bluuebunny/crossref_metadata_2025 huggingface dataset:
Spectroscopic characterization of laser-induced tin plasma
Authors: Harilal S. S. , O’Shay Beau , Tillack Mark. S. , Mathew Manoj V.
Published: July 2005

Optical emission spectroscopic studies have been carried out on a tin plasma generated using 1064-nm, 8-ns pulses from a Nd:yttrium aluminum garnet laser. Temperature and density were estimated from the analysis of spectral data. The temperature measurements have been performed by Boltzmann diagram method using singly ionized Sn lines, while density measurements were made using the Stark broadening method. An initial temperature of 3.2 eV and density of 7.7×1017cm−3 were measured. Temporal and spatial behaviors of electron temperature and density in the laser-generated tin plasma have been analyzed. Time evolutions of density and temperature are found to decay adiabatically at early times. The spatial variation of density shows approximately 1∕z dependence. The time-integrated temperature exhibits an appreciable rise at distances greater than 7 mm. This may be caused by the deviation from local thermodynamic equilibrium at larger distances from the target surface.
Temperature of ion cyclotron heated impurity ions in fusion plasmas
Authors: Pilipenko D. , Tokar M. Z. , Pavlenko I. , Weyssow B.
Published: July 2005

The temperature of impurity ions in fusion plasmas is normally assumed to be the same as that of background particles. This assumption can be, however, violated for selective impurity species intensively heated by radio frequency waves or in reactor plasmas of low collisionality. An approach to compute the impurity temperature under such conditions is elaborated. It is based on the construction of a hierarchy of approximate solutions to the impurity heat balance equation and takes into account that the density and, thus, the heat conductivity of heated ion species can change by many orders of magnitude with the position in the plasma. Coupled with the wave propagation code, the particle and heat balances for impurity and main plasma species provide a self-consistent approach to model the ion cyclotron resonance heating scenario.
Asymmetry-induced particle drift in a rotating flow
Authors: Bluemink J. J. , van Nierop E. A. , Luther S. , Deen N. G. , Magnaudet J. , Prosperetti A. , Lohse D.
Published: July 2005

We report on an intriguing phenomenon taking place in a liquid rotating around a fixed horizontal axis. Under suitable conditions, bubbles and particles are observed to drift along the axis of rotation maintaining a constant distance from it and a constant angle of elevation above the horizontal. Absence of fore-aft symmetry of the bubble or particle shape is a prerequisite for this phenomenon. For bubbles, this requires a volume sufficiently large for surface-tension effects to be small and large deformations to be possible. Particle image velocimetry and flow visualization suggest that the wake does not play a role. The dependence on bubble radius, particle shape, liquid viscosity, and speed of rotation is investigated.
Fabrication of spatial transient-density structures as high-field plasma photonic devices
Authors: Pai C.-H. , Huang S.-Y. , Kuo C.-C. , Lin M.-W. , Wang J. , Chen S.-Y. , Lee C.-H. , Lin J.-Y.
Published: July 2005

Fabrication of periodic transient-density structures in a gas jet with a boundary scale length approaching 10μm was demonstrated. This was achieved by passing an ultrashort high-intensity laser pulse through a patterned mask and imaging the mask onto the target plane. Gas/plasma density at the laser-irradiated regions drops as a result of hydrodynamic expansion following ionization and heating by the laser pulse. The fabrication of gas/plasma density structures with such a scheme is an essential step in the development of plasma photonic devices for applications in high-field physics.
Study of the current stressing in nanomanipulated three-dimensional carbon nanotube structures
Authors: Cox D. C. , Forrest R. D. , Smith P. R. , Stolojan V. , Silva S. R. P.
Published: July 2005

We report the fabrication of free-standing carbon nanotube structures. The welding of individual carbon nanotubes to other nanotubes and metal substrates has been performed, on a selective basis, to produce joints of both good electrical conductivity and mechanical integrity, without the need for a joining material. As a result of this unique process, we study the damage to the microstructure of the nanotube as a function of current. When the current densities are in excess of 2×106A∕cm2, particular care must be taken with regard to the quality of the nanotube and the heat dissipation. This is crucial for the use and application of nanotubes in any future device structure for it gives the upper limits to the “average” current density calculations. This process now allows for the fabrication of bespoke carbon nanotube devices for the prototyping of device performance.
Low-dimensional phonon specific heat of titanium dioxide nanotubes
Authors: Dames C. , Poudel B. , Wang W. Z. , Huang J. Y. , Ren Z. F. , Sun Y. , Oh J. I. , Opeil C. , Naughton M. J. , Chen G.
Published: July 2005

The specific heat of multiwalled titanium dioxide (anatase phase) nanotubes has been measured between 1.5 and 95K. Bulk anatase and rutile were also measured. The nanotube specific heat approaches that of bulk anatase at high temperatures. Below about 50K the nanotube specific heat begins to show large enhancements compared to bulk. Using an isotropic elastic continuum model, this can be understood qualitatively as a transition to low-dimensional behavior. Below about 3K there is a second transition and the nanotube specific heat becomes nearly constant, exceeding bulk anatase by an order of magnitude or more at 1.5K.
A 1 bit binary-decision-diagram adder circuit using single-electron transistors made by selective-area metalorganic vapor-phase epitaxy
Authors: Miyoshi Yoshihito , Nakajima Fumito , Motohisa Junichi , Fukui Takashi
Published: July 2005

We demonstrate single-electron operation of a 1 bit adder circuit using GaAs single-electron tunneling transistors (SETs). GaAs dot and wire coupled structures for the fabrication of SETs were grown by a selective-area metalorganic vapor-phase epitaxy technique. The logic circuit was realized based on a binary decision diagram architecture using Coulomb blockade (CB) in GaAs dots and switching operations were achieved in a single-electron mode because of the CB effects. Through this architecture, a 1 bit adder circuit was realized with three SETs, two of which were for AND logic and one with two input gates for exclusive OR (XOR). Both AND and XOR operations were demonstrated at 1.9 K, which indicated successful fabrication of the 1 bit adder.
Variable holographic femtosecond laser processing by use of a spatial light modulator
Authors: Hayasaki Yoshio , Sugimoto Takashi , Takita Akihiro , Nishida Nobuo
Published: July 2005

We propose a holographic femtosecond laser processing system capable of parallel, arbitrary, and variable patterning. These features are achieved by introducing a spatial light modulator displaying a hologram into the femtosecond laser processing system. We demonstrate the variable parallel processing of a glass sample.
Polyfluorene distributed feedback lasers operating in the green-yellow spectral region
Authors: Xia R. , Heliotis G. , Stavrinou P. N. , Bradley D. D. C.
Published: July 2005

We report solid-state, optically pumped poly(9,9-dioctylfluorene-co-benzothiadiazole) (F8BT), distributed feedback lasers that operate in the green-yellow spectral region, previously unaddressed with conjugated polymer gain media. The lasers were fabricated by spin coating F8BT (the gain medium) onto one-dimensional gratings patterned in silica substrates. The emission wavelength could be selected to lie within the range from 558 to 591 nm by controlling the F8BT film thickness and grating periodicity. The minimum lasing threshold of 6.5 nJ per pump pulse (10 ns, 10 Hz, 450 nm) was achieved for a 350 nm spatial period grating with a 180 nm thickness F8BT film. The corresponding emission wavelength was 573 nm and the laser slope efficiency was a relatively high 3%.
Element-selective vertical height determination for an organic monolayer by a scanned-energy photoelectron-yield soft x-ray standing wave technique
Authors: Kondoh H. , Yokota R. , Amemiya K. , Shimada T. , Nakai I. , Nagasaka M. , Ohta T. , Nakamura T. , Takenaka H.
Published: July 2005

A photoelectron-yield soft x-ray standing wave (SW) technique with the scanned-energy mode has been applied to the vertical height determination of the atoms of specific elements involved in an organic monolayer prepared by the Langmuir–Blodgett method on a W∕C superlattice substrate (d=30.9Å) that serves as a SW generator. The vertical positions of two different-element atoms were determined from the SW profiles. This kind of information is complementary to the molecular-orientation estimation by the polarized x-ray absorption spectroscopy and the combination of these techniques will be a powerful tool to understand the structures of organic monolayers.
Atomically straight steps on vicinal Si(111) surfaces prepared by step-parallel current in the kink-up direction
Authors: Yoshida S. , Sekiguchi T. , Itoh K. M.
Published: July 2005

We demonstrate that annealing of a vicinal Si(111) surface at about 800°C with a direct current in the direction that ascends the kinks enhances the formation of atomically straight step edges over micrometer lengths, while annealing with a current in the opposite direction does not. Every straight step edge has the same atomic configuration U(2, 0), which is useful as a template for the formation of a variety of nanostructures. A phenomenological model based on electromigration of charged mobile atoms explains the observed current-polarity dependent behavior.
Influence of Mg content on the band alignment at CdS∕(Zn,Mg)O interfaces
Authors: Rao G. Venkata , Säuberlich F. , Klein A.
Published: July 2005

In this investigation, we studied electronic properties of the CdS∕Zn1−xMgxO (x=0,0.15) interface using photoelectron spectroscopy. ZnO and (Zn,Mg)O films were deposited by magnetron sputtering from ceramic targets on thermally evaporated CdS. Valence-band offsets of ΔEV=1.2±0.1eV are determined for both interfaces. The gap difference of 0.3eV between ZnO and Zn0.85Mg0.15O is therefore fully accommodated by a different conduction-band energy, which should be well suited for modulation doping in ZnO∕(Zn,Mg)O heterostructures.
Strong polarization-dependent photoluminescence from silicon nanowire fibers
Authors: Ma D. D. D. , Lee S. T. , Shinar J.
Published: July 2005

Fibers of highly oriented Si nanowires (SiNWs) were formed by drawing from a condensed SiNW suspension. The SiNW fiber, excited at 514.5nm, produces a strong photoluminescence (PL) at room temperature. The PL spectrum shows three bands at 565–580, 605–640, and 680–690nm, respectively, which are consistent with the PL of porous silicon. The relative intensity of these bands and the integrated intensity of the PL vary with the angle θ between the electric field of the polarized laser excitation and the fiber axis. The dependence on θ is attributed to the combined effects of the one-dimensional shape of the SiNW and the large dielectric contrast between the SiNW and the ambient.
Electron spin injection into GaAs from ferromagnetic contacts in remanence
Authors: Gerhardt N. C. , Hövel S. , Brenner C. , Hofmann M. R. , Lo F.-Y. , Reuter D. , Wieck A. D. , Schuster E. , Keune W. , Westerholt K.
Published: July 2005

We demonstrate electrical spin injection into a (GaIn)As∕GaAs light-emitting diode from the remanent state of ferromagnetic contacts in perpendicular geometry. Using a Fe∕Tb multilayer structure with perpendicular magnetic anisotropy and a reverse-biased Schottky contact, we achieve a circular polarization degree of the emitted light of 0.75% at 90K.
Superconducting metamaterials
Authors: Ricci Michael , Orloff Nathan , Anlage Steven M.
Published: July 2005

Evanescent wave amplification has been predicted under the ideal condition that the index of refraction, n=−1+i0 precisely, but is difficult to observe in practice because current metamaterials suffer from high losses. We present experimental results on a metamaterial that employs superconducting Nb metals and low-loss dielectric materials. Results include transmission data on a wire, split-ring resonator, and a combination medium at temperatures between 4.2 and 297K. Evidence of negative effective permittivity, permeability, and a negative effective index passband are seen in the superconducting state between 50MHz and 18GHz. We find a dielectric loss of εeff,2=2.6×10−3 in a superconducting wire array at 10.75GHz.
Free-standing epitaxial La1−x(Sr,Ca)xMnO3 membrane on Si for uncooled infrared microbolometer
Authors: Kim J.-H. , Grishin A. M.
Published: July 2005

Ar ion beam etching and inductively coupled SF6 and C4F8 plasma-etching processes have been employed to fabricate free standing membrane from the heteroepitaxial La1−x(Sr,Ca)xMnO3(50nm)∕Bi4Ti3O12(100nm)∕CeO2(40nm)∕YSZ(30nm) film structure pulsed laser deposited on Si(001) wafer. We demonstrate feasibility to use epitaxial colossal magnetoresistive manganite film as thermally isolated self-supporting membrane for uncooled infrared microbolometer applications.
Reversible blue light emission from self-assembled silica nanocords
Authors: Hao Yufeng , Meng Guowen , Ye Changhui , Zhang Lide
Published: July 2005

Self-assembled silica nanocords were synthesized through a vapor-solid process without the assistance of catalyst. The rope-like nanostructures were formed by splitting and connecting of lots of amorphous silica nanowires. Appropriate water vapor partial pressure and reaction temperature play critical roles in determining the morphologies. Blue light emission of these nanocords can dramatically be strengthened and weakened in the process of alternative dry and humid treatments. We propose that hydroxyl groups and adsorbed–desorbed ambient water on the nanocords surface are responsible for the reversible blue light emission behavior through analyzing photoluminescence and infrared spectra. Silica nanocords with such blue light emission may be used as effective optoelectronic devices and optical signal humid sensors.
Super-Poissonian shot noise in the resonant tunneling due to coupling with a localized level
Authors: Djuric Ivana , Dong Bing , Cui H. L.
Published: July 2005

We report our studies of the shot noise spectrum in tunneling through an interacting quantum dot when an additional single-level quantum dot without tunnel coupling to leads is coherently side connected to it. We show that the zero-frequency shot noise could reach a super-Poissonian value for appropriate ratios between dot-dot hoppings and dot-lead couplings, but the current is independent on the hopping. Moreover, the frequency spectrum of shot noise shows an obvious peak at the Rabi frequency, which is controllable by tuning the dot-lead couplings.
Efficient continuous-wave holey fiber Raman laser
Authors: Travers J. C. , Popov S. V. , Taylor J. R.
Published: July 2005

A continuous wave Raman laser, with only 100m of holey fiber as the Raman gain medium, is reported in a linear cavity all-fiber configuration. Slope efficiencies of 29% with a threshold of 2.7W and 77% with a threshold of 3.7W were achieved with a maximum output power of 3.6W at 1.12μm. The estimated holey fiber Raman gain coefficient of ∼17W−1km−1 is over 40 times larger than that of a standard telecommunication fiber.
Memory effect of Al-rich AlN films synthesized with rf magnetron sputtering
Authors: Liu Y. , Chen T. P. , Zhao P. , Zhang S. , Fung S. , Fu Y. Q.
Published: July 2005

Al-rich AlN thin film, which is deposited onto n-type Si substrate by radio frequency sputtering of Al target in an argon and N2 gas mixture, can exhibit a large memory effect as a result of charge trapping in the Al nanoparticles/nanoclusters embedded in the AlN matrix. For the metal-insulator-semiconductor structure with a 60nm Al-rich AlN thin film, a voltage of −15V applied to the metal electrode for 10−6s causes a flatband voltage shift of ∼1.5V. Both electron trapping and hole trapping are possible, depending on the polarity of the applied voltage. In addition, whether the electron trapping or the hole trapping is the dominant process also depends on the charging time and the magnitude of the voltage. The Al-rich AlN thin films provide the possibility of memory applications with low cost.
Synthesis and Characterization of p-t-Butyl Calix[4]crown-4 and its Double Calix[4]arene Dimer
Authors: Asfari Zouhair , Thuéry Pierre , Nierlich Martine , Vicens Jacques
Published: July 2005

The preparation, separation, characterization and crystal structure
determinations of the 1+1 and 2+2 condensation products,
p-t-butyl calix[4]crown-4 (1) and its dimer
double calix[4]arene double crown-4 (2), resulting from the reaction
of p-t-butylcalix[4]arene with triethylene
glycol ditosylate in the presence of a base are reported.
New Macrocyclic Ligands. VIII Di- and Tri-linked Macrocyclic Systems Incorporating N2O2-Donor Atoms
Authors: Atkinson Ian M. , Boghai Davar M. , Lindoy Leonard F. , Ghanbari Bahram , Meehan George V. , Saini Vinod
Published: July 2005

The synthesis and characterization of new lipophilic di- and tri-linked
O2N2-donor macrocycles is
reported. The synthesis of the dilinked species involved the initial
alkylation of one secondary nitrogen of the parent 15-membered,
O2N2-donor macrocycle (1) with
2-bromoethanol or with ethylene oxide to yield (2), followed by protection of
the appended alcohol group by reaction with t-butyldiphenylsilyl chloride to
give (3). Two such moieties were then bridged via a diacylation reaction with
ClCO(CH2)8COCl to yield the
corresponding diamide product (4). Deprotection of the alcohol functions
followed by reduction of the both amide linkages resulted in formation of
theN,N′-alkyl-linked species
(5) incorporating two pendant hydroxyethyl groups. This product was then
converted [via the corresponding dichloro derivative (6)] into the
diether (7) by condensation with 4-t-butylphenol.
By use of analogous chemistry, the trilinked trismacrocycle species (12),
based on a phloroglucinol core, has also been synthesized. An aim of the
present study was thus the preparation of new ‘linked’ macrocyclic
systems that might be expected to show higher lipophilicity than their
corresponding single-ring systems. These were designed for future use as
ionophores in metal ion membrane transport (and solvent extraction)
experiments.
A uniquely preserved Ediacaran fossil with direct evidence for a quilted bodyplan
Authors: Xiao Shuhai , Shen Bing , Zhou Chuanming , Xie Guwei , Yuan Xunlai
Published: July 2005

Ediacara fossils are among the oldest known macroscopic and complex life forms. Their bodyplan, ecology, and phylogenetic affinities have been controversial. On the basis of taphonomic observations, Seilacher [Seilacher, A. (1989)Lethaia22, 229–239] proposed that the core elements of the Ediacara biota, the vendobionts, were constructed with serially or fractally arranged quilts or tube-like units. However, anatomy of quilt walls has been rarely reported, because most Ediacara fossils are preserved as casts and molds in siliciclastic rocks with inadequate morphological resolution. Here, we report an Ediacara form, uniquely preservedin situand in three dimensions with its organic walls cast by early diagenetic calcite, from bituminous limestone of the 551- to 542-mega-annum Dengying Formation of South China. Despite diagenetic tampering, serial sections show that the Dengying form consists of biserially arranged, tube-like quilts, each with two vertical side walls, a floor, a roof, and an open distal end. Three-dimensional morphological complexity of the Dengying form excludes a microbial interpretation but is broadly consistent with vendobionts. Unlike classic frondose vendobiontssensuSeilacher, however, the Dengying form probably lacked a smooth margin and had distally open quilts. It probably lived procumbently at or near the water–sediment interface and shows evidence for substrate utilization. Despite its uncertain phylogeny, ontogeny, and functional biology, the Dengying form adds to Ediacaran biodiversity, places key constraints on the ecology and extinction of Ediacara organisms, and points to the need to explore an alternative taphonomic window for Ediacara biology.
An N-glucosylated peptide detecting disease-specific autoantibodies, biomarkers of multiple sclerosis
Authors: Lolli Francesco , Mulinacci Barbara , Carotenuto Alfonso , Bonetti Bruno , Sabatino Giuseppina , Mazzanti Benedetta , D'Ursi Anna Maria , Novellino Ettore , Pazzagli Marta , Lovato Laura , Alcaro Maria C. , Peroni Elisa , Pozo-Carrero Maria C. , Nuti Francesca , Battistini Luca , Borsellino Giovanna , Chelli Mario , Rovero Paolo , Papini Anna Maria
Published: July 2005

Multiple sclerosis (MS) is a complex disease that seems to depend on several pathophysiological processes. Because of its varied clinical presentation, natural history, and response to therapeutic interventions, MS can be considered to be a group of diseases that have not been yet characterized, thus resulting in difficult evaluation of prognosis. In the last few years, the role of autoAbs in MS has been reevaluated, and, therefore, their identification as specific biomarkers became a relevant target. In this paper, we demonstrate that an aberrant
N
-glucosylation is a fundamental determinant of autoAb recognition in MS. Thus, we developed CSF114(Glc), an antigenic probe accurately measuring IgM autoAbs in the sera of a patient population, as disease biomarker. The relevance of CSF114(Glc) is demonstrated by its clinical application and correlation with disease activity and prognosis. In fact, CSF114(Glc), a structure-based designed glycopeptide, is able to recognize, by ELISA, the presence of specific IgM autoAbs in the sera of a MS patient population but not in blood donors and other autoimmune conditions. AutoAbs specific for CSF114(Glc) isolated from MS patients recognized myelin and oligodendrocyte antigens by immunohistochemistry but not other nonrelevant tissues. We demonstrate that CSF114(Glc) is a reliable, specific probe in a longitudinal study of untreated MS patients. Development of IgG/IgM anti-CSF114(Glc) Abs paralleled clinical activity and brain lesions positive to MRI. Therefore, a CSF114(Glc)-based immunoassay on sera may have important prognostic value in monitoring MS disease progression guiding optimal therapeutic treatment.
Activation of hypoxia-inducible factors in hyperoxia through prolyl 4-hydroxylase blockade in cells and explants of primate lung
Authors: Asikainen Tiina M. , Schneider Barbara K. , Waleh Nahid S. , Clyman Ronald I. , Ho Wen-Bin , Flippin Lee A. , Günzler Volkmar , White Carl W.
Published: July 2005

Preterm neonates with respiratory distress syndrome (RDS) often develop a chronic form of lung disease called bronchopulmonary dysplasia (BPD), characterized by decreased alveolar and vascular development. Ventilator treatment with supraphysiological O
2
concentrations (hyperoxia) contribute to the development of BPD. Hyperoxia down-regulates and hypoxia up-regulates many angiogenic factors in the developing lung. We investigated whether angiogenic responses could be augmented through enhancement of hypoxia-inducible factors 1α and 2α (HIF-1α and -2α, respectively) via blockade of prolyl hydroxylase domain-containing proteins (HIF-PHDs) in human microvascular endothelial cells from developing and adult lung, in epithelial A549 cells, and in fetal baboon explants in relative or absolute hyperoxia. PHD inhibitor (FG-4095) and positive control dimethyloxaloylglycine (DMOG), selective and nonselective HIF-PHD inhibitors, respectively, enhanced HIF-1α and -2α, vascular endothelial growth factor (VEGF), and platelet-endothelial cell adhesion molecule 1 expression
in vitro
in 95% and 21% O
2
. Furthermore, VEGF receptor fms-like tyrosine kinase 1 (Flt-1) was elevated, whereas kinase insert domain-containing receptor/fetal liver kinase 1 (KDR) was diminished in endothelial, but not epithelial, cells. Intracellular Flt-1 and KDR locations were unchanged by PHD blockade. Like VEGF, FG-4095 and DMOG increased angiogenesis
in vitro
, both in 95% and 21% O
2
, an effect that could be blocked through either Flt-1 or KDR. Notably, FG-4095 was effective in stimulating HIFs and VEGF also in fetal baboon lung explants. FG-4095 or DMOG treatment appeared to stimulate the feedback loop promoting HIF degradation in that PHD-2 and/or -3, but not PHD-1, were enhanced. Through actions characterized above, FG-4095 could have desirable effects in enhancing lung growth in BPD.
CAPRI and RASAL impose different modes of information processing on Ras due to contrasting temporal filtering of Ca2+
Authors: Liu Qing , Walker Simon A. , Gao Dingcheng , Taylor James A. , Dai Yan-Feng , Arkell Rebecca S. , Bootman Martin D. , Roderick H. Llewelyn , Cullen Peter J. , Lockyer Peter J.
Published: July 2005

The versatility of Ca2+ as a second messenger lies in the complex manner in which Ca2+ signals are generated. How information contained within the Ca2+ code is interpreted underlies cell function. Recently, we identified CAPRI and RASAL as related Ca2+-triggered Ras GTPase-activating proteins. RASAL tracks agonist-stimulated Ca2+ oscillations by repetitively associating with the plasma membrane, yet CAPRI displays a long-lasting Ca2+-triggered translocation that is refractory to cytosolic Ca2+ oscillations. CAPRI behavior is Ca2+- and C2 domain–dependent but sustained recruitment is predominantly Ca2+ independent, necessitating integration of Ca2+ by the C2 domains with agonist-evoked plasma membrane interaction sites for the pleckstrin homology domain. Using an assay to monitor Ras activity in real time, we correlate the spatial and temporal translocation of CAPRI with the deactivation of H-Ras. CAPRI seems to low-pass filter the Ca2+ signal, converting different intensities of stimulation into different durations of Ras activity in contrast to the preservation of Ca2+ frequency information by RASAL, suggesting sophisticated modes of Ca2+-regulated Ras deactivation.
Defective thrombus formation in mice lacking coagulation factor XII
Authors: Renné Thomas , Pozgajová Miroslava , Grüner Sabine , Schuh Kai , Pauer Hans-Ulrich , Burfeind Peter , Gailani David , Nieswandt Bernhard
Published: July 2005

Blood coagulation is thought to be initiated by plasma protease factor VIIa in complex with the membrane protein tissue factor. In contrast, coagulation factor XII (FXII)–mediated fibrin formation is not believed to play an important role for coagulation in vivo. We used FXII-deficient mice to study the contributions of FXII to thrombus formation in vivo. Intravital fluorescence microscopy and blood flow measurements in three distinct arterial beds revealed a severe defect in the formation and stabilization of platelet-rich occlusive thrombi. Although FXII-deficient mice do not experience spontaneous or excessive injury-related bleeding, they are protected against collagen- and epinephrine-induced thromboembolism. Infusion of human FXII into FXII-null mice restored injury-induced thrombus formation. These unexpected findings change the long-standing concept that the FXII-induced intrinsic coagulation pathway is not important for clotting in vivo. The results establish FXII as essential for thrombus formation, and identify FXII as a novel target for antithrombotic therapy.
Principal bundles with parabolic structure
Authors: Balaji V. , Biswas I. , Nagaraj D.
Published: July 2005

We define a principal bundle analog of vector bundles with parabolic structure over a normal crossing divisor. Various results on parabolic vector bundles and usual principal bundles are extended to the context of parabolic principal bundles.
Induction of Cytokinesis Is Independent of Precisely Regulated Microtubule Dynamics
Authors: Strickland Laila I. , Donnelly Erin J. , Burgess David R.
Published: July 2005

Astral microtubules (MTs) emanating from the mitotic apparatus (MA) during anaphase are required for stimulation of cytokinesis in eggs. We have used green fluorescent protein-labeled EB1 to observe MT dynamics during mitosis and cytokinesis in normal sea urchin eggs. Analysis of astral MT growth rates during anaphase shows that MTs contact the polar cortex earlier than the equatorial cortex after anaphase onset but that a normal cleavage furrow is not induced until contact with MTs has been achieved throughout the cortex. To assess the role of MT dynamics in initiation of cytokinesis, we used a collection of small molecule drugs to affect dynamics. Hexylene glycol resulted in rapid astral elongation due to decreased MT catastrophe and precocious furrowing. Taxol suppressed MT dynamics but did not inhibit furrow induction when the MA was manipulated toward the cortex. Urethane resulted in short, highly dynamic astral MTs with increased catastrophe that also stimulated furrowing upon being brought into proximity to the cortex. Our findings indicate that astral MT contact with the cortex is necessary for furrow initiation but that the dynamic state of astral MTs does not affect their competency to stimulate furrowing.
Transmural inflammation by interferon‐γ‐producing T cells correlates with outward vascular remodeling and intimal expansion of ascending thoracic aortic aneurysms
Authors: Tang Paul C. Y. , Yakimov Alexander O. , Teesdale Michael A. , Coady Michael A. , Dardik Alan , Elefteriades John A. , Tellides George
Published: July 2005

Arterial pathology manifests as aneurysmal or obstructive disease depending on changes in lumen size due to vascular remodeling (change in vessel external diameter) and/or intimal expansion. Recent clinical and experimental observations in abdominal aortic aneurysms have led to the emerging dogma that Th2‐dominant immune responses result in expansive vascular remodeling and luminal ectasia, whereas Th1 immune responses cause intimal hyperplasia and luminal stenosis. We tested this hypothesis by descriptive analyses of 31 non‐aneurysmal and 29 aneurysmal ascending thoracic aortic specimens. Approximately half the aneurysms were distinguished by transmural inflammation. The remaining aneurysms and all the non‐aneurysmal aortas had a similar leukocytic infiltrate that spared the inner media. Aneurysm tissue had increased expression of the prototypical Th1 cytokine, interferon (IFN)‐γ, and undetectable Th2 cytokines. Specimens with inner media infiltration displayed robust production of IFN‐γ, induction of the IFN‐γ‐inducible chemokines IP‐10 and Mig, and recruitment of lymphocytes bearing their cognate receptor CXCR3. Transmural inflammation and IFN‐γ production were associated with increased aortic external diameter, intimal thickening, preserved vascular smooth muscle cell density, and decreased matrix proteins. Th1, but not Th2, immune responses have a positive correlation with both outward vascular remodeling and intimal expansion of ascending thoracic aortic aneurysms.
Prodynorphin transcripts and proteins differentially expressed and regulated in the adult human brain
Authors: Nikoshkov Andrej , Hurd Yasmin L. , Yakovleva Tatiana , Bazov Igor , Marinova Zoya , Cebers Gvido , Pasikova Natalia , Gharibyan Anna , Terenius Lars , Bakalkin Georgy
Published: July 2005

Transcription from multiple promoters along with alternative mRNA splicing constitutes the basis for cell‐specific gene expression and mRNA and protein diversity. The prodynorphin gene (PDYN) gives rise to prodynorphin (PDYN), precursor to dynorphin opioid peptides that regulate diverse physiological functions and are implicated in various neuropsychiatric disorders. Here, we characterized PDYN transcripts and proteins in the adult human brain and studied PDYN processing and intracellular localization in model cell lines. Seven PDYN mRNAs were identified in the human brain; two of the transcripts, FL1 and FL2, encode the full‐length PDYN. The dominant, FL1 transcript shows high expression in limbic‐related structures such as the nucleus accumbens and amygdala. The second, FL2 transcript is only expressed in few brain structures such as the claustrum and hypothalamus. FL‐PDYN was identified for the first time in the brain as the dominant PDYN protein product. Three novel PDYNs expressed from spliced or truncated PDYN transcripts either lack a central segment but are still processed into dynorphins, or are translated into N‐terminally truncated proteins. One truncated PDYN is located in the cell nucleus, suggesting a novel nonopioid function for this protein. The complexity of PDYN expression and diversity of its protein products may be relevant for diverse levels of plasticity in adaptive responses for the dynorphin system.
3,5‐Diiodo‐L‐thyronine powerfully reduces adiposity in rats by increasing the burning of fats
Authors: Lanni Antonia , Moreno Maria , Lombardi Assunta , De Lange Pieter , Silvestri Elena , Ragni Maurizio , Farina Paola , Baccari Gabriella Chieffi , Fallahi Pupah , Antonelli Alessandro , Goglia Fernando
Published: July 2005

The effect of thyroid hormones on metabolism has long supported their potential as drugs to stimulate fat reduction, but the concomitant induction of a thyrotoxic state has greatly limited their use. Recent evidence suggests that 3,5‐diiodo‐L‐thyronine (T2), a naturally occurring iodothyronine, stimulates metabolic rate via mechanisms involving the mitochondrial apparatus. We examined whether this effect would result in reduced energy storage. Here, we show that T2 administration to rats receiving a high‐fat diet (HFD) reduces both adiposity and body weight gain without inducing thyrotoxicity. Rats receiving HFD + T2 showed (when compared with rats receiving HFD alone) a 13% lower body weight, a 42% higher liver fatty acid oxidation rate, ∼50% less fat mass, a complete disappearance of fat from the liver, and significant reductions in the serum triglyceride and cholesterol levels (−52% and −18%, respectively). Thyroid hormones and thyroid‐stimulating hormone (TSH) serum levels were not influenced by T2 administration. The biochemical mechanism underlying the effects of T2 on liver metabolism involves the carnitine palmitoyl‐transferase system and mitochondrial uncoupling. If the results hold true for humans, pharmacological administration of T2 might serve to counteract the problems associated with overweight, such as accumulation of lipids in liver and serum, without inducing thyrotoxicity. However, the results reported here do not exclude deleterious effects of T2 on a longer time scale as well as do not show that T2 acts in the same way in humans.
Experimental validation of a critical domain size in reaction–diffusion systems with
Escherichia coli
populations
Authors: Perry Nicolas
Published: July 2005

In a one-variable, finite size reaction–diffusion system, the existence of a minimal domain size required for the existence of a non-zero steady state is predicted, provided that the reaction–diffusion variable has a fixed value of zero at the boundaries of the domain (Dirichlet boundary conditions). This type of reaction diffusion model can be applied in population biology, in which the finite domain of the system represents a refuge where individuals can live normally immersed in a desert, or region where the conditions are so unfavourable that individuals cannot live in it. Building on a suggestion by Kenkre and Kuperman, and using non-chemotactic
E. coli
populations and a quasi-one-dimensional experimental design, we were able to find a minimal size (approximately 0.8 cm) for a refuge immersed in a region irradiated with intense UV light. The observed minimal size is in reasonable agreement with theory.
Estimation of effective population sizes from data on genetic markers
Authors: Wang Jinliang
Published: July 2005

The effective population size (Ne) is an important parameter in ecology, evolutionary biology and conservation biology. It is, however, notoriously difficult to estimate, mainly because of the highly stochastic nature of the processes of inbreeding and genetic drift for whichNeis usually defined and measured, and because of the many factors (such as time and spatial scales, systematic forces) confounding such processes. Many methods have been developed in the past three decades to estimate the current, past and ancient effective population sizes using different information extracted from some genetic markers in a sample of individuals. This paper reviews the methodologies proposed for estimatingNefrom genetic data using information on heterozygosity excess, linkage disequilibrium, temporal changes in allele frequency, and pattern and amount of genetic variation within and between populations. For each methodology, I describe mainly the logic and genetic model on which it is based, the data required and information used, the interpretation of the estimate obtained, some results from applications to simulated or empirical datasets and future developments that are needed.
Reclassification of Leptospira parva Hovind-Hougen et al. 1982 as Turneriella parva gen. nov., comb. nov.
Authors: Levett P. N. , Morey R. E. , Galloway R. , Steigerwalt A. G. , Ellis W. A.
Published: July 2005

Analysis of the G+C content, DNA–DNA relatedness to other leptospires and 16S rRNA gene sequence of Leptospira parva showed that this species was not related to other Leptospira species. On the basis of these data, it is proposed that Leptospira parva should be transferred to the genus Turneriella as Turneriella parva gen. nov., comb. nov., with strain HT (=NCTC 11395T=ATCC BAA-1111T) as the type strain.
Photobacterium frigidiphilum sp. nov., a psychrophilic, lipolytic bacterium isolated from deep-sea sediments of Edison Seamount
Authors: Seo Hae Jeom , Bae Seung Seob , Lee Jung-Hyun , Kim Sang-Jin
Published: July 2005

A Gram-negative, motile, rod-shaped, psychrophilic and weakly halophilic bacterial strain, SL13T, was isolated from deep-sea sediments (1450 m depth) of Edison Seamount in the western Pacific Ocean. Optimal growth of SL13Trequires the presence of 1·5 % (w/v) NaCl, a pH of 6·0 and a temperature of 14 °C. The whole-cell fatty acid profile of the isolate includes C16 : 1 and C16 : 0 as major fatty acids and contains C20 : 5ω3. This is consistent with corresponding data forPhotobacterium profundum. The DNA G+C content of strain SL13Tis 43·8 mol%. Phylogenetic analyses of 16S rRNA gene sequences place this bacterium in the ‘Gammaproteobacteria’, within the genusPhotobacterium. Sequence similarity analysis indicates that the closest relatives of strain SL13TarePhotobacterium indicum(99·3 %),P. profundum(98·5 %) andPhotobacterium lipolyticum(98·2 %). The DNA–DNA hybridization levels between the isolate and its closest known phylogenetic relatives,P. indicum,P. profundumandP. lipolyticum, are 27·1, 52·4 and 20·2 %, respectively. Thus strain SL13Trepresents a novel species of the genusPhotobacterium, for which the namePhotobacterium frigidiphilumsp. nov. is proposed. The type strain is SL13T(=KCTC 12384T=JCM 12947T).
Geobacter bemidjiensis sp. nov. and Geobacter psychrophilus sp. nov., two novel Fe(III)-reducing subsurface isolates
Authors: Nevin Kelly P. , Holmes Dawn E. , Woodard Trevor L. , Hinlein Erich S. , Ostendorf David W. , Lovley Derek R.
Published: July 2005

Fe(III)-reducing isolates were recovered from two aquifers in which Fe(III) reduction is known to be important. Strain BemTwas enriched from subsurface sediments collected in Bemidji, MN, USA, near a site where Fe(III) reduction is important in aromatic hydrocarbon degradation. Strains P11, P35Tand P39 were isolated from the groundwater of an aquifer in Plymouth, MA, USA, in which Fe(III) reduction is important because of long-term inputs of acetate as a highway de-icing agent to the subsurface. All four isolates were Gram-negative, slightly curved rods that grew best in freshwater media. Strains P11, P35Tand P39 exhibited motility via means of monotrichous flagella. Analysis of the 16S rRNA andnifDgenes indicated that all four strains areδ-proteobacteria and members of theGeobactercluster of theGeobacteraceae. Differences in phenotypic and phylogenetic characteristics indicated that the four isolates represent two novel species within the genusGeobacter. All of the isolates coupled the oxidation of acetate to the reduction of Fe(III) [iron(III) citrate, amorphous iron(III) oxide, iron(III) pyrophosphate and iron(III) nitrilotriacetate]. All four strains utilized ethanol, lactate, malate, pyruvate and succinate as electron donors and malate and fumarate as electron acceptors. Strain BemTgrew fastest at 30 °C, whereas strains P11, P35Tand P39 grew equally well at 17, 22 and 30 °C. In addition, strains P11, P35Tand P39 were capable of growth at 4 °C. The namesGeobacter bemidjiensissp. nov. (type strain BemT=ATCC BAA-1014T=DSM 16622T=JCM 12645T) andGeobacter psychrophilussp. nov. (strains P11, P35Tand P39; type strain P35T=ATCC BAA-1013T=DSM 16674T=JCM 12644T) are proposed.
Tetragenococcus koreensis sp. nov., a novel rhamnolipid-producing bacterium
Authors: Lee Myungjin , Kim Myung Kyum , Vancanneyt Marc , Swings Jean , Kim Seong-Hye , Kang Myung Suk , Lee Sung-Taik
Published: July 2005

A Gram-positive, non-motile, non-spore-forming coccus (strain JST) was isolated from kimchi (a traditional Korean food) and investigated using a polyphasic taxonomic approach. The 16S rRNA gene sequence similarity between strain JST and its closest relative, Tetragenococcus halophilus IAM 1676T, was 98·1 %. The level of DNA–DNA relatedness between the two strains was 9·7 %. Strain JST had a DNA G+C content of 38·3 % and a cellular fatty acid profile containing 16 : 0, 18 : 1 and cyclo fatty acids. Phylogenetic data and genomic and phenotypic features demonstrated that strain JST represents a novel species, for which the name Tetragenococcus koreensis sp. nov. is proposed. The type strain is JST (=KCTC 3924T=DSM 16501T=LMG 22864T).
Nocardioides oleivorans sp. nov., a novel crude-oil-degrading bacterium
Authors: Schippers Axel , Schumann Peter , Spröer Cathrin
Published: July 2005

The crude-oil-degrading strain BAS3Trepresents a novelNocardioidesspecies, according to a taxonomic study. The 16S rRNA gene sequence of strain BAS3Twas most similar to that ofNocardioides ganghwensis(IMSNU 14028T; 99 % similarity), but the DNA–DNA relatedness to this type strain was only 32 %. The physiological properties of strain BAS3Tdiffer from those ofN. ganghwensis(IMSNU 14028T) and other species ofNocardioides. The diamino acid in the cell-wall peptidoglycan of strain BAS3Tisll-diaminopimelic acid and the major menaquinone is MK-8(H4). The nameNocardioides oleivoranssp. nov. is proposed for the novelNocardioidesspecies, since its type strain, BAS3T(=DSM 16090T=NCIMB 14004T), is able to degrade crude oil.
Aquimonas voraii gen. nov., sp. nov., a novel gammaproteobacterium isolated from a warm spring of Assam, India
Authors: Saha P. , Krishnamurthi S. , Mayilraj S. , Prasad G. S. , Bora T. C. , Chakrabarti T.
Published: July 2005

A bacterial strain designated GPTSA 20T, which was isolated from a warm spring in Assam, India, was characterized by using a polyphasic approach. The cells were Gram-negative, aerobic rods, which could not utilize or produce acid from most of the carbohydrates tested. The predominant fatty acids were C15 : 0iso (25·04 %), C17 : 1isoω9c(19·28 %), C16 : 0iso (17·73 %) and C11 : 0iso 3-OH (9·34 %). The G+C content was 75 mol%. From 16S rRNA gene sequence analysis (1433 nucleotides, continuous stretch), it was confirmed that strain GPTSA 20Tbelonged to the class ‘Gammaproteobacteria’. The closest 16S rRNA gene sequence similarity found (98·2 %) was with an uncultured bacterium clone, NB-03 (accession no. AB117707), from an autotrophic nitrifying biofilm. Among culturable bacteria, the closest sequence similarities were withFulvimonas soli(93·0 %),Silanimonas lenta(92·8 %),Thermomonas hydrothermalis(92·4 %),Frateuria aurantia(91·9 %),Rhodanobacter lindaniclasticus(91·9 %),Thermomonas haemolytica(91·9 %) andPseudoxanthomonas taiwanensis(91·8 %); similarities of less than 91·8 % were obtained with other members of the class ‘Gammaproteobacteria’. From the biochemical, physiological, chemotaxonomic and phylogenetic analysis, it was clear that strain GPTSA 20Twas quite different from members of known genera of the class ‘Gammaproteobacteria’. Therefore, it is proposed that strain GPTSA 20Trepresents a novel species within a new genus, with the nameAquimonas voraiigen. nov., sp. nov. The type strain is GPTSA 20T(=MTCC 6713T=JCM 12896T).
Atopococcus tabaci gen. nov., sp. nov., a novel Gram-positive, catalase-negative, coccus-shaped bacterium isolated from tobacco
Authors: Collins Matthew D. , Wiernik Anna , Falsen Enevold , Lawson Paul A.
Published: July 2005

A novel Gram-positive, aerobic, catalase-negative, coccus-shaped organism originating from tobacco was characterized using phenotypic and molecular taxonomic methods. The organism contained a cell wall murein based on l-lysine (variation A4α, type l-lysine–l-glutamic acid), synthesized long-chain cellular fatty acids of the straight-chain saturated and monounsaturated types (with C16 : 1
ω9, C16 : 0 and C18 : 1
ω9 predominating) and possessed a DNA G+C content of 46 mol%. Based on morphological, biochemical and chemical characteristics, the coccus-shaped organism did not conform to any presently recognized taxon. Comparative 16S rRNA gene sequencing studies confirmed the distinctiveness of the unknown coccus, with the bacterium displaying sequence divergence values of greater than 7 % with other recognized Gram-positive taxa. Treeing analysis reinforced its distinctiveness, with the unidentified organism forming a relatively long subline branching at the periphery of an rRNA gene sequence cluster which encompasses the genera Alloiococcus, Allofustis, Alkalibacterium, Atopostipes, Dolosigranulum and Marinilactibacillus. Based on phenotypic and molecular phylogenetic evidence, it is proposed that the unknown organism from tobacco be classified as a new genus and species, Atopococcus tabaci gen. nov., sp. nov. The type strain of Atopococcus tabaci is CCUG 48253T (=CIP 108502T).
Pseudoalteromonas spongiae sp. nov., a novel member of the γ-Proteobacteria isolated from the sponge Mycale adhaerens in Hong Kong waters
Authors: Lau Stanley C. K. , Tsoi Mandy M. Y. , Li Xiancui , Dobretsov Sergey , Plakhotnikova Yulia , Wong Po-Keung , Qian Pei-Yuan
Published: July 2005

A Gram-negative, non-spore-forming, short rod-shaped bacterium (UST010723-006T) was isolated from the surface of the sponge Mycale adhaerens in Hong Kong waters. Cells of UST010723-006T did not have flagella and were non-motile. Colonies were pale orange in colour, 2–4 mm in diameter, convex with a smooth surface and an entire translucent margin. Gas bubbles were observed in the colonies and also in the agar matrix underneath and adjacent to the colonies. UST010723-006T was heterotrophic, strictly aerobic and required NaCl for growth (2·0–6·0 %). It grew at pH 5·0–10·0 and between 12 and 44 °C. Phylogenetic analysis of the 16S rRNA gene sequence placed UST010723-006T within the genus Pseudoalteromonas of the γ-subclass of the Proteobacteria. The DNA G+C content is 40·6 mol% and the dominant fatty acids were 12 : 0 3-OH, 14 : 0, 15 : 0 iso 2-OH, 16 : 0, 16 : 1ω7, 17 : 1ω8 and 18 : 1ω7 (altogether representing 75·9 % of the total).These data supported the affiliation of UST010723-006T to the genus Pseudoalteromonas. The closest relatives were Pseudoalteromonas luteviolacea, P. phenolica, P. rubra and P. ruthenica with similarity values ranging from 95·4 to 96·8 %. UST010723-006T differed from these closest relatives by 9–19 traits. Molecular evidence, together with phenotypic characteristics, suggests that UST010723-006T constitutes a novel species within the genus Pseudoalteromonas. The name Pseudoalteromonas spongiae sp. nov. is proposed for this bacterium. The type strain is UST010723-006T (=NRRL B-41100T=JCM 12884T).