bluuebunny/crossref_metadata_2025 huggingface dataset:
Simulating Brownian suspensions with fluctuating hydrodynamics
Authors: Delmotte Blaise , Keaveny Eric E.
Published: December 2015

Fluctuating hydrodynamics has been successfully combined with several computational methods to rapidly compute the correlated random velocities of Brownian particles. In the overdamped limit where both particle and fluid inertia are ignored, one must also account for a Brownian drift term in order to successfully update the particle positions. In this paper, we present an efficient computational method for the dynamic simulation of Brownian suspensions with fluctuating hydrodynamics that handles both computations and provides a similar approximation as Stokesian Dynamics for dilute and semidilute suspensions. This advancement relies on combining the fluctuating force-coupling method (FCM) with a new midpoint time-integration scheme we refer to as the drifter-corrector (DC). The DC resolves the drift term for fluctuating hydrodynamics-based methods at a minimal computational cost when constraints are imposed on the fluid flow to obtain the stresslet corrections to the particle hydrodynamic interactions. With the DC, this constraint needs only to be imposed once per time step, reducing the simulation cost to nearly that of a completely deterministic simulation. By performing a series of simulations, we show that the DC with fluctuating FCM is an effective and versatile approach as it reproduces both the equilibrium distribution and the evolution of particulate suspensions in periodic as well as bounded domains. In addition, we demonstrate that fluctuating FCM coupled with the DC provides an efficient and accurate method for large-scale dynamic simulation of colloidal dispersions and the study of processes such as colloidal gelation.
The development and interaction of instabilities in intense relativistic electron beams
Authors: Kurkin S. A. , Badarin A. A. , Koronovskii A. A. , Hramov A. E.
Published: December 2015

We report on the physical mechanisms of development, coexistence and interaction of Pierce-Bursian and diocotron instabilities in the non-neutral relativistic electron beam (REB) in the classic vircator. The analytical and numerical analysis is provided by means of 3D electromagnetic simulation. We conducted an extensive study of characteristic regimes of REB dynamics determined by the instabilities development. As a result, a regime map has been obtained. It demonstrates sequential switching of the REB dynamics from the regime with N=1 to the regime with N = 7 electron bunches in the azimuth direction with the beam current growth for the different external magnetic fields. The numerical analysis of bunch equilibrium states has identified the physical causes responsible for the REB regime switchings.
Initial-value semiclassical propagators for the Wigner phase space representation: Formulation based on the interpretation of the Moyal equation as a Schrödinger equation
Authors: Koda Shin-ichi
Published: December 2015

We formulate various semiclassical propagators for the Wigner phase space representation from a unified point of view. As is shown in several studies, the Moyal equation, which is an equation of motion for the Wigner distribution function, can be regarded as the Schrödinger equation of an extended Hamiltonian system where its “position” and “momentum” correspond to the middle point of two points of the original phase space and the difference between them, respectively. Then we show that various phase-space semiclassical propagators can be formulated just by applying existing semiclassical propagators to the extended system. As a result, a phase space version of the Van Vleck propagator, the initial-value Van Vleck propagator, the Herman-Kluk propagator, and the thawed Gaussian approximation are obtained. In addition, we numerically compare the initial-value phase-space Van Vleck propagator, the phase-space Herman-Kluk propagator, and the classical mechanical propagation as approximation methods for the time propagation of the Wigner distribution function in terms of both accuracy and convergence speed. As a result, we find that the convergence speed of the Van Vleck propagator is far slower than others as is the case of the Hilbert space, and the Herman-Kluk propagator keeps its accuracy for a long period compared with the classical mechanical propagation while the convergence speed of the latter is faster than the former.
Towards an automated and efficient calculation of resonating vibrational states based on state-averaged multiconfigurational approaches
Authors: Meier Patrick , Oschetzki Dominik , Pfeiffer Florian , Rauhut Guntram
Published: December 2015

Resonating vibrational states cannot consistently be described by single-reference vibrational self-consistent field methods but request the use of multiconfigurational approaches. Strategies are presented to accelerate vibrational multiconfiguration self-consistent field theory and subsequent multireference configuration interaction calculations in order to allow for routine calculations at this enhanced level of theory. State-averaged vibrational complete active space self-consistent field calculations using mode-specific and state-tailored active spaces were found to be very fast and superior to state-specific calculations or calculations with a uniform active space. Benchmark calculations are presented for trans-diazene and bromoform, which show strong resonances in their vibrational spectra.
Calculation of membrane bending rigidity using field-theoretic umbrella sampling
Authors: Smirnova Y. G. , Müller M.
Published: December 2015

The free-energy change of membrane shape transformations can be small, e.g., as in the case of membrane bending. Therefore, the calculation of the free-energy difference between different membrane morphologies is a challenge. Here, we discuss a computational method — field-theoretic umbrella sampling — to compute the local chemical potential of a non-equilibrium configuration and illustrate how one can apply it to study free-energy changes of membrane transformations using simulations. Specifically, the chemical potential profile of the bent membrane and the bending rigidity of membrane are calculated for a soft, coarse-grained amphiphile model and the MARTINI model of a dioleoylphosphatidylcholine (DOPC) membrane.
Star-type oscillatory networks with generic Kuramoto-type coupling: A model for “Japanese drums synchrony”
Authors: Vlasov Vladimir , Pikovsky Arkady , Macau Elbert E. N.
Published: December 2015

We analyze star-type networks of phase oscillators by virtue of two methods. For identical oscillators we adopt the Watanabe-Strogatz approach, which gives full analytical description of states, rotating with constant frequency. For nonidentical oscillators, such states can be obtained by virtue of the self-consistent approach in a parametric form. In this case stability analysis cannot be performed, however with the help of direct numerical simulations we show which solutions are stable and which not. We consider this system as a model for a drum orchestra, where we assume that the drummers follow the signal of the leader without listening to each other and the coupling parameters are determined by a geometrical organization of the orchestra.
Efficient spin filter and spin valve in a single-molecule magnet Fe4 between two graphene electrodes
Authors: Zu Feng-Xia , Gao Guo-Ying , Fu Hua-Hua , Xiong Lun , Zhu Si-Cong , Peng Li , Yao Kai-Lun
Published: December 2015

We propose a magnetic molecular junction consisting of a single-molecule magnet Fe4 connected two graphene electrodes and investigate transport properties, using the nonequilibrium Green's function method in combination with spin-polarized density-functional theory. The results show that the device can be used as a nearly perfect spin filter with efficiency approaching 100%. Our calculations provide crucial microscopic information how the four iron cores of the chemical structure are responsible for the spin-resolved transmissions. Moreover, it is also found that the device behaves as a highly efficient spin valve, which is an excellent candidate for spintronics of molecular devices. The idea of combining single-molecule magnets with graphene provides a direction in designing a new class of molecular spintronic devices.
Etching of germanium-tin using ammonia peroxide mixture
Authors: Dong Yuan , Ong Bin Leong , Wang Wei , Zhang Zheng , Pan Jisheng , Gong Xiao , Tok Eng-Soon , Liang Gengchiau , Yeo Yee-Chia
Published: December 2015

The wet etching of germanium-tin (Ge1-xSnx) alloys (4.2% < x < 16.0%) in ammonia peroxide mixture (APM) is investigated. Empirical fitting of the data points indicates that the etch depth of Ge1-xSnx is proportional to the square root of the etch time t and decreases exponentially with increasing x for a given t. In addition, X-ray photoelectron spectroscopy results show that increasing t increases the intensity of the Sn oxide peak, whereas no obvious change is observed for the Ge oxide peak. This indicates that an accumulation of Sn oxide on the Ge1-xSnx surface decreases the amount of Ge atoms exposed to the etchant, which accounts for the decrease in etch rate with increasing etch time. Atomic force microscopy was used to examine the surface morphologies of the Ge0.918Sn0.082 samples. Both root-mean-square roughness and undulation periods of the Ge1-xSnx surface were observed to increase with increasing t. This work provides further understanding of the wet etching of Ge1-xSnx using APM and may be used for the fabrication of Ge1-xSnx-based electronic and photonic devices.
The influence of hold time on the onset of plastic deformation in silicon
Authors: Wong S. , Haberl B. , Williams J. S. , Bradby J. E.
Published: December 2015

The transformation of diamond-cubic silicon to the metallic β-Sn phase is known to be “sluggish,” even when the critical pressure (∼11 GPa) for the transformation is reached. In this letter, we use nanoindentation to apply pressures to just above the critical threshold. In this regime, the sample displays purely elastic behavior at zero hold time. As the hold time at maximum load is increased up to 180 s, the percentage of indents that plastically deform also increase. Interestingly, the indents deform via one of two distinct processes: either via a phase transformation to a mixed bc8/r8-Si end phase, or by initiation of crystalline defects. Raman spectroscopy and cross-sectional transmission electron microscopy are used to show that the two deformation mechanisms are mutually exclusive under the indentation conditions presented here, and elastic modelling was utilized to propose a model for this mutually exclusive behavior. Hence, this behavior enhances the potential for application of the exotic bc8/r8-Si end phase.
Theoretical modeling of the plasma-assisted catalytic growth and field emission properties of graphene sheet
Authors: Sharma Suresh C. , Gupta Neha
Published: December 2015

A theoretical modeling for the catalyst-assisted growth of graphene sheet in the presence of plasma has been investigated. It is observed that the plasma parameters can strongly affect the growth and field emission properties of graphene sheet. The model developed accounts for the charging rate of the graphene sheet; number density of electrons, ions, and neutral atoms; various elementary processes on the surface of the catalyst nanoparticle; surface diffusion and accretion of ions; and formation of carbon-clusters and large graphene islands. In our investigation, it is found that the thickness of the graphene sheet decreases with the plasma parameters, number density of hydrogen ions and RF power, and consequently, the field emission of electrons from the graphene sheet surface increases. The time evolution of the height of graphene sheet with ion density and sticking coefficient of carbon species has also been examined. Some of our theoretical results are in compliance with the experimental observations.
Observation of upper drift modes in radio frequency produced magnetized plasmas with frequency above ion cyclotron frequency
Authors: Ghosh Abhijit , Saha S. K. , Chowdhury S. , Janaki M. S.
Published: December 2015

In a RF produced magnetized argon plasma expanding into a larger expansion chamber, electrostatic modes propagating azimuthally in the direction of the electron diamagnetic drift and frequency greater than the ion cyclotron frequency are observed. In the radial direction, the mode amplitude peaks at a location where the radial density gradient is maximum. The modes are detected at axial locations up to 16 cm away from the entrance aperture. For fixed values of the neutral pressure and magnetic field, the mode frequency is found to be independent of the location at which it is measured. The modes exhibit drift wave characteristics revealing a radial structure with the azimuthal mode number m = 1 at the lower radial locations (r ∼ 3.0 cm) while the m = 2 mode is located in the outer region. Theoretical modeling using a local dispersion relation based on the fluid equations predicts destabilization of the modes with frequency greater than the ion-cyclotron frequency by electron-neutral collisions and exhibiting other drift wave features.
Dynamics of optical breakdown in air induced by single and double nanosecond laser pulses
Authors: Mahdieh Mohammad Hossein , Akbari Jafarabadi Marzieh
Published: December 2015

In this paper, an optical breakdown in air induced by single and double nanosecond laser pulses was studied. A high power Nd:YAG laser beam was used for producing optical breakdown plasma in the air. The dynamics of breakdown plasma were studied using an optical probe beam. A portion of the laser beam was used, as the probe beam and was aligned to propagate (perpendicular to the pump beam) through the breakdown region. The transmission of the probe beam (through the breakdown region) was temporally measured for both single and double pulse irradiations. The results were used to describe the evolution of the induced plasma in both conditions. These results show that the plasma formation time and its absorptivity are strongly dependent on the single or double pulse configurations.
Note: Inhibiting bottleneck corrosion in electrical calcium tests for ultra-barrier measurements
Authors: Nehm F. , Müller-Meskamp L. , Klumbies H. , Leo K.
Published: December 2015

A major failure mechanism is identified in electrical calcium corrosion tests for quality assessment of high-end application moisture barriers. Accelerated calcium corrosion is found at the calcium/electrode junction, leading to an electrical bottleneck. This causes test failure not related to overall calcium loss. The likely cause is a difference in electrochemical potential between the aluminum electrodes and the calcium sensor, resulting in a corrosion element. As a solution, a thin, full-area copper layer is introduced below the calcium, shifting the corrosion element to the calcium/copper junction and inhibiting bottleneck degradation. Using the copper layer improves the level of sensitivity for the water vapor transmission rate (WVTR) by over one order of magnitude. Thin-film encapsulated samples with 20 nm of atomic layer deposited alumina barriers this way exhibit WVTRs of 6 × 10−5 g(H2O)/m2/d at 38 °C, 90% relative humidity.
Electron beam guiding by grooved SiO2 parallel plates without energy loss
Authors: Xue Yingli , Yu Deyang , Liu Junliang , Zhang Mingwu , Yang Bian , Zhang Yuezhao , Cai Xiaohong
Published: December 2015

Using a pair of grooved SiO2 parallel plates, stably guided electron beams were obtained without energy loss at 800–2000 eV. This shows that the transmitted electrons are guided by a self-organized repulsive electric field, paving the way for a self-adaptive manipulation of electron beams.
Conversion efficiency improvement of inverted CH3NH3PbI3 perovskite solar cells with room temperature sputtered ZnO by adding the C60 interlayer
Authors: Lai Wei-Chih , Lin Kun-Wei , Guo Tzung-Fang , Chen Peter , Wang Yuan-Ting
Published: December 2015

We have demonstrated the performance of inverted CH3NH3PbI3 perovskite-based solar cells (SCs) with a room temperature (RT) sputtered ZnO electron transport layer by adding fullerene (C60) interlayer. ZnO exhibits a better matched conduction band level with perovskite and Al work function and around energy offset of 2.2 eV between highest occupied molecular orbital level of CH3NH3PbI3 perovskite and valance band level of ZnO. However, the CH3NH3PbI3 perovskite layer will be damaged during direct RT sputtering deposition of ZnO. Therefore, the C60 interlayer having matched conduction band level with ZnO and CH3NH3PbI3 perovskite added between the CH3NH3PbI3 perovskite and RT sputtered ZnO layers for protection prevents sputtering damages on the CH3NH3PbI3 perovskite layer. The short-circuit current density (JSC, 19.41 mA/cm2) and open circuit voltage (VOC, 0.91 V) of the SCs with glass/ITO/poly(3,4-ethylenedioxythiophene):poly(styrene-sulfonate) (PEDOT:PSS)/perovskite/C60/RT sputtered ZnO/Al structure is higher than the JSC (16.23 mA/cm2) and VOC (0.90 V) of the reference SC with glass/ITO/PEDOT:PSS/perovskite/C60/bathocuproine (BCP)/Al structure. Although the SCs with the former structure has a lower fill factor (FF%) than the SCs with the latter structure, its conversion efficiency η% (10.93%) is higher than that (10.6%) of the latter.
Luminescent down shifting effect of Ce-doped yttrium aluminum garnet thin films on solar cells
Authors: Shao Guojian , Lou Chaogang , Kang Jian , Zhang Hao
Published: December 2015

Ce-doped yttrium aluminum garnet (YAG:Ce) thin films as luminescent down shifting (LDS) materials are introduced into the module of crystalline silicon solar cells. The films are deposited by RF magnetron sputtering on the lower surface of the quartz glass. They convert ultraviolet and blue light into yellow light. Experiments show that the introduction of YAG:Ce films improves the conversion efficiency from 18.45% of the cells to 19.27% of the module. The increasing efficiency is attributed to LDS effect of YAG:Ce films and the reduced reflection of short wavelength photons. Two intentionally selected samples with similar reflectivities are used to evaluate roughly the effect of LDS alone on the solar cells, which leads to a relative increase by 2.68% in the conversion efficiency.
Kinetics of liquid-mediated crystallization of amorphous Ge from multi-frame dynamic transmission electron microscopy
Authors: Santala M. K. , Raoux S. , Campbell G. H.
Published: December 2015

The kinetics of laser-induced, liquid-mediated crystallization of amorphous Ge thin films were studied using multi-frame dynamic transmission electron microscopy (DTEM), a nanosecond-scale photo-emission transmission electron microscopy technique. In these experiments, high temperature gradients are established in thin amorphous Ge films with a 12-ns laser pulse with a Gaussian spatial profile. The hottest region at the center of the laser spot crystallizes in ∼100 ns and becomes nano-crystalline. Over the next several hundred nanoseconds crystallization continues radially outward from the nano-crystalline region forming elongated grains, some many microns long. The growth rate during the formation of these radial grains is measured with time-resolved imaging experiments. Crystal growth rates exceed 10 m/s, which are consistent with crystallization mediated by a very thin, undercooled transient liquid layer, rather than a purely solid-state transformation mechanism. The kinetics of this growth mode have been studied in detail under steady-state conditions, but here we provide a detailed study of liquid-mediated growth in high temperature gradients. Unexpectedly, the propagation rate of the crystallization front was observed to remain constant during this growth mode even when passing through large local temperature gradients, in stark contrast to other similar studies that suggested the growth rate changed dramatically. The high throughput of multi-frame DTEM provides gives a more complete picture of the role of temperature and temperature gradient on laser crystallization than previous DTEM experiments.
Note: Decoupling design for high frequency piezoelectric ultrasonic transducers with their clamping connections
Authors: Wang F. J. , Zhang H. J. , Liang C. M. , Tian Y. L. , Zhao X. Y. , Zhang D. W.
Published: December 2015

This work presents the flexure-mechanism based decoupling design between high frequency piezoelectric ultrasonic transducers and their clamping connections to improve ultrasonic energy transmission efficiency. The ring, prismatic beam, and circular notched hinge based flanges were presented, and the crucial geometric dimensions of the transducers with the flexure decoupling flanges were determined. Finite element analysis (FEA) was carried out to investigate the dynamic characteristics of the transducers. Finally, experiments were conducted to examine and verify the effects of the proposed decoupling flanges. FEA and experimental results show that smaller frequency deviations and larger tip displacement amplitudes have been achieved by using the transducers with the flexure flanges compared with the transducer with a rigid ring-type flange, and thus the ultrasonic transmission efficiency can be improved through the flexure flanges.
Thermal expansion accompanying the glass-liquid transition and crystallization
Authors: Jiang M. Q. , Naderi M. , Wang Y. J. , Peterlechner M. , Liu X. F. , Zeng F. , Jiang F. , Dai L. H. , Wilde G.
Published: December 2015

We report the linear thermal expansion behaviors of a Zr-based (Vitreloy 1) bulk metallic glass in its as-cast, annealed and crystallized states. Accompanying the glass-liquid transition, the as-cast Vitreloy 1 shows a continuous decrease in the thermal expansivity, whereas the annealed glass shows a sudden increase. The crystallized Vitreloy 1 exhibits an almost unchanged thermal expansivity prior to its melting. Furthermore, it is demonstrated that the nucleation of crystalline phases can induce a significant thermal shrinkage of the supercooled liquid, but with the growth of these nuclei, the thermal expansion again dominates. These results are explained in the framework of the potential energy landscape, advocating that the configurational and vibrational contributions to the thermal expansion of the glass depend on both, structure and temperature.
Capacitive micromachined ultrasonic transducer for ultra-low pressure measurement: Theoretical study
Authors: Li Zhikang , Zhao Libo , Jiang Zhuangde , Akhbari Sina , Ding Jianjun , Zhao Yihe , Zhao Yulong , Lin Liwei
Published: December 2015

Ultra-low pressure measurement is necessary in many areas, such as high-vacuum environment monitoring, process control and biomedical applications. This paper presents a novel approach for ultra-low pressure measurement where capacitive micromachined ultrasonic transducers (CMUTs) are used as the sensing elements. The working principle is based on the resonant frequency shift of the membrane under the applied pressure. The membranes of the biased CMUTs can produce a larger resonant frequency shift than the diaphragms with no DC bias in the state-of-the-art resonant pressure sensors, which contributes to pressure sensitivity improvement. The theoretical analysis and finite element method (FEM) simulation were employed to study the relationship between the resonant frequency and the pressure. The results demonstrated excellent capability of the CMUTs for ultra-low pressure measurement. It is shown that the resonant frequency of the CMUT varies linearly with the applied pressure. A sensitivity of more than 6.33 ppm/Pa (68 kHz/kPa) was obtained within a pressure range of 0 to 100 Pa when the CMUTs were biased at a DC voltage of 90% of the collapse voltage. It was also demonstrated that the pressure sensitivity can be adjusted by the DC bias voltage. In addition, the effects of air damping and ambient temperature on the resonant frequency were also studied. The effect of air damping is negligible for the pressures below 1000 Pa. To eliminate the temperature effect on the resonant frequency, a temperature compensating method was proposed.
Broadbanding of circularly polarized patch antenna by waveguided magneto-dielectric metamaterial
Authors: Yang Xin Mi , Wen Juan , Liu Chang Rong , Liu Xue Guan , Cui Tie Jun
Published: December 2015

Design of bandwidth-enhanced circularly polarized (CP) patch antenna using artificial magneto-dielectric substrate was investigated. The artificial magneto-dielectric material adopted here takes the form of waveguided metamaterial (WG-MTM). In particular, the embedded meander line (EML) structure was employed as the building element of the WG-MTM. As verified by the retrieved effective medium parameters, the EML-based waveguided magneto-dielectric metamaterial (WG-MDM) exhibits two-dimensionally isotropic magneto-dielectric property with respect to TEM wave excitations applied in two orthogonal directions. A CP patch antenna loaded with the EML-based WG-MDM (WG-MDM antenna) has been proposed and its design procedure is described in detail. Simulation results show that the impedance and axial ratio bandwidths of the WG-MDM antenna have increased by 125% and 133%, respectively, compared with those obtained with pure dielectric substrate offering the same patch size. The design of the novel WG-MDM antenna was also validated by measurement results, which show good agreement with their simulated counterparts.
Influence of sea ice on Arctic precipitation
Authors: Kopec Ben G. , Feng Xiahong , Michel Fred A. , Posmentier Eric S.
Published: December 2015

Significance

There has been a growing consensus that a decrease in sea ice would cause an increase in Arctic precipitation because of the potential for increased local evaporation. We quantify the effect of sea ice on the percentage of moisture sourced from the Arctic, using measurements of the isotopic composition of precipitation at six sites across the Arctic. These moisture proportion changes are important in that they indicate systematic adjustment and/or reorganization of the global hydrological cycle with climate change and provide validation for climate models. We explore how much these changes may increase Arctic precipitation and its impact on the energy balance.
Effects of aging on circadian patterns of gene expression in the human prefrontal cortex
Authors: Chen Cho-Yi , Logan Ryan W. , Ma Tianzhou , Lewis David A. , Tseng George C. , Sibille Etienne , McClung Colleen A.
Published: December 2015

Significance

Circadian rhythms are important in nearly all processes in the brain. Changes in rhythms that come with aging are associated with sleep problems, problems with cognition, and nighttime agitation in elderly people. In this manuscript, we identified transcripts genome-wide that have a circadian rhythm in expression in human prefrontal cortex. Moreover, we describe how these rhythms are changed during normal human aging. Interestingly, we also identified a set of previously unidentified transcripts that become rhythmic only in older individuals. This may represent a compensatory clock that becomes active with the loss of canonical clock function. These studies can help us to develop therapies in the future for older people who suffer from cognitive problems associated with a loss of normal rhythmicity.
High risk of near-crash driving events following night-shift work
Authors: Lee Michael L. , Howard Mark E. , Horrey William J. , Liang Yulan , Anderson Clare , Shreeve Michael S. , O’Brien Conor S. , Czeisler Charles A.
Published: December 2015

Significance

Drowsy driving is a major public health issue, particularly impacting the 9.5 million shift workers in America. Previous reports have assessed the impact of night work on driving in driving simulators. This real-vehicle driving study demonstrated increased objective and subjective drowsiness and degraded daytime driving performance in 16 night-shift workers while driving after a night of work, deteriorating with drive duration. No near-crashes occurred during driving after a night of sleep; 11 occurred during driving after night-work; all near-crashes occurred after at least 45 min of driving. Policy makers and night-workers should consider avoiding/minimizing driving or deploying effective countermeasures when driving after night-shift work to reduce drowsy driving and preventable crashes and injuries in this high-risk population.
Cryptochrome 1 interacts with PIF4 to regulate high temperature-mediated hypocotyl elongation in response to blue light
Authors: Ma Dingbang , Li Xu , Guo Yongxia , Chu Jingfang , Fang Shuang , Yan Cunyu , Noel Joseph P. , Liu Hongtao
Published: December 2015

Significance

Blue light and temperature are two key environmental signals that profoundly affect plant growth and development responses, but how these two abiotic factors integrate remains largely unknown. This study demonstrates a mechanism of multiple photoreceptors and temperature coactions.
Arabidopsis
blue light photoreceptor cryptochrome 1 (CRY1) represses high temperature-induced hypocotyl elongation through PHYTOCHROME-INTERACTING FACTOR 4 (PIF4). CRY1 physically interacts with PIF4 in a blue light-dependent manner to repress the transcription activity of PIF4. Because PIF4 also plays a role in ambient temperature, PIF4 appears to be the molecular basis of cross-talk among blue and red light and ambient temperature signal pathways.
Seed exchange networks, ethnicity, and sorghum diversity
Authors: Labeyrie Vanesse , Thomas Mathieu , Muthamia Zachary K. , Leclerc Christian
Published: December 2015

Significance

This study helps untangle the multiscale processes involved in the relationships between crop genetic and human cultural diversity patterns. It quantifies the effect of homophily on seed exchange networks and details the major role played by kinship systems. By bridging anthropology and crop genetics through an in-depth social network analysis, this study provides a better understanding of the social processes involved in crop diversity dynamics. These findings urgently call for a specification of social and cultural factors in crop metapopulation models, which has been neglected so far.
How learning shapes the empathic brain
Authors: Hein Grit , Engelmann Jan B. , Vollberg Marius C. , Tobler Philippe N.
Published: December 2015

Significance

Deficits in empathy for out-group members are pervasive, with negative societal impact. It is therefore important to ascertain whether empathy toward out-groups can be learned and how learning experiences change empathy-related brain responses. We used a learning intervention during which participants experienced help from a member of their own social group or of a generally depreciated out-group. Our results show that the intervention successfully increased empathy-related brain responses toward the out-group. These changes in out-group empathy were triggered by the learning signal (prediction error) elicited during the first two positive out-group experiences. Together, our results show that classical learning signals update empathic brain responses and that surprisingly few positive experiences with an out-group member are sufficient to increase out-group empathy.
CO and CN
−
syntheses by [FeFe]-hydrogenase maturase HydG are catalytically differentiated events
Authors: Pagnier Adrien , Martin Lydie , Zeppieri Laura , Nicolet Yvain , Fontecilla-Camps Juan C.
Published: December 2015

Significance

The normally biologically unusual CO and CN
−
diatomic compounds are characteristic iron ligands of hydrogen-metabolizing enzymes. In [FeFe]-hydrogenase, these ligands are synthesized from tyrosine-derived dehydroglycine (DHG) by the radical
S
-adenosyl-L-methionine (SAM) enzyme HydG. Although the SAM-based cleavage of tyrosine is fairly well understood, the mechanism of CO and CN
–
synthesis from DHG, which occurs at an unprecedented second iron-sulfur cluster, remains controversial. We report experiments showing that CN
–
and CO syntheses are independent catalytic events. Whereas CN
–
synthesis is iron-sulfur cluster-independent, the concomitantly produced
–
:CO
2
(H) is converted to CO and H
2
O at the second cluster. We unambiguously establish this reaction sequence by detecting
–
:CO
2
(H)-derived formate that accumulates when the second iron-sulfur cluster is either absent or impaired.
Deep sequencing as a probe of normal stem cell fate and preneoplasia in human epidermis
Authors: Simons Benjamin D.
Published: December 2015

Significance

The sporadic acquisition of somatic DNA mutation confers a hereditary label that can be used to trace the fate behavior of cells in normal and diseased states. Applied to human tumor samples, DNA deep sequencing methods have revealed the landscape of somatic mutations and have identified a repertoire of genes implicated in cancer. By adapting statistical methods used to analyze lineage tracing data in transgenic animal models, we use the example of epidermis to show how deep sequencing data can provide quantitative insight into the self-renewal properties of normal human tissues and can serve as a platform to define rare nonneutral field transformations.
Typical action perception and interpretation without motor simulation
Authors: Vannuscorps Gilles , Caramazza Alfonso
Published: December 2015

Significance

How do we perceive and interpret others’ actions? In recent years, the dominant view on this issue is that efficient perceptual processing of others’ actions cannot be achieved by visual analysis of the movements alone but requires unconscious, covert motor simulation of the observed movements. This idea has developed a large following in many disciplines such as psychology, neuroscience, neurology, psychiatry, and philosophy of mind and has started to influence the study and treatment protocols of patients suffering from conditions affecting the perception and interpretation of action (such as autism, schizophrenia, and various dementias). In this paper, however, we report evidence that efficient perception and interpretation of actions can be achieved without motor simulation.
Understanding the kinetic mechanism of RNA single base pair formation
Authors: Xu Xiaojun , Yu Tao , Chen Shi-Jie
Published: December 2015

Significance

This paper addresses a long-standing unsolved issue in RNA folding, namely, the kinetics for the very elementary steps of RNA folding. Lacking the ability to identify the exact microscopic, molecular level processes has been responsible for a variety of inaccurate predictions for RNA dynamics and RNA biochemical, such as enzymatic, reactions. Unlike previous unfolding (pulling) simulations, we here perform a direct folding study for the process. The misfolded states and the kinetic role of ions discovered in the study may provide significant insights into the physical mechanism of RNA conformational changes in biology.
Agriculture, population growth, and statistical analysis of the radiocarbon record
Authors: Zahid H. Jabran , Robinson Erick , Kelly Robert L.
Published: December 2015

Significance

We statistically analyze the radiocarbon record and show that early farming societies in Europe grew at the same rate as contemporaneous foraging societies in North America. Thus, our results challenge the commonly held view that the advent of agriculture was linked to accelerated growth of the human population. The same rates of prehistoric population growth measured worldwide suggest that the global climate and/or biological factors intrinsic to the species and not factors related to the regional environment or subsistence practices regulated the growth of the human population for most of the last 12,000 y. This study demonstrates that statistical analysis of the radiocarbon record is a robust quantitative approach for studying prehistoric human demography.
Quantitative regulation of
FLC
via coordinated transcriptional initiation and elongation
Authors: Wu Zhe , Ietswaart Robert , Liu Fuquan , Yang Hongchun , Howard Martin , Dean Caroline
Published: December 2015

Significance

The textbook view of how transcription is quantitatively regulated is through changes in transcription initiation. However, the arrangement of DNA in chromatin in eukaryotes and the frequent occurrence of noncoding transcripts add to the complexity of transcriptional regulation. Here, we explore the quantitative transcriptional regulation of
FLC
, a gene important for developmental timing in
Arabidopsis
.
FLC
expression correlates with altered antisense transcript processing and different chromatin states. Through experiments and mathematical modeling, we discover that transcription initiation and elongation are tightly coordinated and both are influenced by the chromatin state at the locus. Modulation of the chromatin environment by noncoding transcripts to coordinately influence transcription initiation and elongation could be a general mechanism to regulate quantitative transcriptional output.
Compliant glass–polymer hybrid single ion-conducting electrolytes for lithium batteries
Authors: Villaluenga Irune , Wujcik Kevin H. , Tong Wei , Devaux Didier , Wong Dominica H. C. , DeSimone Joseph M. , Balsara Nitash P.
Published: December 2015

Significance

This study describes hybrid single ion-conducting electrolytes based on inorganic sulfide glasses and perfluoropolyether polymers for lithium batteries. Herein, it is shown that hybrid electrolytes provide a compelling alternative to the traditional glass, ceramic, or polymer battery electrolytes. These electrolytes present high transference numbers, unprecedented ionic conductivities at room temperature, and excellent electrochemical stability, and they limit the dissolution of lithium polysulfides. The results in this work represent a significant step toward addressing the challenges of enabling the next generation cathodes, such as lithium nickel manganese cobalt oxide and sulfur.
Molecular stripping in the
NF-κB/IκB/DNA
genetic regulatory network
Authors: Potoyan Davit A. , Zheng Weihua , Komives Elizabeth A. , Wolynes Peter G.
Published: December 2015

Significance

The classic models of genetic switches are based on thermodynamic control via binding affinities. Complex nonequilibrium eukaryotic gene networks with many targets such as the

N
F
-
κ
B

/

I
κ
B

/

D
N
A

system challenge this picture. Waiting for unbinding from the numerous

N
F
-
κ
B

binding sites takes time that would allow wasteful overexpression of many genes. Active molecular stripping of

N
F
-
κ
B

from the DNA by

I
κ
B

solves the timescale problem raised in the classic picture based on thermodynamics alone.
Chromatographically isolated CD63
+
CD81
+
extracellular vesicles from mesenchymal stromal cells rescue cognitive impairments after TBI
Authors: Kim Dong-ki , Nishida Hidetaka , An Su Yeon , Shetty Ashok K. , Bartosh Thomas J. , Prockop Darwin J.
Published: December 2015

Significance

It has gradually been recognized that the vesicles secreted by cells are a major means by which cells communicate with each other. This recognition has stimulated interest in using vesicles to deliver therapeutic agents. The results presented here address several limitations to progress in the field by developing protocols to produce and isolate large numbers of extracellular vesicles (EVs) from stem-like cells found in the bone marrow. The isolated EVs were found to reduce the adverse effects of traumatic injury to the brain in mice.
Mouse embryonic fibroblasts exhibit extensive developmental and phenotypic diversity
Authors: Singhal Prabhat K. , Sassi Slim , Lan Lan , Au Patrick , Halvorsen Stefan C. , Fukumura Dai , Jain Rakesh K. , Seed Brian
Published: December 2015

Significance

Embryonic fibroblasts have long been considered a relatively homogeneous cell type, and many studies have been conducted on fibroblasts of varying provenance. The results of the present study indicate that embryonic fibroblasts are highly heterogeneous and exhibit anatomic and developmental variation that has both practical consequences for the interpretation of experimental results and theoretical implications for the nature and organization of metazoan organisms. Studies using embryonic fibroblasts to explore the consequences of altered alleles should take into account the possibility that fibroblast composition may be altered by allele expression.
APOL1 kidney disease risk variants cause cytotoxicity by depleting cellular potassium and inducing stress-activated protein kinases
Authors: Olabisi Opeyemi A. , Zhang Jia-Yue , VerPlank Lynn , Zahler Nathan , DiBartolo Salvatore , Heneghan John F. , Schlöndorff Johannes S. , Suh Jung Hee , Yan Paul , Alper Seth L. , Friedman David J. , Pollak Martin R.
Published: December 2015

Significance

People of recent African ancestry develop chronic kidney disease and end stage kidney failure at rates five times that of European-Americans. Two coding variants in the apolipoprotein-L1 (APOL1) gene account for nearly all this excess risk. The mechanisms by which APOL1 variants cause kidney failure are not understood. Recent evidence suggests that APOL1 transports cations, including K
+
, across lipid bilayers. Here, we show that tetracycline-induced expression of APOL1 kidney risk variants in T-REx-293 cells causes significant net efflux of intracellular K
+
, which, in turn, activates the stress-activated protein kinases (SAPKs) p38 MAPK and JNK, ultimately resulting in cytotoxicity. We propose that APOL1 nephropathy may be mediated by APOL1 risk variant-induced loss of intracellular K
+
and aberrant activation of SAPK signaling.
Functions of vasopressin and oxytocin in bone mass regulation
Authors: Sun Li , Tamma Roberto , Yuen Tony , Colaianni Graziana , Ji Yaoting , Cuscito Concetta , Bailey Jack , Dhawan Samarth , Lu Ping , Calvano Cosima D. , Zhu Ling-Ling , Zambonin Carlo G. , Di Benedetto Adriana , Stachnik Agnes , Liu Peng , Grano Maria , Colucci Silvia , Davies Terry F. , New Maria I. , Zallone Alberta , Zaidi Mone
Published: December 2015

Significance

We show that oxytocin and vasopressin, which are released from the posterior pituitary gland to regulate lactation and water balance, respectively, are potent regulators of skeletal integrity. Using genetically modified mice and chemical inhibitors, we provide evidence that the two hormones interact with each other’s receptors to control precisely the formation of new bone.
Status and Genetic Character of Atlantic Sturgeon in the Satilla River, Georgia
Authors: Fritts Mark W. , Grunwald Cheryl , Wirgin Isaac , King Tim L. , Peterson Douglas L.
Published: December 2015

The Atlantic Sturgeon Acipenser oxyrinchus oxyrinchus is an important component of biodiversity along the Atlantic coast of North America, but most populations have been decimated by habitat degradation and chronic overfishing. Historically, spawning populations existed in all major Atlantic coast rivers from the St. Lawrence River, Quebec, to the St. Johns River, Florida, but fisheries surveys conducted in the past two decades suggest that several populations at the southern extent of this range are now extirpated or have declined to remnant status. Our objective was to assess the abundance and genetic character of Atlantic Sturgeon in the Satilla River, Georgia. Using entanglement gears, we expended over 2,800 h of sampling effort and captured a total of 193 Atlantic Sturgeon in tidally influenced reaches of the river during 2008–2010. Of the 157 fish that were collected in 2010, 72 were identified as river‐resident juveniles (ages 0–1). Genetic analyses of a subset (n = 61) of these juveniles revealed (1) depauperate levels of mitochondrial DNA (mtDNA) haplotype diversity and (2) the presence of large family units based on microsatellite DNA multilocus genotypes, collectively suggesting that very few parents produced the 2008 year‐class. The mtDNA and microsatellite analyses both indicated that juveniles in the Satilla River population were genetically distinct from other populations in the South Atlantic Distinct Population Segment. Atlantic Sturgeon life history characteristics and the present results suggest that sampled juveniles from the 2008 year‐class were the offspring of a small remnant pool of Satilla River adults; however, a full description of the population's genetic character and origin will require additional juvenile samples from future year‐classes.
Dynamics of Near‐Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico
Authors: Schaefer Jacob , Frazier Nkrumah , Barr Jonathan
Published: December 2015

Coastal ecosystems along the northern Gulf of Mexico are highly productive and are affected by fishing and petroleum industries in different, sometimes contrasting, ways. As a result of the Deepwater Horizon (DWH) oil spill in April 2010, oil and oil dispersants were introduced into the northern Gulf of Mexico. At the same time, large portions of the Gulf of Mexico were closed to commercial and recreational fishing for most of the 2010 summer. This presented a unique opportunity to study the dynamics of a fish assemblage exposed to changes in two disparate types of anthropogenic disturbances. We compared assemblage data for near‐coastal fish (456 samples representing over 45,000 individuals and 109 species) from pre‐DWH (before 2010) and post‐DWH (2011–2014) to assess potential changes in abundance, diversity (alpha, beta, and gamma), and assemblage structure. In contrast to predicted oil‐induced mortality, post‐DWH assemblages were characterized by high abundance in 2011 (CPUE across all species pooled was 2.5 times higher than in any other year). This high abundance was most pronounced in medium‐sized fish species that are direct targets of commercial fishing or likely bycatch. Abundances returned to levels similar to pre‐DWH in 2012, 2013, and 2014. There were no differences in pre‐ and post‐DWH levels of diversity, and shifts in assemblage structure may be consistent with increases driven by reduced fishing pressure. While other assemblages and ecosystems may respond differently, our data for the near‐coastal fish assemblage indicated the effects of the DWH were minimal. Rigorous empirical data from other systems are required to assess potential DWH impacts across the range of ecosystems potentially affected.
The effect of body composition and BMI on 25(OH)D response in vitamin D‐supplemented athletes
Authors: Cassity Evan P. , Redzic Maja , Teager Cassidy R. , Thomas D. Travis
Published: December 2015

Fat mass is inversely associated with vitamin D status, and athletes with the most adipose tissue may have the greatest risk for insufficient (25(OH)D 20–32 ng mL−1) or deficient (25(OH)D < 20 ng ml−1) status. The effects of fat and lean mass on 25(OH)D change in response to vitamin D supplementation have yet to be elucidated in athletes. In addition, vitamin D has a known role in bone health yet a link between short‐term changes in 25(OH)D and bone turnover in indoor athletes have not yet been described. Thirty‐two collegiate swimmers and divers (19 male, 13 female; 19 (1) years) participated in a 6‐month randomized controlled trial and consumed either 4000 IU d−1 of vitamin D3 (n = 19) or placebo (PLA; n = 13). Anthropometry and blood collection of 25(OH)D, bone‐specific alkaline phosphatase (B‐ALP) and N‐terminal telopeptide (NTx) occurred at three time points. Dual‐energy X‐ray absorptiometry measured body composition analysis at baseline and endpoint. In the vitamin D group, BMI was negatively correlated with 6‐month 25(OH)D change (R = −0.496; P = .03) and a stronger predictor of 25(OH)D change (P = .04) than ultraviolet B exposure and fat mass change. Athletes in the high bone turnover group showed significantly greater losses of 25(OH)D over 6‐months compared to athletes in the low bone turnover group (P = .03). These results suggest athletes within the normal BMI category experience a diminished response to 4000 IU d−1 of vitamin D3 supplementation, and periods of high bone turnover may be an additional risk factor for developing compromised vitamin D status in athletes.