. The plasmonic membrane consists of an ultrathin gold film perforated with a two-dimensional array of holes. The device was fabricated using an imprint and transfer process and fixed on a low-emissivity metal grid. The thermal radiation characteristics of the plasmonic membrane can be engineered by controlling the array period and the thickness of the gold membrane. Plasmonic membranes with two different periods were designed using electromagnetic simulation and then characterized for their transmission and infrared radiation properties. The free-standing membranes exhibit extraordinary optical transmissions with the resonant transmission coefficient as high as 76.8%. After integration with a customized heater, the membranes demonstrate narrowband thermal emission in the wavelength range of 2.5 μm to 5.5 μm. The emission signatures, including peak emission wavelength and bandwidth, are associated with the membrane geometry. The ultrathin membrane infrared emitter can be adopted in applications, such as chemical analysis and thermal imaging.
Post-release survival of two elasmobranchs, the eastern shovelnose ray (Aptychotrema rostrata) and the common stingaree (Trygonoptera testacea), discarded from a prawn trawl fishery in southern Queensland, Australia
Authors: Campbell Matthew J. , McLennan Mark F. , Courtney Anthony J. , Simpfendorfer Colin A.
Published: January 2018

Post-trawl survival (PTS) is an important metric used in determining the ecological risk posed by prawn (shrimp) trawling on discarded elasmobranchs. Despite this, PTS of elasmobranchs is poorly understood. The present study quantified the PTS of two small batoids caught incidentally by prawn trawlers in southern Queensland, Australia, namely the common stingaree (Trygonoptera testacea) and the eastern shovelnose ray (Aptychotrema rostrata). Field studies using on-board tanks revealed that A. rostrata were more resilient to trawl capture and release than T. testacea. For both species, survival was found to increase with size, whereas increasing time on deck resulted in lower survival. Female T. testacea were found to be more resilient than males, and increased tow duration resulted in lower survival for A. rostrata. The mean (±s.e.m.) PTS for female and male T. testacea was 33.5±6.0 and 17.3±5.5% respectively, compared with a mean PTS for A. rostrata of 86.8±3.2%. The survival estimates derived in the present study provide an insight into the effects of trawling on these species and will improve their ecological risk assessment and management.
Targeted knockout of a chemokine-like gene increases anxiety and fear responses
Authors: Choi Jung-Hwa , Jeong Yun-Mi , Kim Sujin , Lee Boyoung , Ariyasiri Krishan , Kim Hyun-Taek , Jung Seung-Hyun , Hwang Kyu-Seok , Choi Tae-Ik , Park Chul O , Huh Won-Ki , Carl Matthias , Rosenfeld Jill A. , Raskin Salmo , Ma Alan , Gecz Jozef , Kim Hyung-Goo , Kim Jin-Soo , Shin Ho-Chul , Park Doo-Sang , Gerlai Robert , Jamieson Bradley B. , Kim Joon S. , Iremonger Karl J. , Lee Sang H. , Shin Hee-Sup , Kim Cheol-Hee
Published: January 2018

Significance

Emotion-related responses, such as fear and anxiety, are important behavioral phenomena in most animal species, as well as in humans. However, the underlying mechanisms of fear and anxiety in animals and in humans are still largely unknown, and anxiety disorders continue to represent a large unmet medical need in the human clinic. Animal models may speed up discovery of these mechanisms and may also lead to betterment of human health. Herein, we report the identification of a chemokine-like gene family,
samdori
(
sam
), and present functional characterization of
sam2
. We observed increased anxiety-related responses in both zebrafish and mouse knockout models. Taken together, these results support a crucial and evolutionarily conserved role of
sam2
in regulating anxiety-like behavior.
Laminar recordings in frontal cortex suggest distinct layers for maintenance and control of working memory
Authors: Bastos André M. , Loonis Roman , Kornblith Simon , Lundqvist Mikael , Miller Earl K.
Published: January 2018

Significance

The anatomy and dynamics of different layers of the cerebral cortex are distinct. Physiological work in the sensory cortex has investigated how different layers process sensory inputs, and how they are engaged during attention tasks. In the frontal and prefrontal cortices, where lamination is present, very few studies have investigated the role of distinct layers for cognition. We studied frontal cortex laminar neuronal activity as monkeys performed working memory tasks. Spiking and gamma-band activity (50–150 Hz) in the superficial layers reflected active maintenance of working memories. Alpha/beta frequencies (4–22 Hz) in the deep layers modulated the gamma activity in the superficial layers. This might serve a control function, allowing information to enter or exit active storage in superficial layers.
Pulsating dissolution of crystalline matter
Authors: Fischer Cornelius , Luttge Andreas
Published: January 2018

Significance

The reaction of crystalline material with fluids is of relevance for natural and technical processes. A basic assumption has been that the reaction products are continuously released from the crystal surface. New experimental and analytical results show something fundamentally different: Material is released in a series of reaction pulses. Applied and theoretical implications impact both the upscaling of crystal dissolution kinetics, and more importantly, the problem of how dissolution and growth are connected via the equilibrium state. These results challenge the prevailing view that crystal dissolution is simply the inverse process of continuous crystal growth at crystal dislocations. Consequently, we need to examine how macroscopic crystal equilibrium reflects continuous or discontinuous processes in the microscopic state.
DNA synthesis from diphosphate substrates by DNA polymerases
Authors: Burke Cassandra R. , Lupták Andrej
Published: January 2018

Significance

All extant cellular organisms are thought to replicate their genomes using triphosphorylated substrates (dNTPs). Because only the α-phosphate is retained in the DNA backbone, both dNTPs and diphosphates (dNDPs) can in principle drive DNA synthesis. The activation barrier for the transphosphorylation is expected to be higher for dNDPs than for dNTPs, rendering the dNDP reactions slower; however, at elevated temperatures this penalty may be less prohibitive. We demonstrate DNA synthesis from dNDPs for a number of DNA polymerases, including bacterial and archaeal replicative and repair enzymes. Activation energy analysis of the forward (DNA synthesis) and reverse (phosphorolysis of DNA) reactions catalyzed by the Taq DNA polymerase shows that DNA synthesis is strongly favored, allowing surprisingly robust replication from low-energy substrates.
MAFA
missense mutation causes familial insulinomatosis and diabetes mellitus
Authors: Iacovazzo Donato , Flanagan Sarah E. , Walker Emily , Quezado Rosana , de Sousa Barros Fernando Antonio , Caswell Richard , Johnson Matthew B. , Wakeling Matthew , Brändle Michael , Guo Min , Dang Mary N. , Gabrovska Plamena , Niederle Bruno , Christ Emanuel , Jenni Stefan , Sipos Bence , Nieser Maike , Frilling Andrea , Dhatariya Ketan , Chanson Philippe , de Herder Wouter W. , Konukiewitz Björn , Klöppel Günter , Stein Roland , Korbonits Márta , Ellard Sian
Published: January 2018

Significance

We report a disease-causing mutation in the β-cell–enriched MAFA transcription factor. Strikingly, the missense p.Ser64Phe
MAFA
mutation was associated with either of two distinct phenotypes, multiple insulin-producing neuroendocrine tumors of the pancreas—a condition known as insulinomatosis—or diabetes mellitus, recapitulating the physiological properties of MAFA both as an oncogene and as a key islet β-cell transcription factor. The implication of MAFA in these human phenotypes will provide insights into how this transcription factor regulates human β-cell activity as well as into the mechanisms of Maf-induced tumorigenesis.
Elevated
d
-2-hydroxyglutarate during colitis drives progression to colorectal cancer
Authors: Han Jie , Jackson Dakota , Holm Janette , Turner Kevin , Ashcraft Paula , Wang Xuan , Cook Beth , Arning Erland , Genta Robert M. , Venuprasad K. , Souza Rhonda F. , Sweetman Lawrence , Theiss Arianne L.
Published: January 2018

d
-2-hydroxyglutarate (D2HG) is produced in the tricarboxylic acid cycle and is quickly converted to α-ketoglutarate by
d
-2-hydroxyglutarate dehydrogenase (D2HGDH). In a mouse model of colitis-associated colon cancer (CAC), urine level of D2HG during colitis correlates positively with subsequent polyp counts and severity of dysplasia. The i.p. injection of D2HG results in delayed recovery from colitis and severe tumorigenesis. The colonic expression of D2HGDH is decreased in ulcerative colitis (UC) patients at baseline who progress to cancer. Hypoxia-inducible factor (Hif)-1α is a key regulator of D2HGDH transcription. Our study identifies urine D2HG and tissue D2HGDH expression as biomarkers to identify patients at risk for progressing from colitis to cancer. The D2HG/D2HGDH pathway provides potential therapeutic targets for the treatment of CAC.
Infected erythrocytes expressing DC13 PfEMP1 differ from recombinant proteins in EPCR-binding function
Authors: Azasi Yvonne , Lindergard Gabriella , Ghumra Ashfaq , Mu Jianbing , Miller Louis H. , Rowe J. Alexandra
Published: January 2018

Significance

Sequestration of
Plasmodium falciparum
-infected erythrocytes (IEs) in the brain microvasculature underlies the pathology of cerebral malaria. Parasites that express
P. falciparum
erythrocyte membrane protein 1 of domain cassette (DC) 8 and DC13 types bind to brain endothelial cells. Recent studies, largely based on recombinant proteins, have identified endothelial protein C receptor (EPCR) as the key receptor for endothelial cell binding. Using DC8- and DC13-expressing IEs, we show that binding of DC13 IEs to brain endothelial cells is not EPCR-dependent and that cytoadhesion of EPCR-binding DC8 IEs to brain endothelial cells is blocked by human serum. This study highlights differences between recombinant protein and native protein in EPCR-binding properties and suggests that other receptors are also required for sequestration in cerebral malaria.
Ultrafast imaging of cell elasticity with optical microelastography
Authors: Grasland-Mongrain Pol , Zorgani Ali , Nakagawa Shoma , Bernard Simon , Paim Lia Gomes , Fitzharris Greg , Catheline Stefan , Cloutier Guy
Published: January 2018

Significance

In wave physics, and especially seismology, uncorrelated vibrations could be exploited using “noise correlation” tools to reconstruct images of a medium. By using a high-frequency vibration, a high-speed tracking device, and a reconstruction technique based on temporal correlations of travelling waves we conceptualized an optical microelastography technique to map elasticity of internal cellular structures. This technique, unlike other methods, can provide an elasticity image in less than a millisecond, thus opening the possibility of studying dynamic cellular processes and elucidating new mechanocellular properties. We call this proposed technique “cell quake elastography.”
Induced
Gnas

R201H

expression from the endogenous
Gnas
locus causes fibrous dysplasia by up-regulating Wnt/β-catenin signaling
Authors: Khan Sanjoy Kumar , Yadav Prem Swaroop , Elliott Gene , Hu Dorothy Zhang , Xu Ruoshi , Yang Yingzi
Published: January 2018

Significance

Understanding molecular and cellular mechanisms of rare genetic diseases provides invaluable insights into the human biology and pathology of both rare and related common diseases. Fibrous dysplasia (FD) is a mosaic disease resulting from postzygotic activating mutations of
GNAS
. The mouse models we created allowed us to precisely model FD by expressing the FD Gα
s
mutation under the control of its endogenous genetic locus. We found in our FD mouse models that up-regulated Wnt/β-catenin signaling resulted in impaired differentiation and proliferation of bone marrow stem cells, which in turn caused marrow fibrosis. Our work provides a solid new foundation for therapeutic development of FD and understanding the principles whereby Gα
s
signaling governs bone formation and maintenance and bone marrow stromal cell differentiation.
Thymic stromal lymphopoietin drives the development of IL-13
+
Th2 cells
Authors: Ochiai Sotaro , Jagot Ferdinand , Kyle Ryan L. , Hyde Evelyn , White Ruby F. , Prout Melanie , Schmidt Alfonso J. , Yamane Hidehiro , Lamiable Olivier , Le Gros Graham , Ronchese Franca
Published: January 2018

Significance

T helper 2 (Th2) cells are defined by their ability to produce the hallmark cytokine IL-4. However, to mediate allergic inflammation in tissues, Th2 cells must secrete additional cytokines including IL-13 and IL-5. We used IL-4 and IL-13 dual-reporter mice to show that naive CD4
+
T cells cultured in the presence of IL-4 and thymic stromal lymphopoietin (TSLP) generate a population of IL-4
neg
IL-13
pos
Th2 cells that develop from IL-4
neg
precursors and express the Th2 effector cytokines IL-5 and IL-9. In vivo, high TSLP levels promote the development of a similar population of IL-4
neg
IL-13
pos
T cells that also express
Gata3
,
Il5
, and
Il3
transcripts. Thus, TSLP drives the early differentiation of a distinct population of effector Th2 cells with pro-inflammatory properties.
Cooperation, clustering, and assortative mixing in dynamic networks
Authors: Melamed David , Harrell Ashley , Simpson Brent
Published: January 2018

Significance

Understanding the patterns and processes of human cooperation is of central scientific importance. Networks can promote cooperation when their existing or emergent topology allows conditional cooperators in the network to isolate themselves from exploitation by noncooperators. We do not know from prior work whether the emergent structures that promote cooperation are driven by reputation or can emerge purely via dynamics, i.e., the severing of ties to noncooperators and the formation of new ties irrespective of reputational information. Here we demonstrate, experimentally, that dynamic networks yield very high rates of cooperation even without reputational knowledge. Further, we identify realistic conditions under which static networks (where ties cannot be altered) yield cooperation rates as high as those in dynamic networks.
Probabilistic switching circuits in DNA
Authors: Wilhelm Daniel , Bruck Jehoshua , Qian Lulu
Published: January 2018

Significance

Biological organisms exhibit sophisticated control over the stochastic states of individual cells, but the understanding of underlying molecular mechanisms remains incomplete. It has been argued that unbiased choices are easy to achieve, but choices biased with specific probabilities are much harder. These natural phenomena raise an engineering challenge: Does there exist a simple method to program molecular systems that control arbitrary probabilities for individual molecular events? Here we show a molecular circuit architecture, using just a simple DNA strand displacement building block that functions as an unbiased switch, for creating a circuit output with any desired probability. We constructed several DNA circuits with multiple layers and feedback, demonstrating complex molecular information processing that exploits the inherent stochasticity of molecular interactions.
Large-scale comparative epigenomics reveals hierarchical regulation of non-CG methylation in
Arabidopsis
Authors: Zhang Yu , Harris C. Jake , Liu Qikun , Liu Wanlu , Ausin Israel , Long Yanping , Xiao Lidan , Feng Li , Chen Xu , Xie Yubin , Chen Xinyuan , Zhan Lingyu , Feng Suhua , Li Jingyi Jessica , Wang Haifeng , Zhai Jixian , Jacobsen Steven E.
Published: January 2018

Genome-wide characterization by next-generation sequencing has greatly improved our understanding of the landscape of epigenetic modifications. Since 2008, whole-genome bisulfite sequencing (WGBS) has become the gold standard for DNA methylation analysis, and a tremendous amount of WGBS data has been generated by the research community. However, the systematic comparison of DNA methylation profiles to identify regulatory mechanisms has yet to be fully explored. Here we reprocessed the raw data of over 500 publicly available
Arabidopsis
WGBS libraries from various mutant backgrounds, tissue types, and stress treatments and also filtered them based on sequencing depth and efficiency of bisulfite conversion. This enabled us to identify high-confidence differentially methylated regions (hcDMRs) by comparing each test library to over 50 high-quality wild-type controls. We developed statistical and quantitative measurements to analyze the overlapping of DMRs and to cluster libraries based on their effect on DNA methylation. In addition to confirming existing relationships, we revealed unanticipated connections between well-known genes. For instance, MET1 and CMT3 were found to be required for the maintenance of asymmetric CHH methylation at nonoverlapping regions of CMT2 targeted heterochromatin. Our comparative methylome approach has established a framework for extracting biological insights via large-scale comparison of methylomes and can also be adopted for other genomics datasets.
Coding of episodic memory in the human hippocampus
Authors: Wixted John T. , Goldinger Stephen D. , Squire Larry R. , Kuhn Joel R. , Papesh Megan H. , Smith Kris A. , Treiman David M. , Steinmetz Peter N.
Published: January 2018

Significance

Neurocomputational models hold that episodic memories are represented by sparse, stimulus-specific neural codes. In tests of episodic memory, single-unit recording studies of the human hippocampus have found neurons that operate as general novelty detectors or general familiarity detectors. Here, we investigated whether neurons can be found that sparsely code some recently studied items and not others. In the left hippocampus, but not the amygdala, we found that small fractions of neurons exhibited strong responses to specific repeated words. The remaining large fractions of neurons exhibited a concurrent reduction in firing rates relative to novel words. Both findings are consistent with predictions made by neurocomputational models of how episodic memory is coded in the hippocampus.
Repetitive aggressive encounters generate a long-lasting internal state in
Drosophila melanogaster
males
Authors: Kim Yong-Kyu , Saver Mathias , Simon Jasper , Kent Clement F. , Shao Lisha , Eddison Mark , Agrawal Pavan , Texada Michael , Truman James W. , Heberlein Ulrike
Published: January 2018

Significance

To survive, an organism must adjust its behavior based upon past experiences. In
Drosophila
, aggression affects fitness as it ensures access to food and mating resources. Here, we show that upon repeated aggressive encounters, males adopt a winner or loser state that shows the qualities of persistence and generalization. Winning is perceived as rewarding, while losing is aversive. We also demonstrate that the activity of specific dopamine neurons is needed for males to avoid an odor previously paired with losing. Although the effects of losing and winning have been extensively studied in other species, our work advances the use of
Drosophila
as a model for circuit dissection of internal states that promote behavioral changes associated with winning or losing fights.
Flexibility of thought in high creative individuals represented by percolation analysis
Authors: Kenett Yoed N. , Levy Orr , Kenett Dror Y. , Stanley H. Eugene , Faust Miriam , Havlin Shlomo
Published: January 2018

Significance

Creative thinking requires flexibility, which facilitates the creation of novel and innovative ideas. However, so far its role in creativity has been measured via indirect measures. We propose a quantitative measure of flexibility based on the robustness of semantic memory networks to attack, assuming that the higher robustness, the higher the flexibility of the network. We show how the semantic network of high creative individuals is more robust to attack, thus more flexible. This is a direct computational investigation on flexibility of semantic memory and creativity. Our approach can be applied to more general questions such as high-level cognitive capacities and clinical populations suffering from atypical thought processes.