bluuebunny/crossref_metadata_2025 huggingface dataset:
A global analysis of ENSO synchrony: The oceans' biological response to physical forcing
Authors: Messié Monique , Chavez Francisco P.
Published: July 2012

A global‐scale Empirical Orthogonal Function (EOF) analysis of physical (sea surface temperatures, sea level height anomalies, atmospheric sea level pressure, photosynthetically active radiation, zonal surface currents and wind‐driven upwelling velocities) and biological (surface chlorophyll concentrations and primary production) variables shows synchronous variations from 1993 to 2010 in the first mode of variability associated with El Niño Southern Oscillation (ENSO). The first EOF of vertical temperature structure along the equatorial Pacific shows identical temporal patterns. The ENSO‐driven biological changes are explained both qualitatively and quantitatively from a subset of the physical variables. During the strong 1997–1998 El Niño a global new production decrease of ∼0.6–0.9 PgC yr−1is estimated from changes in the depth of the nutricline and wind‐driven upwelling. This is consistent with the 3.0 PgC yr−1decrease in global primary production observed by satellite remote sensing. A simple two‐layer model of chlorophyll and primary production driven by changes in nitrate and light reproduces the patterns and magnitude of changes observed by satellite. Changes in the depth of the nutricline are found to be the primary driver of the biological anomalies. The ENSO mode of zonal currents in the equatorial Pacific shows that horizontal advection is responsible for changes in chlorophyll in the central Pacific not explained by the two‐layer model.
Planetary boundary layer heights from GPS radio occultation refractivity and humidity profiles
Authors: Ao Chi O. , Waliser Duane E. , Chan Steven K. , Li Jui‐Lin , Tian Baijun , Xie Feiqin , Mannucci Anthony J.
Published: July 2012

The height of the planetary boundary layer (PBL) is an important parameter that relates to the various processes associated with the PBL. In this paper, we use Global Positioning System radio occultation (GPSRO) measurements to derive a global climatology of PBL heights. Utilizing the strength of GPSRO in capturing fine vertical structures, the top of the PBL is defined to be the height at which the vertical gradient of the refractivity or water vapor partial pressure is minimum, corresponding to the height where the refractivity or water vapor pressure changes most rapidly. A “sharpness parameter” is defined that quantifies the applicability of these definitions. The sharpness parameter is largest over the subtropical regions characterized by strong subsidence. When the sharpness parameter is large, the refractivity‐ and moisture‐based heights are shown to converge. We derived global PBL height climatology using three years (Dec. 2006–Nov. 2009) of COSMIC/FORMOSAT‐3 measurements and compared with values calculated from ECMWF Reanalysis Interim (ERA‐Int). We found that the mean PBL heights from GPSRO shared similar spatial and seasonal variations with ERA‐Int; however, GPSRO heights were higher by 500 m. The standard deviation was also higher from GPSRO, especially in the tropics. We present detailed comparisons between GPSRO and ERA‐Int over the Pacific Ocean and the Sahara desert and examine the PBL height distributions as well as its annual and diurnal variabilities. These results suggest that the underlying causes of the bias between GPSRO and ERA‐Int likely vary from region to region.
Spatial uncertainty to determine reliable daily precipitation maps
Authors: Chappell Adrian , Renzullo Luigi , Haylock Malcolm
Published: July 2012

Daily precipitation observations are commonly used with related variables to make estimates at unsampled locations to provide maps and gridded data for hydrological and climate model applications. Uncertainty in the way gridded data (maps) are prepared, given the available information, is rarely considered. Over a study period of one year, we used conditional simulations to produce multiple equally likely realizations of Australian precipitation per day. Together those realizations represented an ensemble measure of spatial uncertainty for rainfall for a given day. An independent gauge data set had values within the 5th–95th percentile uncertainty range 94% of the time. Combined with other measures they confirmed the reliability of the ensemble spatial uncertainty ranges. We compared several established mapping techniques to an independent gauge data set using local error statistics and to the spatial uncertainty maps. Those statistics showed little difference between the mapping techniques and overall assessment of performance was largely dependent on skill scores. However, the mapping techniques were different when compared to the spatial uncertainty ranges. These findings support the assertion that assessment of mapping techniques using local error statistics is insensitive to the uncertainty in producing the maps as a whole. We conclude that uncertainty information in precipitation estimates should not be overlooked when comparing precipitation estimation techniques. The focus of performance assessment is traditionally on local error estimates, and this tradition diverts attention away from the issues of uncertainty and reliability. Reliable uncertainty characterization is necessary for the rigorous detection of spatial patterns and longer time series trends in precipitation.
Neutron spectrometry—An essential tool for diagnosing implosions at the National Ignition Facility (invited)
Authors: Johnson M. Gatu , Frenje J. A. , Casey D. T. , Li C. K. , Séguin F. H. , Petrasso R. , Ashabranner R. , Bionta R. M. , Bleuel D. L. , Bond E. J. , Caggiano J. A. , Carpenter A. , Cerjan C. J. , Clancy T. J. , Doeppner T. , Eckart M. J. , Edwards M. J. , Friedrich S. , Glenzer S. H. , Haan S. W. , Hartouni E. P. , Hatarik R. , Hatchett S. P. , Jones O. S. , Kyrala G. , Le Pape S. , Lerche R. A. , Landen O. L. , Ma T. , MacKinnon A. J. , McKernan M. A. , Moran M. J. , Moses E. , Munro D. H. , McNaney J. , Park H. S. , Ralph J. , Remington B. , Rygg J. R. , Sepke S. M. , Smalyuk V. , Spears B. , Springer P. T. , Yeamans C. B. , Farrell M. , Jasion D. , Kilkenny J. D. , Nikroo A. , Paguio R. , Knauer J. P. , Yu Glebov V. , Sangster T. C. , Betti R. , Stoeckl C. , Magoon J. , Shoup M. J. , Grim G. P. , Kline J. , Morgan G. L. , Murphy T. J. , Leeper R. J. , Ruiz C. L. , Cooper G. W. , Nelson A. J.
Published: July 2012

DT neutron yield (Yn), ion temperature (Ti), and down-scatter ratio (dsr) determined from measured neutron spectra are essential metrics for diagnosing the performance of inertial confinement fusion (ICF) implosions at the National Ignition Facility (NIF). A suite of neutron-time-of-flight (nTOF) spectrometers and a magnetic recoil spectrometer (MRS) have been implemented in different locations around the NIF target chamber, providing good implosion coverage and the complementarity required for reliable measurements of Yn, Ti, and dsr. From the measured dsr value, an areal density (ρR) is determined through the relationship ρRtot (g/cm2) = (20.4 ± 0.6) × dsr10-12 MeV. The proportionality constant is determined considering implosion geometry, neutron attenuation, and energy range used for the dsr measurement. To ensure high accuracy in the measurements, a series of commissioning experiments using exploding pushers have been used for in situ calibration of the as-built spectrometers, which are now performing to the required accuracy. Recent data obtained with the MRS and nTOFs indicate that the implosion performance of cryogenically layered DT implosions, characterized by the experimental ignition threshold factor (ITFx), which is a function of dsr (or fuel ρR) and Yn, has improved almost two orders of magnitude since the first shot in September, 2010.
Testing a new NIF neutron time-of-flight detector with a bibenzyl scintillator on OMEGA
Authors: Glebov V. Yu. , Forrest C. , Knauer J. P. , Pruyne A. , Romanofsky M. , Sangster T. C. , Shoup M. J. , Stoeckl C. , Caggiano J. A. , Carman M. L. , Clancy T. J. , Hatarik R. , McNaney J. , Zaitseva N. P.
Published: July 2012

A new neutron time-of-flight (nTOF) detector with a bibenzyl crystal as a scintillator has been designed and manufactured for the National Ignition Facility (NIF). This detector will replace a nTOF20-Spec detector with an oxygenated xylene scintillator currently operational on the NIF to improve the areal-density measurements. In addition to areal density, the bibenzyl detector will measure the D–D and D–T neutron yield and the ion temperature of indirect- and direct-drive-implosion experiments. The design of the bibenzyl detector and results of tests on the OMEGA Laser System are presented.
Characterizing time decay of bibenzyl scintillator using time correlated single photon counting
Authors: Hatarik R. , Bernstein L. A. , Caggiano J. A. , Carman M. L. , Schneider D. H. G. , Zaitseva N. P. , Wiedeking M.
Published: July 2012

The time decay of several scintillation materials has been measured using the time correlated single photon counting method and a new organic crystal with a highly suppressed delayed light has been identified. Results comparing the light decay of the bibenzyl crystal with a xylene based detector, which is currently installed at National Ignition Facility will be presented.
Ultra-fast charge exchange spectroscopy for turbulent ion temperature fluctuation measurements on the DIII-D tokamak (invited)
Authors: Uzun-Kaymak I. U. , Fonck R. J. , McKee G. R.
Published: July 2012

A novel two-channel, high throughput, high efficiency spectrometer system has been developed to measure impurity ion temperature and toroidal velocity fluctuations associated with long-wavelength turbulence and other plasma instabilities. The spectrometer observes the emission of the n = 8–7 hydrogenic transition of C+5 ions (λair = 529.06 nm) resulting from charge exchange reactions between deuterium heating beams and intrinsic carbon. Novel features include a large, prism-coupled high-dispersion, volume-phase-holographic transmission grating and high-quantum efficiency, high-gain, low-noise avalanche photodiode detectors that sample emission at 1 MHz. This new diagnostic offers an order-of-magnitude increase in sensitivity compared to earlier ion thermal turbulence measurements. Increased sensitivity is crucial for obtaining enough photon statistics from plasmas with much less impurity content. The irreducible noise floor set by photon statistics sets the ultimate sensitivity to plasma fluctuations. Based on the measured photon flux levels for the entire spectral line, photon noise levels for $\tilde T_i /T_i$T̃i/Ti and $\tilde V_i /V_i$Ṽi/Vi of ∼1% are expected, while statistical averaging over long data records enables reduction in the detectable plasma fluctuation levels to values less than that. Broadband ion temperature fluctuations are observed to near 200 kHz in an L-mode discharge. Cross-correlation with the local beam emission spectroscopy measurements demonstrates a strong coupling of the density and temperature fields, and enables the cross-phase measurements between density and ion temperature fluctuations.
A Thomson scattering diagnostic on the Pegasus Toroidal experiment
Authors: Schlossberg D. J. , Schoenbeck N. L. , Dowd A. S. , Fonck R. J. , Moritz J. I. , Thome K. E. , Winz G. R.
Published: July 2012

By exploiting advances in high-energy pulsed lasers, volume phase holographic diffraction gratings, and image intensified CCD cameras, a new Thomson scattering system has been designed to operate from 532 – 592 nm on the Pegasus Toroidal Experiment. The system uses a frequency-doubled, Q-switched Nd:YAG laser operating with an energy of 2 J at 532 nm and a pulse duration of 7 ns FWHM. The beam path is < 7m, the beam diameter remains ≤ 3 mm throughout the plasma, and the beam dump and optical baffling is located in vacuum but can be removed for maintenance by closing a gate valve. A custom lens system collects scattered photons from 15 cm < Rmaj < 85 cm at ∼F/6 with 14 mm radial resolution. Initial measurements will be made at 12 spatial locations with 12 simultaneous background measurements at corresponding locations. The estimated signal at the machine-side collection optics is ∼3.5 × 104 photons for plasma densities of 1019 m−3. Typical plasmas measured will range from densities of mid-1018 to mid-1019 m−3 with electron temperatures from 10 to 1000 eV.
Plasma relaxation and topological aspects in Hall magnetohydrodynamics
Authors: Shivamoggi B. K.
Published: July 2012

Parker’s formulation of isotopological plasma relaxation process in magnetohydrodynamics (MHD) is extended to Hall MHD. The torsion coefficient α in the Hall MHD Beltrami condition turns out now to be proportional to the potential vorticity. The Hall MHD Beltrami condition becomes equivalent to the potential vorticity conservation equation in two-dimensional (2D) hydrodynamics if the Hall MHD Lagrange multiplier β is taken to be proportional to the potential vorticity as well. The winding pattern of the magnetic field lines in Hall MHD then appears to evolve in the same way as potential vorticity lines in 2D hydrodynamics.
Entropy of single-file water in (6,6) carbon nanotubes
Authors: Waghe Aparna , Rasaiah Jayendran C. , Hummer Gerhard
Published: July 2012

We used molecular dynamics simulations to investigate the thermodynamics of filling of a (6,6) open carbon nanotube (diameter D = 0.806 nm) solvated in TIP3P water over a temperature range from 280 K to 320 K at atmospheric pressure. In simulations of tubes with slightly weakened carbon-water attractive interactions, we observed multiple filling and emptying events. From the water occupancy statistics, we directly obtained the free energy of filling, and from its temperature dependence the entropy of filling. We found a negative entropy of about −1.3 kB per molecule for filling the nanotube with a hydrogen-bonded single-file chain of water molecules. The entropy of filling is nearly independent of the strength of the attractive carbon-water interactions over the range studied. In contrast, the energy of transfer depends strongly on the carbon-water attraction strength. These results are in good agreement with entropies of about −0.5 kB per water molecule obtained from grand-canonical Monte Carlo calculations of water in quasi-infinite tubes in vacuum under periodic boundary conditions. Overall, for realistic carbon-water interactions we expect that at ambient conditions filling of a (6,6) carbon nanotube open to a water reservoir is driven by a favorable decrease in energy, and opposed by a small loss of water entropy.
Random sequential adsorption on fractals
Authors: Ciesla Michal , Barbasz Jakub
Published: July 2012

Irreversible adsorption of spheres on flat collectors having dimension d < 2 is studied. Molecules are adsorbed on Sierpinski's triangle and carpet-like fractals (1 < d < 2), and on general Cantor set (d < 1). Adsorption process is modeled numerically using random sequential adsorption (RSA) algorithm. The paper concentrates on measurement of fundamental properties of coverages, i.e., maximal random coverage ratio and density autocorrelation function, as well as RSA kinetics. Obtained results allow to improve phenomenological relation between maximal random coverage ratio and collector dimension. Moreover, simulations show that, in general, most of known dimensional properties of adsorbed monolayers are valid for non-integer dimensions.
Temperature diagnostics of ECR plasma by measurement of electron bremsstrahlung
Authors: Kasthurirangan S. , Agnihotri A. N. , Desai C. A. , Tribedi L. C.
Published: July 2012

The x-ray bremsstrahlung spectrum emitted by the electron population in a 14.5 GHz ECR plasma source has been measured using a NaI(Tl) detector, and hence the electron temperature of the higher energy electron population in the plasma has been determined. The x-ray spectra for Ne and Ar gases have been systematically studied as a function of inlet gas pressure from 7 × 10−7 mbar to 7 × 10−5 mbar and for input microwave power ∼1 W to ∼300 W. At the highest input power and optimum pressure conditions, the end point bremsstrahlung energies are seen to reach ∼700 keV. The estimated electron temperatures (Te) were found to be in the range 20 keV–80 keV. The Te is found to be peaking at a pressure of 1 × 10−5 mbar for both gases. The Te is seen to increase with increasing input power in the intermediate power region, i.e., between 100 and 200 W, but shows different behaviour for different gases in the low and high power regions. Both gases show very weak dependence of electron temperature on inlet gas pressure, but the trends in each gas are different.
Canonical and micro-canonical analysis of folding of trpzip2: An all-atom replica exchange Monte Carlo simulation study
Authors: Liu Yuan , Kellogg Elizabeth , Liang Haojun
Published: July 2012

The density of states of trpzip2, a β-hairpin peptide, has been explored at all-atom level. Replica exchange Monte Carlo method was used for sufficient sampling over a wide range of temperature. Micro-canonical analysis was performed to confirm that the phase transition behavior of this two-state folder is first-order-like. Canonical analysis of heat capacity suggests that hydrogen bonding interaction exerts a considerable positive influence on folding cooperativity, in contrast, hydrophobic interaction is insufficient for high degree of folding cooperativity. Furthermore, we explain physical nature of the folding process from free energy landscape perspective and extensively analyse hydrogen bonding and stacking energy.
Gas phase hyper-Rayleigh scattering measurements
Authors: Shelton David P.
Published: July 2012

Measurements of hyper-Rayleigh scattering intensities and polarization ratios are presented for nine small molecules in the gas phase [CH4, CF4, CCl4, N2O, NH3, D2O, SO2, CF2Cl2, and (CH3)2CO]. In four cases [CH4, CF4, CCl4, and N2O] all molecular hyperpolarizability tensor components can be determined from the measurements. The results of this experiment are compared with the results of previous ab initio calculations, finding discrepancies up to 60%. Including vibrational contributions decreases the discrepancies for CH4 and CF4 and increases them for CCl4, D2O, and NH3.
A single-spin-current thermal generator
Authors: Liu Y. S. , Yang X. F. , Hong X. K. , Chi F.
Published: July 2012

We theoretically propose a single-spin-current thermal generator consisting of a Rashba quantum dot (QD), one hot electrode and two cold electrodes. The Rashba QD is directly coupled to the three electrodes, and there exists a bridge channel between the two cold electrodes. Our results show the QD device can be used to generate pure spin-up or spin-down currents in cold electrodes in the absence of bias voltages and magnetic materials. The underlying reason is a cooperative effect of the spin-dependent quantum interference effects originating from Rashba spin-orbit interaction in the QD and temperature gradients among the three electrodes. The working conditions for the single-spin-current thermal generator are also clearly presented. Moreover, we also find that the device can be converted from n-type to p-type or vice versa by a gate voltage.
Proof of damage-free selective removal of thin dielectric coatings on silicon wafers by irradiation with femtosecond laser pulses
Authors: Rublack Tino , Schade Martin , Muchow Markus , Leipner Hartmut S. , Seifert Gerhard
Published: July 2012

The microstructural impact of selective femtosecond laser ablation of thin dielectric layers from monocrystalline silicon wafers was investigated. Various spots opened by 280 fs laser pulses at λ = 1.03 μm wavelength and 50 fs pulses at 800 nm, respectively, were analyzed in detail using Raman and transmission electron microscopy. The results show clearly that the thin dielectric films can be removed without any detectable modification of the Si crystal structure in the opened area. In contrast, in adjacent regions corresponding to laser fluence slightly below the breaking threshold, a thin layer of amorphous silicon with a maximum thickness of about 50 nm is found at the Si/SiO2 interface after laser irradiation. More than one pulse on the same position, however, causes structural modification of the silicon after thin film ablation in any case.
Note: Low temperature superconductor superconducting quantum interference device system with wide pickup coil for detecting small metallic particles
Authors: Kandori Akihiko , Ogata Kuniomi , Kawabata Ryuzo , Tanimoto Sayaka , Seki Yusuke
Published: July 2012

A one-channel low temperature superconductor superconducting quantum interference device system comprising a second-order axial gradiometer with a sensing area of 10 mm × 190 mm was developed. The gradiometer was mounted in a liquid-helium dewar (450-mm diameter; 975-mm length), with a gap of 12 mm between the pickup coil and the dewar-tail surface. The magnetic field sensitivity was measured to be 16 fT/Hz1/2 in the white noise regime above 2 Hz. The system was used to measure stainless steel particles of different sizes passing through the sensing area. A 100-μm diameter SUS304 particle was readily detected passing at different positions underneath the large pickup coil by measuring its 1.3-pT magnetic field. Thus, the system was shown to be applicable to quality control of lamination sheet products such as lithium ion batteries.
Interfacial electronic properties of the heterojunctions C60/rubrene/Au and rubrene/C60/Au
Authors: Cheng Chiu-Ping , Chan Yi-Wei , Hsueh Chih-Feng , Pi Tun-Wen
Published: July 2012

Using synchrotron-radiation photoemission, we have studied the electronic structures of rubrene:C60 heterojunctions on Au substrates. The photoelectron spectra show that the interfacial properties at the C60/rubrene/Au and rubrene/C60/Au interfaces are asymmetric and do not follow the commutation rule. In the C60/rubrene case, a gap state appearing in the initial deposition stage results from negative charges transferred from rubrene to C60, while in the inverse deposition process, no strong chemical reaction could be found. A significant shift of the vacuum level induced by alignment of the charge neutrality levels of the two materials was observed in both cases. Furthermore, the charge transfer strongly enhances the dipole potential of the C60/rubrene interface. The energy level diagrams show that the C60-on-rubrene process has a superior number of advantages in the photovoltaic applications.
Study of exciton dynamics in garnets by low temperature thermo-luminescence
Authors: Mackay D. T. , Varney C. R. , Buscher J. , Selim F. A.
Published: July 2012

Shallow traps that affect exciton dynamics in undoped and Ce doped yttrium aluminum garnet (CeYAG) single crystals were studied by low temperature thermo-luminescence spectroscopy. The nature of traps was identified and their energy levels in the band gap were measured. Three types of traps were found: two very shallow traps with activation energy of less than 0.2 eV associated with electronic defects, one trap with activation energy of 0.5 eV associated with oxygen vacancies, and one relatively deeper trap with activation energy of 0.7 eV associated with hydrogen impurities. The association of oxygen vacancies with shallow traps as evident from this work and with deep traps as reported by Varney et al. [J. Appl. Phys. 111, 063505 (2012)] suggest their presence in the lattice in more than one charge state.
Investigation of chemical reactivity at the M/CuO interfaces (where M = Fe, Co, or Ni)
Authors: Chourasia A. R.
Published: July 2012

The chemical reactivity at the M/CuO interfaces (where M is Fe, Co, or Ni) has been studied. Thin films (of thickness 0.5 nm) of the metal M were deposited at room temperature on the CuO substrate by the e-beam method. The interfaces have been characterized in situ by the technique of x-ray photoelectron spectroscopy. The 2p core level regions of the metals have been investigated. The spectral data show considerable reactivity at the interfaces formed at room temperature. The core level peaks of the metal M have been observed to shift to the high binding energy side. Intense satellites appear on the high binding energy side of these core level peaks. The spectral data have been compared with those of the oxidized metal. These spectral features conform to each other confirming the formation of the metal oxide. The satellite structure in the copper region was observed to disappear, and the spectral features approach those of elemental copper after the deposition of the metallic overlayer. The data, therefore, suggest that the copper oxide gets reduced to elemental copper, and the metal M is oxidized to the metal oxide. The presence of the high binding energy satellite has been used to identify the phase of the metal oxide formed at the interface. The uniformity of the initial 0.5 nm overlayer has also been investigated. A second overlayer of 0.5 nm was deposited over the first layer. The characterization of these samples showed core level peaks at the elemental positions. The spectral features correspond to the presence of unreacted metal in these samples. The content of this unreacted metal was determined and is observed to increase in the order from iron to cobalt to nickel. The investigation shows room temperature chemical reactivity at the M/CuO interface and provides a new method to prepare sub-nano-oxide films of iron, cobalt, and nickel.
Understanding helicon plasmas
Authors: Tarey R. D. , Sahu B. B. , Ganguli A.
Published: July 2012

This paper presents a comprehensive overview of work on the helicon plasmas and also discusses various aspects of RF power deposition in such plasmas. Some of the work presented here is a review of earlier work on theoretical [A. Ganguli et al., Phys. Plasmas 14, 113503 (2007)] and experimental [A. Ganguli et al., Plasma Sources Sci. Technol. 20(1), 015021 (2011)] investigations on helicon plasmas in a conducting cylindrical waveguide for m = −1 mode. This work also presents an approach to investigate the mechanisms by which the helicon and associated Trivelpiece-Gould (TG) waves are responsible for RF power deposition in Helicon discharges. Experiment design adopts the recent theory of damping and absorption of Helicon modes in conducting waveguides [A. Ganguli et al., Phys. Plasmas 14, 113503 (2007)]. The effort has also been made to detect the warm electrons, which are necessary for ionization, because Helicon discharges are of high density, low Te discharges and the tail of the bulk electron population may not have sufficient high-energy electrons. Experimental set up also comprises of the mirror magnetic field. Measurements using RF compensated Langmuir probes [A. Ganguli et al., Plasma Sources Sci. Technol. 17, 015003 (2008)], B-dot probe and computations based on the theory shows that the warm electrons at low pressure (0.2–0.3 mTorr) Helicon discharges, are because of the Landau damping of TG waves. In collisional environment, at a pressure ≈10 mTorr, these high-energy electrons are due to the acceleration of bulk electrons from the neighboring regions across steep potential gradients possibly by the formation of double layers.
Linear and nonlinear electrostatic modes in a strongly coupled quantum plasma
Authors: Ghosh Samiran , Chakrabarti Nikhil , Shukla P. K.
Published: July 2012

The properties of linear and nonlinear electrostatic waves in a strongly coupled electron-ion quantum plasma are investigated. In this study, the inertialess electrons are degenerate, while non-degenerate inertial ions are strongly correlated. The ion dynamics is governed by the continuity and the generalized viscoelastic momentum equations. The quantum forces associated with the quantum statistical pressure and the quantum recoil effect act on the degenerate electron fluid, whereas strong ion correlation effects are embedded in generalized viscoelastic momentum equation through the viscoelastic relaxation of ion correlations and ion fluid shear viscosities. Hence, the spectra of linear electrostatic modes are significantly affected by the strong ion coupling effect. In the weakly nonlinear limit, due to ion-ion correlations, the quantum plasma supports a dispersive shock wave, the dynamics of which is governed by the Korteweg-de Vries Burgers’ equation. For a particular value of the quantum recoil effect, only monotonic shock structure is observed. Possible applications of our investigation are briefly mentioned.
Light sensitivity of shoot hydraulic conductance in five temperate deciduous tree species
Authors: Aasamaa Krõõt , Sõber Anu
Published: July 2012

The light sensitivity of the shoot hydraulic conductance in five temperate deciduous tree species was measured using two methods to clarify the role of light sensitivity and the suitability of the methods used to study it. The light sensitivity measured using a method that included an interruption of ≤10 min in shoot light acclimation did not differ from that measured using a method with continuous illumination. The ‘noncontinuous light’ methods are suitable for measuring hydraulic conductance and its light response. Light sensitivity correlated with other leaf water traits as follows: positively with the ion-mediated increase in xylem hydraulic conductance; a relative decrease in the hydraulic conductance of the laminae in response to HgCl2; a relative change in stomatal conductance in response to changes in PAR intensity or atmospheric CO2 concentration, or to a decrease in air humidity or leaf water potential; and with instantaneous water use efficiency. The traits correlated negatively with shoot hydraulic conductance, stomatal conductance and relative increases in stomatal conductance in response to increases in leaf water potential. We suggest that high light sensitivity should be considered as one of the characteristics of conservative water use in trees. Low blue light increased shoot hydraulic conductance to a similar extent to moderate white light and twice as much as moderate red light. Blue light perception is important in the light sensitivity mechanism.
A new wildland fire danger index for a Mediterranean region and some validation aspects
Authors: de Vicente Javier , Crespo Fortunato
Published: July 2012

Wildland fires are the main cause of tree mortality in Mediterranean Europe and a major threat to Spanish forests. This paper focuses on the design and validation of a new wildland fire index especially adapted to a Mediterranean Spanish region. The index considers ignition and spread danger components. Indicators of natural and human ignition agents, historical occurrence, fuel conditions and fire spread make up the hierarchical structure of the index. Multi-criteria methods were used to incorporate experts’ opinion in the process of weighting the indicators and to carry out the aggregation of components into the final index, which is used to map the probability of daily fire occurrence on a 0.5-km grid. Generalised estimating equation models, which account for possible correlated responses, were used to validate the index, accommodating its values onto a larger scale because historical records of daily fire occurrence, which constitute the dependent variable, are referred to cells on a 10-km grid. Validation results showed good index performance, good fit of the logistic model and acceptable discrimination power. Therefore, the index will improve the ability of fire prevention services in daily allocation of resources.
Human embryonic germ cell derivatives express a broad range of developmentally distinct markers and proliferate extensively
in vitro
Authors: Shamblott Michael J. , Axelman Joyce , Littlefield John W. , Blumenthal Paul D. , Huggins George R. , Cui Yan , Cheng Linzhao , Gearhart John D.
Published: July 2012

Human pluripotent stem cells (hPSCs) have been derived from the
inner cell mass cells of blastocysts (embryonic stem cells) and
primordial germ cells of the developing gonadal ridge (embryonic germ
cells). Like their mouse counterparts, hPSCs can be maintained in
culture in an undifferentiated state and, upon differentiation,
generate a wide variety of cell types. Embryoid body (EB) formation is
a requisite step in the process of
in vitro
differentiation of these stem cells and has been used to derive neurons
and glia, vascular endothelium, hematopoietic cells, cardiomyocytes,
and glucose-responsive insulin-producing cells from mouse PSCs. EBs
generated from human embryonic germ cell cultures have also been found
to contain a wide variety of cell types, including neural cells,
vascular endothelium, muscle cells, and endodermal derivatives. Here,
we report the isolation and culture of cells from human EBs as well as
a characterization of their gene expression during growth in several
different culture environments. These heterogeneous cell cultures are
capable of robust and long-term [>70 population doublings (PD)]
proliferation in culture, have normal karyotypes, and can be
cryopreserved, clonally isolated, and stably transfected. Cell cultures
and clonal lines retain a broad pattern of gene expression including
simultaneous expression of markers normally associated with cells of
neural, vascular/hematopoietic, muscle, and endoderm lineages. The
growth and expression characteristics of these EB-derived cells suggest
that they are relatively uncommitted precursor or progenitor cells.
EB-derived cells may be suited to studies of human cell differentiation
and may play a role in future transplantation therapies.
Disruption of matrix metalloproteinase 2 binding to integrin α
v
β
3
by an organic molecule inhibits angiogenesis and tumor growth
in vivo
Authors: Silletti Steve , Kessler Torsten , Goldberg Joel , Boger Dale L. , Cheresh David A.
Published: July 2012

Matrix metalloproteinase 2 (MMP2) can associate with
integrin α
v
β
3
on the surface of endothelial
cells, thereby promoting vascular invasion. Here, we describe an
organic molecule (TSRI265) selected for its ability to bind to integrin
α
v
β
3
and block
α
v
β
3
interaction with MMP2. Although
disrupting α
v
β
3
/MMP2 complex formation,
TSRI265 has no effect on α
v
β
3
binding to
its extracellular matrix ligand vitronectin and does not influence MMP2
activation or catalytic activity directly. However, TSRI265 acts as a
potent antiangiogenic agent and thereby blocks tumor growth
in
vivo
. These findings suggest that activated MMP2 does not
facilitate vascular invasion during angiogenesis unless it forms a
complex with α
v
β
3
on the endothelial cell
surface. By disrupting endothelial cell invasion without broadly
suppressing cell adhesion or MMP function, the use of compounds such as
TSRI265 may provide a novel therapeutic approach for diseases
associated with uncontrolled angiogenesis.
PKN delays mitotic timing by inhibition of Cdc25C: Possible involvement of PKN in the regulation of cell division
Authors: Misaki Kazuyo , Mukai Hideyuki , Yoshinaga Chiho , Oishi Kumiko , Isagawa Takayuki , Takahashi Mikiko , Ohsumi Keita , Kishimoto Takeo , Ono Yoshitaka
Published: July 2012

The role of PKN, a fatty acid- and Rho small GTPase-activated
protein kinase, in cell-cycle regulation was analyzed. Microinjection
of the active form of PKN into a
Xenopus
embryo caused
cleavage arrest, whereas normal cell division proceeded in the control
embryo microinjected with buffer or the inactive form of PKN. Exogenous
addition of the active form of PKN delayed mitotic timing in
Xenopus
egg cycling extracts judging by morphology of
sperm nuclei and Cdc2/cyclin B histone H1 kinase activity. The
kinase-negative form of PKN did not affect the timing, suggesting that
delayed mitotic timing depends on the kinase activity of PKN. The
dephosphorylation of Tyr-15 of Cdc2 was also delayed in correlation
with Cdc2/cyclin B histone H1 kinase activation in extracts
containing active PKN. The Cdc25C activity for the dephosphorylation of
Tyr-15 in Cdc2 was suppressed by pretreatment with the active form of
PKN. Furthermore, PKN efficiently phosphorylated Cdc25C
in
vitro
, indicating that PKN directly inhibits Cdc25C activity by
phosphorylation. These results suggest that PKN plays a significant
role in the control of mitotic timing by inhibition of Cdc25C.
A multiple-site-specific heteroduplex tracking assay as a tool for the study of viral population dynamics
Authors: Resch Wolfgang , Parkin Neil , Stuelke Erin L. , Watkins Terri , Swanstrom Ronald
Published: July 2012

Rapidly evolving entities, such as viruses, can undergo complex
genetic changes in the face of strong selective pressure. We have
developed a modified heteroduplex tracking assay (HTA) capable of
detecting the presence of single, specific mutations or sets of linked
mutations. The initial application of this approach, termed
multiple-site-specific (MSS) HTA, was directed toward the detection of
mutations in the HIV-1
pro
gene at positions 46, 48, 54,
82, 84, and 90, which are associated with resistance to multiple
protease inhibitors. We demonstrate that MSS HTA is sensitive and
largely specific to all targeted mutations. The assay allows the
accurate and reproducible quantitation of viral subpopulations
comprising 3% or more of the total population. Furthermore, we used
MSS HTA in longitudinal studies of
pro
gene evolution
in vitro
and
in vivo
. In the examples
shown here, populations turned over rapidly and more than one
population was present frequently. To demonstrate the versatility of
MSS HTA, we also constructed a probe sensitive to changes at positions
181 and 184 of the RT coding domain. Changes at these positions are
involved in resistance to nevirapine and 2′,3′-dideoxy-3′-thiacytidine
(3TC), respectively. This assay easily detected the evolution of
resistance to 3TC. MSS HTA provides a rapid and sensitive approach for
detecting the presence of and quantifying complex mixtures of distinct
genotypes, including genetically linked mutations, and, as one example,
represents a useful tool for following the evolution of drug resistance
during failure of HIV-1 antiviral therapy.
Effects of replication termination mutants on chromosome partitioning in
Bacillus subtilis
Authors: Lemon Katherine P. , Kurtser Iren , Grossman Alan D.
Published: July 2012

Many circular genomes have replication termination systems, yet
disruption of these systems does not cause an obvious defect in growth
or viability. We have found that the replication termination system of
Bacillus subtilis
contributes to accurate chromosome
partitioning. Partitioning of the terminus region requires that
chromosome dimers, that have formed as a result of RecA-mediated
homologous recombination, be resolved to monomers by the site-specific
recombinase encoded by
ripX
. In addition, the chromosome
must be cleared from the region of formation of the division septum.
This process is facilitated by the
spoIIIE
gene product
which is required for movement of a chromosome out of the way of the
division septum during sporulation. We found that deletion of
rtp
, which encodes the replication termination protein,
in combination with mutations in
ripX
or
spoIIIE
, led to an increase in production of anucleate
cells. This increase in production of anucleate cells depended on
recA
, indicating that there is probably an increase in
chromosome dimer formation in the absence of the replication
termination system. Our results also indicate that SpoIIIE probably
enhances the function of the RipX recombinase system. We also
determined the subcellular location of the replication termination
protein and found that it is a good marker for the position of the
chromosome terminus.
Genome-wide analysis of developmental and sex-regulated gene expression profiles in
Caenorhabditis elegans
Authors: Jiang Min , Ryu Jubin , Kiraly Monika , Duke Kyle , Reinke Valerie , Kim Stuart K.
Published: July 2012

We have constructed DNA microarrays containing 17,871 genes,
representing about 94% of the 18,967 genes currently annotated in the
Caenorhabditis elegans
genome. These DNA
microarrays can be used as a tool to define a nearly complete molecular
profile of gene expression levels associated with different
developmental stages, growth conditions, or worm strains. Here, we used
these full-genome DNA microarrays to show the relative levels of gene
expression for nearly every gene during development, from eggs through
adulthood. These expression data can help reveal when a gene may act
during development. We also compared gene expression in males to that
of hermaphrodites and found a total of 2,171 sex-regulated genes
(
P
< 0.05). The sex-regulated genes provide a
global view of the differences between the sexes at a molecular level
and identify many genes likely to be involved in sex-specific
differentiation and behavior.
HPP1
: A transmembrane protein-encoding gene commonly methylated in colorectal polyps and cancers
Authors: Young Joanne , Biden Kelli G. , Simms Lisa A. , Huggard Phillip , Karamatic Rozemary , Eyre Helen J. , Sutherland Grant R. , Herath Nirmitha , Barker Melissa , Anderson Gregory J. , Fitzpatrick David R. , Ramm Grant A. , Jass Jeremy R. , Leggett Barbara A.
Published: July 2012

Adenomas are the precursors of most colorectal cancers.
Hyperplastic polyps have been linked to the subset of colorectal
cancers showing DNA microsatellite instability, but little is known of
their underlying genetic etiology. Using a strategy that isolates
differentially methylated sequences from hyperplastic polyps and normal
mucosa, we identified a 370-bp sequence containing the 5′ untranslated
region and the first exon of a gene that we have called
HPP1.
Rapid amplification of cDNA ends was used to
isolate
HPP1
from normal mucosa. Using reverse
transcription–PCR,
HPP1
was expressed in 28 of 30
(93%) normal colonic samples but in only seven of 30 (23%) colorectal
cancers (
P
< 0.001). The 5′ region of
HPP1
included a CpG island containing 49 CpG sites, of
which 96% were found to be methylated by bisulfite sequencing of DNA
from colonic tumor samples. By COBRA analysis, methylation was detected
in six of nine (66%) adenomas, 17 of 27 (63%) hyperplastic polyps,
and 46 of 55 (84%) colorectal cancers. There was an inverse
relationship between methylation level and mRNA expression in cancers
(
r
= −0.67;
P
< 0.001), and
5-aza-2-deoxycytidine treatment restored
HPP1
expression
in two colorectal cancer cell lines.
In situ
hybridization of
HPP1
indicated that expression occurs
in epithelial and stromal elements in normal mucosa but is silenced in
both cell types in early colonic neoplasia
. HPP1
is
predicted to encode a transmembrane protein containing follistatin and
epidermal growth factor-like domains. Silencing of
HPP1
by methylation may increase the probability of neoplastic
transformation.
Malaria parasite exit from the host erythrocyte: A two-step process requiring extraerythrocytic proteolysis
Authors: Salmon Brandy L. , Oksman Anna , Goldberg Daniel E.
Published: July 2012

Intraerythrocytic malaria parasites replicate by the process of schizogeny, during which time they copy their genetic material and package it into infective merozoites. These merozoites must then exit the host cell to invade new erythrocytes. To better characterize the events of merozoite escape, erythrocytes containingPlasmodium falciparumschizonts were cultured in the presence of the cysteine protease inhibitor,l-transepoxy-succinyl-leucylamido-(4-guanidino)butane (E64). This treatment resulted in the accumulation of extraerythrocytic merozoites locked within a thin, transparent membrane. Immunomicroscopy demonstrated that the single membrane surrounding the merozoites is not erythrocytic but rather is derived from the parasitophorous vacuolar membrane (PVM). Importantly, structures identical in appearance can be detected in untreated cultures at low frequency. Further studies revealed that (i) merozoites from the PVM-enclosed merozoite structures (PEMS) are invasive, viable, and capable of normal development; (ii) PEMS can be purified easily and efficiently; and (iii) when PEMS are added to uninfected red blood cells, released merozoites can establish a synchronous wave of infection. These observations suggest thatl-transepoxy-succinyl-leucylamido-(4-guanidino)butane (E64) causes an accumulation of an intermediate normally present during the process of rupture. We propose a model for the process of rupture: merozoites enclosed within the PVM first exit from the host erythrocyte and then rapidly escape from the PVM by a proteolysis-dependent mechanism.
A secondary drug resistance mutation of TEM-1 β-lactamase that suppresses misfolding and aggregation
Authors: Sideraki Vera , Huang Wanzhi , Palzkill Timothy , Gilbert Hiram F.
Published: July 2012

In Gram-negative bacteria, TEM-1 β-lactamase provides the major
mechanism of plasmid-mediated β-lactam resistance. Natural variants
of TEM-1 with increased antibiotic resistance have appeared in response
to the use of extended-spectrum β-lactam antibiotics (e.g.,
ceftazidime) and β-lactamase inhibitors (e.g., clavulanic acid). Some
of the variant enzymes are more efficient at catalyzing β-lactam
hydrolysis, whereas others are more resistant to inhibitors. M182T is a
substitution observed in both types of variant TEM-1 β-lactamases.
This mutation is found only in combination with other amino acid
substitutions, suggesting that it may correct defects introduced by
other mutations that alter the specificity. An engineered core
mutation, L76N, which diminishes the periplasmic β-lactamase activity
by 100-fold, was used as a model to understand the mechanism of
suppression of the M182T mutation. Biochemical studies of the L76N
enzyme alone and in combination with the M182T mutation indicate that
the M182T substitution acts at the level of folding but does not affect
the thermodynamic stability of TEM-1 β-lactamase. Thus, the M182T
substitution is an example of a naturally occurring mutation that has
evolved to alter the folding pathway of a protein and confer a
selective advantage during the evolution of drug resistance.
HrpZ
Psph
from the plant pathogen
Pseudomonas syringae
pv.
phaseolicola
binds to lipid bilayers and forms an ion-conducting pore
in vitro
Authors: Lee Justin , Klüsener Birgit , Tsiamis George , Stevens Conrad , Neyt Cécile , Tampakaki Anastasia P. , Panopoulos Nickolas J. , Nöller Joachim , Weiler Elmar W. , Cornelis Guy R. , Mansfield John W. , Nürnberger Thorsten
Published: July 2012

The
hrp
gene clusters of plant pathogenic bacteria
control pathogenicity on their host plants and ability to elicit the
hypersensitive reaction in resistant plants. Some
hrp
gene products constitute elements of the type III secretion system, by
which effector proteins are exported and delivered into plant cells.
Here, we show that the
hrpZ
gene product from the bean
halo-blight pathogen,
Pseudomonas syringae
pv.
phaseolicola
(HrpZ
Psph
), is secreted in an
hrp
-dependent manner in
P. syringae
pv.
phaseolicola
and exported by the type III secretion
system in the mammalian pathogen
Yersinia
enterocolitica
. HrpZ
Psph
was found to associate
stably with liposomes and synthetic bilayer membranes. Under symmetric
ionic conditions, addition of 2 nM of purified recombinant
HrpZ
Psph
to the cis compartment of planar lipid bilayers
provoked an ion current with a large unitary conductivity of 207 pS.
HrpZ
Psph
-related proteins from
P. syringae
pv.
tomato
or
syringae
triggered ion
currents similar to those stimulated by HrpZ
Psph
. The
HrpZ
Psph
-mediated ion-conducting pore was permeable for
cations but did not mediate fluxes of Cl
−
. Such
pore-forming activity may allow nutrient release and/or delivery of
virulence factors during bacterial colonization of host plants.