bluuebunny/crossref_metadata_2025 huggingface dataset:
Role of vertical eddy heat flux in the response of tropical tropopause temperature to changes in tropical sea surface temperature
Authors: Yoshida Kohei , Yamazaki Koji
Published: January 2010

We performed numerical experiments using an atmospheric general circulation model to assess the effect of convections associated with various tropical sea surface temperature (SST) fields on the tropical tropopause (TT). Three experiments were designed with different patterns of tropical SST: increasing and decreasing mean tropical SST, enhanced and weakened longitudinal gradient of tropical SST, and observed SST corresponding to strong El Niño–Southern Oscillation (ENSO) events. The results reveal that vertical advection plays an important role in controlling seasonal variation in TT temperature. In the case of a large (small) longitudinal gradient of tropical SST, the vertical eddy heat flux () diverges strongly (weakly) around the TT, resulting in cooling (warming) of the TT. Divergence of the vertical eddy heat flux is a primary controlling factor of variations in interannual TT temperature, especially during the peak of El Niño events. Analysis of ERA‐Interim and ERA‐40 data supports our results regarding the influence of vertical eddy heat flux on TT temperature. Divergence of vertical eddy heat flux at the TT layer is sensitive to the “strength” of the Matsuno‐Gill–type tropical stationary wave response; this divergence appears to explain variations in the observed TT temperature associated with ENSO.
VCAM‐1 blockade delays disease onset, reduces disease severity and inflammatory cells in an atopic dermatitis model
Authors: Chen Lin , Lin Shao‐xia , Amin Sanober , Overbergh Lut , Maggiolino Giacomo , Chan Lawrence S
Published: January 2010

We investigated the functions of critical adhesion molecules ICAM‐1 and VCAM‐1 in a keratin‐14 IL‐4‐transgenic (Tg) mouse model of atopic dermatitis, the skin lesions of which are characterized by prominent inflammatory cell infiltration, significantly increased mRNAs and proteins of ICAM‐1, VCAM‐1, E‐selectin, P‐selectin, L‐selectin, and PSGL‐1, and significantly increased numbers of dermal vessels expressing these adhesion molecules. We tested the hypotheses that deletion or blockade of these molecules may impede the inflammation by examining the disease progresses in the Tg mice crossed with ICAM‐1‐knockout mice and Tg mice received anti‐VCAM‐1‐neutralizing antibody. Although the findings of the ICAM‐1‐knockout Tg mice (Tg/ICAM‐1−/−) developed skin lesions similar to wide‐type ICAM‐1 Tg mice (Tg/ICAM‐1+/+) were surprising, a compensatory mechanism may account for it: the frequency of VCAM‐1 ligand, CD49d, on CD3+ T cells in the lesional skin significantly increased in the Tg/ICAM‐1−/− mouse, compared with the Tg/ICAM‐1+/+ mice. In contrast, anti‐VCAM‐1‐treated Tg/ICAM‐1−/− or Tg/ICAM‐1+/+ mice had significantly delayed onset of skin inflammation compared with isotype antibody‐treated groups. Moreover, anti‐VCAM‐1 significantly reduced the skin inflammation severity in Tg/ICAM‐1+/+ mice, accompanied with reduction of mast cell, eosinophil, and CD3+ T cell infiltration. VCAM‐1 is more critical in developing skin inflammation in this model.
Antiviral protection following immunization correlates with humoral but not cell‐mediated immunity
Authors: Panchanathan Vijay , Chaudhri Geeta , Karupiah Gunasegaran
Published: January 2010

Smallpox was a deadly disease when it was rife yet despite its eradication more than 30 years ago, the possibility of accidental or intentional release has driven research in search of better definitions of correlates of protective immunity. Mousepox, a disease caused by ectromelia virus (ECTV), is arguably one of the best surrogate small animal models for smallpox. Correlates of protection in mousepox are well defined during primary infection, whereas those in a secondary infection, which have definite relevance to vaccination strategies, are less well understood. We previously established that neutralizing antibody (Ab), which is generated far more rapidly during a secondary infection compared with a primary infection, has a key role during a secondary virus challenge. In this study, we show that the route of immunization or the use of homologous or heterologous virus vaccines for immunization does not influence the ability of mice to control high‐dose virulent ECTV challenge or to mount a substantial secondary neutralizing Ab response. In contrast, the recall cytotoxic T lymphocyte (CTL) responses generated under these regimes of immunization were varied and did not correlate with virus control. Furthermore, unlike the recall Ab response that was generated rapidly, the kinetics of the secondary antiviral CTL response was no different to a primary infection and peaked only at day 8 post‐challenge. This finding further underscores the importance of Ab in conferring protection during secondary poxvirus infection. This information could potentially prove useful in the design of safer and more efficacious vaccines against poxviruses or other diseases using poxvirus vectors.
Transcriptional regulation of Th2 cell differentiation
Authors: Zhu Jinfang
Published: January 2010

CD4 T helper 2 (Th2) cells have critical functions in immune responses against extracellular parasites and are involved in asthma and other allergic diseases. The differentiation of naïve CD4 T cells into Th2 cells is initiated from T‐cell receptor and cytokine‐mediated signaling followed by upregulation of GATA3 and activation of signal transducer and activator of transcription 5 (STAT5), two indispensable events for this differentiation process. In this review, regulation of GATA3 expression and STAT5 activation and functions of these two transcription factors in inducing the expression of Th2 cytokines, cytokine receptors as well as epigenetic modification at Th2 cytokine locus are summarized. Furthermore, I present positive and negative regulatory networks important for Th2 cell commitment, selective growth of committed Th2 cells and suppression of alternative lineage fates. Finally, the difference between in vitro and in vivo Th2 differentiation is discussed.
Electrochemical differential photoacoustic cell to study in situ the growing process of porous materials
Authors: Gutiérrez Adriana , Giraldo Jairo , Velázquez-Hernández Rubén , Mendoza-López Maria Luisa , Espinosa-Arbeláez Diego G. , del Real Alicia , Rodríguez-García Mario E.
Published: January 2010

In order to study in situ the growing process of porous materials, a new electrochemical differential photoacoustic cell (DPC) was developed. This system allows to obtain the thermal signals coming from the growing process of the pores without the external noise component. The DPC is a good system to growth porous silicon and study their growing process with reproducibility. The porous silicon samples were obtained by using electrochemical etching of (100) n-type silicon wafers with different nominal resistivity values in the range of 1–25 Ω cm. The samples were formed in a solution of hydrofluoric acid and ethanol having a composition ratio of 1:1 in volume with etching voltage of 10V and an etching time of 2 min using back illumination provided by a laser beam with a wavelength of 808 nm. The porous samples were characterized by means of Raman microscopy, x-ray diffraction, and scanning electron microscopy. The crystallite sizes of the samples were obtained through the analysis of the micro-Raman spectra using a phonon confinement model, and the analysis of the x-ray diffractograms.
Optical properties of bismuth germanate
Authors: Jellison G. E. , Auluck S. , Singh D. J. , Boatner L. A.
Published: January 2010

The optical dielectric function of bismuth germanate (Bi4Ge3O12) has been measured using spectroscopic ellipsometry and optical transmission. Analysis near the direct band edge indicates that there are at least three critical points at 4.44 (low intensity) and at 4.75 and 4.91 (high intensity). Using transmission measurements, the band gap is determined to be 4.20 eV, which is likely determined by the defects in the material. Comparisons are made with relativistic electronic structure and optical calculations based on the Engel–Vosko generalized gradient approximation. The near-absorption-edge critical points are associated with spin-orbit-split bands which significantly modify the conduction bands.
Fabrication and characterization of a porous silicon based microarray for label-free optical monitoring of biomolecular interactions
Authors: Rea Ilaria , Lamberti Annalisa , Rendina Ivo , Coppola Giuseppe , Gioffrè Mariano , Iodice Mario , Casalino Maurizio , De Tommasi Edoardo , De Stefano Luca
Published: January 2010

We have fabricated a microarray of porous silicon Bragg reflectors on a crystalline silicon substrate using a technological process based on standard photolithography and electrochemical anodization of the silicon. The array density is of 170 elements/cm2 and each element has a diameter of 200 μm. The porous silicon structures have been used as platform to immobilize an amino terminated DNA single strand probe. All fabrication steps have been monitored by spectroscopic reflectometry, optical and electron microscopy, and Fourier transform infrared spectroscopy. A label-free detection method has been employed to investigate the hybridization between micromolar DNA probe and its complementary target. Due to fast and low cost production, good reproducibility, and high quality optical features, this platform could be adopted also for other different microarray applications such as proteomics and medical diagnostics.
Propagation length of surface plasmon polaritons determined by emission from introduced surface discontinuities
Authors: Flynn Richard A. , Bussmann Konrad , Simpkins B. S. , Vurgaftman Igor , Kim Chul Soo , Long James P.
Published: January 2010

Flexible far-field microscopy methods suitable for directly measuring surface plasmon polariton propagation along optically thick or buried waveguides are introduced. The methods monitor the local intensity of surface plasmon polaritons by imaging the light scattered when the plasmons encounter discontinuities in the form of (i) the terminal end of the guide, (ii) randomly dispersed nanoparticles, and (iii) nanoholes drilled through the guide. Measurements by these three methods give consistent values to within ∼15% of 39 μm for the propagation length along 5-μm-wide Au-stripe waveguides deposited on an oxidized silicon wafer and excited at a wavelength of 860 nm. This range is due to varying losses associated with the introduction of the nanoholes and nanoparticles. These losses are quantified and could be reduced with realistic experimental improvements. Finite-element computations find that propagation in these optically thick (107 nm) guides is intrinsically limited not only by Ohmic losses, but also by radiation emitted into the substrate from the stripe edges. The radiative loss depends on the slope of the edge sidewall and on the wafer oxide thickness, both of which must be considered when reconciling experiment with theory.
Periodic magnetic field as a polarized and focusing thermal neutron spectrometer and monochromator
Authors: Cremer J. T. , Williams D. L. , Fuller M. J. , Gary C. K. , Piestrup M. A. , Pantell R. H. , Feinstein J. , Flocchini R. G. , Boussoufi M. , Egbert H. P. , Kloh M. D. , Walker R. B.
Published: January 2010

A novel periodic magnetic field (PMF) optic is shown to act as a prism, lens, and polarizer for neutrons and particles with a magnetic dipole moment. The PMF has a two-dimensional field in the axial direction of neutron propagation. The PMF alternating magnetic field polarity provides strong gradients that cause separation of neutrons by wavelength axially and by spin state transversely. The spin-up neutrons exit the PMF with their magnetic spins aligned parallel to the PMF magnetic field, and are deflected upward and line focus at a fixed vertical height, proportional to the PMF period, at a downstream focal distance that increases with neutron energy. The PMF has no attenuation by absorption or scatter, as with material prisms or crystal monochromators. Embodiments of the PMF include neutron spectrometer or monochromator, and applications include neutron small angle scattering, crystallography, residual stress analysis, cross section measurements, and reflectometry. Presented are theory, experimental results, computer simulation, applications of the PMF, and comparison of its performance to Stern–Gerlach gradient devices and compound material and magnetic refractive prisms.
Influence of oxygen partial pressure on surface tension of molten silver
Authors: Ozawa S. , Morohoshi K. , Hibiya T. , Fukuyama H.
Published: January 2010

Influences of oxygen partial pressure, PO2, of ambient atmosphere and temperature on surface tension of molten silver were experimentally investigated by an oscillating droplet method using an electromagnetic levitation furnace. We successfully measured surface tension of molten silver within a very wide temperature range of over 550 K under a well-controlled PO2 atmosphere. Surface tension of pure melt surface, σp, was determined without any contamination such as oxygen adsorption and the reaction between the melt and a measurement device at a PO2 of less than 10−12 Pa. When the PO2 was controlled at 102 Pa, the “boomerang shape” temperature dependence of surface tension was experimentally observed; surface tension was increased and then decreased with increasing temperature. From these experimental data, the temperature dependence of equilibrium constant for oxygen adsorption was determined using the Szyszkowski equation. We successfully expressed the surface tension of molten silver as functions of both PO2 and temperature. Furthermore, the changes in enthalpy and entropy for oxygen adsorption on molten silver were also estimated.
Electrical and optical characterization of n-InAsSb/n-GaSb heterojunctions
Authors: Lackner D. , Martine M. , Cherng Y. T. , Steger M. , Walukiewicz W. , Thewalt M. L. W. , Mooney P. M. , Watkins S. P.
Published: January 2010

We report the electrical properties of n-InAsSb/n-GaSb heterojunctions as a function of the GaSb doping concentration. Because of the staggered type II band alignment, strong electron accumulation occurs on the InAsSb side. For low GaSb doping, depletion occurs on the GaSb side resulting in a Schottky-like junction as previously reported. As the GaSb doping increases, the built-in voltage as well as depletion width decreases as shown using self-consistent simulations. For GaSb doping levels above 5×1017 cm−3, the junction loses its rectifying properties due to tunneling. Under zero and reverse bias voltage, the photoresponse of these diodes is solely due to the photovoltaic effect in the GaSb depletion region. For forward bias voltages >400 mV, we also observed a photoconductive response from the InAsSb layer. The proposed physical mechanism is quite different from the one suggested in a recent paper.
Ferromagnetic exchange interaction between Co and Mn in the Heusler alloy CuCoMnAl
Authors: Feng L. , Ma L. , Zhu Z. Y. , Zhu W. , Liu E. K. , Chen J. L. , Wu G. H. , Meng F. B. , Liu H. Y. , Luo H. Z. , Li Y. X.
Published: January 2010

The ferromagnetic exchange interaction between Co and Mn in Heusler alloys has been phenomenologically investigated by analyzing the composition dependence of the magnetic moment and the Curie temperature in a series of quaternary CuCoMnAl alloys. The curves of the composition dependence of the magnetic moment show an interesting valleylike profile and their minima are positioned at different Co contents for different Mn concentrations. The ferromagnetic Co–Mn exchange interaction is a short-range effect which is only effective at the nearest-neighbor distance. At this distance, the exchange interaction can be further enhanced by a Mn-rich composition, but it might be destroyed by the lattice distortion due to the martensitic transformation.
Molecular dynamics simulation of hyperthermal neutrals generated by energetic ion impact on a metal plate
Authors: Park Seung-hoon , Yoo Suk Jae , Chang Choong-Seock
Published: January 2010

A hyperthermal neutral beam (HNB) source is one of candidate methods to reduce plasma-induced damage problems. The HNB is generated by vertical collisions between energetic ions and a reflector composed of a tungsten plate. We perform a HNB generation simulation using a molecular dynamics algorithm. The roughness of the reflector surface is experimentally measured and the surface structure is taken into consideration in the simulation. The energy and angular distributions of the HNB are obtained by the simulation and the energy yield of the reflected neutral particles is found to be in good agreement with experimental data.
Adsorption of random copolymers from a melt onto a solid surface: Monte Carlo studies
Authors: Kłos J. S. , Romeis D. , Sommer J.-U.
Published: January 2010

We study the behavior of random AB-copolymer melts near a selective surface. We consider the case where the copolymers do not display phase segregation behavior in the bulk but the surface is strongly selective for the A-component and the probability of finding an A-monomer along the chain is p⪡1. Using self-consistent field theory and scaling arguments, we discuss some aspects of conformational rearrangements and composition selection in the surface layer. For strong selectivity we discuss the formation of a polydisperse brush on the surface. Next, we consider selection mechanisms of chains and sequences of A-species in the surface layer. We used the bond-fluctuation method to simulate copolymer melts at different values of the surface selectivity. Several aspects of the surface layer are analyzed, such as the composition profiles, chemical composition of chains on the surface, chain extension, and dynamics. We find evidence for conformational rearrangements in the surface layer according to the polydisperse brush model, as well as enrichment of A-monomers in the adosorbed chains, stretching of chains in the direction perpendicular to the surface, and selection of multiple A-sequences. Slight but systematic variation of the properties of surface layer at long simulation times indicates that selection processes require very long time scales as expected from theoretical arguments.
Molecular adsorption of small alkanes on a PdO(101) thin film: Evidence of σ-complex formation
Authors: Weaver Jason F. , Hakanoglu Can , Hawkins Jeffery M. , Asthagiri Aravind
Published: January 2010

We investigated the molecular adsorption of methane, ethane, and propane on a PdO(101) thin film using temperature programmed desorption (TPD) and density functional theory (DFT) calculations. The TPD data reveal that each of the alkanes adsorbs into a low-coverage molecular state on PdO(101) in which the binding is stronger than that for alkanes physically adsorbed on Pd(111). Analysis of the TPD data using limiting values of the desorption prefactors predicts that the alkane binding energies on PdO(101) increase linearly with increasing chain length, but that the resulting line extrapolates to a nonzero value between about 22 and 26 kJ/mol at zero chain length. This constant offset implies that a roughly molecule-independent interaction contributes to the alkane binding energies for the molecules studied. DFT calculations predict that the small alkanes bind on PdO(101) by forming dative bonds with coordinatively unsaturated Pd atoms. The resulting adsorbed species are analogous to alkane σ-complexes in that the bonding involves electron donation from C–H σ bonds to the Pd center as well as backdonation from the metal, which weakens the C–H bonds. The binding energies predicted by DFT lie in a range from 16 to 24 kJ/mol, in good agreement with the constant offsets estimated from the TPD data. We conclude that both the dispersion interaction and the formation of σ-complexes contribute to the binding of small alkanes on PdO(101), and estimate that σ-complex formation accounts for between 30% and 50% of the total binding energy for the molecules studied. The predicted weakening of C–H bonds resulting from σ-complex formation may help to explain the high activity of PdO surfaces toward alkane activation.
Dielectrophoretic separation of colorectal cancer cells
Authors: Yang Fang , Yang Xiaoming , Jiang Hong , Bulkhaults Phillip , Wood Patricia , Hrushesky William , Wang Guiren
Published: January 2010

Separation of colorectal cancer cells from other biological materials is important for stool-based diagnosis of colorectal cancer. In this paper, we use conventional dielectrophoresis in a microfluidic chip to manipulate and isolate HCT116 colorectal cancer cells. It is noticed that at a particular alternating current frequency band, the HCT116 cells are clearly deflected to a side channel from the main channel after the electric activation of an electrode pair. This motion caused by negative dielectrophoresis can be used to simply and rapidly separate cancer cells from other cells. In this manuscript, we report the chip design, flow conditions, dielectrophoretic spectrum of the cancer cells, and the enrichment factor of the colorectal cancer cells from other cells.
Scaling law analysis of paraffin thin films on different surfaces
Authors: Dotto M. E. R. , Camargo S. S.
Published: January 2010

The dynamics of paraffin deposit formation on different surfaces was analyzed based on scaling laws. Carbon-based films were deposited onto silicon (Si) and stainless steel substrates from methane (CH4) gas using radio frequency plasma enhanced chemical vapor deposition. The different substrates were characterized with respect to their surface energy by contact angle measurements, surface roughness, and morphology. Paraffin thin films were obtained by the casting technique and were subsequently characterized by an atomic force microscope in noncontact mode. The results indicate that the morphology of paraffin deposits is strongly influenced by substrates used. Scaling laws analysis for coated substrates present two distinct dynamics: a local roughness exponent (αlocal) associated to short-range surface correlations and a global roughness exponent (αglobal) associated to long-range surface correlations. The local dynamics is described by the Wolf–Villain model, and a global dynamics is described by the Kardar–Parisi–Zhang model. A local correlation length (Llocal) defines the transition between the local and global dynamics with Llocal approximately 700nm in accordance with the spacing of planes measured from atomic force micrographs. For uncoated substrates, the growth dynamics is related to Edwards–Wilkinson model.
Dissipative particle dynamics simulation of the interplay between spinodal decomposition and wetting in thin film binary fluids
Authors: Hore Michael J. A. , Laradji Mohamed
Published: January 2010

The dynamics of phase separation of thin film binary fluids is investigated via dissipative particle dynamics simulation. We consider both cases of symmetric and asymmetric interactions between the walls and the two components. In the case of walls interacting symmetrically with the two fluid components, corresponding to a nonwetting case, relatively fast kinetics is observed when the average domain size is smaller than the slit thickness. A crossover to a slow Lifshitz–Slyozov growth is observed at late times. Faster dynamics is observed when the walls act as a slip boundary condition to the velocity field. In the case of asymmetric interactions, such that the system is in the wetting regime, the interplay between wetting kinetics and spinodal decomposition leads to rich dynamics. The phase separation proceeds through three stages. During the first stage, the dynamics is characterized as surface-directed spinodal decomposition, with growth of both average domain size and thickness of the wetting layers. The domain morphology is three dimensional and bicontinuous during the first stage, with kinetics reminiscent of that in bulk systems is observed. The second stage of the phase separation is characterized by the breakup of the bicontinuous domain morphology into small tubular domains bridging the two wetting layers and depletion of the core of the film from the wetting component. During this stage, domains with diameter smaller than thickness of the film shrink and disappear while those with diameter larger that the film thickness grow. The third stage is characterized by growth induced by the backflow of A-component from the wetting layers to the core of the film, leading to the decay in the thickness of the film and growth of the domains bridging the wetting layers. At even later times of the third stage, when the wetting layers become very depleted in the wetting component, growth becomes mediated by diffusion followed by collision of the tubular domains.
Computed tomographic x-ray velocimetry
Authors: Dubsky S. , Jamison R. A. , Irvine S. C. , Siu K. K. W. , Hourigan K. , Fouras A.
Published: January 2010

An x-ray velocimetry technique is described which provides three components of velocity measurement in three dimensional space. Current x-ray velocimetry techniques, which use particle images taken at a single projection angle, are limited to two components of velocity measurement, and are unable to measure in three dimensions without a priori knowledge of the flow field. The proposed method uses multiple projection angles to overcome these limitations. The technique uses a least-squares iterative scheme to tomographically reconstruct the three-dimensional velocity field directly from two-dimensional image pair cross-correlations, without the need to reconstruct three-dimensional particle images. Synchrotron experiments demonstrate the effectiveness of the technique for blood flow measurement in opaque vessels, with applications for the diagnosis and treatment of cardiovascular disease.
Fabrication of graphene nanogap with crystallographically matching edges and its electron emission properties
Authors: Wang H. M. , Zheng Z. , Wang Y. Y. , Qiu J. J. , Guo Z. B. , Shen Z. X. , Yu T.
Published: January 2010

We demonstrate the fabrication of graphene nanogap with crystallographically matching edges on SiO2/Si substrates by divulsion. The current-voltage measurement is then performed in a high-vacuum chamber for a graphene nanogap with few hundred nanometers separation. The parallel edges help to build uniform electrical field and allow us to perform electron emission study on individual graphene. It was found that current-voltage (I-V) characteristics are governed by the space-charge-limited flow of current at low biases while the Fowler–Nordheim model fits the I-V curves in high voltage regime. We also examined electrostatic gating effect of the vacuum electronic device. Graphene nanogap with atomically parallel edges may open up opportunities for both fundamental and applied research of vacuum nanoelectronics.
Interfacial intermixing in InAs/GaSb short-period-superlattices grown by molecular beam epitaxy
Authors: Luna E. , Satpati B. , Rodriguez J. B. , Baranov A. N. , Tournié E. , Trampert A.
Published: January 2010

The unique properties of the noncommon-atom InAs/GaSb short-period-superlattices (SPSL) strongly depend on the interface structure. These interfaces are characterized using transmission electron microscopy (TEM). The compositional sharpness is obtained from the comparison of the experimental contrast in g002 two-beam dark-field TEM images with simulated intensity profiles, which are calculated assuming that the element distribution profiles are described by sigmoidal functions. The interfacial intermixing, defined by the chemical width, is obtained for SPSL with different periods and layer thicknesses, even in the extreme case of nominally less than 3 ML thick InAs layers. Nominal 1 ML InSb layers intentionally inserted are also identified.
Vertical absorption edge and temperature dependent resistivity in semihydrogenated graphene
Authors: Chen Lei , Ma Zhongshui , Zhang C.
Published: January 2010

We show that for graphene with any finite asymmetry in the on-site energy between the two sublattices (Δ), the optical absorption edge is determined by the Δ. The universal conductance will be broken and the conductance near the band edge varies with frequency as 1/ω2. The onset conductance is σc=2σ0=πe2/2h, independent of the size of the band gap. The total integrated optical response is nearly conserved despite of the opening of the band gap. Moreover, near the band edge, there is a change over of the electrical resistivity from temperature independent to a linear temperature dependence.
Effect of contact barrier on electron transport in graphene
Authors: Zhou Yang-Bo , Han Bing-Hong , Liao Zhi-Min , Zhao Qing , Xu Jun , Yu Da-Peng
Published: January 2010

The influence of the barrier between metal electrodes and graphene on the electrical properties was studied on a two-electrode device. A classical barrier model was used to analyze the current-voltage characteristics. Primary parameters including barrier height and effective resistance were achieved. The electron transport properties under magnetic field were further investigated. An abnormal peak-valley-peak shape of voltage-magnetoresistance curve was observed. The underlying mechanisms were discussed under the consideration of the important influence of the contact barrier. Our results indicate electrical properties of graphene based devices are sensitive to the contact interface.
Memory for Time Distinguishes between Perception and Action
Authors: Bueti Domenica , Walsh Vincent
Published: January 2010

Our experience of time is unlike that of other features of the sensory world such as colour, movement, touch, or sound because there is no unique receptor system through which it is received. However, since time can be perceived, remembered, estimated, and compared in a way analogous to other sensory experiences, it should perhaps be subject to some of the same architectures or principles that have advanced understanding in these other domains. By adapting a task designed to test visual memory within a perception/action framework we investigated whether memory for time is affected by the use to which temporal information is put. When remembering a visual or auditory duration for subsequent motor production, storage is biased by a delay of up to 8 s. When the same duration is remembered for subsequent perception, however, there is no such effect of delay on memory. The results suggest a distinction in temporal memory that parallels the perception/action dichotomy in vision.
Archaea and bacteria with surprising microdiversity show shifts in dominance over 1,000-year time scales in hydrothermal chimneys
Authors: Brazelton William J. , Ludwig Kristin A. , Sogin Mitchell L. , Andreishcheva Ekaterina N. , Kelley Deborah S. , Shen Chuan-Chou , Edwards R. Lawrence , Baross John A.
Published: January 2010

The Lost City Hydrothermal Field, an ultramafic-hosted system located 15 km west of the Mid-Atlantic Ridge, has experienced at least 30,000 years of hydrothermal activity. Previous studies have shown that its carbonate chimneys form by mixing of ∼90 °C, pH 9–11 hydrothermal fluids and cold seawater. Flow of methane and hydrogen-rich hydrothermal fluids in the porous interior chimney walls supports archaeal biofilm communities dominated by a single phylotype ofMethanosarcinales. In this study, we have extensively sampled the carbonate-hosted archaeal and bacterial communities by obtaining sequences of >200,000 amplicons of the 16S rRNA V6 region and correlated the results with isotopic (230Th) ages of the chimneys over a 1,200-year period. Rare sequences in young chimneys were commonly more abundant in older chimneys, indicating that members of the rare biosphere can become dominant members of the ecosystem when environmental conditions change. These results suggest that a long history of selection over many cycles of chimney growth has resulted in numerous closely related species at Lost City, each of which is preadapted to a particular set of reoccurring environmental conditions. Because of the unique characteristics of the Lost City Hydrothermal Field, these data offer an unprecedented opportunity to study the dynamics of a microbial ecosystem’s rare biosphere over a thousand-year time scale.
Reconstructed evolutionary adaptive paths give polymerases accepting reversible terminators for sequencing and SNP detection
Authors: Chen Fei , Gaucher Eric A. , Leal Nicole A. , Hutter Daniel , Havemann Stephanie A. , Govindarajan Sridhar , Ortlund Eric A. , Benner Steven A.
Published: January 2010

Any system, natural or human-made, is better understood if we analyze both its history and its structure. Here we combine structural analyses with a “Reconstructed Evolutionary Adaptive Path” (REAP) analysis that used the evolutionary and functional history of DNA polymerases to replace amino acids to enable polymerases to accept a new class of triphosphate substrates, those having their 3′-OH ends blocked as a 3
′
-ONH
2
group (dNTP-ONH
2
). Analogous to widely used 2′,3′-dideoxynucleoside triphosphates (ddNTPs), dNTP-ONH
2
s terminate primer extension. Unlike ddNTPs, however, primer extension can be resumed by cleaving an O-N bond to restore an -OH group to the 3′-end of the primer. REAP combined with crystallographic analyses identified 35 sites where replacements might improve the ability of
Taq
to accept dNTP-ONH
2
s. A library of 93
Taq
variants, each having replacements at three or four of these sites, held eight variants having improved ability to accept dNTP-ONH
2
substrates. Two of these (A597T, L616A, F667Y, E745H, and E520G, K540I, L616A) performed notably well. The second variant incorporated both dNTP-ONH
2
sand ddNTPs faithfully and efficiently, supporting extension-cleavage-extension cycles applicable in parallel sequencing and in SNP detection through competition between reversible and irreversible terminators. Dissecting these results showed that one replacement (L616A), not previously identified, allows
Taq
to incorporate both reversible and irreversible terminators. Modeling showed how L616A might open space behind Phe-667, allowing it to move to accommodate the larger 3′-substituent. This work provides polymerases for DNA analyses and shows how evolutionary analyses help explore relationships between structure and function in proteins.
A gene therapy approach for long-term normalization of blood pressure in hypertensive mice by ANP-secreting human skin grafts
Authors: Therrien Jean-Philippe , Kim Soo Mi , Terunuma Atsushi , Qin Yan , Tock Christine L. , Pfützner Wolfgang , Ohyama Manabu , Schnermann Jurgen , Vogel Jonathan C.
Published: January 2010

The use of bioengineered human skin as a bioreactor to deliver therapeutic factors has a number of advantages including accessibility that allows manipulation and monitoring of genetically modified cells. We demonstrate a skin gene therapy approach that can regulate blood pressure and treat systemic hypertension by expressing atrial natriuretic peptide (
ANP
), a hormone able to decrease blood pressure, in bioengineered human skin equivalents (HSE). Additionally, the expression of a selectable marker gene, multidrug resistance (
MDR
) type 1, is linked to ANP expression on a bicistronic vector and was coexpressed in the human keratinocytes and fibroblasts of the HSE that were grafted onto immunocompromised mice. Topical treatments of grafted HSE with the antimitotic agent colchicine select for keratinocyte progenitors that express both MDR and ANP. Significant plasma levels of human ANP were detected in mice grafted with HSE expressing ANP from either keratinocytes or fibroblasts, and topical selection of grafted HSE resulted in persistent high levels of ANP expression in vivo. Mice with elevated plasma levels of human ANP showed lower renin levels and, correspondingly, had lower systemic blood pressure than controls. Furthermore, mice with HSE grafts expressing human ANP did not develop elevated blood pressure when fed a high-salt diet. These findings illustrate the potential of this human skin gene therapy approach to deliver therapeutic molecules systemically for long-term treatment of diverse diseases.
Dissecting the paradoxical effects of hydrogen bond mutations in the ketosteroid isomerase oxyanion hole
Authors: Kraut Daniel A. , Sigala Paul A. , Fenn Timothy D. , Herschlag Daniel
Published: January 2010

The catalytic importance of enzyme active-site interactions is frequently assessed by mutating specific residues and measuring the resulting rate reductions. This approach has been used in bacterial ketosteroid isomerase to probe the energetic importance of active-site hydrogen bonds donated to the dienolate reaction intermediate. The conservative Tyr16Phe mutation impairs catalysis by 10
5
-fold, far larger than the effects of hydrogen bond mutations in other enzymes. However, the less-conservative Tyr16Ser mutation, which also perturbs the Tyr16 hydrogen bond, results in a less-severe 10
2
-fold rate reduction. To understand the paradoxical effects of these mutations and clarify the energetic importance of the Tyr16 hydrogen bond, we have determined the 1.6-Å resolution x-ray structure of the intermediate analogue, equilenin, bound to the Tyr16Ser mutant and measured the rate effects of mutating Tyr16 to Ser, Thr, Ala, and Gly. The nearly identical 200-fold rate reductions of these mutations, together with the 6.4-Å distance observed between the Ser16 hydroxyl and equilenin oxygens in the x-ray structure, strongly suggest that the more moderate rate effect of this mutant is not due to maintenance of a hydrogen bond from Ser at position 16. These results, additional spectroscopic observations, and prior structural studies suggest that the Tyr16Phe mutation results in unfavorable interactions with the dienolate intermediate beyond loss of a hydrogen bond, thereby exaggerating the apparent energetic benefit of the Tyr16 hydrogen bond relative to the solution reaction. These results underscore the complex energetics of hydrogen bonding interactions and site-directed mutagenesis experiments.
Micron-scale holes terminate the phage infection cycle
Authors: Dewey Jill S. , Savva Christos G. , White Rebecca L. , Vitha Stanislav , Holzenburg Andreas , Young Ry
Published: January 2010

Holins are small phage-encoded proteins that accumulate harmlessly in the cytoplasmic membrane during the infection cycle until suddenly, at an allele-specific time, triggering to form lethal lesions, or “holes.” In the phages λ and T4, the holes have been shown to be large enough to allow release of prefolded active endolysin from the cytoplasm, which results in destruction of the cell wall, followed by lysis within seconds. Here, the holes caused by S105, the λ-holin, have been captured in vivo by cryo-EM. Surprisingly, the scale of the holes is at least an order of magnitude greater than any previously described membrane channel, with an average diameter of 340 nm and some exceeding 1 μm. Most cells exhibit only one hole, randomly positioned in the membrane, irrespective of its size. Moreover, on coexpression of holin and endolysin, the degradation of the cell wall leads to spherically shaped cells and a collapsed inner membrane sac. To obtain a 3D view of the hole by cryo-electron tomography, we needed to reduce the average size of the cells significantly. By taking advantage of the coupling of bacterial cell size and growth rate, we achieved an 80% reduction in cell mass by shifting to succinate minimal medium for inductions of the
S105
gene. Cryotomographic analysis of the holes revealed that they were irregular in shape and showed no evidence of membrane invagination. The unexpected scale of these holes has implications for models of holin function.
Inherited genetic variant predisposes to aggressive but not indolent prostate cancer
Authors: Xu Jianfeng , Zheng Siqun Lilly , Isaacs Sarah D. , Wiley Kathleen E. , Wiklund Fredrik , Sun Jielin , Kader A. Karim , Li Ge , Purcell Lina D. , Kim Seong-Tae , Hsu Fang-Chi , Stattin Pär , Hugosson Jonas , Adolfsson Jan , Walsh Patrick C. , Trent Jeffrey M. , Duggan David , Carpten John , Grönberg Henrik , Isaacs William B.
Published: January 2010

Autopsy studies suggest that most aging men will develop lesions that, if detected clinically, would be diagnosed as prostate cancer (PCa). Most of these cancers are indolent and remain localized; however, a subset of PCa is aggressive and accounts for more than 27,000 deaths in the United States annually. Identification of factors specifically associated with risk for more aggressive PCa is urgently needed to reduce overdiagnosis and overtreatment of this common disease. To search for such factors, we compared the frequencies of SNPs among PCa patients who were defined as having either more aggressive or less aggressive disease in four populations examined in the Genetic Markers of Susceptibility (CGEMS) study performed by the National Cancer Institute. SNPs showing possible associations with disease severity were further evaluated in an additional three independent study populations from the United States and Sweden. In total, we studied 4,829 and 12,205 patients with more and less aggressive disease, respectively. We found that the frequency of the TT genotype of SNP rs4054823 at 17p12 was consistently higher among patients with more aggressive compared with less aggressive disease in each of the seven populations studied, with an overall
P
value of 2.1 × 10
−8
under a recessive model, exceeding the conservative genome-wide significance level. The difference in frequency was largest between patients with high-grade, non–organ-confined disease compared with those with low-grade, organ-confined disease. This study demonstrates that inherited variants predisposing to aggressive but not indolent PCa exist in the genome, and suggests that the clinical potential of such variants as potential early markers for risk of aggressive PCa should be evaluated.
Managing the Miombo Woodlands of Southern Africa: Policies, Incentives and Options for the Rural Poor
Authors: Dewees Peter A. , Campbell Bruce M. , Katerere Yemi , Sitoe Almeida , Cunningham Anthony B. , Angelsen Arild , Wunder Sven
Published: January 2010

Miombo woodlands cover vast areas of southern Africa. Of comparatively little interest for export-oriented commercial logging, they are part of a complex system of rural land use that integrates woodland management with crops and livestock. There is also evidence that woodland resources are extensively used for household consumption, greatly reducing the risk of households falling deeper into poverty as a result of environmental or economic stress. New opportunities for improving the management of miombo woodlands, with poverty mitigation in mind, suggest four policy options. First, communities are becoming more active in managing local natural resources, a result of decentralization and land reforms, which suggests that there may be good scope for strengthening related policy and legal frameworks and the measures to implement them. Second, new and integrated conservation-development approaches are emerging, which suggests possible scope for providing payments for environmental services to increase the value of managed woodlands. Third, markets throughout the region are developing and expanding, which suggests great scope for enhancing forest-based markets by removing restrictive legislation and by supporting local producers and forest enterprises. Fourth, all these opportunities suggest that public forest institutions can be revitalized by strengthening their service delivery orientations, with poverty mitigation as a main objective.
Spatial and seasonal variability in cetacean distribution in the fjords of northern Patagonia, Chile
Authors: Viddi Francisco A. , Hucke-Gaete Rodrigo , Torres-Florez Juan P. , Ribeiro Sandra
Published: January 2010

Viddi, F. A., Hucke-Gaete, R., Torres-Florez, J. P., and Ribeiro, S. 2010. Spatial and seasonal variability in cetacean distribution in the fjords of northern Patagonia, Chile. – ICES Journal of Marine Science, 67: 959–970. Compared with other Chilean coastal areas, little is known about the diversity and distribution of cetaceans in northern Patagonian fjords. Between December 2000 and November 2001, surveys on platforms of opportunity were undertaken in southern Chile to evaluate species richness and the spatial and seasonal distribution of cetaceans. Nine species were recorded, blue, humpback, and minke whales, Peale's dolphin, Chilean dolphin, killer whale, false killer whale, bottlenose dolphin, and Cuvier's beaked whale. The pattern of cetacean distribution displayed significant seasonal differences, with most baleen whales (mysticetes) observed during late summer and autumn, and toothed cetaceans (odontocetes) mostly during spring. Generalized additive models, used to assess the spatial distribution of cetaceans, showed that mysticetes were distributed disproportionately along a north–south gradient, in open gulfs with oceanic influence, and close to shore. In contrast, odontocetes were observed mainly within narrow channels, areas with complex coastal morphology, peaking at different water depths. These findings, although from a single year of data, increase our understanding of habitat determinants of cetacean distribution in southern Chile. The results have the potential to be applied to coastal conservation and management in the region.
Recent advances in the understanding of iron overload in sideroblastic myelodysplastic syndrome
Authors: Cuijpers Maria L. H. , Raymakers Reinier A. P. , MacKenzie Marius A. , De Witte Theo J. M. , Swinkels Dorine W.
Published: January 2010

Myelodysplastic syndromes (MDS) are a heterogeneous group of clonal haematopoietic stem cell malignancies. A subgroup, the so‐called sideroblastic MDS, shows ring sideroblasts in the bone marrow aspirate that represent mitochondrial iron accumulation. Patients with sideroblastic MDS also develop systemic iron overload and generally have a low‐risk MDS. Therefore it is important to understand the mechanisms responsible for iron accumulation and the associated toxicity in these patients. Recently, low levels of the iron‐regulatory peptide hepcidin were found to contribute to body iron overload in β‐thalassaemia patients. A similar mechanism may account for systemic iron accumulation in sideroblastic MDS. Mitochondrial iron accumulation is observed in several subtypes of MDS, and predominantly in refractory anaemia with ring sideroblasts. The presence of ring sideroblasts is also the diagnostic hallmark in patients with inherited forms of sideroblastic anaemia. The ever‐increasing insights into the affected pathways in inherited sideroblastic anaemia may lead to a better comprehension of the pathogenesis of mitochondrial iron accumulation in MDS patients. Overall, an improved understanding of the mechanisms responsible for iron overload in MDS will lead to novel treatment strategies to reduce both systemic and mitochondrial iron overload, resulting in less tissue damage and more effective erythropoiesis.