bluuebunny/crossref_metadata_2025 huggingface dataset:
A soluble nonionic surfactant as electron injection material for high-efficiency inverted bottom-emission organic light emitting diodes
Authors: Xiong Tao , Wang Fengxia , Qiao Xianfeng , Ma Dongge
Published: September 2008

A soluble nonionic surfactant, polyethylenimine 80% ethoxylated (PEIE) solution, was used as the electron injection material in inverted bottom-emission organic light emitting diodes (OLEDs). The transparent PEIE film was formed on indium-tin-oxide cathode by simple spin-coating method and it was found that the electron injection was greatly enhanced. The devices with PEIE electron injection layer had achieved significant enhancement in luminance and efficiency. The maximum luminance reached 47 000 cd/m2, and the maximum luminance efficiency and power efficiency arrived at 19.7 cd/A and 10.6 lm/W, respectively. Our results indicate that PEIE is a promising electron injection material to realize high performance OLEDs.
Pinned emission from ultrasmall cadmium selenide nanocrystals
Authors: Dukes Albert D. , Schreuder Michael A. , Sammons Jessica A. , McBride James R. , Smith Nathanael J. , Rosenthal Sandra J.
Published: September 2008

We report pinning of the emission spectrum in ultrasmall CdSe nanocrystals with a diameter of 1.7 nm and smaller. It was observed that the first emission feature ceased to blueshift once the band edge absorption reached 420 nm, though the band edge absorption continued to blueshift with decreasing nanocrystal diameter.
Statistical analysis of the turbulent Reynolds stress and its link to the shear flow generation in a cylindrical laboratory plasma device
Authors: Yan Z. , Yu J. H. , Holland C. , Xu M. , Müller S. H. , Tynan G. R.
Published: September 2008

The statistical properties of the turbulent Reynolds stress arising from collisional drift turbulence in a magnetized plasma column are studied and a physical picture of turbulent driven shear flow generation is discussed. The Reynolds stress peaks near the maximal density gradient region, and is governed by the turbulence amplitude and cross-phase between the turbulent radial and azimuthal velocity fields. The amplitude probability distribution function (PDF) of the turbulent Reynolds stress is non-Gaussian and positively skewed at the density gradient maximum. The turbulent ion-saturation (Isat) current PDF shows that the region where the bursty Isat events are born coincides with the positively skewed non-Gaussian Reynolds stress PDF, which suggests that the bursts of particle transport appear to be associated with bursts of momentum transport as well. At the shear layer the density fluctuation radial correlation length has a strong minimum (∼4–6mm∼0.5Cs∕Ωci, where Cs is the ion acoustic speed and Ωci is the ion gyrofrequency), while the azimuthal turbulence correlation length is nearly constant across the shear layer. The results link the behavior of the Reynolds stress, its statistical properties, generation of bursty radially going azimuthal momentum transport events, and the formation of the large-scale shear layer.
Potential energy surfaces for the 1 A4′, 2 A4′ 1 A4″ and 2 A4″ states of Li3
Authors: Li Xuan , Brue Daniel A. , Parker Gregory A.
Published: September 2008

Global potential energy surfaces for the 1 A4′, 2 A4′, 1 A4″, and 2 A4″ spin-aligned states of Li3 are constructed as sums of a diatomics-in-molecules (DIM) term plus a three-body term. The DIM model, using a large basis set of 15 A4″ and 22 A4′ states, is used to obtain a “mixed-pairwise additive” contribution to the potential. A global fit of the three-body terms conserves the accuracy of the ab initio points of a full configuration-interaction calculation. The resulting fit accurately describes conical intersections for both the 1 A4′ and 2 A4′ surfaces with a root-mean-square (rms) deviation of 5.4×10−5 hartree in D∞h geometries and 1.2×10−4 hartree in C∞v geometries. The global fit appears to be quantitatively correct with a rms deviation of 1.8×10−4hartree for 1 A4′, 9.2×10−4 hartree for 2 A4′, 2.5×10−4 hartree for 1 A4″, and 5.1×10−4 hartree for 2 A4″. A possible diabolic conical intersection, also called an accidental degeneracy, in C2v geometries, indicating a seam of conical intersections in Cs geometries, is also found in ab initio calculations for A2 states. As shown in this example, the DIM procedure can be optimized to describe the geometric phase and nonadiabatic effects in multisurface potentials.
Fractional spins and static correlation error in density functional theory
Authors: Cohen Aron J. , Mori-Sánchez Paula , Yang Weitao
Published: September 2008

Electronic states with fractional spins arise in systems with large static correlation (strongly correlated systems). Such fractional-spin states are shown to be ensembles of degenerate ground states with normal spins. It is proven here that the energy of the exact functional for fractional-spin states is a constant, equal to the energy of the comprising degenerate pure-spin states. Dramatic deviations from this exact constancy condition exist with all approximate functionals, leading to large static correlation errors for strongly correlated systems, such as chemical bond dissociation and band structure of Mott insulators. This is demonstrated with numerical calculations for several molecular systems. Approximating the constancy behavior for fractional spins should be a major aim in functional constructions and should open the frontier for density functional theory to describe strongly correlated systems. The key results are also shown to apply in reduced density-matrix functional theory.
A mass analysis technique using coincidence measurements from the Interstellar Boundary Explorer-Hi (∼0.3–∼6 keV) detector
Authors: Allegrini F. , Ebert R. W. , Alquiza J. , Broiles T. , Dunn C. , McComas D. J. , Silva I. , Valek P. , Westlake J.
Published: September 2008

NASA’s Interstellar Boundary Explorer (IBEX) mission, scheduled to launch in October 2008, will make the first observations of charge exchange energetic neutral atoms (ENAs) produced near the edge of the heliosphere. IBEX will measure these ENAs with two ultra-high sensitivity, single-pixel ENA sensors in the energy range of ∼0.01–∼2 keV (IBEX-Lo) and ∼0.3–∼6 keV (IBEX-Hi), respectively. The primary purpose of IBEX is to measure hydrogen ENAs from the outer heliosphere, but it will also be sensitive to heavier species of ENAs produced anywhere throughout the solar system. For this study, we measured the coincidence response of the IBEX-Hi detector section to H, He, N, and O ions. Based on these results, we have developed an innovative technique in estimating the hydrogen to heavy ion ratio in the signal. This new technique can be applied more widely than the IBEX-Hi detector section, and the basic principle may be useful for other, future space and ground-based measurements.
Spin injection effects on exciton formation in organic semiconductors
Authors: Yunus M. , Ruden P. P. , Smith D. L.
Published: September 2008

The effects of spin-polarized electron and hole injection from ferromagnetic contacts on the formation and distribution of singlet and triplet excitons in a conjugated organic semiconductor are modeled. Electron and hole transport in the semiconductor are described by spin-dependent device equations for a structure resembling an organic light emitting diode. The formation of electron-hole pairs at a given site is modeled as a Langevin process, and the subsequent local relaxation into the lowest energy exciton states is described by rate equations. Once formed, excitons may recombine in the semiconductor or diffuse through the material and recombine at the contact interfaces. The model calculations yield steady-state spatial profiles for singlet and triplet excitons. It is shown that spin-polarized injection increases the formation of singlet excitons, and that the diffusion of excitons has significant effects on the triplet exciton profile.
Ultrafast imaging of transient electronic plasmas produced in conditions of femtosecond waveguide writing in dielectrics
Authors: Gawelda W. , Puerto D. , Siegel J. , Ferrer A. , Ruiz de la Cruz A. , Fernández H. , Solis J.
Published: September 2008

Femtosecond laser-induced plasmas in bulk dielectrics are imaged under waveguide writing conditions, for different polarizations, pulse durations, and processing depths, and their temporal evolution is measured using ultrafast pump-probe microscopy. The irradiation beam profile is elliptically shaped yielding a disklike focal volume. We demonstrate for doped phosphate glass that increasing the pulse duration improves the spatial distribution of deposited energy by minimizing beam filamentation and prefocal depletion effects. As a consequence, energy deposition in the desired volume is greatly enhanced. Our results identify key parameters for optimizing femtosecond laser processing of dielectrics and different strategies to minimize energy loss channels.
Escape patterns of chaotic magnetic field lines in a tokamak with reversed magnetic shear and an ergodic limiter
Authors: Kroetz T. , Roberto M. , da Silva E. C. , Caldas I. L. , Viana R. L.
Published: September 2008

The existence of a reversed magnetic shear in tokamaks improves the plasma confinement through the formation of internal transport barriers that reduce radial particle and heat transport. However, the transport poloidal profile is much influenced by the presence of chaotic magnetic field lines at the plasma edge caused by external perturbations. Contrary to many expectations, it has been observed that such a chaotic region does not uniformize heat and particle deposition on the inner tokamak wall. The deposition is characterized instead by structured patterns called magnetic footprints, here investigated for a nonmonotonic analytical plasma equilibrium perturbed by an ergodic limiter. The magnetic footprints appear due to the underlying mathematical skeleton of chaotic magnetic field lines determined by the manifold tangles. For the investigated edge safety factor ranges, these effects on the wall are associated with the field line stickiness and escape channels due to internal island chains near the flux surfaces. Comparisons between magnetic footprints and escape basins from different equilibrium and ergodic limiter characteristic parameters show that highly concentrated magnetic footprints can be avoided by properly choosing these parameters.
Solutions and symmetries of force-free magnetic fields
Authors: Tassi E. , Pegoraro F. , Cicogna G.
Published: September 2008

New analytical results concerning force-free magnetic fields are presented. A number of examples of exact solutions for two-dimensional nonlinear force-free fields described by the Liouville equation are shown. These include classical solutions, such as, the Gold–Hoyle field and the force-free Harris sheet as special cases. The connection between these solutions and the Lie point symmetries of the Liouville equation is illustrated. Lie point symmetries of the equation describing force-free magnetic fields in helical symmetry in cylindrical geometry are also investigated and an infinitesimal generator that, in the vicinity of the cylinder axis, makes it possible to transform purely radially dependent solutions into helically symmetric solutions, is found. Finally we point out the existence of a formal analogy between the equations for the vector potential components of a class of force-free fields and the equations of motion of a charged particle in a magnetic field. This analogy makes it possible to transfer known results from the theory of the motion of a charged particle, into the context of force-free magnetic fields. Explicit examples of such application are given.
Spin dependent tunneling spectroscopy in single crystalline bcc-Co/MgO/bcc-Co(001) junctions
Authors: Nishioka Shingo , Matsumoto Rie , Tomita Hiroyuki , Nozaki Takayuki , Suzuki Yoshishige , Itoh Hiroyoshi , Yuasa Shinji
Published: September 2008

We have measured the derivative conductance spectra of magnetic tunnel junctions with fully epitaxial bcc-Co electrodes and MgO barrier layers of various thicknesses. For all samples, clear peaks, caused by a minority Δ1 band in the bcc Co(001) electrodes, were observed at around 0.5 V. Below 0.7 V, the dI/dV spectra are essentially independent of the barrier layer thickness indicating the absence of scattering of any significance in the barrier layer and the validity of the coherent tunneling description in the single crystalline structure. Above 0.7 V, the spectra depend on the MgO barrier layer thickness. The contribution made to the conductivity by the intrinsic electronic structure in the MgO layer is discussed.
Transparent polymer Schottky contact for a high performance visible-blind ultraviolet photodiode based on ZnO
Authors: Nakano M. , Makino T. , Tsukazaki A. , Ueno K. , Ohtomo A. , Fukumura T. , Yuji H. , Akasaka S. , Tamura K. , Nakahara K. , Tanabe T. , Kamisawa A. , Kawasaki M.
Published: September 2008

We report on a high performance visible-blind Schottky ultraviolet photodiode composed of a ZnO (0001) bulk single crystal and a transparent conducting polymer, poly(3,4-ethylenedioxythiophene) poly(styrenesulfonate), fabricated with a simple spin-coating process at room temperature in air. The quantum efficiency as high as unity in ultraviolet region and a visible rejection ratio of about 103 were achieved in the spectral response of the photodiode under zero-bias condition. The normalized detectivity of the photodiode was evaluated to be 3.6×1014 cm Hz1/2/W at 370 nm.
Lateral diffusion of minority carriers in nBn based type-II InAs/GaSb strained layer superlattice detectors
Authors: Plis E. , Kim H. S. , Bishop G. , Krishna S. , Banerjee K. , Ghosh S.
Published: September 2008

We report on the investigation of lateral diffusion of minority carriers in nBn based InAs/GaSb strained layer superlattice photodetectors. Values of diffusion length of minority carriers were extracted from temperature dependent I-V measurements. The behavior of diffusion length as a function of applied bias, temperature, and composition of the barrier layer and the values ranging by two orders of magnitude from 77 to 250 K at the same value of applied bias were investigated. The obtained results suggest that at this point the lateral diffusion current could be the limiting factor of the MWIR nBn detector performance at low (<150 K) temperatures.
Atomic structure of postgrowth annealed epitaxial Fe/(001)GaAs interfaces
Authors: LeBeau James M. , Hu Qi O. , Palmstrøm Christopher J. , Stemmer Susanne
Published: September 2008

The interfacial atomic structure of epitaxial Fe films grown by molecular beam epitaxy on c(4×4) reconstructed (001) GaAs was investigated using high-angle annular dark-field imaging in scanning transmission electron microscopy. No extended interfacial reaction phase is observed and the image contrast is discussed in terms of the interface atomic configuration. The images show an As-terminated semiconductor. The interface consists of a single partially occupied plane inserted between the Fe film and the GaAs, which most likely is occupied by Fe. This interface structure provides strong evidence for preferential Fe–As bonding across the interface.
Current-perpendicular-to-plane giant magnetoresistance in spin-valve structures using epitaxial Co2FeAl0.5Si0.5/Ag/Co2FeAl0.5Si0.5 trilayers
Authors: Furubayashi T. , Kodama K. , Sukegawa H. , Takahashi Y. K. , Inomata K. , Hono K.
Published: September 2008

A current-perpendicular-to-plane giant magnetoresistance (CPP-GMR) spin valve using epitaxial layers of Co2FeAl0.5Si0.5 (CFAS) Heusler alloy as ferromagnetic electrodes is reported. A multilayer stack of Cr/Ag/CFAS/Ag/CFAS/Co75Fe25/Ir22Mn78/Ru was deposited on a MgO (001) single crystal substrate. Epitaxial growth of the Cr, Ag, and CFAS layers in the (001) orientation up to the top CFAS layer was confirmed. Large MR ratios of 6.9% at room temperature and 14% at 6 K were observed for the CPP-GMR device. High spin polarization of epitaxial CFAS is the possible reason for high MR ratios.
Origin of threshold voltage instability in indium-gallium-zinc oxide thin film transistors
Authors: Jeong Jae Kyeong , Won Yang Hui , Jeong Jong Han , Mo Yeon-Gon , Kim Hye Dong
Published: September 2008

We investigated the impact of the passivation layer on the stability of indium-gallium-zinc oxide (IGZO) thin film transistors. While the device without any passivation layer showed a huge threshold voltage (Vth) shift under positive gate voltage stress, the suitably passivated device did not exhibit any Vth shift. The charge trapping model, which has been believed to be a plausible mechanism, cannot by itself explain this behavior. Instead, the Vth instability was attributed to the interaction between the exposed IGZO backsurface and oxygen and/or water in the ambient atmosphere during the gate voltage stress.
High efficient photovoltaics in nanoscaled ferroelectric thin films
Authors: Qin Meng , Yao Kui , Liang Yung C.
Published: September 2008

Photovoltaic effect in ferroelectric thin films with thickness below 100nm was investigated through both theoretical and experimental approaches. Unprecedented high photovoltaic power conversion efficiency around ∼0.28% was achieved with epitaxial (Pb0.97La0.03)(Zr0.52Ti0.48)O3 ferroelectric thin films, which is about 2 orders of magnitude higher than the reported in literature for ferroelectrics. Theoretical analysis indicated that efficiency can be further significantly improved by reducing the thickness in nanoscale. Extremely high efficient bulk photovoltaic effect is predicted in high quality ferroelectric ultrathin films.
p
-type Fermi level pinning at a Si:Al2O3 model interface
Authors: Fonseca L. R. C. , Liu D. , Robertson J.
Published: September 2008

To understand the origin of p-type work function shifts in Al2O3-based gate stacks, we constructed two O-rich Si:Al2O3 interface models. A small periodic model is found to be insulating, with no interface states in the Si gap. A larger amorphous Al2O3 interface is found to have its Fermi level pinned in the Si valence band, due to an oxygen deficiency at the interface. This is a mechanism for p-type Fermi level shifts found in gate stacks containing Al2O3 layers.
High-power 1 kHz laser-plasma x-ray source for ultrafast x-ray absorption near-edge spectroscopy in the keV range
Authors: Dorchies F. , Harmand M. , Descamps D. , Fourment C. , Hulin S. , Petit S. , Peyrusse O. , Santos J. J.
Published: September 2008

A high average power broadband x-ray source is developed in the multi-keV range, based on the thermal emission of plasmas produced with a 1 kHz fs laser focused on high Z element target. This compact ultrafast x-ray source is used to measure the x-ray absorption near-edge spectroscopy of aluminum K-edge (1.559 keV) with noise lower than 1% of the absorption edge when accumulating laser shots over a few tens of seconds. That demonstrates its suitability to study atomic and electronic structures of matter during ultrafast phase transitions among solid, liquid, or higher energy density states.
Comparative Sb and As segregation at the InP on GaAsSb interface
Authors: Wallart X. , Godey S. , Douvry Y. , Desplanque L.
Published: September 2008

We study the formation of the InP on GaAsSb interface grown by molecular beam epitaxy at 450 °C. Using angle resolved x-ray photoemission spectroscopy (XPS), we show that Sb strongly segregates whereas As does not, leading to a Sb-rich InP surface. Similarly, XPS spectra recorded on air-exposed samples reveal oxidized Sb but no oxidized As. We perform a quantitative analysis and determine a Sb segregation coefficient very near to 1. This result is in good agreement with previous reflectance anisotropy spectroscopy observations on the same interface.
Performance enhancement of n-channel inversion type InxGa1−xAs metal-oxide-semiconductor field effect transistor using ex situ deposited thin amorphous silicon layer
Authors: Sonnet A. M. , Hinkle C. L. , Jivani M. N. , Chapman R. A. , Pollack G. P. , Wallace R. M. , Vogel E. M.
Published: September 2008

Significant enhancement in metal-oxide-semiconductor field effect transistor (MOSFET) transport characteristics is achieved with InxGa1−xAs (x=0.53, x=0.20) channel material using ex situ plasma enhanced chemical vapor deposited amorphous Si layer. InxGa1−xAs MOSFETs (L=2 μm, Vgs-Vt=2.0 V) with Si interlayer show a maximum drain current of 290 mA/mm (x=0.53) and 2 μA/mm (x=0.20), which are much higher compared to devices without a Si interlayer. However, charge pumping measurements show a lower average interface state density near the intrinsic Fermi level for devices without the silicon interlayer indicating that a reduction in the midgap interface state density is not responsible for the improved transport characteristics.
Microscopic theory of the electrocaloric effect in the paraelectric phase of potassium dihydrogen phosphate
Authors: Dunne Lawrence J. , Valant Matjaz , Manos George , Axelsson Anna-Karin , Alford Neil
Published: September 2008

Here we present a microscopic theory of the electrocaloric effect in potassium dihydrogen phosphate, KH2PO4, based on Slater’s lattice model. The model reproduces the essential features of the experimentally observed behavior and also gives a remarkably accurate description of the electric field dependence of the electrocaloric effect. The basic principle of the theory also gives guidelines for a theoretical analysis of other dielectrics and for the further development of materials with an enhanced electrocaloric effect.
Si metal-oxide-semiconductor field-effect transistor on Si-on-SiC directly bonded wafers with high thermal conductance
Authors: Shinohara Hiroshi , Kinoshita Hiroyuki , Yoshimoto Masahiro
Published: September 2008

Single-crystalline Si wafers were directly bonded to single-crystalline 6H-SiC wafers (Si-on-SiC), followed by thinning of the Si wafers to around 1μm. A Si metal-oxide-semiconductor field-effect transistor (MOSFET) was then fabricated on the Si layer. In a high-temperature atmosphere (∼300°C), the channel mobility of a Si MOSFET on a conventional Si wafer degraded by around 80%. The Si MOSFET fabricated on the Si-on-SiC wafer, however, showed almost no degradation in its channel mobility from heating. This confirmed that the high thermal conductivity of single-crystalline 6H-SiC improves the heat dissipation performance of Si MOSFETs.
Alkali incorporation control in Cu(In,Ga)Se2 thin films using silicate thin layers and applications in enhancing flexible solar cell efficiency
Authors: Ishizuka Shogo , Yamada Akimasa , Matsubara Koji , Fons Paul , Sakurai Keiichiro , Niki Shigeru
Published: September 2008

Control of the alkali doping level in Cu(In,Ga)Se2 (CIGS) films was demonstrated using alkali-silicate thin layers of various thickness deposited on substrates prior to the sputtering of the Mo back contact layer. Not only the alkali density in the CIGS film, but also the Ga composition distribution in CIGS films, CIGS grain size, and consequent photovoltaic performance showed variations with the silicate layer thickness. Using alkali-silicate thin layers as an alkali source material, 17.4% and 17.7% efficiency flexible CIGS solar cells have been demonstrated on Ti and zirconia substrates, respectively.
Antireflection coatings for two-dimensional photonic crystals using a rigorous impedance definition
Authors: Lawrence Felix J. , Botten Lindsay C. , Dossou Kokou B. , de Sterke C. Martijn
Published: September 2008

We show that no consistent scalar definition of impedance is generally possible for photonic crystals. Instead, we present a rigorous semianalytic matrix definition of impedance for square lattice photonic crystals, defined in terms of Bloch modes. We then apply our definition to design a range of multilayer photonic crystal antireflection coatings efficiently.
Characterization of Mn-modified Pb(Mg1∕3Nb2∕3)O3–PbZrO3–PbTiO3 single crystals for high power broad bandwidth transducers
Authors: Zhang Shujun , Lee Sung-Min , Kim Dong-Ho , Lee Ho-Yong , Shrout Thomas R.
Published: September 2008

The effect of MnO2 addition on the dielectric and piezoelectric properties of 0.4Pb(Mg1∕3Nb2∕3)O3–0.25PbZrO3–0.35PbTiO3 single crystals was investigated. Analogous to acceptor doping in “hard” Pb(Zr,Ti)O3 based polycrystalline materials, the Mn doped crystals exhibited enhanced mechanical Q (∼1050) with low dielectric loss (∼0.2%), while maintaining ultrahigh electromechanical coupling k33>90%, inherent in domain engineered single crystals. The effect of acceptor doping was also evident in the build-up of an internal bias (Ei∼1.6kV∕cm), shown by a horizontal offset in the polarization-field behavior. Together with the relatively high usage temperature (TR-T∼140°C), the Mn doped crystals are promising candidates for high power and broad bandwidth transducers.
Precision proteomics: The case for high resolution and high mass accuracy
Authors: Mann Matthias , Kelleher Neil L.
Published: September 2008

Proteomics has progressed radically in the last 5 years and is now on par with most genomic technologies in throughput and comprehensiveness. Analyzing peptide mixtures by liquid chromatography coupled to high-resolution mass spectrometry (LC-MS) has emerged as the main technology for in-depth proteome analysis whereas two-dimensional gel electrophoresis, low-resolution MALDI, and protein arrays are playing niche roles. MS-based proteomics is rapidly becoming quantitative through both label-free and stable isotope labeling technologies. The latest generation of mass spectrometers combines extremely high resolving power, mass accuracy, and very high sequencing speed in routine proteomic applications. Peptide fragmentation is mostly performed in low-resolution but very sensitive and fast linear ion traps. However, alternative fragmentation methods and high-resolution fragment analysis are becoming much more practical. Recent advances in computational proteomics are removing the data analysis bottleneck. Thus, in a few specialized laboratories, “precision proteomics” can now identify and quantify almost all fragmented peptide peaks. Huge challenges and opportunities remain in technology development for proteomics; thus, this is not “the beginning of the end” but surely “the end of the beginning.”
AP4 encodes a c-MYC-inducible repressor of
p21
Authors: Jung Peter , Menssen Antje , Mayr Doris , Hermeking Heiko
Published: September 2008

In the majority of human tumors, expression of the
c-MYC
oncogene becomes constitutive. Here, we report that c-MYC directly regulates the expression of
AP4
via CACGTG motifs in the first intron of the
AP4
gene. Induction of AP4 was required for c-MYC-mediated cell cycle reentry of anti-estrogen arrested breast cancer cells and mitogen-mediated repression of the CDK inhibitor p21. AP4 directly repressed
p21
by occupying four CAGCTG motifs in the
p21
promoter via its basic region. AP4 levels declined after DNA damage, and ectopic AP4 interfered with p53-mediated cell cycle arrest and sensitized cells to apoptosis induced by DNA damaging agents. AP4 expression blocked induction of
p21
by TGF-β in human keratinocytes and interfered with up-regulation of p21 and cell cycle arrest during monoblast differentiation. Notably, AP4 is specifically expressed in colonic progenitor and colorectal carcinoma cells. In conclusion, our results indicate that c-MYC employs AP4 to maintain cells in a proliferative, progenitor-like state.
The steady-state level of Mg-protoporphyrin IX is not a determinant of plastid-to-nucleus signaling in
Arabidopsis
Authors: Mochizuki Nobuyoshi , Tanaka Ryouichi , Tanaka Ayumi , Masuda Tatsuru , Nagatani Akira
Published: September 2008

The plastid plays a vital role in various cellular activities within plant cells including photosynthesis and other metabolic pathways. It is believed that the functional status of the plastid is somehow monitored by the nucleus to optimize the expression of genes encoding plastid proteins. The currently dominant model for plastid-derived signaling (“plastid signaling”) proposes that Mg-protoporphyrin IX (MgProto) is a negative signal that represses the expression of a wide range of nuclear genes encoding plastid-localized proteins when plastid development is inhibited. In this study, we have re-evaluated this hypothesis by quantifying the steady-state levels of MgProto (as well as its neighboring intermediates protoporphyrin IX and Mg-Proto monomethyl ester [MgProtoMe]) in
Arabidopsis
plants with altered plastid signaling responses as monitored by expression of the
Lhcb1
,
RBCS
,
HEMA1
,
BAM3
and
CA1
genes. In addition, we have examined the correlation between gene expression and MgProto (MgProtoMe) in a range of mutants and conditions in which the steady-state levels of MgProto (MgProtoMe) have been modified. Overall we found that there was no correlation between the steady-state levels of MgProto (MgProtoMe) and
Lhcb1
expression or with any of the other genes tested. Taking these results together, we propose that the current model on plastid signaling must be revised.
CTLA-4 blockade increases IFNγ-producing CD4
+
ICOS
hi
cells to shift the ratio of effector to regulatory T cells in cancer patients
Authors: Liakou Chrysoula I. , Kamat Ashish , Tang Derek Ng , Chen Hong , Sun Jingjing , Troncoso Patricia , Logothetis Christopher , Sharma Padmanee
Published: September 2008

Significant anti-tumor responses have been reported in a small subset of cancer patients treated with the immunotherapeutic agent anti-CTLA-4 antibody. All clinical trials to date, comprising over 3,000 patients, have been conducted in the metastatic disease setting, which allows for correlation of drug administration with clinical outcome but has limited analyses of intermediate biomarkers to indicate whether the drug has impacted human immune responses within the tumor microenvironment. We conducted a pre-surgical clinical trial in six patients with localized bladder cancer, which allowed for correlation of drug administration with biomarkers in both blood and tumor tissues but did not permit correlation with clinical outcome. We found that CD4 T cells from peripheral blood and tumor tissues of all treated patients had markedly increased expression of inducible costimulator (ICOS). These CD4
+
ICOS
hi
T cells produced IFN-gamma (IFNγ) and could recognize the tumor antigen NY-ESO-1. Increase in CD4
+
ICOS
hi
cells led to an increase in the ratio of effector to regulatory T cells. To our knowledge, these are the first immunologic changes reported in both tumor tissues and peripheral blood as a result of treatment with anti-CTLA-4 antibody, and they may be used to guide dosing and scheduling of this agent to improve clinical responses.
New auxin analogs with growth-promoting effects in intact plants reveal a chemical strategy to improve hormone delivery
Authors: Savaldi-Goldstein Sigal , Baiga Thomas J. , Pojer Florence , Dabi Tsegeye , Butterfield Cristina , Parry Geraint , Santner Aaron , Dharmasiri Nihal , Tao Yi , Estelle Mark , Noel Joseph P. , Chory Joanne
Published: September 2008

Plant growth depends on the integration of environmental cues and phytohormone-signaling pathways. During seedling emergence, elongation of the embryonic stem (hypocotyl) serves as a readout for light and hormone-dependent responses. We screened 10,000 chemicals provided exogenously to light-grown seedlings and identified 100 compounds that promote hypocotyl elongation. Notably, one subset of these chemicals shares structural characteristics with the synthetic auxins, 2,4-dichlorophenoxyacetic acid (2,4-D), and 1-naphthaleneacetic acid (1-NAA); however, traditional auxins (e.g., indole-3-acetic acid [IAA], 2,4-D, 1-NAA) have no effect on hypocotyl elongation. We show that the new compounds act as “proauxins” akin to prodrugs. Our data suggest that these compounds diffuse efficiently to the hypocotyls, where they undergo cleavage at varying rates, releasing functional auxins. To investigate this principle, we applied a masking strategy and designed a pro-2,4-D. Unlike 2,4-D alone, this pro-2,4-D enhanced hypocotyl elongation. We further demonstrated the utility of the proauxins by characterizing auxin responses in light-grown hypocotyls of several auxin receptor mutants. These new compounds thus provide experimental access to a tissue previously inaccessible to exogenous application of auxins. Our studies exemplify the combined power of chemical genetics and biochemical analyses for discovering and refining prohormone analogs with selective activity in specific plant tissues. In addition to the utility of these compounds for addressing questions related to auxin and light-signaling interactions, one can envision using these simple principles to study other plant hormone and small molecule responses in temporally and spatially controlled ways.
Identification of amino acids essential for the antiangiogenic activity of tumstatin and its use in combination antitumor activity
Authors: Eikesdal Hans Petter , Sugimoto Hikaru , Birrane Gabriel , Maeshima Yohei , Cooke Vesselina G. , Kieran Mark , Kalluri Raghu
Published: September 2008

Tumstatin is an angiogenesis inhibitor that binds to αvβ3 integrin and suppresses tumor growth. Previous deletion mutagenesis studies identified a 25-aa fragment of tumstatin (tumstatin peptide) within vitroantiangiogenic activity. Here, we demonstrate that systemic administration of this tumstatin peptide inhibits tumor growth and angiogenesis. Site-directed mutagenesis identified amino acids L, V, and D as essential for the antiangiogenic activity of tumstatin. The tumstatin peptide binds to αvβ3 integrin on proliferating endothelial cells and localizes to select tumor endotheliumin vivo. Using 3D molecular modeling, we identify a putative interaction interface for tumstatin peptide on αvβ3 integrin. The antitumor activity of the tumstatin peptide, in combination with bevacizumab (anti-VEGF antibody), displays significant improvement in efficacy against human renal cell carcinoma xenografts when compared with the single-agent use. Collectively, our results demonstrate that tumstatin peptide binds specifically to the tumor endothelium, and its antiangiogenic action is mediated by αvβ3 integrin, and, in combination with an anti-VEGF antibody it exhibits enhanced tumor suppression of renal cell carcinoma.
The effects of perceived parenting style on the propensity for illicit drug use: the importance of parental warmth and control
Authors: MONTGOMERY CATHARINE , FISK JOHN E. , CRAIG LAURA
Published: September 2008

Introduction and Aims. Research in adolescents has shown that parental warmth and control are important factors in drug use. The present study focused upon investigating perceived parental warmth and control in a sample of post‐adolescent ecstasy/polydrug users, and investigating their relationship to severity of drug use. Design and Methods. A total of 128 (65 male) ecstasy/polydrug users, 51 (17 male), cannabis‐only users and 54 (13 male) non‐users were recruited from a university population. All participants completed the parenting styles and drug use questionnaires. Results. Compared to non‐users, a greater proportion of ecstasy/polydrug users characterised their parents' style as neglectful. The modal style endorsed by non‐users was authoritative. Those who rated their parents' style as authoritative had significantly lower lifetime consumption and average dose of ecstasy relative to those describing their parents as neglectful. Again, relative to those describing their parents as neglectful, participants from authoritarian backgrounds had significantly smaller lifetime consumption of ecstasy and cocaine and significantly smaller average doses of cannabis, ecstasy and cocaine. Contrary to expectation, there was no significant association between perceived parental warmth and the severity of ecstasy use. Discussion and Conclusions. The present study is, to our knowledge, the first to quantify drug use, and relate it to perceived parental practices in a post‐adolescent sample of ecstasy/polydrug users. The results provide further support for the relationship between perceived parental control and drug use.
Bicoherence during confinement transitions in the TJ-II stellarator
Authors: van Milligen B.Ph. , Kalhoff T. , Pedrosa M.A. , Hidalgo C.
Published: September 2008

Bicoherence was computed for a number of discharges having confinement transitions, either induced by biasing or spontaneous, at the TJ-II stellarator. The bicoherence was computed for a variety of signals obtained using a reciprocating Langmuir probe system, but the main emphasis here is on the analysis of the poloidal electric field (E
θ).

During biasing, the auto-bicoherence of E
θ was significant only in a narrow radial range, in contrast to the fluctuation level of E
θ and the linear coherence between E
θ and E

r
(the radial electric field), which were affected over a very broad radial extension.

With spontaneous transitions, significant bicoherence was again detected only in a narrow radial range, associated with the position of the flow shear layer. The observations are consistent with the standard sheared flow model for confinement transitions.

The temporal asymmetry A of E
θ was also computed. During biasing, the region of strongly modified asymmetry was located inwards from the bicoherence maximum. This suggests that the detected bicoherence is not merely due to a change in the temporal shape of the signal.
Between a rock and a hot place: the core–mantle boundary
Authors: Wookey James , Dobson David P
Published: September 2008

The boundary between the rocky mantle and iron core, almost 2900 km below the surface, is physically the most significant in the Earth's interior. It may be the terminus for subducted surface material, the source of mantle plumes and a control on the Earth's magnetic field. Its properties also have profound significance for the thermochemical and dynamic evolution of the solid Earth. Evidence from seismology shows that D″ (the lowermost few hundred kilometres of the mantle) has a variety of anomalous features. Understanding the origin of these observations requires an understanding of the elastic and deformation properties of the deep Earth minerals. Core–mantle boundary pressures and temperatures are achievable in the laboratory using diamond anvil cell (DAC) apparatus. Such experiments have led to the recent discovery of a new phase, ‘post-perovskite’, which may explain many hitherto poorly understood properties of D″. Experimental work is also done using analogue minerals at lower pressures and temperatures; these circumvent some of the limits imposed by the small sample size allowed by the DAC. A considerable contribution also comes from theoretical methods that provide a wealth of otherwise unavailable information, as well as verification and refinement of experimental results. The future of the study of the lowermost mantle will involve the linking of the ever-improving seismic observations with predictions of material properties from theoretical and experimental mineral physics in a quantitative fashion, including simulations of the dynamics of the deep Earth. This has the potential to dispel much of the mystery that still surrounds this remote but important region.
The atmospheric ocean: eddies and jets in the Antarctic Circumpolar Current
Authors: Thompson Andrew F
Published: September 2008

Although the Antarctic Circumpolar Current (ACC) is the longest and the strongest oceanic current on the Earth and is the primary means of inter-basin exchange, it remains one of the most poorly represented components of global climate models. Accurately describing the circulation of the ACC is made difficult owing to the prominent role that mesoscale eddies and jets, oceanic equivalents of atmospheric storms and storm tracks, have in setting the density structure and transport properties of the current. The successes and limitations of different representations of eddy processes in models of the ACC are considered, with particular attention given to how the circulation responds to changes in wind forcing. The dynamics of energetic eddies and topographically steered jets may both temper and enhance the sensitivity of different aspects of the ACC's circulation to changes in climate.
Mathematical models of plant–soil interaction
Authors: Roose Tiina , Schnepf Andrea
Published: September 2008

In this paper, we set out to illustrate and discuss how mathematical modelling could and should be applied to aid our understanding of plants and, in particular, plant–soil interactions. Our aim is to persuade members of both the biological and mathematical communities of the need to collaborate in developing quantitative mechanistic models. We believe that such models will lead to a more profound understanding of the fundamental science of plants and may help us with managing real-world problems such as food shortages and global warming. We start the paper by reviewing mathematical models that have been developed to describe nutrient and water uptake by a single root. We discuss briefly the mathematical techniques involved in analysing these models and present some of the analytical results of these models. Then, we describe how the information gained from the single-root scale models can be translated to root system and field scales. We discuss the advantages and disadvantages of different mathematical approaches and make a case that mechanistic rather than phenomenological models will in the end be more trustworthy. We also discuss the need for a considerable amount of effort on the fundamental mathematics of upscaling and homogenization methods specialized for branched networks such as roots. Finally, we discuss different future avenues of research and how we believe these should be approached so that in the long term it will be possible to develop a valid, quantitative whole-plant model.
Introduction. Progress in Earth science and climate studies
Authors: Thompson J. Michael T
Published: September 2008

In this introductory paper, I review the ‘visions of the future’ articles prepared by top young scientists for the second of the two Christmas 2008 Triennial Issues of
Phil. Trans. R. Soc.
A
, devoted respectively to astronomy and Earth science. Topics covered in the Earth science issue include: trace gases in the atmosphere; dynamics of the Antarctic circumpolar current; a study of the boundary between the Earth's rocky mantle and its iron core; and two studies of volcanoes and their plumes. A final section devoted to ecology and climate covers: the mathematical modelling of plant–soil interactions; the effects of the boreal forests on the Earth's climate; the role of the past palaeoclimate in testing and calibrating today's numerical climate models; and the evaluation of these models including the quantification of their uncertainties.
Sequencing of natural strains of Arabidopsis thaliana with short reads
Authors: Ossowski Stephan , Schneeberger Korbinian , Clark Richard M. , Lanz Christa , Warthmann Norman , Weigel Detlef
Published: September 2008

Whole-genome hybridization studies have suggested that the nuclear genomes of accessions (natural strains) of Arabidopsis thaliana can differ by several percent of their sequence. To examine this variation, and as a first step in the 1001 Genomes Project for this species, we produced 15- to 25-fold coverage in Illumina sequencing-by-synthesis (SBS) reads for the reference accession, Col-0, and two divergent strains, Bur-0 and Tsu-1. We aligned reads to the reference genome sequence to assess data quality metrics and to detect polymorphisms. Alignments revealed 823,325 unique single nucleotide polymorphisms (SNPs) and 79,961 unique 1- to 3-bp indels in the divergent accessions at a specificity of >99%, and over 2000 potential errors in the reference genome sequence. We also identified >3.4 Mb of the Bur-0 and Tsu-1 genomes as being either extremely dissimilar, deleted, or duplicated relative to the reference genome. To obtain sequences for these regions, we incorporated the Velvet assembler into a targeted de novo assembly method. This approach yielded 10,921 high-confidence contigs that were anchored to flanking sequences and harbored indels as large as 641 bp. Our methods are broadly applicable for polymorphism discovery in moderate to large genomes even at highly diverged loci, and we established by subsampling the Illumina SBS coverage depth required to inform a broad range of functional and evolutionary studies. Our pipeline for aligning reads and predicting SNPs and indels, SHORE, is available for download at http://1001genomes.org.
Characterization of expressed sequence tags from turkey skeletal muscle
Authors: Reed K. M. , Mendoza K. M. , Juneja B. , Fahrenkrug S. C. , Velleman S. , Chiang W. , Strasburg G. M.
Published: September 2008

This study was designed to identify important muscle gene homologues in the turkey. Three skeletal muscle cDNA libraries representing distinct muscle developmental stages were constructed. A total of 20 042 clones were sequenced resulting in 13 023 finished high‐quality sequences (trimmed, quality scored and masked) for analysis. Sequence clustering produced 1113 contigs and 4144 singletons (5257 putative transcripts). Sequences were compared by blastn to the chicken whole‐genome sequence and to the Ensembl and NCBI databases to identify homologous sequences. These surveys indicated that most of the important muscle genes are included in the sequence collection. Examination of contigs identified 1288 single nucleotide polymorphisms and in 320 of those the minor allele was observed to be present in more than one sequence. This resource provides sequence variants for numerous genes in the turkey, as demonstrated by the SNP haplotypes that were constructed for 10 genes. Sequences obtained in this study provide the basis for constructing a skeletal muscle‐focused microarray, a tool that will facilitate the analysis of genes expressed during turkey muscle development, as well as the expression of genes underlying the genetic basis of muscle characteristics associated with meat quality.
Polymorphisms in eggshell organic matrix genes are associated with eggshell quality measurements in pedigree Rhode Island Red hens
Authors: Dunn I. C. , Joseph N. T. , Bain M. , Edmond A. , Wilson P. W. , Milona P. , Nys Y. , Gautron J. , Schmutz M. , Preisinger R. , Waddington D.
Published: September 2008

Novel and traditional eggshell quality measurements were made from up to 2000 commercial pedigree hens for a candidate gene association analysis with organic eggshell matrix genes: ovocleidin‐116, osteopontin (SPP1), ovocalyxin‐32 (RARRES1), ovotransferrin (LTF), ovalbumin and ovocalyxin‐36, as well as key genes in the maintenance and function of the shell gland [estrogen receptor (ESR1) and carbonic anhydrase II (CAII)]. Associations were found for (i) ovalbumin with breaking strength and shell thickness; (ii) ovocleidin‐116 with elastic modulus, shell thickness and egg shape; (iii) RARRES1 with mammillary layer thickness; (iv) ESR1 with dynamic stiffness; (v) SPP1 with fracture toughness and (vi) CAII with egg shape. The marker effects are as large as 17% of trait standard deviations and could be used to improve eggshell quality.