bluuebunny/crossref_metadata_2025 huggingface dataset:
Beyond (the Scope of) Conflict: National Black and Latino Advocacy Group Relations in the Congressional and Legal Arenas
Authors: Hero Rodney E. , Preuhs Robert R.
Published: August 2009

We examine activities of and between minority advocacy groups in the U.S., particularly similarities and differences in positions of Blacks and Latinos in their efforts to influence national-level policies. Findings highlight several points. Analysis of Congressional scorecard data indicates only modest overlap among the issues identified by the minority advocacy groups, though there is complete “congruence” on the issues that are identified by both groups. The highest degree of “independence” of the activities examined occurs in Congressional testimony. Regarding legal advocacy, analysis ofamicus curiaebriefs further affirms the general finding that there is little if any outright competition between Black and Latino advocacy groups. There appears to be considerable “tacit non-cooperation” which varies by policy-type and between these national institutions.
Review Editor's Introduction
Authors: Isaac Jeffrey C.
Published: August 2009

The constant stream—deluge might be a better word—of new books making their way to our offices makes vivid, on a daily basis, how productive is our discipline. There is so much work being done, on such a range of topics and employing such a range of approaches. And—as we have understood ever since Thomas Kuhn—while academic fields and subfields most assuredly are organized in part to channel and “discipline” such intellectual energies, the contemporary academy is at the same time a space of extraordinary intellectual diversity. There is no overall “plan” to this outpouring of ideas, no single “method” to the madness that drives us continually and persistently to research and write, to revise and resubmit, and to enter the fray with ideas that, at their best, will prove their true worth by serving as fodder for the next generation of scholars.
Low efficiency of nutrient translocation for enhancing oceanic uptake of carbon dioxide
Authors: Yool Andrew , Shepherd John G. , Bryden Harry L. , Oschlies Andreas
Published: August 2009

Anthropogenic emissions of carbon dioxide (CO2) are steadily increasing the concentration of this greenhouse gas in the Earth's atmosphere. The possible long‐term consequences of this elevated concentration have led to proposals for a number of large‐scale geoengineering schemes that aim to enhance or augment natural sinks for CO2. One such scheme proposes deploying a large number of floating “pipes” in the ocean that act to translocate nutrient‐rich seawater from below the mixed layer to the ocean's surface: the nutrient supplied should enhance the growth of phytoplankton and consequently the export of organic carbon to the deep ocean via the biological pump. Here we examine the practical consequences of this scheme in a global ocean general circulation model that includes a nitrogen‐based ecosystem and the biogeochemical cycle of carbon. While primary production is generally enhanced by the modeled pipes, as expected, the effect on the uptake of CO2 from the atmosphere is much smaller, may be negative, and shows considerable spatiotemporal variability.
A dual‐pass variational data assimilation framework for estimating soil moisture profiles from AMSR‐E microwave brightness temperature
Authors: Tian Xiangjun , Xie Zhenghui , Dai Aiguo , Shi Chunxiang , Jia Binghao , Chen Feng , Yang Kun
Published: August 2009

To overcome the difficulties in determining the optimal parameters needed for a radiative transfer model (RTM), which acts as the observational operator in a land data assimilation system, we have designed a dual‐pass assimilation (DP‐En4DVar) framework to optimize the model state (volumetric soil moisture content) and model parameters simultaneously using the gridded Advanced Microwave Scanning Radiometer–EOS (AMSR‐E) satellite brightness temperature data. This algorithm embeds a dual‐pass (the state assimilation pass and the parameter optimization pass) optimization technique based on an ensemble‐based four‐dimensional variational assimilation method and a shuffled complex evolution approach (SCE‐UA). The SCE‐UA method optimizes the parameters using observational information, thereby leading to improved simulations. The RTM is used to estimate brightness temperature from surface temperature and soil moisture. This algorithm is implemented differently in two phases: the parameter calibration phase and the pure assimilation phase. Both passes are applied in each assimilation time window during the parameter calibration phase. However, only the state assimilation pass is used in the pure assimilation phase after the parameters are determined during the parameter calibration phase. Several experiments conducted using this framework coupled partially with a land surface model (the NCAR CLM3) show that volumetric soil moisture content can be significantly improved to be comparable with in situ observations by assimilating only daily satellite brightness temperature. Furthermore, the improvement in surface soil moisture also propagates to lower layers where no observations are available.
Snow and ice facies variability and ice layer formation on Canadian Arctic ice caps, 1999–2005
Authors: Wolken Gabriel J. , Sharp Martin , Wang Libo
Published: August 2009

Time series of enhanced resolution data from the SeaWinds scatterometer aboard QuikScat were used to map the distribution of snow and ice surface facies and ice layer formation in the percolation zone on ice caps in the Queen Elizabeth Islands during the period 1999–2005. Iterative Self‐Organizing Data Analysis classification of the mean postfreeze‐up biweekly average σ0 signal for the 7‐year period resulted in the delineation of four snow and ice surface facies (interpreted as the percolation, saturation, superimposed ice, and glacier ice zones). Analysis with National Centers for Environmental Prediction/National Center for Atmospheric Research Reanalysis reveals that changes in geopotential height in the troposphere (700, 500, and 300 hPa) and air temperature (700 hPa level) are positively (negatively) correlated with area changes in the glacier ice (percolation and saturation) zones and changes in facies boundary elevation. The change in biweekly‐averaged backscatter following the freeze‐up periods between successive autumns was used to map changes in the distribution of ice layers formed by meltwater percolation and refreezing in the snowpack within the percolation zone. Strongly positive air temperature anomalies at the 700 hPa level in 2001 and 2005 are consistent with extensive ice layer formation in the percolation zones of all ice caps. Such large interannual changes in ice layer formation are likely associated with large changes to the density profile of the snowpack and may be associated with surface elevation changes that are unrelated to changes in surface mass balance.
Water supply risk on the Colorado River: Can management mitigate?
Authors: Rajagopalan Balaji , Nowak Kenneth , Prairie James , Hoerling Martin , Harding Benjamin , Barsugli Joseph , Ray Andrea , Udall Bradley
Published: August 2009

Population growth and a changing climate will tax the future reliability of the Colorado River water supply. Using a heuristic model, we assess the annual risk to the Colorado River water supply for 2008–2057. Projected demand growth superimposed upon historical climate variability results in only a small probability of annual reservoir depletion through 2057. In contrast, a scenario of 20% reduction in the annual Colorado River flow due to climate change by 2057 results in a near tenfold increase in the probability of annual reservoir depletion by 2057. However, our analysis suggests that flexibility in current management practices could mitigate some of the increased risk due to climate change–induced reductions in flows.
C/NOFS and radar observations during a convective ionospheric storm event over South America
Authors: Kelley M. C. , Rodrigues F. S. , Makela J. J. , Tsunoda R. , Roddy P. A. , Hunton D. E. , Retterer J. M. , de La Beaujardiere O. , de Paula E. R. , Ilma R. R.
Published: August 2009

The development of a convective ionospheric storm is studied using three radars, the C/NOFS satellite, airglow instrumentation, and a numerical model. First detected in the form of convective plumes over the Eastern Pacific, plasma irregularities, airglow signatures, plumes, and irregularities were also detected over Brazil and then Peru. Dynamo conditions were such that a modest prereversal enhancement was recorded at both Christmas Island and Peru and probably over Brazil as well. No prereversal enhancement occurred during the next two days and no plumes were detected. The numerical model reproduced the results quite well over Peru. Evidence for seeding by both gravity waves and the Kelvin‐Helmholtz instability is presented.
Polymerase chain reaction primers miss half of rRNA microbial diversity
Authors: Hong SunHee , Bunge John , Leslin Chesley , Jeon Sunok , Epstein Slava S
Published: August 2009

The rRNA approach is the principal tool to study microbial diversity, but it has important biases. These include polymerase chain reaction (PCR) primers bias, and relative inefficiency of DNA extraction techniques. Such sources of potential undersampling of microbial diversity are well known, but the scale of the undersampling has not been quantified. Using a marine tidal flat bacterial community as a model, we show that even with unlimited sampling and sequencing effort, a single combination of PCR primers/DNA extraction technique enables theoretical recovery of only half of the richness recoverable with three such combinations. This shows that different combinations of PCR primers/DNA extraction techniques recover in principle different species, as well as higher taxa. The majority of earlier estimates of microbial richness seem to be underestimates. The combined use of multiple PCR primer sets, multiple DNA extraction techniques, and deep community sequencing will minimize the biases and recover substantially more species than prior studies, but we caution that even this—yet to be used—approach may still leave an unknown number of species and higher taxa undetected.
Women With Hypertensive Pregnancies Have Difficulties in Regaining Pre‐pregnancy Weight and Show Metabolic Disturbances
Authors: Suntio Katariina , Saarelainen Heli , Laitinen Tomi , Valtonen Pirjo , Heiskanen Nonna , Lyyra‐Laitinen Tiina , Vanninen Esko , Heinonen Seppo
Published: August 2009

The aim was to determine maternal weight gain and body composition during pregnancy and 3 months postpartum in women with uncomplicated singleton and twin pregnancies and in women with gestational diabetes (GDM) and gestational hypertension (GH). This prospective study includes four groups of subjects: those with an uncomplicated pregnancy (n = 32), those with a diagnosis of GH (n = 28), those with a diagnosis of GDM (n = 52), and those with twin pregnancy (n = 11). Their body compositions were estimated by a bioimpedance analysis and fasting lipids and glucose levels were determined during the pregnancy and 3 months after pregnancy. Women with GDM were 11.7 kg heavier than the reference group before pregnancy, whereas weight before pregnancy was not different in other investigated groups. Weight loss after delivery was attenuated in GH group. Percentage body fat remained elevated in women with GDM (34.1 ± 7.0%) and hypertension (31.5 ± 6.4%) at 3 months after pregnancy. Also their total cholesterol and low‐density lipoprotein (LDL)‐cholesterol levels as well as fasting glucose remained elevated in comparison to values of the reference group. In conclusion, women with hypertensive pregnancies, though not overweight before pregnancy, gain and retain excess gestational weight and this leads to metabolic abnormalities similar to those seen in women GDM. Thus, postpartum period appears to be critical for weight management and interventional programs are called for.
Adaptive Visualization of Search Results: Bringing User Models to Visual Analytics
Authors: Ahn Jae-Wook , Brusilovsky Peter
Published: August 2009

Adaptive visualization is a new approach at the crossroads of user modeling and information visualization. Taking into account information about a user, adaptive visualization attempts to provide user-adapted visual presentation of information. This paper proposes Adaptive VIBE, an approach for adaptive visualization of search results in an intelligence analysis context. Adaptive VIBE extends the popular VIBE visualization framework by infusing user model terms as reference points for spatial document arrangement and manipulation. We explored the value of the proposed approach using data obtained from a user study. The result demonstrated that user modeling and spatial visualization technologies are able to reinforce each other, creating an enhanced level of user support. Spatial visualization amplifies the user model's ability to separate relevant and non-relevant documents, whereas user modeling adds valuable reference points to relevance-based spatial visualization.
Advancing User-Centered Evaluation of Visual Analytic Environments through Contests
Authors: Costello Loura , Grinstein Georges , Plaisant Catherine , Scholtz Jean
Published: August 2009

In this paper, the authors describe the Visual Analytics Science and Technology (VAST) Symposium contests run in 2006 and 2007 and the VAST 2008 and 2009 challenges. These contests were designed to provide researchers with a better understanding of the tasks and data that face potential end users. Access to these end users is limited because of time constraints and the classified nature of the tasks and data. In that respect, the contests serve as an intermediary, with the metrics and feedback serving as measures of utility to the end users. The authors summarize the lessons learned and the future directions for VAST Challenges.
Visual Analysis of Dynamic Data Streams
Authors: Chin George , Singhal Mudita , Nakamura Grant , Gurumoorthi Vidhya , Freeman-Cadoret Natalie
Published: August 2009

For scientific data visualizations, real-time data streams present many interesting challenges when compared to static data. Real-time data are dynamic, transient, high-volume and temporal. Effective visualizations need to be able to accommodate dynamic data behavior as well as Abstract and present the data in ways that make sense to and are usable by humans. The Visual Content Analysis of Real-Time Data Streams project at the Pacific Northwest National Laboratory is researching and prototyping dynamic visualization techniques and tools to help facilitate human understanding and comprehension of high-volume, real-time data. The general strategy of the project is to develop and evolve visual contexts that will organize and orient high-volume dynamic data in conceptual and perceptive views. The goal is to allow users to quickly grasp dynamic data in forms that are intuitive and natural without requiring intensive training in the use of specific visualization or analysis tools and methods. Thus far, the project has prototyped five different visualization prototypes that represent and convey dynamic data through human-recognizable contexts and paradigms such as hierarchies, relationships, time and geography. We describe the design considerations and unique features of these dynamic visualization prototypes as well as our findings in the exploration and evaluation of their use.
Bend-twist-stretch model for coarse elastic network simulation of biomolecular motion
Authors: Stember Joseph N. , Wriggers Willy
Published: August 2009

The empirical harmonic potential function of elastic network models (ENMs) is augmented by three- and four-body interactions as well as by a parameter-free connection rule. In the new bend-twist-stretch (BTS) model the complexity of the parametrization is shifted from the spatial level of detail to the potential function, enabling an arbitrary coarse graining of the network. Compared to distance cutoff-based Hookean springs, the approach yields a more stable parametrization of coarse-grained ENMs for biomolecular dynamics. Traditional ENMs give rise to unbounded zero-frequency vibrations when (pseudo)atoms are connected to fewer than three neighbors. A large cutoff is therefore chosen in an ENM (about twice the average nearest-neighbor distance), resulting in many false-positive connections that reduce the spatial detail that can be resolved. More importantly, the required three-neighbor connectedness also limits the coarse graining, i.e., the network must be dense, even in the case of low-resolution structures that exhibit few spatial features. The new BTS model achieves such coarse graining by extending the ENM potential to include three-and four-atom interactions (bending and twisting, respectively) in addition to the traditional two-atom stretching. Thus, the BTS model enables reliable modeling of any three-dimensional graph irrespective of the atom connectedness. The additional potential terms were parametrized using continuum elastic theory of elastic rods, and the distance cutoff was replaced by a competitive Hebb connection rule, setting all free parameters in the model. We validate the approach on a carbon-alpha representation of adenylate kinase and illustrate its use with electron microscopy maps of E. coli RNA polymerase, E. coli ribosome, and eukaryotic chaperonin containing T-complex polypeptide 1, which were difficult to model with traditional ENMs. For adenylate kinase, we find excellent reproduction (>90% overlap) of the ENM modes and B factors when BTS is applied to the carbon-alpha representation as well as to coarser descriptions. For the volumetric maps, coarse BTS yields similar motions (70%–90% overlap) to those obtained from significantly denser representations with ENM. Our Python-based algorithms of ENM and BTS implementations are freely available.
Properties of silicon homojunctions with pulse-magnetron sputtered crystalline n+-emitter layers
Authors: Fenske Frank , Fuhs Walther
Published: August 2009

Highly phosphorus doped crystalline silicon films were grown by pulse-magnetron sputter deposition on (100) and (111) oriented silicon wafer substrates at low temperatures of 450–550 °C. Rapid thermal annealing (RTA) and plasma hydrogenation (PH) were applied as postgrowth treatments. To explore the nature of the junction transport processes the I-V characteristics were studied in different device geometries as a function of temperature. The analysis suggests that depending on the substrate orientation (hkl) both postgrowth treatments influence the bulk-related current component J0b(hkl) of the saturation current density in different manners and introduce additional conduction paths at the perimeter of the measured diode structures. For diodes grown on Si(100) postgrowth treatment by RTA results in a decrease in J0b(100) to respectable 4×10−11 A cm−2, whereas no major influence of RTA for the Si(111) based junctions could be obtained. They prove to be sensitive to PH post-treatment, which resulted in a reduction in J0b(111) to 8×10−11 A cm−2. The perimeter induced excess current is most strongly pronounced for the hydrogenated diodes on Si(111) and much less relevant for the RTA treated Si(100) structures.
Current-induced spin polarization in gallium nitride
Authors: Koehl W. F. , Wong M. H. , Poblenz C. , Swenson B. , Mishra U. K. , Speck J. S. , Awschalom D. D.
Published: August 2009

Electrically generated spin polarization is probed directly in bulk GaN using Kerr rotation spectroscopy. A series of n-type GaN epilayers are grown in the wurtzite phase both by molecular beam epitaxy and metalorganic chemical vapor deposition with a variety of doping densities chosen to broadly modulate the transverse spin lifetime, T2∗. The spin polarization is characterized as a function of electrical excitation energy over a range of temperatures. Despite weak spin-orbit interactions in GaN, a current-induced spin polarization is observed in the material at temperatures of up to 200 K.
Pitfalls of choosing an order parameter for rare event calculations
Authors: Dickson Bradley M. , Makarov Dmitrii E. , Henkelman Graeme
Published: August 2009

The mechanism of rare events in complex systems can be found by sampling dynamical paths that connect stable states. To calculate a rate using transition paths, an order parameter is required to describe the progress of the reaction and to distinguish the initial and final states. In this work, we compare two implementations of transition path sampling for Langevin paths, one for which paths are sampled in configuration space and the other in the space of the random variables that describe the thermostat. These two approaches are found to give different rates for the rearrangement of a seven-particle cluster despite the fact that both are formally exact. The difference is understood in terms of how efficiently the methods sample states along the order parameter. The more efficient approach takes the system to unexpected states that are allowed by a poor choice of order parameter. While transition path sampling is formally correct, we show how mistakes can be made when the system escapes to unknown states along an order parameter represented in terms of collective variables.
Preparation and characterization of Eu: Ti codoped LiNbO3 films prepared by the sol-gel method
Authors: Takahashi Makoto , Iyoda Kazuki , Miyauchi Toshiyuki , Ohkido Sadao , Tahashi Masahiro , Wakita Koichi , Kajitani Naofumi , Kurachi Masato , Hotta Kazutoshi
Published: August 2009

Europium (Eu3+) and titanium (Ti4+) codoped lithium niobate (LiNbO3; LN) thick films were deposited on z-cut congruent LiNbO3 (CLN) substrate by the sol-gel method from precursor solutions containing various Eu3+ concentration, 1.5 mol % Ti4+ and 0.10 mol dm−3 polyvinyl alcohol, and their crystal characteristics were evaluated. The Eu3+ and Ti4+ concentration in the LN film was controlled by the Eu3+ and Ti4+ concentration in the starting solution. The orientation relationships between Eu and Ti codoped LN (Eu:Ti:LN) films and CLN substrates were determined by x-ray diffraction, and (006) oriented Eu:Ti:LN films could be grown on the z-cut CLN substrate. The refractive indices of Eu3+ and Ti4+ codoped LN films decreased with increasing Eu3+ concentration. Refractive indices (ne) of these codoped LN films were higher than those of CLN substrate. Transmission losses of films were measured in the transverse magnetic mode. The transmission loss increased linearly from 0.09 to 0.21 dB/cm at 632.8 nm with increasing Eu3+ ion concentration.
Edge turbulence measurements in electron-heated Helically Symmetric Experiment plasmas
Authors: Guttenfelder W. , Anderson D. T. , Anderson F. S. B. , Canik J. M. , Likin K. M. , Talmadge J. N.
Published: August 2009

This paper presents edge measurements utilizing Langmuir probes to characterize plasma turbulence in the Helically Symmetric Experiment (HSX) [F. S. B. Anderson et al., Fusion Technol. 27, 273 (1995)]. Normalized density and potential fluctuations exhibit strong intensities but are comparable to mixing length estimates using measured correlation lengths. The correlation lengths are isotropic with respect to radial and poloidal directions and follow local (gyro-Bohm) drift wave expectations. These observations are common to measurements in both the optimized quasihelically symmetric (QHS) configuration, as well as a configuration where the symmetry is degraded intentionally. The resulting turbulent particle flux in higher density QHS discharges is in good quantitative agreement with transport analysis using three-dimensional neutral gas simulations. The measured turbulence characteristics are compared to a quasilinear trapped electron mode (TEM) drift wave model [H. Nordman, J. Weiland, and A. Jarmén, Nucl. Fusion 30, 983 (1990)] that has been used to predict the anomalous transport in HSX. While quantitative differences exist (factors of 2–3), there is a general consistency between the turbulence measurements and the TEM drift wave model.
Mode-coupling instability of two-dimensional plasma crystals
Authors: Zhdanov S. K. , Ivlev A. V. , Morfill G. E.
Published: August 2009

The dispersion relations for three principal wave modes sustained in two-dimensional (2D) plasma crystals are derived taking into account particle-wake interactions. The rigorous analysis of the mode coupling shows that if the normalized frequency of the vertical confinement is below a certain critical value, then resonance coupling between the longitudinal in-plane mode and out-of-plane mode sets in. This results in the emergence of a hybrid mode and drives the mode-coupling instability. The universal dependence of the critical confinement frequency on plasma parameters is calculated, which allows us to specify the conditions when stable 2D plasma crystals can be formed in experiments.
Response to “Comment on ‘Guiding center plasma models in three dimensions’ ” [Phys. Plasmas 16, 084701 (2009)]
Authors: Sugiyama Linda E.
Published: August 2009

In response to the Comment [J. A. Krommes, Phys. Plasmas 16, 084701 (2009)], this note extends the original paper [L. E. Sugiyama, Phys. Plasmas 15, 092112 (2008)] to consider the breakdown of good magnetic flux surfaces. The validity of the noncanonical Lagrangian (NCL) guiding center model of Littlejohn and Brizard depends directly on the existence of sufficiently smooth, structured solutions for the three-dimensional magnetic field in a plasma. In general, such fields are chaotic. Local existence of the parameter R=(∇ê1)⋅ê2, which measures the rotation of the magnetic coordinate system for the gyroangle, determines the existence of the NCL expansion at second order. Globally, sufficient smoothness that R is definable almost everywhere requires zero magnetic field line torsion or two-dimensional (planar) symmetry, although limited regions of validity may exist otherwise. The original anholonomy analysis of Littlejohn for the gyroangle assumes field smoothness and concludes that R almost always exists.
Effects of backward-propagating waves and lumped mirror losses on self-induced transparency modelocking in quantum cascade lasers
Authors: Talukder Muhammad Anisuzzaman , Menyuk Curtis R.
Published: August 2009

Work to date on self-induced transparency modelocking in quantum cascade lasers (QCLs) has neglected backward-propagating waves and lumped mirror losses. In this work, we remove these unrealistic assumptions. The qualitative features of the modelocking are unaffected by this improvement in the model, but the parameter regime in which stable modelocked pulses may be found is reduced. This reduction is due to incomplete gain recovery near the edges of the QCL when pulses pass through after reflecting from the mirrors, coincident with the loss of pulse energy at the mirrors. Spatial hole burning is observed in parameter regimes in which continuous waves can grow, but it does not affect the stability of the modelocking.
Phonon recycling in ion-doped lasers
Authors: Kim Jedo , Kaviany Massoud
Published: August 2009

Phonon emission is an energy-conversion efficiency loss in photonic transition processes. Phonon recycling by the anti-Stokes cooling results in a lower operating temperature. Transmitted optical phonons cross heterogeneous boundary and the upconverted acoustic phonons contribute to higher occupancy of the optical phonon and increase the second-order transition rate. Optimization of phonon spectra makes upconversion favorable. We present theoretical study and quantitative efficiency results for phonon recycling in Yb3+ doped yttria alumina garnet lasing layer and its adjacent Yb3+:ZrF2 cooling layers and examine the thermodynamic limits. It is predicted that 30% of emitted phonons are recycled and further improvement is possible.
Ghost “pinhole” imaging in Fraunhofer region
Authors: Gong Wenlin , Zhang Pengli , Shen Xia , Han Shensheng
Published: August 2009

For an aperture with transverse size D, Fraunhofer region is named when the distance between the aperture and the detector is larger than D2/λ, where λ is the wavelength of the illuminating light. For a lensless system, when both reference detector and the object are located in Fraunhofer region relative to the thermal source, we demonstrate that a ghost “pinhole” camera with magnification M=z/z1 can be obtained by the second-order correlation of two light fields even if the test detector is a single pointlike detector. Effects determining the quality of ghost pinhole imaging and its potential applications are also discussed.
The coefficient of restitution for air bubbles colliding against solid walls in viscous liquids
Authors: Zenit Roberto , Legendre Dominique
Published: August 2009

The motion of air bubbles undergoing collisions with solid walls was studied experimentally. Using a high speed camera, the processes of approach, contact, and rebound were recorded for a wide range of fluid properties. The process is characterized considering a modified Stokes number, St∗=(CAMρdeqU0)/(9μ), which compares the inertia associated with the bubble (added mass) and viscous dissipation. We found that the dependence of the coefficient of restitution, ϵ=−Ureb/U0, with the impact Stokes number can be approximated by −log ϵ∼(Ca/St∗)1/2, where Ca is the capillary number; this behavior is very different from that found for the case of solid spheres. Most importantly, it shows that ϵ does not depend on the approach velocity. Considering a model for the process of contact and rebound of a deformable particle, this dependence is validated. Furthermore, by comparing the experimental trajectories and velocities of the bubble approach with model predictions, it was found that the film drainage is dominated by inertial effects; viscous effects, which would dominate for the case of approaching solid particles, are of secondary importance in this case.
High resolution photoemission study of SiOx/Si(111) interface disruption following in situ HfO2 deposition
Authors: McDonnell Stephen , Brennan Barry , Hughes Greg
Published: August 2009

We report on an in situ high resolution core level photoemission study of the early stages of interface formation between an ultrathin SiOx layer (∼0.3 nm) grown on the atomically clean Si(111) surface and a HfO2 dielectric layer. Si 2p core level spectra acquired at 130 eV photon energy reveal evidence of a chemically shifted component on the lower binding energy side of the substrate peak which is attributed to interface defect states resulting from the incorporation of silicon atoms from the substrate into the interfacial oxide at room temperature. This evidence of Si/SiOx interface disruption would be expected to increase charge carrier scattering mechanisms in the silicon and contribute to the generally observed mobility degradation in high-k stacks with ultrathin silicon oxide interface layers.
Deuterium NMR study of mobility and fluctuations in nematic and isotropic elastomers
Authors: Feio G. , Figueirinhas J. L. , Tajbakhsh A. R. , Terentjev E. M.
Published: August 2009

Orientational ordering in polydomain nematic and isotropic elastomers with identical polysiloxane backbone and different deuterium-labeled side groups is studied by D-NMR. In the nematic elastomer the orientational order parameter grows in a critical fashion on crossing the I-N transition implying a continuous phase transition driven by critical fluctuations of local director. The orientational (nematic) ordering occurs on the background of the polymer dynamics exhibited by the backbone, which is similar in the nematic and the analogous isotropic elastomers. The temperature dependence of NMR linewidths is compatible with a Vogel–Fulcher glassy dynamics.
Role of the renin-angiotensin system in autoimmune inflammation of the central nervous system
Authors: Stegbauer Johannes , Lee De-Hyung , Seubert Silvia , Ellrichmann Gisa , Manzel Arndt , Kvakan Heda , Muller Dominik N. , Gaupp Stefanie , Rump Lars Christian , Gold Ralf , Linker Ralf A.
Published: August 2009

Angiotensin II is the principle effector molecule of the renin angiotensin system (RAS). It exerts its various actions on the cardiovascular and renal system, mainly via interaction with the angiotensin II type-1 receptor (AT1R), which contributes to blood pressure regulation and development of hypertension but may also mediate effects on the immune system. Here we study the role of the RAS in myelin-oligodendrocyte glycoprotein-induced experimental autoimmune encephalomyelitis (MOG-EAE), a model mimicking many aspects of multiple sclerosis. Quantitative RT-PCR analyses showed an up-regulation of renin, angiotensin-converting enzyme, as well as AT1R in the inflamed spinal cord and the immune system, including antigen presenting cells (APC). Treatment with the renin inhibitor aliskiren, the angiotensin II converting-enzyme inhibitor enalapril, as well as preventive or therapeutic application of the AT1R antagonist losartan, resulted in a significantly ameliorated course of MOG-EAE. Blockade of AT1R did not directly impact on T-cell responses, but significantly reduced numbers of CD11b+or CD11c+APC in immune organs and in the inflamed spinal cord. Additionally, AT1R blockade impaired the expression of CCL2, CCL3, and CXCL10, and reduced CCL2-induced APC migration. Our findings suggest a pivotal role of the RAS in autoimmune inflammation of the central nervous system and identify RAS blockade as a potential new target for multiple sclerosis therapy.
Intracellular cleavage of osteopontin by caspase-8 modulates hypoxia/reoxygenation cell death through p53
Authors: Kim Hyo-Jin , Lee Ho-June , Jun Joon-Il , Oh Yumin , Choi Seon-Guk , Kim Hyunjoo , Chung Chul-Woong , Kim In-Ki , Park Il-Sun , Chae Han-Jung , Kim Hyung-Ryong , Jung Yong-Keun
Published: August 2009

Osteopontin (OPN) is highly expressed in cancer patients and plays important roles in many stages of tumor progression, such as anti-apoptosis, proliferation, and metastasis. From functional screening of human cDNA library, we isolated OPN as a caspase-8 substrate that regulates cell death during hypoxia/reoxygenation (Hyp/RO). In vitro cleavage assays demonstrate that OPN is cleaved at Asp-135 and Asp-157 by caspase-8. Cellular cleavage of OPN is observed in apoptotic cells exposed to Hyp/RO among various apoptotic stimuli and its cleavage is blocked by zVAD or IETD caspase inhibitor. Further, over-expression of OPN, the form with secretion signal, inhibits Hyp/RO-induced cell death. Caspase cleavage-defective OPN mutant (OPN D135A/D157A) is more efficient to suppress Hyp/RO-induced cell death than wild-type OPN. OPN D135A/D157A sustains AKT activity to increase cell viability through inhibition of caspase-9 during Hyp/RO. In addition, OPN is highly induced in some tumor cells during Hyp/RO, such as HeLa and Huh-7 cells, which is associated with their resistance to Hyp/RO by sustaining AKT activity. Notably, OPN C-terminal cleavage fragment produced by caspase-8 is detected in the nucleus. Plasmid-encoded expression of OPN C-terminal cleavage fragment increases p53 protein level and induces apoptosis of wild-type mouse embryonic fibroblast cells, but not p53
−/−
mouse embryonic fibroblast cells. These observations suggest that the protective function of OPN during Hyp/RO is inactivated via the proteolytic cleavage by caspase-8 and its cleavage product subsequently induces cell death via p53, postulating caspase-8 as a negative regulator of tumorigenic activity of OPN.
Blocking angiotensin-converting enzyme induces potent regulatory T cells and modulates TH1- and TH17-mediated autoimmunity
Authors: Platten Michael , Youssef Sawsan , Hur Eun Mi , Ho Peggy P. , Han May H. , Lanz Tobias V. , Phillips Lori K. , Goldstein Matthew J. , Bhat Roopa , Raine Cedric S. , Sobel Raymond A. , Steinman Lawrence
Published: August 2009

The renin-angiotensin-aldosterone system (RAAS) is a major regulator of blood pressure. The octapeptide angiotensin II (AII) is proteolytically processed from the decapeptide AI by angiotensin-converting enzyme (ACE), and then acts via angiotensin type 1 and type 2 receptors (AT1R and AT2R). Inhibitors of ACE and antagonists of the AT1R are used in the treatment of hypertension, myocardial infarction, and stroke. We now show that the RAAS also plays a major role in autoimmunity, exemplified by multiple sclerosis (MS) and its animal model, experimental autoimmune encephalomyelitis (EAE). Using proteomics, we observed that RAAS is up-regulated in brain lesions of MS. AT1R was induced in myelin-specific CD4
+
T cells and monocytes during autoimmune neuroinflammation. Blocking AII production with ACE inhibitors or inhibiting AII signaling with AT1R blockers suppressed autoreactive TH1 and TH17 cells and promoted antigen-specific CD4+FoxP3+ regulatory T cells (T
reg
cells) with inhibition of the canonical NF-κB1 transcription factor complex and activation of the alternative NF-κB2 pathway. Treatment with ACE inhibitors induces abundant CD4+FoxP3+ T cells with sufficient potency to reverse paralytic EAE. Modulation of the RAAS with inexpensive, safe pharmaceuticals used by millions worldwide is an attractive therapeutic strategy for application to human autoimmune diseases.
Human deoxyhypusine hydroxylase, an enzyme involved in regulating cell growth, activates O
2
with a nonheme diiron center
Authors: Vu Van V. , Emerson Joseph P. , Martinho Marlène , Kim Yeon Sook , Münck Eckard , Park Myung Hee , Que Lawrence
Published: August 2009

Deoxyhypusine hydroxylase is the key enzyme in the biosynthesis of hypusine containing eukaryotic translation initiation factor 5A (eIF5A), which plays an essential role in the regulation of cell proliferation. Recombinant human deoxyhypusine hydroxylase (hDOHH) has been reported to have oxygen- and iron-dependent activity, an estimated iron/holoprotein stoichiometry of 2, and a visible band at 630 nm responsible for the blue color of the as-isolated protein. EPR, Mössbauer, and XAS spectroscopic results presented herein provide direct spectroscopic evidence that hDOHH has an antiferromagnetically coupled diiron center with histidines and carboxylates as likely ligands, as suggested by mutagenesis experiments. Resonance Raman experiments show that its blue chromophore arises from a (μ-1,2-peroxo)diiron(III) center that forms in the reaction of the reduced enzyme with O
2
, so the peroxo form of hDOHH is unusually stable. Nevertheless we demonstrate that it can carry out the hydroxylation of the deoxyhypusine residue present in the elF5A substrate. Despite a lack of sequence similarity, hDOHH has a nonheme diiron active site that resembles both in structure and function those found in methane and toluene monooxygenases, bacterial and mammalian ribonucleotide reductases, and stearoyl acyl carrier protein Δ
9
-desaturase from plants, suggesting that the oxygen-activating diiron motif is a solution arrived at by convergent evolution. Notably, hDOHH is the only example thus far of a human hydroxylase with such a diiron active site.
Pre-Neolithic wild boar management and introduction to Cyprus more than 11,400 years ago
Authors: Vigne Jean-Denis , Zazzo Antoine , Saliège Jean-François , Poplin François , Guilaine Jean , Simmons Alan
Published: August 2009

The beginnings of pig domestication in Southwest Asia are controversial. In some areas, it seems to have occurred abruptly
ca.
10,500 years ago, whereas in nearby locations, it appears to have resulted from a long period of management of wild boar starting at the end of the Late Pleistocene. Here, we present analyses of suid bones from Akrotiri
Aetokremnos
, Cyprus. This site has provided the earliest evidence for human occupation of the Mediterranean islands. Morphological analysis and direct radiocarbon dating of both degraded collagen and apatite of these bones reveal that small-sized suids were living on Cyprus 11,400–11,700 years ago. We demonstrate that these suids were introduced by humans and that, at this early date, their small size must result from island isolation. This sheds light on the early Holocene colonization of Cyprus and on pre-Neolithic Mediterranean seafaring. We further argue that wild boar were managed on the mainland before their introduction to Cyprus (i.e., before the beginning of the Neolithic and at least 1 millennium before the earliest known morphological modifications attributable to domestication). This adds weight to the theory that pig domestication involved a long period of wild boar management that started about the time of the Pleistocene/Holocene transition.
Biochemical basis for the essential genetic requirements of RecA and the β-clamp in Pol V activation
Authors: Fujii Shingo , Fuchs Robert P.
Published: August 2009

In
Escherichia coli
, it is genetically well established that the β-clamp and RecA are essential cofactors that endow DNA polymerase (Pol) V with lesion bypass activity. However, the biochemical basis for these requirements is still largely unknown. Because the process of translesion synthesis (TLS) requires that the specialized DNA polymerase synthesize in a single binding event a TLS patch that is long enough to resist external proofreading, it is critical to monitor Pol V burst synthesis. Here, we dissect the distinct roles that RecA and the β-clamp perform during the Pol V activation process using physiologically relevant long single-stranded template DNA, similar to those used in genetic assays. Our data show that the β-clamp endows the complex between Pol V and the template DNA with increased stability. Also, the RecA filament formed in
cis
on the single-stranded DNA produced downstream from the lesion stretches the template DNA to allow smooth elongation of the nascent strand by Pol V. The concurrent action of both cofactors is required for achieving productive TLS events. The present article presents an integrated view of TLS under physiologically relevant conditions in
E. coli
that may represent a paradigm for lesion bypass in other organisms.
Src family protein tyrosine kinase (PTK) modulates the effect of SGK1 and WNK4 on ROMK channels
Authors: Yue Peng , Lin Dao-Hong , Pan Chun-Yang , Leng Qiang , Giebisch Gerhard , Lifton Richard P. , Wang Wen-Hui
Published: August 2009

WNK4 (with no lysine kinase 4) inhibits ROMK channel activity in the distal nephron by stimulating clathrin-dependent endocytosis, an effect attenuated by SGK1 (serum-glucocorticoids-induced kinase)-mediated phosphorylation. It has been suggested that increased ROMK activity because of SGK1-mediated inhibition of WNK4 plays a role in promoting renal K secretion in response to elevated serum K or high K (HK) intake. In contrast, intravascular volume depletion also increases SGK1 activity but fails to stimulate ROMK channels and K secretion. Because HK intake decreases Src family protein tyrosine kinase (PTK) activity an inhibitor of ROMK channels, it is possible that Src family PTK may modulate the effects of SGK1 on WNK4. Here, we show that c-Src prevents SGK1 from attenuating WNK4's inhibition of ROMK activity. This effect of c-Src was WNK4-dependent because c-Src had no effect on ROMK harboring mutation at the site of c-Src phosphorylation (R1Y337A) in the absence of WNK4. Moreover, expression c-Src diminished the SGK1-mediated increase in serine phosphorylation of WNK4, suggesting that c-Src enhances WNK4-mediated inhibition of ROMK channels by suppressing the SGK1-induced phosphorylation. This notion is also supported by the observation that c-Src was not able to modulate the interaction between SGK1 and WNK4 mutants (WNK4
S1169A
or WNK4
S1169D
) in which an SGK1-phosphorylation site (serine 1169) was mutated by alanine or aspartate. We conclude that c-Src inhibits SGK1-mediated phosphorylation hereby restoring the WNK4-mediated inhibition of ROMK channels thus suppressing K secretion.
Toxicity of paraquat to Daphnia magna under different exposure conditions associated with Korean agricultural conditions
Authors: Kim B. S. , Park Y. K. , Jeong M. H. , You A. S. , Lee Y. H. , Yang Y. J. , Ahn Y. J.
Published: August 2009

This study was conducted to examine the toxic effects of paraquat on Daphnia magna and its behavior in Korean agricultural conditions. Acute immobilization toxicity tests on D. magna were performed for 48 h at three different exposure systems: water-alone (System A), water-sediment system (System B), and an equilibrated water-sediment system (System C). The concentration of paraquat in the System A was very stable over 48 h and the EC50 was 6.39 ppm. In contrast, the concentration of paraquat in water phase of the System B drastically decreased. The dissipation time in water (DT50) in the System B ranged from 5.45 h to 13.05 h, while the EC50 increased 3 times to 20.8 ppm. The concentration of paraquat in the water phase of the System C decreased over 90%, and no adverse effect was observed at 80 ppm. Considering that the toxicity of paraquat greatly decreased in the System B, there was a large margin between predicted environmental concentration (PEC) and the concentration that would cause adverse effects on D. magna in environmentally relevant conditions. This study clearly indicated that paraquat equilibrated in the water sediment system did not acutely affect D. magna dwelling in the aquatic ecosystems, including rice paddies of Korea.
Protein Tyrosine Phosphatase Epsilon Regulates Integrin-mediated Podosome Stability in Osteoclasts by Activating Src
Authors: Granot-Attas Shira , Luxenburg Chen , Finkelshtein Eynat , Elson Ari
Published: August 2009

The nonreceptor isoform of tyrosine phosphatase epsilon (cyt-PTPe) supports osteoclast adhesion and activity in vivo, leading to increased bone mass in female mice lacking PTPe (EKO mice). The structure and organization of the podosomal adhesion structures of EKO osteoclasts are abnormal; the molecular mechanism behind this is unknown. We show here that EKO podosomes are disorganized, unusually stable, and reorganize poorly in response to physical contact. Phosphorylation and activities of Src, Pyk2, and Rac are decreased and Rho activity is increased in EKO osteoclasts, suggesting that integrin signaling is defective in these cells. Integrin activation regulates cyt-PTPe by inducing Src-dependent phosphorylation of cyt-PTPe at Y638. This phosphorylation event is crucial because wild-type—but not Y638F—cyt-PTPe binds and further activates Src and restores normal stability to podosomes in EKO osteoclasts. Increasing Src activity or inhibiting Rho or its downstream effector Rho kinase in EKO osteoclasts rescues their podosomal stability phenotype, indicating that cyt-PTPe affects podosome stability by functioning upstream of these molecules. We conclude that cyt-PTPe participates in a feedback loop that ensures proper Src activation downstream of integrins, thus linking integrin signaling with Src activation and accurate organization and stability of podosomes in osteoclasts.
Glycosylation Regulates Pannexin Intermixing and Cellular Localization
Authors: Penuela Silvia , Bhalla Ruchi , Nag Kakon , Laird Dale W.
Published: August 2009

The pannexin family of mammalian proteins, composed of Panx1, Panx2, and Panx3, has been postulated to be a new class of single-membrane channels with functional similarities to connexin gap junction proteins. In this study, immunolabeling and coimmunoprecipitation assays revealed that Panx1 can interact with Panx2 and to a lesser extent, with Panx3 in a glycosylation-dependent manner. Panx2 strongly interacts with the core and high-mannose species of Panx1 but not with Panx3. Biotinylation and dye uptake assays indicated that all three pannexins, as well as the N-glycosylation-defective mutants of Panx1 and Panx3, can traffic to the cell surface and form functional single-membrane channels. Interestingly, Panx2, which is also a glycoprotein and seems to only be glycosylated to a high-mannose form, is more abundant in intracellular compartments, except when coexpressed with Panx1, when its cell surface distribution increases by twofold. Functional assays indicated that the combination of Panx1 and Panx2 results in compromised channel function, whereas coexpressing Panx1 and Panx3 does not affect the incidence of dye uptake in 293T cells. Collectively, these results reveal that the functional state and cellular distribution of mouse pannexins are regulated by their glycosylation status and interactions among pannexin family members.