bluuebunny/crossref_metadata_2025 huggingface dataset:
Anomalous thermomechanical properties and laser-induced densification of vitreous silica
Authors: Huang Liping , Kieffer John
Published: October 2006

The authors studied the anomalous behaviors of vitreous silica under the combined influence of high temperature and pressure, by using molecular dynamics simulations based on a charge-transfer three-body potential. Accordingly, anomalous properties, such as the minimum in the bulk modulus at ∼2–3GPa and the negative thermal expansion while under pressure, are inherently connected to the ability of the glass to undergo irreversible densification. Their simulations reveal the structural features responsible for this behavior, as well as the extent to which these properties can be tailored through specific processing routes and hence create glass that is less susceptible to radiation damage.
White organic light-emitting device based on a compound fluorescent-phosphor-sensitized-fluorescent emission layer
Authors: Kanno Hiroshi , Sun Yiru , Forrest Stephen R.
Published: October 2006

The authors demonstrate a combination fluorescent and phosphor-sensitized-fluorescent white organic light-emitting device (WOLED), employing the conductive host material, 4,4′-bis(9-ethyl-3-carbazovinylene)-1,1′-biphenyl, doped with the phosphorescent green, and the fluorescent red and blue emitters, fac-tris(2-phenylpyridinato-N,C2′) iridium (III), 4-(dicyanomethylene)-2-t-butyl-6-(1,1,7,7-tetramethyljulolidyl-9-enyl)-4H-pyran, and 4,4′-bis (9-ethy-3-carbazolvinylene)-1-1′-biphenyl, respectively. Although two fluorescent dopants are employed along with only a single phosphor, this simple structure can, in principle, achieve 100% internal quantum efficiency. In the prototype, the phosphor-sensitized WOLED exhibits total external quantum and power efficiencies of ηext,tot=13.1±0.5% and ηp,tot=20.2±0.7lm∕W, respectively, at a luminance of 800cd∕m2 with Commission Internationale de L’Eclairage chromaticity coordinates of (x=0.38, y=0.42) and a color rendering index of 79.
Pulsed molecular beam scattering of a planar-shaped organic molecule on regularly stepped surfaces of hydrogen-terminated Si(111)
Authors: Shimada Toshihiro , Ichikawa Hisashi , Saiki Koichiro
Published: October 2006

Strong dependence of surface residence time of a planar organic molecule (hydrogen phthalocyanine) on vicinal surfaces of hydrogen-terminated Si(111) was observed in pulsed molecular beam scattering experiments. These results can be explained by the difference in the microscopic contact area of the molecules on the surface, which determines the binding force between the migrating molecules and the surface. The relationship between the observed behavior and the organic thin film growth is discussed.
Effect of axial finiteness on electron heating in low-frequency inductively coupled plasmas
Authors: Aman-ur-Rehman  , Pu Yi-Kang
Published: October 2006

Total power absorption inside the plasma (by taking the thermal motion of the electrons into account) has been calculated using different inductively coupled plasma models. The comparison shows that in the low-frequency region the results of the semi-infinite plasma models are different from those of the finite-length plasma models. The semi-infinite plasma models show net reduction of heating in the low-frequency region, due to thermal motion of the electrons from inside the skin region to outside the skin region. The finite-length plasma models on the other hand (due to change in the skin depth owing to the boundary condition of E=0 at z=L, and reflection of electrons from the plasma boundary) show that the decrease in heating due to the motion of the electrons from inside the skin depth to outside the skin depth is recovered by the reflection of the electrons from the plasma boundary. Hence, it is concluded that the results of the semi-infinite plasma models presented by Tyshetskiy et al. [Phys Rev. Lett. 90, 255002 (2003)] can be misleading (in the low-frequency region), since they overlooked the effect of axial finiteness of the plasma.
Center of mass method for exchange bias measurements
Authors: Hovorka Ondrej , Berger Andreas , Friedman Gary
Published: October 2006

Exchange bias measurement techniques are tested using an Ising model for exchange-coupled bilayer structures. In the presence of hysteresis loop asymmetry, the conventional exchange bias characterization method of measuring the sum of the coercive fields is found to be rather inaccurate if compared to the interface coupling energy. An alternative method based on the analysis of entire hysteresis loops is proposed, tested, and found to be substantially more robust.
Construction of three-dimensional biomolecule structures employing femtosecond lasers
Authors: Drakakis Theodore S. , Papadakis George , Sambani Kyriaki , Filippidis George , Georgiou Savas , Gizeli Electra , Fotakis Costas , Farsari Maria
Published: October 2006

The authors demonstrate here a method for three-dimensional patterning of proteins and other biological molecules. The method employs femtosecond-laser-induced three-photon polymerization, a technique which enables the construction of arbitrary two- and three-dimensional structures of submicron resolution. Biotin is subsequently attached to the three-dimensional (3D) structures via UV-activated cross-linking. The integrity of the photolytically immobilized biotin is confirmed by detecting the binding of fluorescently labeled avidin via fluorescence microscopy and via a surface acoustic sensor technique. In all, the technique opens the way for the fabrication of structures with a wide range of biomaterials as well as studying their dynamics within complex 3D structures.
Temperature dependence of solubility limits of transition metals (Co, Mn, Fe, and Ni) in ZnO nanoparticles
Authors: Mandal S. K. , Das A. K. , Nath T. K. , Karmakar Debjani
Published: October 2006

X-ray diffraction studies on bulk amount of chemically prepared nanocrystalline powder of Zn1−xTMxO (TM=Co, Mn, Fe, and Ni) show that the evolution of secondary phases (Co3O4, Mn3O4, Fe3O4, or NiO) along with the single phase Zn1−xTMxO strongly depend on growth temperature and doping concentration. The highest solubility limits of Co, Mn, Fe, and Ni in ZnO are 30%, 30%, 20%, and 3% (atomic weight), respectively. The magnetization measurement shows that the secondary phase formation reduces the magnetization of single phase Zn1−xTMxO, which may be the important clue that the secondary phase is not responsible for magnetism in Zn1−xTMxO.
Defect passivation in HfO2 gate oxide by fluorine
Authors: Tse K. , Robertson J.
Published: October 2006

The authors have calculated that fluorine substituting for oxygen gives no gap states in HfO2. This accounts for the good passivation of oxygen vacancies by F seen experimentally. Bonding arguments are used to account for why F may be the most effective passivant in ionic oxides such as HfO2, whereas hydrogen is effective in covalent solids. General principles of defect passivation in ionic oxides are discussed. Vacancies are more detrimental in ionic oxides than in SiO2 because they are more likely to be charged in the presence of a gate electrode.
Enhancement of hole injection in pentacene organic thin-film transistor of O2 plasma-treated Au electrodes
Authors: Kim Woong-Kwon , Hong Kihyon , Lee Jong-Lam
Published: October 2006

The effect of oxygen plasma treatment on enhancement of hole mobility was demonstrated using pentacene organic thin-film transistors (OTFTs) with bottom-contact Au electrodes. Linear field-effect mobility increased from 3.2×10−2to7.4×10−2cm2∕Vs as the Au electrodes were treated with O2 plasma. Secondary electron emission spectra revealed that the work function of oxygen plasma-treated Au is 0.5eV higher than that of untreated Au. This led to a reduced hole injection barrier at the interface of Au with pentacene, increasing the field-effect mobility of OTFTs.
Enhanced light-extraction in GaInN near-ultraviolet light-emitting diode with Al-based omnidirectional reflector having NiZn∕Ag microcontacts
Authors: Kim Jong Kyu , Xi J.-Q. , Luo Hong , Fred Schubert E. , Cho Jaehee , Sone Cheolsoo , Park Yongjo
Published: October 2006

Enhancement of light extraction in a GaInN near-ultraviolet light-emitting diode (LED) employing an Al-based omnidirectional reflector (ODR) consisting of GaN, a SiO2 low-refractive-index layer perforated by an array of NiZn∕Ag microcontacts, and an Al layer is presented. A theoretical calculation reveals that a SiO2∕Al ODR has much higher reflectivity than both a SiO2∕Ag ODR and a Ag reflector at a wavelength of 400nm. It is experimentally shown that GaInN near-ultraviolet LEDs with GaN∕SiO2∕Al ODR have 16% and 38% higher light output than LEDs with SiO2∕Ag ODR and Ag reflector, respectively. The higher light output is attributed to enhanced reflectivity of the Al-based ODR in the near-ultraviolet wavelength range.
Effect of aggregation on thermal conduction in colloidal nanofluids
Authors: Prasher Ravi , Evans William , Meakin Paul , Fish Jacob , Phelan Patrick , Keblinski Pawel
Published: October 2006

Using effective medium theory the authors demonstrate that the thermal conductivity of nanofluids can be significantly enhanced by the aggregation of nanoparticles into clusters. Predictions of the effective medium theory are in excellent agreement with detailed numerical calculation on model nanofluids involving fractal clusters and show the importance of cluster morphology on thermal conductivity enhancements.
Origin of the blue photoluminescence from SiO2(SiC)∕SiC on Si substrate
Authors: Chen Zheng , Wang Yuxia , Zou Youming , Wang Jianwen , Li Yun , Zhang Hongjuan
Published: October 2006

SiC film is prepared by heating the polystyrene/Si in 1atm ambient Ar at 1270°C. The as-grown SiC film is characterized by scanning electron microscopy, x-ray diffraction, and x-ray photoelectron spectroscopy. Based on the results, it is suggested that a SiO2(SiC) layer is located on the top of the as-grown SiC film. A blue photoluminescence band is observed from the as-grown sample. The photoluminescence band has the same origin as those from silica nanowires and SiC nanostructures and is associated with the near interface traps at the interface of SiO2∕SiC or SiO2∕Si.
Fine-feature patterning of self-aligned polymeric thin-film transistors fabricated by digital lithography and electroplating
Authors: Wong W. S. , Chow E. M. , Lujan R. , Geluz-Aguilar V. , Chabinyc M. L.
Published: October 2006

Spatially controlled jet-printed etch masks, having a minimum drop size of 40–50μm, were used to define gap patterns having a minimum feature size of ∼10μm. The defined gaps, in combination with nickel electroplating, were used to create bottom-gate electrode thin-film transistors (TFTs) with gate lengths of 10–20μm and gate widths of 150μm. Self-aligned source/drain top contacts were used for fabricating polythiophene-based TFT devices having channel width-to-length ratios of ∼4. A typical p-channel TFT device had an on/off ratio of 107, threshold voltage of −1V, and field-effect mobility of 0.034cm2∕Vs.
Confined Brownian motion of individual magnetic nanoparticles on a chip: Characterization of magnetic susceptibility
Authors: van Ommering Kim , Nieuwenhuis Jeroen H. , van IJzendoorn Leo J. , Koopmans Bert , Prins Menno W. J.
Published: October 2006

An increasing number of biomedical applications requires detailed knowledge of the magnetic susceptibility of individual particles. With conventional techniques it is very difficult to analyze individual particles smaller than 1μm. The authors demonstrate how the susceptibility of individual nanoparticles can be determined in an efficient way by optically analyzing the confined Brownian motion of a nanoparticle trapped in a known magnetic potential well on a chip. A setup is introduced that has a controllable two-dimensional magnetic potential well, which is defined by an integrated microscopic current wire. Susceptibility measurements have been performed on 150–450nm superparamagnetic beads. They found differences in bead susceptibility of an order of magnitude and differences in volumetric susceptibility of more than a factor of 2.
Observation of numerous E2 mode phonon replicas in the room temperature photoluminescence spectra of ZnO nanowires: Evidence of strong deformation potential electron-phonon coupling
Authors: Ramanathan S. , Bandyopadhyay S. , Hussey L. K. , Muñoz M.
Published: October 2006

The authors report the observation of numerous (>20) phonon replica peaks in the room temperature photoluminescence spectrum of ZnO nanowires embedded in 50nm diameter pores of an anodic alumina film. The peaks are spaced in energy by ∼54meV, which is the energy of a nonpolar phonon with symmetry E2 in ZnO. These peaks are possibly caused by resonant phonon-assisted decay of photoexcited electrons to an impurity band, followed by radiative recombination. These results suggest that even though ZnO is strongly polar, deformation potential coupling to a nonpolar phonon mode may be stronger than Fröhlich coupling to polar phonon modes.

At the request of the authors and editor, this article is being retracted effective 27 March 2009.
Charge state dependence of cathodic vacuum arc ion energy and velocity distributions
Authors: Rosén Johanna , Schneider Jochen M. , Anders André
Published: October 2006

In the literature, conflicting conclusions are reported concerning the charge state dependence of cathodic arc ion energy and velocity distributions. It appears that data from electrostatic energy analyzers indicate charge state dependence of ion energy, whereas time-of-flight methods support charge state independence of ion velocity. Here the authors present charge-state-resolved ion energy distributions and calculate the corresponding ion velocity distributions in aluminum vacuum arc plasma. They show that the conflicting conclusions reported in the literature for the two different characterization techniques may originate from the commonly employed data interpretation of energy and velocity, in which peak values and average values are not carefully distinguished.
Mapping protein dynamics in catalytic intermediates of the redox-driven proton pump cytochrome
c
oxidase
Authors: Busenlehner Laura S. , Salomonsson Lina , Brzezinski Peter , Armstrong Richard N.
Published: October 2006

Redox-driven proton pumps such as cytochrome
c
oxidase (C
c
O) are fundamental elements of the energy transduction machinery in biological systems. C
c
O is an integral membrane protein that acts as the terminal electron acceptor in respiratory chains of aerobic organisms, catalyzing the four-electron reduction of O
2
to H
2
O. This reduction also requires four protons taken from the cytosolic or negative side of the membrane, with an additional uptake of four protons that are pumped across the membrane. Therefore, the proton pump must embody a “gate,” which provides alternating access of protons to one or the other side of the membrane but never both sides simultaneously. However, the exact mechanism of proton translocation through C
c
O remains unknown at the molecular level. Understanding pump function requires knowledge of the nature and location of these structural changes that is often difficult to access with crystallography or NMR spectroscopy. In this paper, we demonstrate, with amide hydrogen/deuterium exchange MS, that transitions between catalytic intermediates in C
c
O are orchestrated with opening and closing of specific proton pathways, providing an alternating access for protons to the two sides of the membrane. An analysis of these results in the framework of the 3D structure of C
c
O indicate the spatial location of a gate, which controls the unidirectional proton flux through the enzyme and points to a mechanism by which C
c
O energetically couples electron transfer to proton translocation.
Gastric stimulation in obese subjects activates the hippocampus and other regions involved in brain reward circuitry
Authors: Wang Gene-Jack , Yang Julia , Volkow Nora D. , Telang Frank , Ma Yeming , Zhu Wei , Wong Christopher T. , Tomasi Dardo , Thanos Panayotis K. , Fowler Joanna S.
Published: October 2006

The neurobiological mechanisms underlying overeating in obesity are not understood. Here, we assessed the neurobiological responses to an Implantable Gastric Stimulator (IGS), which induces stomach expansion via electrical stimulation of the vagus nerve to identify the brain circuits responsible for its effects in decreasing food intake. Brain metabolism was measured with positron emission tomography and 2-deoxy-2[
18
F]fluoro-
d
-glucose in seven obese subjects who had the IGS implanted for 1–2 years. Brain metabolism was evaluated twice during activation (on) and during deactivation (off) of the IGS. The Three-Factor Eating Questionnaire was obtained to measure the behavioral components of eating (cognitive restraint, uncontrolled eating, and emotional eating). The largest difference was in the right hippocampus, where metabolism was 18% higher (
P
< 0.01) during the “on” than “off” condition, and these changes were associated with scores on “emotional eating,” which was lower during the on than off condition and with “uncontrolled eating,” which did not differ between conditions. Metabolism also was significantly higher in right anterior cerebellum, orbitofrontal cortex, and striatum during the on condition. These findings corroborate the role of the vagus nerve in regulating hippocampal activity and the importance of the hippocampus in modulating eating behaviors linked to emotional eating and lack of control. IGS-induced activation of regions previously shown to be involved in drug craving in addicted subjects (orbitofrontal cortex, hippocampus, cerebellum, and striatum) suggests that similar brain circuits underlie the enhanced motivational drive for food and drugs seen in obese and drug-addicted subjects, respectively.
A deletion defining a common Asian lineage ofMycobacterium tuberculosisassociates with immune subversion
Authors: Newton Sandra M. , Smith Rebecca J. , Wilkinson Katalin A. , Nicol Mark P. , Garton Natalie J. , Staples Karl J. , Stewart Graham R. , Wain John R. , Martineau Adrian R. , Fandrich Sarah , Smallie Timothy , Foxwell Brian , Al-Obaidi Ahmed , Shafi Jamila , Rajakumar Kumar , Kampmann Beate , Andrew Peter W. , Ziegler-Heitbrock Loems , Barer Michael R. , Wilkinson Robert J.
Published: October 2006

Six major lineages ofMycobacterium tuberculosisappear preferentially transmitted amongst distinct ethnic groups. We identified a deletion affectingRv1519in CH, a strain isolated from a large outbreak in Leicester U.K., that coincidentally defines the East African-Indian lineage matching a major ethnic group in this city. In broth media, CH grew less rapidly and was less acidic and H2O2-tolerant than reference sequenced strains (CDC1551 and H37Rv). Nevertheless, CH was not impaired in its ability to grow in human monocyte-derived macrophages. When compared with CDC1551 and H37Rv, CH induced less protective IL-12p40 and more antiinflammatory IL-10 and IL-6 gene transcription and secretion from monocyte-derived macrophages. It thus appears that CH compensates microbiological attenuation by skewing the innate response toward phagocyte deactivation. Complementation ofRv1519, but none of nine additional genes absent from CH compared with the type strain, H37Rv, reversed the capacity of CH to elicit antiinflammatory IL-10 production by macrophages. TheRv1519polymorphism inM. tuberculosisconfers an immune subverting phenotype that contributes to the persistence and outbreak potential of this lineage.
The plasma membrane Na
+
/H
+
antiporter SOS1 interacts with RCD1 and functions in oxidative stress tolerance in
Arabidopsis
Authors: Katiyar-Agarwal Surekha , Zhu Jianhua , Kim Kangmin , Agarwal Manu , Fu Xinmiao , Huang Alex , Zhu Jian-Kang
Published: October 2006

The adverse effects of high salt on plants include Na
+
toxicity and hyperosmotic and oxidative stresses. The plasma membrane-localized Na
+
/H
+
antiporter SOS1 functions in the extrusion of toxic Na
+
from cells and is essential for plant salt tolerance. We report here that, under salt or oxidative stress, SOS1 interacts through its predicted cytoplasmic tail with RCD1, a regulator of oxidative-stress responses. Without stress treatment, RCD1 is localized in the nucleus. Under high salt or oxidative stress, RCD1 is found not only in the nucleus but also in the cytoplasm. Like
rcd1
mutants,
sos1
mutant plants show an altered sensitivity to oxidative stresses. The
rcd1
mutation causes a decrease in salt tolerance and enhances the salt-stress sensitivity of
sos1
mutant plants. Several genes related to oxidative-stress tolerance were found to be regulated by both RCD1 and SOS1. These results reveal a previously uncharacterized function of a plasma membrane Na
+
/H
+
antiporter in oxidative-stress tolerance and shed light on the cross-talk between the ion-homeostasis and oxidative-stress detoxification pathways involved in plant salt tolerance.
Recent progress in understanding hydrophobic interactions
Authors: Meyer Emily E. , Rosenberg Kenneth J. , Israelachvili Jacob
Published: October 2006

We present here a brief review of direct force measurements between hydrophobic surfaces in aqueous solutions. For almost 70 years, researchers have attempted to understand the hydrophobic effect (the low solubility of hydrophobic solutes in water) and the hydrophobic interaction or force (the unusually strong attraction of hydrophobic surfaces and groups in water). After many years of research into how hydrophobic interactions affect the thermodynamic properties of processes such as micelle formation (self-assembly) and protein folding, the results of direct force measurements between macroscopic surfaces began to appear in the 1980s. Reported ranges of the attraction between variously prepared hydrophobic surfaces in water grew from the initially reported value of 80–100 Å to values as large as 3,000 Å. Recent improved surface preparation techniques and the combination of surface force apparatus measurements with atomic force microscopy imaging have made it possible to explain the long-range part of this interaction (at separations >200 Å) that is observed between certain surfaces. We tentatively conclude that only the short-range part of the attraction (<100 Å) represents the true hydrophobic interaction, although a quantitative explanation for this interaction will require additional research. Although our force-measuring technique did not allow collection of reliable data at separations <10 Å, it is clear that some stronger force must act in this regime if the measured interaction energy curve is to extrapolate to the measured adhesion energy as the surface separation approaches zero (i.e., as the surfaces come into molecular contact).
Similarities between heterophilic and homophilic cadherin adhesion
Authors: Prakasam A. K. , Maruthamuthu V. , Leckband D. E.
Published: October 2006

The mechanism that drives the segregation of cells into tissue-specific subpopulations during development is largely attributed to differences in intercellular adhesion. This process requires the cadherin family of calcium-dependent glycoproteins. A widely held view is that protein-level discrimination between different cadherins on cell surfaces drives this sorting process. Despite this postulated molecular selectivity, adhesion selectivity has not been quantitatively verified at the protein level. In this work, molecular force measurements and bead aggregation assays tested whether differences in cadherin bond strengths could account for cell sorting
in vivo
and
in vitro
. Studies were conducted with chicken N-cadherin, canine E-cadherin, and
Xenopus
C-cadherin. Both qualitative bead aggregation and quantitative force measurements show that the cadherins cross-react. Furthermore, heterophilic adhesion is not substantially weaker than homophilic adhesion, and the measured differences in adhesion do not correlate with cell sorting behavior. These results suggest that the basis for cell segregation during morphogenesis does not map exclusively to protein-level differences in cadherin adhesion.
Red blood cells in the metabolism of nitric oxide‐derived peroxynitrite
Authors: Romero Natalia , Denicola Ana , Radi Rafael
Published: October 2006

In this review we have analyzed the reactions of nitric oxide (·NO) with superoxide radical (O2·‐) at the vascular compartment which results in limitation of the bioavailability of ·NO and the formation of peroxynitrite (ONOO‐), a strong oxidant species. The intravascular formation of peroxynitrite can result in oxidative modifications of plasma and vessel wall proteins including the formation of protein‐3‐nitrotyrosine. The role of red blood cells (RBC) and oxyhemoglobin in the metabolism of intravascular peroxynitrite will be discussed. While RBC constitute an important 'sink' of both ·NO and peroxynitrite, redox reactions of these species with oxyhemoglobin may in part contribute to erythrocyte aging. The intravascular formation, reactions and detoxification of peroxynitrite are revealed as important factors controlling vascular dysfunction and degeneration in a variety of pathophysiologically‐relevant conditions.
iubmb Life, 58: 572‐580, 2006
Recovery of Small‐Sized Blood Vessels in Ischemic Bone under Static Magnetic Field
Authors: Xu Shenzhi , Tomita Naohide , Ikeuchi Ken , Ikada Yoshito
Published: October 2006

Effects of static magnetic field (SMF) on the vascularization in bone were evaluated using an ischemic bone model, where rat femoral artery was ligated. Magnetized and unmagnetized samarium–cobalt rods were implanted transcortically into the middle diaphysis of the ischemic femurs. Collateral circulation was evaluated by injection of microspheres into the abdominal aorta at the third week after ligation. It was found that the bone implanted with a magnetized rod showed a larger amount of trapped microspheres than that with an unmagnetized rod at the proximal and the distal region (P < 0.05 proximal region). There were no significant differences at the middle and the distal region. This tendency was similar to that of the bone mineral density in the SMF‐exposed ischemic bone.
Olfactory memory capacity of the cricketGryllus bimaculatus
Authors: Matsumoto Yukihisa , Mizunami Makoto
Published: October 2006

Olfactory learning in insects is a useful model for studying neural mechanisms underlying learning and memory, but memory storage capacity for olfactory learning in insects has not been studied. We investigate whether crickets are capable of simultaneously memorizing seven odour pairs. Fourteen odours were grouped into seven A/B pairs, and crickets in one group were trained to associate A odours with water reward and B odours with saline punishment for all the seven pairs. Crickets in another group were trained with the opposite stimulus arrangement. Crickets in all the groups exhibited significantly greater preference for the odours associated with water reward for all the seven odour pairs. We conclude that crickets are capable of memorizing seven odour pairs at the same time.
On electromagnetics of an isotropic chiral medium moving at constant velocity
Authors: Mackay Tom G , Lakhtakia Akhlesh
Published: October 2006

A medium which is an isotropic chiral medium from the perspective of a co-moving observer is a Faraday chiral medium (FCM) from the perspective of a non-co-moving observer. The Tellegen constitutive relations for this FCM are established. By an extension of the Beltrami field concept, these constitutive relations are exploited to show that plane wave propagation is characterized by four generally independent wavenumbers. This FCM can support negative phase velocity at certain translational velocities and with certain wavevectors, even though the corresponding isotropic chiral medium does not. The constitutive relations and Beltrami-like fields are also used to develop a convenient spectral representation of the dyadic Green functions for the FCM.
Experimental evidence for the role of ions in particle nucleation under atmospheric conditions
Authors: Svensmark Henrik , Pedersen Jens Olaf P , Marsh Nigel D , Enghoff Martin B , Uggerhøj Ulrik I
Published: October 2006

Experimental studies of aerosol nucleation in air, containing trace amounts of ozone, sulphur dioxide and water vapour at concentrations relevant for the Earth's atmosphere, are reported. The production of new aerosol particles is found to be proportional to the negative ion density and yields nucleation rates of the order of 0.1–1 cm
−3
 s
−1
. This suggests that the ions are active in generating an atmospheric reservoir of small thermodynamically stable clusters, which are important for nucleation processes in the atmosphere and ultimately for cloud formation.
Metapopulation extinction risk is increased by environmental stochasticity and assemblage complexity
Authors: Bull James C , Pickup Nicola J , Pickett Brian , Hassell Michael P , Bonsall Michael B
Published: October 2006

Extinction risk is a key area of investigation for contemporary ecologists and conservation biologists. Practical conservation efforts for vulnerable species can be considerably enhanced by thoroughly understanding the ecological processes that interact to determine species persistence or extinction. Theory has highlighted the importance of both extrinsic environmental factors and intrinsic demographic processes. In laboratory microcosms, single-species single-habitat patch experimental designs have been widely used to validate the theoretical prediction that environmental heterogeneity can increase extinction risk. Here, we develop on this theme by testing the effects of fluctuating resource levels in experimental multispecies metapopulations. We compare a three-species host–parasitoid assemblage that exhibits apparent competition to the individual pairwise, host–parasitoid interactions. Existing theory is broadly supported for two-species assemblages: environmental stochasticity reduces trophic interaction persistence time, while metapopulation structure increases persistence time. However, with increasing assemblage complexity, the effects of trophic interactions mask environmental impacts and persistence time is further reduced, regardless of resource renewal regime. We relate our findings to recent theory, highlighting the importance of taking into account both intrinsic and extrinsic factors, over a range of spatial scales, in order to understand resource–consumer dynamics.
Consequences of prenatal androgen exposure for the reproductive performance of female pheasants (
Phasianus colchicus
)
Authors: Rubolini Diego , Martinelli Roberta , von Engelhardt Nikolaus , Romano Maria , Groothuis Ton G.G , Fasola Mauro , Saino Nicola
Published: October 2006

Maternal hormones in vertebrate eggs can mediate important forms of maternal effects. However, the function of hormone transfer to the eggs is still debated, especially because long-term fitness consequences have been little studied. We investigated the effect of prenatal exposure to physiologically elevated yolk testosterone (T) levels on reproduction of female pheasants (
Phasianus colchicus
) in captivity. We found that females hatching from T-injected eggs (T-females) had a lower egg-laying rate than controls, and their eggs were more frequently infertile than those laid by control females. There were no effects of prenatal maternal treatment on egg size and yolk T concentration, but eggs carrying a female embryo laid by T-females had smaller yolks than eggs with a male embryo, while there was no sex difference in yolk size among the eggs laid by control females. Progeny sex ratio was unaffected by maternal treatment. These findings suggest that the transfer of high androgen levels to the eggs by the mother is constrained by complex trade-offs between direct effects on her daughters’ reproduction and by trans-generational differential consequences on male and female descendants.
Grading system of lymphatic invasion according to D2‐40 immunostaining is useful for the prediction of nodal metastasis in squamous cell carcinoma of the uterine cervix
Authors: Urabe A , Matsumoto T , Kimura M , Sonoue H , Kinoshita K
Published: October 2006

Aims To determine the relationship between lymphatic invasion detected by D2‐40 immunostaining and nodal metastasis in squamous cell carcinoma (SCC) of the cervix.

Methods and results Seventy‐five cases of FIGO stage IB to IIB SCC of the cervix, treated by radical hysterectomy and lymph node dissection, were examined. Immunohistochemistry for D2‐40 was performed. Overestimation of lymphatic invasion on conventional histological examination was demonstrated by assessment of D2‐40 immunoreactivity in 22 cases. A significant difference in lymphatic invasion detected by D2‐40 immunostaining was found between the metastatic group (30 cases) and the non‐metastatic group (45 cases) (P < 0.001). A grading system (grade 0–2) of lymphatic invasion according to D2‐40 immunostaining was devised. Subsequently, the frequency of nodal metastasis significantly increased in accordance with the grade of lymphatic invasion (P < 0.001) and in eight cases with grade 2, seven cases (87.5%) had nodal metastasis.

Conclusions In cervical SCC, a grading system for lymphatic invasion according to D2‐40 immunostaining is useful for the prediction of nodal metastasis and grade 2 lymphatic invasion is a strong predictor of nodal metastasis.
Effects of F‐encoded components and F‐pilin domains on the synthesis and membrane insertion of TraA'‐'PhoA fusion proteins
Authors: Paiva William D. , Silverman Philip M.
Published: October 2006

F‐pilin, the 70‐amino‐acid F‐pilus subunit, accumulates in the cell envelope of F+strains in a process that requires interactions between its precursor (the traA gene product) and other host and F‐encoded proteins. Here, we have used a set of (traA‐phoA) genes to explore the effects of different TraA domains on the synthesis and membrane insertion of TraA‐PhoA fusion proteins, particularly in relation to other F‐encoded gene products. The 51‐amino‐acid TraA leader peptide fused directly to alkaline phosphatase was synthesized at comparable rates and incorporated rapidly and efficiently into the inner membrane in F' and F− cells. A second fusion gene encoded the TraA leader peptide and the first 51 amino acids of F‐pilin itself fused to PhoA (TraA'‐'PhoA‐102 polypeptide). Alkaline phosphatase activities and patterns of pulse‐labelled polypeptides indicated that TraA'‐'PhoA‐102 was synthesized at comparable rates in F' and F− cells, but in neither was the TraA'‐'PhoA‐102 polypeptide efficiently processed as a membrane protein. A third gene encoded the entire 121‐amino‐acid TraA polypeptide fused to PhoA (TraA‐'PhoA‐121 polypeptide). About 70% of the pulse‐labelled TraA‐'PhoA‐121 polypeptide was rapidly processed in F'cells, where it accumulated in the cell envelope as active alkaline phosphatase, whereas in F‐ cells, >5% of the pulse‐labelled polypeptide was processed. Additionally, the apparent rate of TraA‐'PhoA‐121 polypeptide synthesis was threefold higher in F'cells. The traQ gene alone could not substitute for F in restoring TraA‐'PhoA‐121 (or wild‐type F‐pilin) accumulation.
Isolation of periplasmic nitrate reductase genes from Rhodobacter sphaeroides DSM 158: structural and functional differences among prokaryotic nitrate reductases
Authors: Reyes Francisca , Roldán M. Dolores , Klipp Werner , Castillo Francisco , Moreno‐Vivián Conrado
Published: October 2006

The prototrophic bacterium Rhodobacter sphaeroides DSM 158 has a periplasmic nitrate reductase which is induced by nitrate and it is not repressed by ammonium or oxygen. In a Tn5 mutant lacking nitrate reductase activity, transposon insertion is localized in a 1.2 kb EcoRI fragment. A 0.6 kb BamHI‐EcoRI segment of this region was used as a probe to isolate, from the wild‐type strain, a 6.8 kb Pstl fragment carrying the putative genes coding for the periplasmic nitrate reductase. In vivo protein expression and DNA sequence analysis reveal the presence in this region of three genes, napABC, probably organized in an operon. These genes are required for nitrate reduction, as deduced by mutational and complementation studies. The napA gene codes for a protein with a high homology to the periplasmic nitrate reductase from Alcali‐genes eutrophus and, to a lesser extent, to other prokaryotic nitrate reductases and molybdenum‐containing enzymes. The napB gene product has two haem c‐binding sites and shows a high homology with the cytochrome c‐type subunit of the periplasmic nitrate reductase from A. eutrophus. NAPA and NAPB proteins appear to be translated with signal peptides of 29 and 24 residues, respectively, indicating that mature proteins are located in the periplasm. The napC gene codes for a 25 kDa protein with a transmembrane sequence of 17 hydrophobic residues. NAPC has four haem c‐binding sites and is homologous to the membrane‐bound c‐type cytochromes encoded by Pseudomonas stutzeri nirT and Escherichia coli torC genes. The phenotypes of defined insertion mutants constructed for each gene also indicate that periplasmic nitrate reductase from R. sphaeroides DSM 158 is a dimeric complex of a 90kDa catalytic subunit (NAPA) and a 15kDa cytochrome c (NAPB), which receives electrons from a membrane‐anchored tetrahaem protein (NAPC), thus allowing electron flow between membrane and periplasm. This nitrate‐reducing system differs from the assimilatory and respiratory bacterial nitrate reductases at the level of cellular localization, regulatory properties, biochemical characteristics and gene organization.
Inducible gene expression mediated by a repressor‐operator system isolated from Lactococcus lactis bacteriophage r1t
Authors: Nauta Arjen , van Sinderen Ouwe , Karsens Harma , Smit Egbert , Venema Gerard , Kok Jan
Published: October 2006

A regulatory region of the temperate Lactococcus lactis bacteriophage r1t chromosome has been cloned and characterized. It encompasses the two divergently oriented genes rro, encoding the phage repressor, and tec. Both genes, of which the transcription start sites have been mapped, are preceded by consensus‐35 and‐10 promoter sequences. The region contains three 21 bp direct repeats with internal dyad symmetry which probably act as operators. Two of these repeats partially overlap the two promoter sequences. The distant third repeat is located within the tec coding sequence. Gel mobility shift assays demonstrated that Rro specifically binds to this sequence. To study possible transcriptional regulation of the region, a lacZ translational fusion with an open reading frame following tec was constructed. Under conditions that favour the lysogenic life cycle of r1t, β‐galactosidase activity was very low. Expression of the lacZ fusion could be induced 70‐fold by the addition of mitomycin C at a concentration which promotes the switch of r1t from the lysogenic to the lytic life cycle. In non‐induced cells, promoter activity was repressed by Rro, as a frameshift mutation in rro resulted in constitutive expression of the lacZ gene fusion.
MicroCorrespondence
Authors: Bachellier S. , Hofnung M.
Published: October 2006

The members of the so‐called BEE95 family of dispersed enterobacterial intergenic elements are already known under the name RSA sequences
Structure, function and controls in microbial division
Authors: Vicente Miguel , Errington Jeffery
Published: October 2006

Several crucial genes required for bacterial division lie close together in a region called the dcw cluster. Within the cluster, gene expression is subject to complex transcriptional regulation, which serves to adjust the cell cycle in response to growth rate. The pivotally important FtsZ protein, which is needed to initiate division, is now known to interact with many other components of the division machinery in Escherichia coli.Some biochemical properties of FtsZ, and of another division protein called FtsA, suggest that they are similar to the eukaryotic proteins tubulin and actin respectively. Cell division needs to be closely co‐ordinated with chromosome partitioning. The mechanism of partitioning is poorly understood, though several genes involved in this process, including several muk genes, have been identified. The min genes may participate in both septum positioning and chromosome partitioning. Coupled transcription and translation of membrane‐associated proteins might also be important for partitioning. In the event of a failure in the normal partitioning process, Bacillus subtilis, at least, has a mechanism for removing a bisected nucleoid from the division septum.
Functional analysis of the Enterococcus faecalis plasmid pAD1‐encoded stability determinant par
Authors: Weaver Keith E. , Jensen Kristi D. , Colwell Amy , Sriram Saileela
Published: October 2006

The molecular organization and functional characteristics of the pAD1 replicon‐encoded par stability determinant were examined, par encodes two convergently transcribed RNAs of 210 and 65 nucleotides designated RNA I and RNA II, respectively. The sequence of RNA II is largely complementary to RNA I, suggesting that RNA II could regulate RNA I function as an anti‐sense RNA. Results of functional studies are consistent with a role for par as a post‐segregational killing system, the first to be identified in Gram‐positive bacteria, with RNA I encoding the toxin and RNA II the antidote. These results include: (i) destabilization of par‐containing replicons in the presence of a second complete par or the RNA II coding sequence in the same cell; (ii) par‐dependent stabilization of a highly unstable vector at the expense of host‐cell growth rate; and (iii) protection of cells from the toxic effects of overexpression of RNA I by RNA II supplied in trans.
Identification of a Salmonella virulence gene required for formation of filamentous structures containing lysosomal membrane glycoproteins within epithelial cells
Authors: Stein Murry A. , Leung Ka Yin , Zwick Michael , Portillo Francisco Garcia‐del , Finlay B. Brett
Published: October 2006

summary

Salmonella species are facultative intracellular pathogens that invade epithelial cells and reside within lysosomal membrane glycoprotein (Igp)‐containing vacuoles. Coincident with the onset of bacterial replication inside these vacuoles, Salmonella induce the formation of stable Igp‐containing filamentous structures that connect with the Salmonella‐containing vacuoles. Salmonella typhimurium SL1344::Tn 10dCm mutant strains unable to induce these structures were isolated. All contained insertions within a novel Salmonella induced filament gene A (sifA). sifA is present only in Salmonella species and encodes a protein with a predicted molecular mass of 38kDa and an apparent molecular mass of 35kDa. sifA is flanked by ∼300 base pairs, and sifA and its flanking DNA show no homology to sequences in DNA databases. sifA is located within the potABCD operon, a housekeeping locus involved in periplasmic transport of polyamines. Fourteen‐base‐pair direct repeats mark the probable site of integration of sifA and its flanking DNA at the 3 end of potB. sifA and its flanking DNA have a significantly reduced G+C content (41%) when compared with the potABCD operon (51%) and the Salmonella genome (52–54%). Deletion mutant strains
Induction of haemolytic activity in Escherichia coli by the slyA gene product
Authors: Oscarsson Jan , Mizunoe Yoshimitsu , Uhlin Bernt Eric , Haydon David J.
Published: October 2006

The Salmonella typhimurium protein SlyAST, originally described as a cytolysin, shows sequence similarities to several known bacterial regulatory proteins. A homologue to the slyASt gene has been localised to min 37 of the Eschericia coli K‐12 chromosome and has been designated slyAEC When introduced in trans on a plasmid, the slyAEC gene conferred a haemolytic phenotype on wild‐type but not clyA‐knockout strains of E. coli K‐12. The clyA gene encodes a novel haemolysin that is not expressed by wild‐type E. coli under tested laboratory conditions. Western and Northern blot analyses, and DNA‐band‐shift assays support a model whereby the SlyAEC protein activates clyA expression by binding to the clyA promoter region, thereby supporting the sequence similarity data in suggesting that SlyAST is a haemolysin activator rather than being a haemolysin per se.
Altering the level and regulation of the major sigma subunit of RNA polymerase affects gene expression and development in Bacillus subtilis
Authors: Hicks Karen A. , Grossman Alan D.
Published: October 2006

In Bacillus subtilis, the major sigma factor, sigma‐A (rpoD), and the minor sigma factor, sigma‐H (spo0H), are present during growth and are required for the initiation of sporulation. Our experiments indicate that sigma‐A and sigma‐H compete for binding to core RNA polymerase. We used a fusion of rpoD to the Lacl‐repressible IPTG‐inducible promoter, Pspac, to vary the levels of sigma‐A in the cell. Increasing the amount of sigma‐A caused a decrease in expression of genes controlled by sigma‐H, and a delay in the production of heat‐resistant spores. Decreasing the amount of sigma‐A, in a strain deleted for the chromosomal rpoD, caused an increase in expression of genes controlled by sigma‐H. As rpoD itself is controlled by at least two promoters recognized by RNA polymerase that contains sigma‐H, the effect of sigma‐A levels on expression of sigma‐H‐controlled promoters represents a feedback mechanism that might contribute to maintaining appropriate levels of sigma‐A. While the level of sigma‐A was important for efficient sporulation, our results indicate that the normal transcriptional control of rpoD, in the context of the rpoD operon and the numerous promoters in that operon, is not required for efficient sporulation or germination, provided that the sigma‐A level from a heterologous promoter is comparable to that in wild‐type cells.
Genetic footprint of the ToxR‐binding site in the promoter for cholera toxin
Authors: Pfau James D. , Taylor Ronald K.
Published: October 2006

The transmembrane DNA‐binding protein, ToxR, of Vibrio cholerae is a global transcriptional regulator of virulence gene expression. ToxR has been shown to interact with promoter regions upstream of both the ctxAB operon encoding cholera toxin, and the regulatory gene toxT. Deletion analysis has shown that a repeated sequence, TTTTGAT, is required for ToxR binding and activation of the ctxAB promoter. However, this sequence is not found upstream of the toxT promoter. Genetic selections using P22 challenge phages were used to define sites within the promoter for ctxAB which are critical for ToxR‐DNA interactions. Single‐base‐pair changes and deletion mutations that impair ToxR binding cluster within two regions: ‐57 to ‐69 within two of three tandem TTTTGAT sequences; and from ‐39 to ‐47, between the repeat sequences; and the ‐35 region of the promoter. ToxR does not bind to a synthetic target that has three tandem repeats which lack a flanking upstream and downstream sequence. These results suggest that the ToxR‐binding site lies immediately upstream of the ‐35 position of the ctx promoter, and that the affinity of ToxR binding to this site is influenced by the repeat sequences.
Phage presentation
Authors: Hill H. Rachael , Stockley Peter G.
Published: October 2006

There has recently been great interest in the use of the filamentous bacteriophage fd as a vehicle for the display of peptides and proteins. Phage libraries displaying random peptides up to 38 amino acids in length can be used (i) to select for ligands able to bind specific target molecules; (ii) to mimic non‐proteinaceous ligands; and (iii) as a tool to map epitopes recognized by antibodies. The display of proteins or their functional domains provides a system for the analysis of structure‐function relationships, and the potential to generate proteins with altered binding characteristics or novel catalytic properties. The display of short immunogenic determinants on fusion phage may provide a basis for the development of novel peptide vaccines, whilst the expression of libraries of antibody fragments may provide a method to by‐pass hybridoma technology in the generation of monoclonal antibodies.