bluuebunny/crossref_metadata_2025 huggingface dataset:
Time evolution of the intensity and size of tropical cyclones
Authors: Musgrave Kate D. , Taft Richard K. , Vigh Jonathan L. , McNoldy Brian D. , Schubert Wayne H.
Published: June 2012

The purpose of this paper is to analyze the life cycle of tropical cyclones in terms of a K‐Vmax diagram. Such a diagram summarizes the time evolution of the integrated kinetic energy K and the maximum tangential wind Vmax, which respectively measure vortex size and intensity. A typical life cycle consists of an incipient stage in which K and Vmax slowly increase until Vmax≈25 m s−1, a deepening stage in which K and Vmax increase more rapidly until Vmax≈60 m s−1, and finally a mature stage in which K continues to grow at approximately the same rate while Vmax remains fixed or even decreases. This typical life cycle can be diagnostically analyzed using a theoretical argument that is based on the balanced vortex model and, in particular, on the associated geopotential tendency equation. This is a second order partial differential equation containing the diabatic forcing and, under idealized conditions, two spatially varying coefficients: the static stability and the inertial stability, whose ratio determines the local Rossby length ℓ. Thus, the balanced azimuthal wind and temperature tendencies in a tropical vortex depend not only on the diabatic forcing, but also on the spatial distribution of ℓ. Under the simplifying assumption that the diabatic heating and the associated response are confined to the first internal vertical mode, the geopotential tendency equation reduces to a radial structure equation, which can be solved numerically. These solutions illustrate how the vortex response to diabatic heating depends on whether this heating lies in the large Rossby length region outside the radius of maximum wind or in the small Rossby length region inside the radius of maximum wind. Tangential wind tendencies are found to be hypersensitive to the location of the diabatic heating relative to the small Rossby length region in the vortex core.
Towards a comprehensive assessment of model structural adequacy
Authors: Gupta Hoshin V. , Clark Martyn P. , Vrugt Jasper A. , Abramowitz Gab , Ye Ming
Published: June 2012

The past decade has seen significant progress in characterizing uncertainty in environmental systems models, through statistical treatment of incomplete knowledge regarding parameters, model structure, and observational data. Attention has now turned to the issue of model structural adequacy (MSA, a term we prefer over model structure “error”). In reviewing philosophical perspectives from the groundwater, unsaturated zone, terrestrial hydrometeorology, and surface water communities about how to model the terrestrial hydrosphere, we identify several areas where different subcommunities can learn from each other. In this paper, we (a) propose a consistent and systematic “unifying conceptual framework” consisting of five formal steps for comprehensive assessment of MSA; (b) discuss the need for a pluralistic definition of adequacy; (c) investigate how MSA has been addressed in the literature; and (d) identify four important issues that require detailed attention—structured model evaluation, diagnosis of epistemic cause, attention to appropriate model complexity, and a multihypothesis approach to inference. We believe that there exists tremendous scope to collectively improve the scientific fidelity of our models and that the proposed framework can help to overcome barriers to communication. By doing so, we can make better progress toward addressing the question “How can we use data to detect, characterize, and resolve model structural inadequacies?”
Rapid surficial oxidation of synthetic Fe‐Ti oxides at high temperature: Observations and consequences for magnetic measurements
Authors: Lattard Dominique , Sauerzapf Ursula , Kontny Agnes
Published: June 2012

Synthetic polycrystalline samples of Fe‐Ti oxides (titanomagnetite, Tmtss; ilmenite‐hematitess, Ilmss; pseudobrookitess, Psbss) are very sensitive to changes in the redox conditions at high temperatures, either during synthesis experiments or during thermomagnetic measurements. For instance, exposure to air for a few seconds at the end of a synthesis run at 1300°C of a Tmtss‐Ilmss sample produces surficial oxidation down to a depth of some 100 μm. This oxidation zone is well visible on backscattered electron images of polished sections through the sample pellet. It is characterized by so‐called trellis “oxyexsolution” textures, i.e., fine lamellae of Ilmss within the Tmtss crystals and lamellae of Psbss within the Ilmss crystals. In this oxidation zone the newly grown Ilmss lamellae and the surrounding Tmtss are more Fe rich than the original crystals. The presence of trellis textures in the crystals of both coexisting phases, Tmtss and Ilmss, show that only short‐scaled elemental transport within the crystals was involved and that equilibrium was not attained. Even though the oxidation zone is very narrow, the imprint of the new Tmtsscompositions is well recognizable in temperature‐dependent magnetic susceptibility curves. In temperature‐dependent saturation magnetization (MS‐T) curves, however, the contribution of more Fe‐rich Tmtss from the oxidation zone can be easily overseen. However, surficial oxidation of Tmtss does occur during MS‐T measurements with a variable field translation balance, apparently in relation with insufficient Ar flowing around the sample. Further examples of rapid surficial oxidation of Fe‐Ti oxide samples are also discussed.
Parameterized lifetime of radiation belt electrons interacting with lower‐band and upper‐band oblique chorus waves
Authors: Gu Xudong , Shprits Yuri Y. , Ni Binbin
Published: June 2012

In order to evaluate the electron lifetimes from quasi‐linear bounce‐averaged diffusion coefficients, a large amount of CPU time is required to compute scattering rates. To reduce computation time, we assume that the electron loss rates are a function of L shell and electron energy, allowing us to derive the parameterization of electron lifetime using a linear regression technique. We also present the parameterizations of lifetimes as a function of electron energy and ratios of plasma frequency to electron gyrofrequency at a fixed L shell. By considering the net loss rates due to lower‐band (0.05–0.5 |Ωce|) and upper‐band (0.5–0.7 |Ωce|) chorus waves propagating obliquely with respect to the ambient magnetic field, the parameterizations of electron lifetime for energies between 1 keV and 2 MeV are investigated in the outer radiation belt. The parameterized lifetimes indicate a strong functional dependence on electron energy, L shell, and the level of geomagnetic activity (Kp index), and are also dependent on the ratios of plasma frequency to electron gyrofrequency. During the storm time, the lifetimes for higher energy (>100 keV) electrons range from hours to days in the heart of the radiation belts. In contrast, the lifetimes for lower energy (<100 keV) electrons are mainly in the range from minutes to hours. Such parameterization efforts of radiation belt electron lifetimes are very significant for multi‐dimensional simulations of the dynamics of the radiation belt and ring current electrons.
Pre‐Columbian deforestation as an amplifier of drought in Mesoamerica
Authors: Cook B. I. , Anchukaitis K. J. , Kaplan J. O. , Puma M. J. , Kelley M. , Gueyffier D.
Published: June 2012

Droughts in pre‐Columbian Mesoamerica caused significant societal disruptions during the Late Classic and Post‐Classic Periods. While the primary causes of these droughts are still debated, it has been speculated that they may be linked to extensive deforestation associated with high population densities during these intervals. Here we show that pre‐Columbian deforestation would have biased the climate in Mesoamerica towards a drier mean state, amplifying drought in the region. In climate model simulations using a pre‐Columbian land cover reconstruction, annual precipitation decreases by 5%–15% throughout southern Mexico and the Yucatán compared to simulations using either natural forest cover or forest regrowth associated with population declines after 1500 C.E. These changes are driven primarily by large reductions (10%–20%) in precipitation during the late summer wet season (August–September). When compared to precipitation changes estimated to have occurred during the Maya collapse, our results suggest that deforestation could account for up to sixty percent of the mean drying during this interval. Many regions previously deforested in the pre‐Columbian era are now under dense forest cover, indicating potential future climate impacts should tropical deforestation of these areas accelerate.
Mid‐latitude ionospheric irregularities persisting into late morning during the magnetic storm on 19 March 2001
Authors: Li Jinghua , Ma Guanyi , Maruyama Takashi , Li Zheng
Published: June 2012

Post‐sunrise intense ionospheric irregularities at low to mid‐latitudes are reported for the first time. A method based on spaced‐receiver technique is proposed to estimate the apparent drift velocity of the irregularities by using the correlation of the slant total electron content (TEC) from 3 GPS receivers. The irregularities were detected at 23∼45°N by the GPS Earth Observation Network (GEONET) of Japan from ∼0455 LT to ∼1051 LT on 21 March 2001 during the recovery phase of the magnetic storm. At the corresponding time spread F was observed with 3 ionosondes located meridionally at Okinawa (127.8°E, 26.3°N; 20.7°N magnetic latitude), Kokubunji (139.5°E, 35.7°N; 30.0°N magnetic latitude) and Wakkanai (141.7°E, 45.4°N; 40.5°N magnetic latitude), while an intense negative ionospheric storm was processing and propagating from mid to lower latitudes. The irregularities were seen as plasma bubbles by the Defense Meteorological Satellite Program (DMSP) in‐situ measurements. Westward drift with the speed of ∼100 m/s was estimated by spaced receivers from GEONET and confirmed by DMSP during the evolution of the irregularities. The plasma bubbles at mid‐latitude sustained ∼1.5 hour after sunrise, and at the lower latitudes they survived more than 4 hours after sunrise. The observations suggested that the irregularities were generated by an eastward electric field associated with the disturbance dynamo, and the long time existence of the irregularities after sunrise seemed to be related to the daytime intense negative ionospheric storm on 21 March.
Effect of depleted continental lithosphere counterflow and inherited crustal weakness on rifting of the continental lithosphere: General results
Authors: Beaumont Christopher , Ings Steven J.
Published: June 2012

Some non‐volcanic rifted continental margins differ from the predictions of uniform lithospheric extension in two significant ways, namely: 1) large tracts of continental mantle lithosphere are exposed at the seafloor or are inferred to have been emplaced beneath the outer regions of the margin; 2) rifting evolves from distributed extension with multiple rifts to terminal focused rifting. These characteristics are explained by depth‐dependent extension. We investigate this type of deformation using 2D upper‐mantle‐scale dynamical finite element models of rifting that include: 1) lithospheric counterflow, the gravitationally driven lateral flow of depleted lower lithosphere during rifting, as a mechanism for underplating and exhuming continental mantle, and; 2) inherited crustal weak zones that cause initially distributed syn‐rift extension. Depleted lower lithosphere (compositionally less dense than sublithospheric mantle by 50–80 kg m−3, with a moderately ‘dry’ olivine rheology) efficiently flows laterally thereby exhuming zones of continental mantle lithosphere that are respectively up to 90 and 140 km wide. Inherited crustal weak zones that are offset from the main central rift axis can be reactivated as offset rift basins. Extension in these basins depends on their proximity to the central rift and the ease with which crust decouples from mantle: narrow (<50 km) basins when crust does not decouple, and longer‐lived wider basins for moderate decoupling. For weak crust that readily decouples during depth‐dependent extension, the offset rift basins may remain active throughout rifting, giving rise to highly allochthonous crustal terranes that are translated toward and over the central rift axis.
Crystals stirred up: 2. Numerical insights into the formation of the earliest crust on the Moon
Authors: Suckale Jenny , Elkins‐Tanton Linda T. , Sethian James A.
Published: June 2012

This is the second paper in a two‐part series examining the fluid dynamics of crystal settling and flotation in the lunar magma ocean. In the first paper, we develop a direct numerical method for resolving the hydrodynamic interactions between crystals and their feedback on the flow field in magmatic liquid. In this paper, we use this computational technique to test the leading model for the formation of the earliest crust on the Moon. The anorthositic lithology of the lunar crust is thought to have been formed by the flotation of buoyant plagioclase crystals at a time when the lunar mantle was still wholly or largely molten. This model is appealing from an observational point of view, but its fluid dynamical validity is not obvious, because (1) plagioclase probably started crystallizing very late (i.e., when the magma ocean was already 80% solidified) and (2) a significant portion of the shallow lunar crust consists of almost pure plagioclase (>90 vol. %), requiring very efficient plagioclase segregation. The goal of this study is to better understand the fluid dynamical conditions that hinder or facilitate crystal settling or flotation. Our approach complements earlier studies by explicitly linking the petrological and fluid dynamical evolution and by focusing on the effect of increasing crystal fraction. We find that crystal settling was probably possible throughout the entire solidification history of the lunar magma ocean as long as crystal sizes were sufficiently large (r > 1 mm) and crystal fraction sufficiently low (ϕ < 13%).
Spreading of energy in the Ding-Dong model
Authors: Roy S. , Pikovsky A.
Published: June 2012

We study the properties of energy spreading in a lattice of elastically colliding harmonic oscillators (Ding-Dong model). We demonstrate that in the regular lattice the spreading from a localized initial state is mediated by compactons and chaotic breathers. In a disordered lattice, the compactons do not exist, and the spreading eventually stops, resulting in a finite configuration with a few chaotic spots.
Telecommunications-band heralded single photons from a silicon nanophotonic chip
Authors: Davanço Marcelo , Ong Jun Rong , Shehata Andrea Bahgat , Tosi Alberto , Agha Imad , Assefa Solomon , Xia Fengnian , Green William M. J. , Mookherjea Shayan , Srinivasan Kartik
Published: June 2012

We demonstrate room temperature heralded single photon generation in a CMOS-compatible silicon nanophotonic device. The strong modal confinement and slow group velocity provided by a coupled resonator optical waveguide produced a large four-wave-mixing nonlinearity coefficient γeff≈4100 W−1 m−1 at telecommunications wavelengths. Spontaneous four-wave-mixing using a degenerate pump beam at 1549.6 nm created photon pairs at 1529.5 nm and 1570.5 nm with a coincidence-to-accidental ratio exceeding 20. A photon correlation measurement of the signal (1529.5 nm) photons heralded by the detection of the idler (1570.5 nm) photons showed antibunching with g(2)(0)=0.19±0.03. The demonstration of a single photon source within a silicon platform holds promise for future integrated quantum photonic circuits.
Modeling and theoretical efficiency of a silicon nanowire based thermoelectric junction with area enhancement
Authors: Seong M. , Sadhu J. S. , Ma J. , Ghossoub M. G. , Sinha S.
Published: June 2012

Recent experimental work suggests that individual silicon nanowires with rough surfaces possess a thermoelectric figure of merit as high as 0.6 near room temperature. This paper addresses the possibility of using an array of such nanowires in a thermoelectric junction for generation. Employing a model of frequency dependent phonon boundary scattering, we estimate the effective thermal conductivity of the array and investigate heat flow through the junction. We show that charge transport is largely unaffected by the roughness scales considered. Enhancing the area for heat exchange at an individual 200 μm × 200 μm p-n junction yields significant temperature differences across the junction leading to power >0.6 mW and efficiency >1.5% for a junction with effective thermal conductivity <5 W/mK, when the source and sink are at 450 K and 300 K, respectively. We show that relatively short nanowires of ∼50 μm length are sufficient for obtaining peak power and reasonable efficiency. This substantially reduces the challenge of engineering low resistivity electrical contacts that critically affect power and efficiency. This paper provides insight into how fundamental transport in relation to bulk heat transfer and charge transport, affects the performance of thermoelectric junctions based on nanostructured materials.
Size dependent carrier thermal escape and transfer in bimodally distributed self assembled InAs/GaAs quantum dots
Authors: Muñoz-Matutano G. , Suárez I. , Canet-Ferrer J. , Alén B. , Rivas D. , Seravalli L. , Trevisi G. , Frigeri P. , Martínez-Pastor J.
Published: June 2012

We have investigated the temperature dependent recombination dynamics in two bimodally distributed InAs self assembled quantum dots samples. A rate equations model has been implemented to investigate the thermally activated carrier escape mechanism which changes from exciton-like to uncorrelated electron and hole pairs as the quantum dot size varies. For the smaller dots, we find a hot exciton thermal escape process. We evaluated the thermal transfer process between quantum dots by the quantum dot density and carrier escape properties of both samples.
Calibration of an advanced neutral particle analyzer for the Madison Symmetric Torus reversed-field pinch
Authors: Reusch J. A. , Anderson J. K. , Belykh V. , Eilerman S. , Liu D. , Fiksel G. , Polosatkin S.
Published: June 2012

A new E∥B neutral particle analyzer, which has recently been installed on Madison Symmetric Torus (MST) reversed-field pinch (RFP), has now been calibrated, allowing the measurement of the fast ion density and energy distribution. This diagnostic, dubbed the advanced neutral particle analyzer (ANPA), can simultaneously produce time resolved measurements of the efflux of both hydrogen and deuterium ions from the plasma over a 35 keV energy range with an energy resolution of 2–4 keV and a time resolution of 10 μs. These capabilities are needed to measure both majority ion heating that occurs during magnetic reconnection events in MST and the behavior of the fast ions from the 1 MW hydrogen neutral beam injector on MST. Calibration of the ANPA was performed using a custom ion source that resides in the flight tube between the MST and the ANPA. In this work, the ANPA will be described, the calibration procedure and results will be discussed, and initial measurements of the time evolution of 25 keV neutral beam injection-born fast ions will be presented.
Electrical transition of (3,3) carbon nanotube on patterned hydrogen terminated Si(001)-2 × 1 driven by electric field
Authors: Gupta Bikash C. , Konar Shyamal , Jena Puru
Published: June 2012

Structure, energetics, and electrical properties of (3,3) carbon nanotube (CNT) supported on patterned hydrogen terminated Si(001): 2 × 1 surface are studied using density functional theory. Our investigation reveals that an otherwise metallic (3,3) CNT when supported becomes semiconducting with a band gap of ≈0.5 eV due to its strong interaction with the surface. During adsorption, Si-C bonds form at the interface and charges transfer from Si surface to CNT. The Si-C bonds at the interface are partially covalent and partially ionic in nature. Under the application of an external electric field, the bandgap of the supported CNT reduces to zero, hence rendering the system metallic.
Non-invasive determination of external forces in vortex-pair-cylinder interactions
Authors: Hartmann D. , Schröder W. , Shashikanth B. N.
Published: June 2012

Expressions for the conserved linear and angular momenta of a dynamically coupled fluid + solid system are derived. Based on the knowledge of the flow velocity field, these expressions allow the determination of the external forces exerted on a body moving in the fluid such as, e.g., swimming fish. The verification of the derived conserved quantities is done numerically. The interaction of a vortex pair with a circular cylinder in various configurations of motions representing a generic test case for a dynamically coupled fluid + solid system is investigated in a weakly compressible Navier-Stokes setting using a Cartesian cut-cell method, i.e., the moving circular cylinder is represented by cut cells on a moving mesh. The objectives of this study are twofold. The first objective is to show the robustness of the derived expressions for the conserved linear and angular momenta with respect to bounded and discrete data sets. The second objective is to study the coupled dynamics of the vortex pair and a neutrally buoyant cylinder free to move in response to the fluid stresses exerted on its surface. A comparison of the vortex-body interaction with the case of a fixed circular cylinder evidences significant differences in the vortex dynamics. When the cylinder is fixed strong secondary vorticity is generated resulting in a repeating process between the primary vortex pair and the cylinder. In the neutrally buoyant cylinder case, a stable structure consisting of the primary vortex pair and secondary vorticity shear layers stays attached to the moving cylinder. In addition to these fundamental cases, the vortex-pair-cylinder interaction is studied for locomotion at constant speed and locomotion at constant thrust. It is shown that a similar vortex structure like in the neutrally buoyant cylinder case is obtained when the cylinder moves away from the approaching vortex pair at a constant speed smaller than the vortex pair translational velocity. Finally, the idealized symmetric settings are complemented by an asymmetric interaction of a vortex pair and a cylinder. This case is discussed for a fixed and a neutrally buoyant cylinder to show the validity of the derived relations for multi-dimensional body dynamics.
Experimental and numerical investigation of binary coalescence: Liquid bridge building and internal flow fields
Authors: Eiswirth R. T. , Bart H.-J. , Ganguli A. A. , Kenig E. Y.
Published: June 2012

In this work, we present the results of experimental and numerical investigation of the liquid bridge building and internal flows during a binary droplet-droplet coalescence event. A system consisting of two rising toluene droplets with different droplet radii that coalesce in surrounding water is considered. The growth of the liquid bridge between the two droplets during the coalescence event is found to be in the inertial regime, whereas the bridge radius grows in proportion to the square root of time. Further, the internal mixing of the two droplets is investigated. It is observed that when two droplets with the same radius coalesce, there is nearly no internal mixing within the first 40 ms after the coalescence start. In contrast, when two droplets with different radii coalesce, a liquid jet directed from the smaller to the larger droplet appears during the coalescence event. A good agreement between the experimental and numerical data is established.
Origin of temperature plateaus in laser-heated diamond anvil cell experiments
Authors: Geballe Zachary M. , Jeanloz Raymond
Published: June 2012

Many high-pressure high-temperature studies using laser-heated diamond cells have documented plateaus in the increase of temperature with increasing laser power or with time. By modeling heat transfer in typical laser-heated diamond anvil cell experiments, we demonstrate that latent heat due to melting or other phase transformation is unlikely to be the source of observed plateaus in any previously published studies, regardless of whether pulsed or continuous lasers were used. Rather, large increases (∼10-fold) in thermal conductivity can explain some of the plateaus, and modest increases in reflectivity (tens of percent) can explain any or all of them. Modeling also shows that the sub-microsecond timescale of heating employed in recent pulsed heating experiments is fast enough compared to heat transport into and through typical insulations, but too slow compared to heat transport into metallic laser absorbers themselves to allow the detection of a large plateau due to latent heat of fusion. Four new designs are suggested for future experiments that could use the simple observation of a latent heat-induced plateau to provide reliable high-pressure melting data.
Perfect spin-filter and quantum-signal generator in a parallel coupled multiple triple-quantum-dots device
Authors: Fu Hua-Hua , Yao Kai-Lun
Published: June 2012

Electronic transport through a parallel coupled multiple triple-quantum-dots (tQDs) chain is theoretical studied. By producing an energy difference between the site energy of the upper QDs and the down ones and considering a Zeeman splitting, several highly to 100% spin-polarized windows (SPWs) with very steep edges appear in the linear conductance spectra due to the Fano antiresonance. Moreover, if the Dicke resonance is considered, some nearest SPWs with opposite direction of the spin polarization just contact with each other in some suitable conditions. These results strongly support that this multi-tQDs device can serve multiple purposes including perfect spin-filtering and quantum-signal generator.
Optically pumped amplified spontaneous emission in an ionic liquid-based polymer light-emitting electrochemical cell
Authors: Sakanoue Tomo , Sawabe Kosuke , Yomogida Yohei , Takenobu Taishi , Seki Shiro , Ono Shimpei
Published: June 2012

Optically pumped amplified spontaneous emission (ASE) is demonstrated in the active layer of the polymer light-emitting electrochemical cells (LECs). The active layer blend of the light-emitting polymer and the ionic liquid retained a high degree of transparency, enabling its use as an optical slab waveguide, allowing a low ASE threshold energy of 4.1 μJ cm−2 to be achieved. We also demonstrate a planar LEC that showed fast turn on, bright linear shape emission in the middle of the two contacts, and a relatively high current density of 36 A cm−2 with a low driving voltage of 6 V.
Kinetics of axial composition evolution in multi-component alloy nanowires
Authors: Ye H. , Yu Z. Y. , Kodambaka S. , Shenoy V. B.
Published: June 2012

The axial composition profiles in two-component alloy semiconductor nanowires are theoretically studied based on a comprehensive transient growth model which accounts for both surface diffusion and direct impingement of atoms to catalyst. The composition variation derives from the different growth rates contributed by each component. Our simulations reveal that the component with larger (smaller) diffusivity will segregate near the bottom (top) of the nanowire. In the presence (absence) of direct deposition on nanowire sidewalls, the steady state alloy composition is determined by the ratio of effective diffusion lengths (impingement rates to the catalyst).
Electric field enhanced conductivity in strongly coupled dense metal plasma
Authors: Stephens J. , Neuber A.
Published: June 2012

Experimentation with dense metal plasma has shown that non-negligible increases in plasma conductivity are induced when a relatively low electric field (∼6 kV/cm) is applied. Existing conductivity models assume that atoms, electrons, and ions all exist in thermal equilibrium. This assumption is invalidated by the application of an appreciable electric field, where electrons are accelerated to energies comparable to the ionization potential of the surrounding atoms. Experimental data obtained from electrically exploded silver wire is compared with a finite difference hydrodynamic model that makes use of the SESAME equation-of-state database. Free electron generation through both thermal and electric field excitations, and their effect on plasma conductivity are applied and discussed.
Treatment surfaces with atomic oxygen excited in dielectric barrier discharge plasma of O2 admixed to N2
Authors: Shun'ko E. V. , Belkin V. S.
Published: June 2012

This paper describes the increase in surface energy of substrates by their treatment with gas composition generated in plasmas of DBD (Dielectric Barrier Discharge) in O2 admixed with N2. Operating gas dissociation and excitation was occurred in plasmas developed in two types of reactors of capacitively-coupled dielectric barrier configurations: coaxial cylindrical, and flat rectangular. The coaxial cylindrical type comprised an inner cylindrical electrode encapsulated in a ceramic sheath installed coaxially inside a cylindrical ceramic (quartz) tube passing through an annular outer electrode. Components of the flat rectangular type were a flat ceramic tube of a narrow rectangular cross section supplied with two flat electrodes mounted against one another outside of the long parallel walls of this tube. The operating gas, mixture of N2 and O2, was flowing in a completely insulated discharge gap formed between insulated electrodes of the devices with an average velocity of gas inlet of about 7 to 9 m/s. Dielectric barrier discharge plasma was excited in the operating gaps with a bipolar pulse voltage of about 6 kV for 2 ms at 50 kHz repetition rate applied to the electrodes of the coaxial device, and of about 14 kV for 7 ms at 30 kHz repetition rate for the flat linear device. A lifetime of excited to the 2s22p4(1S0) state in DBD plasma and streaming to the surfaces with a gas flow atomic oxygen, responsible presumably for treating surfaces, exceeded 10 ms in certain cases, that simplified its separation from DBD plasma and delivery to substrates. As it was found in particular, surfaces of glass and some of polymers revealed significant enhancement in wettability after treatment.
Magnetic hysteresis of an artificial square ice studied by in-plane Bragg x-ray resonant magnetic scattering
Authors: Morgan J. P. , Kinane C. J. , Charlton T. R. , Stein A. , Sánchez-Hanke C. , Arena D. A. , Langridge S. , Marrows C. H.
Published: June 2012

We report X-ray resonant magnetic scattering studies of a Permalloy artificial square ice nanomagnet array, focussing on the field-driven evolution of the sum Σ and difference Δ signals of left and right handed circularly polarized synchrotron X-rays at different lateral positions in reciprocal space Qx. We used X-rays tuned to the Fe L3 resonance energy, with the scattering plane aligned along a principal symmetry axis of the array. Details of the specular Δ hysteresis curve are discussed, following the system magnetization from an initial demagnetized state. The periodic structure gives rise to distinct peaks at in-plane reciprocal Bragg positions, as shown by fitting Σ(Qx) to a model based on a simple unit cell structure. Diffraction order-dependent hysteresis in Δ is observed, indicative of the reordering of magnetization on the system's two interpenetrating sublattices, which markedly deviates from an ideal Ising picture under strong applied fields.
Critical role for calcium mobilization in activation of the NLRP3 inflammasome
Authors: Murakami Tomohiko , Ockinger Johan , Yu Jiujiu , Byles Vanessa , McColl Aisleen , Hofer Aldebaran M. , Horng Tiffany
Published: June 2012

The NLRP3 (nucleotide-binding domain, leucine-rich-repeat-containing family, pyrin domain-containing 3) inflammasome mediates production of inflammatory mediators, such as IL-1β and IL-18, and as such is implicated in a variety of inflammatory processes, including infection, sepsis, autoinflammatory diseases, and metabolic diseases. The proximal steps in NLRP3 inflammasome activation are not well understood. Here we elucidate a critical role for Ca
2+
mobilization in activation of the NLRP3 inflammasome by multiple stimuli. We demonstrate that blocking Ca
2+
mobilization inhibits assembly and activation of the NLRP3 inflammasome complex, and that during ATP stimulation Ca
2+
signaling is pivotal in promoting mitochondrial damage. C/EPB homologous protein, a transcription factor that can modulate Ca
2+
release from the endoplasmic reticulum, amplifies NLRP3 inflammasome activation, thus linking endoplasmic reticulum stress to activation of the NLRP3 inflammasome. Our findings support a model for NLRP3 inflammasome activation by Ca
2+
-mediated mitochondrial damage.
Transformation of a transposon into a derived prolactin promoter with function during human pregnancy
Authors: Emera Deena , Wagner Günter P.
Published: June 2012

Transposable elements (TEs) are known to provide DNA for host regulatory functions, but the mechanisms underlying the transformation of TEs into
cis
-regulatory elements are unclear. In humans two TEs—MER20 and MER39—contribute the enhancer/promoter for decidual prolactin (
dPRL
), which is dramatically induced during pregnancy. We show that evolution of the strong human
dPRL
promoter was a multistep process that took millions of years. First, MER39 inserted near MER20 in the primate/rodent ancestor, and then there were two phases of activity enhancement in primates. Through the mapping of causal nucleotide substitutions, we demonstrate that strong promoter activity in apes involves epistasis between transcription factor binding sites (TFBSs) ancestral to MER39 and derived sites. We propose a mode of molecular evolution that describes the process by which MER20/MER39 was transformed into a strong promoter, called “epistatic capture.” Epistatic capture is the stabilization of a TFBS that is ancestral but variable in outgroup lineages, and is fixed in the ingroup because of epistatic interactions with derived TFBSs. Finally, we note that evolution of human promoter activity coincides with the emergence of a unique reproductive character in apes, highly invasive placentation. Because prolactin communicates with immune cells during pregnancy, which regulate fetal invasion into maternal tissues, we speculate that ape
dPRL
promoter activity evolved in response to increased invasiveness of ape fetal tissue.
Ume6 transcription factor is part of a signaling cascade that regulates autophagy
Authors: Bartholomew Clinton R. , Suzuki Tsukasa , Du Zhou , Backues Steven K. , Jin Meiyan , Lynch-Day Melinda A. , Umekawa Midori , Kamath Avani , Zhao Mantong , Xie Zhiping , Inoki Ken , Klionsky Daniel J.
Published: June 2012

Autophagy has been implicated in a number of physiological processes important for human heath and disease. Autophagy involves the formation of a double-membrane cytosolic vesicle, an autophagosome. Central to the formation of the autophagosome is the ubiquitin-like protein autophagy-related (Atg)8 (microtubule-associated protein 1 light chain 3/LC3 in mammalian cells). Following autophagy induction, Atg8 shows the greatest change in expression of any of the proteins required for autophagy. The magnitude of autophagy is, in part, controlled by the amount of Atg8; thus, controlling Atg8 protein levels is one potential mechanism for modulating autophagy activity. We have identified a negative regulator of
ATG8
transcription, Ume6, which acts along with a histone deacetylase complex including Sin3 and Rpd3 to regulate Atg8 levels; deletion of any of these components leads to an increase in Atg8 and a concomitant increase in autophagic activity. A similar regulatory mechanism is present in mammalian cells, indicating that this process is highly conserved.
Neuritin produces antidepressant actions and blocks the neuronal and behavioral deficits caused by chronic stress
Authors: Son Hyeon , Banasr Mounira , Choi Miyeon , Chae Seung Yeon , Licznerski Pawel , Lee Boyoung , Voleti Bhavya , Li Nanxin , Lepack Ashley , Fournier Neil M. , Lee Ka Rim , Lee In Young , Kim Juhyun , Kim Joung-Hun , Kim Yong Ho , Jung Sung Jun , Duman Ronald S.
Published: June 2012

Decreased neuronal dendrite branching and plasticity of the hippocampus, a limbic structure implicated in mood disorders, is thought to contribute to the symptoms of depression. However, the mechanisms underlying this effect, as well as the actions of antidepressant treatment, remain poorly characterized. Here, we show that hippocampal expression of neuritin, an activity-dependent gene that regulates neuronal plasticity, is decreased by chronic unpredictable stress (CUS) and that antidepressant treatment reverses this effect. We also show that viral-mediated expression of neuritin in the hippocampus produces antidepressant actions and prevents the atrophy of dendrites and spines, as well as depressive and anxiety behaviors caused by CUS. Conversely, neuritin knockdown produces depressive-like behaviors, similar to CUS exposure. The ability of neuritin to increase neuroplasticity is confirmed in models of learning and memory. Our results reveal a unique action of neuritin in models of stress and depression, and demonstrate a role for neuroplasticity in antidepressant treatment response and related behaviors.
Phosphoinositide isoforms determine compartment-specific ion channel activity
Authors: Zhang Xiaoli , Li Xinran , Xu Haoxing
Published: June 2012

Phosphoinositides serve as address labels for recruiting peripheral cytoplasmic proteins to specific subcellular compartments, and as endogenous factors for modulating the activity of integral membrane proteins. Phosphatidylinositol 4,5-bisphosphate (PI(4,5)P
2
) is a plasma-membrane (PM)–specific phosphoinositide and a positive cofactor required for the activity of most PM channels and transporters. This requirement for phosphoinositide cofactors has been proposed to prevent PM channel/transporter activity during passage through the biosynthetic/secretory and endocytic pathways. To determine whether intracellularly localized channels are similarly “inactivated” at the PM, we studied PIP
2
modulation of intracellular TRPML1 channels. TRPML1 channels are primarily localized in lysosomes, but can also be detected temporarily in the PM upon lysosomal exocytosis. By directly patch-clamping isolated lysosomes, we previously found that lysosomal, but not PM-localized, TRPML1 is active with PI(3,5)P
2
, a lysosome-specific PIP
2
, as the underlying positive cofactor. Here we found that “silent” PM-localized TRPML1 could be activated by depleting PI(4,5)P
2
levels and/or by adding PI(3,5)P
2
to inside-out membrane patches. Unlike PM channels, surface-expressed TRPML1 underwent a unique and characteristic run-up upon patch excision, and was potently inhibited by a low micromolar concentration of PI(4,5)P
2
. Conversely, depletion of PI(4,5)P
2
by either depolarization-induced activation or chemically induced translocation of 5′-phosphatase potentiated whole-cell TRPML1 currents. PI(3,5)P
2
activation and PI(4,5)P
2
inhibition of TRPML1 were mediated by distinct basic amino acid residues in a common PIP
2
-interacting domain. Thus, PI(4,5)P
2
may serve as a negative cofactor for intracellular channels such as TRPML1. Based on these results, we propose that phosphoinositide regulation sets compartment-specific activity codes for membrane channels and transporters.
Multistep molecular mechanism for Bone morphogenetic protein extracellular transport in the
Drosophila
embryo
Authors: Sawala Annick , Sutcliffe Catherine , Ashe Hilary L.
Published: June 2012

In the
Drosophila
embryo, formation of a bone morphogenetic protein (BMP) morphogen gradient requires transport of a heterodimer of the BMPs Decapentaplegic (Dpp) and Screw (Scw) in a protein shuttling complex. Although the core components of the shuttling complex—Short Gastrulation (Sog) and Twisted Gastrulation (Tsg)—have been identified, key aspects of this shuttling system remain mechanistically unresolved. Recently, we discovered that the extracellular matrix protein collagen IV is important for BMP gradient formation. Here, we formulate a molecular mechanism of BMP shuttling that is catalyzed by collagen IV. We show that Dpp is the only BMP ligand in
Drosophila
that binds collagen IV. A collagen IV binding–deficient Dpp mutant signals at longer range in vivo, indicating that collagen IV functions to immobilize free Dpp in the embryo. We also provide in vivo evidence that collagen IV functions as a scaffold to promote shuttling complex assembly in a multistep process. After binding of Dpp/Scw and Sog to collagen IV, protein interactions are remodeled, generating an intermediate complex in which Dpp/Scw-Sog is poised for release by Tsg through specific disruption of a collagen IV–Sog interaction. Because all components are evolutionarily conserved, we propose that regulation of BMP shuttling and immobilization through extracellular matrix interactions is widely used, both during development and in tissue homeostasis, to achieve a precise extracellular BMP distribution.
Intestinal synthesis and secretion of bile salts as an adaptation to developmental biliary atresia in the sea lamprey
Authors: Yeh Chu-Yin , Chung-Davidson Yu-Wen , Wang Huiyong , Li Ke , Li Weiming
Published: June 2012

Bile salt synthesis is a specialized liver function in vertebrates. Bile salts play diverse roles in digestion and signaling, and their homeostasis is maintained by controlling input (biosynthesis) and intestinal conservation. Patients with biliary atresia (i.e., obliteration of the biliary tree) suffer liver fibrosis and cirrhosis. In contrast, sea lamprey thrives despite developmental biliary atresia. We discovered that the sea lamprey adapts to biliary atresia through a unique mechanism of de novo synthesis and secretion of bile salts in intestine after developmental biliary atresia, in addition to known mechanisms, such as the reduction of bile salt synthesis in liver. During and after developmental biliary atresia, expression of
cyp7a1
in intestine increased by more than 100-fold (
P
< 0.001), whereas in liver it decreased by the same magnitude (
P
< 0.001). Concurrently, bile salt pools changed in similar patterns and magnitudes in these two organs and the composition shifted from C24 bile alcohol sulfates to taurine-conjugated C24 bile acids. In addition, both in vivo and ex vivo experiments showed that aductular sea lamprey secreted taurocholic acid into its intestinal lumen. Our results indicate that the sea lamprey, a jawless vertebrate, may be in an evolutionarily transitional state where bile salt synthesis occurs in both liver and intestine. Understanding the molecular basis of these mechanisms may shed light on the evolution of bile salt synthesis and possible therapy for infant biliary atresia.
Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples
Authors: Lange Oliver F. , Rossi Paolo , Sgourakis Nikolaos G. , Song Yifan , Lee Hsiau-Wei , Aramini James M. , Ertekin Asli , Xiao Rong , Acton Thomas B. , Montelione Gaetano T. , Baker David
Published: June 2012

We have developed an approach for determining NMR structures of proteins over 20 kDa that utilizes sparse distance restraints obtained using transverse relaxation optimized spectroscopy experiments on perdeuterated samples to guide RASREC Rosetta NMR structure calculations. The method was tested on 11 proteins ranging from 15 to 40 kDa, seven of which were previously unsolved. The RASREC Rosetta models were in good agreement with models obtained using traditional NMR methods with larger restraint sets. In five cases X-ray structures were determined or were available, allowing comparison of the accuracy of the Rosetta models and conventional NMR models. In all five cases, the Rosetta models were more similar to the X-ray structures over both the backbone and side-chain conformations than the “best effort” structures determined by conventional methods. The incorporation of sparse distance restraints into RASREC Rosetta allows routine determination of high-quality solution NMR structures for proteins up to 40 kDa, and should be broadly useful in structural biology.
Polyene antibiotic that inhibits membrane transport proteins
Authors: te Welscher Yvonne Maria , van Leeuwen Martin Richard , de Kruijff Ben , Dijksterhuis Jan , Breukink Eefjan
Published: June 2012

The limited therapeutic arsenal and the increase in reports of fungal resistance to multiple antifungal agents have made fungal infections a major therapeutic challenge. The polyene antibiotics are the only group of antifungal antibiotics that directly target the plasma membrane via a specific interaction with the main fungal sterol, ergosterol, often resulting in membrane permeabilization. In contrast to other polyene antibiotics that form pores in the membrane, the mode of action of natamycin has remained obscure but is not related to membrane permeabilization. Here, we demonstrate that natamycin inhibits growth of yeasts and fungi via the immediate inhibition of amino acid and glucose transport across the plasma membrane. This is attributable to ergosterol-specific and reversible inhibition of membrane transport proteins. It is proposed that ergosterol-dependent inhibition of membrane proteins is a general mode of action of all the polyene antibiotics, of which some have been shown additionally to permeabilize the plasma membrane. Our results imply that sterol-protein interactions are fundamentally important for protein function even for those proteins that are not known to reside in sterol-rich domains.
Rapid hybridization of nucleic acids using isotachophoresis
Authors: Bercovici Moran , Han Crystal M. , Liao Joseph C. , Santiago Juan G.
Published: June 2012

We use isotachophoresis (ITP) to control and increase the rate of nucleic acid hybridization reactions in free solution. We present a new physical model, validation experiments, and demonstrations of this assay. We studied the coupled physicochemical processes of preconcentration, mixing, and chemical reaction kinetics under ITP. Our experimentally validated model enables a closed form solution for ITP-aided reaction kinetics, and reveals a new characteristic time scale which correctly predicts order 10,000-fold speed-up of chemical reaction rate for order 100 pM reactants, and greater enhancement at lower concentrations. At 500 pM concentration, we measured a reaction time which is 14,000-fold lower than that predicted for standard second-order hybridization. The model and method are generally applicable to acceleration of reactions involving nucleic acids, and may be applicable to a wide range of reactions involving ionic reactants.
Antisilencing role of the RNA-directed DNA methylation pathway and a histone acetyltransferase in
Arabidopsis
Authors: Li Xiaojie , Qian Weiqiang , Zhao Yusheng , Wang Chunlei , Shen Jie , Zhu Jian-Kang , Gong Zhizhong
Published: June 2012

REPRESSOR OF SILENCING 1 (ROS1) is a DNA demethylation enzyme that was previously identified during a genetic screen for the silencing of both
RD29A-LUC
and
35S-NPTII
transgenes on a T-DNA construct. Here we performed a genetic screen to identify additional mutants in which the
35S-NPTII
transgene is silenced. We identified several alleles of
ros1
and of the following components of the RNA-directed DNA methylation (RdDM) pathway: NRPD1 (the largest subunit of polymerase IV), RDR2, NRPE1 (the largest subunit of polymerase V), NRPD2, AGO4, and DMS3. Our results show that the silencing of
35S-NPTII
in the RdDM pathway mutants is due to the reduced expression of
ROS1
in the mutants. We also identified a putative histone acetyltransferase (ROS4) from the genetic screen. The acetyltransferase contains a PHD-finger domain that binds to unmethylated histone H3K4. The mutation in
ROS4
led to reduction of H3K18 and H3K23 acetylation levels. We show that the silencing of
35S-NPTII
and some transposable element genes was released by the
ddm1
mutation but that this also required ROS4. Our study identifies a unique antisilencing factor, and reveals that the RdDM pathway has an antisilencing function due to its role in maintaining
ROS1
expression.