bluuebunny/crossref_metadata_2025 huggingface dataset:
Plasticity of the α4βδ GABAA receptor
Authors: Shen Hui , Smith Sheryl S.
Published: November 2009

The GABAR [GABAA (γ-aminobutyric acid type A) receptor], which mediates most inhibition in the brain, is regulated homoeostatically to maintain an optimal level of neuronal excitability. In particular, the α4βδ subtype of the GABAR plays a pivotal role in this regulation. This receptor, which is expressed extrasynaptically on the dendrites, normally has low expression in the brain, but displays a remarkable degree of plasticity. It can also be a sensitive target for endogenous neurosteroids such as THP (3α-hydroxy-5[α]β-pregnan-20-one (allo-pregnanolone); a neurosteroid and positive modulator of the GABAR), which is released during stress, although the effect of the steroid is polarity-dependent, such that it increases inward current, but decreases outward current, at α4β2δ GABAR. Expression of α4β2δ GABAR in CA1 hippocampus is also tightly regulated by fluctuating levels of neurosteroids, as seen at the onset of puberty. Declining levels of inhibition resulting from the decrease in THP at puberty are compensated for by an increase in α4βδ GABAR along the apical dendrites of CA1 hippocampal pyramidal cells, which reduces neuronal excitability by decreasing the input resistance. However, excessive decrease of neuronal function is averted when THP levels rise, as would occur during stress, because this steroid decreases the outward GABAergic tonic current via inhibition of α4β2δ GABAR, thereby restoring measures of neuronal excitability to pre-pubertal levels. Thus the homoeostatic regulation of α4βδ GABAR expression plays an important role in maintaining ambient levels of neuronal excitability at puberty.
RDL receptors
Authors: McGonigle Ian , Lummis Sarah C.R.
Published: November 2009

RDL receptors are invertebrate members of the Cys-loop family of ligand-gated ion channels. They are GABA (γ-aminobutyric acid)-activated chloride-selective receptors that are closely related to their vertebrate orthologues, the GABAA receptors, as well as other Cys-loop receptors such as the ionotropic glycine, nicotinic acetylcholine and 5-HT3 receptors. RDL receptors are widely expressed throughout the insect CNS (central nervous system) and are important in inhibitory neurotransmission. They are therefore a major insecticidal target site.
Inhibition of recombinant GluN1/GluN2A and GluN1/GluN2B N-methyl-D-aspartate receptors by single malt whiskies
Authors: Otton Hannah J. , Janssen Ariane , Wyllie David J.A.
Published: November 2009

NMDARs (N-methyl-D-aspartate receptors) are considered to be a target for the inhibitory actions of ethanol. While profound inhibition of both native and recombinant NMDARs can be observed following the application of high concentrations of ethanol the levels of inhibition seen with lower concentrations of ethanol are more modest. Here, we report the effects of inhibiting NMDAR-mediated responses with ethanol concentrations that are experienced during the social consumption of alcohol comparing levels of inhibition seen with ‘pure’ ethanol with those produced by ethanol contained in three popular single malt whiskies.
Visualization of highly graded oxygen vacancy profiles in lead-zirconate-titanate by spectrally resolved cathodoluminescence spectroscopy
Authors: Matsutani Atsuo , Luo Zhenhua (Jerry) , Pojprapai Soodkhet , Hoffman Mark , Pezzotti Giuseppe
Published: November 2009

The ultraviolet and visible cathodoluminescence (CL) emitted at room temperature from bulk hard lead-zirconate-titanate polycrystalline perovskite has been systematically collected before and after an annealing cycle conducted in a reducing atmosphere. Spectroscopic assessments have been made of the in-depth stoichiometric profile developed upon annealing from the sample surface toward the subsurface. Trapping of electronic charge and local atomic scale distortions in the perovskite oxygen octahedron influences the variation observed in visible CL emission, while lattice distortions upon annealing directly arise from the formation of oxygen vacancies.
Clebsch parameterization: Basic properties and remarks on its applications
Authors: Yoshida Z.
Published: November 2009

The Clebsch parameterization (u=∇φ+α∇β) has advantages in elucidating structural properties of vector fields; for example, it helps formulating the Hamiltonian form of ideal fluid mechanics, representing topological constraints (Casimir invariants), integrating the Cauchy characteristics of vortex fields, etc. Because of its “nonlinear” formulation, however, there are some difficulties which must be carefully overcome. (1) It is not complete, i.e., for an arbitrary vector field u, we may fail to find three scalar fields (Clebsch parameters) φ, α, and β that satisfy u=∇φ+α∇β globally in space. (2) It is not uniquely determined, i.e., the map (u1,u2,u3)↦(φ,α,β) is not injective. A generalized form such that u=∇φ+∑j=1ναj∇βj is complete if ν=n−1 (n is the space dimension). However, when we need to control the boundary values of φ, αj, and βj (for example, to determine them uniquely), we have to set ν=n.
Quantifying fatigue generated in high strain rate cyclic loading of Norway spruce
Authors: Salmi Ari , Salminen Lauri , Hæggström Edward
Published: November 2009

Papermaking, especially mechanical pulping, consumes much energy. To reduce this energy consumption one has to understand and exploit the phenomena present during the pulping. An important phenomenon to understand is wood fatigue. We quantitatively measure the fatigue generated during high strain rate cyclic loading of spruce wood performed under conditions resembling those present during mechanical pulping. We impacted the samples with 5% strain pulses at 500 Hz. The radial direction stiffness drop in the samples was quantified by 500 kHz ultrasonic through-transmission postimpacting. The depth profile of the generated fatigue was also determined. A dependency of the amount of fatigue generated during cyclic straining on the moisture content was detected. A hypothesis about the temporal and spatial evolution of the fatigue during the process is presented. The results, supporting the hypothesis, provide insight into wood behavior under mechanical pulping conditions.
Effects of methanol on nanoparticle self-assembly at liquid-liquid interfaces: A molecular dynamics approach
Authors: Luo Mingxiang , Song Yanmei , Dai Lenore L.
Published: November 2009

Molecular dynamics simulations have been performed to study the influence of methanol on the self-assembly of nanoparticles at liquid-liquid interfaces. The simulation shows that the methanol molecules, at low volume fraction, stay in the aqueous phase but with a preference of the water-trichloroethylene (TCE) interfaces. However, at higher methanol volume fraction, methanol dominates the aqueous phase and no preferable location of methanol molecules is observed. The simulations also suggest that the interfacial tension decreases and the interfacial thickness increases with increasing methanol concentration. The presence of the nanoparticles at water-TCE interfaces has minor effect on the interfacial properties compared to those of methanol, and the presence of methanol drives the noncharged nanoparticle clusters closer to the interfaces. Although the methanol molecules do not affect the monolayer distribution of the negatively charged nanoparticles at the water-TCE interfaces, they increase the three-phase contact angles of these nanoparticles.
Comparison of amorphous silicon photodiodes and photoconductors for detection of quantum dot biomolecular tags
Authors: Pimentel A. C. , Prazeres D. M. F. , Chu V. , Conde J. P.
Published: November 2009

A comparative study of the performance of hydrogenated amorphous silicon photosensors based on two different device configurations for integration in a microarray platform for biomolecular detection is presented. A perpendicular contact p-i-n photodiode and a parallel contact intrinsic photoconductor, both with an integrated fluorescence filter, are microfabricated for the detection in solution of the fluorescence of the quantum dot Evitag 604 nm, a tag commonly used to label biological molecules. The minimum quantities of quantum dot detected by the p-i-n photodiode and the parallel contact photoconductor were 1 fmol (0.1 nM) and 30 fmol (3 nM), respectively.
Metal-semiconductor transition in epitaxial ZnO thin films
Authors: Nistor M. , Gherendi F. , Mandache N. B. , Hebert C. , Perrière J. , Seiler W.
Published: November 2009

We report on the formation and transport properties of ZnO thin films which are grown by pulsed-electron beam deposition under a low residual oxygen pressure (10−5 mbar). ZnO films presenting metallic conductivity at room temperature, and a metal-semiconductor transition at low temperature, were epitaxially grown on Al2O3 single crystal substrates for growth temperatures in the 300–450 °C range. These results have been interpreted through the quantum corrections to conductivity in a disordered oxide conductor, implying first a high density of carriers leading to degenerate semiconductor ZnO films, and then a sufficient disorder in these films. These characteristics could be related to the nature of the ZnO films formed by pulsed-electron deposition: a high density of carriers related to an oxygen deficiency in the films and a high density of defects related to the high deposition rate of the pulsed-electron beam deposition method.
Simultaneous low-frequency noise characterization of gate and drain currents in AlGaN/GaN high electron mobility transistors
Authors: Rao Hemant , Bosman Gijs
Published: November 2009

Room temperature low frequency noise characteristics of gate and drain currents of an AlGaN/GaN high electron mobility transistor are reported. A Hooge parameter (αH) ranging from 10−3 to 10−4 is extracted for drain current noise as a function of sheet carrier density. Gate current noise is simultaneously measured with drain noise both in the time and frequency domain. A weak correlation is seen between the drain and gate noise. Temporally unstable Lorentzian components on top of stable 1/fγ noise are observed in the gate noise spectra which also show up as random telegraph signal noise in the time domain. It is proposed that the gate Schottky contact is of high quality but that electrically unstable point defects in the AlGaN layer are the cause of Lorentzians and random telegraph switching noise.
Charge order, dielectric response, and local structure of La5/3Sr1/3NiO4 system
Authors: Filippi M. , Kundys B. , Agrestini S. , Prellier W. , Oyanagi H. , Saini N. L.
Published: November 2009

Charge ordering, dielectric permittivity, and local structure of La5/3Sr1/3NiO4 system have been explored by x-ray charge scattering, complex dielectric impedance spectroscopy, and extended x-ray absorption fine structure (EXAFS) measurements, made on the same single crystal sample. The local structure measured by the temperature-dependent, polarized Ni K-edge EXAFS shows significant distortions in the NiO2 planes. These local distortions could be reasonable cause of high dielectric permittivity of the title system (ε≈100 at 5 K) with the charge ordering in this system being a ferroelectriclike second order transition.
First-principles simulations on bulk Ta2O5 and Cu/Ta2O5/Pt heterojunction: Electronic structures and transport properties
Authors: Gu Tingkun , Wang Zhongchang , Tada Tomofumi , Watanabe Satoshi
Published: November 2009

Electronic structures and transport properties of bulk Ta2O5 and Cu/Ta2O5/Pt heterojunction have been studied from first principles. Of the two room-temperature phases of bulk Ta2O5, β-, and δ-Ta2O5, our calculated results showed that the β phase has much narrower band gap than the δ-Ta2O5. For Cu/δ-Ta2O5/Pt heterojunction, the p-type Schottky barriers between the Cu (Pt) and Ta2O5 were estimated as 0.9–1.2 eV. Both the standard density-functional calculation and the nonequilibrium Green’s function showed that no conducting channels were formed from Cu to Pt through δ-Ta2O5.
Electrical control of magnetic remanent states in a magnetoelectric layered nanostructure
Authors: Chung Tien-Kan , Wong Kin , Keller Scott , Wang Kang L. , Carman Gregory P.
Published: November 2009

We report experimental results on electrical control of magnetic remanent states (i.e., nanoscale remanent domain patterns) in a magnetoelectric layered nanostructure, Ni nanobar/lead zirconate titanate film. First, with application of different external magnetic fields as a baseline characterization, the magnetic single domain in the Ni nanobar presents time-dependent nanoscale remanent domain patterns which were observed under a magnetic force microscope. Based on this baseline characterization, we further successfully demonstrate that these time-dependent nanoscale magnetic domain patterns could be instantaneously controlled with an application of electric fields due to the converse magnetoelectric effect. The magnetic-field-induced changes are correlated with the electric-field-induced changes.
Photoinduced spin-polarized current in InSb-based structures
Authors: Frazier M. , Cates J. G. , Waugh J. A. , Heremans J. J. , Santos M. B. , Liu X. , Khodaparast G. A.
Published: November 2009

We demonstrate the observation of spin-polarized photocurrent in InSb films grown on GaAs and InP substrates and InSb quantum wells where a nonequilibrium spin population has been achieved by using circularly polarized radiation. The characteristics of our observations indicated that the circular photo galvanic effect could be responsible for the generation of the photocurrents.
Inertial range scaling of the scalar flux spectrum in two-dimensional turbulence
Authors: Bos W. J. T. , Kadoch B. , Schneider K. , Bertoglio J.-P.
Published: November 2009

Two-dimensional statistically stationary isotropic turbulence with an imposed uniform scalar gradient is investigated. Dimensional arguments are presented to predict the inertial range scaling of the turbulent scalar flux spectrum in both the inverse cascade range and the enstrophy cascade range for small and unity Schmidt numbers. The scaling predictions are checked by direct numerical simulations and good agreement is observed.
Sound control by temperature gradients
Authors: Sánchez-Dehesa José , Angelov Mitko I. , Cervera Francisco , Cai Liang-Wu
Published: November 2009

This work reports experiments showing that airborne sound propagation can be controlled by temperature gradients. A system of two heated tubes is here used to demonstrate the collimation and focusing of an ultrasonic beam by the refractive index profile created by the temperature gradients existing around the tubes. Numerical simulations supporting the experimental findings are also reported.
Emergence of complex behavior in gelling systems starting from simple behavior of single clusters
Authors: Fierro A. , Abete T. , Coniglio A.
Published: November 2009

A theoretical and numerically study of dynamical properties in the sol-gel transition is presented. In particular, the complex phenomenology observed experimentally and numerically in gelling systems is reproduced in the framework of percolation theory, under simple assumptions on the relaxation of single clusters. By neglecting the correlation between particles belonging to different clusters, the quantities of interest (such as the self intermediate scattering function, the dynamical susceptibility, the Van-Hove function, and the non-Gaussian parameter) are written as superposition of those due to single clusters. Connection between these behaviors and the critical exponents of percolation are given. The theoretical predictions are checked in a model for permanent gels, where bonds between monomers are described by a finitely extendable nonlinear elastic potential. The data obtained in the numerical simulations are in good agreement with the analytical predictions.
Charge transport in polypyrrole:ZnO-nanowires composite films
Authors: Singh A. , Joshi Aditee , Samanta S. , Debnath A. K. , Aswal D. K. , Gupta S. K. , Yakhmi J. V.
Published: November 2009

Low temperature electrical transport properties of composite polypyrrole (PPy) films having ZnO-nanowires (ZnONWs) in the range of 0–50 wt. % have been investigated. It has been found that pure PPy film is in the critical regime of the metal-to-insulator transition, and adding ZnONWs drive composite films into the insulating regime. For PPy films, the transport is governed by Motts three-dimensional-variable range hopping (VRH) (ln ρ∼T−1/4) conduction and with increasing ZnONWs content above 10 wt. % results in a crossover to one-dimensional-VRH conduction (ln ρ∼T−1/2). It has been observed that films having ZnONWs content ≥10 wt. % exhibit reproducible hysteresis in the current-voltage characteristics.
Comment on “Heat transfer in vacuum packaged microelectromechanical system devices” [Phys. Fluids 20, 017103 (2008)]
Authors: Sone Yoshio
Published: November 2009

It is pointed out that the solution of a free molecular gas in a bounded domain proposed as speculation in Sec. II of Cai [Phys. Fluids 20, 017103 (2008)] and in Sec. II of Cai and Liu [Phys. Fluids 20, 067105 (2008)] and its result of the vanishing of flow velocity were rigorously derived under a more general situation and boundary condition more than 20 years ago.
Development and fertility studies on post-bio-electrosprayed Drosophila melanogaster embryos
Authors: Joly Pascal , Jennings Barbara H. , Jayasinghe Suwan N.
Published: November 2009

Bio-electrosprays (BESs) provide a means of precisely manipulating cells and thus have the potential for many clinical uses such as the generation of artificial tissues/organs. Previously we tested the biological safety of this technology with a variety of living cells and also embryos from the vertebrate model organisms Danio rerio (zebrafish) and Xenopus tropicalis (frog). However, the viability and fertility of the treated embryos could not be fully assessed due to animal licensing laws. Here we assay the viability and fertility of Drosophila melanogaster (fruit fly) embryos in conjunction with the bio-electrospray procedure. Bio-electrosprayed Drosophila embryos developed into fully fertile adult flies that were indistinguishable from wild-type. Thus, we demonstrate that the bio-electrospray procedure does not induce genetic or physical damage that significantly affects the development or fertility of a multicellular organism. This study along with our previous investigations demonstrates the potential of this approach to be developed for the precise manipulation of sensitive biological materials.
Regulation of Hsp90 client proteins by a Cullin5-RING E3 ubiquitin ligase
Authors: Ehrlich Elana S. , Wang Tao , Luo Kun , Xiao Zuoxiang , Niewiadomska Anna Maria , Martinez Tara , Xu Wanping , Neckers Len , Yu Xiao-Fang
Published: November 2009

We report a link between Cullin5 (Cul5) E3 ubiquitin ligase and the heat shock protein 90 (Hsp90) chaperone complex. Hsp90 participates in the folding of its client proteins into their functional conformation. Many Hsp90 clients have been reported to be aberrantly expressed in a number of cancers. We demonstrate Cul5 interaction with members of the Hsp90 chaperone complex as well as the Hsp90 client, ErbB2. We observed recruitment of Cul5 to the site of ErbB2 at the plasma membrane and subsequent induction of polyubiquitination and proteasomal degradation. We also demonstrate Cul5 involvement in regulation of another Hsp90 client, Hif-1α. We observed Cul5 degradation of ErbB2 to occur independently of ElonginB-ElonginC function. The involvement of Cul5 in Hsp90 client regulation has implications in the effectiveness of Hsp90 targeted chemotherapy, which is currently undergoing clinical trials. The link between Cul5 and Hsp90 client regulation may represent an avenue for cancer drug development.
Ca2+, cAMP, and transduction of non-self perception during plant immune responses
Authors: Ma Wei , Qi Zhi , Smigel Andries , Walker Robin K. , Verma Rajeev , Berkowitz Gerald A.
Published: November 2009

Ca2+influx is an early signal initiating cytosolic immune responses to pathogen perception in plant cells; molecular components linking pathogen recognition to Ca2+influx are not delineated. Work presented here provides insights into this biological system of non-self recognition and response activation. We have recently identified a cyclic nucleotide-activated ion channel as facilitating the Ca2+flux that initiates immune signaling in the plant cell cytosol. Work in this report shows that elevation of cAMP is a key player in this signaling cascade. We show that cytosolic Ca2+elevation, nitric oxide (NO) and reactive oxygen species generation, as well as immune signaling, lead to a hypersensitive response upon application of pathogens and/or conserved molecules that are components of microbes and are all dependent on cAMP generation. Exogenous cAMP leads to Ca2+channel-dependent cytosolic Ca2+elevation, NO generation, and defense response gene expression in the absence of the non-self pathogen signal. Inoculation of leaves with a bacterial pathogen leads to cAMP elevation coordinated with Ca2+rise. cAMP acts as a secondary messenger in plants; however, no specific protein has been heretofore identified as activated by cAMP in a manner associated with a signaling cascade in plants, as we report here. Our linkage of cAMP elevation in pathogen-inoculated plant leaves to Ca2+channels and immune signaling downstream from cytosolic Ca2+elevation provides a model for how non-self detection can be transduced to initiate the cascade of events in the cell cytosol that orchestrate pathogen defense responses.
A minimal sequence code for switching protein structure and function
Authors: Alexander Patrick A. , He Yanan , Chen Yihong , Orban John , Bryan Philip N.
Published: November 2009

We present here a structural and mechanistic description of how a protein changes its fold and function, mutation by mutation. Our approach was to create 2 proteins that (i) are stably folded into 2 different folds, (ii) have 2 different functions, and (iii) are very similar in sequence. In this simplified sequence space we explore the mutational path from one fold to another. We show that an IgG-binding, 4β+α fold can be transformed into an albumin-binding, 3-α fold via a mutational pathway in which neither function nor native structure is completely lost. The stabilities of all mutants along the pathway are evaluated, key high-resolution structures are determined by NMR, and an explanation of the switching mechanism is provided. We show that the conformational switch from 4β+α to 3-α structure can occur via a single amino acid substitution. On one side of the switch point, the 4β+α fold is >90% populated (pH 7.2, 20 °C). A single mutation switches the conformation to the 3-α fold, which is >90% populated (pH 7.2, 20 °C). We further show that a bifunctional protein exists at the switch point with affinity for both IgG and albumin.
Illuminating cell-cycle progression in the developing zebrafish embryo
Authors: Sugiyama Mayu , Sakaue-Sawano Asako , Iimura Tadahiro , Fukami Kiyoko , Kitaguchi Tetsuya , Kawakami Koichi , Okamoto Hitoshi , Higashijima Shin-ichi , Miyawaki Atsushi
Published: November 2009

By exploiting the cell-cycle-dependent proteolysis of two ubiquitination oscillators, human Cdt1 and geminin, which are the direct substrates of SCF
Skp2
and APC
Cdh1
complexes, respectively, Fucci technique labels mammalian cell nuclei in G
1
and S/G
2
/M phases with different colors. Transgenic mice expressing these G
1
and S/G
2
/M markers offer a powerful means to investigate the coordination of the cell cycle with morphogenetic processes. We attempted to introduce these markers into zebrafish embryos to take advantage of their favorable optical properties. However, although the fundamental mechanisms for cell-cycle control appear to be well conserved among species, the G
1
marker based on the SCF
Skp2
-mediated degradation of human Cdt1 did not work in fish cells, probably because the marker was not ubiquitinated properly by a fish E3 ligase complex. We describe here the generation of a Fucci derivative using zebrafish homologs of Cdt1 and geminin, which provides sweeping views of cell proliferation in whole fish embryos. Remarkably, we discovered two anterior-to-posterior waves of cell-cycle transitions, G
1
/S and M/G
1
, in the differentiating notochord. Our study demonstrates the effectiveness of using the Cul4
Ddb1
-mediated Cdt1 degradation pathway common to all metazoans for the development of a G
1
marker that works in the nonmammalian animal model.
A microRNA regulatory mechanism of osteoblast differentiation
Authors: Inose Hiroyuki , Ochi Hiroki , Kimura Ayako , Fujita Koji , Xu Ren , Sato Shingo , Iwasaki Makiko , Sunamura Satoko , Takeuchi Yasuhiro , Fukumoto Seiji , Saito Kuniaki , Nakamura Takashi , Siomi Haruhiko , Ito Hiroshi , Arai Yoshiyasu , Shinomiya Ken-ichi , Takeda Shu
Published: November 2009

Growing evidence shows that microRNAs (miRNAs) regulate various developmental and homeostatic events in vertebrates and invertebrates. Osteoblast differentiation is a key step in proper skeletal development and acquisition of bone mass; however, the physiological role of non-coding small RNAs, especially miRNAs, in osteoblast differentiation remains elusive. Here, through comprehensive analysis of miRNAs expression during osteoblast differentiation, we show that miR-206, previously viewed as a muscle-specific miRNA, is a key regulator of this process. miR-206 was expressed in osteoblasts, and its expression decreased over the course of osteoblast differentiation. Overexpression of miR-206 in osteoblasts inhibited their differentiation, and conversely, knockdown of miR-206 expression promoted osteoblast differentiation. In silico analysis and molecular experiments revealed connexin 43 (Cx43), a major gap junction protein in osteoblasts, as a target of miR-206, and restoration of Cx43 expression in miR-206-expressing osteoblasts rescued them from the inhibitory effect of miR-206 on osteoblast differentiation. Finally, transgenic mice expressing miR-206 in osteoblasts developed a low bone mass phenotype due to impaired osteoblast differentiation. Our data show that miRNA is a regulator of osteoblast differentiation.
Glycogen synthase kinase-3/Shaggy mediates ethanol-induced excitotoxic cell death of Drosophila olfactory neurons
Authors: French Rachael L. , Heberlein Ulrike
Published: November 2009

It has long been known that heavy alcohol consumption leads to neuropathology and neuronal death. While the response of neurons to an ethanol insult is strongly influenced by genetic background, the underlying mechanisms are poorly understood. Here, we show that even a single intoxicating exposure to ethanol causes non-cell-autonomous apoptotic death specifically of
Drosophila
olfactory neurons, which is accompanied by a loss of a behavioral response to the smell of ethanol and a blackening of the third antennal segment. The
Drosophila
homolog of glycogen synthase kinase-3 (GSK-3)β, Shaggy, is required for ethanol-induced apoptosis. Consistent with this requirement, the GSK-3β inhibitor lithium protects against the neurotoxic effects of ethanol, indicating the possibility for pharmacological intervention in cases of alcohol-induced neurodegeneration. Ethanol-induced death of olfactory neurons requires both their neural activity and functional NMDA receptors. This system will allow the investigation of the genetic and molecular basis of ethanol-induced apoptosis in general and provide an understanding of the molecular role of GSK-3β in programmed cell death.
Social Marketing Approach to a Successful Oral Cancer Case-Finding Pilot
Authors: Lowry Ray , Archer Anne , Howe Debora , Russell Rebecca , Hiom Sara
Published: November 2009

The incidence of oral cancer is increasing. Cases often present too late for treatment to be successful due to lack of awareness of the disease and reluctance to access services. The objective of this project was to implement a social marketing oral cancer pilot case-finding service for an at-risk population. The project used specific awareness-raising techniques in a defined catchment population to engage with those at risk from oral cancer and encourage them to seek early case-finding and diagnosis or elimination from follow-up, in a uniquely designed case-finding/referral intervention based on social marketing techniques. Of those who went on to make a case-finding appointment following an initial risk assessment, 96% kept their appointment and 10% were referred to specialist services. The system developed proved that it is possible to engage with a hard-to-reach target population at risk from a serious disease and draw significant numbers into case-finding/health service contact. This intervention illustrates the value of complex target-population tracking systems; shows the application of social marketing techniques in drawing in a target audience hard-to-reach; and how much social marketing is about the product or service rather than just the communication strategy.
Newborns' Mooney‐Face Perception
Authors: Leo Irene , Simion Francesca
Published: November 2009

The aim of this study is to investigate whether newborns detect a face on the basis of a Gestalt representation based on first‐order relational information (i.e., the basic arrangement of face features) by using Mooney stimuli. The incomplete 2‐tone Mooney stimuli were used because they preclude focusing both on the local features (i.e., the fine details of the individual features) and on the second‐order relational information (i.e., the distance between the internal elements); therefore, face detection can rely only on a Gestalt representation of a face. Two experiments were carried out by using a preferential looking procedure. Experiment 1 demonstrated that newborns prefer upright Mooney faces to inverted Mooney faces (180° rotated). Experiment 2 showed that newborns prefer a Mooney face as compared to a Mooney‐like object equated for the number of elements in the upper part. Overall, the results indicate that newborns bind and organize the fragmentary parts of the Mooneized face stimulus into a whole and detect the first‐order relations of a face on the basis of holistic processing.
Variational and exact solutions of the wavefunction at origin (WFO) for heavy quarkonium by using a global potential
Authors: Boroun G R , Abdolmalki H
Published: November 2009

In this paper, we discuss the wavefunction at origin (WFO) for , and massive quarks systems. Using the variational method and an exact computation of the Schrödinger equation, we computed the WFO and also expectation values of ⟨ 1/r⟩, ⟨r⟩ for massive mesons, while we had global potential in the form of . We show that the final results of this potential include and cover all other results by other potential models (Cornell, Martin, logarithmic, Lichtenberg, etc). Also, the energy values obtained from this model have the highest level compared with other models.
Hole spin precession in semiconductors: Clifford algebra approach
Authors: Dargys A
Published: November 2009

Recently the Clifford (geometrical) algebra was addressed to describe dynamical properties of electron spin in semiconductors (Dargys 2009 Phys. Scr. 79 055702). In this paper, the Clifford algebra is used to investigate heavy and light hole spins in valence bands of cubic semiconductors. Owing to strong spin–orbit interaction in the valence band, the precession trajectories of hole spin polarization are ellipses, or even lines, rather than circles as usually found in the case of electrons. The paper shows how one can investigate the valence band spectrum and free-hole spin precession trajectories within a framework of the Clifford algebra Cl
4, 1. General formulae that describe free heavy- and light-mass hole spin precession are presented.
Simulation estimation of RB1 station's sensitivities and hit rates for e+/e− particles by RPCs
Authors: Jamil M , Rhee J T , Jeon Y J
Published: November 2009

Resistive plate chambers (RPCs) have been chosen as a part of the muon trigger detector, in both the endcap and barrel regions of a compact muon solenoid (CMS) experiment, which will work in extreme radiation backgrounds. In order to evaluate the response of the RPC detector in the CMS background environment, the RB1 barrel region has been investigated. The present simulation for e+/e− using GEANT3.21 code predicts hit rates of 0.048 (0.045) and 0.040 (0.038) Hz cm−2 using a bakelite and glass-based RPC setup. A similar trend in the results of GEANT4 Monte Carlo code with the same RPC configurations is also reported.
Bayesian variable selection for disease classification using gene expression data
Authors: Ai-Jun Yang , Xin-Yuan Song
Published: November 2009

Motivation: An important application of gene expression microarray data is the classification of samples into categories. Accurate classification depends upon the method used to identify the most relevant genes. Owing to the large number of genes and relatively small sample size, the selection process can be unstable. Modification of existing methods for achieving better analysis of microarray data is needed.

Results: We propose a Bayesian stochastic variable selection approach for gene selection based on a probit regression model with a generalized singular g-prior distribution for regression coefficients. Using simulation-based Markov chain Monte Carlo methods for simulating parameters from the posterior distribution, an efficient and dependable algorithm is implemented. It is also shown that this algorithm is robust to the choices of initial values, and produces posterior probabilities of related genes for biological interpretation. The performance of the proposed approach is compared with other popular methods in gene selection and classification via the well-known colon cancer and leukemia datasets in microarray literature.

Availability: A free Matlab code to perform gene selection is available at http://www.sta.cuhk.edu.hk/xysong/geneselection/.

Contact:  ajyang81@gmail.com; xysong@sta.cuhk.edu.hk.

Supplementary information:  Supplementary data are available at Bioinformatics online.
MAVEN: a tool for visualization and functional analysis of genome-wide association results
Authors: Narayanan Kanchana , Li Jing
Published: November 2009

Summary: We describe the features and implementation of a web application tool named MAVEN—for Management, Analysis, Visualization and rEsults shariNg of genome-wide association data using cutting edge technologies. Main capabilities include user data uploading and management, queries using a variety of criteria, visualization of results, interactive selections and seamless integration of users' data with databases at the National Center for Biotechnology Information (NCBI) for functional annotations of single nucleotide polymorphisms (SNPs) and genes.

Availability:  http://cbc.case.edu/maven

Contact:  jingli@case.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
LegumeTFDB: an integrative database of Glycine max, Lotus japonicus and Medicago truncatula transcription factors
Authors: Mochida Keiichi , Yoshida Takuhiro , Sakurai Tetsuya , Yamaguchi-Shinozaki Kazuko , Shinozaki Kazuo , Tran Lam-Son Phan
Published: November 2009

Summary: We have established a database named LegumeTFDB to provide access to transcription factor (TF) repertoires of three major legume species: soybean (Glycine max), Lotus japonicus and Medicago truncatula. LegumeTFDB integrates unique information for each TF gene and family, including sequence features, gene promoters, domain alignments, gene ontology (GO) assignment and sequence comparison data derived from comparative analysis with TFs found within legumes, in Arabidopsis, rice and poplar as well as with proteins in NCBI nr and UniProt. We also analyzed the promoter regions for all of the TFs to identify all types of cis-motifs provided by the PLACE database. Additionally, we supply hyperlinks to make available expression data of 2411 soybean TF genes. LegumeTFDB provides an important user-friendly public resource for comparative genomics and understanding of transcriptional regulation in agriculturally important legumes.

Availability:  http://legumetfdb.psc.riken.jp/

Contact:  tran@psc.riken.jp; mochida@psc.riken.jp

Supplementary information:  Supplementary data available at Bioinformatics online.
Propofol Facilitates Glutamatergic Transmission to Neurons of the Ventrolateral Preoptic Nucleus
Authors: Li Ke Y. , Guan Yan-zhong , Krnjević Kresimir , Ye Jiang H.
Published: November 2009

Background

There is much evidence that the sedative component of anesthesia is mediated by gamma-aminobutyric acid type A (GABA(A)) receptors on hypothalamic neurons responsible for arousal, notably in the tuberomammillary nucleus. These GABA(A) receptors are targeted by gamma-aminobutyric acid-mediated (GABAergic) neurons in the ventrolateral preoptic area (VLPO): When these neurons become active, they inhibit the arousal-producing nuclei and induce sleep. According to recent studies, propofol induces sedation by enhancing VLPO-induced synaptic inhibition, making the target cells more responsive to GABA(A). The authors explored the possibility that propofol also promotes sedation less directly by facilitating excitatory inputs to the VLPO GABAergic neurons.

Methods

Spontaneous excitatory postsynaptic currents were recorded from VLPO cells-principally mechanically isolated, but also in slices from rats.

Results

In isolated VLPO GABAergic neurons, propofol increased the frequency of glutamatergic spontaneous excitatory postsynaptic currents without affecting their mean amplitude. The action of propofol was mimicked by muscimol and prevented by gabazine, respectively a specific agonist and antagonist at GABA(A) receptors. It was also suppressed by bumetanide, a blocker of Na-K-Cl cotransporter-mediated inward Cl transport. In slices, propofol also increased the frequency of spontaneous excitatory postsynaptic currents and, at low doses, accelerated firing of VLPO cells.

Conclusion

Propofol induces sedation, at least in part, by increasing firing of GABAergic neurons in the VLPO, indirectly by activation of GABA(A) receptors on glutamatergic afferents: Because these axons/terminals have a relatively high internal Cl concentration, they are depolarized by GABAergic agents such as propofol, which thus enhance glutamate release.
Ants defend aphids against lethal disease
Authors: Nielsen Charlotte , Agrawal Anurag A. , Hajek Ann E.
Published: November 2009

Social insects defend their own colonies and some species also protect their mutualist partners. In mutualisms with aphids, ants typically feed on honeydew produced by aphids and, in turn guard and shelter aphid colonies from insect natural enemies. Here we report that
Formica podzolica
ants tending milkweed aphids,
Aphis asclepiadis
, protect aphid colonies from lethal fungal infections caused by an obligate aphid pathogen,
Pandora neoaphidis
. In field experiments, bodies of fungal-killed aphids were quickly removed from ant-tended aphid colonies. Ant workers were also able to detect infective conidia on the cuticle of living aphids and responded by either removing or grooming these aphids. Our results extend the long-standing view of ants as mutualists and protectors of aphids by demonstrating focused sanitizing and quarantining behaviour that may lead to reduced disease transmission in aphid colonies.
Intra-individual variation allows an explicit test of the hygric hypothesis for discontinuous gas exchange in insects
Authors: Williams Caroline M. , Pelini Shannon L. , Hellmann Jessica J. , Sinclair Brent J.
Published: November 2009

The hygric hypothesis postulates that insect discontinuous gas exchange cycles (DGCs) are an adaptation that reduces respiratory water loss (RWL), but evidence is lacking for reduction of water loss by insects expressing DGCs under normal ecological conditions. Larvae ofErynnis propertius(Lepidoptera: Hesperiidae) naturally switch between DGCs and continuous gas exchange (CGE), allowing flow-through respirometry comparisons of water loss between the two modes. Water loss was lower during DGCs than CGE, both between individuals using different patterns and within individuals using both patterns. The hygric cost of gas exchange (water loss associated with carbon dioxide release) and the contribution of respiratory to total water loss were lower during DGCs. Metabolic rate did not differ between DGCs and CGE. Thus, DGCs reduce RWL inE. propertius, which is consistent with the suggestion that water loss reduction could account for the evolutionary origin and/or maintenance of DGCs in insects.
Mechanical loading ofin situchondrocytes in lapine retropatellar cartilage after anterior cruciate ligament transection
Authors: Han Sang-Kuy , Seerattan Ruth , Herzog Walter
Published: November 2009

The aims of this study were (i) to quantify chondrocyte mechanics in fully intact articular cartilage attached to its native bone and (ii) to compare the chondrocyte mechanics for cells in healthy and early osteoarthritis (OA) tissue. We hypothesized that cells in the healthy tissue would deform less for given articular surface pressures than cells in the early OA tissue because of a loss of matrix integrity in early OA and the associated loss of structural integrity that is thought to protect chondrocytes. Chondrocyte dynamics were quantified by measuring the deformation response of the cells to controlled loading of fully intact cartilage using a custom-designed confocal indentation system. Early OA was achieved nine weeks following transection of the anterior cruciate ligament (ACL) in rabbit knees. Experiments were performed on the retropatellar cartilage of early OA rabbit knees (four joints and 48 cells), the corresponding intact contralateral control knees (four joints and 48 cells) and knees from normal control rabbits (four joints and 48 cells). Nine weeks following ACL transection, articular cartilage of the experimental joints showed substantial increases in thickness, and progression towards OA as assessed using histological grading. Local matrix strains in the superficial zone were greater for the experimental (38 ± 4%) compared with the contralateral (27 ± 5%) and normal (28 ± 4%) joints (p= 0.04). Chondrocyte deformations in the axial and depth directions were similar during indentation loading for all experimental groups. However, cell width increased more for the experimental cartilage chondrocytes (12 ± 1%) than the contralateral (6 ± 1%) and normal control chondrocytes (6 ± 1%;p< 0.001). On average, chondrocyte volume increased with indentation loading in the early OA cartilage (8 ± 3%,p= 0.001), while it decreased for the two control groups (−8 ± 2%,p= 0.002 for contralateral and −8 ± 1%,p= 0.004 for normal controls). We conclude from these results that our hypothesis of cell deformations in the early OA tissue was only partially supported: specifically, changes in chondrocyte mechanics in early OA were direction-specific with the primary axial deformations remaining unaffected despite vastly increased average axial matrix deformations. Surprisingly, chondrocyte deformations increased in early OA in specific transverse directions which have received little attention to date but might be crucial to chondrocyte signalling in early OA.
Agromyces bauzanensis sp. nov., isolated from soil
Authors: Zhang De-Chao , Schumann Peter , Liu Hong-Can , Xin Yu-Hua , Zhou Yu-Guang , Schinner Franz , Margesin Rosa
Published: November 2009

A Gram-stain-positive, aerobic bacterium, designated strain BZ41T, was isolated from hydrocarbon-contaminated soil. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BZ41T was related to members of the genus Agromyces and showed highest similarity with the type strain of Agromyces ramosus (96.8 %). The morphological, biochemical and chemotaxonomic characteristics of the new isolate were consistent with the description of the genus Agromyces. The cell-wall peptidoglycan of strain BZ41T was of type B2γ and contained the amino acids 2,4-diaminobutyric acid, alanine, glycine and glutamic acid in an approximate molar ratio of 1.8 : 0.7 : 1.1 : 1.0. The predominant cell-wall sugars were galactose, glucose, mannose and rhamnose. Strain BZ41T had MK-12 and MK-11 as major menaquinones and contained anteiso-C15 : 0 and anteiso-C17 : 0 as major fatty acids. The genomic DNA G+C content of strain BZ41T was 69.7 mol%. On the basis of phenotypic characteristics and genotypic analysis, strain BZ41T is considered to represent a novel species of the genus Agromyces, for which the name Agromyces bauzanensis sp. nov. is proposed. The type strain is BZ41T (=DSM 22275T =CGMCC 1.8984T).
Pseudonocardia babensis sp. nov., isolated from plant litter
Authors: Sakiyama Yayoi , Thao Nguyen K. N. , Vinh Hoang V. , Giang Nguyen M. , Miyadoh Shinji , Hop Duong V. , Ando Katsuhiko
Published: November 2009

A novel actinomycete, designated strain VN05A0561T, was isolated from plant litter collected at Ba Be National Park, Vietnam. The substrate mycelia and spore chains fragmented in a manner similar to nocardioform actinomycetes; the spores had smooth surfaces and were rod-shaped. Strain VN05A0561Thad the following chemotaxonomic characteristics:meso-diaminopimelic acid in the cell-wall peptidoglycan, arabinose and galactose as characteristic sugars, MK-8(H4) as the major isoprenoid quinone, phosphatidylcholine as the diagnostic phospholipid and iso-C16 : 0as the major cellular fatty acid. Strain VN05A0561Tshared low levels of 16S rRNA gene sequence similarity (<97 %) with the type strains of recognized species of the genusPseudonocardiaand could be differentiated from its closest phylogenetic relatives based on phenotypic characteristics. These results suggested that strain VN05A0561Trepresents a novel species of the genusPseudonocardia, for which the namePseudonocardia babensissp. nov. is proposed. The type strain is VN05A0561T(=VTCC-A-1757T=NBRC 105793T).
Sphingobacterium shayense sp. nov., isolated from forest soil
Authors: He Xiang , Xiao Ting , Kuang Haiju , Lan Xiaojun , Tudahong Maripat , Osman Ghenijan , Fang Chengxiang , Rahman Erkin
Published: November 2009

A Gram-staining-negative, yellow-coloured, strictly aerobic, non-spore-forming, rod-shaped bacterium, designated HS39T, isolated from a soil sample collected from a natural Populus euphratica forest in Xinjiang, China, was characterized using a polyphasic approach. The isolate grew optimally at 30–37 °C, at pH 6.5–8.0 and with 0–3 % NaCl. Analysis of the 16S rRNA gene sequence of strain HS39T revealed that it is a member of the genus Sphingobacterium. Sphingobacterium mizutaii ATCC 33299T was the nearest relative (94.0 % 16S rRNA gene sequence similarity). The G+C content of the genomic DNA was 40.2 mol%. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1
ω6c and/or C16 : 1
ω7c). The predominant isoprenoid quinone was MK-7. On the basis of phenotypic properties and phylogenetic inference, strain HS39T represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium shayense sp. nov. is proposed. The type strain is HS39T (=CCTCC AB 209006T =NRRL B-59203T).