bluuebunny/crossref_metadata_2025 huggingface dataset:
Interleukin‐1β, clinical parameters and matched cellular‐histopathologic changes of biopsied gingival tissue from periodontitis patients
Authors: Hou Lein‐Tuan , Liu Cheing‐Meei , Liu Bu‐Yuan , Lin Shih‐Jung , Liao Chia‐Shih , Rossomando Edward F.
Published: September 2009

Objective:  The aim of the present study was to investigate whether interleukin (IL)‐1β in diseased tissues adjacent to periodontal pockets can reflect the degree of inflammation and destruction of these tissues pathologically.

Background:  IL‐1β‐dependent mechanisms have been strongly implicated in contributing to inflammation and destruction of bone and attachment loss, which are characteristic features of periodontal disease. This biochemical mediator released during pro‐inflammatory processes has not been objectively integrated with clinical and histopathologic features of periodontal disease.

Methods:  Periodontitis‐affected inflamed tissue and clinically nonaffected healthy gingivae were harvested from 14 periodontal patients, respectively. The severity of tissue inflammation was illustrated by clinical parameters and cellular histologic changes and quantified by histometric assessments. IL‐1β in these extracted specimens was measured with an enzyme‐linked immunosorbent assay (ELISA) technique. Pathogenic roles that IL‐1β plays in gingival inflammation and pathologic tissue changes in tissue sections were analyzed statistically.

Results:  The overall total tissue IL‐1β, tissue concentration of IL‐1β, and percentage of inflammatory cell infiltration (PICI) determined from diseased gingivae were obviously higher than those of controls from both healthy sites of periodontitis and non‐periodontitis subjects. With increasing gingival index (GI), plaque index (PlI), and probing depth (PD), there was a marked elevation in total tissue IL‐1β. Total tissue IL‐1β was significantly correlated with GI, PlI, the PICI, and tissue alterations. Polymorphonuclear leukocytes (PMNs) and monocyte‐macrophage cells seemed to predominate in heavily infiltrated areas of diseased gingiva. These cell types were confirmed by immunocytochemical localization with either monoclonal mouse antihuman neutrophil elastase antibody or monoclonal mouse antihuman macrophage (CD68) antibody, respectively. Total tissue IL‐1β and the PICI were also elevated in diseased gingivae near deeper PD, while neither total IL‐1β nor tissue concentration was statistically correlated with PD. Thus, correlation analysis indicates that IL‐1β level in inflamed periodontal tissues correlates highly with clinical parameters (GI and PlI) and PICI (the degree of inflammation).

Conclusions:  These observations suggest that IL‐1β plays a significant role in the pathogenic mechanisms of periodontal tissue destruction, and that measurement of tissue IL‐1β would be a valuable aid and useful for diagnostic markers of periodontal diseases.
Field dependences of the magnetization and exchange bias in ferro/antiferromagnetic systems. II. Continuum model of a ferromagnetic layer
Authors: Grechnev A. G. , Kovalev A. S. , Pankratova M. L.
Published: September 2009

A model giving a qualitative explanation of the results of an experimental investigation of the field dependences of the magnetization in ferro- and antiferromagnetic media in contact with one another is proposed. In this model a thin ferromagnetic (FM) film with strong easy-plane anisotropy is described in the continuum approximation. It is shown that collinear and canted structures of the ferromagnetic layer can co-exist in the system studied. The ranges of the parameters (exchange interactions in the FM layer and through the FM/AFM interface, thickness of the FM layer, and magnitude of the external magnetic field) where a nonuniform state of the FM exists are found and explicit analytic expressions are obtained for the distribution of the magnetization in this state. The dependences of the total magnetization of the system on the magnitude of the external field are constructed in the physically important cases of “thin” and “thick” FM layers, and it is demonstrated that the experimentally observed unsymmetric dependence M(H) is possible. The results of the present work are compared with our previous results obtained using simpler model of a two-layer FM subsystem.
Electron-phonon interaction function in the layered dichalcogenide 2Ha-TaSe2
Authors: Kamarchuk G. V. , Khotkevich A. V. , Savitskiĭ A. V. , Molinié P. , Leblanc A. , Faulques E.
Published: September 2009

Point-contact spectroscopy is used to investigate experimentally the electron-phonon interaction spectrum in the layered quasi-two-dimensional dichalcogenide 2Ha-TaSe2. The measurements are performed on 2Ha-TaSe2∕Cu heterocontacts. The point-contact spectra reflecting the effects of the electron-phonon interaction are recorded in the spectral regime of current flow and delocalization of the electronic states near point contacts for small momentum free-path lengths of electrons. The electron-phonon interaction function in this compound is determined for the first time. Calculations of important integral parameters of the electron-phonon system of the experimental material confirm the good reproducibility of the results.
Evolution and collapse of quasistationary states of an electron in planar symmetric three-barrier resonance-tunneling structures
Authors: Tkach N. V. , Seti Yu. A.
Published: September 2009

A theory of the evolution and collapse of pairs of resonances because of a change in the strength (thickness) of the inner barrier is developed in a model of effective masses and symmetric, square, potential barriers for an electron in a planar three-barrier structure. Analytical and numerical calculations of the spectral parameters (resonance energies and widths) are performed by the transmission coefficient and probability distribution function method using the transfer and S matrices. It is shown that the collapse of the resonance energies and widths of all quasistationary states in a symmetric three-barrier structure occurs for practically the same thicknesses of the inner barriers, somewhat greater than the total thickness of the outer barriers. It is established that with respect to the square-barrier model the δ model overestimates the resonance energies by 10% and the resonance widths by almost a factor of 2.
Hall effect and magnetic ordering in RB12
Authors: Baranovskiy A. E. , Grechnev G. E. , Shitsevalova N. Yu. , Sluchanko D. N. , Glushkov V. V. , Demishev S. V. , Sluchanko N. E.
Published: September 2009

The concentration of carriers in LuB12 is evaluated theoretically by applying ab initio FP-LMTO calculations. Theoretical results are found to be in agreement with high-precision measurements of the Hall coefficient RH(T) carried out on single crystals of the rare-earth dodecaborides RB12 (R=Ho,Er,Tm,Lu) at temperatures 1.8–300K. The nature of the antiferromagnetic ordering in RB12 is investigated within an RKKY-like model supplemented by comprehensive electronic structure calculations for paramagnetic, ferromagnetic, and antiferromagnetic phases.
Structure and time-resolved phosphorescence spectra of crystalline and glassy 2-bromobenzophenone
Authors: Pyshkin O. S. , Buravtseva L. M. , Romashkin R. V. , Strzhemechny M. A. , Zloba D. I. , Baumer V. N.
Published: September 2009

Microsecond-level time-resolved photoluminescence spectra of 2-bromobenzophenone are measured on crystalline (at 1.6, 52, and 300K) and glassy (at 1.6 and 95K) samples. For each of these physical situations the characteristic decay times are determined for the 0–0 band of monomer emission from metastable (blue 0–0 band) and global (red 0–0 band) excited states of the 2-benzophenone molecule in the crystal and also for the bimolecular excimer emission. The time dependence of the intensity of the red 0–0 band at 52K in the crystal is found to be nonmonotonic, a fact that provides yet another beautiful demonstration of the presence of two excited states and is indicative of thermally activated nonradiative transitions from the metastable excited state to the global. The corresponding kinetics is well described by a system of equations for joint radiative decay. To gain a better understanding of the nature of the anomalies of the phosphorescence, the crystal and molecular structures of 2-benzophenone at 100 and 200K are determined by the single-crystal x-ray diffraction method. Within the temperature interval 100–300K the crystal structure of 2-benzophenone remains monoclinic, with symmetry space group P21∕a (Z=4). The coefficient of linear thermal expansion is anisotropic and of a magnitude (10−5−10−4K−1) typical for organic molecular crystals. The conformation parameters of the molecule vary relatively strongly with temperature; the behavior of the C–Br and C=O bonds is most interesting: they become shorter with increasing temperature, possibly indicating a weakening of the weak hydrogen bonds of the peripheral oxidizer atoms with the acceptors of the neighboring molecules.
Quasi-two-dimensional features in the phonon spectrum of graphite
Authors: Gospodarev I. A. , Kravchenko K. V. , Syrkin E. S. , Feodos’ev S. B.
Published: September 2009

The phonon spectrum of graphite is analyzed in detail at the microscopic level and the partial contributions from the displacement of atoms in and perpendicular to the plane of the layers to the phonon density of states are calculated. The main distinctive features of the phonon spectrum of graphite are determined; they are due to the quasi-two-dimensional character of phonon propagation as is characteristic for graphite, specifically, the feature arising in the spectral density as a result of the displacement of atoms along the c axis, analogous to the Dirac singularity in the electron spectrum of graphene. This makes it possible to predict the general changes occurring in the phonon and electron spectra as a result of the intercalation of different metals in graphite as well as to explain the change of the superconducting transition temperature in intercalated graphite.
Time-dependent density functional theory study of cobalt corrinoids: Electronically excited states of coenzyme B12
Authors: Andruniów Tadeusz , Jaworska Maria , Lodowski Piotr , Zgierski Marek Z. , Dreos Renata , Randaccio Lucio , Kozlowski Pawel M.
Published: September 2009

The analysis of the electronic spectra of adenosylcobalamin (AdoCbl) and its derivative in which the trans axial base was replaced by a water molecule (AdoCbi–H2O) has been performed by means of time-dependent density functional theory (TDDFT). The latter corresponds to the situation encountered in strongly acidic conditions. The TDDFT electronic transitions and oscillator strengths were calculated at the optimized B3LYP and BP86 ground state equilibrium geometries. A comparison of the orbital energy diagrams obtained with the B3LYP and BP86 functionals reveals a different orbital order and composition of the highest occupied and lowest unoccupied molecular orbitals. In B3LYP the lowest-energy transitions are of π∕d→π*, π∕d→σ*, and π∕d→d characters while in the case of BP86 they are mainly d∕π→π* and d→π*. The long range charge transfer transitions involving excitations from adenine π orbitals to antibonding corrin π* orbital can be observed at low energies, especially in BP86 results. Calculated electronic excitations were used to simulate the absorption spectra for a direct comparison with the absorption spectra recorded for AdoCbl at different pH values. As previously found for methylcobalamin [see Andruniów et al., J. Chem. Phys. 129, 085101 (2008)] also for AdoCbl the two-parameter scaling technique is required to obtain a satisfactory agreement between theoretical and experimental spectra. Both functionals correctly predict the shifting of the lowest intense transition toward blue by approximately 13nm upon changing pH from 7 to 1.
Landau and non-Landau linear damping: Physics of the dissipation
Authors: Chust T. , Belmont G. , Mottez F. , Hess S.
Published: September 2009

For linear Langmuir waves, it is well known that the energy exchanges generally lead to a continuous dissipation, on average, from the electric form to the kinetic one. Many papers have estimated these exchanges and indeed shown that the classical Landau value γL, characterizing the electric field damping, can be derived from this estimation. The paper comes back to this demonstration and its implicit assumption of “forgetting the initial conditions.” The limits of the usual energy calculations have become much apparent recently when non-Landau solutions, decreasing with damping rates smaller than γL, have been evidenced [Belmont et al., Phys. Plasmas 15, 052310 (2008)]. Taking advantage of the explicit form provided in this paper for the perturbed distribution function, the dissipation process is revisited here in a more general way. It is shown that the energy calculations, when complete (i.e., when the role of the initial conditions is not excluded by the very hypotheses of the calculations), are indeed in full agreement with the existence of non-Landau solutions; Landau damping, by the way, appears as a particular mode of dissipation, in which the ballistic transport of the initial plasma perturbation leads to negligible effects. Two approaches are presented for this demonstration, Eulerian and Lagrangian, the first one starting from the Vlasov equation and the second from the dynamics of the individual particles. The specific role of the so-called resonant particles is investigated in both formalisms, which provides complementary pictures of the microphysics involved in the energy transfers between field and particles for Landau as well as for non-Landau solutions.
Surface acoustic wave propagation in Y- and Z-cut 0.67PbMgNbO3–0.33PbTiO3 single crystals
Authors: Li Xiuming , Zhang Rui , Huang Naixing , Lü Tianquan , Cao Wenwu
Published: September 2009

Surface acoustic wave (SAW) propogation in Y-cut and Z-cut relaxor-based 0.67Pb(Mg1/3Nb2/3)O3–0.33PbTiO3 (PMN-33%PT) ferroelectric single crystals poled along [001]c cubic direction has been analyzed theoretically. Characteristic curves were obtained for the phase velocity, electromechanical coupling coefficient and PFA of SAW in Y-cut and Z-cut PMN-33%PT single crystals. It was found that the phase velocity is lower, while the electromechanical coupling coefficient is much higher, than that of traditional piezoelectric materials. The power flow angle (PFA) can be zero in certain directions, which makes this crystal system a promising material for future SAW devices with smaller size and enhanced performance. The directions near 45° and 135° of Y-cut PMN-33%PT crystals are found to be optimum directions for SAW device applications.
Dynamic charge transfer effects in two-dimensional silicon nanocrystal layers embedded within SiO2
Authors: Ioannou-Sougleridis V. , Nassiopoulou A. G.
Published: September 2009

In this work, we study two distinct electrical behaviors, which are often observed in Si nanocrystal memory gate stacks: the transient peak of the current-voltage characteristics and the frequency dependence of the admittance characteristics at strong accumulation. These effects are manifestations of a high electrical transparency tunnel oxide in conjunction with a good quality control oxide. The high electrical transparency tunnel oxide results from hydrogen-related defects that are formed within it during the high temperature processing steps and promotes the electrical communication between the silicon substrate and the silicon nanocrystal layer at low electric fields, while no significant charge transfer is observed at low voltages between the silicon nanocrystals and the gate electrode. These conditions favor the electrical charging/discharging of the silicon nanocrystal layer via the trap-assisted tunneling mechanism and to the appearance of electrostatic screening effects. These dynamic phenomena appear either as a displacement current peak at the onset of accumulation or as frequency dependent admittance characteristics at strong accumulation.
A silicon photomultiplier readout for time of flight neutron spectroscopy with γ-ray detectors
Authors: Pietropaolo A. , Gorini G. , Festa G. , Andreani C. , De Pascale M. P. , Reali E. , Grazzi F. , Schooneveld E. M.
Published: September 2009

The silicon photomultiplier (SiPM) is a recently developed photosensor used in particle physics, e.g., for detection of minimum ionizing particles and/or Cherenkov radiation. Its performance is comparable to that of photomultiplier tubes, but with advantages in terms of reduced volume and magnetic field insensitivity. In the present study, the performance of a gamma ray detector made of an yttrium aluminum perovskite scintillation crystal and a SiPM-based readout is assessed for use in time of flight neutron spectroscopy. Measurements performed at the ISIS pulsed neutron source demonstrate the feasibility of γ-detection based on the new device.
Rapid and reversible hydrogen sorption in Mg–Fe–Ti thin films
Authors: Zahiri Beniamin , Harrower Chris T. , Shalchi Amirkhiz Babak , Mitlin David
Published: September 2009

This study focused on hydrogen sorption properties of 1.5 μm thick Mg–10 at. % Fe–10 Ti, Mg–15 at. % Fe–15 Ti, and Mg–20 at. % Fe–20 Ti films. We show that the alloys display remarkable sorption behavior: At 200 °C the films are capable of absorbing nearly 5 wt % hydrogen in seconds and desorbing in minutes. Furthermore this sorption behavior is stable over cycling. In the Mg–15 at. % Fe–15 Ti alloy there is no kinetic or capacity degradation even after 100 absorption/desorption cycles. Pressure–composition isotherm data for Mg–10 at. % Fe–10 Ti indicates that the sorption enhancement is due to improved kinetics rather than any altered thermodynamics. We envision these alloys as becoming the material of choice for a variety of sensing and storage applications.
Loading path and rate dependence of inelastic deformation: x-cut quartz
Authors: Root S. , Asay J. R.
Published: September 2009

Shockless compression experiments were performed on x-cut quartz single crystals to examine the effect of loading path and rate on the inelastic behavior. The Lagrangian wave velocity and stress were determined from the measured particle velocities and compared to the previously measured elastic values. The data show that x-cut quartz remains essentially elastic up to stresses greater than 10GPa during ramp loading, but that the elastic yield behavior is dependent on the sample thickness. These results indicate that the elastic response of x-cut quartz is dependent on the loading path, rate, and sample thickness.
Band alignment at the hybrid heterojunction between S-passivated III–V semiconductors and C60
Authors: Helander M. G. , Greiner M. T. , Wang Z. B. , Lu Z. H.
Published: September 2009

The interface between C60 and several commonly used S-passivated III–V semiconductors was studied using x-ray and ultraviolet photoelectron spectroscopy. It is found that the band alignment for S-passivated III–V semiconductors used in real devices differs significantly from that of in situ-prepared surfaces previously reported. The energy-level alignment is found to be nearly identical for the different III–V semiconductors. This phenomenon is explained by Fermi level pinning, which is consistent with interface dipole theory from traditional semiconductor device physics.
Determination of plasma velocity from light fluctuations in a cutting torch
Authors: Prevosto L. , Kelly H. , Mancinelli B.
Published: September 2009

Measurements of plasma velocities in a 30 A high energy density cutting torch are reported. The velocity diagnostic is based on the analysis of the light fluctuations emitted by the arc which are assumed to propagate with the flow velocity. These light fluctuations originate from plasma temperature and plasma density fluctuations mainly due to hydrodynamic instabilities. Fast photodiodes are employed as the light sensors. The arc core velocity was obtained from spectrally filtered light fluctuations measurements using a band-pass filter to detect light emission fluctuations emitted only from the arc axis. Maximum plasma jet velocities of 5000 m s−1 close to the nozzle exit and about 2000 m s−1 close to the anode were found. The obtained velocity values are in good agreement with those values predicted by a numerical code for a similar torch to that employed in this work.
One- and two-photon absorption in transition metal oxide glasses
Authors: El-Diasty Fouad , Abdel-Baki Manal
Published: September 2009

Scaling of nonlinear two-photon absorption to optical bandgap (which describes the electronic structure of material) in transition metal glasses is given through a proposed empirical equation. A wide applicability of the relation is proven through the 21 studied glasses. The relationship between the calculated nonlinear absorption coefficient and the measured bandgap energy using Tauc’s parabolic band model is discussed in terms of electronic structure of constituent oxides, ionic polarizability, hyperpolarizability of cations, nonbridging oxygen bonds, and the cationic bond-length approach.
Geometric bonding effects in the X A21, A Σ2u+, and B Π2g states of Li2F
Authors: Wright Kris W. A. , Rogers Daniel E. , Lane Ian C.
Published: September 2009

Published ab initio and pseudopotential calculations for the dialkali halide systems suggest that the preferred colinear geometry is for the metal to approach the metal end of the alkali halide. Here, ab initio calculations on the Li2F system reveal that the well depth on the halide side in this radical is much deeper and is a local saddle point associated with the ionic nonlinear global minima. Although many features of the pseudopotential surfaces are confirmed, significant differences are apparent including the existence of a linear excited A Σ2u+ state instead of a triangular one, a considerably deeper global minimum some 50% lower in energy and a close approach between the X A21 and the A Σ2u+ states, with the A Σ2u+ minimum 87 kJ mol−1 below the ground state asymptote. All the results can be rationalised as the avoided crossings between a long range, covalent potential dominant within the LiLiF geometry and an ionic state that forms the global minimum. Calculations on the third A2′ potential indicate that even for Li+LiF collisions at ultracold temperatures the collision dynamics could involve as many as three electronic states.
Highly efficient energy excitation transfer in light-harvesting complexes: The fundamental role of noise-assisted transport
Authors: Caruso F. , Chin A. W. , Datta A. , Huelga S. F. , Plenio M. B.
Published: September 2009

Excitation transfer through interacting systems plays an important role in many areas of physics, chemistry, and biology. The uncontrollable interaction of the transmission network with a noisy environment is usually assumed to deteriorate its transport capacity, especially so when the system is fundamentally quantum mechanical. Here we identify key mechanisms through which noise such as dephasing, perhaps counter intuitively, may actually aid transport through a dissipative network by opening up additional pathways for excitation transfer. We show that these are processes that lead to the inhibition of destructive interference and exploitation of line broadening effects. We illustrate how these mechanisms operate on a fully connected network by developing a powerful analytical technique that identifies the invariant (excitation trapping) subspaces of a given Hamiltonian. Finally, we show how these principles can explain the remarkable efficiency and robustness of excitation energy transfer from the light-harvesting chlorosomes to the bacterial reaction center in photosynthetic complexes and present a numerical analysis of excitation transport across the Fenna–Matthew–Olson complex together with a brief analysis of its entanglement properties. Our results show that, in general, it is the careful interplay of quantum mechanical features and the unavoidable environmental noise that will lead to an optimal system performance.
Spiral instabilities in media supporting complex oscillations under periodic forcing
Authors: Gao Qingyu , Li Jun , Zhang Kailong , Epstein Irving R.
Published: September 2009

The periodically forced Brusselator model displays temporal mixed-mode and quasiperiodic oscillations, period doubling, and chaos. We explore the behavior of such media as reaction-diffusion systems for investigating spiral instabilities. Besides near-core breakup and far-field breakup resulting from unstable modes in the radial direction or Doppler-induced instability (destabilization of the core’s location), the observed complex phenomena include backfiring, spiral regeneration, and amplitude modulation from line defects. Amplitude modulation of spirals can evolve to chambered spirals resembling those found in nature, such as pine cones and sunflowers. When the forcing amplitude is increased, the spiral-tip meander evolves from simple rotation to complex petals, corresponding to transformation of the local dynamics from simple oscillations to mixed-mode, period-2, and quasiperiodic oscillations. The number of petals is related to the complexity of the mixed-mode oscillations. Spiral turbulence, standing waves, and homogeneous synchronization permeate the entire system when the forcing amplitude is further increased.
Photodetachment, photofragmentation, and fragment autodetachment of [O2n(H2O)m]− clusters: Core-anion structures and fragment energy partitioning
Authors: Goebbert Daniel J. , Sanov Andrei
Published: September 2009

Building on the past studies of the O2n− and O2−(H2O)m cluster anion series, we assess the effect of the strong hydration interactions on the oxygen-core clusters using photoelectron imaging and photofragment mass spectroscopy of [O2n(H2O)m]− (n=1–4, m=0–3) at 355 nm. The results show that both pure-oxygen and hydrated clusters with n≥2 form an O4− core anion, indicated in the past work on the pure-oxygen clusters. All clusters studied can be therefore described in terms of O4−(H2O)m(O2)n−2 structures, although the O4− core may be strongly perturbed by hydration in some of these clusters. Fragmentation of these clusters yields predominantly O2− and O2−(H2O)l (l<m) anionic products. The low-electron kinetic energy O2− autodetachment features, prominent in the photoelectron images, signal that the fragments are vibrationally excited. The relative intensity of photoelectrons arising from O2− fragment autodetachment is used to shed light on the varying degree of fragment excitation resulting from the cluster fragmentation process depending on the solvent conditions.
Packaging-ejection phase transitions of a polymer chain: Theory and Monte Carlo simulation
Authors: Matsuyama Akihiko , Yano Masato , Matsuda Akiyoshi
Published: September 2009

We theoretically study packaging-ejection phase transitions of a flexible polymer chain, translocating through a spherical cavity. Based on the Flory model for coil-globule transitions of a single flexible polymer, we derive the free energy of the polymer chain through a spherical cavity. Depending on the size of the cavity, the attractive interaction between the polymer and cavity, solvent quality, and the length of the polymer chain, we find continuous and discontinuous phase transitions between a packaged state and an ejected one of the polymer chain. These results suggest a possibility of the control of DNA packing and ejection. We also perform a Monte Carlo simulation to confirm the theoretical results.
Experimental modeling of intergranular exchange coupling for perpendicular thin film media
Authors: Sokalski Vincent , Laughlin David E. , Zhu Jian-Gang
Published: September 2009

We present an experimental model system that enables quantitative assessment of intergranular exchange coupling in CoCrPt-oxide perpendicular magnetic recording media. A thin film structure consisting of a high coercivity CoPt unicrystal layer and a lower coercivity CoPt layer separated by a thin oxide interlayer is used to model perpendicularly magnetized grains separated by oxide grain boundaries. Exchange coupling energy between the CoPt layers was obtained for SiOx, TiOx, and CrOx interlayers by measuring field shifts from the lower coercivity layer. Cr segregation in CoCrPt grains to grain boundaries is also modeled experimentally and found to significantly suppress exchange coupling.
Low-temperature fluid-phase behavior of ST2 water
Authors: Liu Yang , Panagiotopoulos Athanassios Z. , Debenedetti Pablo G.
Published: September 2009

We perform histogram-reweighting Monte Carlo simulations of the ST2 model of water in the grand-canonical ensemble in order to investigate its low-temperature fluid-phase behavior. Using Ewald summation treatment of long-range electrostatic interactions, we locate the critical point of the liquid-liquid transition at T=237±4 K, ρ=0.99±0.02 g/cc, P=167±24 MPa. Contrary to previous reports in the literature [Brovchenko et al., J. Chem. Phys. 118, 9473 (2003); Brovchenko et al., J. Chem. Phys. 123, 044515 (2005)], according to which there are three liquid-liquid transitions in ST2 with simple truncation of electrostatic interactions, and two in ST2 with reaction field treatment of long-range Coulombic forces, we find only one liquid-liquid transition. Our work points to the sensitivity of results to the proper treatment of electrostatic interactions, and to the introduction of artificial constraints that limit the magnitude of density fluctuations.
Profiling protein thiol oxidation in tumor cells using sulfenic acid-specific antibodies
Authors: Seo Young Ho , Carroll Kate S.
Published: September 2009

Hydrogen peroxide (H
2
O
2
) functions as a second messenger that can activate cell proliferation through chemoselective oxidation of cysteine residues in signaling proteins. The connection between H
2
O
2
signaling, thiol oxidation, and activation of growth pathways has emerged as fertile ground for the development of strategies for cancer treatment. Central to achieving this goal is the development of tools and assays that facilitate characterization of the molecular events associated with tumorigenesis and evaluation of patient response to therapy. Here we report on the development of an immunochemical method for detecting sulfenic acid, the initial oxidation product that results when a thiolate reacts with H
2
O
2
. For this approach, the sulfenic acid is derivatized with a chemical tag to generate a unique epitope for recognition. The elicited antibody is exquisitely specific, context-independent, and capable of visualizing sulfenic acid formation in cells. Applying this approach to several systems, including cancer cell lines, shows it can be used to monitor differences in thiol redox status and reveals a diverse pattern of sulfenic acid modifications across different subtypes of breast tumors. These studies demonstrate a general strategy for producing antibodies against a specific oxidation state of cysteine and show the utility of these reagents for profiling thiol oxidation associated with pathological conditions such as breast cancer.
The cytochrome

ba
3

oxygen reductase from
Thermus thermophilus
uses a single input channel for proton delivery to the active site and for proton pumping
Authors: Chang Hsin-Yang , Hemp James , Chen Ying , Fee James A. , Gennis Robert B.
Published: September 2009

The heme-copper oxygen reductases are redox-driven proton pumps that generate a proton motive force in both prokaryotes and mitochondria. These enzymes have been divided into 3 evolutionarily related groups: the A-, B- and C-families. Most experimental work on proton-pumping mechanisms has been performed with members of the A-family. These enzymes require 2 proton input pathways (D- and K-channels) to transfer protons used for oxygen reduction chemistry and for proton pumping, with the D-channel transporting all pumped protons. In this work we use site-directed mutagenesis to demonstrate that the

ba
3

oxygen reductase from
Thermus thermophilus
, a representative of the B-family, does not contain a D-channel. Rather, it utilizes only 1 proton input channel, analogous to that of the A-family K-channel, and it delivers protons to the active site for both O
2
chemistry and proton pumping. Comparison of available subunit I sequences reveals that the only structural elements conserved within the oxygen reductase families that could perform these functions are active-site components, namely the covalently linked histidine-tyrosine, the Cu
B
and its ligands, and the active-site heme and its ligands. Therefore, our data suggest that all oxygen reductases perform the same chemical reactions for oxygen reduction and comprise the essential elements of the proton-pumping mechanism (e.g., the proton-loading and kinetic-gating sites). These sites, however, cannot be located within the D-channel. These results along with structural considerations point to the A-propionate region of the active-site heme and surrounding water molecules as the proton-loading site.
Ubiquitination of histone H2B regulates chromatin dynamics by enhancing nucleosome stability
Authors: Chandrasekharan Mahesh B. , Huang Fu , Sun Zu-Wen
Published: September 2009

The mechanism by which ubiquitination of histone H2B (H2Bub1) regulates H3-K4 and -K79 methylation and the histone H2A-H2B chaperone Spt16-mediated nucleosome dynamics during transcription is not fully understood. Upon investigating the effect of H2Bub1 on chromatin structure, we find that contrary to the supposed role for H2Bub1 in opening up chromatin, it is important for nucleosome stability. First, we show that H2Bub1 does not function as a “wedge” to non-specifically unfold chromatin, as replacement of ubiquitin with a bulkier SUMO molecule conjugated to the C-terminal helix of H2B cannot functionally support H3-K4 and -K79 methylation. Second, using a series of biochemical analyses, we demonstrate that nucleosome stability is reduced or enhanced, when the levels of H2Bub1 are abolished or increased, respectively. Besides transcription elongation, we show that H2Bub1 regulates initiation by stabilizing nucleosomes positioned over the promoters of repressed genes. Collectively, our study reveals an intrinsic difference in the property of chromatin assembled in the presence or absence of H2Bub1 and implicates the regulation of nucleosome stability as the mechanism by which H2Bub1 modulates nucleosome dynamics and histone methylation during transcription.
Overview of the Alcator C-Mod Research Program
Authors: Marmar E. , Bader A. , Bakhtiari M. , Barnard H. , Beck W. , Bespamyatnov I. , Binus A. , Bonoli P. , Bose B. , Bitter M. , Cziegler I. , Dekow G. , Dominguez A. , Duval B. , Edlund E. , Ernst D. , Ferrara M. , Fiore C. , Fredian T. , Graf A. , Granetz R. , Greenwald M. , Grulke O. , Gwinn D. , Harrison S. , Harvey R. , Hender T.C. , Hosea J. , Hill K. , Howard N. , Howell D.F. , Hubbard A. , Hughes J.W. , Hutchinson I. , Ince-Cushman A. , Irby J. , Izzo V. , Kanojia A. , Kessel C. , Ko J.S. , Koert P. , LaBombard B. , Lau C. , Lin L. , Lin Y. , Lipschultz B. , Liptac J. , Ma Y. , Marr K. , May M. , McDermott R. , Meneghini O. , Mikkelsen D. , Ochoukov R. , Parker R. , Phillips C.K. , Phillips P. , Podpaly Y. , Porkolab M. , Reinke M. , Rice J. , Rowan W. , Scott S. , Schmidt A. , Sears J. , Shiraiwa S. , Sips A. , Smick N. , Snipes J. , Stillerman J. , Takase Y. , Terry D. , Terry J. , Tsujii N. , Valeo E. , Vieira R. , Wallace G. , Whyte D. , Wilson J.R. , Wolfe S. , Wright G. , Wright J. , Wukitch S. , Wurden G. , Xu P. , Zhurovich K. , Zaks J. , Zweben S.
Published: September 2009

This paper summarizes highlights of research results from the Alcator C-Mod tokamak covering the period 2006–2008. Active flow drive, using mode converted ion cyclotron waves, has been observed for the first time in a tokamak plasma, using a mix of D and 3He ion species; toroidal and poloidal flows are driven near the location of the mode conversion layer. ICRF induced edge sheaths are implicated in both the erosion of thin boron coatings and the generation of metallic impurities. Lower hybrid range of frequencies (LHRF) microwaves have been used for efficient current drive, current profile modification and toroidal flow drive. In addition, LHRF has been used to modify the H-mode pedestal, increasing temperature, decreasing density and lowering the pedestal collisionality. Studies of hydrogen isotope retention in solid metallic plasma facing components reveal significantly higher retention than expected from ex situ laboratory studies; a model to explain the results, based on plasma/neutral induced lattice damage, has been developed and tested. During gas-puff mitigation of disruptions, induced MHD instabilities cause the magnetic field to become stochastic, resulting in reduction of halo currents, spreading of plasma power loading and loss of runaway electrons before they cause damage. Detailed pedestal rotation profile measurements have been used to infer E
r profiles, and correlation with global H-mode confinement. An improved L-mode regime, obtained at q
95 ⩽ 3 with ion drift away from the active X-point, shows very good energy confinement with a strong temperature pedestal, a weak density pedestal, and no evidence of particle or impurity accumulation, without the need for ELMs or any additional edge density regulation mechanism.
Development of net-current free heliotron plasmas in the Large Helical Device
Authors: Komori A. , Yamada H. , Sakakibara S. , Kaneko O. , Kawahata K. , Mutoh T. , Ohyabu N. , Imagawa S. , Ida K. , Nagayama Y. , Shimozuma T. , Watanabe K.Y. , Mito T. , Kobayashi M. , Nagaoka K. , Sakamoto R. , Yoshida N. , Ohdachi S. , Ashikawa N. , Feng Y. , Fukuda T. , Igami H. , Inagaki S. , Kasahara H. , Kubo S. , Kumazawa R. , Mitarai O. , Murakami S. , Nakamura Yuji , Nishiura M. , Hino T. , Masuzaki S. , Tanaka K. , Toi K. , Weller A. , Yoshinuma M. , Narushima Y. , Ohno N. , Okamura T. , Tamura N. , Saito K. , Seki T. , Sudo S. , Tanaka H. , Tokuzawa T. , Yanagi N. , Yokoyama M. , Yoshimura Y. , Akiyama T. , Chikaraishi H. , Chowdhuri M. , Emoto M. , Ezumi N. , Funaba H. , Garcia L. , Goncharov P. , Goto M. , Ichiguchi K. , Ichimura M. , Idei H. , Ido T. , Iio S. , Ikeda K. , Irie M. , Isayama A. , Ishigooka T. , Isobe M. , Ito T. , Itoh K. , Iwamae A. , Hamaguchi S. , Hamajima T. , Kitajima S. , Kado S. , Kato D. , Kato T. , Kobayashi S. , Kondo K. , Masamune S. , Matsumoto Y. , Matsunami N. , Minami T. , Michael C. , Miura H. , Miyazawa J. , Mizuguchi N. , Morisaki T. , Morita S. , Motojima G. , Murakami I. , Muto S. , Nagasaki K. , Nakajima N. , Nakamura Y. , Nakanishi H. , Nakano H. , Narihara K. , Nishimura A. , Nishimura H. , Nishimura K. , Nishimura S. , Nishino N. , Notake T. , Obana T. , Ogawa K. , Oka Y. , Ohishi T. , Okada H. , Okuno K. , Ono K. , Osakabe M. , Osako T. , Ozaki T. , Peterson B.J. , Sakaue H. , Sasao M. , Satake S. , Sato K. , Sato M. , Shimizu A. , Shiratani M. , Shoji M. , Sugama H. , Suzuki C. , Suzuki Y. , Takahata K. , Takahashi H. , Takase Y. , Takeiri Y. , Takenaga H. , Toda S. , Todo Y. , Tokitani M. , Tsuchiya H. , Tsumori K. , Urano H. , Veshchev E. , Watanabe F. , Watanabe T. , Watanabe T.H. , Yamada I. , Yamada S. , Yamagishi O. , Yamaguchi S. , Yoshimura S. , Yoshinaga T. , Motojima O.
Published: September 2009

Remarkable progress in the physical parameters of net-current free plasmas has been made in the Large Helical Device (LHD) since the last Fusion Energy Conference in Chengdu, 2006 (Motojima et al
2007 Nucl. Fusion
47 S668). The beta value reached 5% and a high-beta state beyond 4.5% from the diamagnetic measurement has been maintained for longer than 100 times the energy confinement time. The density and temperature regimes have also been extended. The central density has exceeded 1 × 1021 m−3 due to the formation of an internal diffusion barrier. The ion temperature has reached 5.2 keV at the density of 1.6 × 1019 m−3, which is associated with the suppression of ion heat conduction loss. Although these parameters have been obtained in separated discharges, each fusion-reactor relevant parameter has elucidated the potential of net-current free heliotron plasmas. Diversified studies in recent LHD experiments are reviewed in this paper.
Confinement transitions in TJ-II under Li-coated wall conditions
Authors: Sánchez J. , Acedo M. , Alonso A. , Alonso J. , Alvarez P. , Ascasíbar E. , Baciero A. , Balbín R. , Barrera L. , Blanco E. , Botija J. , de Bustos A. , de la Cal E. , Calvo I. , Cappa A. , Carmona J.M. , Carralero D. , Carrasco R. , Carreras B.A. , Castejón F. , Castro R. , Catalán G. , Chmyga A.A. , Chamorro M. , Eliseev L. , Esteban L. , Estrada T. , Fernández A. , Fernández-Gavilán R. , Ferreira J.A. , Fontdecaba J.M. , Fuentes C. , García L. , García-Cortés I. , García-Gómez R. , García-Regaña J.M. , Guasp J. , Guimarais L. , Happel T. , Hernanz J. , Herranz J. , Hidalgo C. , Jiménez J.A. , Jiménez-Denche A. , Jiménez-Gómez R. , Jiménez-Rey D. , Kirpitchev I. , Komarov A.D. , Kozachok A.S. , Krupnik L. , Lapayese F. , Liniers M. , López-Bruna D. , López-Fraguas A. , López-Rázola J. , López-Sánchez A. , Lysenko S. , Marcon G. , Martín F. , Maurin V. , McCarthy K.J. , Medina F. , Medrano M. , Melnikov A.V. , Méndez P. , van Milligen B. , Mirones E. , Nedzelskiy I.S. , Ochando M. , Olivares J. , de Pablos J.L. , Pacios L. , Pastor I. , Pedrosa M.A. , de la Peña A. , Pereira A. , Pérez G. , Pérez-Risco D. , Petrov A. , Petrov S. , Portas A. , Pretty D. , Rapisarda D. , Rattá G. , Reynolds J.M. , Rincón E. , Ríos L. , Rodríguez C. , Romero J.A. , Ros A. , Salas A. , Sánchez M. , Sánchez E. , Sánchez-Sarabia E. , Sarksian K. , Sebastián J.A. , Silva C. , Schchepetov S. , Skvortsova N. , Solano E.R. , Soleto A. , Tabarés F. , Tafalla D. , Tarancón A. , Taschev Yu. , Tera J. , Tolkachev A. , Tribaldos V. , Vargas V.I. , Vega J. , Velasco G. , Velasco J.L. , Weber M. , Wolfers G. , Zurro B.
Published: September 2009

This paper presents the latest results on confinement studies in the TJ-II stellarator. The inherently strong plasma–wall interaction of TJ-II has been successfully reduced after lithium coating by vacuum evaporation. Besides H retention and low Z, Li was chosen because there exists a reactor-oriented interest in this element, thus giving special relevance to the investigation of its properties. The Li-coating has led to important changes in plasma performance. Particularly, the effective density limit in NBI plasmas has been extended reaching central values of 8 × 1019 m−3 and T
e ≈ 250–300 eV, with peaked density, rather flat T
e profiles and higher ion temperatures. Due to the achieved density control, a second type of transition has been added to the low density ones previously observed in ECRH plasmas: higher density transitions characterized by the fall in Hα emission, the onset of steep density gradient and the reduction in the turbulence; which are characteristics of transition to the H mode. Confinement studies in ECH plasmas indicate that lowest order magnetic resonances, even in a low shear environment, locally reduce the effective electron heat diffusivities, while Alfven eigenmodes destabilized in NBI plasmas can influence fast ion confinement.
Overview of RFX-mod results
Authors: Martin P. , Apolloni L. , Puiatti M.E. , Adamek J. , Agostini M. , Alfier A. , Annibaldi S.V. , Antoni V. , Auriemma F. , Barana O. , Baruzzo M. , Bettini P. , Bolzonella T. , Bonfiglio D. , Bonomo F. , Brombin M. , Brotankova J. , Buffa A. , Buratti P. , Canton A. , Cappello S. , Carraro L. , Cavazzana R. , Cavinato M. , Chapman B.E. , Chitarin G. , Dal Bello S. , De Lorenzi A. , De Masi G. , Escande D.F. , Fassina A. , Ferro A. , Franz P. , Gaio E. , Gazza E. , Giudicotti L. , Gnesotto F. , Gobbin M. , Grando L. , Guazzotto L. , Guo S.C. , Igochine V. , Innocente P. , Liu Y.Q. , Lorenzini R. , Luchetta A. , Manduchi G. , Marchiori G. , Marcuzzi D. , Marrelli L. , Martini S. , Martines E. , McCollam K. , Menmuir S. , Milani F. , Moresco M. , Novello L. , Ortolani S. , Paccagnella R. , Pasqualotto R. , Peruzzo S. , Piovan R. , Piovesan P. , Piron L. , Pizzimenti A. , Pomaro N. , Predebon I. , Reusch J.A. , Rostagni G. , Rubinacci G. , Sarff J.S. , Sattin F. , Scarin P. , Serianni G. , Sonato P. , Spada E. , Soppelsa A. , Spagnolo S. , Spolaore M. , Spizzo G. , Taliercio C. , Terranova D. , Toigo V. , Valisa M. , Vianello N. , Villone F. , White R.B. , Yadikin D. , Zaccaria P. , Zamengo A. , Zanca P. , Zaniol B. , Zanotto L. , Zilli E. , Zohm H. , Zuin M.
Published: September 2009

With the exploration of the MA plasma current regime in up to 0.5 s long discharges, RFX-mod has opened new and very promising perspectives for the reversed field pinch (RFP) magnetic configuration, and has made significant progress in understanding and improving confinement and in controlling plasma stability. A big leap with respect to previous knowledge and expectations on RFP physics and performance has been made by RFX-mod since the last 2006 IAEA Fusion Energy Conference. A new self-organized helical equilibrium has been experimentally achieved (the Single Helical Axis—SHAx—state), which is the preferred state at high current. Strong core electron transport barriers characterize this regime, with electron temperature gradients comparable to those achieved in tokamaks, and by a factor of 4 improvement in confinement time with respect to the standard RFP. RFX-mod is also providing leading edge results on real-time feedback control of MHD instabilities, of general interest for the fusion community.
Recent fast electron energy transport experiments relevant to fast ignition inertial fusion
Authors: Norreys P.A. , Scott R.H.H. , Lancaster K.L. , Green J.S. , Robinson A.P.L. , Sherlock M. , Evans R.G. , Haines M.G. , Kar S. , Zepf M. , Key M.H. , King J. , Ma T. , Yabuuchi T. , Wei M.S. , Beg F.N. , Nilson P. , Theobald W. , Stephens R.B. , Valente J. , Davies J.R. , Takeda K. , Azechi H. , Nakatsutsumi M. , Tanimoto T. , Kodama R. , Tanaka K.A.
Published: September 2009

A number of experiments have been undertaken at the Rutherford Appleton Laboratory that were designed to investigate the physics of fast electron transport relevant to fast ignition inertial fusion. The laser, operating at a wavelength of 1054 nm, provided pulses of up to 350 J of energy on target in a duration that varied in the range 0.5–5 ps and a focused intensity of up to 1021 W cm−2. A dependence of the divergence of the fast electron beam with intensity on target has been identified for the first time. This dependence is reproduced in two-dimensional particle-in-cell simulations and has been found to be an intrinsic property of the laser–plasma interaction. A number of ideas to control the divergence of the fast electron beam are described. The fractional energy transfer to the fast electron beam has been obtained from calibrated, time-resolved, target rear-surface radiation temperature measurements. It is in the range 15–30%, increasing with incident laser energy on target. The fast electron temperature has been measured to be lower than the ponderomotive potential energy and is well described by Haines' relativistic absorption model.
Theory and observations of magnetic islands
Authors: Waelbroeck F.L.
Published: September 2009

Magnetic islands are a ubiquitous feature of magnetically confined plasmas. They arise as the result of plasma instabilities as well as externally imposed symmetry-breaking perturbations. In the core, effective suppression techniques have been developed. Even thin islands, however, are observed to have nonlocal effects on the profiles of rotation and current. This has stimulated interest in using magnetic islands to control plasma transport, particularly in the edge. They are also of interest as a tool to improve our understanding of microscopic plasma dynamics.
A life course approach to women’s reproductive health
Authors: Rich-Edwards Janet , Morton Susan
Published: September 2009

This chapter explores the emerging evidence that adult reproductive function is shaped by intergenerational, in utero, and childhood factors, as well as adult environment. It opens with a discussion of early life factors that shape women's reproductive health, with a focus on determinants of pregnancy outcome. It then presents evidence that the gynecological and obstetric health status of young women reveals latent chronic disease processes.