bluuebunny/crossref_metadata_2025 huggingface dataset:
Origin of Ultra-High Energy Cosmic Rays: Nuclear Composition of Gamma-Ray Burst Jets
Authors: Shibata Sanshiro , Tominaga Nozomu
Published: September 2012

Ultra-high energy cosmic rays (UHECRs) are the most energetic particles flying from space and their source is not clarified yet. Recently, the Pierre Auger Observatory (PAO) suggests that UHECRs involve heavy nuclei. The PAO results require that a considerable fraction of metal nuclei must exist in the accelerating site, which can be realized only in the stellar interior. This puts strong constraints on the origin of UHECRs. In order to definitize the constraints from PAO results, we investigate the fraction of metal nuclei in a relativistic jet in gamma-ray burst associated with core-collapse supernova. If the jet is initially dominated by radiation field, quasi-statistical equilibrium (QSE) is established and heavy nuclei are dissociated to light particles such as 4He during the acceleration and expansion. On the other hand, if the jet is mainly accelerated by magnetic field heavy or intermediate mass nuclei can survive. The criterion to contain the metal nuclei is that the temperature at the launch site is below 4.5 × 109K. Therefore, if the composition of UHECRs is dominated by metal nuclei, a GRB with the magnetized jet is the most plausible candidate of the accelerating site.
Radio Insight into the Nature of Type IIb Progenitors
Authors: Stockdale Christopher J. , Ryder S. D. , Horesh A. , Weiler K. W. , Panagia N. , Van Dyk S. D. , Bauer F. E. , Immler S. , Sramek R. A. , Pooley D. , Marcaide J. M. , Kassim N.
Published: September 2012

We present the results of over two decades of radio observations of type IIb Supernovae with the Very Large Array and the Australia Telescope Compact Array. These radio studies illustrate the need for multi-wavelength follow-up to determine the progenitor scenario for type IIb events.
On the importance of the equation of state for the neutrino-driven supernova explosion mechanism
Authors: Suwa Yudai
Published: September 2012

We present two-dimensional numerical simulations of core-collapse supernova including multi-energy neutrino radiative transfer. We aim to examine the influence of the equation of state (EOS) for the dense nuclear matter. We employ four sets of EOSs, namely, those by Lattimer and Swesty (LS) and Shen et al., which became standard EOSs in the core-collapse supernova community. We reconfirm that not every EOS produces an explosion in spherical symmetry, which is consistent with previous works. In two-dimensional simulations, we find that the structure of the accretion flow is significantly different between LS EOS and Shen EOS, inducing an even qualitatively different evolution of the shock wave, namely, the LS EOS leads to shock propagation beyond 2000 km from the center, while the Shen EOS shows only oscillations within 500 km. The possible origins of the difference are discussed.
Optical to X-rays SNe light curves following shock breakout through a thick wind
Authors: Svirski Gilad , Nakar Ehud , Sari Re'em
Published: September 2012

We present luminosity and temperature light curves following supernova shock breakouts through a thick wind. These events are very luminous and their spectrum may contain both an X-ray and a UV/optical component. For breakout pulse durations between a week and a month, the X-ray component luminosity peaks 100-500 days after the explosion, respectively.
Type II-P supernovae in the mid-infrared
Authors: Szalai Tamás , Vinkó József
Published: September 2012

We present detailed analysis of mid-infrared (MIR) data for 9 type II-P supernovae from the public Spitzer database. Spectral energy distributions (SEDs) from observed fluxes are fitted with simple models to get basic information about the dust as the presumed source of MIR radiation. We found two SNe, 2005ad and 2005af, which likely have newly-formed dust in their environment, while in the other seven cases the observed MIR flux may originate from pre-existing circumstellar or interstellar dust.
The Effects of Sibling Relationships on Social Adjustment Among Japanese Twins Compared With Singletons
Authors: Nozaki Mari , Fujisawa Keiko K. , Ando Juko , Hasegawa Toshikazu
Published: September 2012

This study examined the link between sibling relationships and children's social adjustment by comparing twin siblings and siblings with different ages (singleton siblings), and clarified the role of reciprocity in sibling relationships on children's social development. Mothers of 58 monozygotic twin pairs, 48 dizygotic twin pairs, and 86 singleton sibling pairs reported their children's sibling relationships and social adjustment. This study showed that the effects of sibling relationships on the prosocial behaviors and conduct problems of each child are stronger for twins than for singleton siblings. Moreover, positivity toward one's sibling increased peer problems only among monozygotic twins. The opposite tendency was present among dizygotic twins and singleton siblings. This study suggests the importance for children's social development of having many interactions with siblings and establishing reciprocity in sibling relationships. Moreover, our results suggest that the quality of sibling relationships among monozygotic twins may be different from those among dizygotic twins and singleton siblings.
The Norwegian Twin Registry
Authors: Nilsen Thomas S. , Brandt Ingunn , Magnus Per , Harris Jennifer R.
Published: September 2012

Norway has a long-standing tradition in twin research, but the data collected in several population-based twin studies were not coordinated centrally or easily accessible to the scientific community. In 2009, the Norwegian Twin Registry was established at the Norwegian Institute of Public Health (NIPH) in Oslo with the purpose of creating a single research resource for Norwegian twin data. As of today, the Norwegian Twin Registry contains 47,989 twins covering birth years 1895–1960 and 1967–1979; 31,440 of these twins consented to participate in health-related research. In addition, DNA from approximately 4,800 of the twins is banked at the NIPH biobank and new studies are continually adding new data to the registry. The value of the Norwegian twin data is greatly enhanced by the linkage opportunities offered by Norway's many nationwide registries, spanning a broad array of medical, demographic, and socioeconomic information.
Flood forecast errors and ensemble spread—A case study
Authors: Nester T. , Komma J. , Viglione A. , Blöschl G.
Published: September 2012

Flood forecasts are generally associated with errors, which can be attributed to uncertainties in the meteorological forecasts and the hydrologic simulations, and ensemble spreads are usually considered capable of representing them. To quantify these two components of the total forecast errors and to compare these to ensemble spreads, an extended data set is used. Four years of operational flood forecasts at hourly time step with lead times up to 48 h are evaluated for 43 catchments in Austria and Germany. Catchment sizes range from 70 to 25,600 km2, elevations from 200 to 3800 m, and mean annual precipitation from 700 to 2000 mm. A combination of ECMWF and ALADIN ensemble forecasts are used as input in a semidistributed conceptual water balance model on an hourly time step. The results indicate that, for short lead times, the ratio of hydrological simulation error to precipitation forecast error is 1.2 to 2.7 with increasing catchment size from 100 to 10,000 km2. For long lead times the ratio of hydrological simulation error to precipitation forecast error decreases from 1.1 to 0.9 with increasing catchment size. Clear scaling relationships of the forecast error components with catchment area are found. A similar scaling is also found for ensemble spreads, which are shown to represent quantitatively the total forecast error when forecasting floods.
Access to the Heads and Chairs Program expands beyond AGU Fall Meeting
Authors: Asher Pranoti M. , Keane Christopher M.
Published: September 2012

The AGU Education and Public Outreach department is pleased to announce a new collaboration with the American Geosciences Institute (AGI) for AGU's existing Heads and Chairs Program. This collaboration developed from a mutual interest in supporting the higher education departments of Earth and space sciences, as well as a desire to combine activities and resources toward strengthening that support. Through this partnership, AGI's Workforce Program and AGU's education staff are hosting hour‐long webinars on various topics each month to engage department heads and chairs in discussions that will help them share, learn, and apply new ideas to their own programs. The ultimate goal is to provide opportunities for open dialogue beyond the annual Heads and Chairs workshops held at the AGU Fall Meeting each year, as well as to support those heads and chairs who are unable to attend Fall Meeting.
Nonbreaking waves cause near‐surface turbulence
Authors: Schultz Colin
Published: September 2012

Surface ocean turbulence is predominantly generated by two forces: near‐surface winds and breaking waves. Where waves crash, strong downwelling can induce mixing of the upper few dozen meters, while winds establish larger turbulent vortices. A third known mechanism exists for generating near‐surface turbulence, the propagation of nonbreaking surface waves. However, it is typically overlooked as being too minute to matter. Recent research has suggested that nonbreaking waves may be a more important mechanism than previously thought. Using a laboratory wave tank and a numerical turbulence model, Savelyev et al. found that propagating nonbreaking waves not only can induce near‐surface eddies but also can modulate and feed into existing turbulent dynamics.
The sources of volatile and fluid‐mobile elements in the Sunda arc: A melt inclusion study from Kawah Ijen and Tambora volcanoes, Indonesia
Authors: Vigouroux Nathalie , Wallace Paul J. , Williams‐Jones Glyn , Kelley Katherine , Kent Adam J. R. , Williams‐Jones Anthony E.
Published: September 2012

Subduction zone recycling of volatiles (H2O, Cl, S, F) is controlled by the nature of subducted materials and the temperature‐pressure profile of the downgoing slab. We investigate the variability in volatile and fluid‐mobile trace element enrichment in the Sunda arc using melt inclusion data from Kawah Ijen and Tambora volcanoes, together with published data from Galunggung, Indonesia. Combining our results with data from other arcs, we investigate the mobility of these elements during slab dehydration and melting. We observe correlations between Sr, H2O and Cl contents, indicating coupling of these elements during subduction zone recycling. Sulfur is more variable, and fluorine contents generally remain at background mantle values, suggesting decoupling of these elements from H2O and Cl. Partial melting and dehydration models constrain the source of Sr and the volatiles and suggest that the altered oceanic crust (AOC) is the main source of the hydrous component that fluxes into the mantle wedge, in agreement with thermo‐mechanical models. Sediment melt remains an important component for other elements such as Ba, Pb, Th and the LREE. The Indonesian volcanoes have variable concentrations of volatile and fluid‐mobile elements, with Kawah Ijen recording higher AOC‐derived fluid fluxes (Sr/Nd and H2O/Nd) compared to Galunggung and Tambora. Kawah Ijen has H2O/Ce ratios that are comparable to some of the most volatile‐rich magmas from other cold slab subduction zones worldwide, and the highest yet measured in the Sunda arc.
Melt inclusions reveal geochemical cross‐arc variations and diversity within magma chambers feeding the Higashi‐Izu Monogenetic Volcano Field, Izu Peninsula, Japan
Authors: Nichols A. R. L. , Wysoczanski R. J. , Tani K. , Tamura Y. , Baker J. A. , Tatsumi Y.
Published: September 2012

The Higashi‐Izu Monogenetic Volcano Field (HIMVF) consists of 70 subaerial monogenetic volcanoes on the northeastern Izu Peninsula, Japan, and 50 submarine monogenetic volcanoes that extend offshore toward Izu‐Oshima on the Izu‐Bonin Arc volcanic front. We investigate olivine‐hosted glassy silicate melt inclusions erupted in scoria from two of the subaerial monogenetic volcanoes, Takatsukayama and Sukumoyama. Major element data (and volatile elements S and Cl) have been collected from 85 inclusions, of which 26 and 41 have been analyzed for trace and volatile (H2O, CO2) elements, respectively. The trace element compositions of the melt inclusions, together with those of the whole rocks from volcanoes within the HIMVF, vary systematically across the HIMVF, even over 5 km between Takatsukayama and Sukumoyama. These variations reflect a decrease in the contribution from slab fluids that leads to melting of the mantle with distance from the volcanic front, and increasing subducting slab depth. The Takatsukayama and Sukumoyama inclusions also reveal an intra‐volcano geochemical diversity; most are low TiO2 (0.81–1.18 wt.%), high Al2O3 (15.88–19.34 wt.%) basalts (low TiO2‐HABs), with a few high TiO2 (1.11–2.19 wt.%), low Al2O3 (11.75–14.04 wt.%) basalts (high TiO2‐LABs) that are sometimes trapped in the same crystal. As both groups show the cross‐HIMVF geochemical variability, we conclude that the heterogeneity does not reflect mantle processes or the true composition of melts in the magma chambers; instead we relate it to interstitial melts within the crystal mush of the magma chambers experiencing distinct crystallization histories.
Large‐scale troughs on Vesta: A signature of planetary tectonics
Authors: Buczkowski D. L. , Wyrick D. Y. , Iyer K. A. , Kahn E. G. , Scully J. E. C. , Nathues A. , Gaskell R. W. , Roatsch T. , Preusker F. , Schenk P. M. , Le Corre L. , Reddy V. , Yingst R. A. , Mest S. , Williams D. A. , Garry W. B. , Barnouin O. S. , Jaumann R. , Raymond C. A. , Russell C. T.
Published: September 2012

Images of Vesta taken by the Dawn spacecraft reveal large‐scale linear structural features on the surface of the asteroid. We evaluate the morphology of the Vesta structures to determine what processes caused them to form and what implications this has for the history of Vesta as a planetary body. The dimensions and shape of these features suggest that they are graben similar to those observed on terrestrial planets, not fractures or grooves such as are found on smaller asteroids. As graben, their vertical displacement versus length relationship could be evaluated to describe and interpret the evolution of the component faults. Linear structures are commonly observed on smaller asteroids and their formation has been tied to impact events. While the orientation of the large‐scale Vesta structures does imply that their formation is related to the impact events that formed the Rheasilvia and Veneneia basins, their size and morphology is greatly different from impact‐formed fractures on the smaller bodies. This is consistent with new analyses that suggest that Vesta is fully differentiated, with a mantle and core. We suggest that impact into a differentiated asteroid such as Vesta could result in graben, while grooves and fractures would form on undifferentiated asteroids.
Crustal changes at Mt. Etna volcano accompanying the 2002–2003 eruption as inferred from a repeating earthquake analysis
Authors: Cannata Andrea
Published: September 2012

In this work, waveform variations in repeating volcano‐tectonic earthquakes occurring from 2001–2009 in the north‐eastern flank of Mt. Etna were studied. Changes in waveform were found mainly during 2002–2003; and consisted of a decreasing similarity in the coda of events in earthquake families, as revealed by cross‐correlation analysis, and delays, increasing proportionally to the lapse time, detected by coda wave interferometry. Such variations, mainly evident at stations located in the north‐eastern flank of the volcano, were likely due to medium changes taking place within this region. Localized medium velocity decreases were inferred to occur in 2002–2003, followed by successive increases. The velocity decrease was interpreted as being caused by the opening or enlargement of cracks, produced by intruding magma bodies, intense ground deformation, and/or VT earthquake activity that accompanied the 2002–2003 Mt. Etna eruption. On the other hand, subsequent velocity increases were interpreted as resulting from healing processes.
Visualization of ion cyclotron wave and particle interactions in the inner magnetosphere via THEMIS‐ASI observations
Authors: Sakaguchi K. , Miyoshi Y. , Spanswick E. , Donovan E. , Mann I. R. , Jordanova V. , Shiokawa K. , Connors M. , Green J. C.
Published: September 2012

Interaction with EMIC (electromagnetic ion cyclotron) waves is thought to be a key component contributing to the very rapid loss of both ring current and radiation belt particles into the atmosphere. Estimated loss rates are heavily dependent on the assumed spatial distribution of the EMIC wave. Statistical maps of the spatial distribution have been produced using in‐situ satellite data. However, with limited satellite data it is impossible to deduce the true spatial distribution. In this study, we present ground‐based observations using all‐sky imager and search coil magnetometer networks, which provide the large‐scale distribution and motion of the EMIC wave‐particle interaction regions. We observed several spots of isolated proton auroras simultaneously with Pc1/EMIC waves at subauroral latitudes during the expansion phase of a storm‐time substorm on 9 March 2008. The isolated auroras were distributed over ∼4‐hours MLT preceding midnight. The POES‐17 satellite confirmed enhancements of 30‐keV proton precipitations over the isolated auroras. The equatorward motion of the auroras and frequency drift of the wave were consistent with the plasmasphere eroding due to a polar cap potential enhancement modeled by a numerical simulation. We also found that relativistic electron precipitation was not always associated with the isolated aurora, depending strongly on the plasma density profile near the plasmapause. This study shows that the specific distribution of ring current proton precipitation can be visualized through the ground network observations. By combining with upcoming inner‐magnetosphere satellite missions, these remote‐sensing observations are very important for quantitative understanding of the particle loss in the inner magnetosphere.
Delineation of catchment zones of geothermal systems in large‐scale rifted settings
Authors: Dempsey D. E. , Simmons S. F. , Archer R. A. , Rowland J. V.
Published: September 2012

Hydrothermal convection in the Taupo Volcanic Zone (TVZ), New Zealand, is driven by heat extracted at the brittle‐ductile transition, which is in turn supplied by magmatic intrusion of the lower‐crust. We present a numerical model that approximates this circulation in a statistical sense, being constrained by TVZ dimensions and mean thermal properties, but incorporating a permeability distribution of arbitrary heterogeneity. A particle tracking methodology that accounts for advective and dispersive transport is introduced, and ensembles of several tens of thousands of flow paths are constructed for each of the modeled geothermal systems. These flow paths reveal the nature of mass recharge in multicell convective systems, and suggest the ages of waters in TVZ geothermal systems vary between 5 and 50 kyr. Flow path ensembles are used to delineate catchments for each of the modeled systems and a method for calculating their areas is introduced. Catchment area is shown to be proportional to system heat output and area, which is consistent with a 1‐D analytical model of heat and mass transfer. As an approximation to catchments delineated by particle tracking, we outline a method of Voronoi tessellation based on the positions and heat outputs of geothermal systems. This method is used to delineate catchments for geothermal systems in the TVZ and Iceland.
A Bayesian methodological framework for accommodating interannual variability of nutrient loading with the SPARROW model
Authors: Wellen Christopher , Arhonditsis George B. , Labencki Tanya , Boyd Duncan
Published: September 2012

Regression‐type, hybrid empirical/process‐based models (e.g., SPARROW, PolFlow) have assumed a prominent role in efforts to estimate the sources and transport of nutrient pollution at river basin scales. However, almost no attempts have been made to explicitly accommodate interannual nutrient loading variability in their structure, despite empirical and theoretical evidence indicating that the associated source/sink processes are quite variable at annual timescales. In this study, we present two methodological approaches to accommodate interannual variability with the Spatially Referenced Regressions on Watershed attributes (SPARROW) nonlinear regression model. The first strategy uses the SPARROW model to estimate a static baseline load and climatic variables (e.g., precipitation) to drive the interannual variability. The second approach allows the source/sink processes within the SPARROW model to vary at annual timescales using dynamic parameter estimation techniques akin to those used in dynamic linear models. Model parameterization is founded upon Bayesian inference techniques that explicitly consider calibration data and model uncertainty. Our case study is the Hamilton Harbor watershed, a mixed agricultural and urban residential area located at the western end of Lake Ontario, Canada. Our analysis suggests that dynamic parameter estimation is the more parsimonious of the two strategies tested and can offer insights into the temporal structural changes associated with watershed functioning. Consistent with empirical and theoretical work, model estimated annual in‐stream attenuation rates varied inversely with annual discharge. Estimated phosphorus source areas were concentrated near the receiving water body during years of high in‐stream attenuation and dispersed along the main stems of the streams during years of low attenuation, suggesting that nutrient source areas are subject to interannual variability.
Use of heat as tracer to quantify vertical streambed flow in a two‐dimensional flow field
Authors: Roshan Hamid , Rau Gabriel C. , Andersen Martin S. , Acworth Ian R.
Published: September 2012

Analytical solutions to the heat transport equation in porous media have been developed in the past to estimate surface water‐groundwater interactions. These solutions, however, are based upon simplifying assumptions that are frequently violated in natural systems. A nonvertical flow field, inherent to most field settings, can violate the one‐dimensional (1‐D) flow assumption and lead to erroneous velocity estimates. In this study, we have developed a 2‐D heat and mass transport finite element‐based numerical model for a stream aquifer cross section experiencing flow‐through. Synthetic multilevel streambed temperature time series were generated with the model using a sinusoidal temperature boundary. The temperature data was used to quantify the vertical flow velocity with a 1‐D analytical solution based on the amplitude decay and phase shift of temperature with depth. Results demonstrate that erroneous vertical components of fluid velocity can be obtained by the 1‐D analytical solution when the true vertical velocity approaches zero and the flow regime becomes almost horizontal. The results also illustrate that the amplitude ratio method performs quite poorly on the gaining side of the stream where the only reliable method is phase shift. On the losing side of the stream, both methods can be employed but a better estimation is obtained from the amplitude ratio method. In general, amplitude ratio and phase shift data should be used in conjunction to maximize the information of the system.
Development and applications of a unitary group adapted state specific multi-reference coupled cluster theory with internally contracted treatment of inactive double excitations
Authors: Sinha Debalina , Maitra Rahul , Mukherjee Debashis
Published: September 2012

Any multi-reference coupled cluster (MRCC) development based on the Jeziorski-Monkhorst (JM) multi-exponential ansatz for the wave-operator Ω suffers from spin-contamination problem for non-singlet states. We have very recently proposed a spin-free unitary group adapted (UGA) analogue of the JM ansatz, where the cluster operators are defined in terms of spin-free unitary generators and a normal ordered, rather than ordinary, exponential parametrization of Ω is used. A consequence of the latter choice is the emergence of the “direct term” of the MRCC equations that terminates at exactly the quartic power of the cluster amplitudes. Our UGA-MRCC ansatz has been utilized to generate both the spin-free state specific (SS) and the state universal MRCC formalisms. It is well-known that the SSMRCC theory requires suitable sufficiency conditions to resolve the redundancy of the cluster amplitudes. In this paper, we propose an alternative variant of the UGA-SSMRCC theory, where the sufficiency conditions are used for all cluster operators containing active orbitals and the single excitations with inactive orbitals, while the inactive double excitations are assumed to be independent of the model functions they act upon. The working equations for the inactive double excitations are thus derived in an internally contracted (IC) manner in the sense that the matrix elements entering the MRCC equations involve excitations from an entire combination of the model functions. We call this theory as UGA-ICID-MRCC, where ICID is the acronym for “Internally Contracted treatment of Inactive Double excitations.” Since the number of such excitations are the most numerous, choosing them to be independent of the model functions will lead to very significant reduction in the number of cluster amplitudes for large active spaces, and is worth exploring. Moreover, unlike for the excitations involving active orbitals, where there is inadequate coupling between the model and the virtual functions in the SSMRCC equations generated from sufficiency conditions, our internally contracted treatment of inactive double excitations involves much more complete couplings. Numerical implementation of our formalism amply demonstrates the efficacy of the formalism.
Analysis of optical properties of porous silicon nanostructure single and gradient-porosity layers for optical applications
Authors: Shokrollahi A. , Zare M. , Mortezaali A. , Ramezani Sani S.
Published: September 2012

The porous silicon (PS) layers with different porosities were prepared by electrochemical anodization method to obtain the desired refractive index in a given range. The optical response of the PS layer has been performed by the reflectance measurements. The obtained data were coupled to Kramers-Kronig analysis and allowed determination of complex refractive index in spectral range extending from 400 to 850 nm. In addition, the dispersion of refractive index of PS was determined from optical reflection measurements experimentally utilizing the relationship between the optical path in the plane-parallel film and the position of extrema. These results were compared and the agreement of them was discussed. The Bruggeman’s effective medium approximation was also used to estimate the porosity of each PS sample from calculated optical characteristics. FESEM analyses revealed vertically aligned silicon nanopillars with diameters on the order of 50 nm perpendicular to the Si substrate surface. A gradient-porosity PS layer was fabricated by modulating applied current density during anodization. Indeed, the elaborated structure is consisted of porous layers with modulated refractive indices. For this structure, normal incident and reflecting light through the layers provide an effective refractive index.
Investigation of the improved performance in a graphene/polycrystalline BiFeO3/Pt photovoltaic heterojunction: Experiment, modeling, and application
Authors: Zang Yongyuan , Xie Dan , Chen Yu , Wu Xiao , Ren Tianling , Zhu Hongwei , Cao Jiang-Li , Plant David
Published: September 2012

We report on the enhancement of photovoltaic performance in a graphene/polycrystalline BiFeO3 (BFO)/Pt heterojunction for the first time. The unique properties of the graphene electrode lead to a short circuit current density of 61 μA/cm2 and an open circuit voltage of 0.52 V in the heterojunction. These values are much higher than the results reported in polycrystalline BFO with indium tin oxide as the top electrode. A theoretical band diagram model and an equivalent electrical model considering the ferroelectric polarization, interface states, and energy band bending effect are constructed to depict the carrier transport behavior. Important photovoltaic parameters, such as conversion efficiency, illumination intensity response, ON/OFF characteristics, minority carrier lifetime, and external quantum efficiency, are investigated experimentally and theoretically. To improve the photovoltaic performance of the graphene/polycrystalline BFO/Pt heterojunction, HNO3 treatment, and CdSe quantum dots (QDs) filling/sensitizing, as two independent chemical and physical routines, were processed and compared. It can be seen that the photocurrent density exhibits a significant improvement from 61 μA/cm2 to 8.67 mA/cm2 (∼150 fold) after HNO3 treatment, while a considerable enhancement of ∼5 fold is seen with QDs filling/sensitizing. We also present and investigate an optical application of our graphene/polycrystalline BFO/Pt heterojunction as a photosensitive detector.
Energy conservation and pulse propagation in an elastic medium with quadratic nonlinearity
Authors: Cantrell John H. , Yost William T.
Published: September 2012

A sinusoidal acoustic tone-burst launched into an elastic medium with weak quadratic nonlinearity is shown to generate a right-triangular static displacement pulse, when conservation of energy is properly imposed on the model equations. The right-triangular displacement profile is shown to occur whether the tone-burst is modeled with displacement-prescribed or traction-prescribed boundary conditions. Definitive experimental evidence is presented confirming the model predictions. Theoretical arguments and experimental evidence are also presented showing that, contrary to the assertion of Qu et al. [J. Acoust. Soc. Am. 131, 1827 (2012)], the right-triangular shape is not in violation of causality.
Strong room-temperature ferromagnetism of high-quality lightly Mn-doped ZnO grown by molecular beam epitaxy
Authors: Zuo Zheng , Zhou Huimei , Olmedo Mario J. , Kong Jieying , Beyermann Ward P. , Zheng Jian-Guo , Xin Yan , Liu Jianlin
Published: September 2012

Strong room-temperature ferromagnetism is demonstrated in single crystalline Mn-doped ZnO grown by molecular beam epitaxy. With a low Mn concentration of 2 × 1019 cm−3, Mn-doped ZnO films exhibited room-temperature ferromagnetism with a coercivity field larger than 200 Oe, a large saturation moment of 6 μB/ion, and a large residue moment that is ∼70% of the saturation magnetization. Isolated ions with long range carrier mediated spin-spin coupling may be responsible for the intrinsic ferromagnetism.
Pressure dependency of thermal boundary conductance of carbon nanotube/silicon interface: A molecular dynamics study
Authors: Liu Huake , Zeng Huizhong , Pan Taisong , Huang Wen , Lin Yuan
Published: September 2012

Thermal boundary conductance (TBC) of open carbon nanotube (CNT) and crystal silicon was investigated by the method of molecular dynamics (MD) simulation. Van der Waals interaction was used to form the interface between the vertically mounted CNT and the silicon surface. The interfacial TBC was extracted from the thermal relaxation between CNT and Si with different initial temperatures. An enhancement of TBC was spotted with the increase of the external pressure. At the interfacial region, the phonon densities of states of CNT and Si were altered by the external pressure, especially at the frequency between 2 THz and 15 THz, which could be associated with the enhancement of TBC.
Study of semiconductor quantum dots influence on photorefractivity of liquid crystals
Authors: Anczykowska A. , Bartkiewicz S. , Nyk M. , Mysliwiec J.
Published: September 2012

In this paper, we present the results of doping nematic liquid crystals (nLCs) with semiconductor quantum dots (QDs) where we discuss the CdS and CdSe QDs influence on the optical properties of investigated liquid crystal structures, i.e., diffraction efficiency enhancement. We also present the mathematical model describing the interaction between QDs and nLC molecules in the liquid crystal volume. The aim of this study is to improve the comprehension of the mechanisms of photorefractive effect observed in functionalized liquid crystal structures, which can lead to the development of more efficient holographic materials for dynamic data processing applications.
Improvement of near-infrared absorption linewidth in AlGaN/GaN superlattices by optimization of delta-doping location
Authors: Edmunds C. , Tang L. , Shao J. , Li D. , Cervantes M. , Gardner G. , Zakharov D. N. , Manfra M. J. , Malis O.
Published: September 2012

We report a systematic study of the near-infrared intersubband absorption in AlGaN/GaN superlattices grown by plasma-assisted molecular-beam epitaxy as a function of Si-doping profile with and without δ-doping. The transition energies are in agreement with theoretical calculations including many-body effects. A dramatic reduction of the intersubband absorption linewidth is observed when the δ-doping is placed at the end of the quantum well. This reduction is attributed to the improvement of interface roughness. The linewidth dependence on interface roughness is well reproduced by a model that considers the distribution of well widths measured with transmission electron microscopy.
Electroluminescence from quantum dots fabricated with nanosphere lithography
Authors: Yu L. , Law S. , Wasserman D.
Published: September 2012

We demonstrate strong carrier confinement in, and electroluminescence (EL) from, quantum nanostructures fabricated from epitaxially grown quantum wells (QWs) using a top-down nanosphere lithography, dry-etch, mass-transport, and overgrowth fabrication process. Optically active nano-pillars with diameters as small as 90 nm are fabricated, and narrow linewidth (18 meV) electroluminescence from a fabricated diode structure is observed, with an emission blue-shift of over 37 meV from the original quantum well sample luminescence. The results presented offer the potential for low-cost, large-area patterning of quantum nanostructures for optoelectronic applications.
Direct observation of a force-induced switch in the anisotropic mechanical unfolding pathway of a protein
Authors: Jagannathan Bharat , Elms Phillip J. , Bustamante Carlos , Marqusee Susan
Published: September 2012

Many biological processes generate force, and proteins have evolved to resist and respond to tension along different force axes. Single-molecule force spectroscopy allows for molecular insight into the behavior of proteins under force and the mechanism of protein folding in general. Here, we have used src SH3 to investigate the effect of different pulling axes under the low-force regime afforded by an optical trap. We find that this small cooperatively folded protein shows an anisotropic response to force; the protein is more mechanically resistant to force applied along a longitudinal axis compared to force applied perpendicular to the terminal β strand. In the longitudinal axis, we observe an unusual biphasic behavior revealing a force-induced switch in the unfolding mechanism suggesting the existence of two parallel unfolding pathways. A site-specific variant can selectively affect one of these pathways. Thus, even this simple two-state protein demonstrates a complex mechanical unfolding trajectory, accessing multiple unfolding pathways under the low-force regime of the optical trap; the specific unfolding pathway depends on the perturbation axis and the applied force.
Cytoplasmic streaming in
Drosophila
oocytes varies with kinesin activity and correlates with the microtubule cytoskeleton architecture
Authors: Ganguly Sujoy , Williams Lucy S. , Palacios Isabel M. , Goldstein Raymond E.
Published: September 2012

Cells can localize molecules asymmetrically through the combined action of cytoplasmic streaming, which circulates their fluid contents, and specific anchoring mechanisms. Streaming also contributes to the distribution of nutrients and organelles such as chloroplasts in plants, the asymmetric position of the meiotic spindle in mammalian embryos, and the developmental potential of the zygote, yet little is known quantitatively about the relationship between streaming and the motor activity which drives it. Here we use Particle Image Velocimetry to quantify the statistical properties of Kinesin-dependent streaming during mid-oogenesis in
Drosophila
. We find that streaming can be used to detect subtle changes in Kinesin activity and that the flows reflect the architecture of the microtubule cytoskeleton. Furthermore, based on characterization of the rheology of the cytoplasm in vivo, we establish estimates of the number of Kinesins required to drive the observed streaming. Using this in vivo data as the basis of a model for transport, we suggest that the disordered character of transport at mid-oogenesis, as revealed by streaming, is an important component of the localization dynamics of the body plan determinant
oskar
mRNA.
TIPE2 protein serves as a negative regulator of phagocytosis and oxidative burst during infection
Authors: Wang Zhaojun , Fayngerts Svetlana , Wang Peng , Sun Honghong , Johnson Derek S. , Ruan Qingguo , Guo Wei , Chen Youhai H.
Published: September 2012

Phagocytosis and oxidative burst are two major effector arms of innate immunity. Although it is known that both are activated by Toll-like receptors (TLRs) and Rac GTPases, how their strengths are controlled in quiescent and TLR-activated cells is not clear. We report here that TIPE2 (TNFAIP8L2) serves as a negative regulator of innate immunity by linking TLRs to Rac. TLRs control the expression levels of TIPE2, which in turn dictates the strengths of phagocytosis and oxidative burst by binding to and blocking Rac GTPases. Consequently, TIPE2 knockout cells have enhanced phagocytic and bactericidal activities and TIPE2 knockout mice are resistant to bacterial infection. Thus, TIPE2 sets the strengths of phagocytosis and oxidative burst and may be targeted to effectively control infections.
Evidence for additive and interaction effects of host genotype and infection in malaria
Authors: Idaghdour Youssef , Quinlan Jacklyn , Goulet Jean-Philippe , Berghout Joanne , Gbeha Elias , Bruat Vanessa , de Malliard Thibault , Grenier Jean-Christophe , Gomez Selma , Gros Philippe , Rahimy Mohamed Chérif , Sanni Ambaliou , Awadalla Philip
Published: September 2012

The host mechanisms responsible for protection against malaria remain poorly understood, with only a few protective genetic effects mapped in humans. Here, we characterize a host-specific genome-wide signature in whole-blood transcriptomes of
Plasmodium falciparum
-infected West African children and report a demonstration of genotype-by-infection interactions in vivo. Several associations involve transcripts sensitive to infection and implicate complement system, antigen processing and presentation, and T-cell activation (i.e.,
SLC39A8
,
C3AR1
,
FCGR3B
,
RAD21
,
RETN
,
LRRC25
,
SLC3A2
, and
TAPBP
), including one association that validated a genome-wide association candidate gene (
SCO1
), implicating binding variation within a noncoding regulatory element. Gene expression profiles in mice infected with
Plasmodium chabaudi
revealed and validated similar responses and highlighted specific pathways and genes that are likely important responders in both hosts. These results suggest that host variation and its interplay with infection affect children’s ability to cope with infection and suggest a polygenic model mounted at the transcriptional level for susceptibility.
Cis-2-dodecenoic acid receptor RpfR links quorum-sensing signal perception with regulation of virulence through cyclic dimeric guanosine monophosphate turnover
Authors: Deng Yinyue , Schmid Nadine , Wang Chao , Wang Jianhe , Pessi Gabriella , Wu Donghui , Lee Jasmine , Aguilar Claudio , Ahrens Christian H. , Chang Changqing , Song Haiwei , Eberl Leo , Zhang Lian-Hui
Published: September 2012

Many bacterial pathogens produce diffusible signal factor (DSF)-type quorum sensing (QS) signals in modulation of virulence and biofilm formation. Previous work onXanthomonas campestrisshowed that the RpfC/RpfG two-component system is involved in sensing and responding to DSF signals, but little is known in other microorganisms. Here we show that inBurkholderia cenocepaciathe DSF-family signalcis-2-dodecenoic acid (BDSF) negatively controls the intracellular cyclic dimeric guanosine monophosphate (c-di-GMP) level through a receptor protein RpfR, which contains Per/Arnt/Sim (PAS)-GGDEF-EAL domains. RpfR regulates the same phenotypes as BDSF including swarming motility, biofilm formation, and virulence. In addition, the BDSF−mutant phenotypes could be rescued byin transexpression of RpfR, or its EAL domain that functions as a c-di-GMP phosphodiesterase. BDSF is shown to bind to the PAS domain of RpfR with high affinity and stimulates its phosphodiesterase activity through induction of allosteric conformational changes. Our work presents a unique and widely conserved DSF-family signal receptor that directly links the signal perception to c-di-GMP turnover in regulation of bacterial physiology.
Oncogenic mutations mimic and enhance dynamic events in the natural activation of phosphoinositide 3-kinase p110α (
PIK3CA
)
Authors: Burke John E. , Perisic Olga , Masson Glenn R. , Vadas Oscar , Williams Roger L.
Published: September 2012

The p110α catalytic subunit (
PIK3CA
) is one of the most frequently mutated genes in cancer. We have examined the activation of the wild-type p110α/p85α and a spectrum of oncogenic mutants using hydrogen/deuterium exchange mass spectrometry (HDX-MS). We find that for the wild-type enzyme, the natural transition from an inactive cytosolic conformation to an activated form on membranes entails four distinct events. Analysis of oncogenic mutations shows that all up-regulate the enzyme by enhancing one or more of these dynamic events. We provide the first insight into the activation mechanism by mutations in the linker between the adapter-binding domain (ABD) and the Ras-binding domain (RBD) (G106V and G118D). These mutations, which are common in endometrial cancers, enhance two of the natural activation events: movement of the ABD and ABD–RBD linker relative to the rest of the catalytic subunit and breaking the C2–iSH2 interface on binding membranes. C2 domain mutants (N345K and C420R) also mimic these events, even in the absence of membranes. A third event is breaking the nSH2–helical domain contact caused by phosphotyrosine-containing peptides binding to the enzyme, which is mimicked by a helical domain mutation (E545K). Interaction of the C lobe of the kinase domain with membranes is the fourth activation event, and is potentiated by kinase domain mutations (e.g., H1047R). All mutations increased lipid binding and basal activity, even mutants distant from the membrane surface. Our results elucidate a unifying mechanism in which diverse
PIK3CA
mutations stimulate lipid kinase activity by facilitating allosteric motions required for catalysis on membranes.
Persistent and reversible consequences of combat stress on the mesofrontal circuit and cognition
Authors: van Wingen Guido A. , Geuze Elbert , Caan Matthan W. A. , Kozicz Tamás , Olabarriaga Silvia D. , Denys Damiaan , Vermetten Eric , Fernández Guillén
Published: September 2012

Prolonged stress can have long-lasting effects on cognition. Animal models suggest that deficits in executive functioning could result from alterations within the mesofrontal circuit. We investigated this hypothesis in soldiers before and after deployment to Afghanistan and a control group using functional and diffusion tensor imaging. Combat stress reduced midbrain activity and integrity, which was associated to compromised sustained attention. Long-term follow-up showed that the functional and structural changes had normalized within 1.5 y. In contrast, combat stress induced a persistent reduction in functional connectivity between the midbrain and prefrontal cortex. These results demonstrate that combat stress has adverse effects on the human mesofrontal circuit and suggests that these alterations are partially reversible.
Linking habitat mosaics and connectivity in a coral reef seascape
Authors: McMahon Kelton W. , Berumen Michael L. , Thorrold Simon R.
Published: September 2012

Tropical marine ecosystems are under mounting anthropogenic pressure from overfishing and habitat destruction, leading to declines in their structure and function on a global scale. Although maintaining connectivity among habitats within a seascape is necessary for preserving population resistance and resilience, quantifying movements of individuals within seascapes remains challenging. Traditional methods of identifying and valuing potential coral reef fish nursery habitats are indirect, often relying on visual surveys of abundance and correlations of size and biomass among habitats. We used compound-specific stable isotope analyses to determine movement patterns of commercially important fish populations within a coral reef seascape. This approach allowed us to quantify the relative contributions of individuals from inshore nurseries to reef populations and identify migration corridors among important habitats. Our results provided direct measurements of remarkable migrations by juvenile snapper of over 30 km, between nurseries and reefs. We also found significant plasticity in juvenile nursery residency. Although a majority of individuals on coastal reefs had used seagrass nurseries as juveniles, many adults on oceanic reefs had settled directly into reef habitats. Moreover, seascape configuration played a critical but heretofore unrecognized role in determining connectivity among habitats. Finally, our approach provides key quantitative data necessary to estimate the value of distinctive habitats to ecosystem services provided by seascapes.
Molecular basis for recognition of methylated and specific DNA sequences by the zinc finger protein Kaiso
Authors: Buck-Koehntop Bethany A. , Stanfield Robyn L. , Ekiert Damian C. , Martinez-Yamout Maria A. , Dyson H. Jane , Wilson Ian A. , Wright Peter E.
Published: September 2012

Methylation of CpG dinucleotides in DNA is a common epigenetic modification in eukaryotes that plays a central role in maintenance of genome stability, gene silencing, genomic imprinting, development, and disease. Kaiso, a bifunctional Cys
2
His
2
zinc finger protein implicated in tumor-cell proliferation, binds to both methylated CpG (mCpG) sites and a specific nonmethylated DNA motif (TCCTGCNA) and represses transcription by recruiting chromatin remodeling corepression machinery to target genes. Here we report structures of the Kaiso zinc finger DNA-binding domain in complex with its nonmethylated, sequence-specific DNA target (KBS) and with a symmetrically methylated DNA sequence derived from the promoter region of
E-cadherin
. Recognition of specific bases in the major groove of the core KBS and mCpG sites is accomplished through both classical and methyl CH···O hydrogen-bonding interactions with residues in the first two zinc fingers, whereas residues in the C-terminal extension following the third zinc finger bind in the opposing minor groove and are required for high-affinity binding. The C-terminal region is disordered in the free protein and adopts an ordered structure upon binding to DNA. The structures of these Kaiso complexes provide insights into the mechanism by which a zinc finger protein can recognize mCpG sites as well as a specific, nonmethylated regulatory DNA sequence.