bluuebunny/crossref_metadata_2025 huggingface dataset:
Wetting and particle adsorption in nanoflows
Authors: Drazer German , Khusid Boris , Koplik Joel , Acrivos Andreas
Published: December 2004

Molecular dynamics simulations are used to study the behavior of closely fitting spherical and ellipsoidal particles moving through a fluid-filled cylinder at nanometer scales. The particle, the cylinder wall, and the fluid solvent are all treated as atomic systems, and special attention is given to the effects of varying the wetting properties of the fluid. Although the modification of the solid-fluid interaction leads to significant changes in the microstructure of the fluid, its transport properties are found to be the same as in bulk. Independently of the shape and the relative size of the particle, we find two distinct regimes as a function of the degree of wetting, with a sharp transition between them. In the case of a highly wetting suspending fluid, the particle moves through the cylinder with an average axial velocity in agreement with that obtained from the solution of the continuum Stokes equations. In contrast, in the case of less-wetting fluids, only the early time motion of the particle is consistent with continuum dynamics. At later times, the particle is eventually adsorbed onto the wall and subsequently executes an intermittent stick-slip motion. We show that van der Waals forces are the dominant contribution to the particle adsorption phenomenon and that depletion forces are weak enough to allow, in the highly wetting situation, an initially adsorbed particle to spontaneously desorb.
Noise selection in multielectrode devices by using a correlation spectrum analyzer
Authors: Ferrari Giorgio , Fumagalli Laura , Sampietro Marco
Published: December 2004

In this article, we present a technique to sort out in a multielectrode device a vanishing small noise component between two electrodes affected by a much larger overall noise. The technique is based on the use of a correlation spectrum analyzer and has proven to detect a current noise of interest as low as 1 fA/Hz in the presence of undesirable noise of 50 fA/Hz. The possibility offered by this technique is useful in a number of applications, ranging from gate current investigation in metal-oxide-semiconductor field effect transistors to the study of leakage currents in nanodevices.
Organic thin-film transistors having inorganic/organic double gate insulators
Authors: Wang Jun , Yan Xuanjun , Xu Yanxia , Zhang Jian , Yan Donghang
Published: December 2004

Bottom-contact organic thin-film transistors (BC OTFTs) based on inorganic/organic double gate insulators were demonstrated. The double gate insulators consisted of tantalum pentoxide (Ta2O5) with high dielectric constant (κ) as the first gate insulator and octadecyltrichlorosilane (OTS) with low κ as the second gate insulator. The devices have carrier mobilities larger than 10−2cm2∕Vs, on/off current ratio greater than 105, and the threshold voltage of −14V, which is threefold larger field-effect mobility and an order of magnitude larger on/off current ratio than the OTFTs with a Ta2O5 gate insulator. The leakage current was decreased from 2.4×10−6 to 7.4×10−8 A due to the introduction of the OTS second dielectric layer. The results demonstrated that using inorganic/organic double insulator as the gate dielectric layer is an effective method to fabricate OTFTs with improved electric characteristics.
Electrical thermo-optic tuning of ultrahigh-Q microtoroid resonators
Authors: Armani Deniz , Min Bumki , Martin Andrea , Vahala Kerry J.
Published: December 2004

The ability to tune resonant frequency in optical microcavities is an essential feature for many applications. Integration of electrical-based tuning as part of the fabrication process has been a key advantage of planar microresonant devices. Until recently, the combination of these features has not been available in devices that operate in the ultrahigh-Q regime where device quality factors (Q) can exceed 100 million. In this letter, we demonstrate an electrically tunable resonator on a chip with ultrahigh-quality factors. Futhermore, the devices have demonstrated tuning rates in excess of 85GHz∕V2 and are capable of tuning more than 300GHz.
Nonthermal decomposition of C60 polymers induced by tunneling electron injection
Authors: Nakamura Yoshiaki , Kagawa Fumitaka , Kasai Koichi , Mera Yutaka , Maeda Koji
Published: December 2004

Scanning tunneling microscopic (STM) studies of C60 films deposited on highly oriented pyrolytic graphite substrates revealed that the electron injection from the STM tip induces the decomposition (isomerization) of the C60 molecules that have been polymerized also by the electron injection into the films. Both reaction rates were characterized by a linear dependence on the injected tunneling current and a common threshold around 2 V in the sample bias dependence. We discuss two nonthermal mechanisms for the polymerization and decomposition reactions: electronic excitation mechanism by Auger decay and a hypothetical ionic reaction model.
Optical nonlinearities in VO2 nanoparticles and thin films
Authors: Lopez Rene , Haglund Richard F. , Feldman Leonard C. , Boatner Lynn A. , Haynes Tony E.
Published: December 2004

Z -scan and pump-probe measurements with ultrafast, 800nm laser pulses were used to compare the ultrafast optical nonlinearities of VO2 nanoparticles and thin films in both semiconducting and metallic states. In the metallic state, both the nanocrystals and thin films exhibit a positive, intensity-dependent nonlinear index of refraction. However, the nonlinear effects are relatively larger in the VO2 nanocrystals, which also reveal a saturable nonlinear absorption. When the semiconductor-to-metal phase transition is induced by the laser pulse, VO2 thin films exhibit a negative equivalent nonlinear index of refraction while the nanocrystals exhibit a smaller but still positive index. Both the VO2 nanocrystals and thin films undergo the phase transition within 120fs.
Internal light source technique free from reabsorption losses for optical characterization of planar photonic crystals
Authors: Lombardet B. , Ferrini R. , Dunbar L. A. , Houdré R. , Cuisin C. , Drisse O. , Lelarge F. , Pommereau F. , Poingt F. , Duan G.-H.
Published: December 2004

An optimization of the internal light source (ILS) technique for optical characterization of planar photonic crystals (PPhCs) is presented. The approach makes use of a double planar waveguide structure that separates the region where the light emitting layers are embedded from the region where the PPhCs are fabricated. This technique is demonstrated to be free from reabsorption losses, thus combining the advantages of standard optical techniques with the versatility of the ILS setup. We validate this method by comparison with standard ILS measurements on several PPhC structures.
Degradation diagnosis of ultrahigh-molecular weight polyethylene with terahertz-time-domain spectroscopy
Authors: Yamamoto Kohji , Yamaguchi Mariko , Tani Masahiko , Hangyo Masanori , Teramura Satoshi , Isu Toshiro , Tomita Naohide
Published: December 2004

We investigated ultrahigh-molecular-weight-polyethylene (UHMWPE) samples prepared by various conditions with terahertz-time-domain spectroscopy (THz-TDS). Degradation of the virgin UHMWPE samples by γ irradiation induced a drastic increase of the absorption ranging continuously over the THz region. The increase of the absorption continuum is interpreted to originate in the oxidation of the amorphous region within the sample. Only slight THz spectral changes induced by the γ irradiation were, however, observed for the UHMWPE samples doped with 0.1 and 0.3 wt % vitamin E. This result agrees with the earlier indication that vitamin E has an antidegradation effect on UHMWPE. The present result shows that the THz-TDS can be used for the quality control of UHMWPE by monitoring the absorption continuum in the THz region.
A resonant detector for high-energy inelastic neutron scattering experiments
Authors: Andreani C. , Pietropaolo A. , Senesi R. , Gorini G. , Perelli-Cippo E. , Tardocchi M. , Rhodes N. , Schooneveld E. M.
Published: December 2004

Results on the application of the resonant detector (RD) for epithermal neutron scattering in an unexplored kinematical region are presented. The RD is based on resonance radiative neutron capture for energy analysis of the scattered neutrons in an inverse geometry time of flight spectrometer. Application of the RD to detection of epithermal neutrons at very low scattering angles allows access to an unexplored scattering kinematical region, the High-energy Inelastic Neutron Scattering (HINS) region, of low wave vector (3Å−1<q<10Å−1) and high energy transfers (0.1eV<ω<10eV). Results of HINS measurements from polycrystalline ice are presented.
Multimode transflective liquid crystal display with a single cell gap using a self-masking process of photoalignment
Authors: Yu Chang-Jae , Kim Dong-Woo , Lee Sin-Doo
Published: December 2004

We demonstrate a transflective liquid crystal display (LCD), doped with a chiral agent to produce a low helical twisting power, in a multimode configuration consisting of the homogeneous alignment and the hybrid alignment. The multimode transflective LCD was fabricated by a single-step exposure of the UV light through an array of metal reflectors used as an amplitude photomask which gives an alternating homogeneous and homeotropic LC geometry. This single-step UV exposure produces no cell gap variations. In our configuration, the electro-optical disparity between the transmissive region and the reflective region was found to be significantly reduced by the low helical twisting power of the chiral dopant.
Fabrication of a metal-oxide-semiconductor-type capacitive microtip array using SiO2 or HfO2 gate insulators
Authors: Kim Kyung-Min , Choi Byung Joon , Kim Seong Keun , Hwang Cheol Seong
Published: December 2004

Capacitive tip arrays having a metal-insulator-semiconductor capacitor structure were fabricated using thermally oxidized SiO2 or atomic-layer-deposited HfO2 gate dielectric films for their application to scanning-probe-array-type memory devices. The SiO2 film showed a nonuniform thickness distribution over the flat and tip areas of the arrays owing to the different oxidation speeds of the flat and tip Si surfaces. This resulted in a smaller sensing margin of the device. However, the high-dielectric HfO2 film showed not only a higher capacitance value but also a more uniform growth behavior over the whole area, which would result in a better device performance. The capacitance–voltage characteristics of both devices coincide well with the simulation results based on conventional metal-insulator-semiconductor theories.
High μτ product in a smectic liquid crystalline photoconductor of a 2-phenylnaphthalene derivative
Authors: Zhang Hong , Hanna Jun-ichi
Published: December 2004

Photoconductive properties in a smectic liquid crystalline photoconductor of 2-(4′-octylpheny)-6-dodecyoxylnaphthalene (8-PNP-O12) were investigated by the time-of-flight measurement. By fitting the collected charges with the Hecht equation as a function of electric field, where the field effect on the photogeneration was taken into account, the μτ product was determined to be as high as 6×10−8 and 5×10−7cm2∕V in the smectic A and B phases, respectively. Judging from the field- and temperature-independent mobility and no electrically active domain boundaries in smectic mesophases, the μτ products in these phases are determined by a common carrier lifetime, which is probably governed by a trace amount of chemical impurities.
Doping of functional materials into poly(p-phenylene vinylene) by the vapor transportation method
Authors: Mochizuki Hiroyuki , Mizokuro Toshiko , Tanigaki Nobutaka , Mo Xiaoliang , Hiraga Takashi
Published: December 2004

Poly(p-phenylene vinylene) (PPV) is a promising material, but shows poor processability, such as doping, due to its insolubility and infusibility. Therefore, the development of a standard and easy method of dye doping into PPV is important for device fabrication using PPV. We developed a simple method for the dispersal of dyes into PPV without deformation. Using this method, it was possible to change the color of PPV from yellow to green by doping with the blue dye 1,4-(N,N’-diethylamino)anthraquinone (SV59). The amount of SV59 doped into PPV was ∼2.7wt%. The fluorescence color of PPV could be changed from green to red by 2 min dispersal of 4-(dicyanomethylene)-2-methyl-6-(4-dimethylaminostyryl)-4H-pyran.
Rib waveguide dye-doped polymer amplifier with up to 26dB optical gain at 625nm
Authors: Reilly M. A. , Marinelli C. , Morgan C. N. , Penty R. V. , White I. H. , Ramon M. , Ariu M. , Xia R. , Bradley D. D. C.
Published: December 2004

We report optical signal amplification in a solid-state dye-doped polymer with a rib waveguide structure. A 625nm pulsed signal and a collinear 575nm pump are coupled into a 1μm×120μm poly(methyl methacrylate) waveguide doped with 1% by weight Rhodamine 640 dye. Depending on the signal intensity, a maximum optical gain in the 21–26dB range is obtained from a 1.2-cm-long device, accompanied by a signal-to-noise ratio in the 9–16dB range.
Frequency response of atomic force microscope cantilever driven by fluid
Authors: Volkov A. O. , Burnell-Gray J. S. , Datta P. K.
Published: December 2004

The most widely used dynamic atomic force microscopy technique in fluids is the piezo-drive, where a cantilever is driven by fluid excited by a piezoelectric. The study of the frequency response of the fluid-driven cantilever is usually interfered by the resonances of a fluid cell. In this work an active cantilever has been used to drive fluid in the vicinity of a passive cantilever. The local drive resulted in the measured response free from spurious resonances. In contrast to a magnetically driven cantilever, the oscillations of the fluid-driven cantilever tend at high frequency to finite amplitude.
Fabrication of functional microstructured optical fibers through a selective-filling technique
Authors: Huang Yanyi , Xu Yong , Yariv Amnon
Published: December 2004

We develop a method for the fabrication of functional microstructured optical fibers (MOFs) by selectively filling the air holes with liquid phase materials, where we utilize the dependence of filling speed on the size of the air holes. As a demonstration, we construct a hybrid MOF by filling the center hollow core of a triangular lattice photonic crystal fiber with dye-doped curable polymer, and experimentally observe the two-photon fluorescence from the hybrid MOF.
High-power 1.3-μm InGaAsN strain-compensated lasers fabricated with pulsed anodic oxidation
Authors: Qu Yi , Liu C. Y. , Yuan Shu
Published: December 2004

Ridge waveguide InGaAsN triple-quantum-well strain-compensated lasers grown by metal-organic chemical vapor deposition were fabricated with pulsed anodic oxidation. Laser output power reached 962mW in cw mode at room temperature from 100-μm stripe lasers with a wavelength of 1297nm. The threshold-current density was 256A∕cm2. The characteristic temperature of the lasers was 138K in the linear region (20–80°C).
Radiation response analysis of wide-gap p-AlInGaP for superhigh-efficiency space photovoltaics
Authors: Khan Aurangzeb , Marupaduga S. , Anandakrishnan S. S. , Alam M. , Ekins-Daukes N. J. , Lee H. S. , Sasaki T. , Yamaguchi M. , Takamoto T. , Agui T. , Kamimura K. , Kaneiwa M. , Imazumi M.
Published: December 2004

We present here the direct observation of the majority and minority carrier defects generation from wide-band-gap (2.04eV) and thick (2μm) p-AlInGaP diodes and solar cells structures before and after 1MeV electron irradiation by deep level transient spectroscopy (DLTS). One dominant hole-emitting trap H1 (EV+0.37±0.05eV) and two electron-emitting traps, E1 (EC−0.22±0.04eV) and E3 (EC−0.78±0.05eV) have been observed in the temperature range, which we could scan by DLTS. Detailed analysis of the minority carrier injection annealing experiment reveals that the H1 center has shown the same annealing characteristics, which has been previously observed in all phosphide-based materials such as InP, InGaP, and InGaAsP. The annealing property of the radiation-induced defects in p-AlInGaP reveals that multijunction solar cells and other optoelectronic devices such as light-emitting diodes based on this material could be considerably better to Si and GaAs in a radiation environment.
Broadband sensitization of 1.53μm Er3+ luminescence in erbium-implanted alumina
Authors: Chryssou C. E. , Kenyon A. J. , Smeeton T. M. , Humphreys C. J. , Hole D. E.
Published: December 2004

Experimental evidence of an efficient broadband sensitization mechanism in erbium-implanted alumina is presented. Alumina thin films were deposited by plasma-enhanced chemical vapor deposition using trimethyl-amine alane and nitrous oxide. The as-grown films, together with sapphire crystals, were implanted with erbium. Photoluminescence excitation spectra showed that erbium-implanted sapphire crystals exhibit characteristic Er3+ luminescence at 1.53μm only when pumped resonantly. In contrast, erbium-implanted alumina thin films exhibit 1.53μm luminescence even when pumped at wavelengths outside Er3+ absorption bands. We postulate that the sensitizing species is either small nanoclusters of aluminum or pairs of aluminum ions.
Catalytic effect on hydrogen desorption in Nb-doped microcrystalline MgH2
Authors: Bazzanella Nicola , Checchetto Riccardo , Miotello Antonio
Published: December 2004

Mg and Nb-doped Mg films were deposited by rf magnetron sputtering. Morphological and structural analysis were performed by scanning electron microscopy and x-ray diffraction. The desorption kinetics has been investigated by using a Sievert-type apparatus. The overall activation energy and the reaction order controlling desorption are (141±5)kJmol−1H and n≈4 for Mg and (51±5)kJmol−1H and n≈1 for Nb-doped (5at.%) Mg. It is suggested that Nb atoms dispersed in the MgH2 grains catalyzes the dissociation of the hydride phase and that the rate limiting step in the H2 desorption is given by the H atomic migration through interconnected transformed domains of h-Mg.
High-resolution x-ray topography and diffraction study of bulk regular domain structures in LiNbO3 crystals
Authors: Antipov V. V. , Blistanov A. A. , Roshchupkina E. D. , Tucoulou R. , Ortega L. , Roshchupkin D. V.
Published: December 2004

Bulk regular domain structures created in a LiNbO3 crystal by aftergrowth thermoelectrical treatment technique were studied by high-resolution x-ray diffraction and topography. Topographic contrast can be observed between neighboring domains and is related to the difference in the direction of spontaneous polarization vectors. In the Y-cut case, x-ray topography allows the determination of positively or negatively charged domain boundaries. It is also shown that x-ray diffraction can be used to study elastic deformation around domain walls.
Catalyst consumption during growth of carbon nanofilaments on Pd seeds
Authors: Breton Yannick , Fleurier Romain , Salvetat Jean-Paul , Thomann Anne-Lise , Verstraete Matthieu , Charlier Jean-Christophe
Published: December 2004

Carbon nanofilaments are produced at 600°C by catalytic decomposition of acetylene on palladium nanoparticles. We observe that nanofilament length is limited to a few hundreds of nm when the size of Pd germs is less than 10nm, possibly due to the incorporation of Pd atoms during growth. We propose a growth model, supported by first-principles calculations which show that Pd atoms are stable when adsorbed on graphene and that a charge transfer occurs, modifying significantly the electronic properties.
Gate bias symmetry dependency of electron mobility and prospect of velocity modulation in double-gate silicon-on-insulator transistors
Authors: Prunnila M. , Ahopelto J. , Henttinen K. , Gamiz F.
Published: December 2004

We report on detailed room-temperature transport properties of a 17nm thick double-gate silicon-on-insulator (DGSOI) transistor. We find that when the electron gas is transferred between the top and the bottom of the silicon-on-insulator (SOI) layer by changing the gate bias symmetry (i.e., applying the gate biases in a push–pull fashion), while keeping the carrier density constant the maximum mobility occurs when the electron gas symmetrically occupies the whole SOI slab. The observed mobility behavior is the fingerprint of volume inversion∕accumulation. This gate bias symmetry dependency of the mobility suggests that DGSOI devices intrinsically can be operated in a velocity modulation transistor (VMT) mode. In the experimental gate bias window, the maximum velocity∕mobility modulation is ∼40%. The VMT transconductance exceeds conventional single-gate transconductance when electron density is above ∼5.3×1016m−2. Improvements of the observed VMT operation in thin DGSOI devices are discussed.
Efficient thin-film organic solar cells based on pentacene/C60 heterojunctions
Authors: Yoo S. , Domercq B. , Kippelen B.
Published: December 2004

We have fabricated an efficient organic photovoltaic cell based on a heterojunction of pentacene and C60. Photocurrent action spectra exhibit broad light-harvesting throughout the visible spectrum with a peak external quantum efficiency (EQE) of 58±4% at short-circuit condition. Modeling studies indicate that this high EQE can be partly attributed to the large exciton diffusion length in the pentacene film as well as efficient dissociation of excitons at the pentacene/C60 heterojunction.
Effect of a trapping molecule on the monolithic organic photorefractive materials
Authors: Hou Zhanjia , You Wei , Yu Luping
Published: December 2004

A peculiar effect of a trapping molecule on two closely related monolithic organic photorefractive (PR) materials was described. It was found that the trapping molecule C affects the PR performances differently in two materials made from either A or B, although the two molecules have similar chemical structures. Detailed studies on the charge mobility with the time-of-flight technique and activation energies for charge transport revealed that the trapping molecule C plays the role of electron trapper in material A and bipolar trapping center for both hole and electron in material B.
Transmittance of a tunable filter at terahertz frequencies
Authors: Drysdale Timothy D. , Gregory Ian S. , Baker Colin , Linfield Edmund H. , Tribe William R. , Cumming David R. S.
Published: December 2004

A metallic photonic crystal filter has been demonstrated at terahertz frequencies, with the passband tunable over the range of 365–386 GHz. Tuning is achieved by a relative lateral shift of two metallic photonic crystal plates. Each plate is comprised of two orthogonal layers of gratings and integral mounting lugs. The plates are micromachined from silicon wafers then coated in gold to provide metallic electromagnetic behavior. An insertion loss of 3–7 dB and Q in the range of 20–30 was achieved. A shift of 140μm gave a tuning range of 21 GHz, tuning sensitivity of 150 GHz/mm, and a fractional tuning range of 6%.
Coherent longitudinal optical phonon and plasmon coupling in the near-surface region of InN
Authors: Chang Y.-M. , Chuang C. T. , Chia C. T. , Tsen K. T. , Lu H. , Schaff W. J.
Published: December 2004

Coherent phonon spectroscopy of a high-quality InN epitaxial layer is carried out using time-resolved second-harmonic generation. A coherent longitudinal optical phonon and plasmon coupling mode only at 447cm−1 can be resolved in the spectrum. Its frequency shows no dependence on the photoinjected carrier density up to 1.5×1019cm−3. This phenomenon is attributed to the hybridization of a coherent A1(LO) phonon with the intrinsic cold plasma accumulated in the near-surface region of InN, where the plasma density could reach on the order of 1020cm−3, much higher than the bulk carrier concentration 1×1018cm−3 determined by Hall effect measurement.
Study of exciton-polariton spin dynamics
Authors: Soleimani H. Rahimpour , Cronenberger S. , Crégut O. , Likforman J.-P. , Gallart M. , Ostatnicky T. , Gilliot P. , Hönerlage B.
Published: December 2004

We study the relaxation dynamics of spin-polarized exciton-polaritons using a technique in a pump-probe configuration: According to their total angular momentum, exciton-polaritons can be excited by circularly polarized light of either σ+ or σ− helicities. In addition, a bound state of two excitons may exist to which the transition is only allowed when using two photons of opposite helicities. After excitation by a pump pulse of σ+ helicity, additional polaritons from a probe pulse of σ− helicity may be absorbed to excite biexcitons, while absorption of those with σ+ helicity becomes possible only after a spin-flip process. It is characterized by a time-constant τs, which can be determined by a time-resolved study of the induced transmission changes at the exciton–biexciton transition. We demonstrate this method using bulk CuCl, in which the biexciton binding energy is large and in which effects due to polariton propagation can be nicely evidenced. We thus identify a spectral region where the spin-flip process is dominating, which is situated just below the polariton bottleneck.
Control of carbon nanotube morphology by change of applied bias field during growth
Authors: Chen L.-H. , AuBuchon J. F. , Gapin A. , Daraio C. , Bandaru P. , Jin S. , Kim D. W. , Yoo I. K. , Wang C. M.
Published: December 2004

Carbon nanotube morphology has been engineered via simple control of applied voltage during dc plasma chemical vapor deposition growth. Below a critical applied voltage, a nanotube configuration of vertically aligned tubes with a constant diameter is obtained. Above the critical voltage, a nanocone-type configuration is obtained. The strongly field-dependent transition in morphology is attributed primarily to the plasma etching and decrease in the size of nanotube-nucleating catalyst particles. A two-step control of applied voltage allows a creation of dual-structured nanotube morphology consisting of a broad base nanocone (∼200nm dia.) with a small diameter nanotube (∼7nm) vertically emanating from the apex of the nanocone, which may be useful for atomic force microscopy.
Genomic data support the hominoid slowdown and an Early Oligocene estimate for the hominoid–cercopithecoid divergence
Authors: Steiper Michael E. , Young Nathan M. , Sukarna Tika Y.
Published: December 2004

Several lines of indirect evidence suggest that hominoids (apes and humans) and cercopithecoids (Old World monkeys) diverged around 23–25 Mya. Importantly, although this range of dates has been used as both an initial assumption and as a confirmation of results in many molecular-clock analyses, it has not been critically assessed on its own merits. In this article we test the robusticity of the 23- to 25-Mya estimate with ≈150,000 base pairs of orthologous DNA sequence data from two cercopithecoids and two hominoids by using quartet analysis. This method is an improvement over other estimates of the hominoid–cercopithecoid divergence because it incorporates two calibration points, one each within cercopithecoids and hominoids, and tests for a statistically appropriate model of molecular evolution. Most comparisons reject rate constancy in favor of a model incorporating two rates of evolution, supporting the “hominoid slowdown” hypothesis. By using this model of molecular evolution, the hominoid–cercopithecoid divergence is estimated to range from 29.2 to 34.5 Mya, significantly older than most previous analyses. Hominoid–cercopithecoid divergence dates of 23–25 Mya fall outside of the confidence intervals estimated, suggesting that as much as one-third of ape evolution has not been paleontologically sampled. Identifying stem cercopithecoids or hominoids from this period will be difficult because derived features that define crown catarrhines need not be present in early members of these lineages. More sites that sample primate habitats from the Oligocene of Africa are needed to better understand early ape and Old World monkey evolution.
Ordered patterns of liquid crystal toroidal defects by microchannel confinement
Authors: Choi Myung Chul , Pfohl Thomas , Wen Zhiyu , Li Youli , Kim Mahn Won , Israelachvili Jacob N. , Safinya Cyrus R.
Published: December 2004

In this article we present experimental results demonstrating an approach to controlling the size and spatial patterning of defect domains in a smectic liquid crystal (LC) by geometric confinement in surface-modified microchannels. By confining the LC 4′-octyl-4-cyanobiphenyl in μm-sized rectangular channels with controlled surface polarity, we were able to generate defect domains that are not only nearly uniform in size but also arranged in quasi-2D ordered patterns. Atomic force microscopy measurements revealed that the defects have a toroidal topology, which we argue is dictated by the boundary conditions imposed by the walls of the microchannel. We show that the defects can be considered to be colloidal objects, which interact with each other to form ordered patterns. This method opens the possibility for exploiting the unique optical and rheological properties associated with LC defects to making new materials. For example, the control of the shape, size, and spatial arrangement of the defects at the mesoscale suggests applications in patterning, templating, and when extended to lyotropic LCs, a process leading to uniform-sized spherical particles for chemical encapsulation and delivery.
Plasma proteome of severe acute respiratory syndrome analyzed by two-dimensional gel electrophoresis and mass spectrometry
Authors: Chen Jenn-Han , Chang Yu-Wang , Yao Chen-Wen , Chiueh Tzong-Shi , Huang Su-Chin , Chien Ko-Yi , Chen An , Chang Feng-Yee , Wong Chi-Huey , Chen Yu-Ju
Published: December 2004

We have investigated the plasma proteome by using 2D gel electrophoresis and MS from patients with severe acute respiratory syndrome (SARS). A complete proteomic analysis was performed on four patients with SARS in different time courses, and a total of 38 differential spots were selected for protein identification. Most of the proteins identified are acute phase proteins, and their presence represents the consequence of serial cascades initiated by SARS-coronavirus infection. There are several proteins that have never been identified in plasma before using 2D gel electrophoresis, among which peroxiredoxin II was chosen for further study by analyzing additional 20 plasma samples from patients with probable and suspected SARS and patients with fever, respectively. The results showed that the level of plasma peroxiredoxin II in patients with SARS is significantly high and could be secreted by T cells. Taken together, our findings indicate that active innate immune responses, along with the oxidation-associated injuries, may play a major role in the pathogenesis of SARS.
Helminths infecting the parthenogenetic whiptail lizard Cnemidophorus nativo in a restinga habitat of Bahia State, Brazil
Authors: Menezes V.A. , Vrcibradic D. , Vicente J.J. , Dutra G.F. , Rocha C.F.D.
Published: December 2004

A sample of 101 specimens of the unisexual whiptail lizard Cnemidophorus nativo (Squamata; Teiidae) from a coastal site in Bahia State, Brazil were examined for the presence of endoparasites. Of these, 35 (34.7%) harboured helminths. Six helminth species were recovered from C. nativo, including five nematodes (Physaloptera retusa, Physalopteroides venancioi, Subulura lacertilia, Skrjabinelazia intermedia and Parapharyngodon sp., and one cestode (Oochoristica ameivae), all representing new host records. Most lizards were infected by a single species of helminth and none by more than three. Infection rates were neither significantly influenced by host body size nor by environmental factors. The results are compared with data from studies on other whiptail species in both South and North America.
Effects of copper sulphate on in vitro encystment of the cercariae of Echinostoma caproni
Authors: Fried B. , Schneck J.L.
Published: December 2004

The effects of various concentrations of copper sulphate were studied on in vitro encystment of Echinostoma caproni in a Locke's–artificial spring water (ASW) (1:1) medium. Cercariae were killed in 10,000 mg l−1 CuSO4 in Locke's–ASW (1:1) within 24 h and extruded cystogenous material to produce an abnormal cyst wall. The ‘emergency response’ of encystment to high concentrations of copper reported for Parorchis acanthus cercariae did not occur in E. caproni. Concentrations of 1000 mg l−1 and 100 mg l−1 CuSO4 in Locke's–ASW (1:1) also killed the cercariae without encystment by 48 h. A concentration of 10 mg l−1 CuSO4 in Locke's–ASW (1:1) allowed for normal in vitro encystment within 48 h and these cysts were capable of excystation in a trypsin–bile salts medium.
The prevalence, intensity and clinical signs of urinary schistosomiasis in Imo state, Nigeria
Authors: Okoli C.G. , Iwuala M.O.E.
Published: December 2004

Urine samples were assayed for urinary schistosomiasis in four local government areas (LGA) of Imo State, Nigeria between May 1998 and September 2000. A total of 3504 persons were sampled, with 880 (25.1%) being positive for urinary schistosomiasis, based on records of eggs ofSchistosoma haematobium. The prevalence ofS. haematobiuminfection differed in the various LGAs, with Oguta (38.9%) and Owerri-West (10.4%) showing the highest and the lowest values, respectively. Prevalence was higher in males (67.4%) than in females (32.6%) and in subjects 11–20 years of age (31.5%), while prevalence varied among different occupational groups, with farmers ranking the highest (41.6%). Visible haematuria was the predominant symptom (P<0.05). Of 880 persons positive for eggs ofS. haematobium, 452 (51.4%) had visible haematuria, followed by suprapubic pains 214 (24.3%) and painful micturition 97 (11.0%). Although 367 (10. 5%) of the sampled subjects with eggs ofS. haematobiumshowed no visible haematuria, 513 (14.6%) clearly demonstrated haematuria.
Delayed macrofilaricidal activity of diethylcarbamazine against Brugia pahangi in Mongolian jirds
Authors: Fujimaki Y. , Sithithaworn P. , Mitsui Y. , Aoki Y.
Published: December 2004

The macrofilaricidal activity of diethylcarbamazine (DEC) was confirmed in jirds infected with Brugia pahangi. Seventy jirds were inoculated subcutaneously with 100 infective larvae. At 20 weeks post-infection, the microfilaraemic jirds were divided into two groups, untreated and treated. For the treated group, 200 mg kg−1 of DEC was injected intraperitoneally for 5 consecutive days. One, 4, 8, 12, 16 and 27 weeks after the final treatment, 4–7 jirds in each group were sacrificed to measure adult worm burdens. The number of adult worms recovered from treated jirds was comparable to controls at earlier necropsy (1 and 4 weeks post-treatment). However, at late necropsy (8 weeks and later) the recovery rate of adult worms in treated jirds was significantly lower than that in untreated controls, indicating an adultcidal effect of DEC. The present study demonstrates that DEC requires 8 weeks to kill B. pahangi adult worms in jirds and that the Mongolian jird is a useful model for screening antifilarial activity.
Influence of cadmium exposure on the incidence of first intermediate host encystment by Echinoparyphium recurvatum cercariae in Lymnaea peregra
Authors: Morley N.J. , Crane M. , Lewis J.W.
Published: December 2004

The effect of cadmium exposure of the snail first intermediate host Lymnaea peregra on the incidence of encystment of Echinoparyphium recurvatum (Digenea: Echinostomatidae) cercariae without emergence from the snail was investigated. Exposure to 100 μg l−1 Cd for 72 h caused a significant increase in the incidence of first host encystment when compared to controls. In addition, autometallographic staining of E. recurvatum daughter rediae and developing cercariae showed that there was metal accumulation within their body tissues. The significance of these findings to parasite transmission in metal-polluted environments is discussed.
Parametric Bäcklund transformations I: Phenomenology
Authors: Clelland Jeanne , Ivey Thomas
Published: December 2004

We begin an exploration of parametric Bäcklund transformations for hyperbolic Monge-Ampère systems. (The appearance of an arbitrary parameter in the transformation is a feature of several well-known completely integrable PDEs.) We compute invariants for such transformations and explore the behavior of four examples, two of which are new, in terms of their invariants, symmetries, and conservation laws. We prove some preliminary results and indicate directions for further research.
Stable and finite Morse index solutions on 𝐑ⁿ or on bounded domains with small diffusion
Authors: Dancer E.
Published: December 2004

In this paper, we study bounded solutions of

−
Δ
u
=
f
(
u
)

- \Delta u = f (u)

on

R

n

\mathbf {R}^n

(where

n
=
2

n = 2

and sometimes

n
=
3

n = 3

) and show that, for most

f
f

’s, the weakly stable and finite Morse index solutions are quite simple. We then use this to obtain a very good understanding of the stable and bounded Morse index solutions of

−

ϵ
2

Δ
u
=
f
(
u
)

- \epsilon ^2 \Delta u = f (u)

on

Ω
\Omega

with Dirichlet or Neumann boundary conditions for small

ϵ
\epsilon

.
On the degenerate Beltrami equation
Authors: Gutlyanskiĭ V. , Martio O. , Sugawa T. , Vuorinen M.
Published: December 2004

We study the well-known Beltrami equation under the assumption that its measurable complex-valued coefficient

μ
(
z
)

\mu (z)

has the norm

‖
μ

‖
∞

=
1.

\|\mu \|_\infty =1.

Sufficient conditions for the existence of a homeomorphic solution to the Beltrami equation on the Riemann sphere are given in terms of the directional dilatation coefficients of

μ
.

\mu .

A uniqueness theorem is also proved when the singular set

Sing
⁡
(
μ
)

\operatorname {Sing} (\mu )

of

μ
\mu

is contained in a totally disconnected compact set with an additional thinness condition on

Sing
⁡
(
μ
)
.

\operatorname {Sing}(\mu ).
Geometry of Fermat adeles
Authors: Buium Alexandru
Published: December 2004

If

L
(
a
,
s
)
:=

∑
n

c
(
n
,
a
)

n

−
s

L(a,s):=\sum _n c(n,a)n^{-s}

is a family of “geometric”

L
−

L-

functions depending on a parameter

a
a

, then the function

(
p
,
a
)
↦
c
(
p
,
a
)

(p,a)\mapsto c(p,a)

, where

p
p

runs through the set of prime integers, is not a rational function and hence is not a function belonging to algebraic geometry. The aim of the paper is to show that if one enlarges algebraic geometry by “adjoining a Fermat quotient operation”, then the functions

c
(
p
,
a
)

c(p,a)

become functions in the enlarged geometry at least for

L
−

L-

functions of curves and Abelian varieties.
A quadratic approximation to the Sendov radius near the unit circle
Authors: Miller Michael
Published: December 2004

Define

S
(
n
,
β
)

S(n,\beta )

to be the set of complex polynomials of degree

n
≥
2

n\ge 2

with all roots in the unit disk and at least one root at

β
\beta

. For a polynomial 

P
P

, define

|

P

|

β

|P|_\beta

to be the distance between

β
\beta

and the closest root of the derivative 

P
′

P’

. Finally, define
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="r Subscript n Baseline left-parenthesis beta right-parenthesis equals sup left-brace right-brace colon vertical-bar vertical-bar upper P beta colon element-of element-of upper P of SS left-parenthesis right-parenthesis comma n comma beta">

r
n

(
β
)
=
sup
{

|

P

|

β

:
P
∈
S
(
n
,
β
)
}

r_n(\beta )=\sup \{ |P|_\beta : P \in S(n,\beta ) \}

. In this notation, a conjecture of Bl. Sendov claims that

r
n

(
β
)
≤
1

r_n(\beta )\le 1

. In this paper we investigate Sendov’s conjecture near the unit circle, by computing constants

C
1

C_1

and

C
2

C_2

(depending only on

n
n

) such that
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="r Subscript n Baseline left-parenthesis beta right-parenthesis tilde 1 plus upper C 1 left-parenthesis 1 minus StartAbsoluteValue beta EndAbsoluteValue right-parenthesis plus upper C 2 left-parenthesis 1 minus StartAbsoluteValue beta EndAbsoluteValue right-parenthesis squared">

r
n

(
β
)
∼
1
+

C
1

(
1
−

|

β

|

)
+

C
2

(
1
−

|

β

|

)
2

r_n(\beta )\sim 1+C_1(1-|\beta |)+C_2(1-|\beta |)^2

for

|

β

|

|\beta |

near

1
1

. We also consider some consequences of this approximation, including a hint of where one might look for a counterexample to Sendov’s conjecture.
Projected products of polygons
Authors: Ziegler Günter
Published: December 2004

It is an open problem to characterize the cone of

f
f

-vectors of

4
4

-dimensional convex polytopes. The question whether the “fatness” of the

f
f

-vector of a

4
4

-polytope can be arbitrarily large is a key problem in this context. Here we construct a

2
2

-parameter family of

4
4

-dimensional polytopes

π
(

P
n

2
r

)

\pi (P^{2r}_n)

with extreme combinatorial structure. In this family, the “fatness” of the

f
f

-vector gets arbitrarily close to 

9
9

; an analogous invariant of the flag vector, the “complexity,” gets arbitrarily close to 

16
16

.

The polytopes are obtained from suitable deformed products of even polygons by a projection to 

R

4

\mathbb {R}^4

.
Dynamics of Relative Chromosome Position during the Cell Cycle
Authors: Essers Jeroen , van Cappellen Wiggert A. , Theil Arjan F. , van Drunen Ellen , Jaspers Nicolaas G.J. , Hoeijmakers Jan H.J. , Wyman Claire , Vermeulen Wim , Kanaar Roland
Published: December 2004

The position of chromosomal neighborhoods in living cells was followed using three different methods for marking chromosomal domains occupying arbitrary locations in the nucleus; photobleaching of GFP-labeled histone H2B, local UV-marked DNA, and photobleaching of fluorescently labeled DNA. All methods revealed that global chromosomal organization can be reestablished through one cell division from mother to daughters. By simultaneously monitoring cell cycle stage in the cells in which relative chromosomal domain positions were tracked, we observed that chromosomal neighborhood organization is apparently lost in the early G1 phase of the cell cycle. However, the daughter cells eventually regain the general chromosomal organization pattern of their mothers, suggesting an active mechanism could be at play to reestablish chromosomal neighborhoods.
Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC)
Authors: Rahman S. A. , Advani P. , Schunk R. , Schrader R. , Schomburg Dietmar
Published: December 2004

Motivation: Pathway Hunter Tool (PHT), is a fast, robust and user-friendly tool to analyse the shortest paths in metabolic pathways. The user can perform shortest path analysis for one or more organisms or can build virtual organisms (networks) using enzymes. Using PHT, the user can also calculate the average shortest path (Jungnickel, 2002 Graphs, Network and Algorithm. Springer-Verlag, Berlin), average alternate path and the top 10 hubs in the metabolic network. The comparative study of metabolic connectivity and observing the cross talk between metabolic pathways among various sequenced genomes is possible.

Results: A new algorithm for finding the biochemically valid connectivity between metabolites in a metabolic network was developed and implemented. A predefined manual assignment of side metabolites (like ATP, ADP, water, CO2 etc.) and main metabolites is not necessary as the new concept uses chemical structure information (global and local similarity) between metabolites for identification of the shortest path.

Availability: PHT is accessible at http://www.pht.uni-koeln.de

Contact:  d.schomburg@uni-koeln.de
MapLinker: a software tool that aids physical map-linked whole genome shotgun assembly
Authors: Xu Jian , Gordon Jeffrey I.
Published: December 2004

Summary: MapLinker is an analysis tool, as well as a browsing interface, that facilitates integration of whole genome sequence assembly with a clone-based physical map. Using the locations of sequence markers on the physical map, MapLinker generates a tentative sequence map of the genome that serves to verify the map and to guide genome-wide finishing.

Availability: MapLinker is freely available at http://gordonlab.wustl.edu/MapLinker

Contact:  jgordon@molecool.wustl.edu, jxu@watson.wustl.edu
Quantile smoothing of array CGH data
Authors: Eilers Paul H. C. , de Menezes Renée X.
Published: December 2004

Motivation: Plots of array Comparative Genomic Hybridization (CGH) data often show special patterns: stretches of constant level (copy number) with sharp jumps between them. There can also be much noise. Classic smoothing algorithms do not work well, because they introduce too much rounding. To remedy this, we introduce a fast and effective smoothing algorithm based on penalized quantile regression. It can compute arbitrary quantile curves, but we concentrate on the median to show the trend and the lower and upper quartile curves showing the spread of the data. Two-fold cross-validation is used for optimizing the weight of the penalties.

Results: Simulated data and a published dataset are used to show the capabilities of the method to detect the segments of changed copy numbers in array CGH data.

Availability: Software for R and Matlab is available.

Contact:  p.eilers@lumc.nl
A role for E2F6 in distinguishing G1/S- and G2/M-specific transcription
Authors: Giangrande Paloma H. , Zhu Wencheng , Schlisio Susanne , Sun Xin , Mori Seiichi , Gaubatz Stefan , Nevins Joseph R.
Published: December 2004

E2F transcription factors play a critical role in the control of cell cycle progression, regulating the expression of genes involved in DNA replication, DNA repair, mitosis, and cell fate. This involves both positive-acting and negative-acting E2F proteins, the latter group including the E2F6 protein, which has been shown to function as an Rb-independent repressor of E2F-target gene transcription. In an effort to better delineate the context of E2F6 function, including the mechanisms of E2F6 functional specificity, we used chromatin immunoprecipitation assays to assess when and with what genes E2F6 associates during a cell cycle. We find that E2F6 associates specifically with the E2F target genes that are activated at G1/S; this interaction occurs during S phase of the cell cycle. In sharp contrast, E2F6 does not bind to E2F-regulated genes activated at G2/M. In the absence of E2F6, E2F4 can bind to the G1/S-regulated promoters and compensate for loss of E2F6 function. Indeed, inhibition of both E2F4 and E2F6 activity results in specific derepression of these genes during S phase. We conclude that E2F6 functions as a repressor of E2F-dependent transcription during S phase and given the specificity for the G1/S-regulated genes, we propose that E2F6 functions to distinguish G1/S and G2/M transcription during the cell cycle.
A systems view of mRNP biology
Authors: Hieronymus Haley , Silver Pamela A.
Published: December 2004

Gene expression occurs through a complex mRNA-protein (mRNP) system that stretches from transcription to translation. Gene expression processes are increasingly studied from global perspectives in order to understand their pathways, properties, and behaviors as a system. Here we review these beginnings of mRNP systems biology, as they have emerged from recent large-scale investigation of mRNP components, interactions, and dynamics. Such work has begun to lay the foundation for a broader, integrated view of mRNP organization in gene expression.