bluuebunny/crossref_metadata_2025 huggingface dataset:
Validation of RADARSAT‐2 fully polarimetric SAR measurements of ocean surface waves
Authors: Zhang Biao , Perrie Will , He Yijun
Published: June 2010

C band RADARSAT‐2 fully polarimetric (fine quad‐polarization mode, HH+VV+HV+VH) synthetic aperture radar (SAR) images are used to validate ocean surface waves measurements using the polarimetric SAR wave retrieval algorithm, without estimating the complex hydrodynamic modulation transfer function, even under large radar incidence angles. The linearly polarized radar backscatter cross sections (RBCS) are first calculated with the copolarization (HH, VV) and cross‐polarization (HV, VH) RBCS and the polarization orientation angle. Subsequently, in the azimuth direction, the vertically and linearly polarized RBCS are used to measure the wave slopes. In the range direction, we combine horizontally and vertically polarized RBCS to estimate wave slopes. Taken together, wave slope spectra can be derived using estimated wave slopes in azimuth and range directions. Wave parameters extracted from the resultant wave slope spectra are validated with colocated National Data Buoy Center (NDBC) buoy measurements (wave periods, wavelengths, wave directions, and significant wave heights) and are shown to be in good agreement.
Gross primary production estimation from MODIS data with vegetation index and photosynthetically active radiation in maize
Authors: Wu Chaoyang , Niu Zheng , Gao Shuai
Published: June 2010

Gross primary production (GPP) is a significant important parameter for carbon cycle and climate change research. Remote sensing combined with other climate and meteorological data offers a convenient tool for large‐scale GPP estimation. GPP was estimated as a product of vegetation indices (VIs) and photosynthetically active radiation (PAR). Four kinds of vegetation indices [the normalized difference vegetation index (NDVI), the weighted difference vegetation index, the soil‐adjusted vegetation index, and the enhanced vegetation index (EVI)] derived from the Moderate Resolution Imaging Spectroradiometer daily surface reflectance product were selected to test our method. The in situ GPP was calculated using the eddy covariance technique and the PAR data were acquired from meteorological measurements. Because VIs were found to be a reliable proxy of both light use efficiency (LUE) and the fraction of absorbed PAR (fAPAR; R2 of 0.63–0.87 for LUE and 0.69–0.76 for fAPAR), the product VI × VI × PAR is used as a measure of GPP according to Monteith logic. Moderate determination coefficients R2 from 0.65 for NDVI to 0.71 for EVI were obtained when GPP was estimated from a single index in maize. When testing our method, calculating GPP as a product of VI × VI × PAR, the determination coefficients R2 largely improved, fluctuating from 0.81 to 0.91. EVI × EVI × PAR provided the best estimation of GPP with the highest R2 of 0.91 because EVI was found to be the best indicator of both LUE and fAPAR (R2 of 0.87 and 0.76, respectively). These results will be helpful for the development of future GPP estimation models.
Defrosting, dark flow features, and dune activity on Mars: Example in Russell crater
Authors: Gardin E. , Allemand P. , Quantin C. , Thollot P.
Published: June 2010

Defrosting processes observed on Mars are among the most unusual features described on high‐resolution images. A defrosting sequence has been observed near the crest of the megadune located in the Russell crater on new high‐resolution images obtained from the HiRISE instrument and on hyperspectral cubes obtained from CRISM instrument, both on board MRO. Hyperspectral images show that frost overlaps the entire megadune in middle winter. This frost is composed mainly of CO2 and of a small amount of water ice. The deepest ice signatures are mainly located near the crest of the megadune. The defrosting sequence monitored by CRISM reveals spatial heterogeneity and refrosting processes. On the morphological counterpart, the defrosting sequence starts with the development of dark spots, similar to those described in the cryptic regions. After few sols, we observe the emplacement of dark linear flow features that start from the dark spots downward of the main slope of the dune. These linear flow features are 1 to 2 m wide and 50 to 100 m long. They settle on the small rills visible on the frost cover. They are interpreted as avalanches of a mixing of sand, dust, and unstable CO2 gas released under pressure. The avalanches would be triggered by the eruption of the dark spots. The flux of material transported by the flow features has been estimated to 0.25 to 0.5 m3 by meter width each year on the megadune. This flux is larger than flux transported by wind. These dark flow features are thus very efficient to transport material on slopes located in frosted areas.
In situ sensing to understand diel turbidity cycles, suspended solids, and nutrient transport in Clear Creek, Iowa
Authors: Loperfido J. V. , Just Craig L. , Papanicolaou Athanasios N. , Schnoor Jerald L.
Published: June 2010

Recent advances in sensor technology have made high‐frequency environmental data readily available. In this study, high‐frequency monitoring of turbidity revealed diel turbidity cycles with peak values during the nighttime and lower values occurring during daytime. Particles responsible for these cycles were fixed suspended solids consisting mostly of aluminosilicates (clay particles) emanating from bed sediments. High‐frequency data were used to investigate the transport of total suspended solids (TSS) during base flow. A majority of the base flow TSS loading occurred during the nighttime in a small agricultural catchment in Iowa, United States. Elevated nighttime turbidity coincided with an increased total suspended phosphorus loading during nighttime. Bioturbation, as a result of nocturnal feeding of fishes, is the suspected cause of the diel turbidity cycles. High‐frequency monitoring was also used to detect TSS loading during storm events. Results from this study highlight the importance of high‐frequency environmental measurements to reveal and understand biogeochemical transport phenomena.
Network model investigation of interfacial area, capillary pressure and saturation relationships in granular porous media
Authors: Joekar‐Niasar V. , Prodanović M. , Wildenschild D. , Hassanizadeh S. M.
Published: June 2010

We have developed a new approach for generating pore throat cross sections of various shapes based on distributions of shape factors and radii of inscribed circles. These distributions are obtained from analysis of grains packing. General formulas for calculating geometrical properties and entry capillary pressure for given shape factor and inscribed circle radius are developed. These relationships are employed in a pore network, which has a number of special features. In particular, it is highly flexible in terms of location of pore bodies, variable coordination number, as well as variable cross‐sectional shapes. The pore network model is employed for simulating the equilibrium distribution of two fluids in a granular porous medium, under both drainage and imbibition conditions. The pore network model is verified by comparing simulation results with experimental data of quasi‐static drainage and imbibition experiments in a glass bead medium. The pore‐level topology and geometrical description of pore bodies and pore throats, essential for building the network, are rigorously extracted from experimental data using image analysis (3DMA‐Rock software). Calculated capillary pressure‐saturation (Pc − Sw) and specific interfacial area‐saturation (anw − Sw) curves show very good agreement with measured ones, for both drainage and imbibition. We show that the shape factor can significantly influence the form of macroscopic Pc − Sw and anw − Sw curves, if the length and volumes associated to the pore throats are considerable. Furthermore, using continuous generation of shape factor distribution, the model can be validated against the grain size distribution. After validating the model against experiments, in addition to primary and main curves, we simulate many scanning curves to generate Pc − Sw − anw surfaces for drainage and imbibition, separately. Results show that these two surfaces lie very close to each other, and the average normalized difference is small, in the range of simulations uncertainty. Our results illustrate that Pc − Sw − anw surfaces show very little hysteresis and, therefore, specific interfacial area can be considered as an essential variable for reducing or eliminating the hysteresis observed in Pc − Sw curves.
Strong Showing for AGU Journals in 2009 Impact Factors
Authors: Cock Bill
Published: June 2010

AGU publishes great science, which is recognized in several ways. One of the most widely recognized is from Thomson Reuters, which provides the Journal Citation Report (JCR) each year as a component of the Web of Science®. JCR reports on several measures of journal usage, including a journal's Eigenfactor score, its Article Influence score, its Impact Factor, and its rank within a cohort of similar journals.

According to the 2009 statistics released last week, AGU again has outperformed its larger competitors. For the twelfth time, two different AGU titles hold the top rank in their categories, and AGU titles hold the second spot in two other categories and third in two more.
Lowering TCR expression on naive CD8+ T cells does not affect memory T‐cell differentiation
Authors: Leignadier Julie , Rooney Julie , Daudelin Jean‐François , Labrecque Nathalie
Published: June 2010

The generation of long‐lived memory T (Tm) cells is critical for the success of vaccination, but the factors controlling their differentiation are still poorly defined. We examined the hypothesis that the level of T‐cell receptor (TCR) engagement contributed to memory CD8+ T‐cell generation. By manipulating TCR expression levels on murine, naive ovalbumin (OVA)‐specific CD8+ T cells, we showed that the expansion of antigen (Ag)‐specific CD8+ T cells is minimally affected by the level of TCR expression. Indeed, naive CD8+ T cells expressing as little as a 1000 TCRs (30‐fold less) show only a 2.5‐fold reduction in the number of effectors generated. Furthermore, the TCR expression levels influenced neither the acquisition of effector functions nor the generation of functional Tm cells. Our data indicate that during an in vivo immune response, a threshold in the number of TCRs engaged by naive CD8+ T cells is required for full T‐cell expansion but not for their differentiation into effector and Tm cells.
Promiscuous partnering and independent activity of MexB, the multidrug transporter protein from Pseudomonas aeruginosa
Authors: Welch Alexander , Awah Chidiebere U. , Jing Shiheng , van Veen Hendrik W. , Venter Henrietta
Published: June 2010

The MexAB–OprM drug efflux pump is central to multidrug resistance of Pseudomonas aeruginosa. The ability of the tripartite protein to confer drug resistance on the pathogen is crucially dependent on the presence of all three proteins of the complex. However, the role of each protein in the formation of the intact functional complex is not well understood. One of the key questions relates to the (in)ability of MexB to act independently of its cognitive partners, MexA and OprM. In the present study, we have demonstrated that, in the absence of MexA and OprM, MexB can: (i) recruit AcrA and TolC from Escherichia coli to form a functional drug-efflux complex; (ii) transport the toxic compound ethidium bromide in a Gram-positive organism where the periplasmic space and outer membrane are absent; and (iii) catalyse transmembrane chemical proton gradient (ΔpH)-dependent drug transport when purified and reconstituted into proteoliposomes. Our results represent the first evidence of drug transport by an isolated RND (resistance–nodulation–cell division)-type multidrug transporter, and provide a basis for further studies into the energetics of RND-type transporters and their assembly into multiprotein complexes.
Dielectrophoretic cell trapping and parallel one-to-one fusion based on field constriction created by a micro-orifice array
Authors: Gel Murat , Kimura Yuji , Kurosawa Osamu , Oana Hidehiro , Kotera Hidetoshi , Washizu Masao
Published: June 2010

Micro-orifice based cell fusion assures high-yield fusion without compromising the cell viability. This paper examines feasibility of a dielectrophoresis (DEP) assisted cell trapping method for parallel fusion with a micro-orifice array. The goal is to create viable fusants for studying postfusion cell behavior. We fabricated a microfluidic chip that contained a chamber and partition. The partition divided the chamber into two compartments and it had a number of embedded micro-orifices. The voltage applied to the electrodes located at each compartment generated an electric field distribution concentrating in micro-orifices. Cells introduced into each compartment moved toward the micro-orifice array by manipulation of hydrostatic pressure. DEP assisted trapping was used to keep the cells in micro-orifice and to establish cell to cell contact through orifice. By applying a pulse, cell fusion was initiated to form a neck between cells. The neck passing through the orifice resulted in immobilization of the fused cell pair at micro-orifice. After washing away the unfused cells, the chip was loaded to a microscope with stage top incubator for time lapse imaging of the selected fusants. The viable fusants were successfully generated by fusion of mouse fibroblast cells (L929). Time lapse observation of the fusants showed that fused cell pairs escaping from micro-orifice became one tetraploid cell. The generated tetraploid cells divided into three daughter cells. The fusants generated with a smaller micro-orifice (diameter∼2 μm) were kept immobilized at micro-orifice until cell division phase. After observation of two synchronized cell divisions, the fusant divided into four daughter cells. We conclude that the presented method of cell pairing and fusion is suitable for high-yield generation of viable fusants and furthermore, subsequent study of postfusion phenomena.
Fabrication and characterization of nanomaterial-based sensors using dielectrophoresis
Authors: Suehiro Junya
Published: June 2010

Dielectrophoresis (DEP) is an electrokinetic motion of dielectrically polarized materials in nonuniform electric fields. DEP has been successfully applied to manipulation of nanomaterials including carbon nanotubes (CNTs), metallic nanoparticles, and semiconducting nanowires. Under positive DEP force, which attracts nanomaterials toward the higher field region, nanomaterials are trapped in the electrode gap and automatically establish good electrical connections between them and the external measuring circuit. This feature allows us a fast, simple, and low-cost fabrication of nanomaterial-based sensors based on a bottom-up approach. This paper first presents a theoretical background of DEP phenomena and then reviews recent works of the present author, which were aimed to develop nanomaterial-based sensors, such as a CNT gas sensor and a ZnO nanowire photosensor, using DEP fabrication technique. It is also demonstrated that DEP technique enables self-formation of interfaces between various nanomaterials, which can be also applicable as novel sensing transducers.
Intuitionistic fuzzy stability of a general mixed additive-cubic equation
Authors: Xu Tian Zhou , Rassias John Michael , Xu Wan Xin
Published: June 2010

We establish some stability results concerning the general mixed additive-cubic functional equation, f(kx+y)+f(kx−y)=kf(x+y)+kf(x−y)+2f(kx)−2kf(x),in intuitionistic fuzzy normed spaces. In addition, we show under some suitable conditions that an approximately mixed additive-cubic function can be approximated by a mixed additive and cubic mapping.
Morita equivalence of noncommutative supertori
Authors: Chang-Young Ee , Kim Hoil , Nakajima Hiroaki
Published: June 2010

In this paper we study the extension of Morita equivalence of noncommutative tori to the supersymmetric case. The structure of the symmetry group yielding Morita equivalence appears to be intact but its parameter field becomes supersymmetrized having both body and soul parts. Our result is mainly in the two dimensional case in which noncommutative supertori have been constructed recently: The group SO(2,2,VZ0), where VZ0 denotes Grassmann even number whose body part belongs to Z, yields Morita equivalent noncommutative supertori in two dimensions.
A noncommutative space approach to confined Dirac fermions in graphene
Authors: Dayi Ömer F. , Jellal Ahmed
Published: June 2010

A generalized algebra of noncommutative coordinates and momenta embracing non-Abelian gauge fields is proposed. Through a two-dimensional realization of this algebra for a gauge field including electromagnetic vector potential and two spin-orbit-like coupling terms, a Dirac-like Hamiltonian in noncommutative coordinates is introduced. We established the corresponding energy spectrum and from that we derived the relation between the energy level quantum number and the magnetic field at the maxima of Shubnikov–de Haas oscillations. By tuning the noncommutativity parameter θ in terms of the values of magnetic field at the maxima of Shubnikov–de Haas oscillations, we accomplished the experimentally observed Landau plot of the peaks for graphene. Accepting that the experimentally observed behavior is due to the confinement of carriers, we conclude that our method of introducing noncommutative coordinates provides another formulation of the confined massless Dirac fermions in graphene.
A boundary element model of the transport of a semi-infinite bubble through a microvessel bifurcation
Authors: Calderon Andres J. , Eshpuniyani Brijesh , Fowlkes J. Brian , Bull Joseph L.
Published: June 2010

Motivated by a developmental gas embolotherapy technique for selective occlusion of blood flow to tumors, we examined the transport of a pressure-driven semi-infinite bubble through a liquid-filled bifurcating channel. Homogeneity of bubble splitting as the bubble passes through a vessel bifurcation affects the degree to which the vascular network near the tumor can be uniformly occluded. The homogeneity of bubble splitting was found to increase with bubble driving pressure and to decrease with increased bifurcation angle. Viscous losses at the bifurcation were observed to affect the bubble speed significantly. The potential for oscillating bubble interfaces to induce flow recirculation and impart high stresses on the vessel endothelium was also observed.
The resonant tunneling through a graphene multiquantum well system
Authors: Xu G. J. , Xu X. G. , Wu B. H. , Cao J. C. , Zhang C.
Published: June 2010

The transport properties of a graphene multiquantum well system are investigated numerically using transfer-matrix method. There are transmission gaps for electrons and holes in the transmission spectra at tilted incidence. In the transmission gaps, a few resonant tunneling peaks appear, defined as transmission windows, which are related with the bound states in the quantum wells. Unlike conventional semiconductor nanostructures, the location and the width of the transmission windows are sensitive not only to the quantum well width but also the incident angle. The number of the quantum wells determines the fine structure of the transmission windows. The anisotropic property is affected in the following way: the increase in well width makes the nonzero-transmission incident angle range decrease, and the interference effect is enhanced as the well number increases. Tiny oscillation of the conductance and fine structures in the middle energy range are due to the resonant tunneling induced by the multiquantum well structure. These oscillating features may be helpful in explaining the oscillatory characteristics in experiment.
Surface chemical reactions during electron beam irradiation of nanocrystalline CaS:Ce3+ phosphor
Authors: Kumar Vinay , Mishra Varun , Pitale Shreyas S. , Nagpure I. M. , Coetsee E. , Ntwaeaborwa O. M. , Terblans J. J. , Swart H. C.
Published: June 2010

The effects of accelerating voltage (0.5–5 keV) on the green cathodoluminescence (CL) of CaS:Ce3+ nanocrystalline powder phosphors is reported. An increase in the CL intensity was observed from the powders when the accelerating voltage was varied from 0.5 to 5 keV, which is a relevant property for a phosphor to be used in field emission displays (FEDs). The CL degradation induced by prolonged electron beam irradiation was analyzed using CL spectroscopy, x-ray photoelectron spectroscopy (XPS) and Auger electron spectroscopy (AES). The AES data showed the decrease in the S peak intensity and an increase in the O peak intensity during electron bombardment. The CL intensity was found to decrease to 30% of its original intensity after about 50 C/cm2. XPS was used to study the chemical composition of the CaS:Ce3+ nanophosphor before and after degradation. The XPS data confirms that a nonluminescent CaSO4 layer has formed on the surface during the degradation process, which may partially be responsible for the CL degradation. The electron stimulated surface chemical reaction mechanism was used to explain the effects of S desorption and the formation of the nonluminescent CaSO4 layer on the surface.
Velocity map imaging the dynamics of the reactions of Cl atoms with neopentane and tetramethylsilane
Authors: Rose Rebecca A. , Greaves Stuart J. , Orr-Ewing Andrew J.
Published: June 2010

The reactions of ground state Cl(P23/2) atoms with neopentane and tetramethylsilane have been studied at collision energies of 7.9±2.0 and 8.2±2.0 kcal mol−1, respectively. The nascent HCl(v=0,J) products were probed using resonance enhanced multiphoton ionization spectroscopy combined with velocity map imaging (VMI) to determine the rotational level population distributions, differential cross sections (DCSs), and product translational energy distributions. The outcomes from PHOTOLOC and dual beam methods are compared and are discussed in light of previous studies of the reactions of Cl atoms with other saturated hydrocarbons, including a recent crossed molecular beam and VMI investigation of the reaction of Cl atoms with neopentane [Estillore et al., J. Chem. Phys. 132, 164313 (2010)]. Rotational distributions were observed to be cold, consistent with the reactions proceeding via a transition state with a collinear Cl–H–C moiety. The DCSs for both reactions are forward peaked but show scatter across a broad angular range. Interpretation using a model based on linear dependence of scattering angle on impact parameter indicates that the probability of reaction is approximately constant across all allowed impact parameters. Product translational energy distributions from dual beam experiments have mean values, expressed as fractions of the total available energy, of 0.67 (Cl+neopentane) and 0.64 (Cl+tetramethylsilane) that are consistent with a kinematic model for the reaction in which the translational energy of the reactants is conserved into product translational energy.
Intrinsic carrier mobility in amorphous In–Ga–Zn–O thin-film transistors determined by combined field-effect technique
Authors: Kimura Mutsumi , Kamiya Toshio , Nakanishi Takashi , Nomura Kenji , Hosono Hideo
Published: June 2010

Amorphous In–Ga–Zn–O (α-IGZO) is expected for thin-film transistors (TFTs) in next-generation flat-panel displays but its intrinsic properties are not understood well and different mobility models have been applied to different films. This letter reports that a universal mobility model is obtained using a field-effect technique and capacitance-voltage method. Electrical characteristics of α-IGZO TFTs subjected to different annealing are reproduced using the mobility model and different trap densities. The present achievement will be a necessary basis to establish device and circuit simulators for α-IGZO-based electronic applications.
Anisotropic surface plasmon excitation in Au/silica nanowire
Authors: Wu Chien-Ting , Chu Ming-Wen , Wang Sheng-Bo , Hu Ming-Shien , Chen Kuei-Hsien , Chen Li-Chyong , Chen Chun-Wei , Chen Cheng-Hsuan
Published: June 2010

The surface plasmon (SP) excitations of gold/silica nanowire, investigated by electron energy-loss spectroscopy in conjunction with scanning transmission electron microscopy, are found to be anisotropic with stronger SP intensities observed along the transverse direction of the nanowire. This indicates that the charge carriers generated near the surface of the nanowires by the decay of SP resonance play a significant role to the enhanced photoconductivity. This conclusion is reaffirmed by the polarization dependent photoconductivity measurement.
Molecular anion formation in 9,10-anthraquinone: Dependence of the electron detachment rate on temperature and incident electron energy
Authors: Pshenichnyuk Stanislav A. , Vorob’ev Alexander S. , Asfandiarov Nail L. , Modelli Alberto
Published: June 2010

Attachment of low-energy electrons to gas phase 9,10-anthraquinone (AQ) was observed with electron transmission (ET) spectroscopy, and interpreted with the support of quantum chemical calculations. The ET spectrum displays three shape resonances at 0.45, 0.7, and 2.2 eV, associated with temporary electron capture into empty π∗ molecular orbitals of AQ, the first two anion states being stable. According to TD-B3LYP calculations, the first π-π∗ core-excited resonance lies at about 1.8 eV, although no experimental evidence for this anion state was found. The long-lived parent molecular anion [AQ]− was observed by means of Electron Attachment Spectroscopy (EAS) using two different mass spectrometers and also by measuring the total anion current at the collision chamber walls. The molecular anion current shows maxima at zero energy, around 0.6 eV and at 1.8 eV. Association of these maxima with the corresponding resonant anion states is discussed. The experimentally measured electron detachment times from [AQ]− as a function of the incident electron energy and the temperature of the target molecule show a pronounced change of slope around 1.5 eV, regardless of the temperature. This unexpected behavior can be qualitatively reproduced within the framework of a multiexponential approach which describes the electron detachment event in terms of a redistribution of the anion excess energy, regardless of the initial mechanism of temporary anion formation.
Preface to Special Topic: Dielectrophoresis
Authors: Pethig Ronald
Published: June 2010

This Special Topic section is on dielectrophoresis, a growing area of widespread interest and relevance to the microfluidics and nanofluidics community.
Current anisotropy of carbon nanotube diodes: Voltage and work function dependence
Authors: Perello David J. , Lim Seong Chu , Chae Seung Jin , Lee Innam , Kim Moon. J. , Lee Young Hee , Yun Minhee
Published: June 2010

Here, we report a performance analysis on carbon nanotube (CNT) Schottky diodes using source-drain current anisotropy. An analytical model is derived based on thermionic field emission and used to correlate experimental data from Pd–Hf, Ti–Hf, Cr–Hf, Ti–Cr, and Pd–Au mixed metal devices fabricated on one single 6 mm long CNT. Results suggest that the difference in work functions of the two contact-metals, and not a dominant Schottky contact, determines diode performance. Results are further applied and demonstrated in a reversible polarity diode.
YbdG in
Escherichia coli
is a threshold-setting mechanosensitive channel with MscM activity
Authors: Schumann Ulrike , Edwards Michelle D. , Rasmussen Tim , Bartlett Wendy , van West Pieter , Booth Ian R.
Published: June 2010

We describe a mechanosensitive (MS) channel that has mechanosensitive channel of miniconductance (MscM) activity, and displays unique properties with respect to gating. Mechanosensitive channels respond to membrane tension, are ubiquitous from bacteria to man, and exhibit a great diversity in structure and function. These channels protect
Bacteria
and
Archaea
against hypoosmotic shock and are critical determinants of shape in chloroplasts. Given the dominant roles played in bacteria by the mechanosensitive channel of small conductance (MscS) and the mechanosensitive channel of large conductance (MscL), the role of the multiple MS channel homologs observed in most organisms remains obscure. Here we demonstrate that a MscS homolog, YbdG, extends the range of hypoosmotic shock that
Escherichia coli
cells can survive, but its expression level is insufficient to protect against severe shocks. Overexpression of the YbdG protein provides complete protection. Transcription and translation of the
ybdG
gene are enhanced by osmotic stress consistent with a role for the protein in survival of hypoosmotic shock. Measurement of the conductance of the native channel by standard patch clamp methods was not possible. However, a fully functional YbdG mutant channel, V229A, exhibits a conductance in membrane patches consistent with MscM activity. We find that MscM activities arise from more than one gene product because
ybdG
deletion mutants still exhibit an occasional MscM-like conductance. We propose that
ybdG
encodes a low-abundance MscM-type MS channel, which in cells relieves low levels of membrane tension, obviating the need to activate the major MS channels, MscS and MscL.
Energy transducing redox steps of the Na
+
-pumping NADH:quinone oxidoreductase from
Vibrio cholerae
Authors: Juárez Oscar , Morgan Joel E. , Nilges Mark J. , Barquera Blanca
Published: June 2010

Na
+
-NQR is a unique respiratory enzyme that couples the free energy of electron transfer reactions to electrogenic pumping of sodium across the cell membrane. This enzyme is found in many marine and pathogenic bacteria where it plays an analogous role to the H
+
-pumping complex I. It has generally been assumed that the sodium pump of Na
+
-NQR operates on the basis of thermodynamic coupling between reduction of a single redox cofactor and the binding of sodium at a nearby site. In this study, we have defined the coupling to sodium translocation of individual steps in the redox reaction of Na
+
-NQR. Sodium uptake takes place in the reaction step in which an electron moves from the 2Fe-2S center to FMN
C
, while the translocation of sodium across the membrane dielectric (and probably its release into the external medium) occurs when an electron moves from FMN
B
to riboflavin. This argues against a single-site coupling model because the redox steps that drive these two parts of the sodium pumping process do not have any redox cofactor in common. The significance of these results for the mechanism of coupling is discussed, and we proposed that Na
+
-NQR operates through a novel mechanism based on kinetic coupling, mediated by conformational changes.
Coaction of intercellular adhesion and cortical tension specifies tissue surface tension
Authors: Manning M. Lisa , Foty Ramsey A. , Steinberg Malcolm S. , Schoetz Eva-Maria
Published: June 2010

In the course of animal morphogenesis, large-scale cell movements occur, which involve the rearrangement, mutual spreading, and compartmentalization of cell populations in specific configurations. Morphogenetic cell rearrangements such as cell sorting and mutual tissue spreading have been compared with the behaviors of immiscible liquids, which they closely resemble. Based on this similarity, it has been proposed that tissues behave as liquids and possess a characteristic surface tension, which arises as a collective, macroscopic property of groups of mobile, cohering cells. But how are tissue surface tensions generated? Different theories have been proposed to explain how mesoscopic cell properties such as cell–cell adhesion and contractility of cell interfaces may underlie tissue surface tensions. Although recent work suggests that both may be contributors, an explicit model for the dependence of tissue surface tension on these mesoscopic parameters has been missing. Here we show explicitly that the ratio of adhesion to cortical tension determines tissue surface tension. Our minimal model successfully explains the available experimental data and makes predictions, based on the feedback between mechanical energy and geometry, about the shapes of aggregate surface cells, which we verify experimentally. This model indicates that there is a crossover from adhesion dominated to cortical-tension dominated behavior as a function of the ratio between these two quantities.
HIV, transmitted drug resistance, and the paradox of preexposure prophylaxis
Authors: Supervie Virginie , García-Lerma J. Gerardo , Heneine Walid , Blower Sally
Published: June 2010

The administration of antiretrovirals before HIV exposure to prevent infection (i.e., preexposure prophylaxis; PrEP) is under evaluation in clinical trials. Because PrEP is based on antiretrovirals, there is considerable concern that it could substantially increase transmitted resistance, particularly in resource-rich countries. Here we use a mathematical model to predict the effect of PrEP interventions on the HIV epidemic in the men-who-have-sex-with-men community in San Francisco. The model is calibrated using Monte Carlo filtering and analyzed by constructing nonlinear response hypersurfaces. We predict PrEP interventions could substantially reduce transmission but significantly increase the proportion of new infections caused by resistant strains. Two mechanisms can cause this increase. If risk compensation occurs, the proportion increases due to increasing transmission of resistant strains and decreasing transmission of wild-type strains. If risk behavior remains stable, the increase occurs because of reduced transmission of resistant strains coupled with an even greater reduction in transmission of wild-type strains. We define this as the paradox of PrEP (i.e., resistance appears to be increasing, but is actually decreasing). We determine this paradox is likely to occur if the efficacy of PrEP regimens against wild-type strains is greater than 30% and the relative efficacy against resistant strains is greater than 0.2 but less than the efficacy against wild-type. Our modeling shows, if risk behavior increases, that it is a valid concern that PrEP could significantly increase transmitted resistance. However, if risk behavior remains stable, we find the concern is unfounded and PrEP interventions are likely to decrease transmitted resistance.
Neural correlates of virtual route recognition in congenital blindness
Authors: Kupers Ron , Chebat Daniel R. , Madsen Kristoffer H. , Paulson Olaf B. , Ptito Maurice
Published: June 2010

Despite the importance of vision for spatial navigation, blind subjects retain the ability to represent spatial information and to move independently in space to localize and reach targets. However, the neural correlates of navigation in subjects lacking vision remain elusive. We therefore used functional MRI (fMRI) to explore the cortical network underlying successful navigation in blind subjects. We first trained congenitally blind and blindfolded sighted control subjects to perform a virtual navigation task with the tongue display unit (TDU), a tactile-to-vision sensory substitution device that translates a visual image into electrotactile stimulation applied to the tongue. After training, participants repeated the navigation task during fMRI. Although both groups successfully learned to use the TDU in the virtual navigation task, the brain activation patterns showed substantial differences. Blind but not blindfolded sighted control subjects activated the parahippocampus and visual cortex during navigation, areas that are recruited during topographical learning and spatial representation in sighted subjects. When the navigation task was performed under full vision in a second group of sighted participants, the activation pattern strongly resembled the one obtained in the blind when using the TDU. This suggests that in the absence of vision, cross-modal plasticity permits the recruitment of the same cortical network used for spatial navigation tasks in sighted subjects.
Proton equilibration in the chloroplast modulates multiphasic kinetics of nonphotochemical quenching of fluorescence in plants
Authors: Joliot Pierre A. , Finazzi Giovanni
Published: June 2010

In plants, the major route for dissipating excess light is the nonphotochemical quenching of absorbed light (NPQ), which is associated with thylakoid lumen acidification. Our data offer an interpretation for the complex relationship between changes in luminal pH and the NPQ response. Upon steady-state illumination, fast NPQ relaxation in the dark reflects the equilibration between the electrochemical proton gradient established in the light and the cellular ATP/ADP+Pi ratio. This is followed by a slower phase, which reflects the decay of the proton motive force at equilibrium, due to gradual cellular ATP consumption. In transient conditions, a sustained lag appears in both quenching onset and relaxation, which is modulated by the size of the antenna complexes of photosystem II and by cyclic electron flow around photosystem I. We propose that this phenomenon reflects the signature of protonation of specific domains in the antenna and of slow H
+
diffusion in the different domains of the chloroplast.
HIV Rev response element (RRE) directs assembly of the Rev homooligomer into discrete asymmetric complexes
Authors: Daugherty Matthew D. , Booth David S. , Jayaraman Bhargavi , Cheng Yifan , Frankel Alan D.
Published: June 2010

RNA is a crucial structural component of many ribonucleoprotein (RNP) complexes, including the ribosome, spliceosome, and signal recognition particle, but the role of RNA in guiding complex formation is only beginning to be explored. In the case of HIV, viral replication requires assembly of an RNP composed of the Rev protein homooligomer and the Rev response element (RRE) RNA to mediate nuclear export of unspliced viral mRNAs. Assembly of the functional Rev-RRE complex proceeds by cooperative oligomerization of Rev on the RRE scaffold and utilizes both protein-protein and protein-RNA interactions to organize complexes with high specificity. The structures of the Rev protein and a peptide-RNA complex are known, but the complete RNP is not, making it unclear to what extent RNA defines the composition and architecture of Rev-RNA complexes. Here we show that the RRE controls the oligomeric state and solubility of Rev and guides its assembly into discrete Rev-RNA complexes. SAXS and EM data were used to derive a structural model of a Rev dimer bound to an essential RRE hairpin and to visualize the complete Rev-RRE RNP, demonstrating that RRE binding drives assembly of Rev homooligomers into asymmetric particles, reminiscent of the role of RNA in organizing more complex RNP machines, such as the ribosome, composed of many different protein subunits. Thus, the RRE is not simply a passive scaffold onto which proteins bind but instead actively defines the protein composition and organization of the RNP.
Cross-reactive CD8
+
T-cell immunity between the pandemic H1N1-2009 and H1N1-1918 influenza A viruses
Authors: Gras Stephanie , Kedzierski Lukasz , Valkenburg Sophie A. , Laurie Karen , Liu Yu Chih , Denholm Justin T. , Richards Michael J. , Rimmelzwaan Guus F. , Kelso Anne , Doherty Peter C. , Turner Stephen J. , Rossjohn Jamie , Kedzierska Katherine
Published: June 2010

Preexisting T-cell immunity directed at conserved viral regions promotes enhanced recovery from influenza virus infections, with there being some evidence of cross-protection directed at variable peptides. Strikingly, many of the immunogenic peptides derived from the current pandemic A(H1N1)-2009 influenza virus are representative of the catastrophic 1918 “Spanish flu” rather than more recent “seasonal” strains. We present immunological and structural analyses of cross-reactive CD8
+
T-cell–mediated immunity directed at a variable (although highly cross-reactive) immunodominant NP
418–426
peptide that binds to a large B7 family (HLA-B*3501/03/0702) found throughout human populations. Memory CD8
+
T-cell specificity was probed for 12 different NP
418
mutants that emerged over the 9 decades between the 1918 and 2009 pandemics. Although there is evidence of substantial cross-reactivity among seasonal NP
418
mutants, current memory T-cell profiles show no preexisting immunity to the 2009-NP
418
variant or the 1918-NP
418
variant. Natural infection with the A(H1N1)-2009 virus, however, elicits CD8
+
T cells specific for the 2009-NP
418
and 1918-NP
418
epitopes. This analysis points to the potential importance of cross-reactive T-cell populations that cover the possible spectrum of T-cell variants and suggests that the identification of key residues/motifs that elicit cross-reactive T-cell sets could facilitate the evolution of immunization protocols that provide a measure of protection against unpredicted pandemic influenza viruses. Thus, it is worth exploring the potential of vaccines that incorporate peptide variants with a proven potential for broader immunogenicity, especially to those that are not recognized by the current memory T-cell pool generated by exposure to influenza variants that cause successive seasonal epidemics.
Differential changes in steroid hormones before competition in bonobos and chimpanzees
Authors: Wobber Victoria , Hare Brian , Maboto Jean , Lipson Susan , Wrangham Richard , Ellison Peter T.
Published: June 2010

A large body of research has demonstrated that variation in competitive behavior across species and individuals is linked to variation in physiology. In particular, rapid changes in testosterone and cortisol during competition differ according to an individual's or species’ psychological and behavioral responses to competition. This suggests that among pairs of species in which there are behavioral differences in competition, there should also be differences in the endocrine shifts surrounding competition. We tested this hypothesis by presenting humans’ closest living relatives, chimpanzees (
Pan troglodytes
) and bonobos (
Pan paniscus
), with a dyadic food competition and measuring their salivary testosterone and cortisol levels. Given that chimpanzees and bonobos differ markedly in their food-sharing behavior, we predicted that they would differ in their rapid endocrine shifts. We found that in both species, males showed an anticipatory decrease (relative to baseline) in steroids when placed with a partner in a situation in which the two individuals shared food, and an anticipatory increase when placed with a partner in a situation in which the dominant individual obtained more food. The species differed, however, in terms of which hormone was affected; in bonobo males the shifts occurred in cortisol, whereas in chimpanzee males the shifts occurred in testosterone. Thus, in anticipation of an identical competition, bonobo and chimpanzee males showed differential endocrine shifts, perhaps due to differences in perception of the situation, that is, viewing the event either as a stressor or a dominance contest. In turn, common selection pressures in human evolution may have acted on the psychology and the endocrinology of our competitive behavior.
Kinase requirements in human cells: V. Synthetic lethal interactions between p53 and the protein kinases SGK2 and PAK3
Authors: Baldwin Amy , Grueneberg Dorre A. , Hellner Karin , Sawyer Jacqueline , Grace Miranda , Li Wenliang , Harlow Ed , Munger Karl
Published: June 2010

Cervical carcinomas are initiated through a series of well-defined stages that rely on the expression of human papillomavirus (HPV) oncogenes. A panel of 100 small hairpin RNAs that target essential kinases in many tumor types was used to study the stepwise appearance of kinase requirements during cervical tumor development. Twenty-six kinases were commonly required in three cell lines derived from frank carcinomas, and each kinase requirement was traced to the specific stage in which the requirement emerged. Six kinases became required following HPV-induced immortalization, and the requirement for two kinases, SGK2 and PAK3, was mapped to the inactivation of p53 in primary human epithelial cells. Loss of the p53 tumor suppressor in other primary epithelial cells also induced dependence on SGK2 and PAK3. Hence, SGK2 and PAK3 provide important cellular functions following p53 inactivation, fulfilling the classical definition of synthetic lethality; loss of p53, SGK2, or PAK3 alone has little effect on cell viability, whereas loss of p53 together with either SGK2 or PAK3 loss leads to cell death. Whereas tumor suppressor gene mutations are not directly druggable, other proteins or pathways that become obligatory to cell viability following tumor suppressor loss provide theoretical targets for tumor suppressor-specific drug discovery efforts. The kinases SGK2 and PAK3 may thus represent such targets for p53-specific drug development.
Reconstitution of RPA-covered single-stranded DNA-activated ATR-Chk1 signaling
Authors: Choi Jun-Hyuk , Lindsey-Boltz Laura A. , Kemp Michael , Mason Aaron C. , Wold Marc S. , Sancar Aziz
Published: June 2010

ATR kinase is a critical upstream regulator of the checkpoint response to various forms of DNA damage. Previous studies have shown that ATR is recruited via its binding partner ATR-interacting protein (ATRIP) to replication protein A (RPA)-covered single-stranded DNA (RPA-ssDNA) generated at sites of DNA damage where ATR is then activated by TopBP1 to phosphorylate downstream targets including the Chk1 signal transducing kinase. However, this critical feature of the human ATR-initiated DNA damage checkpoint signaling has not been demonstrated in a defined system. Here we describe an in vitro checkpoint system in which RPA-ssDNA and TopBP1 are essential for phosphorylation of Chk1 by the purified ATR-ATRIP complex. Checkpoint defective RPA mutants fail to activate ATR kinase in this system, supporting the conclusion that this system is a faithful representation of the in vivo reaction. Interestingly, we find that an alternative form of RPA (aRPA), which does not support DNA replication, can substitute for the checkpoint function of RPA in vitro, thus revealing a potential role for aRPA in the activation of ATR kinase. We also find that TopBP1 is recruited to RPA-ssDNA in a manner dependent on ATRIP and that the N terminus of TopBP1 is required for efficient recruitment and activation of ATR kinase.
Democracy, knowledge and critique: rethinking European universities beyond tradition and the market
Authors: Weymans Wim
Published: June 2010

In many European countries, universities are asked to become more market-oriented. Those who oppose this trend mostly invoke a traditional university ideal to make their case. This paper aims to look for a third way to conceptualise a university that is neither market-oriented nor traditionalist.
It finds such an alternative by looking at a democratic culture in which knowledge remains indeterminate and subject to debate. It concretely demonstrates that this alternative view allows us to identify problematic aspects of contemporary discourses on universities, as exemplified by the
European Commission's discourse. It ends by arguing that the alternative vision is more in tune with the grassroots reality of research and education than the market-oriented view.
Monoculture on the intellectual landscape: research performance evaluation
Authors: Ruth Damian
Published: June 2010

The metaphor of 'monoculture on the intellectual landscape' is used to analyse the effects of large-scale research management regimes. The metaphor of 'monoculture on the intellectual landscape', derived from Shiva's 'monocultures of the mind', is developed and illustrated with respect
to gender and ethnicity. The paper then discusses the production of knowledge in the context of monocultures of the mind, and concludes that large-scale research management regimes are inimical to healthy and diverse intellectual habitats.