bluuebunny/crossref_metadata_2025 huggingface dataset:
Probabilistic identification of high‐frequency radar backscatter from the ground and ionosphere based on spectral characteristics
Authors: Blanchard G. T. , Sundeen S. , Baker K. B.
Published: October 2009

We present an analysis of the spectral characteristics of 1‐hop HF radar ground scatter and ‐ and 1‐hop ionospheric scatter as measured by the Super Dual Auroral Radar Network. Our objective is to determine criteria that separate signals scattered from the ground and the ionosphere. We find that for both ground scatter and ionospheric scatter that the probability density function of backscatter Doppler velocity decreases exponentially with velocity, but with significantly different e‐folding velocities for the two types of backscatter. We use this observation to separate the total probability density of Doppler velocity and spectral width into two component distributions. This process yields the posterior probability that a signal of given Doppler velocity and spectral width is ground scatter. The resulting criterion for classification of a particular signal as ground scatter, v < 33.1 m/s + 0.139w − (0.00133 s/m)w2, significantly reduces the probability that a signal will be erroneously classified as ionospheric scatter, while only moderately increasing the probability that an ionospheric scatter signal will be erroneously classified as ground scatter. Finally, we validate the ground scatter probability function by demonstrating that the backscatter virtual height increases as expected with increasing probability of ground scatter.
Structural basis for recognition of H3K4 methylation status by the DNA methyltransferase 3A ATRX–DNMT3–DNMT3L domain
Authors: Otani Junji , Nankumo Toshiyuki , Arita Kyohei , Inamoto Susumu , Ariyoshi Mariko , Shirakawa Masahiro
Published: October 2009

DNMT3 proteins are de novo DNA methyltransferases that are responsible for the establishment of DNA methylation patterns in mammalian genomes. Here, we have determined the crystal structures of the ATRX–DNMT3–DNMT3L (ADD) domain of DNMT3A in an unliganded form and in a complex with the amino‐terminal tail of histone H3. Combined with the results of biochemical analysis, the complex structure indicates that DNMT3A recognizes the unmethylated state of lysine 4 in histone H3. This finding indicates that the recruitment of DNMT3A onto chromatin, and thereby de novo DNA methylation, is mediated by recognition of the histone modification state by its ADD domain. Furthermore, our biochemical and nuclear magnetic resonance data show mutually exclusive binding of the ADD domain of DNMT3A and the chromodomain of heterochromatin protein 1α to the H3 tail. These results indicate that de novo DNA methylation by DNMT3A requires the alteration of chromatin structure.
Modifications of RNA polymerase II are pivotal in regulating gene expression states
Authors: Brookes Emily , Pombo Ana
Published: October 2009

The regulation of gene expression programmes is essential for the generation of diverse cell types during development and for adaptation to environmental signals. RNA polymerase II (RNAPII) transcribes genetic information and coordinates the recruitment of accessory proteins that are responsible for the establishment of active chromatin states and transcript maturation. RNAPII is post‐translationally modified at active genes during transcription initiation, elongation and termination, and thereby recruits specific histone and RNA modifiers. RNAPII complexes are also located at silent genes in promoter‐proximal paused configurations that provide dynamic transcriptional regulation downstream from initiation. In embryonic stem cells, silent developmental regulator genes that are repressed by Polycomb are associated with a form of RNAPII that can elongate through coding regions but that lacks the post‐translational modifications that are important for coupling RNA synthesis to co‐transcriptional maturation. Here, we discuss the mechanisms through which the transcription of silent genes might be dissociated from productive expression, and the sophisticated interplay between the transcriptional machinery, Polycomb repression and RNA processing.
Towards a small animal model for hepatitis C
Authors: Ploss Alexander , Rice Charles M.
Published: October 2009

Hepatitis C virus (HCV) causes chronic liver disease and affects an estimated 3% of the world's population. Options for the prevention or therapy of HCV infection are limited; there is no vaccine and the nonspecific, interferon‐based treatments now in use are frequently ineffective and have significant side effects. A small‐animal model for HCV infection would significantly expedite antiviral compound development and preclinical testing, as well as open new avenues to decipher the mechanisms that underlie viral pathogenesis. The natural species tropism of HCV is, however, limited to humans and chimpanzees. Here, we discuss the prospects of developing a mouse model for HCV infection, taking into consideration recent results on HCV entry and replication, and new prospects in xenotransplantation biology. We highlight three independent, but possibly complementary, approaches towards overcoming current species barriers and generating a small‐animal model for HCV pathogenesis.
Beyond us
Authors: Rull Valentí
Published: October 2009

Although humans have become the predominant species on Earth, it is not a given that they will remain so. Valentí Rull explores possible future scenarios for humanity and explains why we should investigate the future evolution of Homo sapiens using the tools of modern science.
Ten Simple Rules for Searching and Organizing the Scientific Literature
Authors: Bauer Denis
Published: October 2009

The exponentially increasing number of published papers (1.4 million per year by one estimate) makes it more and more difficult for us to manage the flood of scientific information. Each of us has acquired some protocol to find and organize journal articles and other references over the course of our careers. Most of those protocols are likely to have been formed by old routines or idleness rather than a structured approach to save time and frustration over the long run. Furthermore, with the Web 2.0 revolution, new ways of handling information are emerging (O’Reilly 2005). For example, traditional standalone tools for reference management like EndNote are being supplemented by centralized resources like RefWorks and social bookmarking sites as described subsequently. This fusion of personal and public information offers the promise of efficiency through better organization, which in turn leads to better science.How can seasoned scientists do better using these tools and those newer to the field start off in the right way? To start to answer that question, I present ten simple rules to master the search and organization of new literature. This is not meant to be comprehensive. It represents the experiences of a few and I welcome your thoughts, through comments to this article, on what you do to keep your references organized.
BioPortal: Ontologies and Integrated Data Resources at the Click of a Mouse
Authors: Whetzel Patricia , Shah Nigam , Noy Natalya , Dai Benjamin , Dorf Michael , Griffith Nicholas , Jonquet Clement , Youn Cherie , Coulet Adrien , Callendar Chris , Rubin Daniel , Smith Barry , Storey Margaret-Anne , Chute Christopher , Musen Mark
Published: October 2009

BioPortal ("http://bioportal.bioontology.org":http://bioportal.bioontology.org) is an open repository of biomedical ontologies that provides programmatic and web-based access to ontologies developed in OBO, OWL, Protégé frames, and RDF. Features include browsing, searching, and visualization of ontologies. Searching of integrated data resources is also possible through ontology-based indexing of biomedical resources with BioPortal ontologies.
Lyn-mediated mitochondrial tyrosine phosphorylation is required to preserve mitochondrial integrity in early liver regeneration
Authors: Gringeri Enrico , Carraro Amedeo , Tibaldi Elena , D'Amico Francesco E. , Mancon Mario , Toninello Antonio , Pagano Mario A. , Vio Claudia , Cillo Umberto , Brunati Anna M.
Published: October 2009

Functional alterations in mitochondria such as overproduction of ROS (reactive oxygen species) and overloading of calcium, with subsequent change in the membrane potential, are traditionally regarded as pro-apoptotic conditions. Although such events occur in the early phases of LR (liver regeneration) after two-thirds PH (partial hepatectomy), hepatocytes do not undergo apoptosis but continue to proliferate until the mass of the liver is restored. The aim of the present study was to establish whether tyrosine phosphorylation, an emerging mechanism of regulation of mitochondrial function, participates in the response to liver injury following PH and is involved in contrasting mitochondrial pro-apoptotic signalling. Mitochondrial tyrosine phosphorylation, negligible in the quiescent liver, was detected in the early phases of LR with a trend similar to the events heralding mitochondrial apoptosis and was attributed to the tyrosine kinase Lyn, a member of the Src family. Lyn was shown to accumulate in an active form in the mitochondrial intermembrane space, where it was found to be associated with a multiprotein complex. Our results highlight a role for tyrosine phosphorylation in accompanying, and ultimately counteracting, mitochondrial events otherwise leading to apoptosis, hence conveying information required to preserve the mitochondrial integrity during LR.
Hypoxia aggravates non-alcoholic steatohepatitis in mice lacking hepatocellular PTEN
Authors: Piguet Anne-Christine , Stroka Deborah , Zimmermann Arthur , Dufour Jean-François
Published: October 2009

The metabolic disorders that predispose patients to NASH (non-alcoholic steatohepatitis) include insulin resistance and obesity. Repeated hypoxic events, such as occur in obstructive sleep apnoea syndrome, have been designated as a risk factor in the progression of liver disease in such patients, but the mechanism is unclear, in particular the role of hypoxia. Therefore we studied the influence of hypoxia on the development and progression of steatohepatitis in an experimental mouse model. Mice with a hepatocellular-specific deficiency in the Pten (phosphatase and tensin homologue deleted on chromosome 10) gene, a tumour suppressor, were exposed to a 10% O2 (hypoxic) or 21% O2 (control) atmosphere for 7 days. Haematocrit, AST (aspartate aminotransferase), glucose, triacylglycerols (triglycerides) and insulin tolerance were measured in blood. Histological lesions were quantified. Expression of genes involved in lipogenesis and mitochondrial β-oxidation, as well as FOXO1 (forkhead box O1), hepcidin and CYP2E1 (cytochrome P450 2E1), were analysed by quantitative PCR. In the animals exposed to hypoxia, the haematocrit increased (60±3% compared with 50±2% in controls; P<0.01) and the ratio of liver weight/body weight increased (5.4±0.2% compared with 4.7±0.3% in the controls; P<0.01). Furthermore, in animals exposed to hypoxia, steatosis was more pronounced (P<0.01), and the NAS [NAFLD (non-alcoholic fatty liver disease) activity score] (8.3±2.4 compared with 2.3±10.7 in controls; P<0.01), serum AST, triacylglycerols and glucose were higher. Insulin sensitivity decreased in mice exposed to hypoxia relative to controls. The expression of the lipogenic genes SREBP-1c (sterol-regulatory-element-binding protein-1c), PPAR-γ (peroxisome-proliferator-activated receptor-γ), ACC1 (acetyl-CoA carboxylase 1) and ACC2 (acetyl-CoA carboxylase 2) increased significantly in mice exposed to hypoxia, whereas mitochondria β-oxidation genes [PPAR-α (peroxisome-proliferator-activated receptor-α) and CPT-1 (carnitine palmitoyltransferase-1)] decreased significantly. In conclusion, the findings of the present study demonstrate that hypoxia alone aggravates and accelerates the progression of NASH by up-regulating the expression of lipogenic genes, by down-regulating genes involved in lipid metabolism and by decreasing insulin sensitivity.
Analysis of generalized Forchheimer flows of compressible fluids in porous media
Authors: Aulisa Eugenio , Bloshanskaya Lidia , Hoang Luan , Ibragimov Akif
Published: October 2009

This work is focused on the analysis of nonlinear flows of slightly compressible fluids in porous media not adequately described by Darcy’s law. We study a class of generalized nonlinear momentum equations which covers all three well-known Forchheimer equations, the so-called two-term, power, and three-term laws. The generalized Forchheimer equation is inverted to a nonlinear Darcy equation with implicit permeability tensor depending on the pressure gradient. This results in a degenerate parabolic equation for the pressure. Two classes of boundary conditions are considered, given pressure and given total flux. In both cases they are allowed to be unbounded in time. The uniqueness, Lyapunov and asymptotic stabilities, and other long-time dynamical features of the corresponding initial boundary value problems are analyzed. The results obtained in this paper have clear hydrodynamic interpretations and can be used for quantitative evaluation of engineering parameters. Some numerical simulations are also included.
Collinear central configurations in the n-body problem with general homogeneous potential
Authors: Woodlin Mervin , Xie Zhifu
Published: October 2009

In this paper we investigate the central configurations of collinear n-body problem given by the general law of attraction of the form f(r)=1/rα. A method involving analysis skills of some elementary algebra and calculus is presented to study the central configurations in the collinear n-body problem. It is well known that for given n positive masses, there are precisely n!/2 collinear central configurations for Newton’s law of gravitation of α=2. However, it is not true that there is always a position that causes a central configuration for any given ordered particles with some positive masses and that there may exist more than one position that make it central for some α<0. We give a generalization of Moulton’s theorem for collinear n-body problem for all α>0. Examples that Moulton’s theorem does not work are also provided.
Deterministic fabrication of carbon nanotube probes using the dielectrophoretic assembly and electrical detection
Authors: Lim Donghyun , Kwon Soongeun , Lee Jonghyun , Shim Hyung Cheoul , Lee Hyung Woo , Kim Soohyun
Published: October 2009

We report the controlled dielectrophoretic assembly for the deterministic fabrication of carbon nanotube (CNT) probes. Electrical detection was applied to the dielectrophoretic assembly of CNT probes. Dielectrophoretic manipulation with an ac electric field of 5 MHz was used to form the CNT bridge across oppositely aligned tungsten tips (W-tips). A dc electric field was simultaneously applied to monitor the direct current flowing through the gap. The detected nanocurrent reveals that the CNT bridge is formed between W-tips in real time. We compared current data with bundle diameter of CNT probes in field emission scanning electron microscopy (FE-SEM) images. As the number of assembled CNTs increased, current was increased. With the obtained linear relationship, the number of the attached CNTs can be estimated without confirmation of the FE-SEM image. This combined use of the current detection method with dielectrophoretic manipulation will provide a reliable process for the fabrication of CNT probes.
Mechanisms of nonstoichiometry in HfN1−x
Authors: Ashley N. J. , Parfitt D. , Chroneos A. , Grimes R. W.
Published: October 2009

Density functional theory is used to calculate defect structures that can accommodate nonstoichiometry in hafnium nitride: HfN1−x, 0≤×≤0.25. It is predicted that a mechanism assuming simple distributions of nitrogen vacancies can accurately describe the variation in the experimentally observed lattice parameter with respect to the nitrogen nonstoichiometry. Although the lattice parameter changes are remarkably small across the whole nonstoichiometry range, the variations in the bulk modulus are much greater.
Sn doped (Cu0.5Tl0.5)Ba2Ca2Cu3−ySnyO10−δ superconductors: Effect on the diamagnetism and phonon modes
Authors: Firdous Tayyaba , Khan Nawazish A.
Published: October 2009

Sn doped (Cu0.5Tl0.5)Ba2Ca2Cu3−ySnyO10−δ (y=0,0.25,0.5,0.75,1.0,1.25,1.50) superconductors have been synthesized by using solid state reaction method. The crystal structure of these Sn doped samples is orthorhombic and the axis lengths are found to increase with enhanced Sn doping concentration. The critical temperature and the magnitude of the diamagnetism are suppressed with enhanced doping of Sn. The samples turn into an insulator with very high room temperature resistivity if the Sn doping concentration is increased beyond y=1.5. The carrier’s concentration in the conducting CuO2/SnO2 planes has been enhanced by carrying out post-annealing experiments in the air and oxygen atmosphere. The increased concentration of holes in CuO2/SnO2 planes resulting out of oxygen diffusion in the material is evidenced by increased intensity of Oδ mode of oxygen measured by Fourier transform infrared absorption measurements and also by oxygen contents measured by iodometric titration method.
Molecular dynamics simulation of delamination of a stiff, body-centered-cubic crystalline film from a compliant Si substrate
Authors: Hale L. M. , Zhou X. W. , Zimmerman J. A. , Moody N. R. , Ballarini R. , Gerberich W. W.
Published: October 2009

Compliant substrate technology offers an effective approach to grow high-quality multilayered films, of importance to microelectronics and microelectromechanical systems devices. By using a thin, soft substrate to relieve the mismatch strain of an epitaxial film, the critical thickness of misfit dislocation formation in the overlayer is effectively increased. Experiments have indicated that stiff films deposited onto Si substrates can delaminate at the interface. However, the atomic mechanisms of the deformation and the fracture of the films have not been well studied. Here, we have applied molecular dynamics simulations to study the delamination of a stiff body-centered-cubic crystalline film from a compliant Si substrate due to tensile loading. The observed mechanical behavior is shown to be relatively independent of small changes in temperature, loading rate, and system size. Fracture occurs at the interface between the two materials resulting in nearly atomically clean surfaces. Dislocations are seen to nucleate in the body-centered-cubic film prior to delamination. At higher strains, a phase change to a face centered cubic is observed within the body-centered-cubic film, facilitating extensive dislocation growth and interaction. The various defects that form prior to fracture are discussed and related to the mechanical properties of the system.
Centrifugal instabilities in curved compressible wakes
Authors: Lin Li , Stephen Sharon O.
Published: October 2009

This investigation is concerned with the linear development of Görtler vortices in the high-Reynolds-number laminar compressible wake behind a flat plate which is aligned with the centerline of a curved mixing-layer system. The Görtler modes were previously found to exist within curved compressible mixing layers by Owen et al. [Phys. Fluids 8, 2506 (1997)]. This study extends that investigation and demonstrates the effect a wake has on the growth rate and location of such modes. The investigations were made by examining the growth rate and the location of the Görtler modes in the limit of large Görtler number and high wave number within the wake-dominated curved compressible mixing-layer systems based on three wake flow models. An analytic Gaussian wake profile is first used to model the behavior of the basic flow within the mixing layer at the trailing edge of the splitter plate. It is found that the wake has an amplification effect on the growth of the Görtler instability within the concavely curved or “unstably” curved compressible mixing layers. It is also found that within the convexly curved or “stably” curved compressible mixing layers wake modes can occur that behave differently to the “thermal modes,” which were previously found within the plain curved compressible system by Owen et al. Another analytic composite model which has some practical applications is then used to predict the behavior of the modes within the systems. Solutions from a numerical wake flow model have been compared with the predictions based on the analytic wake flow models.
Development of high critical current density in multifilamentary round-wire Bi2Sr2CaCu2O8+δ by strong overdoping
Authors: Shen T. , Jiang J. , Yamamoto A. , Trociewitz U. P. , Schwartz J. , Hellstrom E. E. , Larbalestier D. C.
Published: October 2009

Bi 2 Sr 2 CaCu 2 O 8 + δ is the only cuprate superconductor that can be made into a round-wire conductor form with a high enough critical current density Jc for applications. Here we show that the Jc(5 T,4.2 K) of such Ag-sheathed filamentary wires can be doubled to more than 1.4×105 A/cm2 by low temperature oxygenation. Careful analysis shows that the improved performance is associated with a 12 K reduction in transition temperature Tc to 80 K, an increase in flux pinning, and particularly a significant enhancement in intergranular connectivity. In spite of the macroscopically untextured nature of the wire, overdoping is highly effective in producing high Jc values.
40 Gb/s surface-illuminated Ge-on-Si photodetectors
Authors: Osmond Johann , Vivien Laurent , Fédéli Jean-Marc , Marris-Morini Delphine , Crozat Paul , Damlencourt Jean-François , Cassan Eric , Lecunff Y.
Published: October 2009

This paper reports on surface illuminated Ge photodetectors monolithically integrated on Si substrate operating in the C and L wavelength bands. The responsivity at a wavelength of 1.5 μm ranges from 0.08 to 0.21 A/W without bias voltage for Ge mesa diameter ranging from 10 to 25 μm, respectively. The measured −3 dB cut-off frequency is as high as 49 GHz under a reverse bias of 5 V at a wavelength of 1.5 μm. An open eye diagram up to 40 Gbit/s is also demonstrated.
The compass rose pattern in electricity prices
Authors: Batten Jonathan A. , Hamada Mahmoud
Published: October 2009

The “compass rose pattern” is known to appear in the phase portraits, or scatter diagrams, of the high-frequency returns of financial series. We first show that this pattern is also present in the returns of spot electricity prices. Early researchers investigating these phenomena hoped that these patterns signaled the presence of rich dynamics, possibly chaotic or fractal in nature. Although there is a definite autoregressive and conditional heteroscedasticity structure in electricity returns, we find that after simple filtering no pattern remains. While the series is non-normal in terms of their distribution and statistical tests fail to identify significant chaos, there is evidence of fractal structures in periodic price returns when measured over the trading day. The phase diagram of the filtered returns provides a useful visual check on independence, a property necessary for pricing and trading derivatives and portfolio construction, as well as providing useful insights into the market dynamics.
Interplay between writhe and knotting for swollen and compact polymers
Authors: Baiesi Marco , Orlandini Enzo , Whittington Stuart G.
Published: October 2009

The role of the topology and its relation with the geometry of biopolymers under different physical conditions is a nontrivial and interesting problem. Aiming at understanding this issue for a related simpler system, we use Monte Carlo methods to investigate the interplay between writhe and knotting of ring polymers in good and poor solvents. The model that we consider is interacting self-avoiding polygons on the simple cubic lattice. For polygons with fixed knot type, we find a writhe distribution whose average depends on the knot type but is insensitive to the length N of the polygon and to solvent conditions. This “topological contribution” to the writhe distribution has a value that is consistent with that of ideal knots. The standard deviation of the writhe increases approximately as N in both regimes, and this constitutes a geometrical contribution to the writhe. If the sum over all knot types is considered, the scaling of the standard deviation changes, for compact polygons, to ∼N0.6. We argue that this difference between the two regimes can be ascribed to the topological contribution to the writhe that, for compact chains, overwhelms the geometrical one, thanks to the presence of a large population of complex knots at relatively small values of N. For polygons with fixed writhe, we find that the knot distribution depends on the chosen writhe, with the occurrence of achiral knots being considerably suppressed for large writhe. In general, the occurrence of a given knot thus depends on a nontrivial interplay between writhe, chain length, and solvent conditions.
Understanding the relation between stress and surface morphology in sputtered films: Atomistic simulations and experiments
Authors: Zepeda-Ruiz Luis A. , Chason Eric , Gilmer George H. , Wang Yinmin , Xu Hongwei , Nikroo Abbas , Hamza Alex V.
Published: October 2009

The relation between stress evolution and surface morphology during deposition of sputtered films is examined by combining kinetic Monte Carlo simulations and stress measurements. We find that the surface morphology is susceptible to an instability, which transforms from layer-by-layer growth to the formation of pillarlike columns. The gaps between these columns prevent complete densification and can lead to a network of pores in the layer. We propose that the formation of this structure changes the stress in the growing layers from compressive to tensile.
Photoinduced homogeneous proton-coupled electron transfer: Model study of isotope effects on reaction dynamics
Authors: Venkataraman Charulatha , Soudackov Alexander V. , Hammes-Schiffer Sharon
Published: October 2009

A model Hamiltonian for photoinduced homogeneous proton-coupled electron transfer reactions is presented, and the equations of motion for the reduced density matrix elements in an electron-proton vibronic basis are derived. This formalism enables a detailed analysis of the proton vibrational dynamics, as well as the dynamics of the electronic state populations, following photoexcitation. The application of this theory to model systems provides insight into the fundamental physical principles underlying these types of processes. The initial nonequilibrium state is prepared by vertical photoexcitation from the ground electronic state to a coherent vibrational mixture in the donor electronic state. This nonstationary state relaxes to the equilibrium distributions in the donor and acceptor electronic states via dynamical processes arising from nonadiabatic transitions between the donor and acceptor vibronic states concurrent with energy dissipation to the bath. During the initial stage, when the proton vibrational population in the donor state is distributed among higher vibrational states and the donor proton wavepacket is oscillating with large amplitude, the electronic state population dynamics exhibits virtually no hydrogen/deuterium isotope effect. After vibrational relaxation, when the proton vibrational population in the donor state becomes concentrated in the lower vibrational states and the donor proton wavepacket becomes more localized near the minimum of the donor potential, a significant hydrogen/deuterium isotope effect on the electronic state population dynamics is exhibited. These model system calculations lead to experimentally testable predictions about the qualitative behavior of these isotope effects.
Direct visualization of the H–Xe bond in xenon hydrides: Xenon isotopic shift in the IR spectra
Authors: Feldman Vladimir I. , Kobzarenko Alexey V. , Baranova Irina A. , Danchenko Alexander V. , Sukhov Fedor F. , Tsivion Ehud , Gerber R. Benny
Published: October 2009

IR spectra of xenon hydrides (HXeCCH, HXeCC, and HXeH) obtained from different xenon isotopes (X129e and X136e) exhibit a small but detectable and reproducible isotopic shift in the absorptions assigned to H–Xe stretching (by 0.17–0.38 cm−1). To our knowledge, it is the first direct experimental evidence for the H–Xe bond in HXeY type compounds. The shift magnitude is in good agreement with quantum-chemical calculations.
Characterization of electrical conductivity in a zeolitelike material
Authors: Soghomonian V. , Heremans J. J.
Published: October 2009

We present the electrical characterization of a zeolitelike oxo-vanadium arsenate framework. The experimentally obtained electronic and ionic conductivities and their interactions are discussed. Further, we investigate the potential use of electrically conducting zeolitelike materials in electrical energy storage applications, in light of the material’s structural and electronic characteristics.
High-mobility enhancement-mode 4H-SiC lateral field-effect transistors utilizing atomic layer deposited Al2O3 gate dielectric
Authors: Lichtenwalner Daniel J. , Misra Veena , Dhar Sarit , Ryu Sei-Hyung , Agarwal Anant
Published: October 2009

Lateral metal-oxide-semiconductor field-effect transistors (MOSFETs) have been fabricated on 4H-SiC utilizing deposited dielectrics and gate-last processing. The bilayer dielectric consists of thin nitrided SiO2 covered by 25 nm of Al2O3 deposited using atomic layer deposition. Field-effect mobility and threshold voltage (VT) vary with SiC nitric oxide (NO) anneal temperature. Peak mobility of 106 cm2/V⋅s was obtained with corresponding VT of 0.8 V. The peak mobility decreases to 61 cm2/V⋅s with a lower temperature NO anneal, while the VT increased to 1.4 V. Thus with proper gate engineering, high-mobility normally off MOSFET devices can be obtained, leading to higher-performance gate-controlled power devices.
Ultralow-voltage transparent electric-double-layer thin-film transistors processed at room-temperature
Authors: Jiang Jie , Wan Qing , Sun Jia , Lu Aixia
Published: October 2009

Electric-double-layer effect is observed in mesoporous SiO2 films deposited by plasma-enhanced chemical vapor deposition at room temperature. Room-temperature processed transparent InGaZnO4 thin film transistors (TFTs) gated with such mesoporous SiO2 dielectric show an ultralow operating voltage of 1.0 V due to the large electric-double-layer capacitance. The InGaZnO4 TFTs exhibit a good performance with a high field-effect mobility of 28.5 cm2/V s, a low subthreshold swing of 110 mV/decade, and a large on-off ratio of 1.1×106, respectively. Such ultralow-voltage devices are very promising for low-power transparent macroelectronics on temperature-sensitive substrates.
Featural, Configural, and Holistic Face-Processing Strategies Evoke Different Scan Patterns
Authors: Bombari Dario , Mast Fred W , Lobmaier Janek S
Published: October 2009

In two experiments we investigated the role of eye movements during face processing. In experiment 1, using modified faces with primarily featural (scrambled faces) or configural (blurred faces) information as cue stimuli, we manipulated the way participants processed subsequently presented intact faces. In a sequential same–different task, participants decided whether the identity of an intact test face matched a preceding scrambled or blurred cue face. Analysis of eye movements for test faces showed more interfeatural saccades when they followed a blurred face, and longer gaze duration within the same feature when they followed scrambled faces. In experiment 2, we used a similar paradigm except that test faces were cued by intact faces, low-level blurred stimuli, or second-order scrambled stimuli (features were cut out but maintained their first-order relations). We found that in the intact condition participants performed fewer interfeatural saccades than in low-level blurred condition and had shorter gaze duration than in second-order scrambled condition. Moreover, participants fixated the centre of the test face to grasp the information from the whole face. Our findings suggest a differentiation between featural, configural, and holistic processing strategies, which can be associated with specific patterns of eye movements.
Illusions Can Warp Visual Space
Authors: Smeets Jeroen B J , Sousa Rita , Brenner Eli
Published: October 2009

Our perception of the space around us is not veridical. It has been reported that the systematic errors in our perception of visual space can be described by a reasonably well-behaving space (the resulting space is approximately projective and complies with an affine geometry). The evidence for this is that the perceived centre of a set of points is independent of the order of the steps taken to construct it. We investigated whether this is also the case in displays with well-known 2-D visual illusions. In two examples (Judd and Poggendorff illusions), we show that the perceptual centre of a set of points depends on how this centre is constructed. The misperceptions induced by visual illusions are thus of a different nature than our everyday misperceptions. We argue that the concept of perceived visual space is not very useful for describing human behaviour. We propose an alternative description whereby illusions do not deform a visual space, but only a single visual attribute, leaving other attributes unaffected.
Letters, Not Words, are Processed Holistically
Authors: Wilson Kevin D , Taylor James M
Published: October 2009

Observers cannot accurately discriminate the top halves of two sequentially presented three-letter words. One interpretation of this effect is that words, like faces, are processed holistically. Here we show, in three simple experiments, that this phenomenon is more consistent with the hypothesis that letters, not words, are processed holistically.
BMPs and Chordin regulate patterning of the directive axis in a sea anemone
Authors: Saina Michael , Genikhovich Grigory , Renfer Eduard , Technau Ulrich
Published: October 2009

The TGF-β molecules Dpp/BMP2/4/7 and their antagonist Sog/Chd play a conserved role in establishing the dorso-ventral (DV) axis in bilaterians. Homologues of BMPs and the antagonist, Chordin, have been isolated from Cnidaria and show a striking asymmetric expression pattern with respect to the primary oral-aboral (OA) axis. We used Morpholino knockdowns of
Nematostella dpp
(
bmp2/4
),
bmp5-8
,
chordin
, and
tolloid
to investigate their function during early development of the sea anemone
Nematostella vectensis
. Molecular analysis of the BMP Morpholino phenotypes revealed an upregulated and radialized expression of
bmps
and
chordin
in ectoderm and endoderm indicating a negative feedback loop. Our data further suggest that BMP signaling is required for symmetry breaking of
bmp
and
chordin
expression during gastrulation. While
bmps
and
chordin
marker genes of the ectodermal OA axis extended aborally, other ectodermal markers of the OA axis were not significantly affected. By contrast, expression of other endodermal marker genes marking both the OA and the directive axis were abolished. Our data suggest that the logic of BMP2/4 signaling and the BMP antagonist, Chordin, differs significantly between Cnidaria and Bilateria, yet the double negative feedback loop detected in
Nematostella
bears systemic similarities with part of the regulatory network of the DV axis patterning system in amphibians.
Late Paleocene fossils from the Cerrejón Formation, Colombia, are the earliest record of Neotropical rainforest
Authors: Wing Scott L. , Herrera Fabiany , Jaramillo Carlos A. , Gómez-Navarro Carolina , Wilf Peter , Labandeira Conrad C.
Published: October 2009

Neotropical rainforests have a very poor fossil record, making hypotheses concerning their origins difficult to evaluate. Nevertheless, some of their most important characteristics can be preserved in the fossil record: high plant diversity, dominance by a distinctive combination of angiosperm families, a preponderance of plant species with large, smooth-margined leaves, and evidence for a high diversity of herbivorous insects. Here, we report on an ≈58-my-old flora from the Cerrejón Formation of Colombia (paleolatitude ≈5 °N) that is the earliest megafossil record of Neotropical rainforest. The flora has abundant, diverse palms and legumes and similar family composition to extant Neotropical rainforest. Three-quarters of the leaf types are large and entire-margined, indicating rainfall >2,500 mm/year and mean annual temperature >25 °C. Despite modern family composition and tropical paleoclimate, the diversity of fossil pollen and leaf samples is 60–80% that of comparable samples from extant and Quaternary Neotropical rainforest from similar climates. Insect feeding damage on Cerrejón fossil leaves, representing primary consumers, is abundant, but also of low diversity, and overwhelmingly made by generalist feeders rather than specialized herbivores. Cerrejón megafossils provide strong evidence that the same Neotropical rainforest families have characterized the biome since the Paleocene, maintaining their importance through climatic phases warmer and cooler than present. The low diversity of both plants and herbivorous insects in this Paleocene Neotropical rainforest may reflect an early stage in the diversification of the lineages that inhabit this biome, and/or a long recovery period from the terminal Cretaceous extinction.
Refolding of the integral membrane protein light-harvesting complex II monitored by pulse EPR
Authors: Dockter Christoph , Volkov Aleksei , Bauer Christian , Polyhach Yevhen , Joly-Lopez Zoé , Jeschke Gunnar , Paulsen Harald
Published: October 2009

The major light-harvesting chlorophyll
a
/
b
complex (LHCII) of the photosynthetic apparatus in plants self-organizes in vitro. The recombinant apoprotein, denatured in dodecyl sulfate, spontaneously folds when it is mixed with its pigments, chlorophylls, and carotenoids in detergent solution, and assembles into structurally authentic LHCII in the course of several minutes. Pulse EPR techniques, specifically double-electron-electron resonance (DEER), have been used to analyze protein folding during this process. Pairs of nitroxide labels were introduced site-specifically into recombinant LHCII and shown not to affect the stability and function of the pigment-protein complex. Interspin distance distributions between two spin pairs were measured at various time points, one pair located on either end of the second transmembrane helix (helix 3), the other one located near the luminal ends of the intertwined transmembrane helices 1 and 4. In the dodecyl sulfate-solubilized apoprotein, both distance distributions were consistent with a random-coil protein structure. A rapid freeze-quench experiment on the latter spin pair indicated that 1 s after initiating reconstitution the protein structure is virtually unchanged. Subsequently, both distance distributions monitored protein folding in the same time range in which the assembly of chlorophylls into the complex had been observed. The positioning of the spin pair spanning the hydrophobic core of LHCII clearly preceded the juxtaposition of the spin pair on the luminal side of the complex. This indicates that superhelix formation of helices 1 and 4 is a late step in LHCII assembly.
Selective oxidation of carbolide C–H bonds by an engineered macrolide P450 mono-oxygenase
Authors: Li Shengying , Chaulagain Mani Raj , Knauff Allison R. , Podust Larissa M. , Montgomery John , Sherman David H.
Published: October 2009

Regio- and stereoselective oxidation of an unactivated C–H bond remains a central challenge in organic chemistry. Considerable effort has been devoted to identifying transition metal complexes, biological catalysts, or simplified mimics, but limited success has been achieved. Cytochrome P450 mono-oxygenases are involved in diverse types of regio- and stereoselective oxidations, and represent a promising biocatalyst to address this challenge. The application of this class of enzymes is particularly significant if their substrate spectra can be broadened, selectivity controlled, and reactions catalyzed in the absence of expensive heterologous redox partners. In this study, we engineered a macrolide biosynthetic P450 mono-oxygenase PikC (PikC
D50N
-RhFRED) with remarkable substrate flexibility, significantly increased activity compared to wild-type enzyme, and self-sufficiency. By harnessing its unique desosamine-anchoring functionality via a heretofore under-explored “substrate engineering” strategy, we demonstrated the ability of PikC to hydroxylate a series of carbocyclic rings linked to the desosamine glycoside via an acetal linkage (referred to as “carbolides”) in a regioselective manner. Complementary analysis of a number of high-resolution enzyme-substrate cocrystal structures provided significant insights into the function of the aminosugar-derived anchoring group for control of reaction site selectivity. Moreover, unexpected biological activity of a select number of these carbolide systems revealed their potential as a previously unrecorded class of antibiotics.
Computational design of ligand binding is not a solved problem
Authors: Schreier Bettina , Stumpp Christian , Wiesner Silke , Höcker Birte
Published: October 2009

Computational design has been very successful in recent years: multiple novel ligand binding proteins as well as enzymes have been reported. We wanted to know in molecular detail how precise the predictions of the interactions of protein and ligands are. Therefore, we performed a structural analysis of a number of published receptors designed onto the periplasmic binding protein scaffold that were reported to bind to the new ligands with nano- to micromolar affinities. It turned out that most of these designed proteins are not suitable for structural studies due to instability and aggregation. However, we were able to solve the crystal structure of an arabinose binding protein designed to bind serotonin to 2.2 Å resolution. While crystallized in the presence of an excess of serotonin, the protein is in an open conformation with no serotonin bound, although the side-chain conformations in the empty binding pocket are very similar to the conformations predicted. During subsequent characterization using isothermal titration calorimetry, CD, and NMR spectroscopy, no indication of binding could be detected for any of the tested designed receptors, whereas wild-type proteins bound their ligands as expected. We conclude that although the computational prediction of side-chain conformations appears to be working, it does not necessarily confer binding as expected. Hence, the computational design of ligand binding is not a solved problem and needs to be revisited.
TDP-43 mutant transgenic mice develop features of ALS and frontotemporal lobar degeneration
Authors: Wegorzewska Iga , Bell Shaughn , Cairns Nigel J. , Miller Timothy M. , Baloh Robert H.
Published: October 2009

Frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS) are neurodegenerative diseases that show considerable clinical and pathologic overlap, with no effective treatments available. Mutations in the RNA binding protein TDP-43 were recently identified in patients with familial amyotrophic lateral sclerosis (ALS), and TDP-43 aggregates are found in both ALS and FTLD-U (FTLD with ubiquitin aggregates), suggesting a common underlying mechanism. We report that mice expressing a mutant form of human TDP-43 develop a progressive and fatal neurodegenerative disease reminiscent of both ALS and FTLD-U. Despite universal transgene expression throughout the nervous system, pathologic aggregates of ubiquitinated proteins accumulate only in specific neuronal populations, including layer 5 pyramidal neurons in frontal cortex, as well as spinal motor neurons, recapitulating the phenomenon of selective vulnerability seen in patients with FTLD-U and ALS. Surprisingly, cytoplasmic TDP-43 aggregates are not present, and hence are not required for TDP-43-induced neurodegeneration. These results indicate that the cellular and molecular substrates for selective vulnerability in FTLD-U and ALS are shared between mice and humans, and suggest that altered DNA/RNA-binding protein function, rather than toxic aggregation, is central to TDP-43-related neurodegeneration.
An enzyme regulating triacylglycerol composition is encoded by the
ROD1
gene of
Arabidopsis
Authors: Lu Chaofu , Xin Zhanguo , Ren Zhonghai , Miquel Martine , Browse John
Published: October 2009

The polyunsaturated fatty acids (PUFAs) linoleic acid (18:2) and α-linolenic acid (18:3) in triacylglycerols (TAG) are major factors affecting the quality of plant oils for human health, as well as for biofuels and other renewable applications. These PUFAs are essential fatty acids for animals and plants, but also are the source of unhealthy
trans
fats during the processing of many foodstuffs. PUFAs 18:2 and 18:3 are synthesized in developing seeds by the desaturation of oleic acid (18:1) esterified on the membrane lipid phosphatidylcholine (PC) on the endoplasmic reticulum. The reactions and fluxes involved in this metabolism are incompletely understood, however. Here we show that a previously unrecognized enzyme, phosphatidylcholine:diacylglycerol cholinephosphotransferase (PDCT), encoded by the
Arabidopsis ROD1
gene, is a major reaction for the transfer of 18:1 into PC for desaturation and also for the reverse transfer of 18:2 and 18:3 into the TAG synthesis pathway. The PDCT enzyme catalyzes transfer of the phosphocholine headgroup from PC to diacylglycerol, and mutation of
rod1
reduces 18:2 and 18:3 accumulation in seed TAG by 40%. Our discovery of PDCT is important for understanding glycerolipid metabolism in plants and other organisms, and provides tools to modify the fatty acid compositions of plant oils for improved nutrition, biofuel, and other purposes.
Methionine oxidation contributes to bacterial killing by the myeloperoxidase system of neutrophils
Authors: Rosen Henry , Klebanoff Seymour J. , Wang Yi , Brot Nathan , Heinecke Jay W. , Fu Xiaoyun
Published: October 2009

Reactive oxygen intermediates generated by neutrophils kill bacteria and are implicated in inflammatory tissue injury, but precise molecular targets are undefined. We demonstrate that neutrophils use myeloperoxidase (MPO) to convert methionine residues of ingested
Escherichia coli
to methionine sulfoxide in high yield. Neutrophils deficient in individual components of the MPO system (MPO, H
2
O
2
, chloride) exhibited impaired bactericidal activity and impaired capacity to oxidize methionine. HOCl, the principal physiologic product of the MPO system, is a highly efficient oxidant for methionine, and its microbicidal effects were found to correspond linearly with oxidation of methionine residues in bacterial cytosolic and inner membrane proteins. In contrast, outer envelope proteins were initially oxidized without associated microbicidal effect. Disruption of bacterial methionine sulfoxide repair systems rendered
E. coli
more susceptible to killing by HOCl, whereas over-expression of a repair enzyme, methionine sulfoxide reductase A, rendered them resistant, suggesting a direct role for methionine oxidation in bactericidal activity. Prominent among oxidized bacterial proteins were those engaged in synthesis and translocation of peptides to the cell envelope, an essential physiological function. Moreover, HOCl impaired protein translocation early in the course of bacterial killing. Together, our findings indicate that MPO-mediated methionine oxidation contributes to bacterial killing by neutrophils. The findings further suggest that protein translocation to the cell envelope is one important pathway targeted for damage.