bluuebunny/crossref_metadata_2025 huggingface dataset:
Seismic evidence for large‐scale compositional heterogeneity of oceanic core complexes
Authors: Canales J. Pablo , Tucholke Brian E. , Xu Min , Collins John A. , DuBois David L.
Published: August 2008

Long‐lived detachment faults at mid‐ocean ridges exhume deep‐seated rocks to form oceanic core complexes (OCCs). Using large‐offset (6 km) multichannel seismic data, we have derived two‐dimensional seismic tomography models for three of the best developed OCCs on the Mid‐Atlantic Ridge. Our results show that large lateral variations in P wave velocity occur within the upper ∼0.5–1.7 km of the lithosphere. We observe good correlations between velocity structure and lithology as documented by in situ geological samples and seafloor morphology, and we use these correlations to show that gabbros are heterogeneously distributed as large (tens to >100 km2) bodies within serpentinized peridotites. Neither the gabbros nor the serpentinites show any systematic distribution with respect to along‐isochron position within the enclosing spreading segment, indicating that melt extraction from the mantle is not necessarily focused at segment centers, as has been commonly inferred. In the spreading direction, gabbros are consistently present toward the terminations of the detachment faults. This suggests enhanced magmatism during the late stage of OCC formation due either to natural variability in the magmatic cycle or to decompression melting during footwall exhumation. Heat introduced into the rift valley by flow and crystallization of this melt could weaken the axial lithosphere and result in formation of new faults, and it therefore may explain eventual abandonment of detachments that form OCCs. Detailed seismic studies of the kind described here, when constrained by seafloor morphology and geological samples, can distinguish between major lithological units such as volcanics, gabbros, and serpentinized peridotites at lateral scales of a few kilometers. Thus such studies have tremendous potential to elucidate the internal structure of the shallow lithosphere and to help us understand the tectonic and magmatic processes by which they were emplaced.
Halo of ice deformation observed over the Maud Rise seamount
Authors: Lindsay R. W. , Kwok R. , de Steur L. , Meier W.
Published: August 2008

A distinctive halo of sea ice deformation was observed above the Maud Rise seamount in the eastern Weddell Sea in the winter of 2005. The deformation halo is coincident with a halo of low mean ice concentration that is often observed in the region. Monthly mean ice vorticity estimates for the months July through November reveal the deformation zone most clearly in an arc about 100 km northwest of the seamount where there is a strong gradient in the bathymetry at depths of 3000–5000 m. The deformation was computed from satellite‐based ice motion vectors derived from Envisat Synthetic Aperture Radar backscatter images. The deformation halo is evidence of a Taylor cap circulation over the seamount, which has been described and analyzed with modeling studies and concurrent oceanographic observations obtained during an extensive field campaign.
Statistical analysis of the location of the Martian magnetic pileup boundary and bow shock and the influence of crustal magnetic fields
Authors: Edberg N. J. T. , Lester M. , Cowley S. W. H. , Eriksson A. I.
Published: August 2008

We use the data set from the magnetometer and electron reflectometer instruments on board the Mars Global Surveyor spacecraft to show that the crustal magnetic fields of Mars affect the location of the magnetic pileup boundary (MPB) and bow shock (BS) globally. We search for crossings of the MPB and BS in the data that were observed over the first 16 months of the mission. To identify the influence of the crustal magnetic fields, all crossings are extrapolated to the terminator plane in order to remove the solar zenith angle (SZA) dependence, and to make it possible to compare crossings independently of location. The MPB crossings that were observed over regions on Mars, which contain strong crustal magnetic fields, are on average located further out than crossings observed over regions with weak crustal fields. This is shown in three separate longitude intervals. We also find that the dayside BS crossings observed over the southern hemisphere of Mars are on average located further out than the BS crossings observed over the northern hemisphere, possibly because of the influence of the crustal fields. We also study the magnetic field strength and its variation at the inside of the MPB and their dependence on the SZA and altitude. We find that the magnitude of the magnetic field in the MPB is closely linked to the altitude of the MPB, with the magnitude increasing as the MPB is observed closer to the planet.
Multiple switching of spin polarization injected into a semiconductor by a multiferroic tunneling junction
Authors: Wang Jian , Li Z. Y.
Published: August 2008

A method for switching between multiple spin polarization of the electric current injected into a semiconductor is proposed, based on injecting spins from a diluted magnetic semiconductor through a multiferroic tunnel barrier. We show that it is important to combine a diluted magnetic semiconductor electrode with a multiferroic barrier to realize multiple switching of spin polarization on wide range. The reversal of either electric polarization or magnetization in a multiferroic barrier results in a sizable change in the spin polarization of the injected current both in magnitude and in sign, thereby providing a four-state electrical control of spin polarization. The electroresistance and electromagnetoresistance effects can be also realized in this structure. Our investigations may stimulate experimental studies of the multiferroic tunnel junctions.
Combining quantum wavepacket ab initio molecular dynamics with QM/MM and QM/QM techniques: Implementation blending ONIOM and empirical valence bond theory
Authors: Sumner Isaiah , Iyengar Srinivasan S.
Published: August 2008

We discuss hybrid quantum-mechanics/molecular-mechanics (QM/MM) and quantum mechanics/quantum mechanics (QM/QM) generalizations to our recently developed quantum wavepacket ab initio molecular dynamics methodology for simultaneous dynamics of electrons and nuclei. The approach is a synergy between a quantum wavepacket dynamics, ab initio molecular dynamics, and the ONIOM scheme. We utilize this method to include nuclear quantum effects arising from a portion of the system along with a simultaneous description of the electronic structure. The generalizations provided here make the approach a potentially viable alternative for large systems. The quantum wavepacket dynamics is performed on a grid using a banded, sparse, and Toeplitz representation of the discrete free propagator, known as the “distributed approximating functional.” Grid-based potential surfaces for wavepacket dynamics are constructed using an empirical valence bond generalization of ONIOM and further computational gains are achieved through the use of our recently introduced time-dependent deterministic sampling technique. The ab initio molecular dynamics is achieved using Born–Oppenheimer dynamics. All components of the methodology, namely, quantum dynamics and ONIOM molecular dynamics, are harnessed together using a time-dependent Hartree-like procedure. We benchmark the approach through the study of structural and vibrational properties of molecular, hydrogen bonded clusters inclusive of electronic, dynamical, temperature, and critical quantum nuclear effects. The vibrational properties are constructed through a velocity/flux correlation function formalism introduced by us in an earlier publication.
Interference and crosstalk in double optical tweezers using a single laser source
Authors: Mangeol Pierre , Bockelmann Ulrich
Published: August 2008

Experimental studies of single molecule mechanics require high force sensitivity and low drift, which can be achieved with optical tweezers. We built an optical tweezer setup for force measurements in a two bead assay. A cw infrared laser beam is split by polarization and focused by a high numerical aperture objective to create two traps. The same laser is used to form both traps and to measure the force by back focal plane interferometry. We show that although the two beams entering the microscope are designed to exhibit orthogonal polarization, interference and a significant parasitic force signal occur. Comparing the experimental results with a ray optics model, we show that the interference patterns are caused by the rotation of polarization on microscope lens surfaces and slides. The model qualitatively describes the pattern and the dependence of the parasitic force signal on the experimental parameters. We present two different approaches to experimentally reduce the crosstalk, namely, polarization rectification and frequency shifting.
Dewetting behavior of polystyrene film filled with (C6H5C2H4NH3)2PbI4
Authors: Xue Longjian , Cheng Ziyong , Fu Jun , Han Yanchun
Published: August 2008

The dewetting behavior of thin (about 30nm) polystyrene (PS) films filled with different amount of (C6H5C2H4NH3)2PbI4 (PhE–PbI4) on the silicon substrate with a native oxide layer was investigated. For different additive concentrations, PhE–PbI4 showed different spatial distributions in the PS films, which had a strong influence on the film wettability, dewetting dynamics, and mechanism. With 0.5wt% additive, PhE–PbI4 formed a noncontinuous diffusion layer, which caused a continuous hole nucleation in the film. With about 1wt% additive, a continuous gradient distribution layer of PhE–PbI4 formed in the film, which inhibited the dewetting. When the concentration is higher (2wt%), large PhE–PbI4 aggregates, in addition to the PhE–PbI4 continuous layer, formed in the film. These large aggregates (larger than radius of gyration of PS) migrated to the interface, resulting in the hole nucleation and eventually the complete dewetting of the film.
Analysis of periodic Schrödinger operators: Regularity and approximation of eigenfunctions
Authors: Hunsicker Eugenie , Nistor Victor , Sofo Jorge O.
Published: August 2008

Let V be a real valued potential that is smooth everywhere on R3, except at a periodic, discrete set S of points, where it has singularities of the Coulomb-type Z/r. We assume that the potential V is periodic with period lattice L. We study the spectrum of the Schrödinger operator H=−Δ+V acting on the space of Bloch waves with arbitrary, but fixed, wavevector k. Let T≔R3/L. Let u be an eigenfunction of H with eigenvalue λ and let ϵ>0 be arbitrarily small. We show that the classical regularity of the eigenfunction u is u∊H5/2−ϵ(T) in the usual Sobolev spaces, and u∊K3/2−ϵm(T\S) in the weighted Sobolev spaces. The regularity index m can be as large as desired, which is crucial for numerical methods. For any choice of the Bloch wavevector k, we also show that H has compact resolvent and hence a complete eigenfunction expansion. The case of the hydrogen atom suggests that our regularity results are optimal. We present two applications to the numerical approximation of eigenvalues: using wave functions and using piecewise polynomials.
Insect normal hovering flight in ground effect
Authors: Gao Tong , Lu Xi-Yun
Published: August 2008

The ground effect on insect normal hovering is investigated using an immersed boundary-lattice Boltzmann method to solve the two-dimensional incompressible Navier–Stokes equations. A virtual model of an elliptic foil with oscillating translation and rotation near a body surface or ground is used. Computations have been carried out for some parameters including the distance between the foil and the surface, phase difference between the rotation and translation, and amplitude of oscillating rotation. The ground effect on the unsteady forces and vortical structures is analyzed. In particular, three typical regimes of force behavior due to the ground effect, i.e., force enhancement, force reduction, and force recovery regime, are identified and closely associated with the evolution of vortex structures. The results obtained in this study provide physical insight into the understanding of aerodynamics and flow structures for insect normal hovering flight with a ground effect and flying mechanisms relevant to insect perching on body.
The spatial resolution of electron energy loss and x-ray absorption fine structure
Authors: Wang Feng , Egerton Ray F. , Malac Marek , McLeod Robert A. , Moreno M. Sergio
Published: August 2008

We have investigated the factors that determine the degree of localization of the information obtainable from electron energy loss or x-ray absorption fine structure. Inelastic scattering of the excited core electron limits the volume of specimen contributing to the backscattered intensity to a diameter in the range of 1–2 nm, dependent on the excited-electron energy and the composition and crystal structure of the sample. Phase cancellation between the backscattered waves further reduces the effective diameter that determines the observed fine structure to below 1 nm. Since the spatial resolution attainable by transmission electron microscopy can approach 0.2 nm or can even be below 0.1 nm (with aberration correction), we predict that delocalization arising from the excited-electron range may limit the resolution of images based on changes in core-loss fine structure.
Hartree-Fock and Kohn-Sham time-dependent response theory in a second-quantization atomic-orbital formalism suitable for linear scaling
Authors: Kjærgaard Thomas , Jørgensen Poul , Olsen Jeppe , Coriani Sonia , Helgaker Trygve
Published: August 2008

We present a second-quantization based atomic-orbital method for the computation of time-dependent response functions within Hartree-Fock and Kohn-Sham density-functional theories. The method is suited for linear scaling. Illustrative results are presented for excitation energies, one- and two-photon transition moments, polarizabilities, and hyperpolarizabilities for hexagonal BN sheets with up to 180 atoms.
Improved thermoelectric performance in polycrystalline p-type Bi2Te3 via an alkali metal salt hydrothermal nanocoating treatment approach
Authors: Ji Xiaohua , He Jian , Su Zhe , Gothard Nick , Tritt Terry M.
Published: August 2008

We report herein a proof-of-principle study of grain boundary engineering in the polycrystalline p-type Bi2Te3 system. Utilizing the recently developed hydrothermal nanocoating treatment technique, we fabricated an alkali-metal(s)-containing surface layer on the p-Bi2Te3 bulk grain, which in turn became part of the grain boundary upon hot pressing densification. Compared to the untreated bulk reference, the dimensionless figure of merit ZT has been improved by ∼30% in the Na-treated sample chiefly due to the reduced thermal conductivity, and ∼38% in the Rb-treated sample mainly owing to the improved power factor. The grain boundary phase provides a new avenue by which one can potentially decouple the otherwise inter-related electrical resistivity, Seebeck coefficient, and thermal conductivity within one thermoelectric material.
Effect of La0.67Sr0.33MnO3 electrodes on organic spin valves
Authors: Majumdar Sayani , Huhtinen H. , Majumdar H. S. , Laiho R. , Österbacka R.
Published: August 2008

We report the effect of La0.7Sr0.3MnO3 (LSMO) electrodes on the temperature dependence of the magnetoresistance (MR) of LSMO/polymer/cobalt spin valves (SVs). LSMO films have been prepared by pulsed laser deposition on three different single crystal substrates using different deposition parameters. The films were characterized for their surface morphologies, structural, magnetic, and magnetotransport properties. Low deposition rate is found to be detrimental for growth of good quality films and polycrystalline films with grain boundary effects are observed in thicker films. The films on MGO (100) substrate show a broad paramagnetic to ferromagnetic transition, accompanied with a metal-insulator transition below room temperature. This indicates growth of some strained structures due to large lattice mismatch (9%) between the substrate and the film and presence of polycrystalline grain boundaries. The deposited films on STO (100) and NGO (001) show much sharper magnetic transition and metallic behavior indicating higher spin polarization (SP) of LSMO on these substrates at room temperature. SVs made on STO (100) show improvement in switching behavior and better MR response compared to the devices made on MGO (100) at low temperatures. No difference in MR response was found at room temperature in either case. We conclude that the bulk spin polarization of LSMO films is not very important in the SV operation. The loss of most of the SP carriers at the LSMO/organic semiconductor interface at room temperature is a more dominant effect and drastically reduces the MR signal.
Surface crystallography and electronic structure of potassium yttrium tungstate
Authors: Atuchin V. V. , Pokrovsky L. D. , Khyzhun O. Yu. , Sinelnichenko A. K. , Ramana C. V.
Published: August 2008

Structural and electronic characteristics of KY(WO4)2 (KYW) (010) crystal surfaces have been studied using reflection high-energy electron diffraction (RHEED) and x-ray photoelectron spectroscopy (XPS). The results indicate that the crystal structure and chemical composition of the mechanically polished pristine surface is stoichiometrically well maintained as expected for KYW crystals. Combined measurements of RHEED and XPS as a function of 1.5 keV Ar+ ion irradiation of the KYW (010) surfaces indicate amorphization, partial loss of potassium atoms, and partial transformation of chemical valence state of tungsten from W6+ to a lower valence state, W0 state predominantly, which induces electronic states at the top of valence band.
Band gap engineering for La aluminate dielectrics on Si (100)
Authors: Jin Hua , Cho Young Joon , Oh Suhk Kun , Kang Hee Jae , Park Ju Chul , Heo Sung , Lee Jae Cheol
Published: August 2008

La aluminate (La2O3)x(Al2O3)1−x films were grown by atomic layer deposition method, for which the conduction band offset, valence band offset, and band gap were obtained by using x-ray photoelectron spectroscopy and reflection electron energy loss spectroscopy. The valence band offsets were nearly unchanged within the range from 2.23to2.37eV with increasing Al content. The conduction band offsets were changed from 2.40to2.86eV for the above dielectrics. Remarkably, the band gap could be engineered from 5.75to6.35eV by increasing Al content. We also found that La aluminate films have symmetric band profiles.
Two-dimensional time resolved measurements of toroidal velocity correlated with density blobs in magnetized plasmas
Authors: Labit B. , Furno I. , Podestà M. , Fasoli A.
Published: August 2008

A new method for toroidal velocity measurements with Mach probes is presented. This technique is based on the conditional sampling technique, the triggering events being density blobs. A reconstruction of the time resolved two-dimensional profile of electron density, electron temperature, plasma potential, and toroidal velocity is possible with a single point measurement on a shot-to-shot basis.
Particle-in-cell simulation of collisionless reconnection with open outflow boundaries
Authors: Klimas Alex , Hesse Michael , Zenitani Seiji
Published: August 2008

A new method for applying open boundary conditions in particle-in-cell (PIC) simulations is utilized to study magnetic reconnection. Particle distributions are assumed to have zero normal derivatives at the boundaries. Advantages and possible limitations of this method for PIC simulations are discussed. Results from a reconnection simulation study are presented. For the purpose of this investigation, a 2 12-dimensional electromagnetic PIC simulation using open conditions at the outflow boundaries and simple reflecting boundaries to the inflow regions is discussed. The electron diffusion region is defined as that region where the out-of-plane electron inertial electric field is positive indicating acceleration and flux transfer; the evolution of this region is analyzed. It is found that this region varies in the range 2.5–4 local electron inertial lengths in total width and in the range 10–15 local electron inertial lengths in total length for the mass ratio 25. The reconnection rate is investigated in terms of the aspect ratio of the electron diffusion region plus inflow and outflow measures at its boundaries. It is shown that a properly measured aspect ratio predicts the flux transfer rate, scaled to account for the decline in field strength and electron density at the inflow boundary to the electron diffusion region. It is concluded that this electron diffusion region either adjusts its aspect ratio for compatibility with the flux transfer rate that is set elsewhere, as in the Hall reconnection model, or that it is this region that controls the reconnection flux transfer rate.
Zr-metal adhesion on graphenic nanostructures
Authors: Sanchez-Paisal Y. , Sanchez-Portal D. , Garmendia N. , Muñoz R. , Obieta I. , Arbiol J. , Calvo-Barrio L. , Ayuela A.
Published: August 2008

Our high resolution transmission electronic microscopy studies of multiwall carbon nanotubes show, after the growth of zirconia nanoparticles by a hydrothermal route, the presence of surface Zr, forming an atomically thin layer. Using first-principles calculations we investigate the nature of the Zr–C interaction, which is neither ionic nor covalent, and the optimal coverage for the Zr metal in a graphene flake. This preferred coverage is in agreement with that deduced from electron energy loss spectra experiments. We show also that the amount of charge transferred to the C layer saturates as the Zr coverage increases and the Zr–C bond becomes weaker.
The solitary wave propagation in a collisional dusty plasma
Authors: Pandey B. P. , Vranjes J.
Published: August 2008

The present work investigates the nonlinear wave properties of a collisional dusty plasma consisting of electrons, ions, and charged grains. It is shown that the collisional dusty medium is inherently dispersive in nature when the electrons and ions are strongly magnetized. In such a plasma, when the fluctuation wavelength is larger than the dust skin depth, the balance between the dispersion and nonlinearity leads to the modified Korteweg–de Vries equation. It is quite plausible that the soliton solutions of the nonlinear equation may explain some of the large scale structures observed in various space plasma settings.
Extreme-ultraviolet frequency comb generation by polarization-gated surface-enhanced optical fields
Authors: Wu Jian , Qi Hongxing , Zeng Heping
Published: August 2008

We show that two synchronized counter-propagating femtosecond pulses could be controlled by adjusting their relative delay to excite surface-enhanced optical fields of time-gated linear polarization in contrast with intrinsic elliptic polarization excited by the conventional one-pulse incidence scheme. Such surface-enhanced optical fields can be used to generate efficient high harmonics and thus extreme-ultraviolet frequency combs. The energy conversion efficiency as well as the frequency span of the generated extreme-ultraviolet frequency combs can be significantly increased with controllable emission probabilities along different directions relative to the surface.
SmScO
3
thin films as an alternative gate dielectric
Authors: Durğun Özben E. , Lopes J. M. J. , Roeckerath M. , Lenk St. , Holländer B. , Jia Y. , Schlom D. G. , Schubert J. , Mantl S.
Published: August 2008

Samarium scandate thin films deposited on (100) Si have been investigated structurally and electrically. Rutherford backscattering spectrometry and transmission electron microscopy results show that the films are stoichiometric, amorphous, and smooth. X-ray diffraction analysis indicates that SmScO3 starts to crystallize at 900 °C. Capacitance and leakage current measurements reveal C-V curves with negligible hysteresis, a dielectric constant around 29 for 6 nm thick films, low leakage current densities in the range of 10−7 A/cm2, an effective oxide charge density of ∼5×1011 cm−2, and an interface trap density of 4.5×1011 (eV cm2)−1.
Agglomeration Mobility: Effects of Localisation, Urbanisation, and Scale on Job Changes
Authors: Eriksson Rikard , Lindgren Urban , Malmberg Gunnar
Published: August 2008

Following increased attention being paid to the importance of labour-market processes in relation to knowledge diffusion and learning, this study addresses the influence of agglomeration economies (localisation, urbanisation, and scale) on the propensity to change jobs between and within local labour markets. From the use of longitudinal individual data (1990–2002), controlling for factors such as age, sex, income, and social relations, the results show that the composition of regional economies influences labour-market dynamism. We identify two cases of intraregional agglomeration mobility, that is, positive effects on job mobility, due to the concentration of similar activities (localisation economies) and the size of the labour market (urbanisation economies). The results also show that localisation economies compensate for regional structural disadvantages connected to small population numbers, as localisation effects in small regions have a significantly positive effect on intraregional job-mobility rates, even compared with localisation effects in large and diversified metropolitan areas. The results indicate that the concentration of similar activities may be useful for small regions, if high levels of job mobility are crucial for the transfer of knowledge and the performance of firms.
Taking the Bus: Incorporating Public Transport Timetable Data into Health Care Accessibility Modelling
Authors: Martin David , Jordan Hannah , Roderick Paul
Published: August 2008

This paper is concerned with geographical access to hospital services by public transport. By taking advantage of newly available public transport timetable data, a software tool is developed for the analysis of bus travel times under specified journey scenarios. The example of population access to Derriford Hospital in Devon, England, is used to illustrate the application of these methods, and the social and spatial pattern of accessibility by bus is explored. The analysis reveals substantial differences between access by public and private transport, and highlights the difficulty of combining conventional drive-time analysis with the discontinuous accessibility provided by public transport. There is a need for more attention to be paid to the incorporation of public transport in accessibility modelling.
Performance Measurement of Local Welfare Programmes: Evidence from Madrid's Regional Government
Authors: Ayala Luis , Pedraja Francisco , Salinas-Jiménez Javier
Published: August 2008

Interest in how social assistance programmes are organized has recently heightened, fed by concerns about the limits on achieving greater efficiency. Most available evidence considers performance indicators that are too general, there being few studies relating the use of inputs to outcomes. We compare different performance indicators of Madrid's programme with resource endowments in a group of local agencies of social services. In addition to constructing a detailed system of input and performance indicators, an empirical analysis of efficiency for each of the social services agencies is carried out using data envelopment analysis. Results confirm that there is a wide margin for obtaining efficiency gains. The empirical analysis shows that some detected inefficiencies arise from an excessive number of staff in relation to the work to be performed. Agencies with a higher incidence of social problems present higher efficiency scores.
Genesis of soils across a late Quaternary volcanic landscape in the humid tropical island of Leyte, Philippines
Authors: Navarrete Ian A. , Tsutsuki Kiyoshi , Kondo Renzo , Asio Victor B.
Published: August 2008

This study evaluated the characteristics and genesis of soils across a young volcanic landscape in the humid tropical island of Leyte, Philippines. Five representative soil pedons (P1–P5) derived from late Quaternary volcanoclastics (i.e. fragmental) on a hillslope sequence were examined and sampled. Results revealed that the soils have generally similar morphological characteristics particularly in terms of soil colour (10YR 3/3–10YR 5/6) and soil structure (granular to subangular blocky), but differed in terms of soil thickness and clay content, which was higher in P3 than the other pedons across the landscape. The high porosities of the soils were the results of high organic matter, the dominance of noncrystalline (short-range order) minerals, as well as the isovolumetric weathering in the subsoils. All soils have very similar chemical properties (e.g. acidic, high organic carbon, low exchangeable bases), except soils from the middle backslope position (P3), which have high cation exchange capacity because higher exchangeable Ca and K result in a higher base saturation. Allophane, goethite, ferrihydrite, and gibbsite are the dominant clay minerals in the soils. Principal component analysis revealed that P3 was distinct from pedons P1, P2, P4, and P5, suggesting that it was substantially different from all other soils across the landscape. Soil formation was relatively fast due to the easy weatherability of the parent materials, high rainfall, and good drainage of the soils along the landscape. This study revealed that on young volcanic soils under humid tropical condition, topography greatly influenced soil development.
Spectroscopic identification and stability of the intermediate in the OH + HONO
2
reaction
Authors: O'Donnell Bridget A. , Li Eunice X. J. , Lester Marsha I. , Francisco Joseph S.
Published: August 2008

The reaction of nitric acid with the hydroxyl radical influences the residence time of HONO
2
in the lower atmosphere. Prior studies [Brown SS, Burkholder JB, Talukdar RK, Ravishankara AR (2001)
J Phys Chem A
105:1605–1614] have revealed unusual kinetic behavior for this reaction, including a negative temperature dependence, a complex pressure dependence, and an overall reaction rate strongly affected by isotopic substitution. This behavior suggested that the reaction occurs through an intermediate, theoretically predicted to be a hydrogen-bonded OH–HONO
2
complex in a six-membered ring-like configuration. In this study, the intermediate is generated directly by the association of photolytically generated OH radicals with HONO
2
and stabilized in a pulsed supersonic expansion. Infrared action spectroscopy is used to identify the intermediate by the OH radical stretch (ν
1
) and OH stretch of nitric acid (ν
2
) in the OH–HONO
2
complex. Two vibrational features are attributed to OH–HONO
2
: a rotationally structured ν
1
band at 3516.8 cm
−1
and an extensively broadened ν
2
feature at 3260 cm
−1
, both shifted from their respective monomers. These same transitions are identified for OD–DONO
2
. Assignments of the features are based on their vibrational frequencies, analysis of rotational band structure, and comparison with complementary high level
ab initio
calculations. In addition, the OH (
v
= 0) product state distributions resulting from ν
1
and ν
2
excitation are used to determine the binding energy of OH–HONO
2
,
D
0
≤ 5.3 kcal·mol
−1
, which is in good accord with
ab initio
predictions.
Y-chromosomal evidence of a pastoralist migration through Tanzania to southern Africa
Authors: Henn Brenna M. , Gignoux Christopher , Lin Alice A. , Oefner Peter J. , Shen Peidong , Scozzari Rosaria , Cruciani Fulvio , Tishkoff Sarah A. , Mountain Joanna L. , Underhill Peter A.
Published: August 2008

Although geneticists have extensively debated the mode by which agriculture diffused from the Near East to Europe, they have not directly examined similar agropastoral diffusions in Africa. It is unclear, for example, whether early instances of sheep, cows, pottery, and other traits of the pastoralist package were transmitted to southern Africa by demic or cultural diffusion. Here, we report a newly discovered Y-chromosome-specific polymorphism that defines haplogroup E3b1f-M293. This polymorphism reveals the monophyletic relationship of the majority of haplotypes of a previously paraphyletic clade, E3b1-M35*, that is widespread in Africa and southern Europe. To elucidate the history of the E3b1f haplogroup, we analyzed this haplogroup in 13 populations from southern and eastern Africa. The geographic distribution of the E3b1f haplogroup, in association with the microsatellite diversity estimates for populations, is consistent with an expansion through Tanzania to southern-central Africa. The data suggest this dispersal was independent of the migration of Bantu-speaking peoples along a similar route. Instead, the phylogeography and microsatellite diversity of the E3b1f lineage correlate with the arrival of the pastoralist economy in southern Africa. Our Y-chromosomal evidence supports a demic diffusion model of pastoralism from eastern to southern Africa ≈2,000 years ago.
Crystal structure of the Agrobacterium virulence complex VirE1-VirE2 reveals a flexible protein that can accommodate different partners
Authors: Dym Orly , Albeck Shira , Unger Tamar , Jacobovitch Jossef , Branzburg Anna , Michael Yigal , Frenkiel-Krispin Daphna , Wolf Sharon Grayer , Elbaum Michael
Published: August 2008

Agrobacterium tumefaciens
infects its plant hosts by a mechanism of horizontal gene transfer. This capability has led to its widespread use in artificial genetic transformation. In addition to DNA, the bacterium delivers an abundant ssDNA binding protein, VirE2, whose roles in the host include protection from cytoplasmic nucleases and adaptation for nuclear import. In
Agrobacterium
, VirE2 is bound to its acidic chaperone VirE1. When expressed
in vitro
in the absence of VirE1, VirE2 is prone to oligomerization and forms disordered filamentous aggregates. These filaments adopt an ordered solenoidal form in the presence of ssDNA, which was characterized previously by electron microscopy and three-dimensional image processing. VirE2 coexpressed
in vitro
with VirE1 forms a soluble heterodimer. VirE1 thus prevents VirE2 oligomerization and competes with its binding to ssDNA. We present here a crystal structure of VirE2 in complex with VirE1, showing that VirE2 is composed of two independent domains presenting a novel fold, joined by a flexible linker. Electrostatic interactions with VirE1 cement the two domains of VirE2 into a locked form. Comparison with the electron microscopy structure indicates that the VirE2 domains adopt different relative orientations. We suggest that the flexible linker between the domains enables VirE2 to accommodate its different binding partners.
A high-throughput screening strategy identifies cardiotonic steroids as alternative splicing modulators
Authors: Stoilov Peter , Lin Chia-Ho , Damoiseaux Robert , Nikolic Julia , Black Douglas L.
Published: August 2008

Alternative splicing has emerged as a promising therapeutic target in a number of human disorders. However, the discovery of compounds that target the splicing reaction has been hindered by the lack of suitable high-throughput screening assays. Conversely, the effects of known drugs on the splicing reaction are mostly unclear and not routinely assessed. We have developed a two-color fluorescent reporter for cellular assays of exon inclusion that can accommodate nearly any cassette exon and minimizes interfering effects from changes in transcription and translation. We used microtubule-associated protein tau (MAPT) exon 10, whose missplicing causes frontotemporal dementia, to test the reporter in screening libraries of known bioactive compounds. These screens yielded several compounds that alter the splicing of the exon, both in the reporter and in the endogenous MAPT mRNA. One compound, digoxin, has long been used in the treatment of heart failure, but was not known to modulate splicing. The positive compounds target different signal transduction pathways, and microarray analysis shows that each compound affects the splicing of a different set of exons in addition to MAPT exon 10. Our results identify currently prescribed cardiotonic steroids as modulators of alternative splicing and demonstrate the feasibility of screening for drugs that alter exon inclusion.
An acutely and latently expressed herpes simplex virus 2 viral microRNA inhibits expression of ICP34.5, a viral neurovirulence factor
Authors: Tang Shuang , Bertke Andrea S. , Patel Amita , Wang Kening , Cohen Jeffrey I. , Krause Philip R.
Published: August 2008

Latency-associated transcript (LAT) sequences regulate herpes simplex virus (HSV) latency and reactivation from sensory neurons. We found a HSV-2 LAT-related microRNA (miRNA) designated miR-I in transfected and infected cells
in vitro
and in acutely and latently infected ganglia of guinea pigs
in vivo
. miR-I is also expressed in human sacral dorsal root ganglia latently infected with HSV-2. miR-I is expressed under the LAT promoter
in vivo
in infected sensory ganglia. We also predicted and identified a HSV-1 LAT exon-2 viral miRNA in a location similar to miR-I, implying a conserved mechanism in these closely related viruses. In transfected and infected cells, miR-I reduces expression of ICP34.5, a key viral neurovirulence factor. We hypothesize that miR-I may modulate the outcome of viral infection in the peripheral nervous system by functioning as a molecular switch for ICP34.5 expression.
Apoptosis leads to a degradation of vital components of active nuclear transport and a dissociation of the nuclear lamina
Authors: Kramer A. , Liashkovich I. , Oberleithner H. , Ludwig S. , Mazur I. , Shahin V.
Published: August 2008

Apoptosis, a physiologically critical process, is characterized by a destruction of the cell after sequential degradation of key cellular components. Here, we set out to explore the fate of the physiologically indispensable nuclear envelope (NE) in this process. The NE mediates the critical nucleocytoplasmic transport through nuclear pore complexes (NPCs). In addition, the NE is involved in gene expression and contributes significantly to the overall structure and mechanical stability of the cell nucleus through the nuclear lamina, which underlies the entire nucleoplasmic face of the NE and thereby interconnects the NPCs, the NE, and the genomic material. Using the nano-imaging and mechanical probing approach atomic force microscopy (AFM) and biochemical methods, we unveiled the fate of the NE during apoptosis. The doomed NE sustains a degradation of both the mediators of the critical selective nucleocytoplasmic transport, namely NPC cytoplasmic filaments and basket, and the nuclear lamina. These observations are paralleled by marked softening and destabilization of the NE and the detection of vesicle-like nuclear fragments. We conclude that destruction of the cell nucleus during apoptosis proceeds in a strategic fashion. Degradation of NPC cytoplasmic filaments and basket shuts down the critical selective nucleocytoplasmic cross-talk. Degradation of the nuclear lamina disrupts the pivotal connection between the NE and the chromatin, breaks up the overall nuclear architecture, and softens the NE, thereby enabling the formation of nuclear fragments at later stages of apoptosis.
Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms
Authors: Okazaki Kei-ichi , Takada Shoji
Published: August 2008

Allostery, the coupling between ligand binding and protein conformational change, is the heart of biological network and it has often been explained by two representative models, the induced-fit and the population-shift models. Here, we clarified for what systems one model fits better than the other by performing molecular simulations of coupled binding and conformational change. Based on the dynamic energy landscape view, we developed an implicit ligand-binding model combined with the double-basin Hamiltonian that describes conformational change. From model simulations performed for a broad range of parameters, we uncovered that each of the two models has its own range of applicability, stronger and longer-ranged interaction between ligand and protein favors the induced-fit model, and weaker and shorter-ranged interaction leads to the population-shift model. We further postulate that the protein binding to small ligand tends to proceed via the population-shift model, whereas the protein docking to macromolecules such as DNA tends to fit the induced-fit model.
Influence of nonlinear electrostatics on transfer energies between liquid phases: Charge burial is far less expensive than Born model
Authors: Gong Haipeng , Hocky Glen , Freed Karl F.
Published: August 2008

The widely used Born model describes the electrostatic response of continuous media using static dielectric constants. However, when applied to a liquid environment, a comparison of Born model predictions with experimental values (e.g., transfer free energies and pK
a
shifts) found that agreement is only achieved by using physically unrealistic dielectric constants for proteins, lipids, etc., and/or equally unrealistic atomic radii. This leads to questions concerning the physical origins for this failure of the Born model. We partially resolve this question by applying the Langevin–Debye (LD) model of a continuous distribution of point, polarizable dipoles, a model that contains an added dependence of the electrostatic response on the solvent's optical dielectric constant and both gas- and liquid-phase dipole moments, features absent in the Born model to which the LD model reduces for weak fields. The LD model is applied to simple representations of three biologically relevant systems: (
i
) globular proteins, (
ii
) lipid bilayers, and (
iii
) membrane proteins. The linear Born treatment greatly overestimates both the self-energy and the transfer free energy from water to hydrophobic environments (e.g., a protein interior). By using the experimental dielectric constant, the energy cost of charge burial in either globular or membrane proteins of the Born model is reduced by almost 50% with the nonlinear theory as is the pK
a
shift, and the shifts agree well with experimental trends.
Demyelination arrest and remyelination induced by glatiramer acetate treatment of experimental autoimmune encephalomyelitis
Authors: Aharoni Rina , Herschkovitz Avia , Eilam Raya , Blumberg-Hazan Michal , Sela Michael , Bruck Wolfgang , Arnon Ruth
Published: August 2008

The interplay between demyelination and remyelination is critical in the progress of multiple sclerosis (MS) and its animal model, experimental autoimmune encephalomyelitis (EAE). In the present study, we explored the capacity of glatiramer acetate (GA, Copaxone) to affect the demyelination process and/or lead to remyelination in mice inflicted by chronic EAE, using both scanning electron microscopy and immunohistological methods. Spinal cords of untreated EAE mice revealed substantial demyelination accompanied by tissue destruction and axonal loss. In contrast, in spinal cords of GA-treated mice, in which treatment started concomitantly with disease induction (prevention), no pathology was observed. Moreover, when treatment was initiated after the appearance of clinical symptoms (suppression) or even in the chronic disease phase (delayed suppression) when substantial demyelination was already manifested, it resulted in a significant decrease in the pathological damage. Detection of oligodendrocyte progenitor cells (OPCs) expressing the NG2 or O4 markers via colocalization with the proliferation marker BrdU indicated their elevated levels in spinal cords of GA-treated mice. The mode of action of GA in this system is attributed to increased proliferation, differentiation, and survival of OPCs along the oligodendroglial maturation cascade and their recruitment into injury sites, thus enhancing repair processes
in situ
.
Pitx2 regulates gonad morphogenesis
Authors: Rodríguez-León Joaquín , Esteban Concepción Rodríguez , Martí Mercè , Santiago-Josefat Belén , Dubova Ilir , Rubiralta Xavier , Belmonte Juan Carlos Izpisúa
Published: August 2008

Organ shape and size, and, ultimately, organ function, relate in part to the cell and tissue spatial arrangement that takes place during embryonic development. Despite great advances in the genetic regulatory networks responsible for tissue and organ development, it is not yet clearly understood how specific gene functions are linked to the specific morphogenetic processes underlying the internal organ asymmetries found in vertebrate animals. During female chick embryogenesis, and in contrast to males where both testes develop symmetrically, asymmetrical gonad morphogenesis results in only one functional ovary. The disposition of paired organs along the left–right body axis has been shown to be regulated by the activity of the homeobox containing gene
pitx2
. We have found that
pitx2
regulates cell adhesion, affinity, and cell recognition events in the developing gonad primordium epithelia. This in turn not only allows for proper somatic development of the gonad cortex but also permits the proliferation and differentiation of primordial germ cells. We illustrate how Pitx2 activity directs asymmetrical gonad morphogenesis by controlling mitotic spindle orientation of the developing gonad cortex and how, by modulating
cyclinD1
expression during asymmetric ovarian development, Pitx2 appears to control gonad organ size. All together our observations indicate that the effects elicited by Pitx2 during the development of the female chick ovary are critical for cell topology, growth, fate, and ultimately organ morphogenesis and function.
The
Fezf2–Ctip2
genetic pathway regulates the fate choice of subcortical projection neurons in the developing cerebral cortex
Authors: Chen Bin , Wang Song S. , Hattox Alexis M. , Rayburn Helen , Nelson Sacha B. , McConnell Susan K.
Published: August 2008

Pyramidal neurons in the deep layers of the cerebral cortex can be classified into two major classes: callosal projection neurons and long-range subcortical neurons. We and others have shown that a gene expressed specifically by subcortical projection neurons,
Fezf2
, is required for the formation of axonal projections to the spinal cord, tectum, and pons. Here, we report that
Fezf2
regulates a decision between subcortical vs. callosal projection neuron fates.
Fezf2
−/−
neurons adopt the fate of callosal projection neurons as assessed by their axonal projections, electrophysiological properties, and acquisition of Satb2 expression.
Ctip2
is a major downstream effector of
Fezf2
in regulating the extension of axons toward subcortical targets and can rescue the axonal phenotype of
Fezf2
mutants. When ectopically expressed, either
Fezf2
or
Ctip2
can alter the axonal targeting of corticocortical projection neurons and cause them to project to subcortical targets, although
Fezf2
can promote a subcortical projection neuron fate in the absence of Ctip2 expression.