bluuebunny/crossref_metadata_2025 huggingface dataset:
Vertical profiles of aerosol volume from high spectral resolution infrared transmission measurements: Results
Authors: Eldering Annmarie , Kahn Brian H. , Mills Franklin P. , Irion Fredrick W. , Steele Helen M. , Gunson Michael R.
Published: October 2004

The high‐resolution infrared absorption spectra of the Atmospheric Trace Molecule Spectroscopy (ATMOS) experiment are utilized to derive vertical profiles of sulfate aerosol volume density and extinction coefficient. Following the eruption of Mt. Pinatubo in June 1991, the ATMOS spectra obtained on three Space Shuttle missions (1992, 1993, and 1994) provide a unique opportunity to study the global stratospheric sulfate aerosol layer shortly after a major volcanic eruption and periodically during the decay phase. Synthetic sulfate aerosol spectra are fit to the observed spectra, and a global fitting inversion routine is used to derive vertical profiles of sulfate aerosol volume density. Vertical profiles of sulfate aerosol volume density for the three missions over portions of the globe are presented, with the peak in aerosol volume density occurring from as low as 10 km (polar latitudes) to as high as 20 km (subtropical latitudes). Derived aerosol volume density is as high as 2–3.5 μm3 cm−3 ±10% in 1992, decreasing to 0.2–0.5 μm3 cm−3 ±20% in 1994, in agreement with other experiments. Vertical extinction profiles derived from ATMOS are compared with profiles from Improved Stratospheric And Mesospheric Sounder (ISAMS) and Cryogenic Limb Array Etalon Spectrometer (CLAES) that coincide in space and time and show good general agreement. The uncertainty of the ATMOS vertical profiles is similar to CLAES and consistently smaller than ISAMS at similar altitudes.
Airborne measurements of ground and cloud spectral albedos under low aerosol loads
Authors: Webb Ann R. , Kylling Arve , Wendisch Manfred , Jäkel Evelyn
Published: October 2004

Spectral albedo measurements have been made by three airborne systems (two aircraft and one balloon) over the flat arable land of East Anglia, UK, and above clouds. The spectral albedos measured at the various flight altitudes include the backscattering of the atmosphere beneath the aircraft/balloon, which has to be removed to get the areal spectral surface albedo. Data derived from the airborne spectroradiometers showed the areal surface albedo to be about 0.02 in the UVB (wavelength range between 280–320 nm), increasing with wavelength to about 0.05 at 500 nm. The cloud albedos were measured above two different stratus layers, one completely overcast and one broken. Above the overcast cloud sheet the albedo was independent of wavelength with values between 0.62 and 0.85 depending on position above cloud and altitude. Above the broken cloud layer the averaged albedo spectra showed clear spectral reflection features from the underlying surface mixed with the cloud albedo signatures.
Tropospheric ozone climatology over Irene, South Africa, from 1990 to 1994 and 1998 to 2002
Authors: Diab R. D. , Thompson A. M. , Mari K. , Ramsay L. , Coetzee G. J. R.
Published: October 2004

Ozonesonde measurements over Irene in South Africa are reported for the period 1990 to 1994 and a more recent period, 1998 to 2002, when the station became part of the Southern Hemisphere Additional Ozonesondes (SHADOZ) network. Irene displays the characteristic Southern Hemisphere springtime tropospheric ozone maximum, but its seasonal features are modulated by both tropical and midlatitude influences because of its location (25°54′S, 28°13′E) on the boundary of zonally defined meteorological regimes. The tropical savanna biomass burning signature, namely, the spring maximum, is less distinct in the lower troposphere than at stations closer to biomass burning source regions nearer the equator, although long‐range transport and recirculation in the subtropical anticyclonic gyre over southern Africa permit the buildup of relatively high springtime midtropospheric ozone. Midlatitude dynamical influences are evident, predominantly in winter when upper tropospheric ozone is enhanced as a result of stratospheric‐tropospheric injection of ozone. Mean tropospheric ozone values range between 40 and 60 ppbv throughout the year and increase by ∼20 ppbv in spring. The increase (∼10 ppbv) in surface and lower tropospheric ozone between the two time periods is attributed to an increase in urban‐industrial emissions. A classification of ozone profiles using a cluster analysis has enabled the delineation of a background and “most polluted” profile. Enhancements of at least 30% occur throughout the troposphere in spring, and in certain layers, increases close to 100% are observed.
Removal of NOxand NOyin Asian outflow plumes: Aircraft measurements over the western Pacific in January 2002
Authors: Takegawa N. , Kondo Y. , Koike M. , Chen G. , Machida T. , Watai T. , Blake D. R. , Streets D. G. , Woo J.‐H. , Carmichael G. R. , Kita K. , Miyazaki Y. , Shirai T. , Liley J. B. , Ogawa T.
Published: October 2004

The Pacific Exploration of Asian Continental Emission Phase A (PEACE‐A) aircraft measurement campaign was conducted over the western Pacific in January 2002. Correlations of carbon monoxide (CO) with carbon dioxide (CO2) and back trajectories are used to identify plumes strongly affected by Asian continental emissions. ΔCO/ΔCO2ratios (i.e., linear regression slopes of CO‐CO2) in the plumes generally fall within the variability range of the CO/CO2emission ratios estimated from an emission inventory for east Asia, demonstrating the consistency between the aircraft measurements and the emission characterization. Removal rates of reactive nitrogen (NOxand NOy) for the study region (altitude <4 km, 124°–140°E, 25°–45°N) are estimated using the correlation with CO2, the photochemical age of the plumes, and the NOx/CO2emission ratio derived from the emission inventory. The plume age is estimated from the rates of hydrocarbon decay and hydroxyl radical (OH) concentration calculated using a constrained photochemical box model. The average lifetime of NOxis estimated to be 1.2 ± 0.4 days. Possible processes controlling the NOxlifetime are discussed in conjunction with results from earlier studies. The average lifetime of NOyis estimated to be 1.7 ± 0.5 days, which is comparable to the NOylifetime of 1.7–1.8 days that has been previously reported for outflow from the United States. This similarity suggests the importance of chemical processing near the source regions in determining the NOyabundance.
First evidence for ultrahigh‐pressure metamorphism of eclogites in Pohorje, Slovenia: Tracing deep continental subduction in the Eastern Alps
Authors: Janák Marian , Froitzheim Nikolaus , Lupták Branislav , Vrabec Mirijam , Ravna Erling J. Krogh
Published: October 2004

The first evidence for ultrahigh‐pressure (UHP) metamorphism in the Eastern Alps is reported from kyanite eclogites of the Pohorje Mountains in Slovenia. Polycrystalline quartz inclusions surrounded by radial fractures in garnet, omphacite, and kyanite are interpreted to be pseudomorphs after coesite. Abundant quartz rods and needles in omphacite indicate an exsolution from a preexisting supersilicic clinopyroxene that contained a Ca‐Eskola component. Geothermobarometry on the mineral assemblage garnet + omphacite + kyanite + phengite + quartz/or coesite yields peak pressure and temperature conditions of 3.0–3.1 GPa and 760°–825°C, well within the stability field of coesite, thus supporting the microtextural evidence for UHP metamorphism. This records the highest‐pressure conditions of Eo‐Alpine metamorphism during the Cretaceous orogeny in the Alps, implying a very deep subduction of the continental crust to at least 90–100 km depths. The new data are evidence for a regional southeastward increase of peak pressures in the Lower Central Austroalpine, indicating a south‐ to eastward dip of the subduction zone. Subduction was intracontinental; northwestern parts of the Austroalpine (Lower Central Austroalpine) were subducted under southeastern parts (Upper Central Austroalpine). The subduction zone formed in the Early Cretaceous in the northwestern foreland of the Meliata suture after Late Jurassic closure of the Meliata Ocean and the resulting collision, by a forward subduction shift to a Permian rift.
The Avez–Seifert theorem for the relativistic Lorentz force equation
Authors: Caponio Erasmo , Masiello Antonio
Published: October 2004

In this paper we prove an extension of the Avez–Seifert theorem to the relativistic Lorentz force equation. Let (M,g) be a globally hyperbolic space–time, F an exact 2-form on M representing the electromagnetic field, F̂ the Lorentz force associated to F, and q a charge for a test particle. Let p0 and p1 be two chronologically related points on M, then there exists a future-pointing timelike solution of the Lorentz force equation Dsż=qF̂(z)[ż], connecting p0 and p1.
Investigation of the time-delay estimation method for turbulent velocity inference
Authors: Holland C. , Tynan G. R. , McKee G. R. , Fonck R. J.
Published: October 2004

A key challenge for the development of practical fusion power is to understand how particle and thermal transport are controlled by plasma turbulence. Of particular interest is the turbulent velocity field, which drives the “anomalous” fluxes. Current measurements of the velocity fluctuations have generally been limited to the outer edges of the plasma, but the recently proposed time-delay estimation method offers the possibility of measuring velocity fluctuations further into the plasma, motivating a comprehensive investigation of this method. The first step of this investigation, reported here, is to develop a greater degree of confidence in the method, by testing the technique on known signals and velocity fields. Issues such as optimal sampling rate, noise sensitivity, and the impact of signal processing techniques such as data windowing and interpolation are discussed. Future steps of the investigation will also be presented.
On the interpretation of fluctuation and E×B turbulent transport measured by Langmuir probes in fusion plasmas
Authors: Calderón E. , Hidalgo C. , Pedrosa M. A. , Silva C.
Published: October 2004

Plasma fluctuations and fluctuation-induced particle fluxes have been investigated in the plasma edge of the TJ-II stellarator using Langmuir probes. Simultaneous measurements of plasma fluctuations carried out by probes located in and out of the probe body sheath show similar results in the normalized level of fluctuations in the ion saturation current. However, floating potential fluctuations measured in the co and counter direction of the magnetic field on the sheath probe body show slight but significant differences. The local radial electrostatic turbulent driven transport measured in and out of the probe body sheath shows consistent results, within the errors bars due to uncertainties in the determination of the effective probe collecting area; the normalized local radial transport to the average ion saturation current (the effective velocity which is not affected by uncertainties in the probe area) show consistent results. These results and previous findings call into question the recent interpretation of probe measurements on the basis of the influence of the probe’s pre-sheath zone [B. Labombard, Phys. Plasmas. 9, 1300 (2002)].
Fluctuation measurements using a five-pin triple probe in the Joint European Torus boundary plasma
Authors: Silva C. , Gonçalves B. , Hidalgo C. , Pedrosa M. A. , Erents K. , Matthews G. , Pitts R. A.
Published: October 2004

A multi-probe system has been developed to investigate the importance of electron temperature fluctuations turbulent transport in the Joint European Torus boundary plasma. The compact five-pin triple probe has been designed to reduce the phase delay of fluctuations due to the finite pin separation in the standard triple probe technique, while still avoiding the effects of probe shadowing. This probe has been found to have advantages over the standard triple probe in the region close to the separatrix (r−rsep<0.01 m), where the fluctuation wavelength is large. Importantly, results obtained with the probe support the standard estimation of cross-field particle flux, which ignores temperature fluctuations. They cannot be ignored, however, in the estimation of energy losses since measurements show that the conducted energy may be as large as the convected component.
Supersonic gas injector for fueling and diagnostic applications on the National Spherical Torus Experiment
Authors: Soukhanovskii V. A. , Kugel H. W. , Kaita R. , Majeski R. , Roquemore A. L.
Published: October 2004

A prototype pulsed supersonic gas injector (SGI) has been developed for the National Spherical Torus Experiment (NSTX). Experiments in NSTX will explore the compatibility of the supersonic gas jet fueling with the H-mode plasma edge, edge localized mode control, edge magnetohydrodynamic stability, radio frequency heating scenarios, and start-up scenarios with a fast plasma density ramp up. The diagnostic applications include localized impurity gas injections for transport and turbulence experiments and edge helium spectroscopy for edge Te and ne profile measurements. Nozzle and gas injector design considerations are presented and four types of supersonic nozzles are discussed. The prototype SGI operates at room temperature. It is comprised of a small graphite Laval nozzle coupled to a modified commercial piezoelectric valve and mounted on a movable vacuum feedthrough. The critical properties of the SGI jet—low divergence, high density, and sharp boundary gradient, achievable only at M>1, have been demonstrated in a laboratory setup simulating NSTX edge conditions. The Mach numbers of about 4, the injection rate up to 1022 particles/s, and the jet divergence half angle of 6° have been inferred from pulsed pressure measurements.
Tunnel probes for measurements of the electron and ion temperature in fusion plasmas
Authors: Gunn J. P. , Schrittwieser R. , Balan P. , Ioniţă C. , Stöckel J. , Adámek J. , Ďuran I. , Hron M. , Pánek R. , Bařina O. , Hrach R. , Vicher M. , Van Oost G. , Van Rompuy T. , Martines E.
Published: October 2004

We have developed tunnel probes for localized measurements of the electron and ion temperature in the edge plasma region of smaller tokamaks and stellarators. A normal tunnel probe for Te measurements consists of a metallic tunnel of 5 mm diameter and 5 mm length, with the axis parallel to the magnetic field. One side is open, the other side is closed by a metallic backplate, isolated from the tunnel. If both electrodes are biased negatively, ions flow into the office, and their current is distributed between the tunnel and the backplate. The ratio of the two ion currents is a function of Te. With an additional diaphragm in front of the orifice, the probe becomes ion sensitive, since the electrons are prevented from the tunnel because of their smaller gyroradius, but ions can still reach it. In this way, the perpendicular ion temperature can be derived. By segmenting the tunnel axially into two parts, also an approximate measure for the parallel ion temperature can be found.
Time resolved neutron flux diagnostics for quasi-steady-state operation study of the HT-7 tokamak
Authors: Zhu Yubao , Chen Juequan , Li Guiming
Published: October 2004

Time resolved neutron flux diagnostic systems based on BF3 proportional counter and ZnS(Ag) scintillator have been developed and implemented on the HT-7 superconducting tokamak. A ten-channel flexible data acquisition system designed with a PCI-8554 general digital counter and industry PC is equipped. Calibrations are made with several neutron sources. The consistencies of experimental data from two techniques have been proven; the BF3 based system is more reliable with better detection efficiency. The measured neutron yield shows good agreement with the simple numerical calculation. The observed photo–neutron production indicates that photon–nuclear reactions are dominant in several special cases such as low density and disruption conditions. Good agreement on ion temperature deduced from neutron diagnosis and neutral particle analyzer under high parameter plasma conditions implies that neutron flux diagnostics can be used as an effective higher temporal resolution ion temperature monitor.
Plasma bolometry using a multislit shutter with piezoelectric actuator
Authors: Kuteev Boris V. , Outkine Andrew A. , Gabdullin Pavel G. , Kostrioukov Artem Yu. , Kapralov Vladimir G.
Published: October 2004

We offer to apply a shutter with a piezoelectric bimorph actuator as a modulator of radiation and particle fluxes. Such shutters may be useful to provide measurements in steady state regimes of tokamaks and stellarators because they allow one to avoid amplifier drifts and to simplify diagnostics calibration. Signal modulation makes it possible to apply the lock-in amplification technique, increasing the sensitivity and reducing the neutron doze collected by sensors. Experiments with pyroelectric sensors (LiTaO3) at 350 Hz modulation frequency have demonstrated the detection limit at 30 Hz equal to 15 μW/cm2, which is comparable to metallic bolometers.
Measurement of the rotational velocity in Hanbit mirror device by using the Gundestrup-emissive-triple probe system
Authors: Chung K.-S. , Kwak G. Y. , Choi Y.-S. , Lee M.-J. , Bak J. G. , Kwon M.
Published: October 2004

A new probe set, called the Gundestrup-emissive-triple (GET) probe, is developed to measure the rotational velocity, plasma potential, electron temperature, and plasma density profiles simultaneously in Hanbit mirror device. The GET probe system is composed of the Gunderstrup, an emissive, and a triple probe installed in one boron nitride probe holder, which is attached on the fast scanning injection system. Rotational and parallel flow velocities are deduced from the measurement of Gundestrup probe by using fluid and kinetic theories for unmagnetized and magnetized plasmas. The E×B drift velocity is also deduced from the measurement of plasma potential by an emissive probe. Electron temperature and plasma density variations are measured by a triple probe. Applicability of various theories will be addressed.
Performance of the magnetic sensor and the integrator for the KSTAR magnetic diagnostics
Authors: Bak J. G. , Lee S. G. ,   the KSTAR Project Team, Son DeRac
Published: October 2004

Magnetic sensors and the integrator for the magnetic field measurement have been developed for the engineering design of the KSTAR magnetic diagnostics (MDs). The frequency characteristics of a magnetic sensor (for magnetic fluctuation measurement) is investigated from the measurement of the response function of the sensor and the analysis of the equivalent electronic circuit in the frequency range of 10 kHz –15 MHz. An analog integrator, which automatically compensates a drift, is fabricated and its performance test (connected with a magnetic sensor) is carried out under a rf environment. The experimental results from the performance test of the sensor and the analog integrator are presented.
Design of the new magnetic sensors for Joint European Torus
Authors: Coccorese V. , Albanese R. , Altmann H. , Cramp S. , Edlington T. , Fullard K. , Gerasimov S. , Huntley S. , Lam N. , Loving A. , Riccardo V. , Sartori F. , Marren C. , McCarron E. , Sowden C. , Tidmarsh J. ,   JET-EFDA Contributors, Basso F. , Cenedese A. , Chitarin G. , DegliAgostini F. , Grando L. , Marcuzzi D. , Peruzzo S. , Pomaro N. , Solano E. R.
Published: October 2004

A new magnetic diagnostics system has been designed for the 2005 Joint European Torus (JET) experimental campaigns onward. The new system, which adds to the existing sensors, aims to improve the JET safety, reliability, and performance, with respect to: (i) equilibrium reconstruction; (ii) plasma shape control; (iii) coil failures; (iv) VDEs; (v) iron modeling; and (vi) magnetohydrodynamics poloidal mode analysis. The system consists of in-vessel and ex-vessel sensors. The former are a set of 38 coil pairs (normal and tangential), located as near as possible to the plasma. Coils are generally grouped in rails, in order to ease remote handling in-vessel installation. The system includes: (i) two outer poloidal limiter arrays (2×7 coil pairs); (ii) two divertor region arrays (2×7 coil pairs); and (iii) two top coil arrays (2×5 coil pairs). Ex-vessel sensors, including discrete coils, Hall probes, and flux loops (26 in total) will be installed on the iron limbs, in order to provide experimental data for the treatment of iron in equilibrium codes. The design is accompanied by a software analysis, aiming to predict the expected improvement.
Ion measurement of the edge plasma in the GAMMA10 tandem mirror device with an ion sensitive probe
Authors: Sekine T. , Saito T. , Tatematsu Y. , Yasuoka T. , Ikegami H. , Nagai D. , Nozaki K. , Ichimura M. , Higaki H. , Cho T.
Published: October 2004

An ion sensitive probe (ISP) has been applied to ion diagnostics of the edge plasma of the GAMMA10 tandem mirror device. Since high energy ions are created by ion cyclotron range of frequency heating in the central cell of GAMMA10, a secondary electron repeller electrode is set in to suppress secondary electrons emitted from the collector due to high energy ions. Then secondary electrons are successfully suppressed. The ion flux flowing into the collector is evaluated with numerical calculation of ion orbits. This calculation includes the potential profile near the tip of the ISP. Then a correction factor Fα of the ion flux to the free streaming one is determined. The calculation yields V–I characteristic of the collector current. The ion density can be estimated by using the measured ion temperature and the factor Fα. Sample data of the ion temperature and the ion density in the edge region of the central cell of GAMMA10 are given. The measurement with the ISP shows that the edge ion temperature of GAMMA10 plasma ranges from 100 to 400 eV, and the ion density from 0.5×1010 to 2×1010 cm−3.
Development, tests, and data acquisition of the integrated system of internal sensors for RFX
Authors: Serianni G. , Bolzonella T. , Cavazzana R. , Marchiori G. , Pomaro N. , Lotto L. , Monari M. , Taliercio C.
Published: October 2004

The RFX reversed field pinch (RFP) has undergone major modifications of the load assembly and is now equipped with a large number of active external coils for magnetohydrodynamics mode control. The study of the effects on the plasma of both the new passive structure and the active coils is then of great importance, as well as the investigation of turbulence due to its influence on plasma transport. An integrated system of magnetic, electrostatic and calorimetric sensors has been realized, fulfilling very challenging requirements in terms of spatial and temporal resolution, which are characteristic features of RFP plasmas. A description of the whole diagnostic system is given, including the original solutions adopted to cope with the limited space available and the thermal and electrical requirements, particularly for the calorimetrical probes. The tests performed on the whole system during the installation are presented. Signal conditioning and data acquisition are described.
Determination of velocity shears in a simple magnetized torus by means of a combined Langmuir and Mach probe
Authors: Riccardi C. , Barni R. , Fredriksen Å.
Published: October 2004

We present a multiple electric probe setup for diagnostics of plasmas which is aimed to simultaneously measure the fluctuations of the ion velocity field along one direction and the (E×B) flux perpendicular to it. The probe design is based on combining a Mach probe with two slightly spatially separated Langmuir probes. The probe has been prepared to operate in the turbulent regime of the simple magnetized torus Blaamann. Experiments have been focused on the measurements of shear in the velocity along the magnetic field and on its correlation with the radial flux. Preliminary results are showing the effectiveness of the proposed diagnostics as well as the relevance of velocity fluctuations and correlations in plasma turbulence and in anomalous transport.
Single channel analog data links for use with high bandwidth recording systems for the National Ignition Facility
Authors: Tran Vu , Bennett Corey V. , Sargis Paul D. , Kimbrough Joseph R. , Bell Perry M. , Blair Jerome J.
Published: October 2004

The National Ignition Facility at the Lawrence Livermore National Laboratory requires high bandwidth and high dynamic range data transmission from the target chamber area to diagnostic recording equipment approximately 46 m away. The systems need to pass short pulse signals with high fidelity, requiring a broadband frequency response from below 10 MHz to greater than 6 GHz, that has flat amplitude and a linear phase response. We present here the characterization of a few selected fiber optic systems and work done to optimize the performance of a fiber link and single-shot transient digitizer system. Each link is evaluated by its bandwidth, the fidelity of its step response, the signal loss, and its usable dynamic range.
Multiarm spirals in a two-dimensional cardiac substrate
Authors: Bursac Nenad , Aguel Felipe , Tung Leslie
Published: October 2004

A variety of chemical and biological nonlinear excitable media, including heart tissue, can support stable, self-organized waves of activity in a form of rotating single-arm spirals. In particular, heart tissue can support stationary and meandering spirals of electrical excitation, which have been shown to underlie different forms of cardiac arrhythmias. In contrast to single-arm spirals, stable multiarm spirals (multiple spiral waves that rotate in the same direction around a common organizing center) have not been demonstrated and studied yet in living excitable tissues. Here, we show that persistent multiarm spirals of electrical activity can be induced in monolayer cultures of neonatal rat heart cells by a short, rapid train of electrical point stimuli applied during single-arm-spiral activity. Stable formation is accomplished only in monolayers that show a relatively broad and steep dependence of impulse wavelength and propagation velocity on rate of excitation. The resulting multiarm spirals emit waves of electrical activity at rates faster than for single-arm spirals and exhibit two distinct behaviors, namely “arm-switching” and “tip-switching.” The phenomenon of rate acceleration due to an increase in the number of spiral arms possibly may underlie the acceleration of functional reentrant tachycardias paced by a clinician or an antitachycardia device.
Dissociation of experience-dependent and -independent changes in excitatory synaptic transmission during development of barrel cortex
Authors: Mierau Susanna B. , Meredith Rhiannon M. , Upton A. Louise , Paulsen Ole
Published: October 2004

A fundamental problem in the study of cortical development is the extent to which the formation and refinement of synaptic circuitry depends upon sensory experience. The barrel cortex is a useful model system to study experience-dependent cortical development because there is a simple mapping of individual whiskers to the corresponding barrel columns in the cortex. We investigated experience-dependent and -independent changes in glutamatergic synaptic transmission in the barrel cortex during the second postnatal week by comparing synaptic responses from whisker-intact mice at postnatal day (P) 7 and P14 with those from whisker-deprived mice at P14. α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) and
N
-methyl-D-aspartate (NMDA)-receptor-mediated excitatory synaptic responses were recorded from layer 2/3 pyramidal cells
in vitro
during voltage-clamp in response to stimulation in layer 4. We observed that the ratio of synaptic AMPA- to NMDA-receptor-mediated current (A/N ratio) increased with developmental age. The development of the A/N ratio was unchanged by deprivation of the whisker input throughout the second postnatal week. In contrast, the NMDA-receptor current decay and sensitivity to the NMDA receptor 2B subunit-selective antagonist ifenprodil was affected strongly by such deprivation. These results demonstrate a concurrent dissociation between sensory experience-dependent and -independent changes of glutamatergic transmission in the barrel cortex during the second postnatal week. Furthermore, they suggest that the development of subunit composition of synaptic receptors is dependent on sensory experience, whereas maturation of the synaptic A/N ratio is independent of such experience. Thus, different components of synaptic development may be governed by different developmental rules.
A system for enhancing genome-wide coexpression dynamics study
Authors: Li Ker-Chau , Liu Ching-Ti , Sun Wei , Yuan Shinsheng , Yu Tianwei
Published: October 2004

Statistical similarity analysis has been instrumental in elucidation of the voluminous microarray data. Genes with correlated expression profiles tend to be functionally associated. However, the majority of functionally associated genes turn out to be uncorrelated. One conceivable reason is that the expression of a gene can be sensitively dependent on the often-varying cellular state. The intrinsic state change has to be plastically accommodated by gene-regulatory mechanisms. To capture such dynamic coexpression between genes, a concept termed “liquid association” (LA) has been introduced recently. LA offers a scoring system to guide a genome-wide search for critical cellular players that may interfere with the coexpression of a pair of genes, thereby weakening their overall correlation. Although the LA method works in many cases, a direct extension to more than two genes is hindered by the “curse of dimensionality.” Here we introduce a strategy of finding an informative 2D projection to generalize LA for multiple genes. A web site is constructed that performs on-line LA computation for any user-specified group of genes. We apply this scoring system to study yeast protein complexes by using the
Saccharomyces cerevisiae
protein complexes database of the Munich Information Center for Protein Sequences. Human genes are also investigated by profiling of 60 cancer cell lines of the National Cancer Institute. In particular, our system links the expression of the Alzheimer's disease hallmark gene
APP
(amyloid-β precursor protein) to the β-site-cleaving enzymes BACE and BACE2, the γ-site-cleaving enzymes presenilin 1 and 2, apolipoprotein E, and other Alzheimer's disease-related genes.
The contribution of epistasis to the architecture of fitness in an RNA virus
Authors: Sanjuán Rafael , Moya Andrés , Elena Santiago F.
Published: October 2004

The tendency for genetic architectures to exhibit epistasis among mutations plays a central role in the modern synthesis of evolutionary biology and in theoretical descriptions of many evolutionary processes. Nevertheless, few studies unquestionably show whether, and how, mutations typically interact. Beneficial mutations are especially difficult to identify because of their scarcity. Consequently, epistasis among pairs of this important class of mutations has, to our knowledge, never before been explored. Interactions among genome components should be of special relevance in compacted genomes such as those of RNA viruses. To tackle these issues, we first generated 47 genotypes of vesicular stomatitis virus carrying pairs of nucleotide substitution mutations whose separated and combined deleterious effects on fitness were determined. Several pairs exhibited significant interactions for fitness, including antagonistic and synergistic epistasis. Synthetic lethals represented 50% of the latter. In a second set of experiments, 15 genotypes carrying pairs of beneficial mutations were also created. In this case, all significant interactions were antagonistic. Our results show that the architecture of the fitness depends on complex interactions among genome components.
TIFA activates IκB kinase (IKK) by promoting oligomerization and ubiquitination of TRAF6
Authors: Ea Chee-Kwee , Sun Lijun , Inoue Jun-Ichiro , Chen Zhijian J.
Published: October 2004

TRAF6 (tumor necrosis factor receptor-associated factor 6) is a RING (
r
eally
i
nteresting
n
ew
g
ene) domain ubiquitin (Ub) ligase that mediates the activation of protein kinases, such as transforming growth factor β-activated kinase (TAK1) and IκB kinase (IKK), by catalyzing the formation of a unique polyubiquitin chain linked through Lys-63 of Ub. Here, we present evidence that TIFA (TRAF-interacting protein with a forkhead-associated domain, also known as T2BP) activates IKK by promoting the oligomerization and Ub ligase activity of TRAF6. We show that recombinant TIFA protein, but not TRAF6-binding-defective mutant, can activate IKK in crude cytosolic extracts. Furthermore, TIFA activates IKK in an
in vitro
reconstitution system consisting of purified proteins, including TRAF6, the TAK1 kinase complex, and Ub-conjugating enzyme complex Ubc13–Uev1A. Interestingly, a fraction of recombinant TIFA protein exists as high-molecular-weight oligomers, and only these oligomeric forms of TIFA can activate IKK. Importantly, TIFA induces the oligomerization and polyubiquitination of TRAF6, which leads to the activation of TAK1 and IKK through a proteasome-independent mechanism.
Coding single-nucleotide polymorphisms associated with complex vs. Mendelian disease: Evolutionary evidence for differences in molecular effects
Authors: Thomas Paul D. , Kejariwal Anish
Published: October 2004

Most Mendelian diseases studied to date arise from mutations that lead to a single amino acid change in an encoded protein. An increasing number of complex diseases have also been associated with amino acid-changing single-nucleotide polymorphisms (coding SNPs, cSNPs), suggesting potential similarities between Mendelian and complex diseases at the molecular level. Here, we use two different evolutionary analyses to compare Mendelian and complex disease-associated cSNPs. In the first, we estimate the likelihood that a specific amino acid substitution in a protein will affect the protein's function, by using amino acid substitution scores derived from an alignment of related protein sequences and statistics from hidden Markov models. In the second, we use standard Ka/Ks ratios to make comparisons at the gene, rather than the individual amino acid, level. We find that Mendelian disease cSNPs have a very strong tendency to occur at highly conserved amino acid positions in proteins, suggesting that they generally have a severe impact on the function of the protein. Perhaps surprisingly, the distribution of amino acid substitution scores for complex disease cSNPs is dramatically different from the distribution for Mendelian disease cSNPs, and is indistinguishable from the distribution for “normal” human variation. Further, the distributions of Ka/Ks ratios for human and mouse orthologs indicate greater positive selection (or less negative selection) pressure on complex disease-associated genes, on average. These findings suggest that caution should be exercised when using Mendelian disease as a model for complex disease, at least with respect to molecular effects on protein function.
Fusogenic supramolecular vesicle systems induced by metal ion binding to amphiphilic ligands
Authors: Richard Antoine , Marchi-Artzner Valérie , Lalloz Marie-Noëlle , Brienne Marie-Josèphe , Artzner Franck , Gulik-Krzywicki Thaddée , Guedeau-Boudeville Marie-Alice , Lehn Jean-Marie
Published: October 2004

The incorporation of lipophilic ligands into the bilayer membrane of vesicles offers the possibility to induce, upon binding of suitable metal ions, a variety of processes, in particular vesicle aggregation and fusion and generation of vesicle arrays, under the control of specific metal–ligand recognition events. Synthetic bipyridine lipoligands Bn bearing a bipyridine unit as head group were prepared and incorporated into large unilamellar vesicles. The addition of Ni
2+
or Co
2+
metal ions led to the formation of complexes MBn and MBn
2
followed by spontaneous fusion to generate giant multilamellar vesicles. The metal ion complexation was followed by UV spectroscopy and the progressive fusion could be visualized by optical dark-field and fluorescence microscopies. Vesicle fusion occurred without leakage of the aqueous compartments and resulted in the formation of multilamellar giant vesicles because of the stacking of the lipoligands Bn. The fusion process required a long enough oligoethylene glycol spacer and a minimal concentration of lipoligand within the vesicle membrane. Metallosupramolecular systems such as the present one offer an attractive way to induce selective intervesicular processes, such as vesicle fusion, under the control of molecular recognition between specific metal ions and lipoligands incorporated in the bilayer membrane. They provide an approach to the design of artificial “tissue-mimetics” through the generation of polyvesicular arrays of defined architecture and to the control of their functional properties.
Clues to understanding cold sensation: Thermodynamics and electrophysiological analysis of the cold receptor TRPM8
Authors: Brauchi Sebastian , Orio Patricio , Latorre Ramon
Published: October 2004

The cold and menthol receptor, TRPM8, also designated CMR1, is a member of the transient receptor potential (TRP) family of excitatory ion channels. TRPM8 is a channel activated by cold temperatures, voltage, and menthol. In this study, we characterize the cold- and voltage-induced activation of TRPM8 channel in an attempt to identify the temperature- and voltage-dependent components involved in channel activation. Under equilibrium conditions, decreasing temperature has two effects. (
i
) It shifts the normalized conductance vs. voltage curves toward the left, along the voltage axis. This effect indicates that the degree of order is higher when the channel is in the open configuration. (
ii
) It increases the maximum channel open probability, suggesting that temperature affects both voltage-dependent and -independent pathways. In the temperature range between 18°C and 25°C, large changes in enthalpy (Δ
H
= -112 kcal/mol) and entropy (Δ
S
= -384 cal/mol K) accompany the activation process. The
Q
10
calculated in the same temperature range is 24. This thermodynamic analysis strongly suggests that the process of opening involves large conformational changes of the channel-forming protein. Therefore, the highly temperature-dependent transition between open and closed configurations is possible because enthalpy and entropy are both large and compensate each other. Our data also demonstrate that temperature and voltage interact allosterically to enhance channel opening.
Role of a transductional-transcriptional processor complex involving MyD88 and IRF-7 in Toll-like receptor signaling
Authors: Honda Kenya , Yanai Hideyuki , Mizutani Tatsuaki , Negishi Hideo , Shimada Naoya , Suzuki Nobutaka , Ohba Yusuke , Takaoka Akinori , Yeh Wen-Chen , Taniguchi Tadatsugu
Published: October 2004

Toll-like receptor (TLR) activation is central to immunity, wherein the activation of the TLR9 subfamily members TLR9 and TLR7 results in the robust induction of type I IFNs (IFN-α/β) by means of the MyD88 adaptor protein. However, it remains unknown how the TLR signal “input” can be processed through MyD88 to “output” the induction of the IFN genes. Here, we demonstrate that the transcription factor IRF-7 interacts with MyD88 to form a complex in the cytoplasm. We provide evidence that this complex also involves IRAK4 and TRAF6 and provides the foundation for the TLR9-dependent activation of the IFN genes. The complex defined in this study represents an example of how the coupling of the signaling adaptor and effector kinase molecules together with the transcription factor regulate the processing of an extracellular signal to evoke its versatile downstream transcriptional events in a cell. Thus, we propose that this molecular complex may function as a cytoplasmic transductional-transcriptional processor.
Kinetic efficiency of endocytosis at mammalian CNS synapses requires synaptotagmin I
Authors: Nicholson-Tomishima Karin , Ryan Timothy A.
Published: October 2004

At nerve terminals, synaptic vesicle components are retrieved from the cell surface and recycled for local reuse soon after exocytosis. The kinetics of this coupling is critical for the proper functioning of synapses during repetitive action potential firing, because deficiencies in this process lead to abnormal depletion of the releasable vesicle pool. Although the molecular basis of this coupling is poorly understood, numerous biochemical data point to a role for synaptotagmin I (SytI), an essential synaptic vesicle protein required for fast calcium-dependent exocytosis. Here, using synapto-pHluorin in an approach that allows the dissection of endocytosis and exocytosis into separate components during periods of stimulation, we examined exocytic–endocytic coupling in synapses from SytI knockout mice and their WT littermates. We show that endocytosis is significantly impaired in the absence of SytI with the relative rates of endocytosis compared with exocytosis reduced ≈3-fold with respect to WT. Thus, in addition to regulating exocytosis, SytI also controls the kinetic efficiency of endocytosis at nerve terminals.
Identification of alternative splicing regulators by RNA interference in
Drosophila
Authors: Park Jung W. , Parisky Katherine , Celotto Alicia M. , Reenan Robert A. , Graveley Brenton R.
Published: October 2004

Alternative splicing is thought to be regulated by nonspliceosomal RNA binding proteins that modulate the association of core components of the spliceosome with the pre-mRNA. Although the majority of metazoan genes encode pre-mRNAs that are alternatively spliced, remarkably few splicing regulators are currently known. Here, we used RNA interference to examine the role of >70% of the
Drosophila
RNA-binding proteins in regulating alternative splicing. We identified 47 proteins as splicing regulators, 26 of which have not previously been implicated in alternative splicing. Many of the regulators we identified are nonspliceosomal RNA-binding proteins. However, our screen unexpectedly revealed that altering the concentration of certain core components of the spliceosome specifically modulates alternative splicing. These results significantly expand the number of known splicing regulators and reveal an extraordinary richness in the mechanisms that regulate alternative splicing.
Triggered amplification by hybridization chain reaction
Authors: Dirks Robert M. , Pierce Niles A.
Published: October 2004

We introduce the concept of hybridization chain reaction (HCR), in which stable DNA monomers assemble only upon exposure to a target DNA fragment. In the simplest version of this process, two stable species of DNA hairpins coexist in solution until the introduction of initiator strands triggers a cascade of hybridization events that yields nicked double helices analogous to alternating copolymers. The average molecular weight of the HCR products varies inversely with initiator concentration. Amplification of more diverse recognition events can be achieved by coupling HCR to aptamer triggers. This functionality allows DNA to act as an amplifying transducer for biosensing applications.
Optical Response Study of the Al/a‐Sic:H Schottky Diode for Different Substrate Temperatures of the R.F. Sputtered a‐Sic:H Thin Film
Authors: Magafas L.
Published: October 2004

In the present work, Schottky diodes of Al/a‐SiC:H included in the structure Al/a‐SiC:H/c‐Si(n)/Al were fabricated and their optical response was studied in the wavelength region from 350 nm up to 1000 nm, for different substrate temperatures, Ts (from 30°C up to 290°C) of the r.f. sputtered a‐SiC:H thin film. The spectral response of these structures exhibits two maximum values of quantum efficiency. The first maximum is presented at wavelength
λ≅525
nm and the other at λ = 850
850 nm, which are attributed to the Aa‐SiC:H Schottky junction and the
a‐SiC:H/c‐Si(n) isotype heterojunction, respectively. The position of the first maximum owing to the Al/a‐SiC:H junction as well as the values of quantum efficiency, for the range of wavelengths from 350 nm up to 700 nm, depends on the substrate temperature, Ts, of the a‐SiC:H thin film. In the case that Ts is 120°C, the spectral response of the Al/a‐SiC:H/c‐Si(n)/Al structure for a reverse bias voltage V = ‐2V exhibits high values of quantum efficiency (up to 40%) with slight variation in the range of wavelength from 475 nm up to 925 nm,
making this structure interesting as a wide band optical sensor device. Finally, the minority carrier (holes) diffusion length of a‐SiC:H for TS = 120°C
was calculated and it was found to be ≅2.200
Å.
Direct Growth of High‐Quality InP Layers on GaAs Substrates by MOCVD
Authors: Yarn K. F. , Chien W. C. , Lin C. L. , Liao C. I.
Published: October 2004

In this report, we have overcome the drawback of surface roughness of metamorphic buffer layer by LP‐MOCVD technique and have grown InP metamorphic buffer layers with various thickness on misoriented GaAs (1 0 0) substrates with 10 degree towards (1 1 1)A. The grown films are characterized by optical microscopy, atomic force microscopy, secondary ion mass spectrometry, transmission electron microscopy and double‐crystal X‐ray diffraction. We also analyze the surface morphology, which is dependent on growth temperature, group III and
group V partial pressure, growth rate and V/III ratios. A mirror‐like, uniform surface and high crystal quality of the metamorphic buffer layer directly grown on a GaAs substrate can be achieved. Finally, to investigate the performance of the metamorphic microwave devices, we also fabricate the InAlAs/InGaAs metamorphic HEMT on GaAs substrates.
Analog Low‐Voltage Current‐Mode Implementation of Digital Logic Gates
Authors: Abuelma′atti Muhammad Taher
Published: October 2004

In this letter a new technique is introduced for implementing the basic logic functions using analog current‐mode techniques. By expanding the logic functions in power series expressions, and using summers and multipliers, realization of the basic logic functions is simplified. Since no transistors are working in saturation, the problem of fan‐out is alleviated. To illustrate the proposed technique, a circuit for simultaneous realization of the logic
functions NOT, OR, NAND and XOR is considered. SPICE simulation results, obtained with 3 V supply, are included
Some Investigations on the Anisotropy of the Chemical Etching of(h k 0)and (h h I)Silicon Plates in a NaOH 35% Solution. Part III: Determination of a Database for the Simulator Tensosim and Prediction of 2D Etching Shapes
Authors: Telliera C. R. , Hodebourg C. , Leblois T. G.
Published: October 2004

The simulation of 2D etching shapes such as surface profiles and out‐of‐roundness profiles related to various (h k 0) and (h h l) silicon plates or cross‐sections is studied. The theoretical basis of the simulation is presented. The database for the simulator TENSOSIM is determined from a systematic analysis of experimental 2D etching shapes. Emphasis
is placed on difficulties encountered in the determination procedure. Theoretical 2D etching shapes are compared with experimental shapes. A correlation between polar plots of the dissolution slowness and corresponding theoretical shapes is established. So we can conclude that the accuracy of the proposed database is sufficient for the simulation of 2D etching shapes.
A Novel Ideal Floating Inductor Using Translinear Conveyors
Authors: Khan Iqbal A. , Zaidi Mehmood H.
Published: October 2004

An ideal floating inductor circuit using translinear conveyors is introduced. The floating inductor simulator uses two translinear conveyors and a single capacitor in its realization. The circuit provides the current controlled ideal floating inductance without any component matching constraints. Simulation results on the floating inductor simulator verify the theory