bluuebunny/crossref_metadata_2025 huggingface dataset:
Permissive transmembrane helix heterodimerization is required for the expression of a functional integrin
Authors: Vararattanavech Ardcharaporn , Tang Man-Li , Li Hoi-Yeung , Wong Chi-Hang , Law S. K. Alex , Torres Jaume , Tan Suet-Mien
Published: February 2008

The current paradigm is that integrin is activated via inside-out signalling when its cytoplasmic tails and TMs (transmembrane helices) are separated by specific cytosolic protein(s). Perturbations of the helical interface between the α- and β-TMs of an integrin, as a result of mutations, affect its function. Previous studies have shown the requirement for specific pairing between integrin subunits by ectodomain-exchange analyses. It remains unknown whether permissive α/β-TM pairing of an integrin is also required for pairing specificity and the expression of a functionally regulated receptor. We performed scanning replacement of integrin β2-TM with a TM of other integrin β-subunits. With the exception of β4 substitution, others presented β2-integrins with modified phenotypes, either in their expression or ligand-binding properties. Subsequently, we adopted αLβ2 for follow-on experiments because its conformation and affinity-state transitions have been well defined as compared with other members of the β2-integrins. Replacement of β2- with β3-TM generated a chimaeric αLβ2 of an intermediate affinity that adhered to ICAM-1 (intercellular adhesion molecule 1) but not to ICAM-3 constitutively. Replacing αL-TM with αIIb-TM, forming a natural αIIb/β3-TM pair, reversed the phenotype of the chimaera to that of wild-type αLβ2. Interestingly, the replacement of αLβ2- with β3-TM showed neither an extended conformation nor the separation of its cytoplasmic tails, which are well-reported hallmarks of an activated αLβ2, as determined by reporter mAb (monoclonal antibody) KIM127 reactivity and FRET (fluorescence resonance energy transfer) measurements respectively. Collectively, our results suggest that TM pairing specificity is required for the expression of a functionally regulated integrin.
A decrease in cellular energy status stimulates PERK-dependent eIF2α phosphorylation and regulates protein synthesis in pancreatic β-cells
Authors: Gomez Edith , Powell Mike L. , Bevington Alan , Herbert Terence P.
Published: February 2008

In the present study, we demonstrate that, in pancreatic β-cells, eIF2α (eukaryotic initiation factor 2α) phosphorylation in response to a decrease in glucose concentration is primarily mediated by the activation of PERK [PKR (protein kinase RNA activated)-like endoplasmic reticulum kinase]. We provide evidence that this increase in PERK activity is evoked by a decrease in the energy status of the cell via a potentially novel mechanism that is independent of IRE1 (inositol requiring enzyme 1) activation and the accumulation of unfolded nascent proteins within the endoplasmic reticulum. The inhibition of eIF2α phosphorylation in glucose-deprived cells by the overexpression of dominant-negative PERK or an N-terminal truncation mutant of GADD34 (growth-arrest and DNA-damage-inducible protein 34) leads to a 53% increase in the rate of total protein synthesis. Polysome analysis revealed that this coincides with an increase in the amplitude but not the number of ribosomes per mRNA, indicating that eIF2α dephosphorylation mobilizes hitherto untranslated mRNAs on to polysomes. In summary, we show that PERK is activated at low glucose concentrations in response to a decrease in energy status and that this plays an important role in glucose-regulated protein synthesis in pancreatic β-cells.
Hepatic NKT cells: friend or foe?
Authors: Swain Mark G.
Published: February 2008

The innate immune system represents a critical first line of host response to infectious, injurious and inflammatory insults. NKT cells (natural killer T-cells) are an important, but relatively poorly understood, component of the innate immune response. Moreover, NKT cells are enriched within the liver, suggesting that within the hepatic compartment NKT cells probably fulfil important roles in the modulation of the immune response to infection or injury. NKT cells are characterized by their rapid activation and secretion of large amounts of numerous types of cytokines, including those within the Th1-type, Th2-type and Th17-type groups, which in turn can interact with a multitude of other cell types within the liver. In addition, NKT cells are capable of participating in a wide array of effector functions with regards to other cell types via NKT cell-surface-molecule expression [e.g. FASL (FAS ligand) and CD40L (CD40 ligand)] and the release of mediators (e.g. perforin and granzyme) contained in cellular granules, which in turn can activate or destroy other cells (i.e. immune or parenchymal cells) within the liver. Given the huge scope of potential actions that can be mediated by NKT cells, it has become increasingly apparent that NKT cells may fulfil both beneficial (e.g. clearance of virally infected cells) and harmful (e.g. induction of autoimmunity) roles in the setting of liver disease. This review will outline the possible roles which may be played by NKT cells in the setting of specific liver diseases or conditions, and will discuss the NKT cell in the context of its role as either a ‘friend’ or a ‘foe’ with respect to the outcome of these liver disorders.
DUHOCAMIS: A dual hollow cathode ion source for metal ion beams
Authors: Zhao W. J. , Müller M. W. O. , Janik J. , Liu K. X. , Ren X. T.
Published: February 2008

In this paper we describe a novel ion source named DUHOCAMIS for multiply charged metal ion beams. This ion source is derived from the hot cathode Penning ion gauge ion source (JINR, Dubna, 1957). A notable characteristic is the modified Penning geometry in the form of a hollow sputter electrode, coaxially positioned in a compact bottle-magnetic field along the central magnetic line of force. The interaction of the discharge geometry with the inhomogeneous but symmetrical magnetic field enables this device to be operated as hollow cathode discharge and Penning discharge as well. The main features of the ion source are the very high metal ion efficiency (up to 25%), good operational reproducibility, flexible and efficient operations for low charged as well as highly charged ions, compact setup, and easy maintenance. For light ions, e.g., up to titanium, well-collimated beams in the range of several tens of milliamperes of pulsed ion current (1ms, 10∕s) have been reliably performed in long time runs.
Mössbauer studies of the magnetic phase transition in Fe1−xZnxCr2S4
Authors: Bae Sung Hwan , Kim Sam Jin , Kim Chul Sung
Published: February 2008

The polycrystalline samples of Zn-doped Fe1−xZnxCr2S4 (0.1⩽x⩽0.9) have been studied with x-ray diffraction, magnetization, and Mössbauer spectra measurements. Magnetic structure transforms from the ferromagnetic (0.1⩽x⩽0.5) to the antiferromagnetic phase (0.7⩽x⩽0.9). The Mössbauer spectra of Fe1−xZnxCr2S4 show asymmetrical eight lines due to electric quadrupole interactions below 10K. The magnetic hyperfine field and electric quadrupole interaction for the sample x=0.5 at 4.2K have been fitted with Mössbauer hyperfine parameters of Hhf=116kOe, θ=27°, φ=0°, η=0.60, EQ=2.28mm∕s, and R=2.9. We have observed that the magnetic hyperfine field Hhf decreases with increasing Zn concentration in the ferrimagnetic range (0.1⩽x⩽0.5) at 4.2K, while it increases in the antiferromagnetic region (0.7⩽x⩽0.9). This indicates the changes in the orbital current field contribution depending on Zn concentration in Fe1−xZnxCr2S4.
Magnetodielectric effect and dielectric relaxation of spinel Cd0.7Fe0.3Cr2S4
Authors: Yan L. Q. , Sun Z. H. , He L. H. , Shen J. , Zhang J. , Wang F. W.
Published: February 2008

Polycrystalline Cd0.7Fe0.3Cr2S4 has been prepared by a solid state reaction. A crystalline structure study shows that the x-ray diffraction pattern can be indexed successfully in a cubic spinel phase. Its magnetic and dielectric properties have been investigated. A ferrimagnetic phase transition of the material was identified at 123K. Larger permittivity and loss tangent are observed than those of CdCr2S4 in the frequency range 300Hz–1MHz. An anomaly cusp induced by the internal magnetic field on ε-T and tanδ-T curves is observed near its magnetic transition point, implying an existence of magnetodielectric effect. At low temperature T<TN, the permittivity variation Δε depends on magnetization M and shows clearly a linear relationship between Δε and M2, indicating an interplay of permittivity and magnetism. Furthermore, compared to CdCr2S4, Cd0.7Fe0.3Cr2S4 exhibits smaller values of dielectric relaxation time and activated energy above TC due to Fe2+ doping.
Effects due to molecular shape and flexibility on the permeability ratio of binary fluid mixtures in a model polymer network via computer simulation
Authors: Hörstermann Henning , Hentschke Reinhard
Published: February 2008

Sorption and diffusion of binary mixtures of small molecules in model polymer networks is studied via computer simulation. Three types of molecules identical in volume but different in shape and flexibility (compact, linear stiff, and linear flexible) are combined into binary mixtures (compact/linear stiff) and (linear stiff/linear flexible). The relative effects of shape and flexibility on separation factor and diffusion coefficient inside random polymer networks are studied using a molecular dynamics/Gibbs-ensemble Monte Carlo hybrid technique. In addition the effects of temperature, pressure, and network strand length are considered. We find that the compact molecules are preferentially absorbed into the network at all strand lengths and temperatures considered here. Flexibility only leads to minor preferential sorption under most conditions. Diffusion coefficients of the competing species inside the network are found to agree within the error bars.
Single-photon emission from single quantum dots in a hybrid pillar microcavity
Authors: Yamaguchi Takao , Tawara Takehiko , Kamada Hidehiko , Gotoh Hideki , Okamoto Hiroshi , Nakano Hidetoshi , Mikami Osamu
Published: February 2008

We demonstrate 1240nm single-photon emissions from InAs quantum dots (QDs) embedded in a hybrid pillar microcavity consisting of dielectric and semiconductor distributed Bragg reflectors. The QDs are grown by metal organic chemical vapor deposition. Discrete emission lines corresponding to isolated QDs in the hybrid pillar are observed with a spontaneous emission rate enhanced by a factor of 2. Single-photon emissions are confirmed by antibunching in a second-order photon correlation function.
Flux amplification in Helicity Injected Torus (HIT–II) coaxial helicity injection discharges
Authors: Redd A. J. , Jarboe T. R. , Hamp W. T. , Nelson B. A. , O’Neill R. G. , Smith R. J.
Published: February 2008

Recent coaxial helicity injection (CHI) studies using the Helicity Injected Torus device [Redd et al., Phys. Plasmas 9, 2006 (2002)] have produced discharges with measured toroidal plasma currents up to 350kA and direct evidence of both poloidal flux amplification and toroidal current buildup, resulting from a steady process on millisecond time scales. Internal magnetic probes directly measure the poloidal flux amplification, and also measure a strong paramagnetism. Equilibrium reconstructions of these flux amplification discharges, using only surface magnetics, match the internal probes and multipoint Thomson scattering, and show current-profile relaxation during toroidal current ramp up. The criteria for producing flux amplification include both a sufficiently thin electrode-driven edge region and a large magnetic shear in the CHI injector region, which allows injector reconnection activity to overcome resistive decay and build up a closed plasma core. If the interelectrode distance d is small, then both criteria can be easily met. If d is comparable to the device minor radius, then the injector must be overdriven to produce significant flux amplification. The physics basis for generating CHI discharges with the theoretically maximum toroidal current is now understood, and this basis can be used to guide CHI experiments in any axisymmetric device.
Magnetoelectric nano-Fe3O4∕CoFe2O4∥PbZr0.53Ti0.47O3 composite
Authors: Ren Shenqiang , Wuttig Manfred
Published: February 2008

A new magnetoelectric hybrid device composed of a nanoparticulate magnetostrictive iron oxide-cobalt ferrite film on a piezoelectric lead zirconic titanate crystal serving as both substrate and straining medium is described. Nano-Fe3O4∕CoFe2O4 particles, ranging from 5to42nm, were prepared using a variation of the sol-gel method. A small electric field, 5–10kVcm−1, applied at the coercive field of the nano-Fe3O4∕CoFe2O4 component modulates the film magnetization up to 10% of the saturation magnetization of ferrite. At the smallest particle size of 5nm, the coercive field is as low as 25Oe and the inverse MEE voltage coefficient is as high as (10.1V∕cmOe)−1.
Analytical model for polyatomic gas expansion under pulsed evaporation
Authors: Morozov A. A.
Published: February 2008

Polyatomic gas expansion under pulsed evaporation is considered in one-dimensional plane approach. A system of balance equations is constructed for gas cloud expansion. The obtained analytical solution allows to predict temporal evolution of the spatially averaged gas dynamic parameters, such as density, temperature, and velocity. The obtained results are in good agreement with results of direct Monte Carlo simulation. Based on the cloud parameters, the number of collisions per molecule during expansion is calculated. This number is used for approximate estimation of gas dynamic parameters (including vibrational temperature) for the case of incomplete vibrational cooling. Based on analytical regularities, analysis of experimental data on pulsed laser evaporation of aniline is performed. The calculated aniline vibrational temperature correlates well with the experimentally measured one.
Characterization of HfTaO films for gate oxide and metal-ferroelectric-insulator-silicon device applications
Authors: Lu Xu-bing , Maruyama Kenji , Ishiwara Hiroshi
Published: February 2008

Characteristics of HfTaO thin films have been investigated from the viewpoints of their applications as insulating buffer layer in the metal-ferroelectric-insulator-semiconductor (MFIS) structure and gate oxide for next generation metal-oxide-silicon devices. HfTaO films with 2, 4, and 6nm in thickness have been deposited on Si substrates using electron beam evaporation and annealed typically at 800°C for 1min in O2 atmosphere. In fabrication of MFIS diodes, SrBi2Ta2O9 (SBT) films have been deposited on HfTaO using a sol-gel spin-coating method. It has been found from C-V (capacitance versus voltage) and I-V (current versus voltage) characteristics of Al∕HfTaO∕Si diodes with different film thicknesses that the optimum annealing temperature is 800°C and the dielectric constant of HfTaO is about 17. For MFIS devices with Pt∕SrBi2Ta2O9 (300nm)∕HfTaO(4nm)∕Si gate structures, a memory window of 0.65V between +4 and −4V gate voltage sweeping was observed. Furthermore, the high and low capacitance values biased at the center of the hysteresis loop are clearly distinguishable for over 24h, demonstrating excellent long-term retentions properties.
Highly coherent thermal emission obtained by plasmonic bandgap structures
Authors: Biener Gabriel , Dahan Nir , Niv Avi , Kleiner Vladimir , Hasman Erez
Published: February 2008

We demonstrate an extraordinary quasimonochromatic thermal emission with high spatial coherence length (lc>2400λ) and a quality factor Q=2320 at radiation frequencies that are much smaller than the plasma frequency of metal (ω≪ωp). This emission is achieved by forming a plasmonic bandgap, which is obtained by a periodic structure on a metallic surface. Such a structure modifies the dynamics of the surface wave and results in a van Hove singularity [Van Hove, Phys. Rev. 89, 1189 (1953)] in the spectral density of states while maintaining a large coherence length.
Gate bias stress effects due to polymer gate dielectrics in organic thin-film transistors
Authors: Ng Tse Nga , Daniel Jürgen H. , Sambandan Sanjiv , Arias Ana-Claudia , Chabinyc Michael L. , Street Robert A.
Published: February 2008

The operational stability of organic thin-film transistors (OTFTs) comprising bilayer polymer dielectric of poly(methylsilsesquioxane) (pMSSQ) and either the epoxy resin SU-8 or poly(4-vinyl phenol) was examined. Although not in direct contact with the semiconductor materials, the bottom dielectric layer did affect OTFT stability through water ion movement or charge injection inside the bottom dielectrics. In the comparison between our best polymer dielectric pMSSQ/SU-8 to the silicon oxide dielectric, the result emphasized that, at equal initial charge concentration, polymer dielectrics did not alleviate threshold-voltage shift but did maintain more stable current due to the lower gate capacitance than silicon oxide.
An excitation wavelength–scanning spectral imaging system for preclinical imaging
Authors: Leavesley Silas , Jiang Yanan , Patsekin Valery , Rajwa Bartek , Robinson J. Paul
Published: February 2008

Small-animal fluorescence imaging is a rapidly growing field, driven by applications in cancer detection and pharmaceutical therapies. However, the practical use of this imaging technology is limited by image-quality issues related to autofluorescence background from animal tissues, as well as attenuation of the fluorescence signal due to scatter and absorption. To combat these problems, spectral imaging and analysis techniques are being employed to separate the fluorescence signal from background autofluorescence. To date, these technologies have focused on detecting the fluorescence emission spectrum at a fixed excitation wavelength. We present an alternative to this technique, an imaging spectrometer that detects the fluorescence excitation spectrum at a fixed emission wavelength. The advantages of this approach include increased available information for discrimination of fluorescent dyes, decreased optical radiation dose to the animal, and ability to scan a continuous wavelength range instead of discrete wavelength sampling. This excitation-scanning imager utilizes an acousto-optic tunable filter (AOTF), with supporting optics, to scan the excitation spectrum. Advanced image acquisition and analysis software has also been developed for classification and unmixing of the spectral image sets. Filtering has been implemented in a single-pass configuration with a bandwidth (full width at half maximum) of 16nm at 550nm central diffracted wavelength. We have characterized AOTF filtering over a wide range of incident light angles, much wider than has been previously reported in the literature, and we show how changes in incident light angle can be used to attenuate AOTF side lobes and alter bandwidth. A new parameter, in-band to out-of-band ratio, was defined to assess the quality of the filtered excitation light. Additional parameters were measured to allow objective characterization of the AOTF and the imager as a whole. This is necessary for comparing the excitation-scanning imager to other spectral and fluorescence imaging technologies. The effectiveness of the hyperspectral imager was tested by imaging and analysis of mice with injected fluorescent dyes. Finally, a discussion of the optimization of spectral fluorescence imagers is given, relating the effects of filter quality on fluorescence images collected and the analysis outcome.
Energy band alignment at TiO2∕Si interface with various interlayers
Authors: Perego M. , Seguini G. , Scarel G. , Fanciulli M. , Wallrapp F.
Published: February 2008

Anatase TiO2 films are grown on Si (100) by atomic layer deposition. Three different interlayers (Si3N4, Al2O3, and Ti-rich SiOx) between the TiO2 films and the Si substrate have been considered. The band alignment of the titanium oxide films with the silicon substrate is investigated by x-ray photoelectron spectroscopy (XPS), internal photoemission (IPE) spectroscopy, and optical absorption (OA) measurements. XPS analysis indicates that TiO2∕Si heterojunctions with different interlayers (ILs) have different valence-band offsets (VBOs). A VBO value of 2.56±0.09eV is obtained for the TiO2∕Ti-rich SiOx∕Si sample. Similarly, we obtain a VBO value of 2.44±0.09 and 2.73±0.10eV for the TiO2∕Si3N4∕Si and TiO2∕Al2O3∕Si samples, respectively. According to IPE and OA measurements, the band gap of the as-grown TiO2 films is 3.3±0.1eV for all the samples. Combining the XPS and IPE data, the conduction band offset values at the TiO2∕Si heterojunction are found to be −0.2±0.1, −0.4±0.1, and −0.5±0.1eV for the TiO2∕Si3N4∕Si, TiO2∕Ti-rich SiOx∕Si, and TiO2∕Al2O3∕Si samples, respectively. According to our experimental results, the band alignment of a TiO2 film with the underlying Si (100) substrate is clearly affected by the presence of an IL, suggesting the possibility to tune the band structure of a TiO2∕Si heterojunction by selecting the proper IL.
Electrospun fibrous nanocomposites as permeable, flexible strain sensors
Authors: Tiwari Manish K. , Yarin Alexander L. , Megaridis Constantine M.
Published: February 2008

Electrospun polymer/nanoparticle composite-fiber structures are investigated as potential lightweight, compliant, porous strain sensors for noncyclic strain sensing. Such composite-fiber-based structures (mats/strips) are referred to as nanocomposites in this study. The fibers in the nanocomposites consist of, for example, poly(ε-caprolactone) dielectric polymer matrix with embedded electrically conductive carbon black (CB) nanoparticles. The effect of CB concentration on the electrical resistance of nanocomposite strips is studied experimentally. The fiber strips with 7wt% or more of CB are electrically conducting in the as-spun, undeformed state and are, thus, called conductive polymer composites. The experiments demonstrate that the electrical resistance of a nanocomposite strip increases with strain it undergoes, and at sufficiently high strains, the strip became nonconductive. It is argued that the stretching process breaches the percolation structure of CB nanoparticles in the dielectric polymer matrix, thereby changing the strip electrical resistance. A two-dimensional layered-percolation model is proposed to describe the resistance increase with stretching. The model is compared to the experimental data for nanocomposite strips containing different CB loadings (7–11wt%), and a reasonable agreement is obtained for these CB loadings. The percolation threshold for electrical conduction of these nanocomposites is found experimentally to be lower than the corresponding theoretical two-dimensional random percolation threshold. The reduction is attributed to formation of oriented clusters of CB nanoparticles inside the fibers during the electrospinning process. The scaling-like increase of the electrical resistance toward percolation breakdown at large strains closely resembles the predictions of the percolation theory. A reproducible correlation between electrical resistance of the nanocomposite strips and their stretching suggests that they can be used as resistive noncyclic strain sensors. Such flexible permeable sensors can be useful, for example, when embedded in filters, to indicate filter overstretching due to clogging. In particular, a clogged section of a filter with an embedded sensor possesses a lower permeability, which increases pressure difference acting on this section at a fixed fluid throughput. The increased pressure difference results in local bending and stretching of the clogged section of the filter with an embedded sensor. In the present work, a formula is derived to relate permeability of a clogged filter to the strain of an embedded sensor and, in turn, to the electrical resistance of the sensor. This formula is a key element of the proposed novel resistive sensor.
Structural, electrical, and magnetic properties of Mo1−xFexO2 (x=0–0.05) thin films grown by pulsed laser ablation
Authors: Prakash Ram , Phase D. M. , Choudhary R. J. , Kumar Ravi
Published: February 2008

We report the growth of undoped and Fe (2 and 5at.%) doped molybdenum oxide thin films on c-plane of sapphire substrate using pulsed laser ablation. X-ray diffraction results show that the films are oriented in the (100) direction and have monoclinic structure based on MoO2 phase as also supported by Raman spectroscopy. The x-ray photoelectron spectroscopy reveals that the chemical state of Fe is +2, which favors the substitutional occupancy of Fe ion in the MoO2 matrix. The room temperature resistivity of all the films is very low (∼100μΩcm). The Fe doped samples show ferromagnetic behavior at room temperature.
Effects of high pressure annealing on the characteristics of solid phase crystallization poly-Si thin-film transistors
Authors: Kim Moojin , Kim Kyoung-Bo , Lee Ki-Yong , Yu CheolHo , Kim Hye-Dong , Chung Ho-Kyoon
Published: February 2008

Integrating circuits into organic light emitting diode displays require fabrication of polycrystalline silicon (poly-Si) based thin-film transistors (TFTs) on glass substrates. In this work we evaluated the use of high pressure annealing (HPA) process of poly-Si films in H2O atmosphere to improve TFT characteristics via reducing defect density in poly-Si films. We attempted to develop a HPA process at temperatures below 600°C without causing any glass distortion and reducing the throughput. The HPA-treated poly-Si film was analyzed using various spectroscopic methods such as Raman, x-ray photoelectron spectroscopy, and transmission electron microscope, and the evaluation of the characteristics of TFTs fabricated by such poly-Si films was made. The heating at 550°C with 1MPa H2O vapor increased the carrier mobility from 8.5to20cm2∕Vs and reduced the absolute value of the threshold voltage from 9.6to6.5V, as compared with the conventional solid phase crystallization (SPC) process. The sub-threshold swings also decreased from 1.2to0.8V/decade. Since the realization of good performance in poly-Si depends on the defect density, the poly-Si formed by a combined process of SPC and HPA may be well suited for fabrication of poly-Si TFTs for flat panel displays such as liquid crystal display and active matrix organic light emitting diode that require circuit integration on panels.
Flux transformers made of commercial high critical temperature superconducting wires
Authors: Dyvorne H. , Scola J. , Fermon C. , Jacquinot J. F. , Pannetier-Lecœur M.
Published: February 2008

We have designed flux transformers made of commercial BiSCCO tapes closed by soldering with normal metal. The magnetic field transfer function of the flux transformer was calculated as a function of the resistance of the soldered contacts. The performances of different kinds of wires were investigated for signal delocalization and gradiometry. We also estimated the noise introduced by the resistance and showed that the flux transformer can be used efficiently for weak magnetic field detection down to 1Hz.
Misfit dislocation blocking by dilute nitride intermediate layers
Authors: Schöne J. , Spiecker E. , Dimroth F. , Bett A. W. , Jäger W.
Published: February 2008

Defect formation and strain relaxation in step-graded GaAs1−xNx and GaAs1−yPy buffer structures grown by metal-organic vapor phase epitaxy on GaAs(001) substrates have been investigated by transmission electron microscopy and high-resolution x-ray diffractometry. From the comparison of different buffer concepts, it is shown that, by introducing intermediate GaAs1−xNx layers with N concentrations x⩾2% into a GaAs1−xPx buffer structure, dislocation formation and strain relaxation are effectively suppressed during subsequent growth of layers with tensile strains. It is argued that a similar concept, however, modified by using layers of differing alloy composition, can be used for layer systems with compressive strains. Appropriately alloyed intermediate dilute nitride layers appear to offer a powerful concept for engineering defect distributions and layer strain in semiconductor technology.
Measuring the interface stress of nanocrystalline iron
Authors: Zimmer Patrik , Birringer Rainer
Published: February 2008

With the ongoing miniaturization of structures and devices down to the nanometer scale, we notice concomitant escalation of atoms located at surfaces or interfaces. Presence of surfaces and interfaces generates stresses in nanoscale structures that can easily exceed 1GPa. We developed and applied a method for measuring the absolute value of grain-boundary stress. Since investigation of grain-boundary stress as well as phase-boundary stress of body-centered-cubic materials has not been addressed so far, we aimed at determining the grain-boundary stress f of nanocrystalline Fe. By means of x-ray diffraction measurements of average grain size and residual-strain-free lattice spacings, we deduced a value of f=1.1±0.2N∕m.
Application of ion scattering spectroscopy to measurement of surface potential of MgO thin film under ion irradiation
Authors: Nagatomi T. , Kuwayama T. , Takai Y. , Yoshino K. , Morita Y. , Kitagawa M. , Nishitani M.
Published: February 2008

An experimental approach was proposed for the measurement of the surface potential (SP) induced on an insulator surface during ion irradiation by ion scattering spectroscopy (ISS). The resultant ISS spectra obtained for a MgO thin film of 600nm thickness on a Si substrate under 950eV He+ irradiation revealed that the surface is positively charged by approximately 230V. In addition, the onset energy of a secondary ion peak indicated a SP of approximately 205V. The present results confirmed that ISS is an effective technique for measuring the SP during ion irradiation.
Post-pollination capsule development in Eucalyptus globulus seed orchards
Authors: Suitor S. , Potts B. M. , Brown P. H. , Gracie A. J. , Gore P. L.
Published: February 2008

Low capsule set is a major factor limiting seed production in Eucalyptus globulus seed orchards. Trials were conducted in E. globulus seed orchards in Tasmania, Australia, to identify the timing of capsule development and abortion, as well as the influence of pollination type, the number of ovules fertilised and weather events on capsule set. Controlled pollination (CP), mass supplementary pollination (MSP), open pollination (OP) and isolated unpollinated control (UP) treatments were performed on 21 genotypes in an orchard in southern Tasmania in 2004–2005 and on six genotypes in a higher-altitude orchard in north-western Tasmania in 2005–2006. No capsules were set in the UP control treatment, and capsule set was significantly lower following CP than OP and MSP. The major period of capsule abortion occurred between 20 and 80 days after pollination for all pollination methods across both sites, coinciding with the period of capsule growth. A positive correlation between the number of fertilised ovules per aborted capsule and the length of time capsules were held on the tree was recorded. Given that capsule abortion occurred during a period of fruit growth and that capsules with the lowest number of fertilised ovules aborted first, it is argued that fertilisation level and the level of resource competition are major factors determining capsule abortion.
Phytoplankton community relationship to environmental variables in three Kenyan Rift Valley saline-alkaline lakes
Authors: Schagerl Michael , Oduor S. O.
Published: February 2008

Temporal changes in total alkalinity, ionic composition and nutrient concentrations were studied in the saline, alkaline endorheic Kenyan Rift Valley Lakes Bogoria, Nakuru and Elmentaita to understand the association of these variables with phytoplankton community structure. In total, 24 taxa were found, with L. Bogoria having the fewest species. Although the cyanobacterium Arthrospira fusiformis dominated the phytoplankton biomass, especially in L. Bogoria, other groups came into play especially during high water levels in L. Nakuru and L. Elmentaita. Cluster analysis based on species biomass resulted in four groups, characterised by 13 indicator taxa. Most of the variation in these groups appeared to be associated with hydrological stability and perhaps biological factors rather than water chemistry, which only explained 44% of the variance in taxa composition on the first four axes derived from redundancy analysis. Species numbers decreased with elevated conductivity and water temperature. Synechocystis sp. occurrence coincided with phosphorus, water temperature and conductivity increase, whereas the distributions of Arthrospira fusiformis and Arthrospira platensis were mainly influenced by both light attenuation and elevated nitrate concentrations. Increases in silica and ammonium and declines in conductivity, total phosphorus and water temperature enhanced diatom abundances. Not only do the results of the present study indicate the unexpectedly high variability of phytoplankton community composition and water chemistry in these three alkaline tropical lakes, but also the data assist our understanding of the factors influencing flamingo populations on these lakes, which are significant conservation reserves and tourist attractions.
Mitochondrial deafness alleles confer misreading of the genetic code
Authors: Hobbie Sven N. , Bruell Christian M. , Akshay Subramanian , Kalapala Sarath K. , Shcherbakov Dmitry , Böttger Erik C.
Published: February 2008

Despite the fact that important genetic diseases are caused by mutant mitochondrial ribosomes, the molecular mechanisms by which such ribosomes result in a clinical phenotype remain largely unknown. The absence of experimental models for mitochondrial diseases has also prevented the rational search for therapeutic interventions. Here, we report on the construction of bacterial hybrid ribosomes that contain various versions of the mitochondrial decoding region of ribosomal RNA. We show that the pathogenic mutations A1555G and C1494T decrease the accuracy of translation and render the ribosomal decoding site hypersusceptible to aminoglycoside antibiotics. This finding suggests misreading of the genetic code as an important molecular mechanism in disease pathogenesis.
Optimal partition and effective dynamics of complex networks
Authors: E Weinan , Li Tiejun , Vanden-Eijnden Eric
Published: February 2008

Given a large and complex network, we would like to find the best partition of this network into a small number of clusters. This question has been addressed in many different ways. Here we propose a strategy along the lines of optimal prediction for the Markov chains associated with the dynamics on these networks. We develop the necessary ingredients for such an optimal partition strategy, and we compare our strategy with the previous ones. We show that when the Markov chain is lumpable, we recover the partition with respect to which the chain is lumpable. We also discuss the case of well-clustered networks. Finally, we illustrate our strategy on several examples.
Conditional MHC class I ligands and peptide exchange technology for the human MHC gene products HLA-A1, -A3, -A11, and -B7
Authors: Bakker Arnold H. , Hoppes Rieuwert , Linnemann Carsten , Toebes Mireille , Rodenko Boris , Berkers Celia R. , Hadrup Sine Reker , van Esch Wim J. E. , Heemskerk Mirjam H. M. , Ovaa Huib , Schumacher Ton N. M.
Published: February 2008

Major histocompatibility complex (MHC) class I multimer technology has become an indispensable immunological assay system to dissect antigen-specific cytotoxic CD8+T cell responses by flow cytometry. However, the development of high-throughput assay systems, in which T cell responses against a multitude of epitopes are analyzed, has been precluded by the fact that for each T cell epitope, a separatein vitroMHC refolding reaction is required. We have recently demonstrated that conditional ligands that disintegrate upon exposure to long-wavelength UV light can be designed for the human MHC molecule HLA-A2. To determine whether this peptide-exchange technology can be developed into a generally applicable approach for high throughput MHC based applications we set out to design conditional ligands for the human MHC gene products HLA-A1, -A3, -A11, and -B7. Here, we describe the development and characterization of conditional ligands for this set of human MHC molecules and apply the peptide-exchange technology to identify melanoma-associated peptides that bind to HLA-A3 with high affinity. The conditional ligand technology developed here will allow high-throughput MHC-based analysis of cytotoxic T cell immunity in the vast majority of Western European individuals.
SPAS-1 (stimulator of prostatic adenocarcinoma-specific T cells)/SH3GLB2: A prostate tumor antigen identified by CTLA-4 blockade
Authors: Fassò Marcella , Waitz Rebecca , Hou Yafei , Rim Tae , Greenberg Norman M. , Shastri Nilabh , Fong Lawrence , Allison James P.
Published: February 2008

Discovery of immunologically relevant antigens in prostate cancer forms the basis for developing more potent active immunotherapy. We report here a strategy using the transgenic adenocarcinoma of mouse prostate (TRAMP) model, which allows for the functional identification of immunogenic prostate tumor antigens with relevance for human immunotherapy. Using a combination of active tumor vaccination in the presence of CTL-associated antigen 4 (CTLA-4)
in vivo
blockade, we elicited tumor-specific T cells used to expression clone the first T cell-defined TRAMP tumor antigen, called
Spas-1
(stimulator of prostatic adenocarcinoma specific T cells-1).
Spas-1
expression was increased in advanced primary TRAMP tumors. We show that the immunodominant SPAS-1 epitope SNC9-H
8
arose from a point mutation in one allele of the gene in TRAMP tumor cells, and that immunization with dendritic cells pulsed with SNC9-H
8
peptide resulted in protection against TRAMP-C2 tumor challenge. In humans, the
Spas-1
ortholog
SH3GLB2
has been reported to be overexpressed in prostate cancer metastases. Additionally, we identified a nonmutated HLA-A2-binding epitope in the human ortholog SH3GLB2, which primed T cells from healthy HLA-A2
+
individuals
in vitro
. Importantly,
in vitro
-primed T cells also recognized naturally processed and presented SH3GLB2. Our findings demonstrate that our
in vivo
CTLA-4 blockade-based T cell expression cloning can identify immunogenic cancer antigens with potential relevance for human immunotherapy.
A translocation causing increased α-Klotho level results in hypophosphatemic rickets and hyperparathyroidism
Authors: Brownstein Catherine A. , Adler Felix , Nelson-Williams Carol , Iijima Junko , Li Peining , Imura Akihiro , Nabeshima Yo-ichi , Reyes-Mugica Miguel , Carpenter Thomas O. , Lifton Richard P.
Published: February 2008

Phosphate homeostasis is central to diverse physiologic processes including energy homeostasis, formation of lipid bilayers, and bone formation. Reduced phosphate levels due to excessive renal loss cause hypophosphatemic rickets, a disease characterized by prominent bone defects; conversely, hyperphosphatemia, a major complication of renal failure, is accompanied by parathyroid hyperplasia, hyperparathyroidism, and osteodystrophy. Here, we define a syndrome featuring both hypophosphatemic rickets and hyperparathyroidism due to parathyroid hyperplasia as well as other skeletal abnormalities. We show that this disease is due to a
de novo
translocation with a breakpoint adjacent to α-
Klotho
, which encodes a β-glucuronidase, and is implicated in aging and regulation of FGF signaling. Plasma α-Klotho levels and β-glucuronidase activity are markedly increased in the affected patient; unexpectedly, the circulating FGF23 level is also markedly elevated. These findings suggest that the elevated α-Klotho level mimics aspects of the normal response to hyperphosphatemia and implicate α-Klotho in the selective regulation of phosphate levels and in the regulation of parathyroid mass and function; they also have implications for the pathogenesis and treatment of renal osteodystrophy in patients with kidney failure.
New phytoplankton species in the Bay of Fundy since 1995
Authors: Martin Jennifer L. , LeGresley Murielle M.
Published: February 2008

Martin, J. L., and LeGresley, M. M. 2008. New phytoplankton species in the Bay of Fundy since 1995. – ICES Journal of Marine Science, 65: 759–764. A monitoring programme was initiated in 1987 to study phytoplankton populations in the Western Isles region of the Bay of Fundy, southwest New Brunswick. Samples are collected weekly from May through October, and monthly during the remaining months, to determine phytoplankton distribution and abundance at Brandy Cove, Lime Kiln Bay, Deadmans Harbour, the Wolves Islands, and mid-Passamaquoddy Bay. Since the programme was initiated, several previously absent or non-indigenous species have been found, suggesting that new species may have been introduced to the area. In order to establish a baseline for species indigenous to Bay of Fundy waters, we have taken a conservative approach and termed species reported for the first time in the Bay of Fundy system since 1995 as “new” species. New species include the following: (dinoflagellates) Alexandrium pseudogonyaulax, Amphidinium carterae, A. sphenoides, Ceratium macroceros, Polykrikos schwartzii, Preperidinium meunieri, Protoperidinium crassipes, and Pyrocystis lunata; (diatoms) Attheya septentrionalis, Attheya longicornis, Chaetoceros radicans, Cylindrotheca gracilis, Grammatophora serpentina, Lithodesmium undulatum, Mediopyxis helysia, Membraneis challengeri, Neodenticula seminae, Odontella sinensis, Proboscia eumorpha, Pseudo-nitzschia subpacifica, Pseudo-nitzschia fraudulenta, and Thalassiosira punctigera.
On the evolution of reproductive restraint in malaria
Authors: Mideo Nicole , Day Troy
Published: February 2008

Malaria is one of the leading causes of death among infectious diseases in the world, claiming over one million lives every year. By these standards, this highly complex parasite is extremely successful at generating new infections. Somewhat surprisingly, however, many malaria species seem to invest relatively little in gametocytes, converting only a small percentage of circulating asexual parasite forms into this transmissible form. In this article, we use mathematical models to explore three of the hypotheses that have been proposed to explain this apparent ‘reproductive restraint’ and develop a novel, fourth hypothesis. We find that only one of the previous three hypotheses we explore can explain such low gametocyte conversion rates, and this hypothesis involves a very specific form of density-dependent transmission-blocking immunity. Our fourth hypothesis also provides a potential explanation and is based on the occurrence of multiple infections and the resultant within-host competition between malaria strains that this entails. Further experimental work is needed to determine which of these two hypotheses provides the most likely explanation.
Developmental plasticity of mating calls enables acoustic communication in diverse environments
Authors: Beckers Oliver M , Schul Johannes
Published: February 2008

Male calls of the katydidNeoconocephalus triopsexhibit substantial developmental plasticity in two parameters: (i) calls of winter males are continuous and lack the verse structure of summer calls and (ii) at equal temperatures, summer males produce calls with a substantially higher pulse rate than winter males. We raised femaleN. triopsunder conditions that reliably induced either summer or winter phenotype and tested their preferences for the call parameters that differ between summer and winter males.

Neither generation was selective for the presence of verses, but females had strong preferences for pulse rates: only a narrow range of pulse rates was attractive. The attractive ranges did not differ between summer and winter females. Both male pulse rate and female preference for pulse rate changed with ambient temperature, but female preference changed more than the male calls.

As a result, the summer call was attractive only at 25°C, whereas the slower winter call was attractive only at 20°C. Thus, developmental plasticity of male calls compensates for differences in temperature dependency between calls and preferences and enables the communication system to function in heterogeneous environments. The potential role of call plasticity during the invasion of new habitats is discussed.
Novel RNA sequences associated with late male killing inHomona magnanima
Authors: Nakanishi Kazuko , Hoshino Mayu , Nakai Madoka , Kunimi Yasuhisa
Published: February 2008

Maternally inherited female-biased sex ratios have been documented in many invertebrate species. One cause of such biased sex ratios is male killing, i.e. only males die. In most species, male killing occurs during embryonic stages (early male killing) and is associated with cytoplasmic bacteria, includingWolbachia,Spiroplasma,Rickettsia, Flavobacteria and gamma proteobacteria. However, the oriental tea tortrix,Homona magnanima, is one of the few species in which male death occurs in the larval or pupal stage, and is thus an example of late male killing. We partially purified the agent causing late male killing inH. magnanimaand showed that it consists of two RNA sequences. This represents an entirely novel agent causing late male killing.
Construction of a dense SNP map for bovine chromosome 6 to assist the assembly of the bovine genome sequence
Authors: Nilsen H. , Hayes B. , Berg P. R. , Roseth A. , Sundsaasen K. K. , Nilsen K. , Lien S.
Published: February 2008

A linkage map was constructed for bovine chromosome 6 (BTA6), using 399 single nucleotide polymorphisms (SNPs) detected primarily from PCR‐resequencing. The efficiency of SNP detection was highly dependent on the source of sequence information chosen for primer design (BAC‐end sequences, introns or promoters). The SNPs were used to build a linkage map comprising 104 cM on BTA6. The SNP order in the linkage map corresponded very well with radiation hybrid (RH) maps available for BTA6 as well as with expected positions in the human comparative map, but diverged significantly from the current assembly of the bovine genome (Btau_3.1). When performing linkage analysis with the marker order suggested from the Btau_3.1 we observed an expansion of the genetic map from 104 cM to 137 cM, strongly suggesting a reordering of scaffolds in the current version of the bovine genome assembly. The extent of LD on BTA6 was evaluated by calculating the average r2 for SNP pairs separated by given distances. The decline of LD was rapid with distance, such that r2 was 0.1 at 100 kb. Our results indicate that linkage mapping will be a valuable source of information for correcting errors in the current bovine assembly. These errors were sufficiently frequent to be of concern for the accuracy of mapping QTL with panels of SNPs whose positions are based on the current assembly.