bluuebunny/crossref_metadata_2025 huggingface dataset:
Human rights obligations in military occupation
Authors: Lubell Noam
Published: August 2012

This article examines the applicability of international human rights law in situations of military occupation. Proceeding from the position that human rights obligations can exist in these circumstances, the article provides an analysis of the precise modalities of application. It examines the tests for the determination of human rights applicability, and how these are linked to the concept of occupation. Finally, it recognizes the practical and legal challenges to the implementation of human rights obligations, and argues for a contextual approach that provides for human rights protection while recognizing the realities of military occupation.
Artificial ducts caused by HF heating of the ionosphere by HAARP
Authors: Vartanyan A. , Milikh G. M. , Mishin E. , Parrot M. , Galkin I. , Reinisch B. , Huba J. , Joyce G. , Papadopoulos K.
Published: August 2012

We report on satellite observations of plasma density enhancements (ducts) in the topside ionosphere during four HAARP/BRIOCHE campaigns during 2009–2010. Artificial ducts, caused by high‐power HF radio wave injections from the HAARP transmitter toward the magnetic zenith, are detected by the DEMETER and DMSP satellites on a regular basis when there is a perceptible ionospheric F2 peak density. Overall, the plasma density enhancements detected between 0930 and 1230 LT varied from 3–13%, while those during ∼1730–2215 LT were typically 15–40%. We also used a modified SAMI2 model to study the artificial ducts' mechanism driven by HF electron heating in the bottomside F2 region. The heating builds up the plasma pressure, thus pushing plasma along the magnetic field. The simulation results performed for the input parameters similar to the conditions of the heating experiments are in fair agreement with the pertinent observations. The ducts seem to be produced most efficiently for heating frequencies quite close to the critical frequency foF2.
Effect of R2‐FAC development on the ionospheric electric field pattern deduced by a global ionospheric potential solver
Authors: Nakamizo Aoi , Hiraki Yasutaka , Ebihara Yusuke , Kikuchi Takashi , Seki Kanako , Hori Tomoaki , Ieda Akimasa , Miyoshi Yoshizumi , Tsuji Yuji , Nishimura Yukitoshi , Shinbori Atsuki
Published: August 2012

Toward the understanding of the effect of the magnetosphere originated disturbances on the global ionospheric electric field and current system, we developed a two‐dimensional ionospheric potential solver based on the so‐called “thin shell model.” The important extension from the previous studies is that our model covers the pole‐to‐pole ionosphere without placing any boundary at the equator. By using this solver, we investigate how the ionospheric electric field changes from undershielding condition to overshielding condition as the field aligned current (FAC) distribution changes. Calculations are performed by changing IR2/IR1 (the ratio of current intensities of region 2 (R2) and region 1 (R1) FACs) and by moving R2‐FAC relative to the fixed R1‐FAC. The results are summarized as follows: (1) The turning point, at which the ionosphere turns from undershielding to overshielding is IR2/IR1 = 0.7 ∼ 0.8. (2) With increasing the local time deference between the R1 and R2‐FAC peaks, the efficiency of the shielding by R2‐FAC increases but the associated potential skews to the nightside. (3) At the same time the shielding effect is weakened around noon, where the R1‐potential intrudes to the low latitude region instead, but the R2‐potential remains dominant at other local times. The result suggests that the overshielding or undershielding should be identified by observations not only in a limited local time sector but also in the overall ionosphere as much as possible. In order to accurately describe the ionospheric condition, we suggest new classification terms, “complete‐overshielding” and “incomplete‐overshielding.”
Modeling the basal melting and marine ice accretion of the Amery Ice Shelf
Authors: Galton‐Fenzi B. K. , Hunter J. R. , Coleman R. , Marsland S. J. , Warner R. C.
Published: August 2012

The basal mass balance of the Amery Ice Shelf (AIS) in East Antarctica is investigated using a numerical ocean model. The main improvements of this model over previous studies are the inclusion of frazil formation and dynamics, tides and the use of the latest estimate of the sub‐ice‐shelf cavity geometry. The model produces a net basal melt rate of 45.6 Gt year−1 (0.74 m ice year−1) which is in good agreement with reviewed observations. The melting at the base of the ice shelf is primarily due to interaction with High Salinity Shelf Water created from the surface sea‐ice formation in winter. The temperature difference between the coldest waters created in the open ocean and thein situ freezing point of ocean water in contact with the deepest part of the AIS drives a melt rate that can exceed 30 m of ice year−1. The inclusion of frazil dynamics is shown to be important for both melting and marine ice accretion (refreezing). Frazil initially forms in the supercooled water layer adjacent to the base of the ice shelf. The net accretion of marine ice is 5.3 Gt year−1, comprised of 3.7 Gt year−1 of frazil accretion and 1.6 Gt year−1 of direct basal refreezing.
Heterogeneous ice nucleation and water uptake by field‐collected atmospheric particles below 273 K
Authors: Wang Bingbing , Laskin Alexander , Roedel Tobias , Gilles Mary K. , Moffet Ryan C. , Tivanski Alexei V. , Knopf Daniel A.
Published: August 2012

Ice formation induced by atmospheric particles through heterogeneous nucleation is not well understood. Onset conditions for heterogeneous ice nucleation and water uptake by particles collected in Los Angeles and Mexico City were determined as a function of temperature (200–273 K) and relative humidity with respect to ice (RHice). Four dominant particle types were identified including soot associated with organics, soot with organic and inorganics, inorganic particles of marine origin coated with organic material, and Pb/Zn‐containing particles apportioned to emissions relevant to waste incineration. Single particle characterization was provided by micro‐spectroscopic analyses using computer controlled scanning electron microscopy with energy dispersive analysis of X‐rays (CCSEM/EDX) and scanning transmission X‐ray microscopy with near edge X‐ray absorption fine structure spectroscopy (STXM/NEXAFS). Above 230 K, significant differences in onsets of water uptake and immersion freezing of different particle types were observed. Below 230 K, particles exhibited high deposition ice nucleation efficiencies and formed ice atRHicewell below homogeneous ice nucleation limits. The data suggest that water uptake and immersion freezing are more sensitive to changes in particle chemical composition compared to deposition ice nucleation. The data demonstrate that anthropogenic and marine influenced particles, exhibiting various chemical and physical properties, possess distinctly different ice nucleation efficiencies and can serve as efficient IN at atmospheric conditions typical for cirrus and mixed‐phase clouds.
Aerosol indirect effect on tropospheric ozone via lightning
Authors: Yuan Tianle , Remer Lorraine A. , Bian Huisheng , Ziemke Jerald R. , Albrecht Rachel , Pickering Kenneth E. , Oreopoulos Lazaros , Goodman Steven J. , Yu Hongbin , Allen Dale J.
Published: August 2012

Tropospheric ozone (O3) is a pollutant and major greenhouse gas and its radiative forcing is still uncertain. Inadequate understanding of processes related to O3 production, in particular those natural ones such as lightning, contributes to this uncertainty. Here we demonstrate a new effect of aerosol particles on O3production by affecting lightning activity and lightning‐generated NOx (LNOx). We find that lightning flash rate increases at a remarkable rate of 30 times or more per unit of aerosol optical depth. We provide observational evidence that indicates the observed increase in lightning activity is caused by the influx of aerosols from a volcano. Satellite data analyses show O3is increased as a result of aerosol‐induced increase in lightning and LNOx, which is supported by modle simulations with prescribed lightning change. O3production increase from this aerosol‐lightning‐ozone link is concentrated in the upper troposphere, where O3 is most efficient as a greenhouse gas. In the face of anthropogenic aerosol increase our findings suggest that lightning activity, LNOx and O3, especially in the upper troposphere, have all increased substantially since preindustrial time due to the proposed aerosol‐lightning‐ozone link, which implies a stronger O3 historical radiative forcing. Aerosol forcing therefore has a warming component via its effect on O3 production and this component has mostly been ignored in previous studies of climate forcing related to O3and aerosols. Sensitivity simulations suggest that 4–8% increase of column tropospheric ozone, mainly in the tropics, is expected if aerosol‐lighting‐ozone link is parameterized, depending on the background emission scenario. We note, however, substantial uncertainties remain on the exact magnitude of aerosol effect on tropospheric O3 via lightning. The challenges for obtaining a quantitative global estimate of this effect are also discussed. Our results have significant implications for understanding past and projecting future tropospheric O3forcing as well as wildfire changes and call for integrated investigations of the coupled aerosol‐cloud‐chemistry system.
A second generation of homogenized Canadian monthly surface air temperature for climate trend analysis
Authors: Vincent Lucie A. , Wang Xiaolan L. , Milewska Ewa J. , Wan Hui , Yang Feng , Swail Val
Published: August 2012

This study presents a second generation of homogenized monthly mean surface air temperature data set for Canadian climate trend analysis. Monthly means of daily maximum and of daily minimum temperatures were examined at 338 Canadian locations. Data from co‐located observing sites were sometimes combined to create longer time series for use in trend analysis. Time series of observations were then adjusted to account for nation‐wide change in observing time in July 1961, affecting daily minimum temperatures recorded at 120 synoptic stations; these were adjusted using hourly temperatures at the same sites. Next, homogeneity testing was performed to detect and adjust for other discontinuities. Two techniques were used to detect non‐climatic shifts in de‐seasonalized monthly mean temperatures: a multiple linear regression based test and a penalized maximal t test. These discontinuities were adjusted using a recently developed quantile‐matching algorithm: the adjustments were estimated with the use of a reference series. Based on this new homogenized temperature data set, annual and seasonal temperature trends were estimated for Canada for 1950–2010 and Southern Canada for 1900–2010. Overall, temperature has increased at most locations. For 1950–2010, the annual mean temperature averaged over the country shows a positive trend of 1.5°C for the past 61 years. This warming is slightly more pronounced in the minimum temperature than in the maximum temperature; seasonally, the greatest warming occurs in winter and spring. The results are similar for Southern Canada although the warming is considerably greater in the minimum temperature compared to the maximum temperature over the period 1900–2010.
Primary and secondary organic aerosols in Fresno, California during wintertime: Results from high resolution aerosol mass spectrometry
Authors: Ge Xinlei , Setyan Ari , Sun Yele , Zhang Qi
Published: August 2012

Organic aerosols (OA) were studied in Fresno, California, in winter 2010 with an Aerodyne High Resolution Time‐of‐Flight Aerosol Mass Spectrometer (HR‐ToF‐AMS). OA dominated the submicron aerosol mass (average = 67%) with an average concentration of 7.9μg m−3 and a nominal formula of C1H1.59N0.014O0.27S0.00008, which corresponds to an average organic mass‐to‐carbon ratio of 1.50. Three primary OA (POA) factors and one oxygenated OA factor (OOA) representative of secondary OA (SOA) were identified via Positive Matrix Factorization of the high‐resolution mass spectra. The three POA factors, which include a traffic‐related hydrocarbon‐like OA (HOA), a cooking OA (COA), and a biomass burning OA (BBOA) released from residential heating, accounted for an average 57% of the OA mass and up to 80% between 6 – 9 P.M., during which enhanced emissions from evening rush hour traffic, dinner cooking, and residential wood burning were exacerbated by low mixed layer height. The mass‐based size distributions of the OA factors were estimated based on multilinear analysis of the size‐resolved mass spectra of organics. Both HOA and BBOA peaked at ∼140 nm in vacuum aerodynamic diameter (Dva) while OOA peaked at an accumulation mode of ∼460 nm. COA exhibited a unique size distribution with two size modes centering at ∼200 nm and 450 nm respectively. This study highlights the leading roles played by anthropogenic POA emissions, primarily from traffic, cooking and residential heating, in aerosol pollution in Fresno in wintertime.
Biogenic ice nuclei in boundary layer air over two U.S. High Plains agricultural regions
Authors: Garcia Elvin , Hill Thomas C. J. , Prenni Anthony J. , DeMott Paul J. , Franc Gary D. , Kreidenweis Sonia M.
Published: August 2012

With 18% of the total U.S. landmass devoted to croplands, farmland and farming activities are potentially major sources of biogenic particles to the atmosphere. Farms harbor large populations of microbes both in the soil and on plant surfaces which, if injected into the atmosphere, may serve as nuclei for clouds. In this study, we investigated two farms as potential sources of biological ice nuclei (IN): an organic farm in Colorado and a cornfield in Nebraska. We used a continuous‐flow diffusion chamber (CFDC) to obtain real‐time measurements of IN at these farm sites. Total aerosol particles were also collected at the sites, and their temperature‐dependent ice nucleating activity was determined using the drop freezing method. Quantitative polymerase chain reaction and DNA sequencing of 16S rDNA clone libraries were used to test aerosols and washings of local vegetation for abundance of theinagene in ice nucleation active bacteria (from the well‐known group within theγ‐Proteobacteria) and to identify airborne primary biological aerosol particles. The vegetation in each of these farms contained 6 × 105 to 2 × 107 ina genes per gram vegetation. In contrast to the vegetation, airborne ina gene concentrations at the organic farm were typically below detectable limits, demonstrating a disconnect between local vegetative sources and the air above them. However, for measurements made during combine harvesting at the Nebraska corn field, ina gene concentrations were 19 L−1, with maximum IN concentrations of 50 L−1 determined from the CFDC at −20°C and above water saturation. At both farms, there was also an apparent biological contribution to the IN population which did not contain the ina gene.
Permittivity estimation over Mars by using SHARAD data: the Cerberus Palus area
Authors: Alberti Giovanni , Castaldo Luigi , Orosei Roberto , Frigeri Alessandro , Cirillo Giuseppe
Published: August 2012

Cerberus Palus is a thoroughly studied region of Mars, characterized by evident platy textures that were interpreted either as evidence for a frozen sea close to Mars' equator or as being resultant of lava, mud or ice‐flows coming from Cerberus Fossae through Athabasca Valles. Radargrams provided by radar sounder SHARAD clearly show the presence of subsurface layers in the area. By exploiting the great amount of available data, authors have performed an accurate quantitative analysis aimed to estimate electromagnetic properties of surface and subsurface layers, in terms of permittivity and attenuation. To this aim, a simplified electromagnetic approach has been used, but taking into account effects of scattering due to surface roughness, for avoiding overestimated results. This has been done by using theory of electromagnetic scattering from fractal surfaces and by estimating needed parameters from topographic data provided by MOLA. Three distinct geologic formations have been analyzed, namely a part of Zephyria Planum, the Cerberus plains and the bedrock beneath the plains. The retrieved electromagnetic parameters have been also modeled as a mixture of volcanic rocks with either ice or air. The Zephyria Planum material was found to be significantly porous [50–60%] with an attenuation more likely compatible with empty pores. Ambiguous results were obtained for the plains material, being the resulting porosity high in both the cases of empty [40–50%] and of ice‐filled [80%] pores. The obtained results do not allow for evidence of a frozen sea on Cerberus Palus area.
Corals record persistent multidecadal SST variability in the Atlantic Warm Pool since 1775 AD
Authors: Vásquez‐Bedoya Luis Fernando , Cohen Anne L. , Oppo Delia W. , Blanchon Paul
Published: August 2012

Accurate low‐latitude sea surface temperature (SST) records that predate the instrumental era are needed to put recent warming in the context of natural climate variability and to evaluate the persistence of lower frequency climate variability prior to the instrumental era and the possible influence of anthropogenic climate change on this variability. Here we present a 235‐year‐long SST reconstruction based on annual growth rates (linear extension) of three colonies of the Atlantic coralSiderastrea sidereasampled at two sites on the northeastern Yucatan Peninsula, Mexico, located within the Atlantic Warm Pool (AWP). AWP SSTs vary in concert the Atlantic Multidecadal Oscillation (AMO), a basin‐wide, quasiperiodic (∼60–80 years) oscillation of North Atlantic SSTs. We demonstrate that the annual linear growth rates of all three coral colonies are significantly inversely correlated with SST. We calibrate annual linear growth rates to SST between 1900 and 1960 AD. The linear correlation coefficient over the calibration period is r = −0.77 and −0.66 over the instrumental record (1860–2008 AD). We apply our calibration to annual linear growth rates to extend the SST record to 1775 AD and show that multidecadal SST variability has been a persistent feature of the AWP, and likely, of the North Atlantic over this time period. Our results imply that tropical Atlantic SSTs remained within 1°C of modern values during the past 225 years, consistent with a previous reconstruction based on coral growth rates and with most estimates based on the Mg/Ca of planktonic foraminifera from marine sediments.
Floodplain channel morphology and networks of the middle Amazon River
Authors: Trigg Mark A. , Bates Paul D. , Wilson Matthew D. , Schumann Guy , Baugh Calum
Published: August 2012

Floodplain channels are important components of river‐floodplain systems and are known to play a key role in hydrodynamic exchange and sediment transport. The Amazon floodplain exhibits complex networks of these channels, and despite their potential importance to this globally important wetland system, these floodplain channels are relatively unstudied. The research presented here is the first systematic and detailed study of the network and morphologic characteristics of a large number of these channels in the middle reach of the central Amazon River using analysis of data derived from Landsat Enhanced Thematic Mapper Plus (ETM+) mosaic and field survey. Our findings show that the channels are ubiquitous, their width varies widely, and some of their characteristics can be fitted using power laws, potentially much like the self‐similar or fractal‐like behavior hypothesized for other types of fluvial networks. In all, 96% of the floodplain channels are not wide enough to be represented well, or at all, in the ∼90 m Shuttle Radar Topography Mission data. Channel depths are tied closely to the local amplitude of the passing main river flood wave (p value of 0.75), except where there are local runoff inputs, which results in substantially deeper channels which provide preferential flow paths across the floodplain. Channel networks imply that areas of the floodplain function for large parts of the flood cycle as separate hydrogeomorphic land units, here termed floodplain hydrological units (FHUs). These hypothesized FHUs also have distinct spatial and pattern characteristics, and it is suggested here that their differences could provide the beginnings of a framework for understanding the detailed hydrodynamics of the floodplain. In particular, different types of FHUs have differences in flood water source, which will have important implications for biogeochemical studies of the wetlands.
Long‐term culture optimization of human omentum fat‐derived mesenchymal stem cells
Authors: Marappagounder Dhanasekaran , Somasundaram Indumathi , Janvikula Rajkumar S. , Dorairaj Sudarsanam
Published: August 2012

Recent scientific explorations in search of novel sources for autologous transplantation transpired an alternative source of MSCs (mesenchymal stem cells) derived from omentum fat. The scarcity of experimental evidences probing into the biosafety concerns of omentum fat‐derived MSC under prolonged culture conditions limits its applicability as an efficient tool in regenerative medicine. This study, thus, aims to optimize human omentum fat‐derived MSC in four different media [DMEM (Dulbecco's modified Eagle's medium) LG (low glucose), DMEM KO (knock out), α‐MEM (α‐minimal essential media) and DMEM F12] in the facets of phenotypic characterization, growth kinetics, differentiation and karyotyping under prolonged culture. The cells exhibited a similarity in expression profile for the majority of markers with evidential variations in certain markers. The relevance of omentum fat‐derived MSCs became evident from its triumphant differentiation potential and karyotypic stability substantiated even at later passage. The results obtained from growth curve and PDT (population doubling time) lead to optimization of appropriate media for omentum fat‐derived stem cell research, thereby bringing omentum fat into the forefront of regenerative medicine.
Development of leaky-wave antenna for digitally controlled millimeter-wave interferometer
Authors: Kogi Yuichiro , Yoshikawa Masayuki , Matsukawa Shingo , Mase Atsushi , Nagayama Yoshio , Kawahata Kazuo
Published: August 2012

We propose a new interferometer concept that can realize electron-density distribution measurement with high spatial and moderate temporal resolution. The image non-radiative dielectric guide antenna can probe a wide measurement area simultaneously. We fabricated the antenna with an electromagnetic simulator and confirmed that the simulated and measured radiation patterns are consistent with each other. In addition, we found that the antenna shows the required characteristics such as scanning characteristics, which depend on the input frequency.
Instrumentation for dual-probe scanning near-field optical microscopy
Authors: Kaneta A. , Fujimoto R. , Hashimoto T. , Nishimura K. , Funato M. , Kawakami Y.
Published: August 2012

To investigate local carrier motions, we developed a dual-probe scanning near-field optical microscope (SNOM) with two fiber probes where one is for photoexcitation and the other is for light collection. This instrumentation is based on two important techniques: the design of probe structures and distance control between the sample surface and the two probes. A finite-difference time-domain method numerically analyzed and optimized the design for high efficiency photoexcitation and light collection, while a dual band modulation realized distance control. Real time detection of the oscillations of the probe tips using different frequencies independently controls the distance between the probe tip and the sample surface as well as the distance between the two probes. Thus, the collection probe can be scanned around an illumination probe without destroying the probe tips. To demonstrate our SNOM, we performed photoluminescence spectroscopy under the dual-probe configuration and observed carrier motions in an InGaN quantum well.
The Radiochemical Analysis of Gaseous Samples (RAGS) apparatus for nuclear diagnostics at the National Ignition Facility (invited)
Authors: Shaughnessy D. A. , Velsko C. A. , Jedlovec D. R. , Yeamans C. B. , Moody K. J. , Tereshatov E. , Stoeffl W. , Riddle A.
Published: August 2012

The Radiochemical Analysis of Gaseous Samples (RAGS) diagnostic apparatus was recently installed at the National Ignition Facility (NIF). Following a NIF shot, RAGS is used to pump the gas load from the NIF chamber for purification and isolation of the noble gases. After collection, the activated gaseous species are counted via gamma spectroscopy for measurement of the capsule areal density and fuel-ablator mix. Collection efficiency was determined by injecting a known amount of 135Xe into the NIF chamber, which was then collected with RAGS. Commissioning was performed with an exploding pusher capsule filled with isotopically enriched 124Xe and 126Xe added to the DT gas fill. Activated xenon species were recovered post-shot and counted via gamma spectroscopy. Results from the collection and commissioning tests are presented. The performance of RAGS allows us to establish a noble gas collection method for measurement of noble gas species produced via neutron and charged particle reactions in a NIF capsule.
Geometric phases in quantum control disturbed by classical stochastic processes
Authors: Viennot David
Published: August 2012

We describe the geometric (Berry) phases arising when some quantum systems are driven by control classical parameters but also by outer classical stochastic processes (as, for example, classical noises). The total geometric phase is then divided into an usual geometric phase associated with the control parameters and a second geometric phase associated with the stochastic processes. The geometric structure in which these geometric phases take place is a composite bundle (and not an usual principal bundle), which is explicitly built in this paper. We explain why the composite bundle structure is the more natural framework to study this problem. Finally, we treat a very simple example of a two-level atom driven by a phase modulated laser field with a phase instability described by a Gaussian white noise. In particular, we compute the average geometric phase issued from the noise.
A molecular dynamics study to determine the solid-liquid interfacial tension using test area simulation method (TASM)
Authors: Nair Anjan R. , Sathian Sarith P.
Published: August 2012

Molecular dynamics (MD) studies on heat transfer from a heated nanoparticle into the surrounding fluid have indicated that the fluid next to a spherical nanoparticle can get heated well above its boiling point without observing a phase change, while a contradicting behavior was observed for a flat surface-fluid interface. Another interesting observation is that the critical heat flux was found to increase with increase in the wetting characteristics of solid. Thus, the interfacial tension or free energy of solid-liquid interface could play a pivotal role in the mechanism of heat transfer. A recent study by Gloor et al. [J. Chem. Phys. 123, 134703 (2005)]10.1063/1.2038827 has proposed test area simulation method (TASM) for the determination of interfacial tension. The present study involves the determination and the comparison of solid-liquid interfacial tension for planar and spherical interfaces using MD based on TASM and analyze the results. A higher interfacial tension value is observed for spherical nanoparticle fluid interface compared to flat surface fluid interface. The results also indicate that the solid-liquid interfacial tension is a size and temperature dependent property. The results from this study are also expected to give better insights into the possible reasons for the observed differences in the thermal transport for spherical nanoparticle-liquid interface compared to planar-liquid interface.
Design and implementation of a versatile and variable-frequency piezoelectric coefficient measurement system
Authors: Wu J. S. , Huang Y. K. , Wu F. L. , Lin D. Y.
Published: August 2012

We present a simple but versatile piezoelectric coefficient measurement system, which can measure the longitudinal and transverse piezoelectric coefficients in the pressing and bending modes, respectively, at different applied forces and a wide range of frequencies. The functionality of this measurement system has been demonstrated on three samples, including a PbZr0.52Ti0.48O3 (PZT) piezoelectric ceramic bulk, a ZnO thin film, and a laminated piezoelectric film sensor. The static longitudinal piezoelectric coefficients of the PZT bulk and the ZnO film are estimated to be around 210 and 8.1 pC/N, respectively. The static transverse piezoelectric coefficients of the ZnO film and the piezoelectric film sensor are determined to be, respectively, −0.284 and −0.031 C/m2.
Quick-scanning x-ray absorption spectroscopy system with a servo-motor-driven channel-cut monochromator with a temporal resolution of 10 ms
Authors: Nonaka T. , Dohmae K. , Araki T. , Hayashi Y. , Hirose Y. , Uruga T. , Yamazaki H. , Mochizuki T. , Tanida H. , Goto S.
Published: August 2012

We have developed a quick-scanning x-ray absorption fine structure (QXAFS) system and installed it at the recently constructed synchrotron radiation beamline BL33XU at the SPring-8. Rapid acquisition of high-quality QXAFS data was realized by combining a servo-motor-driven Si channel-cut monochromator with a tapered undulator. Two tandemly aligned monochromators with channel-cut Si(111) and Si(220) crystals covered energy ranges of 4.0–28.2 keV and 6.6–46.0 keV, respectively. The system allows the users to adjust instantly the energy ranges of scans, the starting angles of oscillations, and the frequencies. The channel-cut crystals are cooled with liquid nitrogen to enable them to withstand the high heat load from the undulator radiation. Deformation of the reflecting planes is reduced by clamping each crystal with two cooling blocks. Performance tests at the Cu K-edge demonstrated sufficiently high data quality for x-ray absorption near-edge structure and extended x-ray absorption fine-structure analyses with temporal resolutions of up to 10 and 25 ms, respectively.
First principles molecular dynamics study of filled ice hydrogen hydrate
Authors: Zhang Jingyun , Kuo Jer-Lai , Iitaka Toshiaki
Published: August 2012

We investigated structural changes, phase diagram, and vibrational properties of hydrogen hydrate in filled-ice phase C2 by using first principles molecular dynamics simulation. It was found that the experimentally reported “cubic” structure is unstable at low temperature and/or high pressure: The “cubic” structure reflects the symmetry at high (room) temperature where the hydrogen bond network is disordered and the hydrogen molecules are orientationally disordered due to thermal rotation. In this sense, the “cubic” symmetry would definitely be lowered at low temperature where the hydrogen bond network and the hydrogen molecules are expected to be ordered. At room temperature and below 30 GPa, it is the thermal effects that play an essential role in stabilizing the structure in “cubic” symmetry. Above 60 GPa, the hydrogen bonds in the framework would be symmetrized and the hydrogen bond order-disorder transition would disappear. These results also suggest the phase behavior of other filled-ice hydrates. In the case of rare gas hydrate, there would be no guest molecules’ rotation-nonrotation transition since the guest molecules keep their spherical symmetry at any temperature. On the contrary methane hydrate MH-III would show complex transitions due to the lower symmetry of the guest molecule. These results would encourage further experimental studies, especially nuclear magnetic resonance spectroscopy and neutron scattering, on the phases of filled-ice hydrates at high pressures and/or low temperatures.
Perspective: Supercooled liquids and glasses
Authors: Ediger M. D. , Harrowell Peter
Published: August 2012

Supercooled liquids and glasses are important for current and developing technologies. Here we provide perspective on recent progress in this field. The interpretation of supercooled liquid and glass properties in terms of the potential energy landscape is discussed. We explore the connections between amorphous structure, high frequency motions, molecular motion, structural relaxation, stability against crystallization, and material properties. Recent developments that may lead to new materials or new applications of existing materials are described.
The effect of anisotropic heat transport on magnetic islands in 3-D configurations
Authors: Schlutt M. G. , Hegna C. C.
Published: August 2012

An analytic theory of nonlinear pressure-induced magnetic island formation using a boundary layer analysis is presented. This theory extends previous work by including the effects of finite parallel heat transport and is applicable to general three dimensional magnetic configurations. In this work, particular attention is paid to the role of finite parallel heat conduction in the context of pressure-induced island physics. It is found that localized currents that require self-consistent deformation of the pressure profile, such as resistive interchange and bootstrap currents, are attenuated by finite parallel heat conduction when the magnetic islands are sufficiently small. However, these anisotropic effects do not change saturated island widths caused by Pfirsch-Schlüter current effects. Implications for finite pressure-induced island healing are discussed.
Transition from interpulse to afterglow plasmas driven by repetitive short-pulse microwaves in a multicusp magnetic field
Authors: Pandey Shail , Sahu Debaprasad , Bhattacharjee Sudeep
Published: August 2012

In the power-off phase, plasmas generated by repetitive short-pulse microwaves in a multicusp magnetic field show a transitive nature from interpulse to afterglow as a function of pulse duration tw = 20–200 μs. The ionized medium can be driven from a highly non equilibrium to an equilibrium state inside the pulses, thereby dictating the behavior of the plasma in the power-off phase. Compared to afterglows, interpulse plasmas observed for tw < 50 μs are characterized by a quasi-steady-state in electron density that persists for ∼ 20–40 μs even after the end of the pulse and has a relatively slower decay rate (∼ 4.3 × 104 s−1) of the electron temperature, as corroborated by optical measurements. The associated electron energy probability function indicates depletion in low energy electrons which appear at higher energies just after the end of the pulse. The transition occurs at tw ∼ 50 μs as confirmed by time evolution of integrated electron numbers densities obtained from the distribution function.
Non-contact monitoring of Ge and B diffusion in B-doped epitaxial Si1-xGex bi-layers on silicon substrates during rapid thermal annealing by multiwavelength Raman spectroscopy
Authors: Hong Min-Hao , Chang Chun-Wei , Perng Dung-Ching , Lee Kuan-Ching , Jian Shiu-Ko Jang , Lee Wei-Fan , Chuang Yen , Fan Yu-Ta , Yoo Woo Sik
Published: August 2012

B-doped, thin Si1-xGex bi-layers with different Ge content and B concentrations were epitaxially grown on Si(100) device wafers. Diffusion behavior of Ge and B atoms during rapid thermal annealing were monitored by multiwavelength micro-Raman spectroscopy. Raman spectra indicating possible Ge and B redistribution by thermal diffusion was observed from B-doped, thin Si1-xGex bi-layers on Si(100) wafers after rapid thermal annealing at 950°C or higher. Significant Ge and B diffusion in Si1-xGex bi-layers and Si substrates was verified by secondary ion mass spectroscopy. Pile up of B atoms at the surface and at the boundary between Si1-xGex bi-layers was observed in the early stages of thermal diffusion.
Luminescence and deep-level transient spectroscopy of grown dislocation-rich Si layers
Authors: Kurkina I. I. , Antonova I. V. , Shklyaev A. A. , Smagulova S. A. , Ichikawa M.
Published: August 2012

The charge deep-level transient spectroscopy (Q-DLTS) is applied to the study of the dislocation-rich Si layers grown on a surface composed of dense arrays of Ge islands prepared on the oxidized Si surface. This provides revealing three deep-level bands located at EV + 0.31 eV, EC – 0.35 eV and EC – 0.43 eV using the stripe-shaped p-i-n diodes fabricated on the basis of these layers. The most interesting observation is the local state recharging process which proceeds with low activation energy (∼50 meV) or without activation. The recharging may occur by carrier tunneling within deep-level bands owing to the high dislocation density ∼ 1011 - 1012 cm-2. This result is in favor of the suggestion on the presence of carrier transport between the deep states, which was previously derived from the excitation dependence of photoluminescence (PL) intensity. Electroluminescence (EL) spectra measured from the stripe edge of the same diodes contain two peaks centered near 1.32 and 1.55 μm. Comparison with PL spectra indicates that the EL peaks are generated from arsenic-contaminated and pure areas of the layers, respectively.
Decreased marine dimethyl sulfide production under elevated CO2 levels in mesocosm and in vitro studies
Authors: Avgoustidi Valia , Nightingale Philip D. , Joint Ian , Steinke Michael , Turner Suzanne M. , Hopkins Frances E. , Liss Peter S.
Published: August 2012

Environmental contextAs atmospheric CO2 levels rise due to human activities, more of the gas dissolves in the oceans, increasing their acidity. The effect of these seawater changes on marine organisms is largely unknown. We examine the consequences of higher CO2 levels on the production by plankton of dimethyl sulfide, a climatically active gas. We find that higher CO2 levels leads to lower concentrations of dimethyl sulfide in the seawater, which has potentially important implications for the future climate.
AbstractThe oceans have absorbed approximately half of the CO2 produced by human activities and it is inevitable that surface seawaters will become increasingly acidified. The effect of lower pH on marine organisms and ocean–atmosphere exchanges is largely unknown but organisms with CaCO3 structural components are likely to be particularly affected. Because calcifying phytoplankton are significant producers of dimethyl sulfide (DMS), it is vital to understand how lower seawater pH may affect DMS production and emission to the atmosphere. Here we show, by mesocosm (Raunefjorden, Norway, April–May 2003) and in vitro studies, that the net production of DMS and its cellular precursor dimethylsulfoniopropionate (DMSP) is approximately halved in microbial communities subjected to doubled CO2 levels. Our findings provide evidence that the amount of DMS entering the atmosphere could decrease in the future. Because atmospheric oxidation of DMS can lead to climate cooling by increasing cloud albedo, a consequence of reduced DMS emissions from a lower pH ocean would be an enhancement in global warming.
Aberrant promoter methylation occurred from multicopy transgene and SU(VAR)3 - 9 homolog 9 (SUVH9) gene in transgenic Nicotiana benthamiana
Authors: Lee Gi-Ho , Sohn Seong-Han , Park Eun-Young , Park Young-Doo
Published: August 2012

The chemical modification of DNA by methylation is a heritable trait and can be subsequently reversed without altering the original DNA sequence. Methylation can reduce or silence gene expression and is a component of a host’s defence response to foreign nucleic acids. In our study, we employed a plant transformation strategy using Nicotiana benthamiana Domin to study the heritable stability of the introduced transgenes. Through the introduction of the cauliflower mosaic virus (CaMV) 35S promoter and the green fluorescent protein (GFP) reporter gene, we demonstrated that this introduced promoter often triggers a homology-dependent gene-silencing (HDGS) response. These spontaneous transgene-silencing phenomena are due to methylation of the CaMV 35S promoter CAAT box during transgenic plant growth. This process is catalysed by SU(VAR)3–9 homologue 9 (SUVH9), histone deacetylase 1 (HDA1) and domains rearranged methylase 2 (DRM2). In particular, we showed from our data that SUVH9 is the key regulator of methylation activity in epigenetically silenced GFP transgenic lines; therefore, our findings demonstrate that an introduced viral promoter and transgene can be subject to a homology-dependent gene-silencing mechanism that can downregulate its expression and negatively influence the heritable stability of the transgene.
Polygonal homographic orbits in spaces of constant curvature
Authors: Tibboel Pieter
Published: August 2012

We prove that the geometry of the 2-dimensional

n
n

-body problem for spaces of constant curvature

κ
≠
0

\kappa \neq 0

,

n
≥
3

n\geq 3

, does not allow for polygonal homographic solutions, provided that the corresponding orbits are irregular polygons of non-constant size.
Efficacy of conservation measures for the American lobster: reproductive value as a criterion
Authors: Xu Cailin , Schneider David C.
Published: August 2012

Xu, C., and Schneider, D. C. 2012. Efficacy of conservation measures for the American lobster: reproductive value as a criterion – ICES Journal of Marine Science, 69: 1831–1839.

Reproductive value takes into account both current and future value, effectively characterizing the value of an individual to the population. In this study, we use reproductive value as a criterion to evaluate the effectiveness of several conservation measures that have been undertaken or proposed for the American lobster (Homarus americanus) fishery in Newfoundland. These measures are slot fishing (i.e. no fishing below or above certain sizes), marine protected areas (MPAs), V-notching, and window fishing (i.e. no fishing within a size window). Reproductive value was estimated by using catch length data available from commercial fisheries and research surveys. We found that MPAs had the greatest effect, followed by V-notching and slot-fishing. MPAs resulted in an average increase of 64.9% in total reproductive value, V-notching an average increase of 18.3%, and slot fishing an average increase of 16.8%. In general, window fishing was not effective unless the size of the window was large. For instance, an average increase of 8.7% in total reproductive value would require a wide window (100–129 mm). Our results provide a scientific basis for evaluating conservation measures in a way that integrates population demographical information with information from commercial fisheries and research surveys.
Structured illumination of the interface between centriole and peri-centriolar material
Authors: Fu Jingyan , Glover David M.
Published: August 2012

The increase in centrosome size in mitosis was described over a century ago, and yet it is poorly understood how centrioles, which lie at the core of centrosomes, organize the pericentriolar material (PCM) in this process. Now, structured illumination microscopy reveals inDrosophilathat, before clouds of PCM appear, its proteins are closely associated with interphase centrioles in two tube-like layers: an inner layer occupied by centriolar microtubules, Sas-4, Spd-2 and Polo kinase; and an outer layer comprising Pericentrin-like protein (Dplp), Asterless (Asl) and Plk4 kinase. Centrosomin (Cnn) and γ-tubulin associate with this outer tube in G2 cells and, upon mitotic entry, Polo activity is required to recruit them together with Spd-2 into PCM clouds. Cnn is required for Spd-2 to expand into the PCM during this maturation process but can itself contribute to PCM independently of Spd-2. By contrast, the centrioles of spermatocytes elongate from a pre-existing proximal unit during the G2 preceding meiosis. Sas-4 is restricted to the microtubule-associated, inner cylinder and Dplp and Cnn to the outer cylinder of this proximal part. γ-Tubulin and Asl associate with the outer cylinder and Spd-2 with the inner cylinder throughout the entire G2 centriole. Although they occupy different spatial compartments on the G2 centriole, Cnn, Spd-2 and γ-tubulin become diminished at the centriole upon entry into meiosis to become part of PCM clouds.
Infectious titres of sheep scrapie and bovine spongiform encephalopathy agents cannot be accurately predicted from quantitative laboratory test results
Authors: González Lorenzo , Thorne Leigh , Jeffrey Martin , Martin Stuart , Spiropoulos John , Beck Katy E. , Lockey Richard W. , Vickery Christopher M. , Holder Thomas , Terry Linda
Published: August 2012

It is widely accepted that abnormal forms of the prion protein (PrP) are the best surrogate marker for the infectious agent of prion diseases and, in practice, the detection of such disease-associated (PrPd) and/or protease-resistant (PrPres) forms of PrP is the cornerstone of diagnosis and surveillance of the transmissible spongiform encephalopathies (TSEs). Nevertheless, some studies question the consistent association between infectivity and abnormal PrP detection. To address this discrepancy, 11 brain samples of sheep affected with natural scrapie or experimental bovine spongiform encephalopathy were selected on the basis of the magnitude and predominant types of PrPd accumulation, as shown by immunohistochemical (IHC) examination; contra-lateral hemi-brain samples were inoculated at three different dilutions into transgenic mice overexpressing ovine PrP and were also subjected to quantitative analysis by three biochemical tests (BCTs). Six samples gave ‘low’ infectious titres (106.5 to 106.7 LD50 g−1) and five gave ‘high titres’ (108.1 to ≥108.7 LD50 g−1) and, with the exception of the Western blot analysis, those two groups tended to correspond with samples with lower PrPd/PrPres results by IHC/BCTs. However, no statistical association could be confirmed due to high individual sample variability. It is concluded that although detection of abnormal forms of PrP by laboratory methods remains useful to confirm TSE infection, infectivity titres cannot be predicted from quantitative test results, at least for the TSE sources and host PRNP genotypes used in this study. Furthermore, the near inverse correlation between infectious titres and Western blot results (high protease pre-treatment) argues for a dissociation between infectivity and PrPres.
Systematic Prediction of cis-Regulatory Elements in the Chlamydomonas reinhardtii Genome Using Comparative Genomics
Authors: Ding Jun , Li Xiaoman , Hu Haiyan
Published: August 2012

Chlamydomonas reinhardtii is one of the most important microalgae model organisms and has been widely studied toward the understanding of chloroplast functions and various cellular processes. Further exploitation of C. reinhardtii as a model system to elucidate various molecular mechanisms and pathways requires systematic study of gene regulation. However, there is a general lack of genome-scale gene regulation study, such as global cis-regulatory element (CRE) identification, in C. reinhardtii. Recently, large-scale genomic data in microalgae species have become available, which enable the development of efficient computational methods to systematically identify CREs and characterize their roles in microalgae gene regulation. Here, we performed in silico CRE identification at the whole genome level in C. reinhardtii using a comparative genomics-based method. We predicted a large number of CREs in C. reinhardtii that are consistent with experimentally verified CREs. We also discovered that a large percentage of these CREs form combinations and have the potential to work together for coordinated gene regulation in C. reinhardtii. Multiple lines of evidence from literature, gene transcriptional profiles, and gene annotation resources support our prediction. The predicted CREs will serve, to our knowledge, as the first large-scale collection of CREs in C. reinhardtii to facilitate further experimental study of microalgae gene regulation. The accompanying software tool and the predictions in C. reinhardtii are also made available through a Web-accessible database (http://hulab.ucf.edu/research/projects/Microalgae/sdcre/motifcomb.html).