bluuebunny/crossref_metadata_2025 huggingface dataset:
Void fraction measurements beneath plunging and spilling breaking waves
Authors: Rojas G. , Loewen M. R.
Published: August 2010

The temporal and spatial variations of the void fraction fields beneath deepwater breaking waves were investigated in the laboratory. There were a total of 13 measurement positions along the plunging wave; the peak void fractions measured varied from 0.024 to 0.96 and the time‐averaged void fractions varied from 0.012 to 0.37. For the spilling wave, there were four measurement positions, and the mean void fractions varied from 0.17 to 0.29. It was found that an energetic spilling breaker may entrain approximately the same volume of air as a steeper, larger‐amplitude plunging breaker. The speed of advance of the air cavity entrained beneath the plunging wave was estimated to be 70% of the phase speed of the breaking wave. The speed of the third bubble cloud entrained by the splash‐up was found to be approximately 90% of the phase speed. Beneath the spilling breaker, the speed of advance of the bubble cloud was estimated to be 100% of the phase speed. These measurements have lead to the identification of four significant events during the breaking of a plunging wave: the plunging water jet impacting the forward face of the wave, the air cavity collapse, the splash‐up impact on the forward wave face, and the location and timing of the peak void fraction in the splashing zone. Numerical models of plunging breakers should be able to accurately predict the timing and nature of these events.
Large‐eddy simulation of the tidal‐cycle variations of an estuarine boundary layer
Authors: Li Ming , Radhakrishnan Senthilkumaran , Piomelli Ugo , Rockwell Geyer W.
Published: August 2010

The estuarine boundary layer affected by a horizontal density gradient exhibits temporal evolution over a tidal cycle, in a manner similar to the diurnal cycle of the ocean surface mixed layer. A large eddy simulation (LES) model is developed to investigate the physics controlling the growth of the boundary layer during the flood tide and restratification during the ebb tide. Turbulent kinetic energy, momentum and salt fluxes, bottom stress, and energy dissipation rates calculated from the LES model all show a strong flood‐ebb asymmetry. Analysis of the turbulent kinetic energy (TKE) budget shows a primary balance between shear production and dissipation in the well‐mixed boundary layer over the tidal cycle. However, TKE transport term is found to be important across the edge of the boundary layer during the flood tide so turbulent energy generated in the bottom boundary layer can be transferred to the stratified pycnocline region. Tidal straining leads to a small and weakly convective region inside the boundary layer during the flood tide but the strain‐induced buoyancy flux does not make a significant contribution to the turbulence generation. Additional LES runs are conducted by switching off the baroclinic pressure gradient term in the momentum equation and the tidal straining term in the salinity equation to show that the baroclinic pressure gradient is the main mechanism responsible for generating the flood‐ebb mixing asymmetry.
A correlation study of high‐altitude and midaltitude clouds and galactic cosmic rays by MIPAS‐Envisat
Authors: Rohs Susanne , Spang Reinhold , Rohrer Franz , Schiller Cornelius , Vos Heinz
Published: August 2010

The cloud index (CI), the cloud occurrence frequency (Occ), and the extinction data (Ext) of the Michelson Interferometer for Passive Atmospheric Sounding instrument on board Envisat (MIPAS‐E) from July 2002 to March 2004 are used to investigate a possible link between galactic cosmic rays (GCRs) and midaltitude and high‐altitude clouds (CI, Occ: 9–18 km, Ext: 12–24 km). The zonally averaged data with 3 km vertical resolution are averaged over six major Forbush decrease (FD) events and subsequently correlated with the Climax neutron monitor data (CNM). In order to allow for nucleation and growth of ice particles, time lags from 0 to 5 days are applied. We find several weak but statistically significant correlations with an excess of positive cloud‐GCR correlations. Introducing a time lag does not enhance the correlations significantly. Subdividing the data in a global grid with 30° × 90° × 3 km resolution shows higher correlations in some regions. The investigation of the individual FD events yields a heterogeneous picture. Overall, there is a weak tendency toward a positive cloud‐CNM correlation. A Kolmogorov‐Smirnov test shows that for time shifts from 0 to +5 days a weak GCR‐cloud effect is evident in the MIPAS‐E measurements. An estimation of the impact of this effect delivers that a 15% increase in CNM would result in a small decrease in CI (corresponding to an increase in cloud opacity) which is most pronounced at 9 km altitude (−9% to +0.5%). For log(Ext) a decrease of −5 to 0% is calculated at 12 km altitude which shifts toward weak positive values at higher altitudes.
Causality across rainfall time scales revealed by continuous wavelet transforms
Authors: Molini Annalisa , Katul Gabriel G. , Porporato Amilcare
Published: August 2010

Rainfall variability occurs over a wide range of time scales owing to processes initiated by cloud microphysics and sustained by atmospheric circulation. A central topic in rainfall research is to determine whether rainfall variability at a given scale is caused by dynamics acting at some other scales. Random multiplicative cascades (RMCs) are standard approaches for describing rainfall variability across such a wide range of time scales. Their popularity stems from their ability to reproduce rainfall self‐similarity and long‐range correlations as well as intermittency buildup at finer scales. However, standard RMCs only predict instantaneous flow of variance (energy or activity) from large to fine scales and cannot account for scale‐wise causal relationships. Such relationships reveal themselves through noninstantaneous cascade mechanisms, namely, large‐scale events influencing finer‐scale events at later times (i.e., forward causal cascade) or conversely (inverse causal cascade). The presence of causal cascade signatures within the rainfall process is explored here using both continuous wavelet decomposition (CWT) and scale‐by‐scale causality measures such as cross‐scale correlation and linearized transfer entropy. The causality hypothesis is further tested against results from toy models, surrogate data, and a scalar turbulence time series (water vapor) to ensure that rainfall causality is not an artifact of the estimation method or resulting from the redundancy in CWT. The analysis demonstrates the presence of causal cascades (mainly forward) in rainfall series when sampled at fine temporal resolutions (seconds). These causal relationships tend to vanish when rainfall is aggregated at coarser time scales (hours and longer).
Relation between optical and chemical properties of dust aerosol over Beijing, China
Authors: Huang Kan , Zhuang Guoshun , Lin Yanfen , Li Juan , Sun Yele , Zhang Wenjie , Fu Joshua S.
Published: August 2010

Characteristics of optical and chemical properties of dust aerosol over Beijing and their relation were studied in the spring dust season, 2006 to understand the impact of dust and anthropogenic aerosol on the regional climate. Two dust plumes (DS1 and DS2) were identified with contrasting physicochemical properties. Strong absorbing of aerosol at 439 nm was observed, probably due to the significant proportion of iron oxides in the dust aerosol other than black carbon. The transport pathways of dust, concentrations of pollutant precursors and meteorological conditions were the main factors affecting the mixing extent of pollutants with dust. Aerosol of DS1 was more “polluted” than that of DS2 and even non‐dust (ND) days. Pollution elements, i.e., Zn, As, Pb, S, and Cd, were greatly enriched in DS1; SO42−, NO3−, NH4+, and K+ significantly increased in dust storm episode, especially in DS1, indicating the strong heterogeneous chemical reaction occurred on dust and the mixing of dust with various pollutants during the long‐range/regional transport of dust plumes. Linear relationship between optical properties and aerosol chemical composition was found. Soluble ions, i.e., SO42−, NO3−, NH4+, and K+, were the major contributors to the light extinction in fine particles, while mineral aerosol contributed more to that in coarse particles. Black carbon, as a strong light absorbing species, was found to contribute to the light extinction in both fine and coarse particles.
Five year (2004–2009) observations of upper tropospheric water vapor and cloud ice from MLS and comparisons with GEOS‐5 analyses
Authors: Jiang Jonathan H. , Su Hui , Pawson Steven , Liu Hui‐Chun , Read William G. , Waters Joe W. , Santee Michelle L. , Wu Dong L. , Schwartz Michael J. , Livesey Nathaniel J. , Lambert Alyn , Fuller Ryan A. , Lee Jae N.
Published: August 2010

This paper gives an overview of August 2004 through February 2010 upper tropospheric (UT) water vapor (H2O) and ice water content (IWC) from the Aura Microwave Limb Sounder (MLS) and comparisons with outputs from the NASA Goddard Earth Observing System Version 5 (GEOS‐5) data assimilation system. Both MLS and GEOS‐5 show that high values of H2O and IWC at 215 to 147 hPa are associated with areas of deep convection. They exhibit good (within ∼15%) agreement in IWC at these altitudes, but GEOS‐5 H2O is ∼50% (215 hPa) to ∼30% (147 hPa) larger than MLS values, possibly due to higher temperatures in the data assimilation system at these altitudes. A seasonally migrating band of tropical deep convection is clearly evident in both the MLS and GEOS‐5 UT H2O and IWC, but GEOS‐5 produces a weaker intertropical convergence zone than MLS. MLS and GEOS‐5 both show spatial anticorrelation between IWC and H2O at 100 hPa, where low H2O is associated with low temperatures in regions of tropical convection. At 100 hPa, GEOS‐5 produces 50% less IWC and 15% less H2O in the tropics, and ∼20% more H2O in the extratropics, than does MLS. Behavior of the 100 hPa H2O is consistent with it being controlled by temperature. The seasonal cycle in the vertical transport of tropical mean H2O from ∼147 hPa to ∼10 hPa appears much stronger in MLS than in GEOS‐5. The UT IWC and H2O interannual variations, from both MLS and GEOS‐5, show clear imprints of the El Niño–Southern Oscillation.
Sensitivity of GCM tropical middle atmosphere variability and climate to ozone and parameterized gravity wave changes
Authors: Bushell A. C. , Jackson D. R. , Butchart N. , Hardiman S. C. , Hinton T. J. , Osprey S. M. , Gray L. J.
Published: August 2010

This paper describes the impact of changing the current imposed ozone climatology upon the tropical Quasi‐Biennial Oscillation (QBO) in a high top climate configuration of the Met Office U.K. general circulation model. The aim is to help distinguish between QBO changes in chemistry climate models that result from temperature‐ozone feedbacks and those that might be forced by differences in climatology between previously fixed and newly interactive ozone distributions. Different representations of zonal mean ozone climatology under present‐day conditions are taken to represent the level of change expected between acceptable model realizations of the global ozone distribution and thus indicate whether more detailed investigation of such climatology issues might be required when assessing ozone feedbacks. Tropical stratospheric ozone concentrations are enhanced relative to the control climatology between 20–30 km, reduced from 30–40 km and enhanced above, impacting the model profile of clear‐sky radiative heating, in particular warming the tropical stratosphere between 15–35 km. The outcome is consistent with a localized equilibrium response in the tropical stratosphere that generates increased upwelling between 100 and 4 hPa, sufficient to account for a 12 month increase of modeled mean QBO period. This response has implications for analysis of the tropical circulation in models with interactive ozone chemistry because it highlights the possibility that plausible changes in the ozone climatology could have a sizable impact upon the tropical upwelling and QBO period that ought to be distinguished from other dynamical responses such as ozone‐temperature feedbacks.
South Pole paleowind from automated synthesis of ice core records
Authors: Bay R. C. , Rohde R. A. , Price P. B. , Bramall N. E.
Published: August 2010

We develop a fully automated reconstruction of South Pole surface roughness as a measure of past wind intensity, using dynamic warping feature recognition and internal consistency checks to reduce subjectivity and analysis time. We synchronized millimeter‐resolution optical profiles of deep South Pole glacial dust together with ice core data between the ages 26 and 90 thousand years B.P. The images were captured using a laser dust logger in six boreholes of the IceCube neutrino detector array, a massive construction project in the ice at South Pole and an unusual opportunity for glaciology and paleoclimate research. South Pole surface roughness anticorrelated with curves of Antarctic pCO2 and temperature, which we propose were connected through secular migrations of the Southern Hemisphere westerlies. This new paleoclimate signal may be direct evidence of atmospheric reorganization during the glacial, helping to deconvolve the thermodynamics and biogeochemistry of climate change. We also found that local intensity of atmospheric circulation roughly tracked the quantity of wind‐borne particulates deposited in Antarctic ice during the glacial period, although the largest dust increases were likely furnished by the source regions.
Mineralogy and stratigraphy of phyllosilicate‐bearing and dark mantling units in the greater Mawrth Vallis/west Arabia Terra area: Constraints on geological origin
Authors: Noe Dobrea E. Z. , Bishop J. L. , McKeown N. K. , Fu R. , Rossi C. M. , Michalski J. R. , Heinlein C. , Hanus V. , Poulet F. , Mustard R. J. F. , Murchie S. , McEwen A. S. , Swayze G. , Bibring J.‐P. , Malaret E. , Hash C.
Published: August 2010

Analyses of MRO/CRISM images of the greater Mawrth Vallis region of Mars affirm the presence of two primary phyllosilicate assemblages throughout a region ∼1000 × 1000 km. These two units consist of an Fe/Mg‐phyllosilicate assemblage overlain by an Al‐phyllosilicate and hydrated silica assemblage. The lower unit contains Fe/Mg‐smectites, sometimes combined with one or more of these other Fe/Mg‐phyllosilicates: serpentine, chlorite, biotite, and/or vermiculite. It is more than 100 m thick and finely layered at meter scales. The upper unit includes Al‐smectite, kaolin group minerals, and hydrated silica. It is tens of meters thick and finely layered as well. A common phyllosilicate stratigraphy and morphology is observed throughout the greater region wherever erosional windows are present. This suggests that the geologic processes forming these units must have occurred on at least a regional scale. Sinuous ridges (interpreted to be inverted channels) and narrow channels cut into the upper clay‐bearing unit suggesting that aqueous processes were prevalent after, and possibly during, the deposition of the layered units. We propose that layered units may have been deposited at Mawrth Vallis and then subsequently altered to form the hydrated units. The Fe/Mg‐phyllosilicate assemblage is consistent with hydrothermal alteration or pedogenesis of mafic to ultramafic rocks. The Al‐phyllosilicate/hydrated silica unit may have formed through alteration of felsic material or via leaching of basaltic material through pedogenic alteration or a mildly acidic environment. These phyllosilicate‐bearing units are overlain by a darker, relatively unaltered, and indurated material that has probably experienced a complex geological history.
Formation constraints on Martian north polar volcanic edifices
Authors: Fagan A. L. , Sakimoto S. E. H. , Hughes S. S.
Published: August 2010

This study focuses on probable volcanic features in the north polar region of Mars in an effort to constrain their formation mechanisms and to estimate the thickness of a possible former ice sheet. Using Mars Orbiter Laser Altimeter (MOLA), High Resolution Imaging Science Experiment (HiRISE), Thermal Emission Imaging System (THEMIS), and Context Camera (CTX) data, we conduct topographic analyses of 108 putative volcanic edifices in the Borealis Volcanic Field within 69°N–81°N and 197°E–330°E. As it is rarely possible to identify rock types on Mars (such as hyaloclastite or palagonite), we are limited to the use of topographic data and images alone in our study. Therefore, we use available data for volcanic features in Iceland to predict the formational mechanisms of similar features on Mars. We examined 21 Icelandic volcanoes of subglacial and postglacial origin using Digital Elevation Models (DEMs) as well as limited differential GPS data and suggest by analogy that many of the features in the Borealis Volcanic Field were likely formed subglacially. We use these data to estimate a minimum ice sheet thickness for the area and suggest a range of minimum ice sheet thickness that varies between 57 and 610m with an average value of 283 m.
Four Martian years of nightside upper thermospheric mass densities derived from electron reflectometry: Method extension and comparison with GCM simulations
Authors: Lillis Robert J. , Bougher Stephen W. , González‐Galindo Francisco , Forget François , Smith Michael D. , Chamberlin Phillip C.
Published: August 2010

The long‐term dynamics of the Martian upper thermosphere near the exobase (∼160–200 km) are still relatively poorly constrained by data. Electron reflectometry (ER) provides a way to derive, from electron loss cones, neutral mass densities at these altitudes in the night hemisphere. Because the Mars Global Surveyor Electron Reflectometer was not designed for this purpose, uncertainties in individual measurements are large and thus upper thermospheric variability can be characterized only on time scales of weeks or longer. Density measurements are presented at 2 A.M. local time and 185 km altitude, from April 1999 until November 2006, spanning ∼4 Martian years. We observe a weaker correlation with lower atmospheric dust activity than is seen in the lower thermosphere and a weaker correlation with solar EUV flux than is observed in the dayside exosphere. Seasonally repeating features are (1) overall expansion/contraction of the nighttime thermosphere with heliocentric distance, (2) much lower densities at the aphelion winter pole compared to the perihelion winter pole, and (3) a short‐lived local density maximum at aphelion in the southern hemisphere. Interannual differences are also observed; in particular, the interval of low densities in the southern winter occurs progressively later as solar EUV flux decreases from solar maximum to solar minimum. Results are compared with predictions from the Mars Thermosphere General Circulation Model and LMD Mars Global Circulation atmospheric model frameworks for Ls = 90°–180°, which generally underestimate and overestimate neutral densities, respectively. This disagreement reflects the difficulty in simulating nightside dynamical and cooling processes.
Constraining uncertainty in regional hydrologic impacts of climate change: Nonstationarity in downscaling
Authors: Raje Deepashree , Mujumdar P. P.
Published: August 2010

Regional impacts of climate change remain subject to large uncertainties accumulating from various sources, including those due to choice of general circulation models (GCMs), scenarios, and downscaling methods. Objective constraints to reduce the uncertainty in regional predictions have proven elusive. In most studies to date the nature of the downscaling relationship (DSR) used for such regional predictions has been assumed to remain unchanged in a future climate. However, studies have shown that climate change may manifest in terms of changes in frequencies of occurrence of the leading modes of variability, and hence, stationarity of DSRs is not really a valid assumption in regional climate impact assessment. This work presents an uncertainty modeling framework where, in addition to GCM and scenario uncertainty, uncertainty in the nature of the DSR is explored by linking downscaling with changes in frequencies of such modes of natural variability. Future projections of the regional hydrologic variable obtained by training a conditional random field (CRF) model on each natural cluster are combined using the weighted Dempster‐Shafer (D‐S) theory of evidence combination. Each projection is weighted with the future projected frequency of occurrence of that cluster (“cluster linking”) and scaled by the GCM performance with respect to the associated cluster for the present period (“frequency scaling”). The D‐S theory was chosen for its ability to express beliefs in some hypotheses, describe uncertainty and ignorance in the system, and give a quantitative measurement of belief and plausibility in results. The methodology is tested for predicting monsoon streamflow of the Mahanadi River at Hirakud Reservoir in Orissa, India. The results show an increasing probability of extreme, severe, and moderate droughts due to climate change. Significantly improved agreement between GCM predictions owing to cluster linking and frequency scaling is seen, suggesting that by linking regional impacts to natural regime frequencies, uncertainty in regional predictions can be realistically quantified. Additionally, by using a measure of GCM performance in simulating natural regimes, this uncertainty can be effectively constrained.
Multi‐centennial summer and winter precipitation variability in southern South America
Authors: Neukom R. , Luterbacher J. , Villalba R. , Küttel M. , Frank D. , Jones P. D. , Grosjean M. , Esper J. , Lopez L. , Wanner H.
Published: August 2010

We present the first spatially and temporally highly resolved gridded reconstruction of multi‐centennial precipitation variability for southern South America (SSA). A novel reconstruction approach of deriving 10,000 ensemble members based on varying predictor networks and methodological settings allows the identification of spatiotemporal changes in SSA precipitation and associated uncertainties. The summer and winter reconstructions back to AD 1498 and AD 1590, respectively, provide new evidence for multi‐centennial increase in summer precipitation and an opposing decrease in winter precipitation into the 20th century. The drying in winter is significant over large parts of SSA, whereas the patterns for summer, possibly representing convective rainfall, have displayed high spatial variability. The fact that such long‐term seasonal and spatial changes have occurred in the past, underlines the complex form that hydroclimatic variability might have in the future. This emphasizes the need for careful adaptation strategies as governments become attuned to the realities of climate change.
Spatial patterns of basal drag inferred using control methods from a full‐Stokes and simpler models for Pine Island Glacier, West Antarctica
Authors: Morlighem M. , Rignot E. , Seroussi H. , Larour E. , Ben Dhia H. , Aubry D.
Published: August 2010

Basal drag is a fundamental control on ice stream dynamics that remains poorly understood or constrained by observations. Here, we apply control methods on ice surface velocities of Pine Island Glacier, West Antarctica to infer the spatial pattern of basal drag using a full‐Stokes (FS) model of ice flow and compare the results obtained with two commonly‐used simplified solutions: the MacAyeal shelfy stream model and the Blatter‐Pattyn model. Over most of the model domain, the three models yield similar patterns of basal drag, yet near the glacier grounding‐line, the simplified models yield high basal drag while FS yields almost no basal drag. The simplified models overestimate basal drag because they neglect bridging effects in an ice stream region of rapidly varying ice thickness. This result reinforces theoretical studies that a FS treatment of ice flow is essential near glacier grounding lines.
Episodic detachment of Martian crustal magnetic fields leading to bulk atmospheric plasma escape
Authors: Brain D. A. , Baker A. H. , Briggs J. , Eastwood J. P. , Halekas J. S. , Phan T.‐D.
Published: August 2010

We present an analysis of magnetic field and suprathermal electron measurements from the Mars Global Surveyor (MGS) spacecraft that reveals isolated magnetic structures filled with Martian atmospheric plasma located downstream from strong crustal magnetic fields with respect to the flowing solar wind. The structures are characterized by magnetic field enhancements and rotations characteristic of magnetic flux ropes, and characteristic ionospheric electron energy distributions with angular distributions distinct from surrounding regions. These observations indicate that significant amounts of atmosphere are intermittently being carried away from Mars by a bulk removal process: the top portions of crustal field loops are stretched through interaction with the solar wind and detach via magnetic reconnection. This process occurs frequently and may account for as much as 10% of the total present‐day ion escape from Mars.
A polar low embedded in a blocking high over the Pacific Arctic
Authors: Inoue Jun , Hori Masatake E. , Tachibana Yoshihiro , Kikuchi Takashi
Published: August 2010

A polar low (PL) is a short‐lived phenomenon involving strong winds that occurs over polar oceans. In October 2009, the R/V Mirai encountered a PL with a 600‐km‐wide, comma‐shaped cloud that developed over the Chukchi Sea. A shipboard Doppler radar and radiosondes were used to understand the fine structure of this PL. Analyses of low‐level winds and the thermodynamic structure indicated that the development of the PL was decoupled from sea surface thermal forcing. The PL was likely triggered by an intrusion of a potential vorticity (PV) anomaly at the tropopause. A southerly warm advection associated with a blocking high over Alaska resulted in rapid development of the PL in front of the cold dome induced by the upper‐level PV anomaly. The westerly winds after passage of the PL seemed to modify the upper‐ocean structure dramatically.
Cadmium regulates copper homoeostasis by inhibiting the activity of Mac1, a transcriptional activator of the copper regulon, in Saccharomyces cerevisiae
Authors: Heo Dong-Hyuk , Baek In-Joon , Kang Hyun-Jun , Kim Ji-Hyun , Chang Miwha , Jeong Mi-Young , Kim Tae-Hyoung , Choi Il-Dong , Yun Cheol-Won
Published: August 2010

Cadmium is a toxic metal and the mechanism of its toxicity has been studied in various model systems from bacteria to mammals. We employed Saccharomyces cerevisiae as a model system to study cadmium toxicity at the molecular level because it has been used to identify the molecular mechanisms of toxicity found in higher organisms. cDNA microarray and Northern blot analyses revealed that cadmium salts inhibited the expression of genes related to copper metabolism. Western blotting, Northern blotting and chromatin immunoprecipitation experiments indicated that CTR1 expression was inhibited at the transcriptional level through direct inhibition of the Mac1 transcriptional activator. The decreased expression of CTR1 results in cellular copper deficiency and inhibition of Fet3 activity, which eventually impairs iron uptake. In this way, cadmium exhibits a negative effect on both iron and copper homoeostasis.
Characterization of the role of dendritic cells in prion transfer to primary neurons
Authors: Langevin Christelle , Gousset Karine , Costanzo Maddalena , Richard-Le Goff Odile , Zurzolo Chiara
Published: August 2010

TSEs (transmissible spongiform encephalopathies) are neurodegenerative diseases caused by pathogenic isoforms (PrPSc) of the host-encoded PrPc (cellular prion protein). After consumption of contaminated food, PrPSc deposits rapidly accumulate in lymphoid tissues before invasion of the CNS (central nervous system). However, the mechanisms of prion spreading from the periphery to the nervous system are still unclear. In the present study, we investigated the role of DCs (dendritic cells) in the spreading of prion infection to neuronal cells. First, we determined that BMDCs (bone-marrow-derived DCs) rapidly uptake PrPSc after exposure to infected brain homogenate. Next, we observed a progressive catabolism of the internalized prion aggregates. Similar experiments performed with BMDCs isolated from KO (knockout) mice or mice overexpressing PrP (tga20) indicate that both PrPSc uptake and catabolism are independent of PrPc expression in these cells. Finally, using co-cultures of prion-loaded BMDCs and cerebellar neurons, we characterized the transfer of the prion protein and the resulting infection of the neuronal cultures. Interestingly, the transfer of PrPSc was triggered by direct cell–cell contact. As a consequence, BMDCs retained the prion protein when cultured alone, and no transfer to the recipient neurons was observed when a filter separated the two cultures or when neurons were exposed to the BMDC-conditioned medium. Additionally, fixed BMDCs also failed to transfer prion infectivity to neurons, suggesting an active transport of prion aggregates, in accordance with a role of TNTs (tunnelling nanotubes) observed in the co-cultures.
Self-association and domain rearrangements between complement C3 and C3u provide insight into the activation mechanism of C3
Authors: Li Keying , Gor Jayesh , Perkins Stephen J.
Published: August 2010

Component C3 is the central protein of the complement system. During complement activation, the thioester group in C3 is slowly hydrolysed to form C3u, then the presence of C3u enables the rapid conversion of C3 into functionally active C3b. C3u shows functional similarities to C3b. To clarify this mechanism, the self-association properties and solution structures of C3 and C3u were determined using analytical ultracentrifugation and X-ray scattering. Sedimentation coefficients identified two different dimerization events in both proteins. A fast dimerization was observed in 50 mM NaCl but not in 137 mM NaCl. Low amounts of a slow dimerization was observed for C3u and C3 in both buffers. The X-ray radius of gyration RG values were unchanged for both C3 and C3u in 137 mM NaCl, but depend on concentration in 50 mM NaCl. The C3 crystal structure gave good X-ray fits for C3 in 137 mM NaCl. By randomization of the TED (thioester-containing domain)/CUB (for complement protein subcomponents C1r/C1s, urchin embryonic growth factor and bone morphogenetic protein 1) domains in the C3b crystal structure, X-ray fits showed that the TED/CUB domains in C3u are extended and differ from the more compact arrangement of C3b. This TED/CUB conformation is intermediate between those of C3 and C3b. The greater exposure of the TED domain in C3u (which possesses the hydrolysed reactive thioester) accounts for the greater self-association of C3u in low-salt conditions. This conformational variability of the TED/CUB domains would facilitate their interactions with a broad range of antigenic surfaces. The second dimerization of C3 and C3u may correspond to a dimer observed in one of the crystal structures of C3b.
Musashi 1‐positive cells derived from mouse embryonic stem cells can differentiate into neural and intestinal epithelial‐like cells in vivo
Authors: Lan Shao‐Yang , Yu Tao , Xia Zhong‐Sheng , Yuan Yu‐Hong , Shi Liu , Lin Ying , Huang Kai‐Hong , Chen Qi‐Kui
Published: August 2010

Msi1 (Musashi 1) is regarded as a marker for neural and intestinal epithelial stem cells. However, it is still unclear whether Msi1‐positive cells derived from mouse embryonic stem cells have the ability to differentiate into neural or intestinal epithelial cells. A pMsi1–GFP (green fluorescent protein) reporter plasmid was constructed in order to sort Msi1‐positive cells out of the differentiated cell population. The GFP‐positive cells (i.e. Msi1‐positive cells) were sorted by FACS and were hypodermically engrafted into the backs of NOD/SCID (non‐obese diabetic/severe combined immunodeficient) mice. The presence of neural and intestinal epithelial cells in the grafts was detected. Msi1 was highly expressed in the GFP‐positive cells, but not in the GFP‐negative cells. The markers for neural cells (Nestin and Tubulin β III) and intestinal epithelial cells [FABP2 (fatty acid binding protein 2), Lyz (lysozyme) and ChA (chromogranin A)] were more highly expressed in the grafts from Msi1‐positive cells than those from Msi1‐negative cells (P<0.05). The grafts from the Msi1‐negative cells contained more mesodermal‐like tissues than those from the Msi1‐positive cells. The pMsi1–GFP vector can be used to sort Msi1‐positive cells from a cell population derived from mouse embryonic stem cells. The Msi1‐positive cells can differentiate into neural and intestinal epithelial‐like cells in vivo.
Global Event-identifier Module: A distributed digital approach to event-of-interest identification logic for physics experiments
Authors: Rani Kusum , Subramaniam E. T.
Published: August 2010

The demands from current data acquisition systems are to acquire data from a large number of detectors (or signals) while providing a high throughput. This can be achieved by having some preprocessing capability in the data acquisition system so that it can identify the events of interest. Precise selection of events with minimal time for identification and preprocessing is an experimental challenge. To address this challenge, we have developed a “Global Event-identifier Module” (GEM) on the CAMAC platform, which can flexibly adapt to the experimental requirements and validate an event with minimal time. GEM is a single width CAMAC module capable of operating in a “distributed” data acquisition environment where multiple CAMAC crates (each with one GEM module) can be used to collect synchronized data from all the crates. Event-of-interest decision can be made on signals connected to different crates. Inter-GEM communication is via the ubiquitous ethernet (unshielded twisted pair, CAT5) cable. The event of interest is decided within 32 ns (excluding cable delay). Implementation is accomplished using field programmable gate array which enables greater flexibility for algorithm modifications and updates without hardware changes. GEM supports unified, distributed, and multi-strobe data acquisition, enabling higher throughput, with data collection from a large number of signals by selective reads of events of interest as determined by the experimenter while providing timestamped data of each event.
A method for measuring in-plane unidirectional electrical properties in a wide band-gap semiconductor using a Brillouin scattering method
Authors: Yanagitani Takahiko , Sano Hiroyuki , Matsukawa Mami
Published: August 2010

It is difficult to measure the in-plane directional electrical properties of a crystal sample without physical contact. This paper describes the measurement of in-plane unidirectional resistivity through electromechanical coupling. The degree of coupling was determined from acoustic velocity data measured using the Brillouin scattering method. The resistivity distribution in a ZnO crystal with a resistivity of less than 1 Ω m, (common in intrinsic wide band-gap semiconductors) was clearly detected through acoustic velocity at gigahertz frequencies. The resistivity values obtained from the acoustic wave velocities showed a good correlation with standard contact electrode measurements in the resistivity range of 0.03–1 Ω m. This noncontact measurement technique should be useful for measuring the microscopic distribution of in-plane resistivity in wide band-gap semiconductors, and is a powerful tool for experiments under extreme conditions, such as high pressure and/or high temperature.
Influence of oscillation modes on the line width of rf emissions in MgO based nanopillars
Authors: Hrkac G. , Goncharov A. , Dean J. , Schrefl T. , Kim Joo-Von , Devolder T. , Chappert C. , Cornelissen S. , van Roy W. , Lagae L.
Published: August 2010

We present a numerical study of oscillation modes in magnetic tunnel junction nanopillars and investigate the frequency and the full width at half maximum of the power spectrum as a function of applied field and applied current. We show that the line width reaches a minimum of 14.5 MHz as the system approaches the threshold current, and increases sharply to 308 MHz as the current is increased beyond the threshold current. The initial line narrowing is due to an increased coherence in the uniform precession mode, while the line broadening above threshold arises from the intrinsic oscillator nonlinearity combined with overlapping contributions from edge modes. We show that these results are in good agreement with recent experiments on MgO-based oscillators.
Reptation of a semiflexible polymer through porous media
Authors: Nam Gimoon , Johner Albert , Lee Nam-Kyung
Published: August 2010

We study the motion of a single stiff semiflexible filament of length S through an array of topological obstacles. By means of scaling arguments and two-dimensional computer simulations, we show that the stiff chain kinetics follows the reptation picture, albeit with kinetic exponents (for the central monomer) different from those for flexible chain reptation. At early times when topological constraints are irrelevant, the chain kinetics is the anisotropic dynamics of a free filament. After the entanglement time τe transverse modes are equilibrated under the topological constraints, but the chain is not yet correlated over its whole length. During the relaxation of longitudinal modes, both the longitudinal fluctuation of the central monomer and the longitudinal correlation length grow as ∼t. After time τr∼S2 chain ends are correlated, the chain then diffuses globally along the tube and tube renewal takes place. In the reptation regime, the longitudinal fluctuation of the central monomer grows like ∼t1. The opening of the intermediate ∼t regime, absent for a free filament, is a signature of the reptation process. Although the underlying physics is quite different, the intermediate regime is reminiscent of the internal Rouse mode relaxation found for reptating flexible chains. In most cases asymptotic power laws from scaling could be complemented by prefactors calculated analytically. Our results are supported by two-dimensional Langevin simulations with fixed obstacles via evaluation of the mean squared displacement of the central monomer. The scaling theory can be extended to long semiflexible polymers adopting random-walk equilibrium configurations and should also apply in three dimensions for porous media with pore diameter smaller than the persistence length of the filament.
Interfacial dipole dynamics of light-emitting diodes incorporating a poly(amidoamine) dendrimer monolayer
Authors: Winroth Gustaf , Fenwick Oliver , Scott Mark A. , Yip Daniel , Howorka Stefan , Cacialli Franco
Published: August 2010

We investigate the effects induced by a nonconjugated self-assembled monolayer of poly(amidoamine) (PAMAM) on the work function of thermally evaporated Al-electrodes. We compare results from Kelvin probe measurement of the electrodes work function with electroabsorption characterization of the built-in voltage of polymer light-emitting diodes incorporating them. Interestingly, we find that the PAMAM monolayer decreases the work function by 0.4 eV in a Kelvin probe measurement but that the dipole induced by the PAMAM monolayer is altered by biasing, and that it exhibits a hysteretic behavior in a cyclic voltage scan.
Impact of ion-implantation-induced band gap engineering on the temperature-dependent photoluminescence properties of InAs/InP quantum dashes
Authors: Hadj Alouane M. H. , Ilahi B. , Maaref H. , Salem B. , Aimez V. , Morris D. , Turala A. , Regreny P. , Gendry M.
Published: August 2010

We report on the effects of the As/P intermixing induced by phosphorus ion implantation in InAs/InP quantum dashes (QDas) on their photoluminescence (PL) properties. For nonintermixed QDas, usual temperature-dependent PL properties characterized by a monotonic redshift in the emission band and a continual broadening of the PL linewidth as the temperature increases, are observed. For intermediate ion implantation doses, the inhomogeneous intermixing enhances the QDas size dispersion and the enlarged distribution of carrier confining potential depths strongly affects the temperature-dependent PL properties below 180 K. An important redshift in the PL emission band occurs between 10 and 180 K which is explained by a redistribution of carriers among the different intermixed QDas of the ensemble. For higher implantation doses, the homogeneous intermixing reduces the broadening of the localized QDas state distribution and the measured linewidth temperature behavior matches that of the nonintermixed QDas. An anomalous temperature-dependent emission energy behavior has been observed for extremely high implantation doses, which is interpreted by a possible QDas dissolution.
Trading sensitivity for information: Carr–Purcell–Meiboom–Gill acquisition in solid-state NMR
Authors: Dey Krishna K. , Ash Jason T. , Trease Nicole M. , Grandinetti Philip J.
Published: August 2010

The Carr–Purcell–Meiboom–Gill (CPMG) experiment has gained popularity in solid-state NMR as a method for enhancing sensitivity for anisotropically broadened spectra of both spin 1/2 and half integer quadrupolar nuclei. Most commonly, the train of CPMG echoes is Fourier transformed directly, which causes the NMR powder pattern to break up into a series of sidebands, sometimes called “spikelets.” Larger sensitivity enhancements are observed as the delay between the π pulses is shortened. As the duration between the π pulses is shortened, however, the echoes become truncated and information about the nuclear spin interactions is lost. We explored the relationship between enhanced sensitivity and loss of information as a function of the product Ω 2τ, where Ω is the span of the anisotropic lineshape and 2τ is the π pulse spacing. For a lineshape dominated by the nuclear shielding anisotropy, we found that the minimum uncertainty in the tensor values is obtained using Ω 2τ values in the range Ω 2τ≈12−1+6 and Ω 2τ≈9−3+3 for ηs=0 and ηs=1, respectively. For an anisotropic second-order quadrupolar central transition lineshape under magic-angle spinning (MAS), the optimum range of Ω 2τ≈9−2+3 was found. Additionally, we show how the Two-dimensional One Pulse (TOP) like processing approach can be used to eliminate the cumbersome sideband pattern lineshape and recover a more familiar lineshape that is easily analyzed with conventional lineshape simulation algorithms.
Hartree–Fock perturbative corrections for total and reaction energies
Authors: Deng Jia , Gilbert Andrew T. B. , Gill Peter M. W.
Published: August 2010

We have performed an assessment of the Hartree–Fock perturbative correction (HFPC) on a large and diverse set of molecules and reactions. Errors in both absolute and reaction energies with respect to converged secondary basis Hartree–Fock results are reported for a wide spectrum of primary/secondary basis set combinations. These results show that using an adequate primary basis, HFPC can accurately reproduce secondary basis energies at a substantially reduced cost. Comparisons of HFPC with the related dual basis Hartree–Fock (DBHF) scheme are also made for several molecules and target secondary basis sets. Our results indicate that HFPC is faster and more accurate than DBHF for approaching triple-ζ basis sets. For quadruple-ζ secondary basis sets, HFPC is capable of yielding more accurate energies at a marginally increased cost over DBHF.
Multi-time density correlation functions in glass-forming liquids: Probing dynamical heterogeneity and its lifetime
Authors: Kim Kang , Saito Shinji
Published: August 2010

A multi-time extension of a density correlation function is introduced to reveal temporal information about dynamical heterogeneity in glass-forming liquids. We utilize a multi-time correlation function that is analogous to the higher-order response function analyzed in multidimensional nonlinear spectroscopy. Here, we provide comprehensive numerical results of the four-point, three-time density correlation function from longtime trajectories generated by molecular dynamics simulations of glass-forming binary soft-sphere mixtures. We confirm that the two-dimensional representations in both time and frequency domains are sensitive to the dynamical heterogeneity and that these reveal the couplings of correlated motions, which exist over a wide range of time scales. The correlated motions detected by the three-time correlation function are divided into mobile and immobile contributions that are determined from the particle displacement during the first time interval. We show that the peak positions of the correlations are in accord with the information on the non-Gaussian parameters of the van Hove self-correlation function. Furthermore, it is demonstrated that the progressive changes in the second time interval in the three-time correlation function enable us to analyze how correlations in dynamics evolve in time. From this analysis, we evaluated the lifetime of the dynamical heterogeneity and its temperature dependence systematically. Our results show that the lifetime of the dynamical heterogeneity becomes much slower than the α-relaxation time that is determined from the two-point density correlation function when the system is highly supercooled.
Defect mediated turbulence in a locally quasiperiodic chemical medium
Authors: St-Yves Ghislain , Davidsen Jörn
Published: August 2010

Under a change of conditions, spiral waves in oscillatory reaction-diffusion media can become unstable and give rise to a multitude of emergent patterns. For example, in bounded domains spiral waves can undergo a resonant Hopf bifurcation leading to period-2 spirals which emit wave trains with doubled wavelength and temporal period and have a characteristic synchronization defect line. Here, we analyze the emergent patterns due to nonresonant Hopf bifurcations in the local dynamics giving rise to quasiperiodicity as reported in systems such as the peroxidase-oxidase and the Belousov–Zhabotinsky reaction. For a conceptual model of the peroxidase-oxidase reaction in a spatially extended medium, we find numerically that the additional frequency leads to defect-mediated turbulence. This proves that defect-mediated turbulence can indeed exist in media where the underlying local dynamics is quasiperiodic. While many statistical features of this turbulent dynamics are similar to those observed for other systems, we show that there are clear differences if higher-order statistics are considered. In particular, we find that the space-time dynamics of the topological defects as characterized by the statistics of defect loops is closely related to the underlying local dynamics.
Finite temperature quantum statistics of H3+ molecular ion
Authors: Kylänpää Ilkka , Rantala Tapio T.
Published: August 2010

Full quantum statistical NVT simulation of the five-particle system H3+ has been carried out using the path integral Monte Carlo method. Structure and energetics are evaluated as a function of temperature up to the thermal dissociation limit. The weakly density dependent dissociation temperature is found to be around 4000 K. Contributions from the quantum dynamics and thermal motion are sorted out by comparing differences between simulations with quantum and classical nuclei. The essential role of the quantum description of the protons is established.