bluuebunny/crossref_metadata_2025 huggingface dataset:
Water storage change in the Himalayas from the Gravity Recovery and Climate Experiment (GRACE) and an empirical climate model
Authors: Moiwo Juana Paul , Yang Yonghui , Tao Fulu , Lu Wenxi , Han Shumin
Published: July 2011

The Himalayas and Tibetan Plateau harbor hundreds of mountain lakes along with thousands of glaciers and high‐elevation snowfields. This is the source of water for the upper reaches of Asia's main river systems, providing the livelihood for millions of people in the subregion. Climate change is therefore critical for the Himalaya snow and glacier hydrology, the dependent ecosystems, and the people. Whereas temperature and precipitation are common indicators for climate change, snow and glacier dynamics are reliable precursors of a warming or cooling climate. This study uses a simple empirical climate model (ECM) and the Gravity Recovery and Climate Experiment (GRACE) satellite data to analyze water storage dynamics in the 5.072 × 106 km2 Himalayas and Tibetan Plateau region. About 72 consecutive months (January 2003 through December 2008) of data are used in the study. The temperature and precipitation (snow plus rain) data are acquired from the Global Land Data Assimilation System (GLDAS) Noah land surface model and are validated with ground truth data from 205 meteorological stations. Total water storage change derived from the GRACE gravity data is fitted with a simple sinusoidal least squares regression model. A favorable agreement exists between the GRACE and sinusoidal curve (R2 = 0.81 and root‐mean‐square error (RMSE) = 8.73 mm), suggesting that random errors in GRACE data are small. However, the sinusoidal fit does not quantify systematic errors in GRACE data. Agreements between the GRACE‐ and ECM‐estimated storage changes are also favorable at both monthly (R2 = 0.93, RMSE = 5.46 mm) and seasonal (R2 = 0.83, RMSE = 7.64 mm) cycles. The agreements (significant at p < 0.01) indicate not only GRACE's ability to detect storage signal but also that of the ECM model to characterize storage change in the snow and glacier hydrology. There is clear seasonality in the storage anomaly, with the highest in summer and lowest in winter. The corresponding storage change is delayed by a quarter of the year. The GRACE and ECM model indicate an overall negative storage trend of 0.36 ± 0.03 mm/month or 21.91 ± 1.95 km3/yr for the study area (significant at p < 0.1). Given that snow and glaciers are particularly sensitive to temperature change, the negative storage trend could be indicative of warming climate conditions in the region. Groundwater abstraction (mainly for irrigation) in the southern plains, coupled with dwindling snowfall in the northern massifs, is a critical storage loss factor in the region. Invariably, storage loss in the Himalayan‐Tibetan Plateau region could have negative implications for the hydrology, dependent ecosystems, and livelihoods of millions of people.
Revitalizing urban waterways
Authors: Showstack Randy
Published: July 2011

Eleven U.S. federal agencies have joined together in a new initiative to protect and revitalize urban waterways and communities. The Urban Waters Federal Partnership, announced on 24 June, is focusing on seven pilot locations to help urban communities reconnect with and revitalize their waterways, according to Lisa Jackson, administrator of the U.S. Environmental Protection Agency (EPA), which launched the initiative. “Urban waters have the potential to support healthy environments, growing businesses, and educational and recreational activities. By bringing together the experience and expertise of multiple federal partners, we have a chance to reconnect local residents, young people, and community groups with the environmental resources all around them,” she said.
Outstanding student paper awards
Authors: Anonymous
Published: July 2011

The following members received Outstanding Student Paper Awards at the 2010 AGU Meeting of the Americas, in Foz do Iguaçu, Brazil.
Hematopoiesis leading to a diversity of dendritic antigen‐presenting cell types
Authors: Petvises Sawang , O'Neill Helen C
Published: July 2011

Hematopoietic stem cells (HSCs) undergo expansion and differentiation, giving rise to all terminally differentiated blood cells throughout life. HSCs are found in distinct anatomical sites during development, and in adults, hematopoiesis occurs predominantly on the luminal side of the bone cavity in bone marrow. Millions of newly formed blood cells are generated per second to accommodate the short half‐life of hematopoietic cells. For this to happen, HSCs must sustain their self‐renewal capacity as well as their capability to commit and differentiate toward multiple cell lineages. Development of the hematopoietic system is finely regulated as the animal ages, so that it does not become exhausted or misdirected. This review covers aspects of hematopoietic development from the embryonic period through adult life in relation to development of dendritic cells. It also considers a role for HSCs in extramedullary sites and their possible role in myelopoiesis, with formation of tissue‐specific antigen‐presenting cells.
Interaction between the SH3 domain of Src family kinases and the proline-rich motif of HTLV-1 p13: a novel mechanism underlying delivery of Src family kinases to mitochondria
Authors: Tibaldi Elena , Venerando Andrea , Zonta Francesca , Bidoia Carlo , Magrin Elisa , Marin Oriano , Toninello Antonio , Bordin Luciana , Martini Veronica , Pagano Mario Angelo , Brunati Anna Maria
Published: July 2011

The association of the SH3 (Src homology 3) domain of SFKs (Src family kinases) with protein partners bearing proline-rich motifs has been implicated in the regulation of SFK activity, and has been described as a possible mechanism of relocalization of SFKs to subcellular compartments. We demonstrate in the present study for the first time that p13, an accessory protein encoded by the HTLV-1 (human T-cell leukaemia virus type 1), binds the SH3 domain of SFKs via its C-terminal proline-rich motif, forming a stable heterodimer that translocates to mitochondria by virtue of its N-terminal mitochondrial localization signal. As a result, the activity of SFKs is dramatically enhanced, with a subsequent increase in mitochondrial tyrosine phosphorylation, and the recognized ability of p13 to insert itself into the inner mitochondrial membrane and to perturb the mitochondrial membrane potential is abolished. Overall, the present study, in addition to confirming that the catalytic activity of SFKs is modulated by interactors of their SH3 domain, leads us to hypothesize a general mechanism by which proteins bearing a proline-rich motif and a mitochondrial localization signal at the same time may act as carriers of SFKs into mitochondria, thus contributing to the regulation of mitochondrial functions under various pathophysiological conditions.
The histone variant H2A.Z interconverts two stable epigenetic chromatin states
Authors: Zhao Jin , Siew Wee Leng , Sun Weiqi , Lehming Norbert
Published: July 2011

The nucleosomes occupying the chromosomal start sites of transcription contain the histone H2A variant H2A.Z in place of H2A. Upon galactose induction, nucleosomes are evicted from the GAL1 locus in Saccharomyces cerevisiae cells. H2A.Z (which is encoded by the HTZ1 gene in S. cerevisiae) is required for the eviction of the GAL1 promoter nucleosome and for the transcriptional activation of the GAL1 gene; however, histones are also important for transcriptional repression and we asked in the present paper if H2A.Z also plays a role in the glucose repression of the GAL1 promoter. With the help of a fusion of the URA3 ORF (open reading frame) to the GAL1 promoter, we were able to detect two different epigenetic transcription states of the GAL1 promoter in glucose-grown cells lacking H2A.Z: a repressed state that is occupied by a H2A-containing nucleosome and a derepressed state that is nucleosome-free. These two chromatin states are inherited stably through many cell divisions. According to the model described in the present paper, the role of H2A.Z is to facilitate the addition and removal of promoter nucleosomes and to prevent the formation of unfavourable stable epigenetic chromatin structures, which are not in accordance with the environmental conditions.
MAL, but not MAL2, expression promotes the formation of cholesterol-dependent membrane domains that recruit apical proteins
Authors: Ramnarayanan Sai P. , Tuma Pamela L.
Published: July 2011

Our recent studies have been aimed at understanding the mechanisms regulating apical protein sorting in polarized epithelial cells. In particular, we have been investigating how lipid rafts serve to sort apical proteins in the biosynthetic pathway. The recent findings that lipid domains are too small or transient to host apically destined cargo have led to newer versions of the hypothesis that invoke proteins required for lipid domain coalescence and stabilization. MAL (myelin and lymphocyte protein) and its highly conserved family member, MAL2, have emerged as possible regulators of this process in the direct and indirect apical trafficking pathways respectively. To test this possibility, we took a biochemical approach. We determined that MAL, but not MAL2, self-associates, forms higher-order cholesterol-dependent complexes with apical proteins and promotes the formation of detergent-resistant membranes that recruit apical proteins. Such biochemical properties are consistent with a role for MAL in raft coalescence and stabilization. These findings also support a model whereby hydrophobic mismatch between the long membrane-spanning helices of MAL and the short-acyl-chain phospholipids in the Golgi drive formation of lipid domains rich in raft components that are characterized by a thicker hydrophobic core to alleviate mismatch.
Thioredoxin and dihydrolipoic acid are required for 3-mercaptopyruvate sulfurtransferase to produce hydrogen sulfide
Authors: Mikami Yoshinori , Shibuya Norihiro , Kimura Yuka , Nagahara Noriyuki , Ogasawara Yuki , Kimura Hideo
Published: July 2011

H2S (hydrogen sulfide) has recently been recognized as a signalling molecule as well as a cytoprotectant. We recently demonstrated that 3MST (3-mercaptopyruvate sulfurtransferase) produces H2S from 3MP (3-mercaptopyruvate). Although a reducing substance is required for an intermediate persulfide at the active site of 3MST to release H2S, the substance has not been identified. In the present study we show that Trx (thioredoxin) and DHLA (dihydrolipoic acid) associate with 3MST to release H2S. Other reducing substances, such as NADPH, NADH, GSH, cysteine and CoA, did not have any effect on the reaction. We also show that 3MST produces H2S from thiosulfate. The present study provides a new insight into a mechanism for the production of H2S by 3MST.
Effect of substrate features and mutagenesis of active site tyrosine residues on the reaction course catalysed by Trypanosoma brucei sterol C-24-methyltransferase
Authors: Liu Jialin , Ganapathy Kulothungan , Wywial Ewa , Bujnicki Janusz M. , Nwogwugwu Chizaram A. , Nes W. David
Published: July 2011

TbSMT [Trypanosoma brucei 24-SMT (sterol C-24-methyltransferase)] synthesizes an unconventional 24-alkyl sterol product set consisting of Δ24(25)-, Δ24(28)- and Δ25(27)-olefins. The C-methylation reaction requires Si(β)-face C-24-methyl addition coupled to reversible migration of positive charge from C-24 to C-25. The hydride shifts responsible for charge migration in formation of multiple ergostane olefin isomers catalysed by TbSMT were examined by incubation of a series of sterol acceptors paired with AdoMet (S-adenosyl-L-methionine). Results obtained with zymosterol compared with the corresponding 24-2H and 27-13C derivatives revealed isotopic-sensitive branching in the hydride transfer reaction on the path to form a 24-methyl-Δ24(25)-olefin product (kinetic isotope effect, kH/kD=1.20), and stereospecific CH3→CH2 elimination at the C28 branch and C27 cis-terminal methyl to form Δ24(28) and Δ25(27) products respectively. Cholesta-5,7,22,24-tetraenol converted into ergosta-5,7,22,24(28)-tetraenol and 24β–hydroxy ergosta-5,7,23-trienol (new compound), whereas ergosta-5,24-dienol converted into 24-dimethyl ergosta-5,25(27)-dienol and cholesta-5,7,24-trienol converted into ergosta-5,7,25(27)trienol, ergosta-5,7,24(28)-trienol, ergosta-5,7,24-trienol and 24 dimethyl ergosta-5,7,25(27)-trienol. We made use of our prior research and molecular modelling of 24-SMT to identify contact amino acids that might affect catalysis. Conserved tyrosine residues at positions 66, 177 and 208 in TbSMT were replaced with phenylalanine residues. The substitutions generated variable loss of activity during the course of the first C-1-transfer reaction, which differs from the corresponding Erg6p mutants that afforded a gain in C-2-transfer activity. The results show that differences exist among 24-SMTs in control of C-1- and C-2-transfer activities by interactions of intermediate and aromatic residues in the activated complex and provide an opportunity for rational drug design of a parasite enzyme not synthesized by the human host.
Temperature dependence of scattering phases and Friedel phase discontinuity in quantum wires
Authors: Vargiamidis Vassilios , Fessatidis Vassilios
Published: July 2011

Two important issues concerning the scattering phases in a quantum wire with an attractive scatterer are investigated. We consider the case of two quasibound states which couple to a scattering channel and give rise to two Fano resonances. First, we examine the effects of temperature on the phase of the transmission amplitude and the Friedel phase. It is shown that temperature effects tend to smear sharp features of the transmission phase; namely, the phase drops become less than π, and acquire finite widths which increase linearly in the low-temperature regime. The influence of temperature on the Friedel phase and density of states becomes stronger as the Fano resonance becomes narrower. Second, we examine the behavior of the Friedel phase when the energy of the incident electron crosses an infinitely narrow Fano resonance, forming bound state in the continuum. It is shown that the Friedel phase exhibits abrupt jump of π at this energy. We discuss this odd behavior in relation to the Friedel sum rule and point out its consequences on the charge in the scattering region.
Effect of metallic Mg insertion on the magnetoresistance effect in MgO-based tunnel junctions using D22-Mn3-δGa perpendicularly magnetized spin polarizer
Authors: Kubota Takahide , Mizukami Shigemi , Watanabe Daisuke , Wu Feng , Zhang Xianmin , Naganuma Hiroshi , Oogane Mikihiko , Ando Yasuo , Miyazaki Terunobu
Published: July 2011

Effects of metallic Mg insertion on tunnel magnetoresistance (TMR) effect were investigated in D022-Mn2.4Ga/Mg/MgO/CoFe magnetic tunnel junctions (MTJs). The thickness of Mg (dMg) was varied from 0 to 1.4 nm. TMR ratio exhibited maximum value of 22% with the dMg = 0.4 nm and a negative value of 14% with the dMg = 1.4 nm at 10 K. The dependence of resistance area products (R × A) on the dMg showed similar trend compared with those of what reported in conventional CoFeB-MgO based MTJs. Bias voltage dependences of differential conductance (dI/dV) and TMR ratio exhibited asymmetry with respect to the zero-bias. The difference of the zero-bias anomaly in the dI/dV spectra was also discussed, and an indication of reducing the inelastic tunneling process was found, implying the improvement of barrier/magnetic-layer interfaces by the Mg insertion. Considering a theoretical work done by Wang et al. [Phys. Rev. B 82, 054405 (2010)], the inversion of the sign and the asymmetric bias voltage dependence of TMR ratio were inferred to be attributed to the minority spin tunneling via a quantum well state in the thin metallic Mg layer between Mn2.4Ga and MgO.
A generalized implicit algorithm for multi-dimensional particle-in-cell simulations in Cartesian geometry
Authors: Petrov G. M. , Davis J.
Published: July 2011

An implicit multi-dimensional particle-in-cell (PIC) code is developed to study the interaction of ultrashort pulse lasers with matter. The algorithm is based on current density decomposition and is only marginally more complicated compared to explicit PIC codes, but it completely eliminates grid heating and possesses good energy conserving properties with relaxed time step and grid resolution. This is demonstrated in a test case study, in which high-energy protons are generated from a thin carbon foil at solid density using linear and circular polarizations. The grid heating rate is estimated to be 1–10 eV/ps.
Space charge mediated negative differential resistance in terahertz quantum well detectors
Authors: Delga A. , Doyennette L. , Buffaz A. , Berger V. , Jasnot F. R. , de Vaulchier L. A. , Péré-Laperne N. , Liu H. C.
Published: July 2011

In terahertz quantum well infrared photodetectors, a built-in-charge-mediated regime transition of the electronic transport is thoroughly investigated. The very strong current discontinuity and negative differential resistivity behavior are explained in terms of band structure reorganizations. The analysis of bias versus current measurements reveals that the transition occurs when the first two wells of the structure become partially drained, and the second well enters the ionized regime before the first one. Both many-body effects and a careful model of the contact have to be considered to account for these features. The source of the built-in charge is identified as intersubband impact ionization. The regime transition is one of its few experimental proofs, and provides an original approach to investigate hot electron kinetics in multi-quantum-well structures.
Modification of a commercial atomic force microscopy for low-noise, high-resolution frequency-modulation imaging in liquid environment
Authors: Rode S. , Stark R. , Lübbe J. , Tröger L. , Schütte J. , Umeda K. , Kobayashi K. , Yamada H. , Kühnle A.
Published: July 2011

A key issue for high-resolution frequency-modulation atomic force microscopy imaging in liquids is minimizing the frequency noise, which requires a detailed analysis of the corresponding noise contributions. In this paper, we present a detailed description for modifying a commercial atomic force microscope (Bruker MultiMode V with Nanoscope V controller), aiming at atomic-resolution frequency-modulation imaging in ambient and in liquid environment. Care was taken to maintain the AFMs original stability and ease of operation. The new system builds upon an optimized light source, a new photodiode and an entirely new amplifier. Moreover, we introduce a home-built liquid cell and sample holder as well as a temperature-stabilized isolation chamber dedicated to low-noise imaging in liquids. The success of these modifications is measured by the reduction in the deflection sensor noise density from initially 100 \documentclass[12pt]{minimal}\begin{document}$\mathrm{fm}/\sqrt{\mathrm{Hz}}$\end{document} fm / Hz to around 10 \documentclass[12pt]{minimal}\begin{document}$\mathrm{fm}/\sqrt{\mathrm{Hz}}$\end{document} fm / Hz after modification. The performance of our instrument is demonstrated by atomically resolved images of calcite taken under liquid conditions.
Design, simulation, fabrication, packaging, and characterization of a MEMS-based mirror array for femtosecond pulse-shaping in phase and amplitude
Authors: Weber Stefan M. , Bonacina Luigi , Noell Wilfried , Kiselev Denis , Extermann Jérôme , Jutzi Fabio , Lani Sébastien , Nenadl Ondrej , Wolf Jean-Pierre , de Rooij Nico F.
Published: July 2011

We present an in-detail description of the design, simulation, fabrication, and packaging of a linear micromirror array specifically designed for temporal pulse shaping of ultrashort laser pulses. The innovative features of this device include a novel comb-drive actuator allowing both piston and tilt motion for phase- and amplitude-shaping, and an X-shaped laterally reinforced spring preventing lateral snap-in while providing high flexibility for both degrees of freedom.
An in-vacuum diffractometer for resonant elastic soft x-ray scattering
Authors: Hawthorn D. G. , He F. , Venema L. , Davis H. , Achkar A. J. , Zhang J. , Sutarto R. , Wadati H. , Radi A. , Wilson T. , Wright G. , Shen K. M. , Geck J. , Zhang H. , Novák V. , Sawatzky G. A.
Published: July 2011

We describe the design, construction, and performance of a 4-circle in-vacuum diffractometer for resonant elastic soft x-ray scattering. The diffractometer, installed on the resonant elastic and inelastic x-ray scattering beamline at the Canadian Light Source, includes 9 in-vacuum motions driven by in-vacuum stepper motors and operates in ultra-high vacuum at base pressure of 2 × 10-10 Torr. Cooling to a base temperature of 18 K is provided with a closed-cycle cryostat. The diffractometer includes a choice of 3 photon detectors: a photodiode, a channeltron, and a 2D sensitive channelplate detector. Along with variable slit and filter options, these detectors are suitable for studying a wide range of phenomena having both weak and strong diffraction signals. Example measurements of diffraction and reflectivity in Nd-doped (La,Sr)2CuO4 and thin film (Ga,Mn)As are shown.
A generalized mathematical framework for thermal oxidation kinetics
Authors: Xu Zhijie , Rosso Kevin M. , Bruemmer Stephen M.
Published: July 2011

We present a generalized mathematical model for thermal oxidation and the growth kinetics of oxide films. The model expands long-standing classical models by taking into account the reaction occurring at the interface as well as transport processes in greater detail. The standard Deal-Grove model (the linear-parabolic rate law) relies on the assumption of quasi-static diffusion that results in a linear concentration profile of, for example, oxidant species in the oxide layer. By relaxing this assumption and resolving the entire problem, three regimes can be clearly identified corresponding to different stages of oxidation. Namely, the oxidation starts with the reaction-controlled regime (described by a linear rate law), is followed by a transitional regime (described by a logarithmic or power law depending on the stoichiometry coefficient m), and ends with the well-known diffusion-controlled regime (described by a parabolic rate law). The theory of Deal-Grove is shown to be the lower order approximation of the proposed model. Various oxidation rate laws are unified into a single model to describe the entire oxidation process.
Phase behavior of symmetric disk-coil macromolecules with stacking interactions
Authors: Kim YongJoo , Alexander-Katz Alfredo
Published: July 2011

We investigate using Monte Carlo simulations in the NPT ensemble the self-assembly of disk-coil macromolecules with stacking interactions. The disk-coil molecules are composed of a planar disk that is covalently bonded to a single coil. In addition to commonly used amphiphilic interactions between the disk and coil portion of the molecules, we employ an attractive interaction between central monomers of the disks, which mimics stacking interactions. This additional force induces a preferential axial packing. The phase diagram of this system is complex and depends crucially on the stacking interactions. In particular, we find a variety of new phases that include for this system an ordered lamellar, ordered perforated lamellar, cylinder and ordered cylinder phases in addition to the disordered, lamellar, perforated lamellar, and crystal phases observed previously [Y. Kim and A. Alexander-Katz, J. Chem. Phys. 132, 174901 (2010)]10.1063/1.3407660. The ordered phases show strong tendency of parallel packing of disks. Among them, the ordered cylinder phase exhibits super-aligned structures which could have uses in many organic optoelectronic applications.
The use of electron scattering for studying atomic momentum distributions: The case of graphite and diamond
Authors: Vos M. , Moreh R. , Tőkési K.
Published: July 2011

The momentum distributions of C atoms in polycrystalline diamond (produced by chemical vapor deposition) and in highly oriented pyrolitic graphite (HOPG) are studied by scattering of 40 keV electrons at 135°. By measuring the Doppler broadening of the energy of the elastically scattered electrons, we resolve a Compton profile of the motion of the C atoms. The aim of the present work is to resolve long-standing disagreements between the calculated kinetic energies of carbon atoms in HOPG and in diamond films and the measured ones, obtained both by neutron Compton scattering (NCS) and by nuclear resonance photon scattering (NRPS). The anisotropy of the momentum distribution in HOPG was measured by rotating the HOPG sample relative to the electron beam. The obtained kinetic energies for the motion component along, and perpendicular to, the graphite planes were somewhat higher than those obtained from the most recent NCS data of HOPG. Monte Carlo simulations indicate that multiple scattering adds about 2% to the obtained kinetic energies. The presence of different isotopes in carbon affects the measurement at a 1% level. After correcting for these contributions, the kinetic energies are 3%–6% larger than the most recent NCS results for HOPG, but 15%–25% smaller than the NRPS results. For diamond, the corrected direction-averaged kinetic energy is ≈ 6% larger than the calculated value. This compares favorably to the ≈25% discrepancy between theory and both the NCS and NRPS results for diamond.
Changes of structure and dipole moment of water with temperature and pressure: A first principles study
Authors: Kang Dongdong , Dai Jiayu , Yuan Jianmin
Published: July 2011

The changes of structure and distribution of dipole moment of water with temperatures up to 2800 K and densities up to 2.2 g/cm3 are investigated using ab initio molecular dynamics. Along the isochore of 1.0 g/cm3, the structure of liquid water above 800 K is dramatically different from that at ambient conditions, where the hydrogen-bonds network collapses. Along the isotherm of 1800 K, the transition from the liquid state to an amorphous superionic phase occurs at 2.0 g/cm3 (32.9 GPa), which is not observed along the isotherm of 2800 K. With increasing temperature, the average dipole moment of water molecules is decreased arising from the weakened polarization by the collapse of the hydrogen-bonds network, while it is contrarily increased with compression due to the strengthening effect upon the polarization of water molecules. Both higher temperature and pressure broaden the distribution of dipole moment of water molecules due to the enhanced intramolecular charge fluctuations.
Investigating the degradation behavior caused by charge trapping effect under DC and AC gate-bias stress for InGaZnO thin film transistor
Authors: Chen Te-Chih , Chang Ting-Chang , Hsieh Tien-Yu , Lu Wei-Siang , Jian Fu-Yen , Tsai Chih-Tsung , Huang Sheng-Yao , Lin Chia-Sheng
Published: July 2011

This letter investigates the degradation mechanism of amorphous indium-gallium-zinc oxide thin-film transistors under gate-bias stress. The larger Vt shift under positive AC gate-bias stress when compared to DC operation indicates that an extra electron trapping mechanism occurs during rising/falling time during the AC pulse period. In contrast, the degradation behavior under illuminated negative gate-bias stress exhibits the opposite degradation tendency. Since electron and hole trapping are the dominant degradation mechanisms under positive and illuminated negative gate-bias stress, respectively, the different degradation tendencies under AC/DC operation can be attributed to the different trapping efficiency of electrons and holes.
Synchrotron-based photoluminescence excitation spectroscopy applied to investigate the valence band splittings in AlN and Al0.94Ga0.06N
Authors: Feneberg Martin , Röppischer Marcus , Esser Norbert , Cobet Christoph , Neuschl Benjamin , Meisch Tobias , Thonke Klaus , Goldhahn Rüdiger
Published: July 2011

We demonstrate that synchrotron-based photoluminescence excitation (PLE) spectroscopy is a versatile tool for determining valence band splittings of AlN and high aluminum content AlGaN. PLE results are independently confirmed by synchrotron-based spectroscopic ellipsometry. The splittings between the ordinary and the extraordinary absorption edges are found to be −240 meV and −170 meV for AlN and Al0.94Ga0.06N, respectively. These values differ from the crystal field energy due to residual strain.
Enhanced bias illumination stability of oxide thin film transistor through insertion of ultrathin positive charge barrier into active material
Authors: Oh Himchan , Ko Park Sang-Hee , Hwang Chi-Sun , Yang Shinhyuk , Ki Ryu Min
Published: July 2011

A novel strategy to enhance the bias and illumination stress stability of oxide thin-film transistors (TFTs) is presented. The ultrathin positive charge barrier is employed to block the movement of photo-generated charges toward the interface between gate insulator and semiconductor under negative gate bias and illumination. This method can break through the limitation in stability enhancement caused by the inevitable oxygen vacancy and facilitates the fabrication of highly stable oxide TFTs at low process temperature.
Ion-mediated compensation for drought-induced loss of xylem hydraulic conductivity in field-growing plants of Laurus nobilis
Authors: Trifilò Patrizia , Nardini Andrea , Raimondo Fabio , Lo Gullo Maria A. , Salleo Sebastiano
Published: July 2011

Xylem cavitation is a common occurrence in drought-stressed plants. Cavitation-induced embolism reduces xylem hydraulic conductivity (kxylem) and may lead to stomatal closure and reduction of photosynthetic rates. Recent studies have suggested that plants may compensate for kxylem loss through ion-mediated enhancement of the residual water transport capacity of functioning conduits. To test this hypothesis, field-grown laurel (Laurus nobilis L.) plants were subjected to mild drought stress by suspending irrigation. Drought treatment induced a significant increase in xylem embolism compared with control (well watered) plants. Xylem sap potassium concentration ([K+]) increased during the day both in control and water stressed plants. Midday values of sap [K+] were significantly higher in water stressed plants. The recorded increase in sap potassium concentration induced significant enhancement of residual kxylem when solutions with different [K+] were perfused through excised stems sampled in the field and measured in the laboratory. In planta measurements of stem hydraulic conductance revealed no change between water stressed plants and controls. Our data suggest that ion-mediated enhancement of residual kxylem buffered the actual loss of hydraulic conductance suffered by plants during the warmest hours of the day as well as under mild drought stress conditions.
Induction and reversal of crassulacean acid metabolism in Calandrinia polyandra: effects of soil moisture and nutrients
Authors: Winter Klaus , Holtum Joseph A. M.
Published: July 2011

Calandrinia polyandra Benth. (Montiaceae), an annual succulent herb endemic to Australia, is an exemplary facultative crassulacean acid metabolism (CAM) plant as demonstrated by continuous whole-plant lifetime CO2 exchange measurements under controlled conditions in the laboratory. Reduced soil water availability induced a shift from solely daytime CO2 fixation to dark CO2 fixation. The shift from C3 photosynthesis to CAM was reversible either upon rewatering alone, or upon a combination of rewatering and addition of nutrients. These observations highlight the role of edaphic conditions in controlling CAM expression in a plant that has the option of fixing CO2 either during the day or during the night, providing further evidence that this extreme form of photosynthetic plasticity is primarily controlled by the environment rather than plant ontogeny. The stimulating effect of soil nutrients on CO2 fixation in the light and its negative effect on dark CO2 fixation have not been described previously and deserve further attention. In the most widely used CAM model system, the halophytic Mesembryanthemum crystallinum L., CAM is typically induced by high salinity, and some metabolic responses may be CAM-unrelated and related to salt stress per se. C. polyandra could be an excellent complementary system for studying the biochemical and molecular foundations of CAM because drought stress elicits a complete C3 to CAM transition.
Effect of composted mulch application on soil and wine grape potassium status
Authors: Chan K. Y. , Fahey D. J.
Published: July 2011

Oversupply of potassium (K) to grape vines can result in high grape berry K and pH, leading to difficulty in wine making and low wine quality. There is concern that application of mulch to grape vines may increase K supply and the associated risks. The effect of composted mulch from green wastes was investigated in a field trial involving six vineyards in New South Wales on soils commonly used for viticulture production in Australia, over three seasons (2006–08). Significant increases in extractable soil K were detected as a result of mulch application. Higher berry K and pH were also observed due to the mulch treatments, with the changes dependent on season and mulch rate. Increases in berry K were significantly related to the higher soil exchangeable K. The mean increase in berry K due to a mulch rate of 153 m3/ha was 123 mg/kg. The mean increase in berry pH was 0.02 units observed in two seasons. Application of mulch can increase berry K and pH, but the changes are small compared with variations observed among vineyard sites and between seasons.
Plasticity of human auditory-evoked fields induced by shock conditioning and contingency reversal
Authors: Kluge Christian , Bauer Markus , Leff Alexander Paul , Heinze Hans-Jochen , Dolan Raymond J. , Driver Jon
Published: July 2011

We used magnetoencephalography (MEG) to assess plasticity of human auditory cortex induced by classical conditioning and contingency reversal. Participants listened to random sequences of high or low tones. A first baseline phase presented these without further associations. In phase 2, one of the frequencies (CS
+
) was paired with shock on half its occurrences, whereas the other frequency (CS
−
) was not. In phase 3, the contingency assigning CS
+
and CS
−
was reversed. Conditioned pupil dilation was observed in phase 2 but extinguished in phase 3. MEG revealed that, during phase-2 initial conditioning, the P1m, N1m, and P2m auditory components, measured from sensors over auditory temporal cortex, came to distinguish between CS
+
and CS
−
. After contingency reversal in phase 3, the later P2m component rapidly reversed its selectivity (unlike the pupil response) but the earlier P1m did not, whereas N1m showed some new learning but not reversal. These results confirm plasticity of human auditory responses due to classical conditioning, but go further in revealing distinct constraints on different levels of the auditory hierarchy. The later P2m component can reverse affiliation immediately in accord with an updated expectancy after contingency reversal, whereas the earlier auditory components cannot. These findings indicate distinct cognitive and emotional influences on auditory processing.
A cyclin-D1 interaction with BAX underlies its oncogenic role and potential as a therapeutic target in mantle cell lymphoma
Authors: Beltran Elena , Fresquet Vicente , Martinez-Useros Javier , Richter-Larrea Jose A. , Sagardoy Ainara , Sesma Izaskun , Almada Luciana L. , Montes-Moreno Santiago , Siebert Reiner , Gesk Stefan , Calasanz Maria J. , Malumbres Raquel , Rieger Melissa , Prosper Felipe , Lossos Izidore S. , Piris Miguel Angel , Fernandez-Zapico Martin E. , Martinez-Climent Jose A.
Published: July 2011

The chromosomal translocation
t
(11;14)(q13;q32) leading to cyclin-D1 overexpression plays an essential role in the development of mantle cell lymphoma (MCL), an aggressive tumor that remains incurable with current treatment strategies. Cyclin-D1 has been postulated as an effective therapeutic target, but the evaluation of this target has been hampered by our incomplete understanding of its oncogenic functions and by the lack of valid MCL murine models. To address these issues, we generated a cyclin-D1–driven mouse model in which cyclin-D1 expression can be regulated externally. These mice developed cyclin-D1–expressing lymphomas capable of recapitulating features of human MCL. We found that cyclin-D1 inactivation was not sufficient to induce lymphoma regression in vivo; however, using a combination of in vitro and in vivo assays, we identified a novel prosurvival cyclin-D1 function in MCL cells. Specifically, we found that cyclin-D1, besides increasing cell proliferation through deregulation of the cell cycle at the G
1
–S transition, sequestrates the proapoptotic protein BAX in the cytoplasm, thereby favoring BCL2’s antiapoptotic function. Accordingly, cyclin-D1 inhibition sensitized the lymphoma cells to apoptosis through BAX release. Thus, genetic or pharmacologic targeting of cyclin-D1 combined with a proapoptotic BH3 mimetic synergistically killed the cyclin-D1–expressing murine lymphomas, human MCL cell lines, and primary lymphoma cells. Our study identifies a role of cyclin-D1 in deregulating apoptosis in MCL cells, and highlights the potential benefit of simultaneously targeting cyclin-D1 and survival pathways in patients with MCL. This effective combination therapy also might be exploited in other cyclin-D1–expressing tumors.
Genome-wide landscape of polyadenylation in
Arabidopsis
provides evidence for extensive alternative polyadenylation
Authors: Wu Xiaohui , Liu Man , Downie Bruce , Liang Chun , Ji Guoli , Li Qingshun Q. , Hunt Arthur G.
Published: July 2011

Alternative polyadenylation (APA) has been shown to play an important role in gene expression regulation in animals and plants. However, the extent of sense and antisense APA at the genome level is not known. We developed a deep-sequencing protocol that queries the junctions of 3′UTR and poly(A) tails and confidently maps the poly(A) tags to the annotated genome. The results of this mapping show that 70% of
Arabidopsis
genes use more than one poly(A) site, excluding microheterogeneity. Analysis of the poly(A) tags reveal extensive APA in introns and coding sequences, results of which can significantly alter transcript sequences and their encoding proteins. Although the interplay of intron splicing and polyadenylation potentially defines poly(A) site uses in introns, the polyadenylation signals leading to the use of CDS protein-coding region poly(A) sites are distinct from the rest of the genome. Interestingly, a large number of poly(A) sites correspond to putative antisense transcripts that overlap with the promoter of the associated sense transcript, a mode previously demonstrated to regulate sense gene expression. Our results suggest that APA plays a far greater role in gene expression in plants than previously expected.
Density hysteresis of heavy water confined in a nanoporous silica matrix
Authors: Zhang Yang , Faraone Antonio , Kamitakahara William A. , Liu Kao-Hsiang , Mou Chung-Yuan , Leão Juscelino B. , Chang Sung , Chen Sow-Hsin
Published: July 2011

A neutron scattering technique was developed to measure the density of heavy water confined in a nanoporous silica matrix in a temperature-pressure range, from 300 to 130 K and from 1 to 2,900 bars, where bulk water will crystalize. We observed a prominent hysteresis phenomenon in the measured density profiles between warming and cooling scans above 1,000 bars. We interpret this hysteresis phenomenon as support (although not a proof) of the hypothetical existence of a first-order liquid–liquid phase transition of water that would exist in the macroscopic system if crystallization could be avoided in the relevant phase region. Moreover, the density data we obtained for the confined heavy water under these conditions are valuable to large communities in biology and earth and planetary sciences interested in phenomena in which nanometer-sized water layers are involved.
Agricultural landscape simplification and insecticide use in the Midwestern United States
Authors: Meehan Timothy D. , Werling Ben P. , Landis Douglas A. , Gratton Claudio
Published: July 2011

Agronomic intensification has transformed many agricultural landscapes into expansive monocultures with little natural habitat. A pervasive concern is that such landscape simplification results in an increase in insect pest pressure, and thus an increased need for insecticides. We tested this hypothesis across a range of cropping systems in the Midwestern United States, using remotely sensed land cover data, data from a national census of farm management practices, and data from a regional crop pest monitoring network. We found that, independent of several other factors, the proportion of harvested cropland treated with insecticides increased with the proportion and patch size of cropland and decreased with the proportion of seminatural habitat in a county. We also found a positive relationship between the proportion of harvested cropland treated with insecticides and crop pest abundance, and a positive relationship between crop pest abundance and the proportion cropland in a county. These results provide broad correlative support for the hypothesized link between landscape simplification, pest pressure, and insecticide use. Using regression coefficients from our analysis, we estimate that, across the seven-state region in 2007, landscape simplification was associated with insecticide application to 1.4 million hectares and an increase in direct costs totaling between $34 and $103 million. Both the direct and indirect environmental costs of landscape simplification should be considered in design of land use policy that balances multiple ecosystem goods and services.
Humanized mice with ectopic artificial liver tissues
Authors: Chen Alice A. , Thomas David K. , Ong Luvena L. , Schwartz Robert E. , Golub Todd R. , Bhatia Sangeeta N.
Published: July 2011

“Humanized” mice offer a window into aspects of human physiology that are otherwise inaccessible. The best available methods for liver humanization rely on cell transplantation into immunodeficient mice with liver injury but these methods have not gained widespread use due to the duration and variability of hepatocyte repopulation. In light of the significant progress that has been achieved in clinical cell transplantation through tissue engineering, we sought to develop a humanized mouse model based on the facile and ectopic implantation of a tissue-engineered human liver. These human ectopic artificial livers (HEALs) stabilize the function of cryopreserved primary human hepatocytes through juxtacrine and paracrine signals in polymeric scaffolds. In contrast to current methods, HEALs can be efficiently established in immunocompetent mice with normal liver function. Mice transplanted with HEALs exhibit humanized liver functions persistent for weeks, including synthesis of human proteins, human drug metabolism, drug–drug interaction, and drug-induced liver injury. Here, mice with HEALs are used to predict the disproportionate metabolism and toxicity of “major” human metabolites using multiple routes of administration and monitoring. These advances may enable manufacturing of reproducible in vivo models for diverse drug development and research applications.
Clone history shapes
Populus
drought responses
Authors: Raj Sherosha , Bräutigam Katharina , Hamanishi Erin T. , Wilkins Olivia , Thomas Barb R. , Schroeder William , Mansfield Shawn D. , Plant Aine L. , Campbell Malcolm M.
Published: July 2011

Just as animal monozygotic twins can experience different environmental conditions by being reared apart, individual genetically identical trees of the genus
Populus
can also be exposed to contrasting environmental conditions by being grown in different locations. As such, clonally propagated
Populus
trees provide an opportunity to interrogate the impact of individual environmental history on current response to environmental stimuli. To test the hypothesis that current responses to an environmental stimulus, drought, are contingent on environmental history, the transcriptome- level drought responses of three economically important hybrid genotypes—DN34 (
Populus deltoides
×
Populus nigra
), Walker [
P
.
deltoides
var. occidentalis × (
Populus laurifolia
×
P
.
nigra
)], and Okanese [Walker × (
P
.
laurifolia
×
P
.
nigra
)]—derived from two different locations were compared. Strikingly, differences in transcript abundance patterns in response to drought were based on differences in geographic origin of clones for two of the three genotypes. This observation was most pronounced for the genotypes with the longest time since establishment and last common propagation. Differences in genome-wide DNA methylation paralleled the transcriptome level trends, whereby the clones with the most divergent transcriptomes and clone history had the most marked differences in the extent of total DNA methylation, suggesting an epigenomic basis for the clone history-dependent transcriptome divergence. The data provide insights into the interplay between genotype and environment in the ecologically and economically important
Populus
genus, with implications for the industrial application of
Populus
trees and the evolution and persistence of these important tree species and their associated hybrids.
Tumorigenesis in tuberous sclerosis complex is autophagy and p62/sequestosome 1 (SQSTM1)-dependent
Authors: Parkhitko Andrey , Myachina Faina , Morrison Tasha A. , Hindi Khadijah M. , Auricchio Neil , Karbowniczek Magdalena , Wu J. Julia , Finkel Toren , Kwiatkowski David J. , Yu Jane J. , Henske Elizabeth Petri
Published: July 2011

Tuberous sclerosis complex (TSC) is a tumor suppressor syndrome characterized by benign tumors in multiple organs, including the brain and kidney. TSC-associated tumors exhibit hyperactivation of mammalian target of rapamycin complex 1 (mTORC1), a direct inhibitor of autophagy. Autophagy can either promote or inhibit tumorigenesis, depending on the cellular context. The role of autophagy in the pathogenesis and treatment of the multisystem manifestations of TSC is unknown. We found that the combination of mTORC1 and autophagy inhibition was more effective than either treatment alone in inhibiting the survival of tuberin (TSC2)-null cells, growth of TSC2-null xenograft tumors, and development of spontaneous renal tumors in
Tsc2
+/−
mice. Down-regulation of Atg5 induced extensive central necrosis in TSC2-null xenograft tumors, and loss of one allele of
Beclin1
almost completely blocked macroscopic renal tumor formation in
Tsc2
+/−
mice. Surprisingly, given the finding that lowering autophagy blocks TSC tumorigenesis, genetic down-regulation of p62/sequestosome 1 (SQSTM1), the autophagy substrate that accumulates in TSC tumors as a consequence of low autophagy levels, strongly inhibited the growth of TSC2-null xenograft tumors. These data demonstrate that autophagy is a critical component of TSC tumorigenesis, suggest that mTORC1 inhibitors may have autophagy-dependent prosurvival effects in TSC, and reveal two distinct therapeutic targets for TSC: autophagy and the autophagy target p62/SQSTM1.