bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular mechanisms of microheterogeneity‐induced defect formation in ferritin crystallization
Authors: Yau S.‐T. , Thomas Bill R. , Galkin Oleg , Gliko Olga , Vekilov Peter G.
Published: October 2004

We apply in situ atomic force microscopy to the crystallization of ferritins from solutions containing ≈5% (w/w) of their inherent molecular dimers. Molecular resolution imaging shows that the dimers consist of two bound monomers. The constituent monomers are likely partially denatured, resulting in increased hydrophobicity of the dimer surface. Correspondingly, the dimers strongly adsorb on the crystal surface. The adsorbed dimers hinder step growth and on incorporation by the crystal initiate stacks of up to 10 triple and single vacancies in the subsequent crystal layers. The molecules around the vacancies are shifted by ≈0.1 molecular dimensions from their crystallographic positions. The shifts strain the lattice and, as a consequence, at crystal sizes > 200 μm, the accumulated strain is resolved by a plastic deformation whereupon the crystal breaks into mosaic blocks 20–50 μm in size. The critical size for the onset of mosaicity is similar for ferritin and apoferritin and close to the value for a third protein, lysozyme; it also agrees with theoretical predictions. Trapped microcrystals in ferritin and apoferritin induce strain with a characteristic length scale equal to that of a single point defect, and, as a consequence, trapping does not contribute to the mosaicity. The sequence of undesired phenomena that include heterogeneity generation, adsorption, incorporation, and the resulting lattice strain and mosaicity in this and other proteins systems, could be avoided by improved methods to separate similar proteins species (microheterogeneity) or by increasing the biochemical stability of the macromolecules against oligomerization. Proteins 2001;43:343–352. © 2001 Wiley‐Liss, Inc.
Significance of aromatic‐backbone amide interactions in protein structure
Authors: Tóth Gergely , Watts Charles R. , Murphy Richard F. , Lovas Sándor
Published: October 2004

Weakly polar interactions between aromatic rings of amino acids and hydrogens of backbone amides (Ar‐HN) have been shown to support local structures in proteins. Their role in secondary structures, however, has not been elucidated. To investigate the relationship between Ar‐HN interaction and the stability of local and secondary structures of polypeptides and to improve the prediction of this interaction based on amino acid sequence, the structures of 560 nonhomologous proteins, from the Protein Data Bank, were searched for Ar–HN interactions between the aromatic ring of each Phe, Tyr, and Trp residue at position i and the backbone amide group of any residue, except Pro, at the positions i, i − 1, i − 2, i − 3, i + 1, i + 2, and i + 3. Ar‐HN interactions were identified by calculating the chemical shift of the amide hydrogen caused by the proximal aromatic ring. Ar(i)–HN(i + 1, i + 2 and i + 3) interactions were more common (7.10%, 2.08%, and 0.54%, respectively) than were Ar(i)–HN(i − 1, i − 2, and i − 3) interactions (0.66%, <0.1%, and 0.18%, respectively). The value of the χ1 torsion angle of the aromatic residue in position i depended on the direction of the Ar–HN interaction. The position of the aromatic ring in Ar(i)–HN(i + 1, i + 2, and i + 3) interactions was mostly trans, in Ar(i)–HN(i − 1, i − 2, and i − 3) interactions mainly gauche(−), and in Ar(i)–HN(i) interactions mostly gauche(+). The analyses of the secondary structures of the protein fragments containing Ar–HN interactions showed that Ar–HN interactions were in all types of secondary structures. Search results suggest that Ar–HN interactions have a stabilizing effect on all types of secondary structures. Proteins 2001;43:373–381. © 2001 Wiley‐Liss, Inc.
Mechanism of NAD(P)H:Quinone reductase: Ab initio studies of reduced flavin
Authors: Cavelier German , Amzel L. Mario
Published: October 2004

NAD(P)H:quinone oxidoreductase type 1 (QR1, NQO1, formerly DT‐diaphorase; EC 1.6.99.2) is an FAD‐containing enzyme that catalyzes the nicotinamide nucleotide‐dependent reduction of quinones, quinoneimines, azo dyes, and nitro groups. Animal cells are protected by QR1 from the toxic and neoplastic effects of quinones and other electrophiles. Alternatively, in tumor cells QR can activate a number of cancer chemotherapeutic agents such as mitomycins and aziridylbenzoquinones. Thus, the same enzyme that protects the organism from the deleterious effects of quinones can activate cytotoxic chemotherapeutic prodrugs and cause cancer cell death. The catalytic mechanism of QR includes an important initial step in which FAD is reduced by NAD(P)H. The unfavorable charge separation that results must be stabilized by the protein. The details of this charge stabilization step are inaccessible to easy experimental verification but can be studied by quantum chemistry methods. Here we report ab initio quantum mechanical calculations in and around the active site of the enzyme that provide information about the fine details of the contribution of the protein to the stabilization of the reduced flavin. The results show that (1) protein interactions provide approximately 2 kcal/mol to stabilize the planar conformation of the reduced flavin isoalloxazine ring observed in the X‐ray structure; (2) the charge separation present in the reduced planar form of the flavin is stabilized by interactions with groups of the protein; (3) even after stabilization, the reduction potential of the cofactor remains more negative than that of the free flavin, making it a better reductant for a larger variety of quinones; and (4) the more negative reduction potential may also result in faster kinetics for the quinone reduction step. Proteins 2001;43:420–432. © 2001 Wiley‐Liss, Inc.
Intrasubthalamic injection of 6‐hydroxydopamine induces changes in the firing rate and pattern of subthalamic nucleus neurons in the rat
Authors: Ni Zhongge , Bouali‐Benazzouz Rabia , Gao Dongming , Benabid Alim‐Louis , Benazzouz Abdelhamid
Published: October 2004

The subthalamic nucleus (STN) receives dopaminergic projections from the substantia nigra pars compacta (SNc). To investigate the role of direct and indirect dopaminergic influences on STN neurons, the spontaneous activity was studied in four groups of animals: normal rats, rats with intrasubthalamic or intranigral injection of 6‐hydroxydopamine (6‐OHDA), and sham STN injection rats by using extracellular recordings 4 weeks postsurgery. After intrasubthalamic injection of 6‐OHDA, the mean firing rate significantly decreased (7.29 ± 0.39 spikes/sec, P < 0.01 vs. 11.13 ± 0.59 spikes/sec in normal or 11.26 ± 0.57 spikes/sec in sham group), and the percentage of STN neurons discharging regularly decreased significantly (81%, P < 0.05 vs. 90% in normal group or P < 0.01 vs. 92% in sham group) and that of bursty cells increased (19%, P < 0.05 vs. 10%; in normal group or P < 0.01 vs. 8% in sham group). In the group of rats with SNc lesion, the firing rate of subthalamic neurons did not show a significant difference (11.61 ± 0.81 spikes/sec) compared with normal group. However, the firing pattern was dramatically changed: 74% of cells exhibited bursty pattern and only 26% of cells discharged regularly or slightly irregularly. Immunohistochemical results showed that intrasubthalamic injection of 6‐OHDA induced a marked degeneration of dopaminergic cells in the lateral part of the ipsilateral SNc, whereas 6‐OHDA injection into the SNc induced a total in situ lesion of dopamine cells. These results suggest that the SNc exerts an excitatory influence on STN neurons and that the loss of this dopaminergic projection could, at least partially, account for the changes in the firing pattern of STN neurons in the 6‐OHDA rat model of parkinsonism. Synapse 40:145–153, 2001. © 2001 Wiley‐Liss, Inc.
Bottom stress generation and sediment transport over the shelf and slope off of Lake Superior's Keweenaw peninsula
Authors: Churchill James H. , Williams Albert J. , Ralph Elise A.
Published: October 2004

Data from near‐bottom instruments reveal that the mechanisms responsible for generating bottom stresses and resuspending sediment over the shelf and slope off of Lake Superior's Keweenaw peninsula exhibit distinct seasonal variations. Notably, near‐bottom flows over the slope are persistently weak (<10 cm s−1) during summer but frequently attain high speeds, in excess of 20 cm s−1, in autumn and winter. During the intense storms of autumn and winter the generation of bottom stress is enhanced by the action of near‐bottom orbital velocities due to surface waves. Even at 90‐m depth, orbital velocities can increase bottom stress by a factor of up to 20% during storms. Where the seasonal thermocline intersects the lake floor, bottom stress is also considerably enhanced, often by more than a factor of 2, by high‐frequency motions in the internal wave band. Over the Keweenaw slope, sediment resuspension is largely confined to autumn and winter episodes of high bottom stress. Our analysis indicates that this resuspended material tends to be carried offshore, a phenomenon that is partly due to the coincidence of the direction of the buoyancy‐driven component of the Keweenaw Current with downwelling favorable alongshore winds. As a result of this coincidence, currents and bottom stresses tend to be greater during periods of downwelling, as opposed to upwelling, circulation. A potential challenge to modeling storm‐driven resuspension in the study region is indicated by observations that the minimum stress required for resuspension may vary significantly with time over the autumn and winter.
The influence of climate on in‐stream removal of nitrogen
Authors: Donner Simon D. , Kucharik Christopher J. , Oppenheimer Michael
Published: October 2004

Nitrogen (N) removal via benthic denitrification in large river systems can be a significant sink of terrestrial N and a source of nitrous oxide (N2O) to the atmosphere. Recent studies have demonstrated the fraction of in‐stream N removed from a river reach is related to the water residence time. We used the HYDRA aquatic transport model to examine the sensitivity of in‐stream N removal and the associated N2O emissions in the Mississippi River system to the interannual variability in climate. The results suggested an almost two‐fold range in the percent of N removed in the Mississippi River system and a three‐fold range in the associated N2O emissions, with the lowest percent removed (10–33%) and the highest N2O emissions (15.5–26.0 106 kg N) occurring in the wettest years. The results demonstrate the importance of considering climate variability and change in the management of nutrient export by large rivers.
Significant crustal thinning beneath the Baikal rift zone: New constraints from receiver function analysis
Authors: Gao Stephen S. , Liu Kelly H. , Chen Chizheng
Published: October 2004

Thinning of the crust of more than 10 km is a major feature of typical continental rifts such as the East African (EAR) and Rio Grande (RGR) rifts. However, numerous previous studies across the Baikal rift zone (BRZ), which has similar surface expressions and tectonic history, and more active seismicity relative to EAR and RGR, have resulted in contradicting amount of thinning, ranging from almost none to more than 10 km. We measure crustal thickness by stacking teleseismic receiver functions beneath 51 sites on the southern and central parts of the BRZ and adjacent Siberian Platform and Sayan‐Baikal‐Mongolian Foldbelt. Our measurements reveal that beneath the southern part of the Platform, the average crustal thickness is about 38 km, which is about 7 km thinner than that beneath the Foldbelt and the un‐rifted part of the BRZ. The thinnest crust, 35 km, is found beneath the central part of the rift, and represents a significant thinning of about 10 km relative to the un‐rifted parts of the BRZ.
Nonstationary seasonality of upper ocean temperature in the California Current
Authors: Mendelssohn Roy , Schwing Franklin B. , Bograd Steven J.
Published: October 2004

State‐space models are used to examine long‐term changes in the seasonal amplitude and phase of upper ocean temperatures from a set of time series representing the meridional and offshore extent of the California Current System (CCS). We use global one‐degree summaries from the World Ocean Database at 11 locations and 10 standard depths in the upper 200 m for the period 1950–1993. The seasonality of upper ocean temperature in the CCS is highly nonstationary, with significant interannual to decadal changes in seasonal amplitude and phase apparent over the period of study. The 1950s and early 1990s were characterized by high seasonal variability in upper ocean temperatures, while the intervening years were characterized by a reduced seasonal cycle. Long‐term changes in phase were also observed, with seasonal extrema occurring 1–2 months earlier in the year by the 1990s. The leading common seasonal components, dominated by the longer (yearly, 6‐month, 4‐month) periodicities, explain most of the seasonal fluctuations in the temperature series and partition the variance into well‐defined dynamic regions. In particular, long‐term changes in seasonality at 30–75 m in the major coastal upwelling centers (34°N–38°N) differed from that observed north of Cape Mendocino, within the Southern California Bight, and farther offshore. The observed spatial patterns suggest that the changes in temperature seasonality off central California reflect a significant low‐frequency modulation of the intensity, timing, and duration of coastal upwelling in the CCS. This nonstationarity of the seasonal temperature cycle is superimposed on both a region‐wide warming trend and spatially heterogeneous responses to low‐frequency climate events, such as regime shifts and El Niño events. Results from this study demonstrate that the character and potential biological impacts of climate variability can only be fully realized by considering a nonstationary, nondeterministic seasonal cycle.
Seasonal characteristics of chemical compositions of the atmospheric aerosols collected in urban seaside area at Tokaimura, eastern central Japan
Authors: Fu FengFu , Watanabe K. , Yabuki S. , Akagi T.
Published: October 2004

To obtain the seasonal characteristics and the size distributions of chemical compositions of the atmospheric aerosols in urban seaside area of eastern central Japan, size‐separated aerosol samples were collected at Tokaimura (36.27°N, 140.36°E) using an Andersen type sampler during July 2002 to July 2003. A maximum mass concentration of aerosols (about 50 μg/m3) during April and May and a minimum one (about 13 μg/m3) in January and a size distribution with two peaks at 0.43–1.5 μm and 3–8 μm were observed. The size‐separated aerosols were divided into water‐soluble and water‐insoluble fractions, and Na+, Cl−, NH4+, NO3−, SO42−, Mg2+, Ca2+, and Pb2+ in water‐soluble fraction and Na, Al, Ca, Mg, Fe, Pb, Th, and U in insoluble fractions were analyzed. Then, the seasonal variations and the size distribution in mass concentration of each chemical composition and the chemistry of sea‐salt particles were also studied in detail. Our results showed that (1) considerable amount of soil‐derived particles was supplied from dust storm incident in China, (2) there was a loss of chlorine in sea‐salt particles and this loss was compensated with the replacement by SO42− and NO3−, (3) the size distribution of Th and U showed a bimodal curve with two peaks at 0.43 μm and bigger than 3 μm and these two elements in the atmosphere seem to have two sources, and (4) aerosols contained both soluble and insoluble Pb and the soluble one became much lower in the colder seasons. The concentrations of soluble Pb showed a close relationship with anions such as Cl− and SO42−.
Deep convective cloud‐top heights and their thermodynamic control during CRYSTAL‐FACE
Authors: Sherwood Steven C. , Minnis Patrick , McGill Matthew
Published: October 2004

Infrared (11 μm) radiances from GOES‐8 and local radiosonde profiles, collected during the Cirrus Regional Study of Tropical Anvils and Cirrus Layers‐Florida Area Cirrus Experiment (CRYSTAL‐FACE) in July 2002, are used to assess the vertical distribution of Florida‐area deep convective cloud‐top height and test predictions as to its variation based on parcel theory. The highest infrared tops (Z11) reached approximately to the cold point at 15.4 km, though these are uncertain by about 1 km due to unknown cloud‐environment temperature differences. Since lidar shows that visible “tops” are generally 1 km or more above Z11, visible cloud tops frequently penetrated the lapse‐rate tropopause (∼15 km). Further, since tropospheric ice concentrations were typically present up to ∼1 km above the visible tops, lofting of moisture through the mean cold point was probably common. Morning clouds, and those near Key West, rarely penetrated the tropopause. As in previous studies, nonentraining parcel theory fails to explain either of these results, though it does show promise in explaining day‐to‐day variations over the peninsula. Moisture variations above the boundary layer account for much of the day‐to‐day Z11 variability, especially over the oceans. In all locations a 20% increase in mean mixing ratio between 750 and 500 hPa was associated with about 1 km deeper maximum cloud penetration, other things being equal. This sensitivity is too large to explain by simple dilution of parcel buoyancy through mixing, implying microphysical or dynamical feedbacks on cloud development. The evident influence of midtropospheric humidity on the depth of the tropical troposphere suggests an interesting climate feedback possibility for stabilizing midtropospheric relative humidity.
A 300 mK ultra-high vacuum scanning tunneling microscope for spin-resolved spectroscopy at high energy resolution
Authors: Wiebe J. , Wachowiak A. , Meier F. , Haude D. , Foster T. , Morgenstern M. , Wiesendanger R.
Published: October 2004

We describe the design and development of a scanning tunneling micoscope (STM) working at very low temperatures in ultra-high vacuum (UHV) and at high magnetic fields. The STM is mounted to the He3 pot of an entirely UHV compatible He3 refrigerator inside a tube which can be baked out to achieve UHV conditions even at room temperature. A base temperature of 315 mK with a hold time of 30 h without any recondensing or refilling of cryogenics is achieved. The STM can be moved from the cryostat into a lower UHV-chamber system where STM-tips and -samples can be exchanged without breaking UHV. The chambers contain standard surface science tools for preparation and characterization of tips and samples in particular for spin-resolved scanning tunneling spectroscopy (STS). Test measurements using either superconducting tips or samples show that the system is adequate for performing STS with both high spatial and high energy resolution. The vertical stability of the tunnel junction is shown to be 5 pmpp and the energy resolution is about 100 μeV.
Poloidal polarimeter for current density measurements in ITER
Authors: Donné A. J. H. , Graswinckel M. F. , Cavinato M. , Giudicotti L. , Zilli E. , Gil C. , Koslowski H. R. , McCarthy P. , Nyhan C. , Prunty S. , Spillane M. , Walker C.
Published: October 2004

One of the systems envisaged for measuring the current density profile in the ITER is a 118 μm poloidal polarimeter system. The proposed system has two independent views: one fan of chords observes the plasma via an equatorial port and a second fan views down from an upper port. This article will present the status of the on-going work and will address issues as sensitivity and accuracy, refraction, Gaussian beam ray-tracing, alignment, and calibration as well as some specific design details.
Lumen: A highly versatile spectrophotometer for measuring the transmittance throughout very long samples as well as microstructures
Authors: Montecchi M. , Baccaro S. , Dafinei I. , Diemoz M. , Montereali R. M. , Somma F.
Published: October 2004

Commercial spectrophotometers are basically designed to measure the absorbance of solutions contained in transparent cuvettes. Although their functions can be generally extended by means of a variety of accessories, these instruments are generally not flexible and do not fit solid samples thicker than some centimeters. This paper describes a highly versatile spectrophotometer, named Lumen, composed of discrete components and suitably arranged on a large breadboard. Two noticeable instrument configurations are discussed: the first allows to measure the transmittance through long samples, like crystals of lengths up to 23 cm; the second was developed to perform the same measurement in microstructures a few tens of micrometers wide, like those obtained in insulating materials by focused radiation beams. The data acquisition software, written in LabVIEW, adopts some original solutions that make Lumen unique.
Broadband multi-interferometer spectroscopy in high magnetic fields: From THz to visible
Authors: Padilla W. J. , Li Z. Q. , Burch K. S. , Lee Y. S. , Mikolaitis K. J. , Basov D. N.
Published: October 2004

We present a system capable of broad band frequency domain spectroscopy in the range 6–20 000 cm−1 at cryogenic temperatures. The apparatus couples two different interferometers to a 9 Tesla superconducting split coil magnet and is designed to work with various detectors, including thermal bolometers and semiconducting detectors. The optical layout utilizes an intermediate focus while preserving optical f/#’s throughout enabling DC magnetic field measurements of small crystals with polarized light in both Voight and Faraday geometries. A reference channel eliminates errors associated with system drift and facilitates determination of the optical constants. For transparent samples, simultaneous reflection and transmission can be performed.
Nonlocal nonlinear electrostatic gyrofluid equations
Authors: Strintzi D. , Scott B.
Published: October 2004

Building on Lagrangian field theory methods of fluid dynamics, we construct a set of equations for an electrostatic gyrofluid model which can treat arbitrarily nonlinear situations. Noether’s theorem is used to find the exact energy theorem satisfied by the equations. The exchange of energy between the E×B fluid drift and thermal/kinetic parts of the dynamics is recovered rigorously. Diamagnetic cancellations are inserted manually.
A fast framing camera system for observation of acceleration and ablation of cryogenic hydrogen pellet in ASDEX Upgrade plasmas
Authors: Kocsis G. , Kálvin S. , Veres G. , Cierpka P. , Lang P. T. , Neuhauser J. , Wittman C. , Team ASDEX Upgrade
Published: October 2004

An observation system using fast digital cameras was developed to measure a cryogenic hydrogen pellet’s cloud structure, trajectory, and velocity changes during its ablation in ASDEX Upgrade plasmas. In this article the system, the applied numerical methods, and the results are presented. The three-dimensional pellet trajectory and velocity components were reconstructed from images of observations from two different directions. Pellet acceleration both in the radial and toroidal directions was detected. The pellet cloud distribution was measured with high spatio-temporal resolution. The cloud surrounding the pellet was found to be elongated along the magnetic field lines. Its typical size is 5–7 cm along the field lines and 2 cm in the perpendicular directions. A cloud extension in the poloidal direction was also observed which may be related to the drift of the detached part of the cloud.
Cross talk between bending, twisting, and buckling modes of three types of microcantilever sensors
Authors: Jeon Sangmin , Braiman Yehuda , Thundat Thomas
Published: October 2004

Microcantilevers generally deflect in three ways: bending, twisting, and buckling. Among these, the accurate measurement of bending is essential for atomic force microscopy imaging and sensing applications. However, it was found that the bending of certain cantilevers can be coupled with twisting and buckling of the cantilever. In this article, cross talk between bending and twisting modes of microcantilevers of three different designs such as rectangular, triangular, and piezoresistive cantilevers is described. For the experiments, a thermal stress was applied to the rectangular and triangular cantilevers, and a Lorentz force was exerted on the triangular and the piezoresistive cantilevers. While the bending of the rectangular cantilever induced a negligible amount of twisting when heated, the triangular cantilevers showed nonlinear twisting responses during bending. This nonlinear response of the triangular cantilever was attributed to the variations in the spring constants between the two legs. When a Lorentz force was exerted on the triangular cantilevers, coupling of the bending and twisting modes depended on the direction of a magnetic field. For the piezoresistive cantilevers, a Lorentz force induced the in-phase buckling which accompanied both the bending and twisting modes.
Design and performance of a variable spectrum synthesizer
Authors: Huebschman M. L. , Hunt J. , Munjuluri B. , Takashima A. , Garner H. R.
Published: October 2004

We present the design and performance of a broadband variable spectrum synthesizer (VSS). The VSS system is capable of synthesizing multiple arbitrary spectra using an arc lamp as a source, a spectrograph to disperse the light, a digital micromirror device to select wavelengths and adjust intensities, and optical components to focus and direct the light. The VSS can provide radiation with a spectrum of selected wavelengths dispersed over an area or recombined into a narrow line. The area mode is most useful when imaging the spectrum across a target area is desired. The wavelength dispersion in this mode provides a spatially modulated spectral profile for comparing responses to the wavelengths in the selected bands. The line mode has utility in cases where a light signal with many superimposed spectra is desired. Both modes can simulate the spectra with a very specific wavelength, intensity, and exposure time characteristic. The current VSS system provides intensity and wavelength variations over a range from 250 to 1100 nm and can level wavelength intensities variations to within 15%. The instrument wavelength resolution was measured as 2.0 nm±0.5 nm and the maximum power density delivered was 220 μW/cm2 nm (365 nm). Although the VSS has applications in a number of physics and engineering disciplines, the control software and application described are tailored for measurement of wavelength-induced apoptosis/necrosis of skin cancer cells in the field of clinical phototherapy. An experiment using psoralens coupled with UVA light and an experiment using visible light in photodynamic therapy are discussed. The experimental results obtained for radiation of wavelengths between 300 and 700 nm at various exposures on living cells are presented.
Design and optimization of a flexible high-peak-power laser-to-fiber coupled illumination system used in digital particle image velocimetry
Authors: Robinson Ronald A. , Ilev Ilko K.
Published: October 2004

We present a study on the design and parameter optimization of a flexible high-peak-power fiber-optic laser delivery system using commercially available solid-core silica fibers and an experimental glass hollow waveguide (HW). The fiber-optic delivery system provides a flexible, safe, and easily and precisely positioned laser irradiation for many applications including uniform illumination for digital particle image velocimetry (DPIV). The delivery fibers, when coupled through a line-generating lens, produce a uniform thin laser sheet illumination for accurate and repeatable DPIV two-dimensional velocity measurements. We report experimental results on homogenizing the laser beam profile using various mode-mixing techniques. Furthermore, because a fundamental problem for fiber-optic-based high-peak-power laser delivery systems is the possible damage effects of the fiber material, we determine experimentally the peak power density damage threshold of various delivery fibers designed for the visible spectral range at a typical DPIV laser wavelength of 532 nm. In the case of solid-core silica delivery fibers using conventional lens-based laser-to-fiber coupling, the damage threshold varies from 3.7 GW/cm2 for a 100-μm-core-diameter high-temperature fiber to 3.9 GW/cm2 for a 200-μm-core-diameter high-power delivery fiber, with a total output laser energy delivered of at least 3–10 mJ for those respective fibers. Therefore, these fibers are marginally suitable for most macro-DPIV applications. However, to improve the high-power delivery capability for close-up micro-DPIV applications, we propose and validate an experimental fiber link with much higher laser power delivery capability than the solid-core fiber links. We use an uncoated grazing-incidence-based tapered glass funnel coupled to a glass HW with hollow air-core diameter of 700 μm, a low numerical aperture of 0.05, and a thin inside cladding of cyclic olefin polymer coating for optimum transmission at 532 nm. Because of the mode homogenizing effect and lower power density, the taper-waveguide laser delivery technique ensured high damage threshold for the delivery HW, and as a result, no damage occurred at the maximum measured input laser energy of 33 mJ used in this study.
Analysis of vibrating mode scanning polarization force microscope
Authors: Chen Yuhang , Li Xiaojun , Zhou Xingfei , Sun Jielin , Huang Wenhao , Hu Jun
Published: October 2004

In this article, the vibrating mode scanning polarization force microscope (VSPFM) is modeled with a spring-mass-damper system under van der Waals forces and polarization forces. The behaviors of VSPFM are analyzed numerically. Numerical analysis shows that by superimposing the long-range polarization interactions upon van der Waals forces, the tip motion can be greatly altered. Through adjusting the ac bias voltage between the conductive tip and dielectric substrate, the working regimes (intermittent contact or pure noncontact) of VSPFM can be controlled freely. The results also indicate that this kind of microscope is suitable for measuring mechanical properties of soft samples, where proper contact force is required. As an application example of VSPFM, the radial Young’s modulus of DNA is determined. It is found the measured DNA modulus increases as deformation increases. This trend is the same with that observed in measuring elastic moduli of thin soft films on hard substrates. The elastic modulus is about 300 MPa if the ratio of deformation to DNA diameter is less than 30%.
Compact device for assessment of microorganism motility
Authors: Pomarico J. A. , DiRocco H. O.
Published: October 2004

We have designed and constructed a simple and reliable instrument, based on dynamic speckle interferometry, which allows the determination of the relative degree of motility for microorganisms. A measurement can be carried out in a few seconds and parasites have been used for test purposes. An ad hoc software was also developed showing easy operation characteristics. This instrument surpasses the purely qualitative methodology employed by human operators, that can be affected by great errors, fatigue, etc. Besides, it does not require using image formation systems (such as a microscope) and a frame grabber is not mandatory.
Debris mitigation in pinhole-apertured point-projection backlit imaging
Authors: Blue B. E. , Hansen J. F. , Tobin M. T. , Eder D. C. , Robey H. F.
Published: October 2004

Pinhole-apertured point-projection x-ray radiography is an important diagnostic technique for obtaining high resolution, high contrast, and large field-of-view images used to diagnose the hydrodynamic evolution of high energy density experiments. In this technique, a pinhole aperture is placed between a laser irradiated foil (x-ray source) and an imaging detector. In the present geometry, the x rays that are not transmitted through the pinhole aperture, ablate the pinhole substrate’s surface, and turn it into a flyer plate. The pinhole substrate then breaks apart into shrapnel, and that shrapnel can damage diagnostics inside the target chamber. In this letter, we present a technique on mitigating the debris by using a tilted pinhole.
Microspot x-ray focusing using a short focal-length compound refractive lenses
Authors: Dudchik Y. I. , Kolchevsky N. N. , Komarov F. F. , Piestrup M. A. , Cremer J. T. , Gary C. K. , Park H. , Khounsary A. M.
Published: October 2004

We have fabricated and tested short focal-length compound refractive lenses (CRLs) composed of microbubbles embedded in epoxy encased in glass capillaries. The interface between the bubbles formed 90 to 350 spherical biconcave microlenses reducing the overall focal length inversely by the number of lenses or bubbles. When compared with CRLs manufactured using other methods, the microbubble lenses have shorter focal lengths with higher transmissions and larger gains for moderate energy x rays (e.g., 7–20 keV). We used beamline 2–3 at the Stanford Synchrotron Radiation Laboratory and beamline 5BM-D-DND at the Advanced Photon Source to measure focal lengths between 100–250 mm with lens apertures varying between 97 and 321 μm. Transmission profiles were measured giving, for example, a peak transmission of 46% for a 240 mm focal length CRL at 20 keV. The focal-spot sizes were also measured yielding, for example, a vertical spot size of 1.2 μm resulting from an approximate 20-fold demagnification of the APS 23 μm source size. The measured gains in intensity over that of unfocused beam were between 9 and 26.
Foam analyzer: An instrument based on the foam pressure drop technique
Authors: Khristov Khr. , Exerowa D. , Christov L. , Makievski A. V. , Miller R.
Published: October 2004

The foam pressure drop technique allows measurement of the characteristic properties of aqueous foams. A new fully automated instrument called the FA1 Foam Analyzer employs this technique. The reduced pressure applied to the measurement cell allows reasonably short experiments even for very stable foams. The technique determines the drainage (water content as a function of time) and lifetime of a foam at an applied reduced pressure. The lifetime as a function of applied reduced pressure depends both on the kind of surfactant stabilizing the foam and the type of liquid films (common thin, common black or Newton black) that built up the foam. We give sample experiments for various surfactant solutions.
Linear radio frequency quadrupole for the cooling and bunching of radioactive ion beams
Authors: Darius G. , Ban G. , Brégeault J. , Delahaye P. , Desrues Ph. , Durand D. , Fléchard X. , Herbane M. , Labalme M. , LeBrun Ch. , Liénard E. , Mauger F. , Merrer Y. , Méry A. , Naviliat-Cuncic O. , Szerypo J. , Vallerand Ph. , Vandamme Ch.
Published: October 2004

A linear radio frequency quadrupole has been built for the transport, cooling, and bunching of radioactive ions extracted from an ECR source. The device uses the buffer gas cooling technique and was designed such as to extend the technique for the cooling of very light ions using H2 as buffer gas. We describe here the technical specifications of the device and present results of the first tests concerning the cooling and bunching of stable ions.
Hyperbolic wavelet family
Authors: Le Khoa N. , Dabke Kishor P. , Egan Gregory K.
Published: October 2004

This article reports early results on digital implementation of first- and nth-order hyperbolic wavelets whose important parameters are explicitly expressed and numerically estimated. The first-order hyperbolic, Morlet and Choi–Williams wavelets are compared in detail by numerically calculating their band-peak frequencies, minimum numbers of sampling points, scale resolutions, and maximum numbers of scales. One of the main aims is to show that there exists a strong link among time–frequency kernels and wavelets. This relationship helps to expand and link time–frequency and wavelet approaches to signal analysis. One example of using the hyperbolic wavelet for speech recognition is also given.
Scatterometer of visible light for 2D rough surfaces
Authors: Rodríguez-Herrera O. G. , Rosete-Aguilar M. , Bruce N. C.
Published: October 2004

A new device designed to measure light scattered from a bi-dimensional rough surface is discussed. A description of the system and some test procedures are presented as is an analysis of the results obtained with the instrument for two different diffraction apertures, a one-dimensional and a bi-dimensional rough surface. The instrument works in the visible and near infrared region of the spectrum and the preliminary results presented here agree with previously obtained data.
Corona discharge ion mobility spectrometry at reduced pressures
Authors: Tabrizchi Mahmoud , Rouholahnejad Fereshteh
Published: October 2004

Ion mobility spectrometers (IMSs) normally operate at ambient pressure. In this work an IMS cell has been designed and constructed to allow the pressure to be reduced inside the IMS cell. In this cell, corona discharge was employed as the ionization source. Reducing pressure affected both the discharge and the performance of the IMS. The discharge current was observed to increase with reducing pressure while the ignition potential decreased. The ion current received at the collector plate was also increased about 50 times when the pressure was reduced from ambient pressure to 15 Torr. The higher ion current can lead to an extended dynamic range. IMS spectra were recorded at various pressures and the results show that the drift times shift perfectly linear with pressure. This suggests that unlike temperature, pressure correction for ion mobility spectra is as simple as multiplying the drift times by a factor of 760/P.
High accuracy velocity control method for the french moving-coil watt balance
Authors: Topcu Suat , Chassagne Luc , Haddad Darine , Alayli Yasser , Juncar Patrick
Published: October 2004

We describe a novel method of velocity control dedicated to the French moving-coil watt balance. In this project, a coil has to move in a magnetic field at a velocity of 2 mm s−1 with a relative uncertainty of 10−9 over 60 mm. Our method is based on the use of both a heterodyne Michelson’s interferometer, a two-level translation stage, and a homemade high frequency phase-shifting electronic circuit. To quantify the stability of the velocity, the output of the interferometer is sent into a frequency counter and the Doppler frequency shift is recorded. The Allan standard deviation has been used to calculate the stability and a σy(τ) of about 2.2×10−9 over 400 s has been obtained.
New getter pump for ultrahigh vacuum systems and transportable enclosure
Authors: Firpo G. , Pozzo A.
Published: October 2004

We have developed a new type of nonevaporable getter (NEG) pump. It is based on the getter strip St707, produced by SAES getters S.p.A, fitted into a CF-flanged container. The pump is activated at 400°C for 1 h and its pumping behavior is studied for H2, CO, and N2. The pumping speed is about 500 liters/s for H2, 230 liters/ for CO, and 130 liters/s for N2, which is in good agreement with our theoretical pumping model. While its performance is similar to those of commercial NEG pumps, it is definitely more compact, inexpensive, and easy to use. When coupled with single-penning cell, our NEG pump can replace conventional ion pumps in the design of compact ultrahigh vacuum (UHV) systems. Its first application will be as an efficient and compact pumping device for portable UHV enclosure.
Estimation of initial conditions and parameters of a chaotic evolution process from a short time series
Authors: Lu Fangfang , Xu Daolin , Wen Guilin
Published: October 2004

Tracing back to the initial state of a time-evolutionary process using a segment of historical time series may lead to many meaningful applications. In this paper, we present an estimation method that can detect the initial conditions, unobserved time-varying states and parameters of a dynamical (chaotic) system using a short scalar time series that may be contaminated by noise. The technique based on the Newton–Raphson method and the least-squares algorithm is tolerant to large mismatch between the initial guess and actual values. The feasibility and robustness of this method are illustrated via the numerical examples based on the Lorenz system and Rössler system corrupted with Gaussian noise.
Effect of altitude on resource allocation in the weed Achillea millefolium (yarrow, Asteraceae) in the Australian Alps
Authors: Johnston Frances Mary , Pickering Catherine Marina
Published: October 2004

Increasing severity of environment associated with increasing altitude in mountain ecosystems (decreasing temperature, increasing duration of snow cover) can affect relative and absolute biomass-allocation patterns in plants. Biomass allocation was examined along a 620-m altitudinal gradient in the Australian Alps for the important environmental weed Achillea millefolium (L., Asteraceae, yarrow). Relative and absolute biomass allocation (dry weight) to reproductive (capitula, flowering stems and associated leaves), vegetative (leaves not on the flowering stem) and below-ground structures (rhizome and roots) were measured at each of nine sites by using quadrats. Increasing altitude resulted in a decrease in relative and absolute allocation of biomass to reproductive structures. For example, the dry weight of inflorescences declined as altitude increased because of a decrease in the weight of the terminal and side branches of the inflorescences, but not the total number of capitula produced. There was also a trend for increased relative allocation to below-ground structures with increasing altitude, even though altitude did not affect absolute allocation to below-ground and vegetative structures, or the total dry weight of A. millefolium. These results are consistent with those for other species growing at high altitude. The management implications for the control of A. millefolium in the Australian Alps are discussed, including in relation to predicted climatic change.
The ecology, phytosociology and stand structure of an ancient endemic plant Lomatia tasmanica (Proteaceae) approaching extinction
Authors: Lynch A. J. J. , Balmer J.
Published: October 2004

Lomatia tasmanica W.M.Curtis is a nationally endangered shrub of the family Proteaceae. It is entirely restricted to one population extending over 1.2 km in south-western Tasmania. The species occupies a variety of riparian vegetation types ranging from sclerophyll scrub to implicate rainforest. The population is dominated by ramets originating after fire in 1934, although the species regenerates in a continuous manner by root suckering. The ramets or stems may reach ages > 300 years. The entire population may be composed of one genet and fruit production has never been observed. The extreme rarity of the species, its inability to reproduce sexually and its lack of genetic diversity suggest that L. tasmanica is heading inevitably towards extinction. One population appears to have disappeared since 1934. Threats such as too frequent firing and the root-rot fungus Phytophthora cinnamomi increase the likelihood of extinction of L. tasmanica in the short term to a very high level.
Ontogenesis of the fruit pulp layer of Hymenaea stigonocarpa (Fabaceae: Caesalpinioideae)
Authors: Paiva E. A. S. , Oliveira D. M. T.
Published: October 2004

Hymenaea, a genus of major economic importance, has been the subject of several botanical studies. However, there is disagreement over the origin of the edible fruit pulp of Hymenaea, as there are no ontogenetic studies on this organ. According to some authors, the edible layer results from transformations of the mesocarp and endocarp, while according to others, it is considered a seed aril. There are still others who regard this layer as originating from an undefined region of the pericarp. To understand the nature and origin of the pulp layer, Hymenaea stigonocarpa Mart. ex Hayne ovaries and fruit were processed according to standard techniques. The production of the fruit pulp layer starts immediately after anthesis. During anthesis, the inner epidermal cells of the ovary show periclinal division and form a new layer of cells towards the mesocarp; this remains meristematic and initiates cell production by predominantly periclinal divisions, producing a compact tissue towards the locule. This tissue will become the fruit pulp layer, the inner endocarp. The seed coat shows typical testal structure without evidence of aril formation. This allows us to conclude that the fruit pulp layers are exclusively made from part of the endocarp. We also observed resin cavities on outer mesocarp and outer endocarp.
Vegetation change in an urban grassy woodland 1974 - 2000
Authors: Kirkpatrick J. B.
Published: October 2004

Few temporal studies document vegetation change in Australian temperate grassy woodlands. Floristic and structural data were collected from 68 randomly located sites in the Queens Domain, an urban grassy woodland remnant, in 1974, 1984, 1994 and 2000 and a search made for rare species. Species of conservation significance were concentrated at highly disturbed sites, whereas vegetation types of conservation significance decreased in area as a result of increases in the numbers of Allocasuarina verticillata, which caused a change in many unmown areas from Eucalyptus viminalis grassy woodland to E. viminalis–A. verticillata woodland/forest or A. verticillata open/closed forest. Structural changes were associated with changes in species composition and an increase in native-species richness. Increases in tree cover occurred where fires were most frequent, possibly as a result of the lack of mammalian herbivores. The frequencies of herbs and annual grasses were strongly affected by precipitation in the month of sampling. Half of the species that showed a consistent rise or fall through time were woody plants, approximately twice the number expected. In the dataset as a whole, species-richness variables were largely explained by varying combinations of variables related to moisture availability, altitude and the incidence of mowing. The strongest influences on species composition were the same, although slope and time since the last fire also contributed to multiple regression and generalised linear models. Compositional stability was positively related to native-species richness, whereas high levels of exotic-species richness occurred at both low and high levels of native-species richness. The maintenance of native-plant biodiversity on the Domain requires such counterintuitive measures as the maintenance of exotic trees and the control of native trees, demonstrating the contingencies of conservation management in fragmented vegetation that consists of a mixture of native and exotic species.