bluuebunny/crossref_metadata_2025 huggingface dataset:
Nonlinear finite-Larmor-radius drift-kinetic equation
Authors: Vernon Wong H.
Published: November 2005

An efficient method is described for deriving the drift-kinetic equation. A maximal ordering is invoked: the ordering parameter ϵ⪡1 is formally taken to be proportional to m∕e, subject to the proviso that the parallel electric field E‖∼ϵ. Electric drifts can be of the order of particle thermal velocities. The drift-kinetic equation is derived up to second order in ϵ, and is in a form such that the phase-space volume following the particle phase-space trajectories is preserved. The mean density, mean velocity, momentum flow tensor, and the presure tensor are evaluated in terms of the electromagnetic fields and the velocity moments of the drift-kinetic distribution function G¯. The moments of the drift-kinetic equation reproduce the corresponding moments of the Vlasov equation up to order ϵ2. A consistent set of fluid-kinetic equations is formulated, with the fluid-like perpendicular motion described by the perpendicular component of the momentum equation. The drift-kinetic equation describes the parallel motion, and the solution G¯ is required to evaluate the velocity moments necessary to close the set of equations.
An elementary method for calculating orientation-averaged fully differential electron-impact ionization cross sections for molecules
Authors: Gao Junfang , Peacher J. L. , Madison D. H.
Published: November 2005

Currently there are no reliable theoretical approaches for calculating fully differential cross sections (FDCS) for low-energy electron-impact ionization of large molecules. We have recently introduced the distorted-wave impulse approximation as a first step in developing improved theoretical approaches. One significant obstacle to evaluating improved theoretical approaches which require significant computer resources lies in the fact that the existing experimental data require taking averages over all molecular orientations. To circumvent this problem, it has been proposed to approximate the orientation-average by using an orientation-averaged molecular orbital in the calculation of the FDCS. The theoretical justification and expected range of validity for the approximation is given in this paper. Examples are presented for electron-impact ionization of H2 and N2.
Yes, pair correlations alone do determine sedimentation profiles of highly charged colloids
Authors: Belloni Luc
Published: November 2005

Recent analyses of sedimentation profiles in charged colloidal suspensions are examined in view of general, somewhat underestimated, concepts. It is recalled that the standard equation for osmotic pressure equilibrium, which involves pair correlations between colloids only, remains valid in the presence of long-range Coulombic interactions. The entropy of the counterions and the electric field generated by the spatial inhomogeneity are implicitly taken into account in the colloid structure factor through the compressibility equation and local electroneutrality conditions. Limiting the macroscopic analysis to the pure electric-field contribution or, equivalently, to the ideal ionic pressure, corresponds to the incorrect, bare Debye-Hückel approximation for the colloid-colloid correlations. A one-component description with reasonable Derjaguin-Landau-Verwey-Overbeek-type ion-averaged effective pair potential between colloids is sufficient to derive the sedimentation profile of highly charged, weakly screened colloidal suspensions. The macroscopic electric field is directly related to the microscopic electrostatic potential around the colloids.
5
f
→
5
f
transitions of U4+ ions in high-field, octahedral fluoride coordination: The Cs2GeF6:U4+ crystal
Authors: Ordejón Belén , Seijo Luis , Barandiarán Zoila
Published: November 2005

The U–F bond length, totally symmetric vibrational frequency, and 5f2 energy levels of the Cs2GeF6:U4+ crystal are predicted through quantum-chemical calculations on the embedded (UF6)2− cluster. The U4+ ions substitute for much smaller Ge4+ retaining octahedral site symmetry, which is useful to interpret the electronic transitions. The structure of the 5f2 manifold: its energy range, the crystal splitting of the 5f2 levels, their parentage with free-ion levels, and the energy gaps appearing within the manifold, is presented and discussed, which allows to suggest which are the possible 5f2 luminescent levels. The effects of Cl-to-F chemical substitution are discussed by comparison with isostructural Cs2ZrCl6:U4+. The energy range of the 5f2 manifold increases by some 6000cm−1 and all levels shift to higher energies, but the shift is not uniform, so that noticeable changes of order are observed from Cs2ZrCl6:U4+ to Cs2GeF6:U4+. The comparison also reveals that the green-to-blue up-conversion luminescence, which has been experimentally detected and theoretically discussed on Cs2ZrCl6:U4+, is quenched in the fluoride host. The results of the Cs2GeF6:U4+ are used as a high-symmetry model to try to understand why efficient radiative cascade emissions in the visible do not occur for charged U4+ defects in low-symmetry YF3 crystals. The results presented here suggest that theoretical and experimental investigations of 4f∕5f ions doped in octahedral, high-symmetry fluoride crystals may be conducted even when the mismatch of ionic radii between the lanthanide/actinide ions and the substituted cations of the host is considerably large. Investigations of these new materials should reveal interesting spectroscopic features without the difficulties associated with more commonly used low-symmetry fluoride hosts.
Optimized ensemble Monte Carlo simulations of dense Lennard-Jones fluids
Authors: Trebst Simon , Gull Emanuel , Troyer Matthias
Published: November 2005

We apply the recently developed adaptive ensemble optimization technique to simulate dense Lennard-Jones fluids and a particle-solvent model by broad-histogram Monte Carlo techniques. Equilibration of the simulated fluid is improved by sampling an optimized histogram in radial coordinates that shifts statistical weight towards the entropic barriers between the shells of the liquid. Interstitial states in the vicinity of these barriers are identified with unprecedented accuracy by sharp signatures in the quickly converging histogram and measurements of the local diffusivity. The radial distribution function and potential of mean force are calculated to high precision.
Ideal collimation, concentration, and imaging with curved diffractive optical elements
Authors: Bokor Nándor , Davidson Nir
Published: November 2005

In this article the design, optimization and characterization of diffractive optical elements formed on a curved surface are reviewed. For such curved diffractive optical elements not only the phase function, but also the surface shape are free parameters that can be used for optimization, yielding much better performances than both flat diffractive optical elements and reflective/refractive optical elements when operating with quasimonochromatic light. We present a new analytic design approach for the surface shape that ensures uniform collimation of a light source with any angular distribution. We demonstrate the usefulness of this design also for ideal (brightness conserving) collimation and concentration of diffuse light, aberration-free imaging, and optical Fourier transform. We present experimental results that confirm our theoretical analysis.
Soft x-ray submicron imaging detector based on point defects in LiF
Authors: Baldacchini G. , Bollanti S. , Bonfigli F. , Flora F. , Di Lazzaro P. , Lai A. , Marolo T. , Montereali R. M. , Murra D. , Faenov A. , Pikuz T. , Nichelatti E. , Tomassetti G. , Reale A. , Reale L. , Ritucci A. , Limongi T. , Palladino L. , Francucci M. , Martellucci S. , Petrocelli G.
Published: November 2005

The use of lithium fluoride (LiF) crystals and films as imaging detectors for EUV and soft-x-ray radiation is discussed. The EUV or soft-x-ray radiation can generate stable color centers, emitting in the visible spectral range an intense fluorescence from the exposed areas. The high dynamic response of the material to the received dose and the atomic scale of the color centers make this detector extremely interesting for imaging at a spatial resolution which can be much smaller than the light wavelength. Experimental results of contact microscopy imaging of test meshes demonstrate a resolution of the order of 400nm. This high spatial resolution has been obtained in a wide field of view, up to several mm2. Images obtained on different biological samples, as well as an investigation of a soft x-ray laser beam are presented. The behavior of the generated color centers density as a function of the deposited x-ray dose and the advantages of this new diagnostic technique for both coherent and noncoherent EUV sources, compared with CCDs detectors, photographic films, and photoresists are discussed.
Broad-range neutron spectra identification in ultraintense laser interactions with carbon-deuterated plasma
Authors: Youssef A. , Kodama R. , Habara H. , Tanaka K. A. , Sentoku Y. , Tampo M. , Toyama Y.
Published: November 2005

Detailed neutron energy spectra produced from a CD2 target irradiated by a 450fs, 20J, 1053nm laser at an intensity of 3×1018W∕cm2 have been studied. Wide-ranging neutron spectra were observed from two different observation angles 20° and 70° relative to the rear-side target normal. The experiment and numerically calculated spectra, by a three-dimensional Monte Carlo code, indicate that the range of the measured spectra is larger than that produced by the D(d,n)He3 reaction. An interpretation for the measured spectra is introduced by considering the C12(d,n)N13 and D(c12,n)N13 reactions. In addition, the study revealed that the neutron spectra produced by the D–C and C–D reactions can overlap that produced by the D–D reaction, and due to their high cross sections, comparing to the D–D reaction, both of them effectively participate in the neutron yield.
Hydrogen softening and optical transparency in Si-incorporated hydrogenated amorphous carbon films
Authors: Abbas G. A. , Papakonstantinou P. , McLaughlin J. A. , Weijers-Dall T. D. M. , Elliman R. G. , Filik J.
Published: November 2005

High-resolution x-ray reflectivity (XRR) and heavy-ion elastic recoil detection were employed to study the role of hydrogen on the softening behavior observed in Si-incorporated hydrogenated amorphous carbon (Si-a-C:H) films synthesized by plasma-enhanced chemical-vapor deposition using tetramethylsilane (TMS) precursor in C2H2∕Ar plasma. An enhancement of the optical band gap and a massive reduction in the density of the films prepared at high TMS flow rate were revealed, respectively, by spectroscopic ellipsometry and XRR analysis with the development of a double critical angle. A hydrogenation process was responsible for a rise in the density of voids and an associated reduction in the connectivity of the carbon network and the release of its residual stress.
Copper nitride thin film prepared by reactive radio-frequency magnetron sputtering
Authors: Yue G. H. , Yan P. X. , Liu J. Z. , Wang M. X. , Li M. , Yuan X. M.
Published: November 2005

Copper nitride (Cu3N) thin films were deposited on glass substrates by reactive radio-frequency magnetron sputtering of a pure copper target in a nitrogen/argon atmosphere. The deposition rate of the films gradually decreased with increasing nitrogen flow rate. The color of the deposited films was a reddish dark brown. The Cu3N films obtained by this method were strongly textured with crystal direction [100]. The grain size of the polycrystalline films ranged from 16 to 26 nm. The Hall effect of the copper nitride (Cu3N) thin films was investigated. The optical energy gap of the films was obtained from the Hall coefficient and found to vary with the nitrogen content. The surface morphology was studied by scanning electron microscopy and atomic force microscopy. The copper nitride thin films are unstable and decompose into nitrogen and copper upon heat treatment when annealed in vacuum with argon protected at 200 °C for 1 h.
Collisionless expansion of a Gaussian plasma into a vacuum
Authors: Mora P.
Published: November 2005

The collisionless expansion into a vacuum of a one-dimensional Gaussian plasma bunch of size much larger than the Debye length is studied both analytically and with a hybrid Lagrangian code. Both the case of an isothermal plasma fed by an external energy source and the case of an energy-conserving plasma are studied. It is shown that charge-separation effects are responsible for deviations with respect to known self-similar solutions. In particular, wave breaking occurs because the inner parts of the expanding plasma acquire faster velocities than the outer parts. As a result an ion front appears at the edge of the plasma. In the isothermal case the self-similar solution progressively applies to the whole plasma, while the fastest ion’s velocity asymptotically reaches the same values as in the sharp boundary case. In the energy-conserving case the self-similar description only applies to a part of the plasma, which approximately corresponds to the part which was initially quasineutral, and the final velocity of the fastest ions is significantly smaller than in the sharp boundary case.
Processing techniques for deoxyribonucleic acid: Biopolymer for photonics applications
Authors: Heckman Emily M. , Hagen Joshua A. , Yaney Perry P. , Grote James G. , Hopkins F. Kenneth
Published: November 2005

Marine-based deoxyribonucleic acid (DNA), purified from waste products of the Japanese fishing industry, has recently become a material of interest in photonics applications. Using highly purified DNA, unique processing techniques developed specifically to transform the purified DNA into a biopolymer suitable for optical device fabrication are reported.
Highly efficient fluorescence detection in picoliter volume liquid-core waveguides
Authors: Yin Dongliang , Barber John P. , Hawkins Aaron R. , Schmidt Holger
Published: November 2005

We report loss improvement and fluorescence detection in integrated antiresonant reflecting optical waveguides with liquid cores. The minimum waveguide loss is reduced to 0.33∕cm by compensating for thickness variations in the fabrication process. We demonstrate fluorescence detection from as few as 490molecules in a 57pl core using these optimized waveguides. We measure angular fluorescence collection factors as high as 15% per facet in good agreement with theory. This demonstrates the potential of integrated hollow-core waveguides as optical sensors for single-molecule spectroscopy.
Intrinsic limit of dielectric loss in several Ba(B1∕3′B2∕3″)O3 ceramics revealed by the whispering-gallery mode technique
Authors: Kolodiazhnyi T. , Annino G. , Shimada T.
Published: November 2005

Whispering-gallery mode spectroscopy is employed to study the dielectric permittivity and losses of Ba(Mg1∕3Ta2∕3)O3, Ba(Mg1∕3Nb2∕3)O3, and Ba(Co1∕3Nb2∕3)O3 ceramics in the frequency range of 40–90GHz and temperature interval of 5–295K. Below 50GHz, the room-temperature extrinsic dielectric losses in Ba(Mg1∕3Ta2∕3)O3 and Ba(Mg1∕3Nb2∕3)O3 manifest themselves as a sublinear loss factor tanδ(ω) dependence until the intrinsic losses start to dominate the spectra around 50–70GHz. Based on these data we obtain the room-temperature intrinsic limit of dielectric loss of Ba(Mg1∕3Ta2∕3)O3 (Q×f=430±20THz) and of Ba(Mg1∕3Nb2∕3)O3 (Q×f=230±20THz). In the case of Ba(Co1∕3Nb2∕3)O3, the extrinsic losses were predominant throughout the studied frequency range. The possible sources of this loss are discussed.
Wide-band transmittance of one-dimensional photonic crystals carved in Si3N4∕SiO2 channel waveguides
Authors: Gerace D. , Galli M. , Bajoni D. , Guizzetti G. , Andreani L. C. , Riboli F. , Melchiorri M. , Daldosso N. , Pavesi L. , Pucker G. , Cabrini S. , Businaro L. , Di Fabrizio E.
Published: November 2005

Experimental and theoretical investigations of photonic crystal (PhC) structures in silicon nitride/silicon dioxide (Si3N4∕SiO2) vertical waveguiding geometry are reported. One-dimensional patterns, either periodic or with cavity layers, are carved onto the channel waveguides by using focused ion beam lithography. Broadband transmittance spectroscopy in the visible and near-infrared frequency ranges is employed to show photonic band gap behavior up to the fourth order. For structures with a cavity layer, resonant peaks appear in transmittance spectra within the photonic gaps, in agreement with theory. The results show the interest of Si3N4∕SiO2-based PhC waveguides for photonics applications from the infrared up to the visible range.
Extrinsic optical recombination in pentacene single crystals: Evidence of gap states
Authors: He Rui , Chi X. , Pinczuk Aron , Lang D. V. , Ramirez A. P.
Published: November 2005

Two luminescence bands observed in pentacene single crystals with different degrees of purity are identified as due to extrinsic optical emissions. A band at 1.49 eV remains in the crystal with the highest purity. Its redshift of about 0.3 eV from the free exciton optical recombination suggests that the extrinsic transitions could involve gap states recently discovered in pentacene transistors. Absence of resonance Raman scattering when photon energies overlap the extrinsic recombination suggests that the gap states are likely due to impurities. The temperature dependence of luminescence intensities is interpreted by activated decay of excitons to radiative and nonradiative states.
Excellent uniaxial alignment of poly(9,9-dioctylfluorenyl-2,7-diyl) induced by photoaligned polyimide films
Authors: Sakamoto Kenji , Usami Kiyoaki , Uehara Yoichi , Ushioda Sukekatsu
Published: November 2005

We have investigated the alignment of poly (9,9-dioctylfluorenyl-2,7-diyl) (PFO) induced by photoaligned polyimide films. To induce anisotropic orientation of polyimide backbone structures by optical treatment, we used a specially designed polyimide (Azo-PI), which contains azobenzene in the backbone structure. The 30-nm-thick PFO layer, spincoated onto a photoaligned Azo-PI film, was heated to the liquid crystalline phase of PFO, and then cooled down to room temperature at −0.1°C∕min. The thermally treated PFO layer showed a polarization ratio of approximately 30 in photoluminescence. This high polarization ratio has not previously been reported in PFO films formed by other alignment techniques. This result indicates that the photoaligned Azo-PI film has an excellent ability to align liquid crystalline polymers.
Blistering of GaAs by low keV H, D, and He ions
Authors: Giguère Alexandre , Desrosiers Nicholas , Terreault Bernard
Published: November 2005

The thermally activated blistering of the GaAs (100) surface after 5- and 10keV H, D, and He ion implantations was investigated. A large isotope effect is observed as the critical blistering fluences are two to three times higher for D than for H ions. Blistering and exfoliation are also obtained for very low He ion fluence, contrary to Si which is impervious to He blistering in the same conditions. The exfoliated crater depth depends strongly on the He fluence, varying, at 10keV, from 75±10nm (for 1.6×1016He∕cm2), consistent with the ion projected range determined by computation, to a saturation value of 155±10nm for doses >4×1016He∕cm2. Our results suggest that the fracture leading to cleavage is triggered at a local He concentration of about 2at.%, where dislocations and nanocavities are created.
Scanning near-field optical microscopy utilizing silicon nitride probe photoluminescence
Authors: Lulevich Valentin , Ducker William A.
Published: November 2005

We describe a simple method for performing high-resolution scanning near-field optical microscopy (SNOM). A commercial Si3N4 tip is illuminated by an intense light source, which causes the tip to emit redshifted (inelastically scattered) light. Part of the redshifted light passes through a sample, allowing transmission light microscopy. By simple modification of a commercial atomic force microscopes (AFM), we are able to image many different samples with high-resolution optical microscopy, achieving 20–30 nm lateral resolution for the best samples. The high resolution of the technique is not only due to the high curvature of the AFM tip, but also to the fact that the intensity of inelastically scattered light transmitted through the sample decays exponentially with the separation between the tip and the sample (decay length ∼100nm). We envisage applications to transmission SNOM, spectroscopic imaging, and imaging of fluorescently labeled bioconjugates. The collection of the optical image does not interfere with the normal operation of the AFM, so deflection, height, or other modes of operation can be captured simultaneously.
Low-threshold field emission from cesiated silicon nanowires
Authors: Kulkarni N. N. , Bae J. , Shih C.-K. , Stanley S. K. , Coffee S. S. , Ekerdt J. G.
Published: November 2005

Field-emission studies on Si nanowires (Si NWs) grown by the vapor-liquid-solid (VLS) technique are presented. The field-emission properties of the Si NWs were characterized in ultrahigh vacuum following several postgrowth processes such as catalyst etching, in situ annealing, and cesiation. The average threshold field of cesiated Si NWs was found to be ∼7.76±0.55V∕μm and showed a significant improvement over that of as-grown NWs (average threshold field ∼11.58V∕μm). The superior field-emission characteristics are attributed to the combination of cesiation and quality of the NWs’ surface grown via hydrogen reduction of silicon tetrachloride.
Nanomesa and nanowell formation in Langmuir–Blodgett polyvinylidene fluoride trifluoroethylene copolymer films
Authors: Li Jiangyu , Luo Yang , Bai Mengjun , Ducharme Stephen
Published: November 2005

In this letter, we report an energetics-based model to explain the self-organizing nanomesa and nanowell patterns recently observed in Langmuir-Blodgett (LB) films of polyvinylidene fluoride trifluoroethylene [P(VDF-TrFE)] copolymers. The feature size of nanomesas and nanowells has been estimated using a linear stability analysis, and the morphology of the nanomesas and nanowells has been revealed by the numerical simulation, both in good agreement with experiments. A number of other model predictions regarding the nanomesa and nanowell formation also agree with experimental observations. The model can be used to guide the design and optimization of nanostructures in the P(VDF-TrFE) LB films and possibly in other thin polymer films.
A mass sensor based on torsional modes in a conical shell
Authors: Yang Jiashi , Guo Shaohua
Published: November 2005

We analyze frequency shifts of torsional modes in a conical elastic shell due to a thin layer of added surface mass. A simple expression is obtained for the mass sensitivity. The result suggests the possibility of a mass sensor operating with torsional modes of a conical shell with certain potential advantages over existing acoustic wave mass sensors.
Terahertz microcavity quantum-cascade lasers
Authors: Fasching G. , Benz A. , Unterrainer K. , Zobl R. , Andrews A. M. , Roch T. , Schrenk W. , Strasser G.
Published: November 2005

We demonstrate circular-shaped microcavity quantum-cascade lasers emitting in the THz region between 3.0 and 3.8 THz. The band structure design of the GaAs∕Al0.15Ga0.85As heterostructure is based on longitudinal-optical phonon scattering for depopulation of the lower radiative state. A double metal waveguide is used to confine the whispering gallery modes in the gain medium. The threshold current density is 900A∕cm2 at 5 K. Lasing takes place in pulsed-mode operation up to a heat-sink temperature of 140 K.
Dust acoustic waves in quantum plasmas
Authors: Shukla P. K. , Ali S.
Published: November 2005

The quantum hydrodynamic model for plasmas is employed to derive a new dispersion relation for the dust acoustic wave. It is found that the dispersion property of the latter is significantly affected by quantum corrections.
Risks and prevention of sexually transmissible infections among women who have sex with women
Authors: McNair Ruth
Published: November 2005

Health care providers working with women who have sex with women (WSW) have been ill-informed about a range of sexual health issues for these women. Pertinent issues include sexual behaviours that carry risks of sexually transmissible infection (STI), prevention strategies for safer sex and understanding experiences of abuse. A relative silence continues in all of these areas within the mainstream medical literature, textbooks, research and policy documents, which perpetuates medical ignorance. There is evidence that the prevalence of STIs among WSW is at least as high as among heterosexual women, if not higher among some sub-groups. Risk factors include the sex and number of sexual partners, minimal use of protected sexual behaviours and low levels of knowledge of STI prevention among WSW. Importantly, marginalisation leading to poorer mental health and experiences of abuse can combine to influence risk taking including substance abuse and risky sexual behaviours. Safe-sex guidelines and the need to recognise the impact of sexual abuse are presented.
An audit of contact tracing for cases of chlamydia in the Australian Capital Territory
Authors: England Danelle O. , Currie Marian J. , Bowden Francis J
Published: November 2005

Background: Contact tracing is one of the central pillars of the management of sexually transmitted infections. The aims of this audit were to determine the yield of chlamydia infection from contact tracing the sexual partners of individuals diagnosed with chlamydia and to evaluate and compare the effectiveness of contact tracing undertaken at the Communicable Diseases Control Section (CDCS) of Australian Capital Territory (ACT) Health and the Canberra Sexual Health Centre (the clinic). Methods: A retrospective review of the notification records and contact-tracing documentation was undertaken at CDCS and the clinic from 1 September 2002 to 30 September 2003 (13 months). Results: The background rate of chlamydia in those tested in the ACT community is 3–5%. During the study period, 512 cases of chlamydia were notified to CDCS. Of these, 351 were referred for contact tracing, 293 by CDCS and 98 by the clinic. Of the 437 nominated sexual contacts (average of 1.12 per index case), 272 (62.2%) were contacted, 125 (28.6%) were tested and 51 (11.7%; 95% CI 8.8–15.1) tested positive for chlamydia (15.5%; 95% CI 11.5–20.6% in sexual contacts of CDCS index cases and 7.8%; 95% CI 4.8–12.5% in those of the clinic patients). Contact tracing through the CDCS reached significantly more nominated sexual contacts (78.4% v. 41.7%; P = 0.001) and significantly more of the nominated sexual contacts of index cases reported to CDCS were described as tested (34.7% v. 20.8%; P = 0.01). The average time taken to identify each chlamydia-positive sexual contact was 6.8 hours. Conclusions: Contact tracing more than doubled the case finding effectiveness of chlamydia screening, but was time consuming. These results suggest that provider-initiated contact tracing has clinical and public health value, but that the cost-effectiveness of this approach to chlamydia control should be further evaluated.
Bacterial vaginosis in female sex workers in Chennai, India
Authors: Uma Shanmugasundaram , Balakrishnan Pachamuthu , Murugavel Kailapuri G. , Srikrishnan Aylur K. , Kumarasamy Nagalingeswaran , Cecelia Jebaraj A. , Anand Santhanam , Mayer Kenneth H. , Celentano David , Thyagarajan Sadras P. , Solomon Suniti
Published: November 2005

Bacterial vaginosis (BV) causes obstetric and gynaecological complications and non-chlamydial/non-gonococcal pelvic inflammatory disease and has been shown to be associated with the risk of acquiring HIV and herpes simplex (HSV)-2 infections. This study investigated both the prevalence of BV and its association with STDs among 582 female sex workers living in Chennai, South India. Blood, vaginal and endocervical swabs were tested for HSV-2, HIV, Treponema pallidum, BV, Chlamydia trachomatis, Neisseria gonorrhoea and Trichomonas vaginalis. The vaginal swabs collected were Gram’s stained and analysed for BV by Nugent’s scoring criteria. Of the women studied, 45% (95% CI, 40.6–48.7) were positive, 39.5% (95% CI, 35.5–43.5) were negative and 16% (95% CI, 12.8–18.7) were intermediate for BV. Bacterial vaginosis positivity was directly related to concurrent infection with HSV-2 (RR 1.3, AR 12, P = 0.00), T. vaginalis (RR 1.5, AR 10, P = 0.01) T. pallidum (RR 2.8, AR 16, P = 0.00) and HIV (RR 4.1, AR 52, P = 0.01). Future studies are needed to focus on the risk factors for BV.
Bayesian coclustering of
Anopheles
gene expression time series: Study of immune defense response to multiple experimental challenges
Authors: Heard Nicholas A. , Holmes Christopher C. , Stephens David A. , Hand David J. , Dimopoulos George
Published: November 2005

We present a method for Bayesian model-based hierarchical coclustering of gene expression data and use it to study the temporal transcription responses of an
Anopheles gambiae
cell line upon challenge with multiple microbial elicitors. The method fits statistical regression models to the gene expression time series for each experiment and performs coclustering on the genes by optimizing a joint probability model, characterizing gene coregulation between multiple experiments. We compute the model using a two-stage Expectation-Maximization-type algorithm, first fixing the cross-experiment covariance structure and using efficient Bayesian hierarchical clustering to obtain a locally optimal clustering of the gene expression profiles and then, conditional on that clustering, carrying out Bayesian inference on the cross-experiment covariance using Markov chain Monte Carlo simulation to obtain an expectation. For the problem of model choice, we use a cross-validatory approach to decide between individual experiment modeling and varying levels of coclustering. Our method successfully generates tightly coregulated clusters of genes that are implicated in related processes and therefore can be used for analysis of global transcript responses to various stimuli and prediction of gene functions.
Single-myosin crossbridge interactions with actin filaments regulated by troponin-tropomyosin
Authors: Kad Neil M. , Kim Scott , Warshaw David M. , VanBuren Peter , Baker Josh E.
Published: November 2005

Striated muscle contraction is governed by the thin filament regulatory proteins troponin and tropomyosin. Here, we investigate the molecular mechanisms by which troponin–tropomyosin inhibits myosin's interactions with the thin filament in the absence of calcium by using a laser trap. The displacement events for a single-myosin molecule interacting with a reconstituted thin filament were shorter (step size = 5 nm) and prolonged (69 ms) compared with actin alone (11 nm and 26 ms, respectively). However, these changes alone do not account for the degree of inhibition of thin filament movement observed in an ensemble assay. Our investigations of single- and multiple-myosin molecules with regulated thin filaments suggest the primary basis for this inhibition derives from a ≈100-fold decrease in the probability of myosin attaching to actin. At higher myosin concentrations, short bursts of motility are observed in a laser trap consistent with the strong binding of a single-myosin crossbridge, resulting in cooperative binding of other cycling crossbridges. We confirmed this cooperativity in the
in vitro
motility assay by observing thin filament translocation in the absence of calcium but at low [ATP], consistent with rigor activation. We have developed a simple mechanistic model that reproduces and provides insight into both the observed single-myosin molecule and ensemble data in the absence of Ca
2+
. These data support the hypothesis that thin filament inhibition in the absence of Ca
2+
is largely achieved by modulating the rate of attachment and/or transition from the weakly to strongly bound state.
Requirement for chitin biosynthesis in epithelial tube morphogenesis
Authors: Devine W. Patrick , Lubarsky Barry , Shaw Ken , Luschnig Stefan , Messina Lisa , Krasnow Mark A.
Published: November 2005

Many organs are composed of branched networks of epithelial tubes that transport vital fluids or gases. The proper size and shape of tubes are crucial for their transport function, but the molecular processes that govern tube size and shape are not well understood. Here we show that three genes required for tracheal tube morphogenesis in
Drosophila melanogaster
encode proteins involved in the synthesis and accumulation of chitin, a polymer of
N
-acetyl-β-
d
-glucosamine that serves as a scaffold in the rigid extracellular matrix of insect cuticle. In all three mutants, developing tracheal tubes bud and extend normally, but the epithelial walls of the tubes do not expand uniformly, and the resultant tubes are grossly misshapen, with constricted and distended regions all along their lengths. The genes are expressed in tracheal cells during the expansion process, and chitin accumulates in the lumen of tubes, forming an expanding cylinder that we propose coordinates the behavior of the surrounding tracheal cells and stabilizes the expanding epithelium. These findings show that chitin regulates epithelial tube morphogenesis, in addition to its classical role protecting mature epithelia.
Suppressor of cytokine signaling-1 selectively inhibits LPS-induced IL-6 production by regulating JAK–STAT
Authors: Kimura Akihiro , Naka Tetsuji , Muta Tatsushi , Takeuchi Osamu , Akira Shizuo , Kawase Ichiro , Kishimoto Tadamitsu
Published: November 2005

Suppressor of cytokine signaling-1 (SOCS-1) is one of the negative-feedback regulators of Janus kinase (JAK)–signal transducer and activator of transcription (STAT) signaling. We previously showed that SOCS-1 participates in LPS signaling, but it is not entirely clear yet how SOCS-1 suppresses LPS signaling. In this study, we demonstrate that SOCS-1 selectively inhibits LPS-induced IL-6 production through regulation of JAK–STAT but not production of TNF-α, granulocyte colony-stimulating factor, IFN-β, and other cytokines. We found that LPS directly activated Jak2 and Stat5, whereas SOCS-1 inhibited LPS-induced Jak2 and Stat5 activation. Furthermore, AG490, a Jak-specific inhibitor, and dominant negative Stat5 only reduced LPS-induced IL-6 production. Additionally, Stat5 interacted with p50, resulting in recruitment of Stat5 to the IL-6 promoter together with p50 in response to LPS stimulation. These findings suggest that the JAK–STAT pathway participates in LPS-induced IL-6 production and that SOCS-1 suppresses LPS signaling by regulating JAK–STAT.
Probing structural heterogeneities and fluctuations of nucleic acids and denatured proteins
Authors: Laurence Ted A. , Kong Xiangxu , Jäger Marcus , Weiss Shimon
Published: November 2005

We study protein and nucleic acid structure and dynamics using single-molecule FRET and alternating-laser excitation. Freely diffusing molecules are sorted into subpopulations based on single-molecule signals detected within 100 μs to 1 ms. Distance distributions caused by fluctuations faster than 100 μs are studied within these subpopulations by using time-correlated single-photon counting. Measured distance distributions for dsDNA can be accounted for by considering fluorophore linkers and fluorophore rotational diffusion, except that we find smaller fluctuations for internally labeled dsDNA than DNA with one of the fluorophores positioned at a terminal site. We find that the electrostatic portion of the persistence length of short single-stranded poly(dT) varies approximately as the ionic strength (
I
) to the –1/2 power (
I
–1/2
), and that the average contribution to the contour length per base is 0.40–0.45 nm. We study unfolded chymotrypsin inhibitor 2 (CI2) and unfolded acyl-CoA binding protein (ACBP) even under conditions where folded and unfolded subpopulations coexist (contributions from folded proteins are excluded by using alternating-laser excitation). At lower denaturant concentrations, unfolded CI2 and ACBP are more compact and display larger fluctuations than at higher denaturant concentrations where only unfolded proteins are present. The experimentally measured fluctuations are larger than the fluctuations predicted from a Gaussian chain model or a wormlike chain model. We propose that the larger fluctuations may indicate transient residual structure in the unfolded state.
Small molecules that reactivate p53 in renal cell carcinoma reveal a NF-κB-dependent mechanism of p53 suppression in tumors
Authors: Gurova Katerina V. , Hill Jason E. , Guo Canhui , Prokvolit Anatoly , Burdelya Lyudmila G. , Samoylova Eugenia , Khodyakova Anna V. , Ganapathi Ram , Ganapathi Mahrukh , Tararova Natalia D. , Bosykh Dmitry , Lvovskiy Dmitriy , Webb Thomas R. , Stark George R. , Gudkov Andrei V.
Published: November 2005

Renal cell carcinomas (RCC) commonly retain wild-type but functionally inactive p53, which is repressed by an unknown dominant mechanism. To help reveal this mechanism, we screened a diverse chemical library for small molecules capable of restoring p53-dependent transactivation in RCC cells carrying a p53-responsive reporter. Among the compounds isolated were derivatives of 9-aminoacridine (9AA), including the antimalaria drug quinacrine, which strongly induced p53 function in RCC and other types of cancer cells. Induction of p53 by these compounds does not involve genotoxic stress and is mediated by suppression of NF-κB activity. In contrast to agents that target IκB kinase 2, 9AA and quinacrine can effectively suppress both basal and inducible activities of NF-κB, representing inhibitors of a previously undescribed type that convert NF-κB from a transactivator into a transrepressor, leading to accumulation of inactive nuclear complexes with unphosphorylated Ser-536 in the p65/RelA subunit. p53 function in RCC can be restored by ectopic expression of a superrepressor of IκB as effectively as by 9AA-derived compounds. These findings suggest that the complete or partial repression of p53 observed in many tumors can be the result of constitutive activation of NF-κB. The results demonstrate, in principle, the possibility to kill cancer cells selectively through simultaneous inhibition of NF-κB and activation of p53 by a single small molecule and suggest anticancer applications for the well known antimalaria drug quinacrine.
Anxiolytic- and antidepressant-like profiles of the galanin-3 receptor (Gal
3
) antagonists SNAP 37889 and SNAP 398299
Authors: Swanson Chad J. , Blackburn Thomas P. , Zhang Xuexiang , Zheng Kang , Xu Zhi-Qing David , Hökfelt Tomas , Wolinsky Toni D. , Konkel Michael J. , Chen Heidi , Zhong Huailing , Walker Mary W. , Craig Douglas A. , Gerald Christophe P. G. , Branchek Theresa A.
Published: November 2005

The neuropeptide galanin mediates its effects through the receptor subtypes Gal
1
, Gal
2
, and Gal
3
and has been implicated in anxiety- and depression-related behaviors. Nevertheless, the receptor subtypes relevant to these behaviors are not known because of the lack of available galanin-selective ligands. In this article, we use behavioral, neurochemical, and electrophysiological approaches to investigate the anxiolytic- and antidepressant-like effects of two potent small-molecule, Gal
3
-selective antagonists, SNAP 37889 and the more soluble analog SNAP 398299. Acute administration of SNAP 37889 or SNAP 398299 enhanced rat social interaction. Furthermore, acute SNAP 37889 was also shown to reduce guinea pig vocalizations after maternal separation, to attenuate stress-induced hyperthermia in mice, to increase punished drinking in rats, and to decrease immobility and increase swimming time during forced swim tests with rats. Moreover, SNAP 37889 increased the social interaction time after 14 days of treatment and maintained its antidepressant effects during forced swim tests with rats after 21 days of treatment. In microdialysis studies, SNAP 37889 partially antagonized the galanin-evoked reduction in hippocampal serotonin (5-hydroxytryptamine, 5-HT), as did the 5-HT
1A
receptor antagonist WAY100635. Their combination produced a complete reversal of the effect of galanin. SNAP 398299 partially reversed the galanin-evoked inhibition of dorsal raphe cell firing and galanin-evoked hyperpolarizing currents. These results indicate that Gal
3
-selective antagonists produce anxiolytic- and antidepressant-like effects, possibly by attenuating the inhibitory influence of galanin on 5-HT transmission at the level of the dorsal raphe nucleus.
Negative regulation of nuclear divisions in
Caenorhabditis elegans
by retinoblastoma and RNA interference-related genes
Authors: Grishok Alla , Sharp Phillip A.
Published: November 2005

Short RNA regulatory molecules, microRNAs, and short interfering RNAs participate in a range of developmental gene networks by base-pairing with their target sequences. Consistent with these findings, genes required for the biogenesis and function of short interfering RNAs and microRNAs,
dicer
(
dcr-1
in
Caenorhabditis elegans
) and
argonaute
homologs, are essential for development in diverse organisms, including
C. elegans
. We demonstrate that genes required for the function of short RNAs synergize with the retinoblastoma tumor suppressor homolog
lin-35
in negative regulation of the nuclear divisions in the intestine of
C. elegans
. The level of cyclin E (
cye-1
) expression is critical for nuclear divisions in the intestine and is elevated in double mutants in
lin-35
and RNA interference pathway genes. We propose that RNA interference-related pathways cooperate with retinoblastoma in transcriptional repression of endogenous genes, an example being cyclin E.
Comparison theorems of Kolmogorov type and exact values of 𝑛-widths on Hardy–Sobolev classes
Authors: Fang Gensun , Li Xuehua
Published: November 2005

Let

S

β

:=
{
z
∈

C

:

|

Im

z

|

>
β
}

S_{\beta }:=\{z\in {\mathbb C}:|\textrm {Im}z|>\beta \}

be a strip in complex plane.

H
~

∞
,
β

r

\widetilde {H}_{\infty ,\beta }^{r}

denotes those

2
π

2\pi

-periodic, real-valued functions on

R

{\mathbb R}

which are analytic in the strip

S

β

S_{\beta }

and satisfy the condition

|

f

(
r
)

(
z
)

|

≤
1

|f^{(r)}(z)|\leq 1

,

z
∈

S

β

z\in S_{\beta }

. Osipenko and Wilderotter obtained the exact values of the Kolmogorov, linear, Gel′fand, and information

n
n

-widths of

H
~

∞
,
β

r

\widetilde {H}_{\infty ,\beta }^{r}

in

L

∞

[
0
,
2
π
]

L_{\infty }[0,2\pi ]

,

r
=
0
,
1
,
2
,
…

r=0,1,2,\ldots

, and 2

n
n

-widths of

H
~

∞
,
β

r

\widetilde {H}_{\infty ,\beta }^{r}

in

L

q

[
0
,
2
π
]

L_{q}[0,2\pi ]

,

r
=
0

r=0

,

1
≤
q
>
∞

1\leq q>\infty

. In this paper we continue their work. Firstly, we establish a comparison theorem of Kolmogorov type on

H
~

∞
,
β

r

\widetilde {H}_{\infty ,\beta }^{r}

, from which we get an inequality of Landau–Kolmogorov type. Secondly, we apply these results to determine the exact values of the Gel′fand

n
n

-width of

H
~

∞
,
β

r

\widetilde {H}_{\infty ,\beta }^{r}

in

L

q

[
0
,
2
π
]

L_{q}[0,2\pi ]

,

r
=
0
,
1
,
2
…
,

r=0,1,2\ldots ,

1
≤
q
>
∞

1\leq q>\infty

. Finally, we calculate the exact values of Kolmogorov

2
n

2n

-width, linear

2
n

2n

-width, and information

2
n

2n

-width of

H
~

∞
,
β

r

\widetilde {H}_{\infty ,\beta }^{r}

in

L

q

[
0
,
2
π
]

L_{q}[0,2\pi ]

,

r
∈

N

r\in {\mathbb N}

,

1
≤
q
>
∞

1\leq q>\infty

.
Homotopic residual correction processes
Authors: Pan V. , Kunin M. , Rosholt R. , Kodal H.
Published: November 2005

We present and analyze homotopic (continuation) residual correction algorithms for the computation of matrix inverses. For complex indefinite Hermitian input matrices, our homotopic methods substantially accelerate the known nonhomotopic algorithms. Unlike the nonhomotopic case our algorithms require no pre-estimation of the smallest singular value of an input matrix. Furthermore, we guarantee rapid convergence to the inverses of well-conditioned structured matrices even where no good initial approximation is available. In particular we yield the inverse of a well-conditioned

n
×
n

n \times n

matrix with a structure of Toeplitz/Hankel type in

O
(
n

log
3

⁡
n
)

O(n\log ^3n)

flops. For a large class of input matrices, our methods can be extended to computing numerically the generalized inverses. Our numerical experiments confirm the validity of our analysis and the efficiency of the presented algorithms for well-conditioned input matrices and furnished us with the proper values of the parameters that define our algorithms.
Global optimization of explicit strong-stability-preserving Runge-Kutta methods
Authors: Ruuth Steven
Published: November 2005

Strong-stability-preserving Runge-Kutta (SSPRK) methods are a type of time discretization method that are widely used, especially for the time evolution of hyperbolic partial differential equations (PDEs). Under a suitable stepsize restriction, these methods share a desirable nonlinear stability property with the underlying PDE; e.g., positivity or stability with respect to total variation. This is of particular interest when the solution exhibits shock-like or other nonsmooth behaviour. A variety of optimality results have been proven for simple SSPRK methods. However, the scope of these results has been limited to low-order methods due to the detailed nature of the proofs. In this article, global optimization software, BARON, is applied to an appropriate mathematical formulation to obtain optimality results for general explicit SSPRK methods up to fifth-order and explicit low-storage SSPRK methods up to fourth-order. Throughout, our studies allow for the possibility of negative coefficients which correspond to downwind-biased spatial discretizations. Guarantees of optimality are obtained for a variety of third- and fourth-order schemes. Where optimality is impractical to guarantee (specifically, for fifth-order methods and certain low-storage methods), extensive numerical optimizations are carried out to derive numerically optimal schemes. As a part of these studies, several new schemes arise which have theoretically improved time-stepping restrictions over schemes appearing in the recent literature.
Sharp 𝐿¹ a posteriori error analysis for nonlinear convection-diffusion problems
Authors: Chen Zhiming , Ji Guanghua
Published: November 2005

We derive sharp

L
∞

(

L
1

)

L^\infty (L^1)

a posteriori error estimates for initial boundary value problems of nonlinear convection-diffusion equations of the form
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="StartLayout 1st Row StartFraction partial-differential u Over partial-differential t EndFraction plus d i v f left-parenthesis u right-parenthesis minus normal upper Delta upper A left-parenthesis u right-parenthesis equals g EndLayout">

∂
u

∂
t

+
div
⁡
f
(
u
)
−
Δ
A
(
u
)
=
g

\begin{eqnarray*} \frac {\partial u}{\partial t}+\operatorname {div}f(u)-\Delta A(u)=g \end{eqnarray*}

under the nondegeneracy assumption

A
′

(
s
)
>
0

A’(s)>0

for any

s
∈

R

s\in \mathbb {R}

. The problem displays both parabolic and hyperbolic behavior in a way that depends on the solution itself. It is discretized implicitly in time via the method of characteristic and in space via continuous piecewise linear finite elements. The analysis is based on the Kružkov “doubling of variables” device and the recently introduced “boundary layer sequence” technique to derive the entropy error inequality on bounded domains. The derived a posteriori error estimators have the correct convergence order in the region where the solution is smooth and recover the standard a posteriori error estimators known for parabolic equations with strong diffusions.
Accurate and efficient evaluation of Schur and Jack functions
Authors: Demmel James , Koev Plamen
Published: November 2005

We present new algorithms for computing the values of the Schursλ(x1,x2,…,xn)s_\lambda (x_1,x_2,\ldots ,x_n)and JackJλα(x1,x2,…,xn)J_\lambda ^\alpha (x_1,x_2,\ldots ,x_n)functions in floating point arithmetic. These algorithms deliver guaranteed high relative accuracy for positive data (xi,α>0x_i, \alpha >0) and run in time that is only linear innn.