bluuebunny/crossref_metadata_2025 huggingface dataset:
Multiferroic behavior and impedance spectroscopy of bilayered BiFeO3/CoFe2O4 thin films
Authors: Wu Jiagang , Wang John
Published: June 2009

Lead-free bilayered multiferroic thin films consisting of BiFeO3 (BFO) and CoFe2O4 (CFO) layers with different thicknesses were grown on SrRuO3-coated Pt/TiO2/SiO2/Si substrates by radio frequency sputtering. The effects of constituent layer thicknesses on the ferroelectric and magnetic behavior have been studied. The physical behaviors are shown to strongly depend on the thicknesses of the constituent layers. BFO (220 nm)/CFO (30 nm) bilayered thin film demonstrated much improved ferroelectric and ferromagnetic behavior (2Pr=144.2 μC/cm2, 2Ec=778.0 kV/cm, Ms=61.2 emu/cm3, and Hc=200.8 Oe) as compared to those of the single layer BFO thin film. The dielectric behavior and conductivity of BFO (220 nm)/CFO (30 nm) bilayered thin film were investigated as a function of both temperature (in the range of 294–534 K) and frequency (in the range of 10−1–106 Hz), where an activation energy of ∼1.11 eV for dielectric relaxation was demonstrated. From the conductivity behavior, an activation energies of ∼0.98 eV was derived for dc conductivity are, implying that oxygen vacancies are involved in the conduction of the BFO (220 nm)/CFO (30 nm) bilayered film.
Charge transfer at n-doped organic-organic heterojunctions
Authors: Zhao Wei , Kahn Antoine
Published: June 2009

The impact of n-doping on the electronic structure of two organic-organic heterojunctions (OOH) is investigated with ultraviolet photoemission spectroscopy. The two OOHs have a type II staggered gap configuration corresponding to donor-acceptor pairs applicable to photovoltaic cells. Both molecular top acceptor layers have large electron affinity, which leads to electron transfer from the donor layer. The result is a significant interface dipole (Δ∼0.4–0.6eV) between the two molecular films, at both undoped and doped interfaces, consistent with a stronger interaction between molecular constituents than in wide, largely overlapping, band gap OOHs.
Properties of undoped GaN/InGaN multi-quantum-wells and GaN/InGaN p-n junctions prepared by epitaxial lateral overgrowth
Authors: Polyakov A. Y. , Govorkov A. V. , Smirnov N. B. , Markov A. V. , Lee In-Hwan , Ju Jin-Woo , Karpov S. Yu. , Shmidt N. M. , Pearton S. J.
Published: June 2009

High resolution x-ray diffraction, electron beam induced current, capacitance-voltage profiling, admittance spectroscopy, deep level transient spectroscopy (DLTS), microcathodoluminescence (MCL) spectra and imaging were performed for multi-quantum-well (MQW) GaN/InGaN p-n junctions grown on epitaxial laterally overgrown (ELOG) n-GaN platform layers. These experiments show a very good crystalline quality of the MQW ELOG GaN/InGaN structures with a dislocation density of ∼106 cm−2 in the laterally overgrown ELOG wings regions. Admittance and DLTS spectra show the presence of a prominent electron-trap signal with activation energy ∼0.4 eV likely originating from electron activation from the lowest occupied state in the quantum wells. MCL spectra clearly show a redshift of luminescence in the laterally grown ELOG wings compared to the normally grown ELOG windows. Modeling based on solving Poisson–Schroedinger equations suggests that the main reason for the observed redshift is a higher indium content in the wings.
Characterization of ZnS-layer-inserted bulk-heterojunction organic solar cells by ac impedance spectroscopy
Authors: Kuwabara Takayuki , Nakamoto Masayuki , Kawahara Yoshitaka , Yamaguchi Takahiro , Takahashi Kohshin
Published: June 2009

A fluorine-doped tin oxide (FTO)/zinc sulfide (ZnS)/[6,6]-phenyl C61 butyric acid methyl ester (PCBM): regioregular poly(3-hexylthiophene) (P3HT)/poly(3,4-ethylenedioxylenethiophene): poly(4-styrene sulfonic acid) (PEDOT:PSS)/Au type organic solar cell (FTO/ZnS/PCBM:P3HT/PEDOT:PSS/Au, ZnS cell) with a 1 cm2 active area was first developed using transparent ZnS prepared on a FTO electrode by a chemical bath deposition method. The ZnS inserted solar cells were investigated by photocurrent-voltage (I-V) and ac impedance spectroscopy (IS) measurements. In photo I-V measurements, the ZnS cell exhibited scattered power conversion efficiencies (η) of 0.7%–1.2% when the FTO/ZnS electrode was not immersed in various aqueous solutions before the fabrication of the ZnS cells. In contrast, the solar cells with a surface-modified FTO/ZnS electrode by immersing in 0.1M Na2S solutions at pH 7–9 containing hydrosulfide ions (HS−) exhibited reproducible η of 1.5%–1.7%. The electric resistance components in the cell consisting of five layers were separately estimated by the IS measurement. The larger η of the solar cell using HS− modified ZnS was explained by the fact that the charge transport resistance at the ZnS/PCBM:P3HT interface became smaller due to this surface modification. When a continuous light irradiation was carried out for the modified cells, the resistance at the ZnS/PCBM:P3HT interface increased, being accompanied by the decrease in the η. That is, the cell performance was controlled mainly by charge transport velocity at the ZnS/PCBM:P3HT interface.
Structural and optical properties of GaAs(001) surfaces thermally annealed in dry N2 atmosphere
Authors: Morota Hiroaki , Adachi Sadao
Published: June 2009

Thermal annealing behaviors of GaAs(001) surfaces in dry N2 atmosphere have been studied by using spectroscopic ellipsometry (SE), optical microscopy, scanning electron microscopy, ex situ atomic force microscopy (AFM), x-ray photoelectron spectroscopy (XPS), and photoluminescence (PL) techniques. The SE data indicate that thermal annealing at temperatures T below 500 °C causes no or a little influence on the surface morphology. Microscopic roughening starts to occur at T>600 °C and exhibits a saturated roughness value at ∼800 °C. AFM observation confirms the presence of a microscopically roughened surface overlayer after annealing at T∼600–750 °C and a macroscopically roughened overlayer at above 700 °C. The XPS data indicate the removal of As2O3 oxide after annealing at above 500 °C; however, the Ga2O3 oxide is always observed regardless of annealing temperature, although its peak intensity becomes remarkably large at T∼700 °C and small at T≥800 °C. Annealing at T=1000 °C leads to deliquesced sample surface. The native GaAs oxide is also found to act as a passivation film against annealing-induced PL degradation for T below ∼400 °C.
Density functional calculations of shallow acceptor levels in Si
Authors: Wang Lin-Wang
Published: June 2009

We present a comprehensive study of the binding energies of B, Al, Ga, In, Tl shallow acceptors in bulk Si using density functional theory. Two approaches are used to calculate the binding energies. One is based on the eigenenergy of the single particle Kohn–Sham equation, and another is based on the total energy change during the impurity ionization process. Planewave pseudopotential Hamiltonian under local density approximation is used. A special potential patching method is presented which allows the calculation of 64 000 atom supercells needed for converging the eigenenergies. We found that the calculated impurity eigenenergies reproduce correctly the trend of the element dependence of the binding energy. But the calculated binding energies for In and Tl are much smaller than the experimental values. A linear response formula is derived which relates the total energy difference between the systems with occupied and unoccupied impurity to the impurity state eigenenergy and the impurity state self-interaction. However, the total energy difference gives much worse binding energies when compared to experiment due to the self-interaction error in the local density approximation. We conclude that one must go beyond the usual approximations of the density functional theory in order to predict accurately the binding energies of these shallow impurities.
Self-assembled chains of single layer InP/(In,Ga)P quantum dots on GaAs (001)
Authors: Ugur Asli , Hatami Fariba , Schmidbauer Martin , Hanke Michael , Masselink W. Ted
Published: June 2009

The formation of well-ordered chains of InP quantum dots on GaAs (001) substrates by using self-organized In0.48Ga0.52P surface undulations as a template is demonstrated. The ordering requires neither stacked layers of quantum dots nor substrate misorientation. The pronounced alignment of the InP quantum dots along [1¯10] is driven by linear undulations in the surface material composition and strain in a In0.48Ga0.52P buffer layer. Although the In0.48Ga0.52P buffer layer is nearly perfectly lattice matched to the GaAs substrate on average, grazing incidence x-ray scattering indicates that the undulation regions are In rich. These regions of increased In content and consequent increased strain act as a template for subsequent InP quantum dot growth. When the buffer layer is grown at lower temperatures, the undulations do not form and the InP quantum dots show no ordering.
Thick C60:ZnPc bulk heterojunction solar cells with improved performance by film deposition on heated substrates
Authors: Pfuetzner Steffen , Meiss Jan , Petrich Annette , Riede Moritz , Leo Karl
Published: June 2009

We study the influence of different substrate temperatures during the deposition of the ZnPc:C60 blend layer in bulk heterojunction organic solar cells. It is shown that substrate heating during evaporation leads to a significant improvement in the solar cell performance mainly due to an increase in photocurrent and fill factor (FF). This is attributed to improved morphology resulting in better charge carrier percolation pathways within the ZnPc:C60 blend, leading to reduced transport losses. Using this method, blend layer thicknesses of 150 nm are possible without loss in FF, which requires a three-dimensional interpenetrating network without isolated clusters. When heating the substrate up to 110 °C, an efficiency of 2.56% is achieved compared to 1.59% for an identical device prepared at room temperature.
Energy integral method model for the nonlinear dynamics of an axisymmetric thin liquid film falling on a vertical cylinder
Authors: Novbari Elena , Oron Alexander
Published: June 2009

The nonlinear dynamics of an axisymmetric liquid film falling on the outer surface of a vertical cylinder is investigated in this paper. Using the energy integral method we derive a set of two coupled evolution equations which constitute a first-order approximation to the original hydrodynamic equations. We carry out the linear stability analysis of the axially uniform axisymmetric flow of a liquid film in the framework of the evolution equations. The results of the linear theory are compared to experimental results and with several other relevant linear stability theories available in literature. Traveling wave solutions of the evolution equations are investigated and favorably compared to experiments and other nonlinear theories describing the dynamics of falling films on a vertical cylinder. A bifurcation structure of traveling wave flows is studied for the cases of fluids with both low and relatively large Kapitza number. Both γ1- and γ2-waves are found and investigated.
Grain boundary wetting and prewetting in Ni-doped Mo
Authors: Shi Xiaomeng , Luo Jian
Published: June 2009

Grain boundary (GB) wetting and prewetting in Ni-doped Mo are systematically evaluated via characterizing well-quenched specimens and thermodynamic modeling. In contrast to prior reports, the δ-NiMo phase does not wet Mo GBs in the solid state. In the solid-liquid two-phase region, the Ni-rich liquid apparently wets Mo GBs completely. Furthermore, high-resolution transmission electron microscopy demonstrates that nanometer-thick quasiliquid films persist at GBs into the single-phase region where the bulk liquid phase is no longer stable. This is interpreted as a case of GB prewetting. An analytical thermodynamic model is developed and validated; this model can be applied to other alloys.
Millimeter wave generation from a pseudospark-sourced electron beam
Authors: Yin H. , Cross A. W. , He W. , Phelps A. D. R. , Ronald K. , Bowes D. , Robertson C. W.
Published: June 2009

Experimental studies of the production and propagation of an electron beam from a multigap pseudospark discharge are presented. From a three-gap pseudospark, a beam up to 680 A was measured at the anode at an applied dc voltage of 23 kV. This beam can propagate downstream as far as 20 cm in a gaseous environment with no guiding magnetic field, which confirms that the transport of the electron beam was based on the neutralization of the space charge of the electron beam due to the ionization of the gas molecules by the beam itself. The beam is of very small size of 1–3 mm in diameter and is ideal to drive high frequency radiation. Higher energy electron beam pulses were generated using a 14-gap pseudospark discharge powered by a cable pulser capable of producing 120 ns duration and 170 kV voltage pulses. The beam measured had a current of up to 110 A. Interactions between the produced beam and a Ka-band Cherenkov maser and a W-band backward wave oscillator slow wave structure were simulated and designed. Millimeter wave pulses were detected from the Cherenkov maser and backward wave oscillator beam-wave interaction experiments.
Making a commercial atomic force microscope more accurate and faster using positive position feedback control
Authors: Mahmood I. A. , Moheimani S. O. Reza
Published: June 2009

This paper presents experimental implementation of a positive position feedback (PPF) control scheme for vibration and cross-coupling compensation of a piezoelectric tube scanner in a commercial atomic force microscope (AFM). The AFM is a device capable of generating images with extremely high resolutions down to the atomic level. It is also being used in applications that involve manipulation of matter at a nanoscale. Early AFMs were operated in open loop. Consequently, they were susceptible to piezoelectric creep, thermal drift, hysteresis nonlinearity, and scan-induced vibration. These effects tend to distort the generated image and slow down the scanning speed of the device. Recently, a new generation of AFMs has emerged that utilizes position sensors to measure displacements of the scanner in three dimensions. These AFMs are equipped with feedback control loops that work to minimize the adverse effects of hysteresis, piezoelectric creep, and thermal drift on the obtained image using proportional-plus-integral (PI) controllers. These feedback controllers are often not designed to deal with the highly resonant nature of an AFM’s scanner nor with the cross coupling between various axes. In this paper we illustrate the improvement in accuracy and imaging speed that can be achieved by using a properly designed feedback controller such as a PPF controller. Such controllers can be incorporated into most modern AFMs with minimal effort since they can be implemented in software with the existing hardware. Experimental results show that by implementing the PPF control scheme, relatively good images in comparison with a well-tuned PI controller can still be obtained up to line scan of 60 Hz.
The structure of a statistically steady turbulent boundary layer near a free-slip surface
Authors: Campagne G. , Cazalbou J.-B. , Joly L. , Chassaing P.
Published: June 2009

The interaction between a free-slip surface with unsheared but sustained turbulence is investigated in a series of direct numerical simulations. By changing (i) the distance between the (plane) source of turbulence and the surface, and (ii) the value of the viscosity, a set of five different data sets has been obtained in which the value of the Reynolds-number varies by a factor of 4. The observed structure of the interaction layer is in agreement with current knowledge, being made of three embedded sublayers: a blockage layer, a slip layer, and a Kolmogorov layer. Practical measures of the different thicknesses are proposed that lead to a new Reynolds-number scaling based on easy-to-evaluate surface quantities. This scaling is consistent with previous proposals but makes easier the comparison between free-surface flows when they differ by the characteristics of the distant turbulent field. Its use will be straightforward in a turbulence-modeling framework.
On the energy transfer to small scales in a discrete model of one-dimensional turbulence
Authors: Carati A. , Galgani L. , Santolini F.
Published: June 2009

We consider a discrete one-dimensional model that was investigated numerically by Daumont and Peyrard [Chaos 13, 624 (2003)] as a model for turbulence in fluids, i.e., for the energy transfer from large to small scales. They found numerically that there exist two different regimes for the energy spectrum at high energies and low energies, respectively, and gave an analytical explanation for the high-energy spectrum. An analytical explanation is given here for the low-energy spectrum, which corresponds to the laminar regime.
Structure of liquid phase change material AgInSbTe from density functional/molecular dynamics simulations
Authors: Akola J. , Jones R. O.
Published: June 2009

The liquid phase of the AgInSbTe phase change material Ag3.5In3.8Sb75.0Te17.7 has been studied using molecular dynamics/density functional simulations. The calculated structure factor and total pair distribution function agree very well with high-energy x-ray diffraction measurements. We find that: (a) there are signs of medium-range order, (b) Ag and In prefer to be near Te rather than Sb atoms, and promote octahedral coordination in association with Te, (c) Ag is the most mobile element, has the shortest bonds (2.8–2.9 Å) and the highest coordination (5.5), and is anionic with the largest effective charge, and (d) there are few cavities (4% of volume).
Optical near-field probe with embedded gallium scattering center
Authors: Isakov D. V. , Zhang Y. , Balk L. J. , Phang J. C. H.
Published: June 2009

An optical near-field probe is proposed in which gallium is embedded into the tip of a tapered optical glass fiber to form a scattering center. Gallium is embedded by implantation during the process of probe sharpening by a raster-scanned focused ion beam. Using quasielectrostatic approximation, it is predicted that the presence of gallium should improve the scattering efficiency by an order of magnitude in comparison with a probe without gallium implantation. Imaging of a polished waveguide with different probes shows that Ga implantation can improve the efficiency by 37 times.
Evaluation of the optical axis tilt of zinc oxide films via noncollinear second harmonic generation
Authors: Bovino F. A. , Larciprete M. C. , Belardini A. , Sibilia C.
Published: June 2009

We investigated noncollinear second harmonic generation form zinc oxide films, grown on glass substrates by dual ion beam sputtering technique. At a fixed incidence angle, the generated signal is investigated by scanning the polarization state of both fundamental beams. We show that the map of the generated signal as a function of polarization states of both pump beams, together with the analytical curves, allows to retrieve the orientation of the optical axis and eventually, its angular tilt, with respect to the surface normal.
Robust room temperature persistent photoconductivity in polycrystalline indium oxide films
Authors: Dixit A. , Panguluri Raghava P. , Sudakar C. , Kharel P. , Thapa P. , Avrutsky I. , Naik R. , Lawes G. , Nadgorny B.
Published: June 2009

We have investigated the effects of UV irradiation on the electrical and optical properties of polycrystalline In2O3 films. We found that UV illumination at a peak wavelength of 365 nm leads to a sharp drop in resistance and increase in carrier concentration. This highly conductive state persists for a timescale of hours in air at room temperature after illumination. We observe distinct changes in the optical absorption spectra and the associated change in carrier concentration, which is consistent with a Burstein–Moss shift of ∼0.1 eV. The relaxation rate of this persistent conducting state depends strongly on temperature. We find that the conductance relaxation in an oxygen-free environment can be described by a stretched exponential while the behavior of the samples in air is better described by a logarithmic relaxation, both of which may be associated with glassy behavior.
Relativistic, QED, and nuclear mass effects in the magnetic shielding of H3e
Authors: Rudziński Adam , Puchalski Mariusz , Pachucki Krzysztof
Published: June 2009

The magnetic shielding σ of H3e is studied. The complete relativistic corrections of order O(α2), leading QED corrections of order O(α3 ln α), and finite nuclear mass effects of order O(m/mN) are calculated with high numerical precision. The resulting theoretical predictions for σ=59.967 43(10)×10−6 are the most accurate to date among all elements and support the use of H3e as a NMR standard.
Resistive dependence of magnetic properties in nonvolatile Ti/Mn:TiO2/SrTi0.993Nb0.007O3/Ti memory device
Authors: Wu S. X. , Li X. Y. , Xing X. J. , Hu P. , Yu Y. P. , Li S. W.
Published: June 2009

We report the relationship of the magnetic properties of the Mn-doped TiO2(Mn:TiO2) thin film on SrTi0.993Ti0.007O3 substrate to the different resistance states of the Ti/Mn:TiO2/Nb:SrTiO3/Ti device. Initially, the device showed paramagnetic behavior without applying voltage. When the device was switched to low resistance state after applying a positive voltage, robust ferromagnetism was observed. In contrast, when a negative voltage was applied to switch to high resistance state, the device exhibited weak ferromagnetism. This electrically controllable ferromagnetism should be attributed to the tunability of oxygen-vacancy concentration in the Mn:TiO2 film by electric field.
Optimal control of the local electromagnetic response of nanostructured materials: Optimal detectors and quantum disguises.
Authors: Grigorenko Ilya , Rabitz Herschel
Published: June 2009

We consider the problem of optimization of an effective trapping potential in a nanostructure with a quasi-one-dimensional geometry. The optimization is performed to achieve certain target optical properties of the system. We formulate and solve the optimization problem for a nanostructure that serves either as a single molecule detector or as a “quantum disguise” for a single molecule.
Resistance to age-dependent thymic atrophy in long-lived mice that are deficient in pregnancy-associated plasma protein A
Authors: Vallejo Abbe N. , Michel Joshua J. , Bale Laurie K. , Lemster Bonnie H. , Borghesi Lisa , Conover Cheryl A.
Published: June 2009

Pregnancy-associated plasma protein A (PAPPA) is a metalloproteinase that controls the tissue availability of insulin-like growth factor (IGF). Homozygous deletion ofPAPPAin mice leads to lifespan extension. Since immune function is an important determinant of individual fitness, we examined the natural immune ecology ofPAPPA−/−mice and their wild-type littermates reared under specific pathogen-free condition with aging. Whereas wild-type mice exhibit classic age-dependent thymic atrophy, 18-month-oldPAPPA−/−mice maintain discrete thymic cortex and medulla densely populated by CD4+CD8+thymocytes that are capable of differentiating into single-positive CD4 and CD8 T cells. OldPAPPA−/−mice have high levels of T cell receptor excision circles, and have bone marrows enriched for subsets of thymus-seeding progenitors.PAPPA−/−mice have an overall larger pool of naive T cells, and also exhibit an age-dependent accumulation of CD44+CD43+memory T cells similar to wild-type mice. However, CD43+T cell subsets of oldPAPPA−/−mice have significantly lower prevalence of 1B11 and S7, glycosylation isoforms known to inhibit T cell activation with normal aging. In bioassays of cell activation, splenic T cells of oldPAPPA−/−mice have high levels of activation antigens and cytokine production, and also elicit Ig production by autologous B cells at levels equivalent to young wild-type mice. These data suggest an IGF-immune axis of healthy longevity. Controlling the availability of IGF in the thymus by targeted manipulation of PAPPA could be a way to maintain immune homeostasis during postnatal development and aging.
National differences in gender–science stereotypes predict national sex differences in science and math achievement
Authors: Nosek Brian A. , Smyth Frederick L. , Sriram N. , Lindner Nicole M. , Devos Thierry , Ayala Alfonso , Bar-Anan Yoav , Bergh Robin , Cai Huajian , Gonsalkorale Karen , Kesebir Selin , Maliszewski Norbert , Neto Félix , Olli Eero , Park Jaihyun , Schnabel Konrad , Shiomura Kimihiro , Tulbure Bogdan Tudor , Wiers Reinout W. , Somogyi Mónika , Akrami Nazar , Ekehammar Bo , Vianello Michelangelo , Banaji Mahzarin R. , Greenwald Anthony G.
Published: June 2009

About 70% of more than half a million Implicit Association Tests completed by citizens of 34 countries revealed expected implicit stereotypes associating science with males more than with females. We discovered that nation-level implicit stereotypes predicted nation-level sex differences in 8th-grade science and mathematics achievement. Self-reported stereotypes did not provide additional predictive validity of the achievement gap. We suggest that implicit stereotypes and sex differences in science participation and performance are mutually reinforcing, contributing to the persistent gender gap in science engagement.
Virtual endocast of
Ignacius graybullianus
(Paromomyidae, Primates) and brain evolution in early primates
Authors: Silcox Mary T. , Dalmyn Claire K. , Bloch Jonathan I.
Published: June 2009

Extant primates are distinctive among mammals in having relatively large brains. As stem primates, Paleogene plesiadapiforms provide direct information relevant to the earliest stages in the evolution of this characteristic. Here we describe a virtual endocast reconstructed from ultra high resolution X-ray computed tomography data for the paromomyid plesiadapiform
Ignacius graybullianus
(USNM 421608) from the early Eocene of Wyoming. This represents the most complete endocast known for a stem primate, allowing for an unprecedented study of both size and fine details of anatomy. Relative to fossil and extant euprimates,
I. graybullianus
had large olfactory lobes, but less caudal development of the cerebrum and a poorly demarcated temporal lobe, suggesting more emphasis on olfaction and a less well developed visual system. Although its brain was small compared to those of extant primates, the encephalization quotient of
I. graybullianus
is higher than that calculated for Paleocene
Plesiadapis cookei
and overlaps the lower portion of the range documented for fossil euprimates. Comparison to the basal gliroid
Rhombomylus
suggests that early primates exhibited some expansion of the cerebrum compared to their ancestors. The relatively small brain size of
I. graybullianus
, an arboreal frugivore, implies that neither arboreality nor frugivory was primarily responsible for the expanded brains of modern primates. However, the contrasts in features related to the visual system between
I. graybullianus
and fossil and extant euprimates suggest that improvements to these portions of the brain contributed to increases in brain size within Euprimates.
Growing up blind does not change the neural bases of Theory of Mind
Authors: Bedny Marina , Pascual-Leone Alvaro , Saxe Rebecca R.
Published: June 2009

Humans reason about the mental states of others; this capacity is called Theory of Mind (ToM). In typically developing adults, ToM is supported by a consistent group of brain regions: the bilateral temporoparietal junction (TPJ), medial prefrontal cortex (MPFC), precuneus (PC), and anterior temporal sulci (aSTS). How experience and intrinsic biological factors interact to produce this adult functional profile is not known. In the current study we investigate the role of visual experience in the development of the ToM network by studying congenitally blind adults. In experiment 1, participants listened to stories and answered true/false questions about them. The stories were either about mental or physical representations of reality (e.g., photographs). In experiment 2, participants listened to stories about people's beliefs based on seeing or hearing; people's bodily sensations (e.g., hunger); and control stories without people. Participants judged whether each story had positive or negative valance. We find that ToM brain regions of sighted and congenitally blind adults are similarly localized and functionally specific. In congenitally blind adults, reasoning about mental states leads to activity in bilateral TPJ, MPFC, PC, and aSTS. These brain regions responded more to passages about beliefs than passages about nonbelief representations or passages about bodily sensations. Reasoning about mental states that are based on seeing is furthermore similar in congenitally blind and sighted individuals. Despite their different developmental experience, congenitally blind adults have a typical ToM network. We conclude that the development of neural mechanisms for ToM depends on innate factors and on experiences represented at an abstract level, amodally.
Essential role of the Ly49A stalk region for immunological synapse formation and signaling
Authors: Ito Daisuke , Iizuka Yoshie-Matsubayashi , Katepalli Madhu P. , Iizuka Koho
Published: June 2009

NK cells use surface NK receptors to discriminate self from non-self. The NK receptor ligand-binding domain (NKD) has been considered the sole regulator of ligand binding. Using a prototypic murine NK receptor, Ly49A, we show that the membrane proximal nonligand binding ecto-domain (the stalk region) is critical to ligand binding and signaling. The stalk region is required for receptor binding to ligand on target cells (
trans
interaction), but is dispensable for receptor binding to ligand on the same cell (
cis
interaction). Also, signaling in a
trans
manner depends on the stalk region mediating the formation of the immunological synapse. Thus, our data modeling receptor function at the cellular level reveal an essential role for the stalk region as a specific mediator of receptor signal integration, by which NKD-ligand interactions at the interface initiate and deliver information to the spatially separated cytoplasmic domain.
Identification of a consensus motif in substrates bound by a Type I Hsp40
Authors: Kota Pradeep , Summers Daniel W. , Ren Hong-Yu , Cyr Douglas M. , Dokholyan Nikolay V.
Published: June 2009

Protein aggregation is a hallmark of a large and diverse number of conformational diseases. Molecular chaperones of the Hsp40 family (
Escherichia coli
DnaJ homologs) recognize misfolded disease proteins and suppress the accumulation of toxic protein species. Type I Hsp40s are very potent at suppressing protein aggregation and facilitating the refolding of damaged proteins. Yet, the molecular mechanism for the recognition of nonnative polypeptides by Type I Hsp40s such as yeast Ydj1 is not clear. Here we computationally identify a unique motif that is selectively recognized by Ydj1p. The motif is characterized by the consensus sequence GX[LMQ]{P}X{P}{CIMPVW}, where [XY] denotes either X or Y and {XY} denotes neither X nor Y. We further verify the validity of the motif by site-directed mutagenesis and show that substrate binding by Ydj1 requires recognition of this motif. A yeast proteome screen revealed that many proteins contain more than one stretch of residues that contain the motif and are separated by varying numbers of amino acids. In light of our results, we propose a 2-site peptide-binding model and a plausible mechanism of peptide presentation by Ydj1p to the chaperones of the Hsp70 family. Based on our results, and given that Ydj1p and its human ortholog Hdj2 are functionally interchangeable, we hypothesize that our results can be extended to understanding human diseases.
Chromosomal translocations induced at specified loci in human stem cells
Authors: Brunet Erika , Simsek Deniz , Tomishima Mark , DeKelver Russell , Choi Vivian M. , Gregory Philip , Urnov Fyodor , Weinstock David M. , Jasin Maria
Published: June 2009

The precise genetic manipulation of stem and precursor cells offers extraordinary potential for the analysis, prevention, and treatment of human malignancies. Chromosomal translocations are hallmarks of several tumor types where they are thought to have arisen in stem or precursor cells. Although approaches exist to study factors involved in translocation formation in mouse cells, approaches in human cells have been lacking, especially in relevant cell types. The technology of zinc finger nucleases (ZFNs) allows DNA double-strand breaks (DSBs) to be introduced into specified chromosomal loci. We harnessed this technology to induce chromosomal translocations in human cells by generating concurrent DSBs at 2 endogenous loci, the
PPP1R12C
/
p84
gene on chromosome 19 and the
IL2R
γ gene on the X chromosome. Translocation breakpoint junctions for t(19;X) were detected with nested quantitative PCR in a high throughput 96-well format using denaturation curves and DNA sequencing in a variety of human cell types, including embryonic stem (hES) cells and hES cell-derived mesenchymal precursor cells. Although readily detected, translocations were less frequent than repair of a single DSB by gene targeting or nonhomologous end-joining, neither of which leads to gross chromosomal rearrangements. While previous studies have relied on laborious genetic modification of cells and extensive growth in culture, the approach described in this report is readily applicable to primary human cells, including mutipotent and pluripotent cells, to uncover both the underlying mechanisms and phenotypic consequences of targeted translocations and other genomic rearrangements.
Extracellular thiol-assisted selenium uptake dependent on the x
c
−
cystine transporter explains the cancer-specific cytotoxicity of selenite
Authors: Olm Eric , Fernandes Aristi P. , Hebert Christina , Rundlöf Anna-Klara , Larsen Erik H. , Danielsson Olof , Björnstedt Mikael
Published: June 2009

The selenium salt selenite (SeO
3
2−
) is cytotoxic in low to moderate concentrations, with a remarkable specificity for cancer cells resistant to conventional chemotherapy. Our data show that selenium uptake and accumulation, rather than intracellular events, are crucial to the specific selenite cytotoxicity observed in resistant cancer cells. We show that selenium uptake depends on extracellular reduction, and that the extracellular environment is a key factor specific to selenite cytotoxicity. The extracellular reduction is mediated by cysteine, and the efficacy is determined by the uptake of cystine by the x
c
−
antiporter and secretion of cysteine by multidrug resistance proteins, both of which are frequently overexpressed by resistant cancer cells. This mechanism provides molecular evidence for the existence of an inverse relationship between resistance to conventional chemotherapy and sensitivity to selenite cytotoxicity, and highlights the great therapeutic potential in treating multidrug-resistant cancer.
The large contribution of projected HFC emissions to future climate forcing
Authors: Velders Guus J. M. , Fahey David W. , Daniel John S. , McFarland Mack , Andersen Stephen O.
Published: June 2009

The consumption and emissions of hydrofluorocarbons (HFCs) are projected to increase substantially in the coming decades in response to regulation of ozone depleting gases under the Montreal Protocol. The projected increases result primarily from sustained growth in demand for refrigeration, air-conditioning (AC) and insulating foam products in developing countries assuming no new regulation of HFC consumption or emissions. New HFC scenarios are presented based on current hydrochlorofluorocarbon (HCFC) consumption in leading applications, patterns of replacements of HCFCs by HFCs in developed countries, and gross domestic product (GDP) growth. Global HFC emissions significantly exceed previous estimates after 2025 with developing country emissions as much as 800% greater than in developed countries in 2050. Global HFC emissions in 2050 are equivalent to 9–19% (CO
2
-eq. basis) of projected global CO
2
emissions in business-as-usual scenarios and contribute a radiative forcing equivalent to that from 6–13 years of CO
2
emissions near 2050. This percentage increases to 28–45% compared with projected CO
2
emissions in a 450-ppm CO
2
stabilization scenario. In a hypothetical scenario based on a global cap followed by 4% annual reductions in consumption, HFC radiative forcing is shown to peak and begin to decline before 2050.
Structure and assembly of immature HIV
Authors: Briggs J. A. G. , Riches J. D. , Glass B. , Bartonova V. , Zanetti G. , Kräusslich H.-G.
Published: June 2009

The major structural components of HIV are synthesized as a 55-kDa polyprotein, Gag. Particle formation is driven by the self-assembly of Gag into a curved hexameric lattice, the structure of which is poorly understood. We used cryoelectron tomography and contrast-transfer-function corrected subtomogram averaging to study the structure of the assembled immature Gag lattice to ≈17-Å resolution. Gag is arranged in the immature virus as a single, continuous, but incomplete hexameric lattice whose curvature is mediated without a requirement for pentameric defects. The resolution of the structure allows positioning of individual protein domains. High-resolution crystal structures were fitted into the reconstruction to locate protein–protein interfaces involved in Gag assembly, and to identify the structural transformations associated with virus maturation. The results of this study suggest a concept for the formation of nonsymmetrical enveloped viruses of variable sizes.
NIH funding trajectories and their correlations with US health dynamics from 1950 to 2004
Authors: Manton Kenneth G. , Gu Xi-Liang , Lowrimore Gene , Ullian Arthur , Tolley H. Dennis
Published: June 2009

To determine optimal future National Institutes of Health (NIH) funding levels, the longitudinal correlation of the level of investment in NIH research with population changes in the risk of specific diseases should be analyzed. This is because NIH research is the primary source of new therapies and treatments for major chronic diseases, many of which were viewed as relatively untreatable in the 1950s. NIH research is also important in developing preventative and screening strategies to support public health interventions. These correlations are examined 1938 to 2004 for 4 major chronic diseases [cardiovascular disease (CVD), stroke, cancer, and diabetes] and the NIH institutes responsible for research for those diseases. This analysis shows consistent non-linear temporal correlations of funding to mortality rates across diseases. The economic implications of this are discussed assuming that improved health at later ages will allow projected declines in the rate of growth of the US labor force to be partly offset by a higher rate of labor force participation in the US elderly population due to reduced chronic disease risks and functional impairment.
MURC/Cavin-4 and cavin family members form tissue-specific caveolar complexes
Authors: Bastiani Michele , Liu Libin , Hill Michelle M. , Jedrychowski Mark P. , Nixon Susan J. , Lo Harriet P. , Abankwa Daniel , Luetterforst Robert , Fernandez-Rojo Manuel , Breen Michael R. , Gygi Steven P. , Vinten Jorgen , Walser Piers J. , North Kathryn N. , Hancock John F. , Pilch Paul F. , Parton Robert G.
Published: June 2009

Polymerase I and transcript release factor (PTRF)/Cavin is a cytoplasmic protein whose expression is obligatory for caveola formation. Using biochemistry and fluorescence resonance energy transfer–based approaches, we now show that a family of related proteins, PTRF/Cavin-1, serum deprivation response (SDR)/Cavin-2, SDR-related gene product that binds to C kinase (SRBC)/Cavin-3, and muscle-restricted coiled-coil protein (MURC)/Cavin-4, forms a multiprotein complex that associates with caveolae. This complex can constitutively assemble in the cytosol and associate with caveolin at plasma membrane caveolae. Cavin-1, but not other cavins, can induce caveola formation in a heterologous system and is required for the recruitment of the cavin complex to caveolae. The tissue-restricted expression of cavins suggests that caveolae may perform tissue-specific functions regulated by the composition of the cavin complex. Cavin-4 is expressed predominantly in muscle, and its distribution is perturbed in human muscle disease associated with Caveolin-3 dysfunction, identifying Cavin-4 as a novel muscle disease candidate caveolar protein.
T-bet is essential for encephalitogenicity of both Th1 and Th17 cells
Authors: Yang Yuhong , Weiner Jeffrey , Liu Yue , Smith Alan J. , Huss David J. , Winger Ryan , Peng Haiyan , Cravens Petra D. , Racke Michael K. , Lovett-Racke Amy E.
Published: June 2009

The extent to which myelin-specific Th1 and Th17 cells contribute to the pathogenesis of experimental autoimmune encephalomyelitis (EAE) is controversial. Combinations of interleukin (IL)-1β, IL-6, and IL-23 with transforming growth factor β were used to differentiate myelin-specific T cell receptor transgenic T cells into Th17 cells, none of which could induce EAE, whereas Th1 cells consistently transferred disease. However, IL-6 was found to promote the differentiation of encephalitogenic Th17 cells. Further analysis of myelin-specific T cells that were encephalitogenic in spontaneous EAE and actively induced EAE demonstrated that T-bet expression was critical for pathogenicity, regardless of cytokine expression by the encephalitogenic T cells. These data suggest that encephalitogenicity of myelin-specific T cells appears to be mediated by a pathway dependent on T-bet and not necessarily pathway-specific end products, such as interferon γ and IL-17.
Cardiac 12/15 lipoxygenase–induced inflammation is involved in heart failure
Authors: Kayama Yosuke , Minamino Tohru , Toko Haruhiro , Sakamoto Masaya , Shimizu Ippei , Takahashi Hidehisa , Okada Sho , Tateno Kaoru , Moriya Junji , Yokoyama Masataka , Nojima Aika , Yoshimura Michihiro , Egashira Kensuke , Aburatani Hiroyuki , Komuro Issei
Published: June 2009

To identify a novel target for the treatment of heart failure, we examined gene expression in the failing heart. Among the genes analyzed, Alox15 encoding the protein 12/15 lipoxygenase (LOX) was markedly up-regulated in heart failure. To determine whether increased expression of 12/15-LOX causes heart failure, we established transgenic mice that overexpressed 12/15-LOX in cardiomyocytes. Echocardiography showed that Alox15 transgenic mice developed systolic dysfunction. Cardiac fibrosis increased in Alox15 transgenic mice with advancing age and was associated with the infiltration of macrophages. Consistent with these observations, cardiac expression of monocyte chemoattractant protein 1 (MCP-1) was up-regulated in Alox15 transgenic mice compared with wild-type mice. Treatment with 12-hydroxy-eicosatetraenoic acid, a major metabolite of 12/15-LOX, increased MCP-1 expression in cardiac fibroblasts and endothelial cells but not in cardiomyocytes. Inhibition of MCP-1 reduced the infiltration of macrophages into the myocardium and prevented both systolic dysfunction and cardiac fibrosis in Alox15 transgenic mice. Likewise, disruption of 12/15-LOX significantly reduced cardiac MCP-1 expression and macrophage infiltration, thereby improving systolic dysfunction induced by chronic pressure overload. Our results suggest that cardiac 12/15-LOX is involved in the development of heart failure and that inhibition of 12/15-LOX could be a novel treatment for this condition.
Investigation and Control of an Outbreak of Enterobacter aerogenes Bloodstream Infection in a Neonatal Intensive Care Unit in Fiji
Authors: Narayan Swastika A. , Kool Jacob L. , Vakololoma Miriama , Steer Andrew C. , Mejia Amelita , Drake Anne , Jenney Adam , Turton Jane F. , Kado Joseph , Tikoduadua Lisi
Published: June 2009

Ten neonates developed blood stream infection with extended-spectrum β-lactamase-producing Enterobacter aerogenes in a neonatal intensive care unit in Fiji. The source of the outbreak was traced to a bag of contaminated normal saline in the ward, which was used for multiple patients. All isolates recovered from patients were indistinguishable from the bacteria recovered from the normal saline by pulsed-field gel electrophoresis. The outbreak was controlled using simple infection control practices such as reinforcement of strict hand hygiene policy, provision of single use vials of normal saline, and strict aseptic technique for injections.
A survey of across-target bioactivity results of small molecules in PubChem
Authors: Han Lianyi , Wang Yanli , Bryant Stephen H.
Published: June 2009

This work provides an analysis of across-target bioactivity results in the screening data deposited in PubChem. Two alternative approaches for grouping-related targets are used to examine a compound's across-target bioactivity. This analysis identifies compounds that are selectively active against groups of protein targets that are identical or similar in sequence. This analysis also identifies compounds that are bioactive across unrelated targets. Statistical distributions of compound' across-target selectivity provide a survey to evaluate target specificity of compounds by deriving and analyzing bioactivity profile across a wide range of biological targets for tested small molecules in PubChem. This work enables one to select target specific inhibitors, identify promiscuous compounds and better understand the biological mechanisms of target-small molecule interactions.

Contact:  ywang@ncbi.nlm.nih.gov; bryant@ncbi.nlm.nih.gov
Prestige centrality-based functional outlier detection in gene expression analysis
Authors: Torkamani Ali , Schork Nicholas J.
Published: June 2009

Motivation: Traditional gene expression analysis techniques capture an average gene expression state across sample replicates. However, the average signal across replicates will not capture activated gene networks in different states across replicates. For example, if a particular gene expression network is activated within a subset or all sample replicates, yet the activation state across the sample replicates differs by the specific genes activated in each replicate, the activation of this network will be washed out by averaging across replicates. This situation is likely to occur in single cell gene expression experiments or in noisy experimental settings where a small sub-population of cells contributes to the gene expression signature of interest.

Results and Implementation: In this light, we developed a novel network-based approach which considers gene expression within each replicate across its entire gene expression profile, and identifies outliers across replicates. The power of this method is demonstrated by its ability to enrich for distant metastasis related genes derived from noisy expression data of CD44+CD24-/low tumor initiating cells.

Contact:  atorkama@scripps.edu; atorkama@scrippshealth.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
Evaluation of the Wound Healing Potential of Achillea biebersteinii Afan. (Asteraceae) by In Vivo Excision and Incision Models
Authors: Akkol Esra Küpeli , Koca Ufuk , Pesin Ipek , Yilmazer Demet
Published: June 2009

Achillea species are widely used for diarrhea, abdominal pain, stomachache and healing of wounds in folk medicine. To evaluate the wound healing activity of the plant, extracts were prepared with different solvents; hexane, chloroform, ethyl acetate and methanol, respectively from the roots of Achillea biebersteinii. Linear incision by using tensiometer and circular excision wound models were employed on mice and rats. The wound healing effect was comparatively evaluated with the standard skin ointment Madecassol. The n‐hexane extract treated groups of animals showed 84.2% contraction, which was close to contraction value of the reference drug Madecassol (100%). On the other hand the same extract on incision wound model demonstrated a significant increase (40.1%) in wound tensile strength as compared to other groups. The results of histoptological examination supported the outcome of linear incision and circular excision wound models as well. The experimental data demonstrated that A. biebersteinii displayed remarkable wound healing activity.