bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural, electronic, and optical properties of crystalline iodoform under high pressure: A first-principles study
Authors: Bao Gang , Duan Defang , Tian Fubo , Wang Liancheng , Liu Bingbing , Cui Tian
Published: January 2011

The high pressure phases, electronic structure, and optical properties of iodoform at zero temperature have been investigated by first-principles pseudopotential plane-wave calculations based on the density-functional theory. A new high pressure polar monoclinic structure with space group Cc, denoted as β phase, has been observed after a series of simulated annealing and geometry optimizations. Our calculated enthalpies showed that the transition from α to β phase occurs at 40.1 GPa. Electronic structure calculated results showed that the insulator–metal transition in α phase due to band overlap is found at about 32 GPa. In addition, the calculated absorption spectra of iodoform are consistent with the experimental results.
The role of range-separated Hartree–Fock exchange in the calculation of magnetic exchange couplings in transition metal complexes
Authors: Phillips Jordan J. , Peralta Juan E.
Published: January 2011

We assess the dependence of magnetic exchange couplings on the variation of Hartree–Fock exchange (HFX) admixture in global hybrid functionals and the range-separation parameter ω in range-separated hybrid functionals in a set of 12 spin-1/2 binuclear transition metal complexes. The global hybrid PBEh (hybrid Perdew-Burke-Ernzerhof) and range-separated hybrids HSE (Heyd-Scuseria-Ernzerhof) and LC-ωPBE (long-range corrected hybrid PBE) are employed for this assessment, and exchange couplings are calculated from energy differences within the framework of the spin-projected approach. It is found that these functionals perform optimally for magnetic exchange couplings with 35% HFX admixture for PBEh, ω = 0.50 a.u.\documentclass[12pt]{minimal}\begin{document}$^{-1}$\end{document}−1 for LC-ωPBE, and ω at or near 0.0 a.u.\documentclass[12pt]{minimal}\begin{document}$^{-1}$\end{document}−1 for HSE (which corresponds to PBEh). We find that in their standard respective forms, LC-ωPBE slightly outperforms PBEh, while PBEh with 35% HFX yields exchange couplings closer to experiment than those of LC-ωPBE with ω = 0.50 a.u.\documentclass[12pt]{minimal}\begin{document}$^{-1}$\end{document}−1. Additionally, we show that the profile of exchange couplings with respect to ω in HSE is appreciably flat from 0 to 0.2 a.u.\documentclass[12pt]{minimal}\begin{document}$^{-1}$\end{document}−1. This combined with the fact that HSE is computationally more tractable than global hybrids makes HSE an attractive alternative for the evaluation of exchange couplings in extended systems. These results are rationalized with respect to how varying the parameters within these functionals affects the delocalization of the magnetic orbitals, and conclusions are made regarding the relative importance of range separation versus global mixing of HFX for the calculation of exchange couplings.
Effect of shock compression on wurtzite-type ZnMgS crystals
Authors: Mashimo Tsutomu , Omurzak Emil , Chen Liliang , Inoue Ryuichi , Kawai Chihiro
Published: January 2011

It is hard to generate twin defects in wurtzite-type ZnMS (M: metal element) crystals by static mechanical method, while it is important for the luminescence. It was found that many twin defects were formed in wurtzite-type ZnMgS crystals by shock compression of >15 GPa in stress, and the absorption and luminescence spectra changed.
Nonsaturable absorption in alumino-silicate bismuth-doped fibers
Authors: Kir’yanov A. V. , Dvoyrin V. V. , Mashinsky V. M. , Barmenkov Yu. O. , Dianov E. M.
Published: January 2011

We report an experimental and theoretical investigation of fluorescence decay and transmission coefficient at ∼1 μm pumping for a series of bismuth (Bi) doped alumino-silicate fibers with different concentrations of Bi centers. By modeling the experimental data, we show that the excited-state absorption (ESA) and up-conversion (UC) processes are responsible for a growth of nonsaturable absorption and deviation from exponential the fluorescence decay in the fibers with an increase in Bi centers content. Assuming that Bi centers ensemble is composed of subsystems of single and paired centers, and an increase in partial weight of the latter with a Bi centers concentration growth, we can successfully explain the experimental data. Also, these assumptions allow us to estimate the constants characterizing the ESA and both homogeneous and inhomogeneous UC processes in the fibers.
Ultrananocrystalline diamond film deposition by direct-current plasma assisted chemical vapor deposition using hydrogen-rich precursor gas in the absence of the positive column
Authors: Lee Hak-Joo , Jeon Hyeongtag , Lee Wook-Seong
Published: January 2011

We have investigated the ultrananocrystalline diamond (UNCD) deposition by direct-current plasma assisted chemical vapor deposition on 4 in. Si wafer using CH4H2 as well as CH4Ar gas chemistry containing additive nitrogen. CH4/N2/H2 (5%/0.5%/94.5%) and CH4/N2/H2/Ar (0.5%/5%/6%/88.5%) gas mixtures were compared as the precursor gas. Molybdenum and tungsten were compared as cathode material. Discharge voltage and current were 480 V/45 A and 320 V/60 A, for respective gas chemistry. Chamber pressure and substrate temperature were 110–150 Torr and 750–850 °C, respectively. The film was characterized by near edge x-ray absorption fine structure spectroscopy, x-ray diffraction, high-resolution transmission electron microscope, electron energy loss spectroscopy, and high-resolution scanning electron microscope. We have demonstrated that (1) elimination of the positive column, by adopting very small interelectrode distance, gave some important and beneficial effects; (2) the plasma stability and impurity incorporation was sensitive to the cathode material and the precursor gas; (3) using the conventional CH4/H2 precursor gas and tungsten cathode, the mirror-smooth 4 in. UNCD film of excellent phase-purity and grain size below 10 nm could be deposited even in the absence of the positive column. The high electric field in the unusually narrow interelectrode space and the consequent high electron kinetic energy, in conjunction with the unusually high electron current thereof, directed to the substrate, i.e., the anode, was proposed to be the source of the grain refinement to achieve UNCD at such high chamber pressure around 110–150 Torr, in the absence of the usual ion bombardment assistance.
Electron capture induced dissociation of doubly protonated pentapeptides: Dependence on molecular structure and charge separation
Authors: Haag N. , Holm A. I. S. , Johansson H. A. B. , Zettergren H. , Schmidt H. T. , Nielsen S. Brøndsted , Hvelplund P. , Cederquist H.
Published: January 2011

We have studied electron capture induced dissociation of a set of doubly protonated pentapeptides, all composed of one lysine (K) and either four glycine (G) or four alanine (A) residues, as a function of the sequence of these building blocks. Thereby the separation of the two charges, sequestered on the N-terminal amino group and the lysine side chain, is varied. The characteristic cleavage of N–C\documentclass[12pt]{minimal}\begin{document}$_\alpha$\end{document}α bonds is observed for all peptides over the whole backbone length, with the charge carrying fragments always containing K. The resulting fragmentation patterns are very similar if G is replaced by A. In the case of [XKXXX+2H]\documentclass[12pt]{minimal}\begin{document}$^{2+}$\end{document}2+ (X=A or G), a distinct feature is observed in the distribution of backbone cleavage fragments and the probability for ammonia loss is drastically reduced. This may be due to an isomer with an amide oxygen as protonation site giving rise to the observed increase in breakage at a specific site in the molecule. For the other peptides, a correlation with the distance between amide oxygen and the charge at the lysine side chain has been found. This may be an indication that it is only the contribution from this site to the charge stabilization of the amide \documentclass[12pt]{minimal}\begin{document}$\pi ^*$\end{document}π* orbitals which determines relative fragment intensities. For comparison, complexes with two crown ether molecules have been studied as well. The crown ether provides a shielding of the charge and prevents the peptide from folding and internal hydrogen bonding, which leads to a more uniform fragmentation behavior.
Structure evolution of magnetron sputtered TiO2 thin films
Authors: Mráz Stanislav , Schneider Jochen M.
Published: January 2011

The structure evolution of TiO2 thin films deposited by rf and dc magnetron sputtering onto nonintentionally heated, floating, glass and Si (100) substrates was investigated. As the total pressure was varied from 0.15 to 4.0 Pa, corresponding to the pressure-distance product values from 10.5 to 280 Pa mm, rutile, anatase, and a mixture thereof were deposited. The pressure-distance induced changes in ion energy were quantified by probing the ion energy distribution functions. The ion energy during synthesis was additionally varied by applying a substrate bias potential ranging from floating to −100 V revealing a similar phase formation characteristic. While the structure evolution of the TiO2 thin films reported in the literature exhibits a rather complex dependence on the process parameters, a simple correlation between the structure evolution and the ratio between the ion energy flux and the deposition flux was identified here. Phase pure anatase films were grown below 540 eV/Ti atom and phase pure rutile films were grown above 1000 eV/Ti atom. The here presented data suggest that the ratio between the ion energy flux and the deposition flux ratio defines the phase formation of TiO2 thin films during magnetron sputtering.
Deep-ultraviolet light excites surface plasmon for the enhancement of photoelectron emission
Authors: Watanabe Yusuke , Inami Wataru , Kawata Yoshimasa
Published: January 2011

We show deep ultraviolet (DUV) light excitation of surface plasmon resonance (SPR) (DUV-SPR) with aluminum (Al) film. DUV-SPR has higher energy than that of visible light opens many applications, such as enhancement of photoelectron emission from metal surface, autofluorescence imaging of biological specimens, and laser ablation with high energy photons. We demonstrated the enhancement of photoelectron emission by DUV-SPR and analyzed protection layer to avoid oxidation of aluminum surface with enhancement of electric field kept as much as possible. The photoelectron emission from the aluminum surface was enhanced nine times with the excitation of SPR.
Structural aggregates of rod–coil copolymer solutions
Authors: Chou Shih-Hao , Tsao Heng-Kwong , Sheng Yu-Jane
Published: January 2011

The optoelectronic properties of rod–coil diblock copolymers with π-conjugation are greatly affected by molecular packing, which is closely related to their micellar morphology. Self-assembly of rod–coil block copolymer \documentclass[12pt]{minimal}\begin{document}${\rm B}_{y}{\rm A}_{x}$\end{document}ByAx in a selective solvent for its coil block is studied by using dissipative particle dynamics, where \documentclass[12pt]{minimal}\begin{document}${\rm B}_{y}{\rm A}_{x}$\end{document}ByAx denotes the polymer comprising of y rodlike B beads and x coil-like A beads. The influences of polymer concentration, component compatibility, solvent quality for coil block, rod-block length, and π − π interaction on the resulting aggregate conformations are examined. It was found that distinctly different from coil–coil copolymers, the aggregates of rod–coil copolymers exhibit morphological and structural diversity induced by the intrinsically rigid nature of the rod blocks. In general, the aggregate adopts the overall shape of sphere, cylinder, perforated sheet, or network. The morphology of the rod-block domain within aggregate is even richer and the interesting structures such as porous sphere, spherical spiral, helical bundles, discrete chunks, and nematic cylinder are observed. The short-range order parameter indicates that as rod length is long enough, neighboring rods begin to orient parallel to one another and nematic domains appear. Moreover, in the presence of π − π interactions, the neighboring rods within the B domains become more coherently oriented and smectic domains can thus be formed.
Slice imaging of nitric acid photodissociation: The O($^1$1D) + HONO channel
Authors: Herath Nuradhika , Everhart Stephanie C. , Suits Arthur G. , Vasyuntinskii Oleg S.
Published: January 2011

We report an imaging study of nitric acid (HNO\documentclass[12pt]{minimal}\begin{document}$_3$\end{document}3) photodissociation near 204 nm with detection of O(\documentclass[12pt]{minimal}\begin{document}$^1$\end{document}1D), one of the major decomposition products in this region. The images show structure reflecting the vibrational distribution of the HONO coproduct and significant angular anisotropy that varies with recoil speed. The images also show substantial alignment of the O(\documentclass[12pt]{minimal}\begin{document}$^1$\end{document}1D) orbital, which is analyzed using an approximate treatment that reveals that the polarization is dominated by incoherent, high order contributions. The results offer additional insight into the dynamics of the dissociation of nitric acid through the S\documentclass[12pt]{minimal}\begin{document}$_3$\end{document}3 (2 \documentclass[12pt]{minimal}\begin{document}$^1$\end{document}1A\documentclass[12pt]{minimal}\begin{document}$^\prime$\end{document}′) excited state, resolving an inconsistency in previously reported angular distributions, and pointing the way to future studies of the angular momentum polarization.
Proper orthogonal decomposition analysis of vortex dynamics of a circular cylinder under synthetic jet control
Authors: Feng Li-Hao , Wang Jin-Jun , Pan Chong
Published: January 2011

Vortex dynamics of a circular cylinder controlled by a synthetic jet positioned at the back stagnation point is experimentally investigated using particle image velocimetry (PIV) technique. The proper orthogonal decomposition (POD) method is adopted to present the variations of the POD energy, mode, coefficient, corresponding dominant frequency, and the reconstructed spanwise vorticity. It is found that the dominant dimensionless control parameters should be the synthetic jet stroke length L0/D, where D is the diameter of the experimental circular cylinder, and the equivalent momentum coefficient Cμ. For the same stroke length L0/D=3.3, the states of the wake vortex shedding are determined by the momentum coefficient. They can be categorized into three groups summarizing all the parameters tested: antisymmetric Karman vortex shedding mode (Cμ≤0.027), vortex synchronization with shedding modes varying between the symmetric and antisymmetric ones (0.061≤Cμ≤0.109), and vortex synchronization with symmetric shedding mode (0.213≤Cμ≤0.378). When the symmetric shedding mode occurs, the corresponding spanwise vorticity modes show two parallel rows of half-arrowhead structures with alternate signs that are antisymmetric about the centerline. The POD modes based on the streamwise and vertical velocities also exhibit regular variations with different wake vortex shedding states.
Influence of hydrogen functionalization on thermal conductivity of graphene: Nonequilibrium molecular dynamics simulations
Authors: Chien Shih-Kai , Yang Yue-Tzu , Chen Cha’o-Kuang
Published: January 2011

The influence of hydrogen coverage on the thermal conductivity of typical armchair hydrogen functionalized graphene is investigated using a nonequilibrium molecular dynamics simulation. We also study the effects of easy-rotation of unsupported sp3 bonds. We find that the system exhibits a rapid drop in thermal conductivity with hydrogen coverage, where hydrogen coverage down to as little as 2.5% of the graphene carbon atoms reduces the thermal conductivity by about 40%. The simulation results indicate that the effect is due to a reduction in the phonon mean free path.
Dynamics of wet particles in rotating drums: Effect of liquid surface tension
Authors: Liu P. Y. , Yang R. Y. , Yu A. B.
Published: January 2011

A numerical model based on the discrete element method was developed to simulate the wet particle flow in a rotating drum. The model explicitly considered the capillary force between particles and liquid distribution within the packed bed. Physical experiments under similar conditions were carried out to validate the model, showing that the simulation and experiment results were quite comparable in terms of the flow patterns, maximum flow repose angle, and the frequency of avalanching. Flow properties in two different states were investigated with the focus on the effect of liquid surface tension. In the quasistatic state with the drum rotating at very low speeds, discrete avalanches were observed after the flow reached the maximum repose angle. However, flow properties had changed well before avalanches occurred. The microscopic analysis indicated that the strength caused by the capillary force reached a minimal when avalanches started. The maximum repose angle increased with increasing capillary force and their relationship was compared with the theoretical models based on the Mohr–Coulomb criterion and force balance. In the dynamic state, the bed showed continuous surface flow at weak surface tensions but transited into discrete avalanches characterized by the plough flow as the surface tension further increased. The flow became more dilated at high surface tensions with increased particle contacts and more uniform stress distribution. The energy and frequency of collisions between particles also decreased as the liquid surface tension increased and more collisions were observed in the region 4–5 particle diameters below the flow surface. The results would be useful to the development of a comprehensive understanding of the mechanisms of particle mixing and segregation.
Radiative versus nonradiative optical processes in PbS nanocrystals
Authors: Dantas N. O. , de Paula P. M. N. , Silva R. S. , López-Richard V. , Marques G. E.
Published: January 2011

The Stokes shift detected in PbS nanocrystals is analyzed by optical absorption (OA), photoluminescence (PL) and atomic force microscopy (AFM). The samples were synthesized by fusion method over two different glass substrates, and identical size PbS dot structures with radius 4.1 nm grown showed PL and OA peaks separated by 0.15 and 0.10 eV. The origin of these large Stokes shifts are analyzed whether they are attributed to the nonradiative recombination associated to impurity states in prepared doped samples or to radiative transitions between exciton states induced by electron-hole (e-h) exchange Coulomb interaction.
Surface modification of a ferroelectric polymer insulator for low-voltage readable nonvolatile memory in an organic field-effect transistor
Authors: Kim Won-Ho , Bae Jin-Hyuk , Kim Min-Hoi , Keum Chang-Min , Park Jaehoon , Lee Sin-Doo
Published: January 2011

We demonstrate that the sequential surface modification of a ferroelectric polymer insulator plays an essential role in both the enhancement of the carrier mobility and the shift in the turn-on voltage (Von) in an organic ferroelectric field-effect transistor (FeFET) for nonvolatile memory. The surface of a ferroelectric polymer insulator, poly(vinylidene fluoride-trifluoroethylene), is physicochemically modified by the successive treatments of ultraviolet-ozone (UVO) and CF4 plasma to understand how the surface morphology and the hydrophobicity affect the grain size, the mobility, and Von in the FeFET. In a pentacene-based FeFET, the CF4 plasma irradiation leads to the mobility enhancement by a factor of about 5 as well as the shift in Von toward a positive voltage direction while the UVO treatment results in only the shift in Von toward a negative voltage direction. It is found that the sequence of the two successive treatments is critical for tailoring interfacial interactions between the ferroelectric polymer insulator and the pentacene layer. The underlying mechanism for the mobility enhancement and the shift in Von is described in terms of the surface morphology and the nature of the built-in electric field.
Spin current generation by adiabatic pumping in monolayer graphene
Authors: Zhang Qingtian , Chan K. S. , Lin Zijing
Published: January 2011

We propose a method of generating spin currents in monolayer graphene through adiabatic quantum pumping by two oscillating potentials. Spin splitting is induced in the graphene layer by ferromagnetic proximity. The pumped charge and spin currents are sensitive functions of the Fermi energy, which can thus be used to control the degree of polarization. The predicted pumped currents are measurable using the current technology. The proposed method is useful in the development of graphene spintronics.
Viscous damping force during head-on collision of two spherical particles
Authors: Marshall J. S.
Published: January 2011

Viscous damping is known to play a critical role in determining the restitution coefficient for the collision of two spherical particles at low and moderate Stokes numbers due to fluid motion in the squeeze-film between the particles. The classical expression for the viscous damping force of approaching spheres, valid prior to collision of the particles, has been used by several investigators to model the effect of viscous damping on the restitution coefficient. However, viscous damping also occurs during the particle collision due to the corner flow associated with a change in the radius of the contact region, within which the particle surfaces deform into flattened parallel surfaces due to high fluid pressure within the squeeze-film. The current paper derives a simple expression for the fluid damping force caused by the squeeze-film dynamics associated with a change in the contact region radius during collision. This expression is then used in conjunction with the damping force expression for spherical particles before and after collision to predict the variation of restitution coefficient with the particle Stokes number and elasticity parameter. The viscous damping force during collision exhibits sensitive dependence on the minimum approach distance separating the particle surfaces within the contact region, which, in turn, is controlled by factors such as microscopic particle surface roughness and pressure-dependent density and viscosity changes of the fluid.
Hemp, an mbt domain-containing protein, plays essential roles in hematopoietic stem cell function and skeletal formation
Authors: Honda Hiroaki , Takubo Keiyo , Oda Hideaki , Kosaki Kenjiro , Tazaki Tatsuya , Yamasaki Norimasa , Miyazaki Kazuko , Moore Kateri A. , Honda Zen-ichiro , Suda Toshio , Lemischka Ihor R.
Published: January 2011

To clarify the molecular pathways governing hematopoietic stem cell (HSC) development, we screened a fetal liver (FL) HSC cDNA library and identified a unique gene,
hematopoietic expressed mammalian polycomb
(
hemp
), encoding a protein with a zinc-finger domain and four malignant brain tumor (mbt) repeats. To investigate its biological role, we generated mice lacking Hemp (
hemp
−/−
).
Hemp
−/−
mice exhibited a variety of skeletal malformations and died soon after birth. In the FL,
hemp
was preferentially expressed in the HSC and early progenitor cell fractions, and analyses of fetal hematopoiesis revealed that the number of FL mononuclear cells, including HSCs, was reduced markedly in
hemp
−/−
embryos, especially during early development. In addition, colony-forming and competitive repopulation assays demonstrated that the proliferative and reconstitution abilities of
hemp
−/−
FL HSCs were significantly impaired. Microarray analysis revealed alterations in the expression levels of several genes implicated in hematopoietic development and differentiation in
hemp
−/−
FL HSCs. These results demonstrate that Hemp, an mbt-containing protein, plays essential roles in HSC function and skeletal formation. It is also hypothesized that Hemp might be involved in certain congenital diseases, such as Klippel-Feil anomaly.
RETRACTED: Gastrin-releasing peptide blockade as a broad-spectrum anti-inflammatory therapy for asthma
Authors: Zhou Shutang , Potts Erin N. , Cuttitta Frank , Foster W. Michael , Sunday Mary E.
Published: January 2011

Gastrin-releasing peptide (GRP) is synthesized by pulmonary neuroendocrine cells in inflammatory lung diseases, such as bronchopulmonary dysplasia (BPD). Many BPD infants develop asthma, a serious disorder of intermittent airway obstruction. Despite extensive research, early mechanisms of asthma remain controversial. The incidence of asthma is growing, now affecting >300 million people worldwide. To test the hypothesis that GRP mediates asthma, we used two murine models: ozone exposure for air pollution-induced airway hyperreactivity (AHR), and ovalbumin (OVA)-induced allergic airway disease. BALB/c mice were given small molecule GRP blocking agent 77427, or GRP blocking antibody 2A11, before exposure to ozone or OVA challenge. In both models, GRP blockade abrogated AHR and bronchoalveolar lavage (BAL) macrophages and granulocytes, and decreased BAL cytokines implicated in asthma, including those typically derived from Th1 (e.g., IL-2, TNFα), Th2 (e.g., IL-5, IL-13), Th17 (IL-17), macrophages (e.g., MCP-1, IL-1), and neutrophils (KC = IL-8). Dexamethasone generally had smaller effects on all parameters. Macrophages, T cells, and neutrophils express GRP receptor (GRPR). GRP blockade diminished serine phosphorylation of GRPR with ozone or OVA. Thus, GRP mediates AHR and airway inflammation in mice, suggesting that GRP blockade is promising as a broad-spectrum therapeutic approach to treat and/or prevent asthma in humans.
Dalliance: interactive genome viewing on the web
Authors: Down Thomas A. , Piipari Matias , Hubbard Tim J. P.
Published: January 2011

Summary: Dalliance is a new genome viewer which offers a high level of interactivity while running within a web browser. All data is fetched using the established distributed annotation system (DAS) protocol, making it easy to customize the browser and add extra data.

Availability and Implementation: Dalliance runs entirely within your web browser, and relies on existing DAS server infrastructure. Browsers for several mammalian genomes are available at http://www.biodalliance.org/, and the use of DAS means you can add your own data to these browsers. In addition, the source code (Javascript) is available under the BSD license, and is straightforward to install on your own web server and embed within other documents.

Contact:  thomas@biodalliance.org
Identical Amino Acid Substitutions in the Repression Domain of Auxin/Indole-3-Acetic Acid Proteins Have Contrasting Effects on Auxin Signaling
Authors: Li Hanbing , Tiwari Shiv B. , Hagen Gretchen , Guilfoyle Tom J.
Published: January 2011

Auxin/indole-3-acetic acid (Aux/IAA) proteins function as repressors of auxin response gene expression when auxin concentrations in a cell are low. At elevated auxin concentrations, these repressors are destroyed via the ubiquitin-proteasome pathway, resulting in derepression/activation of auxin response genes. Most Aux/IAA repressors contain four conserved domains, with one of these being an active, portable repression domain (domain I) and a second being an auxin-dependent instability domain (domain II). Here, we have analyzed the effects of amino acid substitutions in the repression domain of selected Aux/IAA proteins. We show that stabilized versions of Aux/IAA proteins with amino acid substitutions in domain I display contrasting phenotypes when expressed in transformed Arabidopsis (Arabidopsis thaliana) plants. An alanine-for-leucine substitution in the LxLxL (where L is leucine and x is another amino acid) repression domain of IAA3, IAA6, or IAA19 confers enhanced auxin response gene expression and “high-auxin” phenotypes when expressed from the 35S or IAA19 promoter (as tested with IAA19) in transformed Arabidopsis plants. In marked contrast, a single alanine-for-leucine substitution in domain I of IAA12 or IAA17 confers repression of auxin response genes and “low-auxin” phenotypes. These results point to intrinsic differences in the repression domain(s) of IAA proteins and suggest that some IAA proteins have stronger or more complex repression domains than others.
Anti‐tumor effect of lentivirus‐mediated gene transfer of alphastatin on human glioma
Authors: Guo Shi‐Wen , Che Hong‐Min , Li Wen‐Zhi
Published: January 2011

Alphastatin, an endogenous angiogenesis inhibitor, has recently been used as an anticancer agent in several tumor models. This study was to investigate whether local sustained long‐term expression of alphastatin could serve to diminish tumor growth of a human xenograft glioma model. We found that the recombinant alphastatin lentiviruses were able to stably infect HUVECs, and infected HUVECs could sustainably secrete alphastatin, which exhibited potent inhibitory effects on HUVECs migration, differentiation but not proliferation induced by vascular endothelial growth factor (VEGF) or basic fibroblast growth factor(bFGF). And the expression of secreted protein alphastatin markedly decreased tumor vascularization and inhibited tumor growth. Additionally, alphastatin inhibited VEGF‐ or bFGF‐induced initial stage of angiogenesis by reducing JNk and ERK phosphorylation in vitro. Taken together, these data demonstrate that secreted protein alphastatin inhibits VEGF‐ or bFGF‐induced angiogenesis by suppressing JNK and ERK kinases activation pathways in HUVECs, and markedly inhibits tumor angiogenesis in vivo. Consequently lentivirus‐mediated gene transfer might represent an effective strategy for expression of alphastatin to achieve inhibition of human malignant glioma proliferation and tumor progression. (Cancer Sci 2011; 102: 1038–1044)
Outdoor immunology: methodological considerations for ecologists
Authors: Boughton Raoul K. , Joop Gerrit , Armitage Sophie A.O.
Published: January 2011

1. Immune defence is an incredibly complicated system, but to understand how it functions in an ecological context is challenging. Our focus is to outline the diversity of ways to measure immune function for ecologists, and to provide some details on the limitations in interpretation of results.

2. There are two broad questions that ecological immunologists have to deal with. The first is what assays are appropriate for the research question of interest? Some researchers assume the biological relevance of an immune assay without investigation or a complete understanding of the immune response. Therefore, the second question is, what parasite challenge does one choose, and does a measurement of immune function reflect the response of the host towards that parasite? There are many assumptions, caveats, and pitfalls facing ecological immunologists, and investigating the relationships between immune assays and whole organismal defence will help us to understand variations in immune responses.

3. We provide an extensive listing of immune function measures, presenting examples from both the vertebrate and invertebrate literature, and wherever possible from non‐model organisms. We also outline how these responses are part of an integrated immune defence and encourage thinking about immune function as a hierarchical defence model. We describe how immune responses interact with one another, identify concerns regarding when to measure an immune response, and describe general problems faced when trying to collect a measure of immune function in wild organisms.

4. Extrinsic factors influence immune measurements and the importance of parasites is often overlooked. We give several examples of how parasites interact with organism’s immune systems, suggest greater inclusion of parasites into ecological immunology experiments, describe how micro‐organisms may interact symbiotically with their host’s immune system, and advocate the inclusion of tolerance and resistance in ecological immunological thinking.
Preference for diverse pastures by sheep in response to intraruminal administrations of tannins, saponins and alkaloids
Authors: Villalba J. J. , Provenza F. D. , K Clemensen A. , Larsen R. , Juhnke J.
Published: January 2011

Plant secondary compounds (PSC) are increasingly recognized as important in animal health, welfare and nutrition, yet little is known about possible complementarities among forages that contain PSC. This study explored how sheep modify their foraging behaviour in pastures containing four forages with different PSC when challenged with intraruminal administration of a single PSC. Six pairs of lambs received a dose of a single PSC in three successive periods (1 – Condensed tannins, 2 – Saponins, and 3 – Ergotamine) of 5 d each. Six other pairs of lambs received just the vehicle. After the early‐morning dosing, lambs were allowed to graze a choice of: 1 –Lotus corniculatus [birdsfoot trefoil (BFT)], 2 –Medicago sativa [alfalfa (AA)], 3 –Festuca arundinacea [endophyte‐infected tall fescue (TF)], high in tannins, saponins and alkaloids, respectively, and 4 –Dactylis glomerata [orchard grass (OG)]. The foraging behaviour of lambs was recorded at 1‐min intervals (scans). Lambs dosed with tannins had more scans than Controls on BFT (P = 0·002) and TF (P = 0·004). Lambs dosed with saponins had more scans than Controls on TF (P = 0·01), and animals treated with ergotamine had more scans than Controls on BFT (P = 0·03). Lambs showed the lowest proportion of scans on AA after a dose of saponin (P ≤ 0·09) and on TF after a dose of ergotamine (P ≤ 0·009). Thus, lambs minimized the negative impacts of PSC through changes in their foraging behaviour by avoiding over‐ingesting any one PSC and by selectively increasing the preference for complementary PSC‐containing forages.
Nurse prescribing in specialist mental health (Part 1): the views and experiences of practising and non‐practising nurse prescribers and service users
Authors: EARLE E. A. , TAYLOR J. , PEET M. , GRANT G.
Published: January 2011

Accessible summary

Prescribing medication used to be the role of the doctor, but in recent years nurses have begun to prescribe following training and supervision.

In this single case study from one NHS Trust, we conducted interviews to look at the views of a practising and non‐practising prescriber to understand and compare their experiences of prescribing in mental health, and also the views of service users receiving this care in the community.

Service users reported that receiving their medication from a nurse was more convenient and less stressful, an issue of particular importance for helping their mental health. The practising nurse prescriber described her experiences and felt she had a good structure of supervision and support from the team. Reasons why trained nurse prescribers may not be practising are discussed, with suggestions for future developments and guidance given.

Nurse prescribing appears to work well in a specialist mental health setting when carried out in a supported and structured way. Offering choice was important; however, for some service users, information about why medication may be helpful was still needed.

Non‐medical prescribing is a relatively new competency that appears to benefit both service users and health professionals alike. However, little is known about its use in mental health settings. This single case study in one UK National Health Service (NHS) Trust aimed to look at these views and consider how the role can be developed further in light of this. Six service users and two nurses trained in nurse prescribing were individually interviewed. One trained nurse had been prescribing for the last 3 years; the other was trained but had never practised. Service users reported that nurse prescribing was more convenient and less anxiety provoking, an issue of particular importance for optimizing mental health services. Offering choice was deemed important; however, for some service users, information about why medication may be beneficial was highlighted as an unmet need in the prescribing process. The practising nurse prescriber described her experiences and credited a good structure of supervision and support from the team. Reasons why trained nurse prescribers may not be practising are discussed, with suggestions for future developments and guidance. This competence appears to work well in a mental health setting when conducted in a supported and structured way.
Large‐scale survey of naturally occurring HBV polymerase mutations associated with anti‐HBV drug resistance in untreated patients with chronic hepatitis B
Authors: Mirandola S. , Campagnolo D. , Bortoletto G. , Franceschini L. , Marcolongo M. , Alberti A.
Published: January 2011

Summary.  Drug resistance is a major limitation for the long‐term efficacy of antiviral therapy with nucleos(t)ide analogues (NAs) in chronic hepatitis B (CHB). Antiviral resistance mutations may pre‐exist in the overall viral population of untreated patients. We aimed to assess the prevalence of such hepatitis B virus (HBV) variants in a large cohort of NAs‐naïve patients with CHB and to explore possible association with viral and host variables. Serum samples from 286 NAs‐naïve consecutive patients with CHB were tested for serum HBV‐DNA, and 255 of them having HBV‐DNA > 1000 IU/mL were further analysed for drug resistance mutations by INNO‐LiPA HBV DRv2/v3. NAs‐naïve patients analysed were mainly men (73%), Caucasians (85%), hepatitis B e Antigen (HBeAg) negative (79%) and genotype D (69%), with a mean age of 43.2 ± 13.4 years. HBV mutations associated with antiviral drug resistance were detected in 13 (5%) patients: three patients infected with HBV genotype C had the rtM204V + rtL180M mutations associated with lamivudine (LMV) resistance. Four patients had the rtI233V mutation that may reduce sensitivity to adefovir, and three patients had the rtM250L/V mutation typical of entecavir resistance. LMV compensatory mutations rtL80V and rtV173L were seen in two and one patients, respectively. No relationship was seen between presence of resistant or compensatory mutations and HBV‐DNA levels, HBeAg/anti‐HBe status or previous IFN therapy. These results confirm that HBV mutations, which confer resistance against currently available anti‐HBV NAs, may already exist in patients who have never received the drug.
Rapid formation of distinct hybrid lineages after secondary contact of two fish species (Cottus sp.)
Authors: STEMSHORN KATHRYN C. , REED FLOYD A. , NOLTE ARNE W. , TAUTZ DIETHARD
Published: January 2011

Homoploid hybridization after secondary contact between related species can lead to mixtures of genotypes which have the potential for rapid adaptation to new environmental conditions. Here, we focus on a case where anthropogenic changes within the past 200 years have allowed the hybridization between two fish species (Cottus rhenanus and Cottus perifretum) in the Netherlands. Specifically, we address the question of the dynamics of the emergence of these hybrids and invasion of the river systems. Using a set of 81 mostly ancestry‐informative SNP markers, as well as broad sample coverage in and around the area of the initial contact, we find a structured hybrid swarm with at least three distinct hybrid lineages that have emerged out of this secondary contact situation. We show that genetically coherent groups can occur at geographically distant locations, while geographically adjacent groups can be genetically different, indicating that some form of reproductive isolation between the lineages is already effective. Using a newly developed modelling approach, we test the relative influence of founding admixture, drift and migration on the allele compositions of the sampling sites. We find that the allele frequency distributions can best be explained if continued gene flow between the parental species and the hybrid lineages is invoked. Genome mapping of the invasive lineage in the Rhine shows that major chromosomal rearrangements were not involved in creating this distinct lineage. Our results show that hybridization after secondary contact can quickly lead to multiple independent new lineages that have the capacity to form hybrid species.
Impact of the unfolded protein response on the pathogenicity of the necrotrophic fungus Alternaria brassicicola
Authors: Joubert A. , Simoneau P. , Campion C. , Bataillé‐Simoneau N. , Iacomi‐Vasilescu B. , Poupard P. , François J. M. , Georgeault S. , Sellier E. , Guillemette T.
Published: January 2011

The unfolded protein response (UPR) is an important stress signalling pathway involved in the cellular development and environmental adaptation of fungi. We investigated the importance of the UPR pathway in the pathogenicity of the plant necrotrophic fungus Alternaria brassicicola, which causes black spot disease on a wide range of Brassicaceae. We identified the AbHacA gene encoding the major UPR transcription regulator in A. brassicicola. Deletion of AbHacA prevented induction of the UPR in response to endoplasmic reticulum stress. Loss of UPR in mutants resulted in a complete loss of virulence and was also associated with a cell wall defect and a reduced capacity for secretion. In addition, our results showed that the UPR was triggered by treatment of mycelia with camalexin, i.e. the major Arabidopsis thaliana phytoalexin, and that strains lacking functional AbHacA exhibited increased in vitro susceptibility to antimicrobial plant metabolites. We hypothesize that the UPR plays a major role in fungal virulence by altering cell protection against host metabolites and by reducing the ability of the fungus to assimilate nutrients required for growth in the host environment. This study suggests that targeting the UPR pathway would be an effective plant disease control strategy.
A bicistronic, Ubiquitin‐10 promoter‐based vector cassette for transient transformation and functional analysis of membrane transport demonstrates the utility of quantitative voltage clamp studies on intact Arabidopsis root epidermis
Authors: CHEN ZHONGHUA , GREFEN CHRISTOPHER , DONALD NAOMI , HILLS ADRIAN , BLATT MICHAEL R.
Published: January 2011

To date the use of fluorescent reporter constructs in analysing membrane transport has been limited primarily to cell lines expressing stably either the tagged transporter protein(s) or markers to identify lineages of interest. Strategies for transient expression have yet to be exploited in transport analysis, despite their wide application in cellular imaging studies. Here we describe a Gateway‐compatible, bicistronic vector, incorporating the constitutive Ubiqutin‐10 gene promoter of Arabidopsis that gives prolonged expression after transient transformation and enables fluorescence marking of cells without a fusion construct. We show that Arabidopsis root epidermal cells are readily transformed by co‐cultivation with Agrobacterium and are tractable for quantitative electrophysiological analysis. As a proof of principle, we transiently transformed Arabidopsis with the bicistronic vector carrying GFP as the fluorescent marker and, separately, the integral plasma membrane protein SYP121 essential for the inward K+ channel current. We demonstrate that transient expression of SYP121 in syp121 mutant plants is sufficient to rescue the K+ current in vivo. The combination of transient expression and use of the bicistronic vector promises significant advantages for studies of membrane transport and nutrient acquisition in roots.
Distinct responses of the mitochondrial respiratory chain to long‐ and short‐term high‐light environments in Arabidopsis thaliana
Authors: YOSHIDA KEISUKE , WATANABE CHIHIRO K. , HACHIYA TAKUSHI , THOLEN DANNY , SHIBATA MASARU , TERASHIMA ICHIRO , NOGUCHI KO
Published: January 2011

In order to ensure the cooperative function with the photosynthetic system, the mitochondrial respiratory chain needs to flexibly acclimate to a fluctuating light environment. The non‐phosphorylating alternative oxidase (AOX) is a notable respiratory component that may support a cellular redox homeostasis under high‐light (HL) conditions. Here we report the distinct acclimatory manner of the respiratory chain to long‐ and short‐term HL conditions and the crucial function of AOX in Arabidopsis thaliana leaves. Plants grown under HL conditions (HL plants) possessed a larger ubiquinone (UQ) pool and a higher amount of cytochrome c oxidase than plants grown under low light conditions (LL plants). These responses in HL plants may be functional for efficient ATP production and sustain the fast plant growth. When LL plants were exposed to short‐term HL stress (sHL), the UQ reduction level was transiently elevated. In the wild‐type plant, the UQ pool was re‐oxidized concomitantly with an up‐regulation of AOX. On the other hand, the UQ reduction level of the AOX‐deficient aox1a mutant remained high. Furthermore, the plastoquinone pool was also more reduced in the aox1a mutant under such conditions. These results suggest that AOX plays an important role in rapid acclimation of the respiratory chain to sHL, which may support efficient photosynthetic performance.
Clinical, biochemical and molecular characterization of Cystinuria in a cohort of 12 patients
Authors: Barbosa M , Lopes A , Mota C , Martins E , Oliveira J , Alves S , De Bonis P , do Céu Mota M , Dias C , Rodrigues‐Santos P , Fortuna AM , Quelhas D , Lacerda L , Bisceglia L , Cardoso ML
Published: January 2011

Barbosa M, Lopes A, Mota C, Martins E, Oliveira J, Alves S, De Bonis P, do Céu Mota M, Dias C, Rodrigues‐Santos P, Fortuna AM, Quelhas D, Lacerda L, Bisceglia L, Cardoso ML. Clinical, biochemical and molecular characterization of Cystinuria in a cohort of 12 patients.

Cystinuria is a rare autosomal inherited disorder characterized by impaired transport of cystine and dibasic aminoacids in the proximal renal tubule. Classically, Cystinuria is classified as type I (silent heterozygotes) and non‐type I (heterozygotes with urinary hyperexcretion of cystine). Molecularly, Cystinuria is classified as type A (mutations on SLC3A1 gene) and type B (mutations on SLC7A9 gene). The goal of this study is to provide a comprehensive clinical, biochemical and molecular characterization of a cohort of 12 Portuguese patients affected with Cystinuria in order to provide insight into genotype–phenotype correlations. We describe seven type I and five non‐type I patients. Regarding the molecular classification, seven patients were type A and five were type B. In SLC3A1 gene, two large genomic rearrangements and 13 sequence variants, including four new variants c.611‐2A>C; c.1136+44G>A; c.1597T (p.Y533N); c.*70A>G, were found. One large genomic rearrangement was found in SLC7A9 gene as well as 24 sequence variants including 3 novel variants: c.216C>T (p.C72C), c.1119G>A (p.S373S) and c.*82C>T. In our cohort the most frequent pathogenic mutations were: large rearrangements (33.3% of mutant alleles) and a missense mutation c.1400T>C ( p.M467T) (11.1%). This report expands the spectrum of SLC3A1 and SLC7A9 mutations and provides guidance in the clinical implementation of molecular assays in routine genetic counseling of Portuguese patients affected with Cystinuria.