bluuebunny/crossref_metadata_2025 huggingface dataset:
Transport of O+ through argon gas
Authors: Danailov Daniel M. , Viehland Larry A. , Johnsen Rainer , Wright Timothy G. , Dickinson Alan S.
Published: April 2008

New experimental and theoretical results are presented that address the movement of O+ ions through argon gas. On the experimental front, improved ion mobility results are presented. These results confirm the presence of the oft-cited mobility minimum as a function of electrostatic field strength at room temperature. On the theoretical side, high-level ab initio potential energy curves are calculated for the Ar–O+ system and, from these, transport properties are calculated and compared to experiment. A crossing between the lowest Π2 curve and the ground state Σ−4 curve near the minimum of each potential becomes an avoided crossing on the inclusion of spin-orbit coupling. It is shown that the more appropriate potential for the description of the motion of O+(S∘4) through Ar at the energies of interest is the diabatic potential, neglecting fine structure. By using an improved Σ−4 potential, agreement with the mobility measurements is obtained for low and intermediate electrostatic field strengths, although small discrepancies remain for high field strengths. The appropriate choice of diabatic or adiabatic potentials is also considered for related systems of interest: He–O+, Ne–O+, and Rg–O− (Rg=He,Ne,Ar).
Convective instability of an Ohmic liquid layer in an unsteady thermal field
Authors: Smorodin Boris L. , Velarde Manuel G.
Published: April 2008

The linear stability problem for an incompressible viscous poorly conducting Ohmic liquid between two rigid horizontal boundaries with time-periodic temperature distribution and under steady transverse electric field is considered. The free charge in the liquid is due only to the nonuniform electroconduction. The electrohydrodynamic (EHD) approximation is used. Floquet theory is applied for finding various instability thresholds in linear approximation. The influence of time-dependent temperature field modulation on the liquid layer behavior is studied with and without an additional steady component. The boundaries of instability and the characteristics of critical disturbances are determined. Depending on the frequency and amplitude of modulation, the temperature gradient can destabilize the equilibrium of the liquid or stabilize otherwise unstable base state. In addition to synchronous and subharmonic responses to external modulation, the instability can be associated with quasiperiodic disturbances. The critical electric Rayleigh number is given as a function of frequency and heating level. The limit of low frequency modulation is studied by an asymptotic method.
Formation of a submillimeter bubble from an orifice using pulsed acoustic pressure waves in gas phase
Authors: Shirota Minori , Sanada Toshiyuki , Sato Ayaka , Watanabe Masao
Published: April 2008

The mechanism of a bubble production method using pulsed acoustic pressure waves in gas phase is investigated using high-speed photography. The acoustic characteristics of the present bubble generator are also investigated. We found out the optimal acoustic waveform for producing only one bubble per one action; the bubble detachment radius is accurately controlled by first applying the positive onset-assistance acoustic pressure wave and then the negative detachment-assistance acoustic pressure wave with an accurately controlled time lapse. From an orifice with a radius of 0.09mm submerged in water, bubbles with radii in the range of 0.28–0.78mm with an extremely small standard deviation of less than 1μm are obtained. The shrinking and pinch-off motions of a capillary bridge connecting the bubble and orifice at the time of bubble detachment are observed in detail. The balancing force on a growing bubble, which is based on a spherical bubble formation model is also estimated. As a result, we reveal that when the gas pressure is decreased due to a negative pressure wave, the capillary bridge submerges into the orifice and an upward added mass force is applied on the bubble, both of which cause the detachment of the bubble from the orifice.
Anisotropic permeability in ultrasoft electroplated NiFeMo/Cu microwires: The Procopiu effect
Authors: Muñoz A. G. , Schiefer C. , Kisker E.
Published: April 2008

The complex magnetoelastic behavior of electroplated NiFeMo/Cu microwires was analyzed by means of the magnetoimpedance and the Procopiu effects. Both phenomena are related through the circular magnetization generated by the ac and were modeled by assuming a magnetic domain and a magnetic relaxation model. From this analysis, information about the frequency and field dependencies of the circular and axial permeabilities was obtained. These results show that the magnetic anisotropy of Cu microwires galvanically coated with a NiFeMo film of 7 μm in thickness is characterized by two circular permeability functions that are ascribed to different types of magnetic domains.
Characterization of Al–As codoped p-type ZnO films by magnetron cosputtering deposition
Authors: Yun Eui-Jung , Park Hyeong-Sik , Lee Kyu H. , Nam Hyoung G. , Jung Myunghee
Published: April 2008

We report the preparation of Al–As codoped p-type ZnO films by rf magnetron cosputtering deposition. The p-type conductivity of the films was revealed by Hall measurements, x-ray photoelectron spectroscopy (XPS), and photoluminescence measurements after being annealed in O2. It was observed by XPS that Al content increased with increasing AlAs target power from 80 to 160 W and reached a maximum value at an AlAs target power of 160 W. Hole concentration decreased with increasing Al content. With increasing AlAs target power greater than 160 W, the samples exhibit increases in As and O contents and decreases in Al and Zn contents, which contribute to the increase in hole concentration. A high hole concentration of 2.354×1020 cm−3, a low resistivity of 2.122×10−2 Ω cm, and a Hall mobility of 0.13 cm2/V s for the films with high As content of 16.59% were obtained. XPS has also been used to address the unresolved issues related to the p-type formation mechanism of As-doped ZnO, supporting that the acceptor is AsZn–2VZn.
Screening and polaronic effects induced by a metallic gate and a surrounding oxide on donor and acceptor impurities in silicon nanowires
Authors: Diarra Mamadou , Delerue Christophe , Niquet Yann-Michel , Allan Guy
Published: April 2008

We present self-consistent tight binding calculations of the electronic structure of donor and acceptor impurities in silicon nanowires surrounded by a gate oxide (SiO2 or HfO2) and a metallic gate. These environments efficiently screen the potential of the impurities so that their ionization energy strongly decreases with respect to the case of freestanding nanowires. It is also shown that the carriers trapped by the impurities form a polaron due to the response of the ions in the surrounding oxide layer. We predict that the polaron shift represents a large part of the impurity ionization energy, in particular, in HfO2. Our work demonstrates the importance of screening and polaronic effects on the transport properties in nanoscale devices based on Si nanowires.
Anomalous low-temperature magnetoresistance dips in sputtered ferromagnetic thin films and multilayers
Authors: Allia Paolo , Celegato Federica , Coïsson Marco , Tiberto Paola , Vinai Franco , Albertini Franca , Casoli Francesca
Published: April 2008

A set of ferromagnetic thin films and multilayers containing 3d metals (Fe, Co) in different amounts was prepared by rf sputtering. Each sample exhibits a specific magnetic and magnetoresistive behavior, as expected for materials having different saturation magnetizations, magnetic anisotropies, and surface-to-volume ratios. From room temperature down to about 10K, the magnetoresistance is explained in terms of well-known mechanisms; at low fields, a negative magnetoresistance is measured. Between ∼10 and 30K, the zero-field electrical resistance appears to be dominated by electron-phonon scattering. At lower temperatures, where the R vs T curve is almost saturated, a sudden drop of the resistance appears, whose magnitude and position vary from sample to sample. Below the drop temperature, a region of positive magnetoresistance is systematically observed at around H=0 in measurements done with the magnetic field applied either parallel or perpendicular to the film plane. The dip magnitude increases with decreasing temperature. The anomaly appears to be related to the presence of magnetic inhomogeneity in the samples. The experimental results are not explained in terms of standard magnetoresistance mechanisms. Effects related to quantum coherence of conduction electrons may be the source of the observed anomalies. The role of weak localization of electrons, inhibited by the additional scattering provided by the magnetic inhomogeneity on the nanometer scale, is discussed.
Reduced leakage current in chemical solution deposited multiferroic BiFeO3∕Ba0.25Sr0.75TiO3 heterostructured thin films on platinized silicon substrates
Authors: Murari N. M. , Kumar A. , Thomas R. , Katiyar R. S.
Published: April 2008

Multilayered metal-insulator-metal structures with BiFeO3 and Ba0.25Sr0.75TiO3 thin films were fabricated by chemical solution deposition to reduce the leakage current through the capacitor stack. The Ba0.25Sr0.75TiO3 layer does not influence the crystalline structure of BiFeO3 and was recognized as rhombohedral by Raman studies. Compared to pure BiFeO3, in the heterostructures, the coercivity increased, but the saturation magnetization and the leakage current were reduced. The frequency and the temperature dependence of the dielectric properties of the heterostructured film showed evidence of space charge developed between the layers of different dielectric constant (Ba0.25Sr0.75TiO3-BiFeO3 interface).
Impact of the strained SiGe source/drain on hot carrier reliability for 45nm p-type metal-oxide-semiconductor field-effect transistors
Authors: Cheng C. Y. , Fang Y. K. , Hsieh J. C. , Hsia H. , Chen W. M. , Lin S. S. , Hou C. S.
Published: April 2008

In this letter, the impact of the uniaxial strain SiGe source/drain (S/D) on hot carrier reliability in 45nm p-type metal-oxide-semiconductor field-effect transistor is investigated in detail. We find that the extra mechanical stress deteriorates the gate oxide and/or generates interface states significantly, resulting in the hot carrier degradation dominantly driven by the drain avalanche hot carrier stress (Vg=1∕2Vd), as opposed to the channel hot electron stress (Vg=Vd), the well-known dominant mechanism for hot carrier degradation in the conventional deep submicron devices. A model to explain the mechanism of these observations is proposed.
All-optical signal amplification in multiple-quantum-well resonant photonic bandgap structures
Authors: Schumacher S. , Kwong N. H. , Binder R.
Published: April 2008

Using a microscopic many-particle theory, we predict all-optical amplification of low-intensity light pulses in resonant photonic bandgap structures realized by Bragg-spaced semiconductor multiple quantum wells. The discussed scheme is based on mirrorless parametric amplification.
Zn
O
∕
Si
O
2
microcavity modulator on silicon
Authors: Batista P. D. , Drescher B. , Seidel W. , Rudolph J. , Jiao S. , Santos P. V.
Published: April 2008

We demonstrate a monolithic acousto-optic light modulator on silicon consisting of a piezoelectric ZnO∕SiO2 microcavity (MC) excited by a surface acoustic wave (SAW). The modulation of the MC optical resonance by the SAW creates an optical grating on the MC, which efficiently diffracts light beams impinging at the Bragg angle.
Anomalous thermal hysteresis in dielectric permittivity of CaCu3Ti4O12
Authors: Wang C. C. , Zhang L. W.
Published: April 2008

We herein report an anomalous thermal hysteresis in dielectric permittivity in CaCu3Ti4O12. The anomalous behavior was well explained in terms of the low-temperature Maxwell–Wagner relaxation induced by frozen carriers. A multirelaxation mechanism, i.e., the coupling of the dipole relaxation to the frozen carrier-induced and blocked carrier-induced Maxwell–Wagner relaxations in the low-temperature and high-temperature regions, respectively, is proposed to be the origin of the colossal dielectric constant.
Domain mapping of a Ca-doped manganite
Authors: Turner Joshua J. , Jordan-Sweet Jean L. , Upton Mary , Hill John P. , Tokura Yoshinori , Tomioka Yasuhide , Kevan Stephen D.
Published: April 2008

We have performed microdiffraction experiments to map the crystallographic domain structure of the Ca-doped manganite Pr0.5Ca0.5MnO3 by microfocusing x-rays through a glass capillary. Domain structure on the order of a few microns is observed. We suggest that this finding implies that the crystallographic domains maybe relevant to the phenomenon of phase separation—such twin boundaries could help determine the submicron size disorder that has been observed recently, and thus may ultimately play a role in colossal magnetoresistance.
Substantial magnetoelectric coupling near room temperature in Bi2Fe4O9
Authors: Singh A. K. , Kaushik S. D. , Kumar Brijesh , Mishra P. K. , Venimadhav A. , Siruguri V. , Patnaik S.
Published: April 2008

We report remarkable multiferroic effects in polycrystalline Bi2Fe4O9. High-resolution x-ray diffraction shows that this compound has orthorhombic structure. Magnetic measurements confirm an antiferromagnetic transition around 260K. A pronounced inverse S-shape anomaly in the loss tangent of dielectric measurement is observed near the Néel temperature. This feature shifts with the application of magnetic field. These anomalies are indicative of substantial coupling between the electric and magnetic orders in this compound.
Control of optical mode distribution through etched microstructures for improved broad area laser performance
Authors: Crump P. , Leisher P. , Matson T. , Anderson V. , Schulte D. , Bell J. , Farmer J. , DeVito M. , Martinsen R. , Kim Y. K. , Choquette K. D. , Erbert G. , Tränkle G.
Published: April 2008

Etching microstructures into broad area diode lasers is found to lead to more uniform near field and increased power conversion efficiency, arising from increased slope. Self-consistent device simulation indicates that this improvement is due to an increase in the effective internal injection efficiency above threshold—the nonuniform near field leads to regions of inefficient clamping of the carrier density in the laser stripe. Measurements of spontaneous emission through the substrate confirm the predicted carrier profile. Both experiment and theory show that improved overlap between carrier and power distributions correlates with improved slope.
Hole mobility in Mg-doped p-type InN films
Authors: Wang Xinqiang , Che Song-Bek , Ishitani Yoshihiro , Yoshikawa Akihiko
Published: April 2008

Mg-doped p-type InN layers with different thicknesses were grown under the same growth/doping conditions so that their net acceptor concentrations were almost the same (3–6)×1018cm−3, which were confirmed by electrolyte capacitance-voltage measurements. The conductivity of p-InN region embedded under high density surface electrons could be extracted through the slope of total sheet conductivity against thickness, which was about 8.1Ω−1cm−1. Then, corresponding hole mobility was determined to be about 17–36cm2∕Vs for the hole concentrations of about (1.4–3.0)×1018cm−3 obtained by providing the hole effective mass and Mg acceptor activation energy as 0.42m0 and 61meV, respectively.
Diffusion and thermal stability of hydrogen in ZnO
Authors: Bang Junhyeok , Chang K. J.
Published: April 2008

We perform both first-principles calculations and kinetic Monte Carlo (kMC) simulations to study the diffusion and thermal stability of hydrogen in ZnO. The migration energy of a substitutional hydrogen (HO) is 1.7eV, much higher than the value of 0.4–0.5eV for an interstitial hydrogen (Hi). Using as input the calculated energy barriers for H diffusion, kMC simulations show that while Hi diffuses out at low temperature, the thermal stability of HO is maintained up to 475°C, in good agreement with the annealing data. In addition, our calculations suggest that injected hydrogen from air turns into HO, causing n-type conductivity.
Large carbon-isotope shift of TC in boron-doped diamond
Authors: Dubrovinskaia Natalia , Dubrovinsky Leonid , Papageorgiou Thomas , Bosak Alexey , Krisch Michael , Braun Hans F. , Wosnitza Joachim
Published: April 2008

We report the carbon-isotope effect for boron-doped diamond (BDD). Resistive as well as specific-heat measurements reveal a 0.2K shift in the superconducting transition temperature Tc between BDDs containing C13 and C12. This is more than two times larger than could be expected from the mass difference by the use of the simple BCS formula in case the phenomenon is related to electron-phonon mediated superconductivity in BDD.
Molecular phylogenetic analysis of Dendrobium (Orchidaceae), with emphasis on the Australian section Dendrocoryne, and implications for generic classification
Authors: Burke Jacinta M. , Bayly Michael J. , Adams Peter B. , Ladiges Pauline Y.
Published: April 2008

Sequences of the internal transcribed spacers (ITS) of nuclear rDNA were obtained for a broad range of dendrobium orchids for phylogenetic analysis using parsimony. A progressive approach was used to identify functional outgroups for analysis of all taxa in Dendrobium sect. Dendrocoryne. Our first, broadest analysis confirmed the results of other workers that Dendrobium sensu lato includes a major Australasian clade and a sister Asian clade. In the Australasian clade, the New Zealand species D. cunninghamii (=gen. Winika, Clements et al. 1997) was identified as the sister group to a well supported clade that includes the genera Cadetia, Diplocaulobium and Flickingeria, and Dendrobium sects Grastidium, Latouria, Spatulata, Australorchis (=gen. Australorchis), Rhizobium (= gen. Dockrillia) and Dendrocoryne. Sect. Dendrocoryne is probably polyphyletic, with two species, D. aemulum and D. callitrophilum (=gen. Tropilis), outside the main group and sect. Rhizobium (= gen. Dockrillia) nested within it. Sect. Australorchis (= gen. Australorchis) is possibly the sister group to the clade of Rhizobium plus the main group of Dendrocoryne. Thelychiton (a genus reinstated for several species in Dendrocoryne) is polyphyletic, given that Tetrabaculum (=D. tetragonum complex) and Dockrillia fall within the same clade. The splitting of the Australasian dendrobiums into various genera by other authors is excessive and unnecessary, and alternative taxonomic treatments are offered here for debate. Our study included accessions for all varieties in the following three widespread eastern Australian species: D. speciosum, D. kingianum and D. tetragonum. Each of these species showed significant sequence divergence between particular geographic regions, but some varieties had identical sequences. The splitting of D. speciosum into 11 species is not supported. We identified pseudogenes in the ITS region for D. fleckeri and D. finniganense, which appear to have evolved before these two species diverged, but support their sister relationship. Sequences for D. callitrophilum and D. (Grastidium) baileyi (the latter from GenBank) also appear to be pseudogenes, and these taxa need further study.
Three-dimensional simulation of powder blasting with a polymer mask using a cellular automaton
Authors: Yagyu Hiromasa , Tabata Osamu
Published: April 2008

A three-dimensional (3D) simulation for micropowder blasting was carried out for the first time to predict the convex corner structure of a processed glass substrate with patterned mask erosion. The simulator utilized a cellular automaton algorithm which consisted of combinations of two orthogonal planes of two-dimensional (2D) cells and a solid particle erosion model. It was confirmed that the effect of erosion at the convex corner of the mask on the glass processing profile, which cannot be predicted in the previous 2D simulation, was successfully simulated using our 3D simulator.
Assigning functional linkages to proteins using phylogenetic profiles and continuous phenotypes
Authors: Gonzalez Orland , Zimmer Ralf
Published: April 2008

Motivation: A class of non-homology-based methods for protein function prediction relies on the assumption that genes linked to a phenotypic trait are preferentially conserved among organisms that share the trait. These methods typically compare pairs of binary strings, where one string encodes the phylogenetic distribution of a trait and the other of a protein. In this work, we extended the approach to automatically deal with continuous phenotypes.

Results: Rather than use a priori rules, which can be very subjective, to construct binary profiles from continuous phenotypes, we propose to systematically explore thresholds which can meaningfully separate the phenotype values. We illustrate our method by analyzing optimal growth temperatures, and demonstrate its usefulness by automatically retrieving genes which have been associated with thermophilic growth. We also apply the general approach, for the first time, to optimal growth pH, and make novel predictions. Finally, we show that our method can also be applied to other properties which may not be classically considered as phenotypes. Specifically, we studied correlations between genome size and the distribution of genes.

Contact:  orlandgonzalez@gmail.com

Supplementary information: Supplementary data are available at Bioinformatics online.
Optical tweezers for single cells
Authors: Zhang Hu , Liu Kuo-Kang
Published: April 2008

Optical tweezers (OT) have emerged as an essential tool for manipulating single biological cells and performing sophisticated biophysical/biomechanical characterizations. Distinct advantages of using tweezers for these characterizations include non-contact force for cell manipulation, force resolution as accurate as 100 aN and amiability to liquid medium environments. Their wide range of applications, such as transporting foreign materials into single cells, delivering cells to specific locations and sorting cells in microfluidic systems, are reviewed in this article. Recent developments of OT for nanomechanical characterization of various biological cells are discussed in terms of both their theoretical and experimental advancements. The future trends of employing OT in single cells, especially in stem cell delivery, tissue engineering and regenerative medicine, are prospected. More importantly, current limitations and future challenges of OT for these new paradigms are also highlighted in this review.
Maximum strength for intermolecular adhesion of nanospheres at an optimal size
Authors: Yao Haimin , Guduru Pradeep , Gao Huajian
Published: April 2008

Previous studies have emphasized that the adhesion strength between solid objects tends to increase as the characteristic size of the objects decreases and eventually saturates at the theoretical adhesion strength below a critical size scale. Here we show that the adhesion strength between two spheres or between a sphere and a solid half-space actually exhibits a peak value at an optimal size. This optimal size arises owing to a transition between surface- and bulk-dominated interaction regimes at the nanoscale.
The bandcount increment scenario. I. Basic structures
Authors: Avrutin Viktor , Eckstein Bernd , Schanz Michael
Published: April 2008

Bifurcation structures in two-dimensional parameter spaces formed only by chaotic attractors are still far away from being understood completely. In a series of three papers, we investigate the chaotic domain without periodic inclusions for a map, which is considered by many authors as some kind of one-dimensional canonical form for discontinuous maps. In the first part, we report a novel bifurcation scenario formed by crises bifurcations, which includes multi-band chaotic attractors with arbitrary high bandcounts and determines the basic structure of the chaotic domain.
The stochastic Mathieu's equation
Authors: Poulin Francis J , Flierl Glenn R
Published: April 2008

In this manuscript, we consider generalizations of the classical Mathieu's equation to stochastic systems. Unlike previous works, we focus on internal frequencies that vary continuously between periodic and stochastic variables. By numerically integrating the system of equations using a symplectic method, we determine the Lyapunov exponents for a wide range of parameters to quantify how the growth rates vary in parameter space.

In the nearly periodic limit, we recover the same growth rates as the classical Mathieu's equation. As the stochasticity increases, the maximum growth decreases and the unstable region broadens, which signifies that the stochasticity can both stabilize and destabilize a system in relation to the deterministic limit. In addition to the classical parametric modes, there is also an unstable stochastic mode that arises only for moderate stochasticity. The power spectrum of the solutions shows that an increase in stochasticity tends to narrow the width of the subharmonic peak and increase the decay away from this peak.
Law of spreading of the crest of a breaking wave
Authors: Pomeau Y , Jamin T , Le Bars M , Le Gal P , Audoly B
Published: April 2008

In a wide range of conditions, ocean waves break. This can be seen as the manifestation of a singularity in the dynamics of the fluid surface, moving under the effect of the fluid motion underneath. We show that, at the onset of breaking, the wave crest expands in the spanwise direction as the square root of time. This is first derived from a theoretical analysis and then compared with experimental findings. The agreement is excellent.
Anisotropic patterned population synchrony in climatic gradients indicates nonlinear climatic forcing
Authors: Hagen Snorre B , Jepsen Jane U , Yoccoz Nigel G , Ims Rolf A
Published: April 2008

Although climatic forcing has been suspected to be the most common cause of spatial population synchrony owing to the Moran effect, it has proved difficult to disentangle the impact of climate from other possible causes of synchrony based on population survey data. Nonlinear population responses to climatic variation may be a part of this difficulty, but they can also provide an opportunity to highlight the climate impacts through targeted survey designs. In particular, when species distribution ranges encompass consistent spatial gradients in climate (e.g. according to latitude or altitude), such gradients can be strategically included in the spatial design of population surveys as to facilitate comparisons of spatial synchrony patterns across and along the gradient. In that case, we predict that nonlinear impacts of climatic variation on population growth rates will result in anisotropic (direction specific) synchrony patterns in the sense that synchrony will drop faster with distance along the climatic gradient than across it. We provide an empirical case study to exemplify survey design and analyses. Of two sympatric species of geometrids, inhabiting an altitudinal gradient in subarctic birch forest, one (
Operophtera brumata
L.) showed anisotropic synchrony consistent with a strongly nonlinear sensitivity to climatic variation, whereas the other (
Epirrita autumnata
Bkh.) did not. These results are interpreted in light of the biological characteristics of the species.
Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition
Authors: Akagi Keiko , Li Jingfeng , Stephens Robert M. , Volfovsky Natalia , Symer David E.
Published: April 2008

Numerous inbred mouse strains comprise models for human diseases and diversity, but the molecular differences between them are mostly unknown. Several mammalian genomes have been assembled, providing a framework for identifying structural variations. To identify variants between inbred mouse strains at a single nucleotide resolution, we aligned 26 million individual sequence traces from four laboratory mouse strains to the C57BL/6J reference genome. We discovered and analyzed over 10,000 intermediate-length genomic variants (from 100 nucleotides to 10 kilobases), distinguishing these strains from the C57BL/6J reference. Approximately 85% of such variants are due to recent mobilization of endogenous retrotransposons, predominantly L1 elements, greatly exceeding that reported in humans. Many genes’ structures and expression are altered directly by polymorphic L1 retrotransposons, including Drosha (also called Rnasen), Parp8, Scn1a, Arhgap15, and others, including novel genes. L1 polymorphisms are distributed nonrandomly across the genome, as they are excluded significantly from the X chromosome and from genes associated with the cell cycle, but are enriched in receptor genes. Thus, recent endogenous L1 retrotransposition has diversified genomic structures and transcripts extensively, distinguishing mouse lineages and driving a major portion of natural genetic variation.
Protective effect of nasal immunization of influenza virus hemagglutinin with recombinant cholera toxin B subunit as a mucosal adjuvant in mice
Authors: Isaka Masanori , Zhao Yanqiu , Nobusawa Eri , Nakajima Setsuko , Nakajima Katsuhisa , Yasuda Yoko , Matsui Hideyuki , Hasegawa Tadao , Maeyama Jun‐ichi , Morokuma Kazunori , Ohkuma Kunio , Tochikubo Kunio
Published: April 2008

To develop an efficient nasal influenza vaccine, influenza A and B virus HA with rCTB as a mucosal adjuvant were administered to mice intranasally. Serum anti‐HA IgG and IgA antibody responses for both HA vaccines were significantly increased in the presence of rCTB. Higher HI and neutralizing antibody titers and higher mucosal IgA antibody responses in the respiratory tract were detected when rCTB was added than without rCTB. When mice were immunized with HA vaccine with or without rCTB and challenged by intranasal administration of mouse‐adapted pathogenic influenza A virus, all mice immunized with HA plus rCTB survived for seven days without any inflammatory changes in the lungs, while not all the mice immunized with HA without rCTB survived, and all of them had lung consolidations. These results demonstrate that intranasal co‐administration of rCTB as a mucosal adjuvant with influenza virus HA is necessary not only for the induction of systemic and mucosal HA antibodies, but also for the protection of mice from morbidity and mortality resulting from virus infection.
Human immunodeficiency virus type‐1 vulnerates nascent neuronal cells
Authors: Kitayama Hiroko , Miura Yoshiharu , Ando Yoshinori , Koyanagi Yoshio
Published: April 2008

Macrophages or microglial cells are the major target cells for HIV‐1 infection in the brain. The infected cells release neurotoxic factors that may cause severe neuronal cell damage, especially in the basal ganglia and hippocampus. In this study, we used rat OHC to examine the region‐specific neuronal cell damage caused by HIV‐1‐infected macrophages. When OHC was cocultured with HIV‐1‐infected MDM, we found that neuronal cells at the GCL of the DG were preferentially killed via apoptosis, and that projection of MF from GCL to PCL of the CA3 region was severely disturbed. We marked precursor cells around the DG region by using an EGFP‐expressing retrovirus vector and found that these cells lost the ability to differentiate into neurons when exposed to HIV‐1‐infected MDM. In the DG, new neurons are normally incorporated into GCL or PCL, while in the presence of HIV‐1‐infected MDM, mature neurons failed to be incorporated into those layers. These data indicate that the neurotoxic factor(s) released from HIV‐1‐infected macrophages impede(s) neuronal cell repair in brain tissue. This suggests that DG is the region of the hippocampus most vulnerable to neuronal damage caused by HIV‐1 infection, and that its selective vulnerability is most likely due to the highly active neurogenesis that takes place in this region.
The Bordetella type III secretion system: its application to vaccine development
Authors: Abe Akio , Nagamatsu Kanna , Watanabe Mineo
Published: April 2008

B. pertussis is a causative agent of whooping cough (pertussis) in humans. Despite wide‐scale vaccination in many countries, there is serious concern about pertussis as a re‐emerging disease. Re‐emergence of pertussis may be explained by several factors: the short duration of protection by the currently available acellular pertussis vaccine, an increase in asymptomatic adult carriers and expansion of strains with certain antigenic variations which are not covered by currently available vaccines. To develop safer and more efficacious vaccines which confer more prolonged protection, researchers are focusing on identification and characterization of new virulence factors. One candidate for protective antigens is the type III secretion system and its secreted proteins.
Submarine and subaerial erosion of volcanic landscapes: comparing Pacific Ocean seamounts with Valencia Seamount, exposed during the Messinian Salinity Crisis
Authors: Mitchell Neil C. , Lofi Johanna
Published: April 2008

Similarity of form between subaerial and submarine landscapes affected by erosion could suggest similarities in the process of erosion, such as by runoff and sedimentary flows, respectively. On the other hand, if aspects of form vary, its characteristics may be used to identify the environmental origin of erosion. Towards these goals, this contribution addresses the morphology of submarine volcanoes (seamounts) with widely differing histories of erosion. One set from the Pacific Ocean never exposed above sea level includes Cretaceous‐age seamounts near Hawai'i (including Apu'upu'u Seamount), two seamounts of <3 Ma in age near a mid‐ocean ridge and the 11–4 Ma Jasper Seamount. These seamounts are all isolated from continents and hence from any erosion associated with mass wasting of unstable terrigenous deposits. In such isolated submarine environments, surfaces erode slowly from in situ weathering, mass wasting and scouring by sedimentary flows initiated by slope failure in pelagic or bedrock materials. The Pacific seamounts are compared with Valencia Seamount in the western Mediterranean, exposed subaerially for 100–400 k.y. during the Messinian Salinity Crisis before 5 Ma. Multibeam and deeply towed sidescan sonar data of Valencia Seamount reveal features typical of subaerial erosion of volcanic islands, such as canyons and relatively uneroded sectors (planezes) between them. Using a simple topographical reconstruction, the apparent erosion depth typically reaches 100 m within canyons and up to 180 m in places. Whereas the younger Pacific seamounts do not show these erosional features, the much older Cretaceous seamounts do have channels, which in one example suggests up to 200 m of incision. Both Valencia and Apu'upu'u seamounts have channel longitudinal profiles that are steep and typically linear to concave upwards. The erosion depth of Apu'upu'u Seamount is significant, despite the seamount's persistent submarine environment, because of its greater age, steeper flanks and greater contributing areas to channels compared with Valencia Seamount. These results illustrate that the channel morphology resulting from submarine erosion can become similar to that produced by subaerial erosion given sufficient time.
Critical issues for e‐learning delivery: what may seem obvious is not always put into practice
Authors: McPherson M.A. , Nunes J.M.
Published: April 2008

Abstract  The successful adoption of information and communication technology to enhance learning can be very challenging, requiring a complex blend of technological, pedagogical and organizational components, which may at times require the resolution of contradictory demands and conflicting needs. The research reported in this paper investigated and analysed critical success factors (CSFs) that are required to deliver e‐learning within higher education (HE) courses and programmes. The research design adopted a critical research approach, instantiated by focus group discussions with e‐learning experts drawn from administrative, educational, technology and research domains. The findings revealed that staffing issues, pedagogically sound delivery models and training of both tutors and students cannot be treated as trivial issues and are critical to the success of e‐learning. Furthermore, this research also shows that there is a strong relationship between these factors and inspirational institutional leadership. The findings also suggest that in order to assure the success of e‐learning, this leadership should guarantee the presence of institutional enablers. It is hoped that the CSFs, described and discussed in depth in this paper, will provide a suitable theoretical foundation to underpin the successful delivery of e‐learning within HE.
Behavioural flexibility in individuals with Angelman syndrome, Down syndrome, non‐specific intellectual disability and Autism spectrum disorder
Authors: Didden R. , Sigafoos J. , Green V. A. , Korzilius H. , Mouws C. , Lancioni G. E. , O'Reilly M. F. , Curfs L. M. G.
Published: April 2008

Background  Little is known about behavioural flexibility in children and adults with Angelman syndrome and whether people with this syndrome have more or less problems in being behaviourally flexible as compared with other people.

Method  Behavioural flexibility scores were assessed in 129 individuals with Angelman syndrome using 11 items from the Behavioural Flexibility Rating Scale‐Revised (Green et al. 2007). Level of behavioural flexibility scores in individuals with Angelman syndrome (N = 129) was compared with that of people with non‐specific intellectual disability (ID) (N = 90), Down syndrome (N = 398) and Autism spectrum disorder (N = 235).

Results  Comparative analyses show that individuals with Angelman syndrome were more flexible than those with non‐specific ID (P < 0.001) and those with Autism spectrum disorder (P < 0.01). There were no differences in behavioural flexibility scores between individuals with Angelman syndrome and those with Down syndrome (P = 0.94).

Conclusion  It is concluded that individuals with Angelman syndrome are comparatively flexible in their behaviour.
Linear spatio‐temporal characterization of a UV microscope objective for nonlinear imaging and spectroscopy by using two‐dimensional spectral interferometry
Authors: AMIR W. , DURFEE C. G. , SCHAFER D. N. , GIBSON E. A. , KOST L. , PRZEKWAS E. , JIMENEZ R. , SQUIER J. A.
Published: April 2008

Two‐dimensional Fourier transform spectral interferometry is used to characterize the spatio‐temporal aberrations of a UV microscope objective. The spatial and temporal profiles of a 420 nm, 38 fs pulse at the focus of a 0.32 NA UV objective are then deduced using a wave propagation code incorporating the measured aberrations.
Quantifying immunogold labelling in transmission electron microscopy
Authors: D'AMICO F. , SKARMOUTSOU E.
Published: April 2008

Gold particles labelling on ultrathin sections is extensively used for antigen localization in transmission electron microscopy. In establishing absolute or relative counts in tissue sections, it would be expedient to use stereologically based unbiased estimates for quantitative results. Nowadays, quantitative immunoelectron microscopy has achieved good and satisfactory results to test whether the gold labelling follows a non‐random or a random pattern and then to draw statistical comparisons between cell subcompartments within a sample of cells or between experimental groups of cells. This brief informal review of literature focuses on the relative quantitative determinations of gold labelling of antigens as well as on the statistical distribution comparisons in transmission electron microscopy.
Spatial control of pa‐GFP photoactivation in living cells
Authors: TESTA I. , PARAZZOLI D. , BAROZZI S. , GARRÈ M. , FARETTA M. , DIASPRO A.
Published: April 2008

Photoactivatable green fluorescent protein (paGFP) exhibits peculiar photo‐physical properties making it an invaluable tool for protein/cell tracking in living cells/organisms. paGFP is normally excited in the violet range (405 nm), with an emission peak centred at 520 nm. Absorption cross‐section at 488 nm is low in the not‐activated form. However, when irradiated with high‐energy fluxes at 405 nm, the protein shows a dramatic change in its absorption spectra becoming efficiently excitable at 488 nm. Confocal microscopes allow to control activation in the focal plane. Unfortunately, irradiation extends to the entire illumination volume, making impracticable to limit the process in the 3D (three‐dimensional) space. In order to confine the process, we used two advanced intrinsically 3D confined optical methods, namely: total internal reflection fluorescence (TIRF) and two‐photon excitation fluorescence (2PE) microscopy. TIRF allows for spatially selected excitation of fluorescent molecules within a thin region at interfaces, i.e. cellular membranes. Optimization of the TIRF optical set‐up allowed us to demonstrate photoactivation of paGFP fused to different membrane localizing proteins. Exploitation of the penetration depth showed that activation is efficiently 3D confined even if limited at the interface. 2PE microscopy overcomes both the extended excitation volume of the confocal case and the TIRF constraint of operating at interfaces, providing optical confinement at any focal plane in the specimen within subfemtoliter volumes. The presented results emphasize how photoactivation by non‐linear excitation can provide a tool to increase contrast in widefield and confocal cellular imaging.
Characterization of the polarization sensitivity anisotropy of a near‐field probe using phase measurements
Authors: FISCHER H. , NESCI A. , LEVEQUE G. , MARTIN O.J.F.
Published: April 2008

Amplitude and phase measurements of the near‐field generated by isolated subwavelength apertures in a gold film are presented. The near‐field distribution of such a structure is complex and the measured signal strongly depends on the electric field components effectively detected by the experimental setup. By comparing this signal with 3D vectorial calculations we are able to determine which electric field components are effectively measured. The sensitivity of the phase distribution is key to this measurement. The proposed characterization technique should prove extremely useful to calibrate a Scanning near‐field optical microscopy (SNOM) beforehand in order to retrieve quantitative information on the polarization of the field distribution under study.
Starch‐based backwards SHG for in situ MEFISTO pulse characterization in multiphoton microscopy
Authors: ANISHA THAYIL K. N. , GUALDA E. J. , PSILODIMITRAKOPOULOS S. , CORMACK I. G. , AMAT‐ROLDÁN I. , MATHEW M. , ARTIGAS D. , LOZA‐ALVAREZ P.
Published: April 2008

We report a simple methodology to provide complete pulse characterization at the sample plane of a two‐photon excited fluorescence (TPEF) microscope. This is achieved by using backward propagating second‐harmonic generation (SHG) from starch granules. Without any modification to the microscope, SHG‐autocorrelation traces were obtained by using a single starch granule that was placed alongside the biological specimen being imaged. A spectrally resolved SHG autocorrelation was acquired by placing a spectrometer at the output port of the microscope. Complete in situ pulse information is then directly retrieved in an analytical way using the measurement of electric filed by interferometric spectral trace observation (MEFISTO) technique.
Study of the structure of the air and blood capillaries of the gas exchange tissue of the avian lung by serial section three‐dimensional reconstruction
Authors: WOODWARD J. D. , MAINA J. N.
Published: April 2008

We have previously reconstructed the gas exchange tissue of the adult muscovy duck, Cairina moschata using a method of manually aligning sections and tracing the contours of the components of the gas exchange tissue. This reconstruction method demonstrated that the air capillaries are comprised of an expanded globular part interconnected by narrow air channels. The blood capillaries completely surround the air capillaries forming an anastomosing meshwork of short segments. However, the resulting reconstruction was limited in scope because of the laborious process of tracing the profiles of each component through the sequence of micrographs. We have now reconstructed a larger proportion of the exchange tissue by using a cross‐correlation based alignment strategy and have demonstrated that the staining intensity of each of the exchange tissue components is sufficiently different to allow them to be identified by simple filtering and thresholding. The resulting reconstructions sample a much larger proportion of the exchange tissue and demonstrate the heterogeneity of structures from different locations in the parabronchus. We have shown that a sheet‐flow‐type arrangement of blood capillaries surrounds the infundibulum; this represents an unexpected functional convergence with the arrangement of blood capillaries surrounding the mammalian alveoli. It is feasible, using this reconstruction strategy, to analyse the exchange tissue of a large number of avian species in order to determine structural correlates of function. The resulting reconstructions could be analysed in order to determine the basis of the functional efficiency and rigidity of the avian lung.
An easily built diffuse illumination system effective at both very low and moderate magnifications, for observing in situ stained slides
Authors: FROHLICH M. W. , MOYROUD E.
Published: April 2008

Effective study of in situ stained sections often requires illumination that is difficult to achieve with commonly used research microscopes. One must be able to switch quickly and conveniently from the very lowest to moderate magnifications. At all magnifications contrast due to light scatter must be minimized, so that the weak staining that signifies low gene expression can be observed reliably. For the lowest power objectives (e.g., 1.25× or 2×) many microscopes require that the condenser be removed to illuminate the full field of view. This is not only very inconvenient when switching magnifications, but without a condenser the low numerical aperture of the illuminating light beam results in unwanted contrast due to light scatter. We have devised a simple system that diffusely illuminates the full field of view of the lowest power objective (1.25×) and has high enough numerical aperture for use with the 25× and 40× objectives. A key feature is the use of a large diameter ring light (internal diameter 5.8 cm), placed on the microscope base, to illuminate a large diameter diffuser placed just below the slide.
Replicate‐based noise corrected correlation for accurate measurements of colocalization
Authors: ADLER J. , PAGAKIS S. N. , PARMRYD I.
Published: April 2008

It is widely recognized that the accuracy of colocalization measurements is dependent upon the quality of the source images. We demonstrate that, as the image quality increases, the measured colocalization, using the Pearson and Spearman rank correlation coefficients, approaches the true colocalization asymptotically. This means that in practice it is difficult to obtain images of sufficient quality for accurate measurements. We introduce the replicate‐based noise corrected correlation (RBNCC) which aligns the measured colocalization with the true colocalization: a noise measurement is made for each fluorophore from a pair of replicate images, the two noise measurements are combined to generate a correction factor which is applied to the measured colocalization between the two fluorophores. In consequence, accurate measurements can be obtained even with noisy images, making RBNCC especially attractive for live imaging. Even with images of apparently good quality we found an average discrepancy of about 20% between the measured and corrected colocalization. A case is made for using the Spearman rank coefficient instead of the Pearson coefficient to measure colocalization.