bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison between radiosonde, rocketsonde, and satellite observations of atmospheric temperatures
Authors: Barnett J. J. , Harwood R. S. , Houghton J. T. , Morgan C. G. , Rodgers C. D. , Williamson E. J.
Published: February 2007

Comparisons have been made between satellite measured radiances and those derived from radiosonde/rocketsonde profiles for several samples for both the Nimbus 4 and Nimbus 5 selective chopper radiometers during the period 1970–1973. Agreement between satellite and radiosonde measurements in the upper troposphere and lower stratosphere is better than 1 K in equivalent temperature. For rocketsonde observations mean differences of up to 3 K in equivalent temperature are found but these are within the combined experimental error of the measurements. Good confidence can, therefore, be placed on the method based on laboratory measured transmissions of deriving weighting functions for the satellite instruments.
A multi‐layer spectral model and the semi‐implicit method
Authors: Hoskins B. J. , Simmons A. J.
Published: February 2007

The formulaton of a multi‐layer primitive equation model on the sphere is described. The horizontal representation is by means of spherical harmonics, truncated either in the triangular or rhomboidal manner. The time integration is performed using the semi‐implicit method in which the linearized gravity wave terms are time averaged and thus the fast moving waves of this type are slowed. For a 5‐layer hemispheric model with triangular truncation at wavenumber 21, storage of 38K words is needed and with the time scheme allowing a time‐step of 90 minutes, one day's simulation requires 11 seconds of CDC 7600 time. The growth of a baroclinic wave on a simple basic state of differential solid body rotation is exhibited. The errors involved in this case in utilizing the large time‐step allowed by the semi‐implicit scheme are thoroughly examined by comparing wave amplitudes and phases, conservation properties and gravity wave treatment for different time‐steps. These errors are found to be negligible. The conservation properties of the model are in fact extremely good. The vertical finite differencing scheme of Arakawa is studied in the same baroclinic instability simulation. The growth is similar though the conservation of angular momentum is greatly improved. The transform method used in all these integrations allows some aliasing, but this is shown to be negligible.
Turbulent wind flow over a low hill
Authors: Jackson P. S. , Hunt J. C. R.
Published: February 2007

An analytical solution is presented for the flow of an adiabatic turbulent boundary layer on a uniformly rough surface over a two‐dimensional hump with small curvature, e.g. a low hill. The theory is valid in the limit L/y0 → ∞ when h/L < 1/8(y0/L)0.1 and δ/L > 2k2/ln(δ/y0) where L and h are the characteristic length and height of the hump, y0 the roughness length of the surface and δ the thickness of the boundary layer. For rural terrain, taking δ ∼ 600m these conditions imply that 102 < L < 104m and h/L < 0·05. Considerations of the turbulent energy balance suggest that the eddy viscosity distribution for equilibrium flow near a wall may still be used to a good approximation to determine the changes in Reynolds stress. This result is only required in a thin layer adjacent to the surface ‐ in the main part of the boundary layer the perturbation stresses are shown to be negligible and the disturbance to be almost irrotational. The theory shows that for a log‐profile upwind the increase in wind speed near the surface of the hill is O((h/L)u0(L)) where u0(L) is the velocity of the incident wind at a height L. Thus the increase in surface winds can be considerably greater than is predicted by potential flow theory based on an upwind velocity u0(h). It is also found that, at the point above the top of a low hill at which the increase in velocity is a maximum, the velocity is approximately equal to the velocity at the same elevation above level ground upwind of the hill. The surface stress is highly sensitive to changes in the surface elevation, being doubled by a slope as small as one in five. The turning of the wind in the Ekman layer may induce a change in direction of the wind above the hill.

The main object of this analysis is to show how the changes in wind speed and shear stress are related to the size and shape of the hill and to the roughness of the surface. Some comparisons are made with measurements of the natural wind and wind tunnel flows. These suggest that the theory may be useful in giving rough estimates of the effect of hills on the wind. The theory and the quoted measurements suggest that the present design recommendation for the increase in wind speeds over hills to be used in wind loading calculations may be an underestimate. It is to be hoped that this analysis will encourage more detailed measurements to be made of the wind over hills.
Rainfall trends in the West African Sahel
Authors: Bunting A. H. , Dennett M. D. , Elston J. , Milford J. R.
Published: February 2007

A statistical analysis has been made of long‐term rainfall records from West Africa. No established trends or periodicities can be detected, and the recent succession of drought years falls within statistical expectation. Sahelian rainfall is not clearly linked to the frequency of westerly weather over Britain.
Baroclinic waves and frontogenesis Part I: Introduction and Eady waves
Authors: Hoskins B. J.
Published: February 2007

The semi‐geostrophic equations are derived from the primitive equations with the momentum approximated by its geostrophic value. Here these equations are used to study the stability of a zonal flow. The quasi‐geostrophic instability criterion is given a more accurate form. The semi‐geostrophic equations are also used for a numerical and analytical study of the development into the nonlinear regime of the Eady wave instability mode of a zonal flow with uniform shear in the vertical. The nonlinear tightening of the low pressure, the occlusion process and the formation of a warm frontal region are all evident in these solutions.
A laboratory model of diffusion into the convective planetary boundary layer
Authors: Willis G. E. , Deardorff J. W.
Published: February 2007

A laboratory model of the convective planetary boundary layer has provided information concerning the evolution of concentration distributions downwind from a simulated continuous point source located near the ground. Results indicate that a Gaussian plume formulation adequately describes the model γ‐concentration distributions, but is useful in predicting the z‐concentration distributions only to a distance downstream of about x = 0.5zi/(w*/U), where zi is the mixed layer depth and w*/U is a dimensionless stability parameter. Near this distance an elevated concentration maximum appears at a height above the source release height. The elevated maximum rises to a height of about 0.8zi at x = 1.7zi/(w*/U) and retains its identity until the pollutants become vertically well mixed farther downstream. Use of the stability parameter w*/U permits the model results to be applied to a range of atmospheric conditions encompassing the Pasquill‐Gifford stability classes A and B. Close agreement is found between the laboratory data and the atmospheric observations of ground‐level lateral spread of Islitzer (1961) and Islitzer and Dumbauld (1963), where the latter measurements extended out to x≃ 3 km.
Infrared absorption and liquid water content in stratocumulus clouds
Authors: Platt C. M. R.
Published: February 2007

Simultaneous measurements of narrow‐beam vertical infrared radiance (10–12μm), cloud dropsize distributions, temperature and humidity in some stratocumulus clouds are reported.

Cloud volume absorption coefficients calculated from mean dropsize distributions are found to be well correlated with the cloud liquid water content. Values of cloud volume absorption coefficient are found to vary from 2 to 20 km−1 for a range in liquid water content from 0.02 to 0.27gm−3. The equivalent variation in cloud mass absorption coefficient is from 700 to 1030g−1 cm2, with a mean value for all clouds of 765g−1 cm2. From the radiance measurements the clouds are found to become ‘black’ for depths ranging from about 100 to 450m. The variation of measured cloud emissivity with liquid water mass is found to be consistent, within the observed variabilities of the clouds, with the emissivities calculated from the above mean absorption coefficient. The results are compared with earlier flux measurements.
Production of nitrogen oxides by lightning discharges
Authors: Tuck A. F.
Published: February 2007

The annual production of nitric oxide by lightning discharges is estimated to be 1.8 × 1035 molecules, within rather large limits of uncertainty. Implications for the global budget of odd nitrogen species are cursorily examined. More data are needed to decide whether or not lightning‐produced nitrogen oxides are transported in significant quantities to the stratosphere.

Closer studies of the budget of nitrate in rainwater, and of air trajectories in large cumulonimbus storms, are also indicated.
A comparative study of radiation balance above forest and grassland
Authors: Moore C. J.
Published: February 2007

Daily net radiation above a Pinus radiata plantation was found to exceed that measured above nearby grassland by about 12% during the winter and 24% during the summer months. This difference was related to differences in the albedo and net longwave radiation associated with the surface temperature of each vegetation. Forest albedo was found to be 0.11 ± 0.001 throughout the winter and did not exhibit a significant diurnal variation. The grassland albedo was found to give the usual diurnal trend and a mean winter albedo of 0.27 ± 0.03 which decreased to 0.24 ± 0.01 in summer, consistent with increasing solar elevation.

Hourly values of net radiation Rn above the forest during daylight hours were found to exceed those for grassland by about 15% during the winter and about 25% during the summer. When the forest was wet and the change in canopy heat storage Q and ground heat flux G were small, such differences also applied to the energy (Rn—G—Q) available for evaporation. However, when the canopy was dry, values of Q during the day were sufficiently large to reduce the forest available energy to about that of the grassland. This forest canopy energy was generally lost during the night.
The propagation of modified flow downstream of a change in roughness
Authors: Jackson N. A.
Published: February 2007

Using published atmospheric and wind tunnel data from a variety of sources, it is established that the rate of propagation of modified flow downstream of a change in surface roughness is determined essentially by the rougher surface. For the data examined neither the ratio of the upstream to downstream roughness lengths nor the ratio of boundary layer height to roughness element height is of itself a significant parameter.

Based on an empirical analogy with Kazanskii and Monin's plume propagation concept, a simple method is proposed for predicting the depth of modified flow. The predictions include an origin correction and are shown to agree satisfactorily with measurements in neutrally stratified boundary layers.
Change in intensity of typhoons which develop cloud‐plume outflow aloft
Authors: Tsui K. S. , Bell G. J. , Fung P. C. W.
Published: February 2007

Satellite and aircraft data indicate an approximate 0–64 probability that the intensity of a typhoon will have increased during the 24 hours prior to the time when a plume of middle and high cloud streaming from the centre of the storm towards the northeast is first seen on satellite photograph.
On the application of some stochastic models to precipitation forecasting
Authors: Dyer T. G. J.
Published: February 2007

The equivalent of 157 rainfall records for South Africa have been subjected to various statistical modelling techniques. These include: autoregression; multiple linear and trigonometric regression; and exponential smoothing. Between them the models cover short‐ and long‐term forecasting. the trigonometric model provides a useful forecasting aid. Estimation of the parameters in this model stem from the spectra of the raw rainfall data. the models described are limited neither to rainfall nor the area of the globe from which the present data were obtained.
Influence of cover on mean column hydraulic characteristics in small pool riffle morphology streams
Authors: Smith David L. , Brannon Ernest L.
Published: February 2007

The field of ecohydraulics tries to link biological‐ and physical‐based processes in order to describe better the distribution of plants and animals in rivers. We tested the hypothesis that the influence of cover in pools and riffles would not be detectable using average velocity, turbulent kinetic energy and turbulent intensity, and compared these measurements to locations distant from cover. We measured water velocity fluctuations using an acoustic Doppler velocimeter. We found that turbulent intensity in the downstream direction (u′) and the transverse or cross‐stream direction (v′) were the most useful in detecting the presence of cover in pools and riffles. Differences were apparent between locations near cover in pools and riffles. Turbulent kinetic energy (k) and vertical turbulent intensity (w′) detected cover in pools but not in riffles. Average downstream velocity ($\bar u$) detected cover in riffles but not in pools. Average cross‐stream ($\bar v$) and vertical ($\bar w$) velocities did not detect any differences at all. We rejected the null hypothesis and concluded that turbulence caused by habitat features such as large rocks, wood or other channel complexities results in a statistically meaningful difference in flow characteristics in locations near cover. This finding was tempered by the fact that knowledge about how fish respond to turbulence is limited in comparison to our understanding of average velocity values. Despite the potential benefits to habitat modelling of incorporating turbulence‐based metrics, application of these findings will be challenging because turbulence modelling is difficult and current models may not be appropriate for application to rivers. Copyright © 2007 John Wiley & Sons, Ltd.
Are clonal plants more tolerant to grazing than co‐occurring non‐clonal plants in inland dunes?
Authors: Liu Hai‐Dong , Yu Fei‐Hai , He Wei‐Ming , Chu Yu , Dong Ming
Published: February 2007

Clonal traits such as clonal integration and storage functions of rhizomes or stolons may provide clonal plants with additional advantages against grazing over non‐clonal plants. Here, we hypothesize that clonal species have a larger capacity for compensatory growth than co‐occurring non‐clonal species. In inland dunes in northern China, individual plants of two rhizomatous clonal species (Bromus ircutensis and Psammochloa villosa) and two non‐clonal ones (Artemisia intramongolica and Astragalus melilotoides) were subjected to 0% (control), 50% (moderate) and 90% (heavy) shoot removal. Compared with control, heavy clipping greatly increased the relative growth rate in Bromus and Psammochloa, but decreased that in Artemisia and Astragalus. Heavy clipping affected above‐ground dry weight and the number of modules more negatively in Artemisia and Astragalus than in Bromus and Psammochloa. These results support the hypothesis and suggest that clonal species are more tolerant to grazing than co‐occurring non‐clonal species in inland dunes.
The oligomeric structure of high molecular weight adiponectin
Authors: Suzuki Shinji , Wilson-Kubalek Elizabeth M. , Wert David , Tsao Tsu-Shuen , Lee David H.
Published: February 2007

There is great interest in the structure of adiponectin as its oligomeric state may specify its biological activities. It occurs as a trimer, a hexamer and a high molecular weight complex. Epidemiological data indicate that the high molecular weight form is significant with low serum levels in type 2 diabetics but to date, has not been well‐defined. To resolve this issue, characterization of this oligomer from bovine serum and 3T3‐L1 adipocytes by sedimentation equilibrium centrifugation and gel electrophoresis respectively, was carried out, revealing that it is octadecameric. Further studies by dynamic light scattering and electron microscopy established that bovine and possibly mouse high molecular weight adiponectin is C1q‐like in structure.
A systematic review and meta-analysis of set-shifting ability in eating disorders
Authors: ROBERTS MARION E. , TCHANTURIA KATE , STAHL DANIEL , SOUTHGATE LAURA , TREASURE JANET
Published: February 2007

Background

The aim was to critically appraise and synthesize the literature relating to set-shifting ability in eating disorders. PsycINFO, Medline, and Web of Science databases were searched to December 2005. Hand searching of eating-disorder journals and relevant reference sections was also undertaken.

Method

The 15 selected studies contained both eating disorder and healthy control groups, and employed at least one of the following six neuropsychological measures of set-shifting ability; Trail Making Test (TMT), Wisconsin Card Sort Test (WCST), Brixton task, Haptic Illusion, CatBat task, or the set-shifting subset of the Cambridge Neuropsychological Test Automated Battery (CANTAB). The outcome variable was performance on the set-shifting aspect of the task. Pooled standardized mean differences (effect sizes) were calculated.

Results

TMT, WCST, CatBat and Haptic tasks had sufficient sample sizes for meta-analysis. These four tasks yielded acceptable pooled standardized effect sizes (0·36; TMT −1·05; Haptic) with moderate variation within studies (as measured by confidence intervals). The Brixton task showed a small pooled mean difference, and displayed more variation between sample results. The effect size for CANTAB set shifting was 0·17.

Conclusion

Problems in set shifting as measured by a variety of neuropsychological tasks are present in people with eating disorders.
The squirrel as a rodent model of the human visual system
Authors: VAN HOOSER STEPHEN D. , NELSON SACHA B.
Published: February 2007

This article appeared in Volume 23, Number 5, 2006, pages
765–778.
Development and quality of porcine embryos in different culture system and embryo-producing methods
Authors: Ock S-A. , Lee S-L. , Kim J-G. , Kumar B-M. , Balasubramanian S. , Choe S-Y. , Rho G-J.
Published: February 2007

In this study, the developmental ability and cellular composition of porcine IVF, parthenote and somatic cell nuclear transfer (SCNT) embryos were evaluated following differentin vitroculture systems. Group 1, embryos were cultured in NCSU-23 with 5.55 mMD-glucose (NCSU+) until day 6 on 20% O2or 5% O2(Group 2). Group 3, embryos were cultured inD-glucose-free NCSU-23 (NCSU−) with 0.17 mM Na pyruvate/2.73 mM Na lactate for 58 h and subsequently cultured in NCSU+ until day 6 (NCSU −/+) on 20% O2or 5% O2(Group 4). IVF blastocysts did not differ significantly with O2concentrations, but differed significantly with major energy source (glucose and pyruvate/lactate). In Group 3 and 4 IVF blastocysts, the total cell number and apoptosis rates were not significantly different with different O2concentrations. Blastocyst rate, total cell number and apoptosis rate in Groups 3 and 4 parthenote embryos also were not significantly different. Parthenote and SCNT, under the same culture treatment, exhibited significant differences in blastocyst and apoptosis rates (47.5 ± 16.1 vs. 24.0 ± 4.0 and 4.9 ± 9.0 vs. 22.8 ± 23.3). Apoptosis-generating rate increased in the order parthenote, IVF and then SCNT. In conclusion,in vitrodevelopment of porcine embryos was not affected by O2concentrations but was affected by major energy source. Even so, the concentration of each major energy source and the timing of its inclusion in culture could accomplish relatively high embryonic development, the apoptosis rate stressed that more work still needs to be done in developing a better defined culture system that could support SCNT embryos equivalent toin vivopreimplantation porcine embryos.
Validation of a food-frequency questionnaire for measurement of nutrient intake in a dietary intervention study
Authors: Segovia-Siapco Gina , Singh Pramil , Jaceldo-Siegl Karen , Sabaté Joan
Published: February 2007

Objective

To validate a 171-item semi-quantitative food-frequency questionnaire (FFQ) for measurement of nutrient intake in an intervention trial based on walnut supplementation.

Design and setting

Free-living adults from Southern California were randomly assigned to either an intervention (walnut-supplemented) or a control diet. The prescribed 6-month intervention was ≥ 28 g of walnuts per day for the walnut-supplemented group and ≤ 2 g of walnuts per day for the control group. Participants provided at least six 24-hour dietary recalls and completed a self-administered FFQ.

Subjects

Eighty-seven adults aged 30–72 years (48 females, 39 males).

Results

Our findings from validation (by correlation with six diet recall measures) of the measurement of 32 nutrients by the FFQ are as follows. We found significant positive correlations (corrected for measurement error) between the FFQ and diet recalls for total energy (r = 0.34), total carbohydrate (r = 0.42), vegetable protein (r = 0.43), total fat (r = 0.51), polyunsaturated fat (r = 0.77), total fibre (r = 0.60), linoleic acid (r = 0.78) and α-linolenic acid (r = 0.79) – the last nutrient being an excellent nutrient biomarker of the intervention (walnut supplementation). Significant positive correlations were also found for vitamin C (r = 0.96) and certain minerals (r = 0.46–0.80 for calcium, phosphorus, magnesium, iron and potassium). Uncorrected correlations were also high (r>0.40) for retinol, β-carotene, folate and alcohol. Both diet recalls and FFQ showed a similar significant difference in α-linolenic acid content between the walnut-supplemented and control diets.

Conclusions

The FFQ demonstrated good relative validity in the estimation intake of some of the major nutrients in a dietary intervention trial and was a particularly valid estimate of an important nutrient biomarker of walnut supplementation.
Gender-Specific Response to Isoflurane Preconditioning in Focal Cerebral Ischemia
Authors: Kitano Hideto , Young Jennifer M , Cheng Jian , Wang Lan , Hurn Patricia D , Murphy Stephanie J
Published: February 2007

Inhalation anesthetics are effective chemical preconditioning agents in experimental cerebral ischemia. However, previous work has been performed exclusively in male animals. We determined if there is a gender difference in ischemic outcome after isoflurane preconditioning (IsoPC), and if this sex-specific response is linked to differences in Akt phosphorylation or expression of neuronal inducible cell-death putative kinase (NIPK), a negative modulator of Akt activation. Young and middle-aged male and female mice were preconditioned for 4 h with air (sham PC) or 1.0% IsoPC and recovered for 24 h. Cortices were subdissected from preconditioned young male and female mice for measurement of Akt phosphorylation (Western blot) and NIPK mRNA (quantitative polymerase chain reaction). Additional cohorts underwent 2 h of reversible middle cerebral artery occlusion. Lastly, male and female Akt1+/+ and Akt1−/– mice were studied to determine if gender differences in ischemic outcome after IsoPC is Akt1-dependent. Infarction volume was determined at 22 h reperfusion (2,3,5-triphenyltetrazolium chloride). As expected, IsoPC decreased ischemic damage as compared with sham PC in young and middle-aged male mice. In contrast, IsoPC markedly increased infarction in young female mice and had no effect in middle-aged female mice. Cortical phospho-Akt was increased by IsoPC versus sham PC only in male mice. No increase was observed in IsoPC female mice. NIPK mRNA was higher in female mice than in male mice regardless of preconditioning status. Male IsoPC neuroprotection was lost in Akt1-deficient male mice. We conclude that IsoPC is beneficial only in ischemic male brain and that sex differences in IsoPC are mediated through Akt activation and basal NIPK expression.
Efficient global biopolymer sampling with end-transfer configurational bias Monte Carlo
Authors: Arya Gaurav , Schlick Tamar
Published: February 2007

We develop an “end-transfer configurational bias Monte Carlo” method for efficient thermodynamic sampling of complex biopolymers and assess its performance on a mesoscale model of chromatin (oligonucleosome) at different salt conditions compared to other Monte Carlo moves. Our method extends traditional configurational bias by deleting a repeating motif (monomer) from one end of the biopolymer and regrowing it at the opposite end using the standard Rosenbluth scheme. The method’s sampling efficiency compared to local moves, pivot rotations, and standard configurational bias is assessed by parameters relating to translational, rotational, and internal degrees of freedom of the oligonucleosome. Our results show that the end-transfer method is superior in sampling every degree of freedom of the oligonucleosomes over other methods at high salt concentrations (weak electrostatics) but worse than the pivot rotations in terms of sampling internal and rotational sampling at low-to-moderate salt concentrations (strong electrostatics). Under all conditions investigated, however, the end-transfer method is several orders of magnitude more efficient than the standard configurational bias approach. This is because the characteristic sampling time of the innermost oligonucleosome motif scales quadratically with the length of the oligonucleosomes for the end-transfer method while it scales exponentially for the traditional configurational-bias method. Thus, the method we propose can significantly improve performance for global biomolecular applications, especially in condensed systems with weak nonbonded interactions and may be combined with local enhancements to improve local sampling.
Electron gun using carbon-nanofiber field emitter
Authors: Sakai Y. , Haga A. , Sugita S. , Kita S. , Tanaka S.-I. , Okuyama F. , Kobayashi N.
Published: February 2007

An electron gun constructed using carbon-nanofiber (CNF) emitters and an electrostatic Einzel lens system has been characterized for the development of a high-resolution x-ray source. The CNFs used were grown on tungsten and palladium tips by plasma-enhanced chemical-vapor deposition. Electron beams with the energies of 10<E<20keV were focused by the electrostatic lens and impinged on a W target for x-ray radiography. Analyzing the recorded x-ray radiographs, the focal spot size of the electron beam extracted from the CNFs was estimated to be D<50μm in diameter. Superior performance was realized by using CNFs with larger fiber radii (100–500nm) grown sparsely on the metal tips, which were installed in a holder at the short length L=0.5mm.
Simulations of edge behavior in a mixed-lipid bilayer: Fluctuation analysis
Authors: Jiang Yong , Kindt James T.
Published: February 2007

Coarse-grained molecular dynamics simulations of lipid bilayer ribbons consisting of a mixture of lipids of different tail lengths have been performed to gain insight into bicelle mixtures. The line tension of the bilayer edge decreases as the mole fraction of short-chain lipids in the system is increased, dropping below zero between 30% and 35%. The mole fraction of short-chain lipids in the ribbon interior is lower than the total mole fraction, as the short-chain lipids segregate towards the edge, but continues to rise even after the line tension vanishes, in contrast to predictions of a two-component two-phase model. The fluctuations of the bilayer edge in both high and low line tension regimes have been analyzed to extract information about the factors that influence the length and shape of the edge. At high line tension the wavelength-dependent in-plane fluctuations of the edge are predicted quantitatively using a simple analytical model using only the line tension as input. Where line tension is vanishing, the fluctuations can be modeled as arising from a combination of harmonic fluctuations around a minimum energy contour length and an in-plane bending elasticity. The estimated value of the in-plane bending modulus is of order 10−29Jm, placing the intrinsic persistence length for the edge near the bilayer thickness of 4nm.
Density functional theory optimized basis sets for gradient corrected functionals: 3d transition metal systems
Authors: Calaminici Patrizia , Janetzko Florian , Köster Andreas M. , Mejia-Olvera Roberto , Zuniga-Gutierrez Bernardo
Published: February 2007

Density functional theory optimized basis sets for gradient corrected functionals for 3d transition metal atoms are presented. Double zeta valence polarization and triple zeta valence polarization basis sets are optimized with the PW86 functional. The performance of the newly optimized basis sets is tested in atomic and molecular calculations. Excitation energies of 3d transition metal atoms, as well as electronic configurations, structural parameters, dissociation energies, and harmonic vibrational frequencies of a large number of molecules containing 3d transition metal elements, are presented. The obtained results are compared with available experimental data as well as with other theoretical data from the literature.
Optical profiles with 180μm resolution of objects hidden in scattering media
Authors: Andreoni Alessandra , Nardo Luca , Brega Adriano , Bondani Maria
Published: February 2007

We measure the time-of-flight distributions of near-infrared photons emerging from thick scattering media within a collection angle of 0.6mrad about the incident light direction by means of a time-correlated single-photon counting apparatus endowed with <35ps resolution. These measurements, which are performed with a picosecond laser beam, allow us to isolate the weakly scattered (ballistic∕snake) photons from the multiply scattered ones. By scanning the incidence position across a target we find variations in the fraction of detected unscattered photons that are significative of local changes in the optical parameters of the target. In particular, if either opaque, light diffusing, or transparent objects are embedded in the scattering medium, their profiles can be reconstructed and their nature can be assessed. Opaque objects embedded in realistic tissue phantoms are detected with <180μm spatial resolution.
Phase separation in potassium-doped ZnPc thin films
Authors: Giovanelli L. , Vilmercati P. , Castellarin-Cudia C. , Themlin J.-M. , Porte L. , Goldoni A.
Published: February 2007

In this study synchrotron radiation was used to investigate the electronic properties of a thin film of zinc-phthalocyanine (ZnPc) deposited on Si(001)-2×1 and progressively doped with K atoms. The molecular orientation was probed by angular-dependent x-ray absorption spectroscopy and the molecules were found to lie with the macrocycle plane roughly perpendicular to the surface. The evolution of the electronic properties of the film was then followed by measuring the photoemission spectra upon in situ evaporation of K atoms on the pristine ZnPc film. The results show that doping proceeds through charge donation from the K atoms to the molecular units whose lowest unoccupied molecular orbital (LUMO) becomes progressively filled. Despite the fact that the LUMO spectral weight increases as the stoichiometry x in the KxZnPc compound varies from about 1 to 4 (as determined by core level photoemission), no detectable density of states was observed at the Fermi level, showing that the film remains insulating for all the investigated stoichiometries. On the other hand the C 1s spectra, which appear merely broadened at the earliest stages of doping (x≈1), clearly develop two distinct components when x exceeds 2, suggesting that the charge state is not the same for all the molecules. At the same time, the modification of the valence band points towards the coexistence of two distinct phases with x=2 and x=4.
Improvements in the electrical properties of high-k HfO2 dielectric films on Si1−xGex substrates by postdeposition annealing
Authors: Park Tae Joo , Kim Jeong Hwan , Jang Jae Hyuk , Seo Minha , Hwang Cheol Seong , Won Jeong Yeon
Published: February 2007

The changes in atomic-layer-deposited HfO2 films on Si and Si1−xGex (x=0.1, 0.2, and 0.3) substrates by postdeposition annealing were studied. The migration of Ge reduced the capacitance equivalent thickness while keeping the leakage current density almost invariant after annealing. High resolution x-ray photoelectron spectroscopy and secondary ion mass spectroscopy analyses confirmed that Ge atoms which had diffused into the HfO2 layer during the deposition were drawn back to the substrate by annealing which was accompanied by the decrease in the interfacial strain energy. A very low interface trap density (1.3×1010cm−2eV−1) was obtained when x=0.3.
Abruptness of a-Si:H∕c-Si interface revealed by carrier lifetime measurements
Authors: De Wolf Stefaan , Kondo Michio
Published: February 2007

Intrinsic hydrogenated amorphous silicon films can yield outstanding electronic surface passivation of crystalline silicon wafers. In this letter the authors confirm that this is strongly determined by the abruptness of the interface. For completely amorphous films the passivation quality improves by annealing at temperatures up to 260°C, most likely by film relaxation. This is different when an epitaxial layer has been grown at the interface during film deposition. Annealing is in such a case detrimental for the passivation. Consequently, the authors argue that annealing followed by carrier lifetime measurements allows determining whether the interface is abrupt.
Entropy change upon magnetic field and pressure variations
Authors: de Oliveira N. A.
Published: February 2007

In this letter it is theoretically discussed the magnetocaloric effect under applied pressure and the barocaloric effect under applied magnetic field in compounds undergoing a first order magnetic phase transition. The theoretical findings of this letter point out that the magnetocaloric effect upon simultaneous variation of the magnetic field and pressure as well as the barocaloric effect in first order phase transition compounds can be very important for magnetic refrigeration technology.
Imaging of hemoglobin oxygen saturation variations in single vessels in vivo using photoacoustic microscopy
Authors: Zhang Hao F. , Maslov Konstantin , Sivaramakrishnan Mathangi , Stoica Gheorghe , Wang Lihong V.
Published: February 2007

Photoacoustic microscopy was used to noninvasively image variations in hemoglobin oxygen saturation (SO2) in the subcutaneous microvasculature of rats in vivo. In phantom tests, the calculated concentration fractions of red ink in double-ink mixtures matched the actual values with a 1% error. In ex vivo studies, the calculated SO2 in bovine blood agreed with the standard spectrophotometric measurements within a 4% systematic difference. In in vivo studies, arteries and veins were separated based on the measured SO2 values and variations in SO2 between different physiological states (hyperoxia, normoxia, and hypoxia) were imaged in single blood vessels.
Direct probe of excitonic and continuum transitions in the photocurrent spectroscopy of individual carbon nanotube p-n diodes
Authors: Lee Ji Ung , Codella Peter J. , Pietrzykowski Matthew
Published: February 2007

The authors show that a carbon nanotube p-n diode is a very sensitive probe of optical transitions in individual single-walled carbon nanotubes. In the photocurrent spectra, an alternating sequence of resonant peaks from dissociation of excitons and exciton-phonon bound states, for the lowest and higher electronic subbands, is observed. At an intermediate energy, the onset of continuum is observed that allows measurement of exciton binding energies. Both the binding energy and the onset of continuum follow the inverse diameter relation as expected from general theory of optical transitions in nanotubes.
Role of interface disorder on thermal boundary conductance using a virtual crystal approach
Authors: Beechem Thomas , Graham Samuel , Hopkins Patrick , Norris Pamela
Published: February 2007

An analytical method is presented to estimate the effects of structural disorder on the thermal boundary conductance (TBC) between two materials. The current method is an extension of the diffuse mismatch model (DMM) where the interface is modeled as a virtual crystal of finite thickness with properties derived from those of the constituent materials. Using this approximation, the TBC for a series of chromium/silicon interfaces is modeled and shown to be within 18% of experimentally obtained values. The methodology improves upon the predictive capabilities of the DMM and allows for quick estimation of the impact of interface mixing on TBC.
Direct evidence of Cu/cap/liner edge being the dominant electromigration path in dual damascene Cu interconnects
Authors: Shao W. , Mhaisalkar S. G. , Sritharan T. , Vairagar A. V. , Engelmann H. J. , Aubel O. , Zschech E. , Gusak A. M. , Tu K. N.
Published: February 2007

In this investigation, Cu/dielectric-cap interface and Cu/cap/liner edge were studied in detail to identify the dominant path in electromigration stressed via-fed test structures that represent the dual damascene architectures in Cu metallization. The impact of the electron wind force on void evolution, agglomeration at the Cu/cap/liner edges, and interface diffusion was investigated based on morphological examinations. The investigations presented here show direct evidence of preferential accumulation of voids at the Cu/cap/liner edges. This preferential void accumulation towards Cu/cap/liner edge is analyzed and explained by means of a simplified Monte Carlo simulation.
The reproductive cycle of the smooth skate, Malacoraja senta, in the Gulf of Maine
Authors: Sulikowski James A. , Elzey Scott , Kneebone Jeff , Jurek Joe , Howell W. Huntting , Tsang Paul C. W.
Published: February 2007

The smooth skate (Malacoraja senta) is a small species of skate that is native to the waters of the north-western Atlantic. Recent assessments in the Gulf of Maine indicate that the biomass of smooth skates has declined below threshold levels mandated by the Sustainable Fisheries Act. This decline, coupled with the paucity of biological data, has prompted the National Marine Fisheries Service to prohibit the possession of smooth skates in this region. Consequently, crucial life history information is now being collected, which could be used in the formulation of a management plan. The present study describes and characterises the reproductive cycle of female and male smooth skates, based on monthly samples taken off the coast of New Hampshire, USA, from May 2001 to April 2002. Gonadosomatic index (GSI), hepatosomatic index (HSI), shell gland weight, follicle size and egg case formation were assessed for 79 female skates. In general, these reproductive parameters remained relatively constant throughout most of the year. Additionally, the size distribution of ovarian follicles in females captured each month did not vary significantly. For males (n = 81), histological stages of spermatogenesis III to VI (SIII-SVI), GSI and HSI were examined. No significant differences were detected in male reproductive parameters, and production and maintenance of mature spermatocysts within the testes were observed throughout the year. Collectively, these findings indicate that, like other north Atlantic skate species, the smooth skate is reproductively active year-round.
Sequential Monte Carlo without likelihoods
Authors: Sisson S. A. , Fan Y. , Tanaka Mark M.
Published: February 2007

Recent new methods in Bayesian simulation have provided ways of evaluating posterior distributions in the presence of analytically or computationally intractable likelihood functions. Despite representing a substantial methodological advance, existing methods based on rejection sampling or Markov chain Monte Carlo can be highly inefficient and accordingly require far more iterations than may be practical to implement. Here we propose a sequential Monte Carlo sampler that convincingly overcomes these inefficiencies. We demonstrate its implementation through an epidemiological study of the transmission rate of tuberculosis.
LARK activates posttranscriptional expression of an essential mammalian clock protein, PERIOD1
Authors: Kojima Shihoko , Matsumoto Ken , Hirose Matsumi , Shimada Miyuki , Nagano Mamoru , Shigeyoshi Yasufumi , Hoshino Shin-ichi , Ui-Tei Kumiko , Saigo Kaoru , Green Carla B. , Sakaki Yoshiyuki , Tei Hajime
Published: February 2007

The mammalian molecular clock is composed of feedback loops to keep circadian 24-h rhythms. Although much focus has been on transcriptional regulation, it is clear that posttranscriptional controls also play important roles in molecular circadian clocks. In this study, we found that mouse LARK (mLARK), an RNA binding protein, activates the posttranscriptional expression of the mouse
Period1
(m
Per1
) mRNA. A strong circadian cycling of the mLARK protein is observed in the suprachiasmatic nuclei with a phase similar to that of mPER1, although the level of the
Lark
transcripts are not rhythmic. We demonstrate that LARK causes increased mPER1 protein levels, most likely through translational regulation and that the LARK1 protein binds directly to a cis element in the 3′ UTR of the m
Per1
mRNA. Alterations of m
Lark
expression in cycling cells caused significant changes in circadian period, with m
Lark
knockdown by siRNA resulting in a shorter circadian period, and the overexpression of mLARK1 resulting in a lengthened period. These data indicate that mLARKs are novel posttranscriptional regulators of mammalian circadian clocks.
Protein ligand migration mapped by nonequilibrium 2D-IR exchange spectroscopy
Authors: Bredenbeck Jens , Helbing Jan , Nienhaus Karin , Nienhaus G. Ulrich , Hamm Peter
Published: February 2007

2D-IR exchange spectroscopy has been introduced recently to map chemical exchange networks in equilibrium with subpicosecond time resolution. Here, we demonstrate the generalization of 2D-IR exchange spectroscopy to nonequilibrium systems and its application to map light-triggered migration of ligands between different sites in a protein. Within picoseconds after a photodissociating laser pulse, carbon monoxide ligands relocate from their binding site A at the heme prosthetic group of myoglobin to a primary docking site B in the distal heme pocket. Multiple CO stretching bands are observed for the CO ligand in sites A and B, indicating that several distinct conformational substates of the myoglobin:ligand complex coexist in solution. Exchange cross-peaks between the bands associated with substates of heme-bound CO and photodissociated CO in the primary docking site reveal the substate connectivity at physiological temperature.
Chromosomal context directs high-frequency precise excision of IS
492
in
Pseudoalteromonas atlantica
Authors: Higgins Brian P. , Carpenter Chandra D. , Karls Anna C.
Published: February 2007

DNA rearrangements, including insertions, deletions, and inversions, control gene expression in numerous prokaryotic and eukaryotic systems, ranging from phase variation of surface antigens in pathogenic bacteria to generation of Ig diversity in human B cells. We report here that precise excision of the mobile element IS
492
from one site on the
Pseudoalteromonas atlantica
chromosome directly correlates with phase variation of peripheral extracellular polysaccharide (
p
EPS) production from OFF (
epsG
::IS
492
) to ON (
epsG
+
). In a previously undescribed application of quantitative PCR, we determined that the frequency of this transposase-dependent precise excision is remarkably high, ranging from 10
−3
to 10
−2
per cell per generation. High-frequency excision resulting in nonmutagenic repair of donor DNA is extremely unusual for classical transposable elements. Interestingly, high-frequency precise excision of IS
492
does not occur at four different insertion sites on the
P. atlantica
chromosome, despite identity in the IS
492
nucleotide sequences and 5- to 7-bp flanking DNA. The genome sequence revealed that
epsG
-associated IS
492
is the only element inserted within a gene. Quantitative RT-PCR assays for externally derived transposase transcripts from each IS
492
copy showed that IS
492
at
epsG
has higher levels of host-initiated transcription through the element, suggesting that transcription
per se
or an increase in transposase (
mooV
) expression is responsible for the effect of chromosomal position on element excision. MooV levels and excision activity for IS
492
inserted in forward and reverse orientations relative to p
lac
and p
T7
in
Escherichia coli
support that external transcription of
mooV
boosts transposase to a critical level required for detectable excision.
The yeast orthologue of GRASP65 forms a complex with a coiled-coil protein that contributes to ER to Golgi traffic
Authors: Behnia Rudy , Barr Francis A. , Flanagan John J. , Barlowe Charles , Munro Sean
Published: February 2007

The mammalian Golgi protein GRASP65 is required in assays that reconstitute cisternal stacking and vesicle tethering. Attached to membranes by an N-terminal myristoyl group, it recruits the coiled-coil protein GM130. The relevance of this system to budding yeasts has been unclear, as they lack an obvious orthologue of GM130, and their only GRASP65 relative (Grh1) lacks a myristoylation site and has even been suggested to act in a mitotic checkpoint. In this study, we show that Grh1 has an N-terminal amphipathic helix that is N-terminally acetylated and mediates association with the cis-Golgi. We find that Grh1 forms a complex with a previously uncharacterized coiled-coil protein, Ydl099w (Bug1). In addition, Grh1 interacts with the Sec23/24 component of the COPII coat. Neither Grh1 nor Bug1 are essential for growth, but biochemical assays and genetic interactions with known mediators of vesicle tethering (Uso1 and Ypt1) suggest that the Grh1–Bug1 complex contributes to a redundant network of interactions that mediates consumption of COPII vesicles and formation of the cis-Golgi.
In vivo imaging of cytotoxic T cell infiltration and elimination of a solid tumor
Authors: Boissonnas Alexandre , Fetler Luc , Zeelenberg Ingrid S. , Hugues Stéphanie , Amigorena Sebastian
Published: February 2007

Although the immune system evolved to fight infections, it may also attack and destroy solid tumors. In most cases, tumor rejection is initiated by CD8+ cytotoxic T lymphocytes (CTLs), which infiltrate solid tumors, recognize tumor antigens, and kill tumor cells. We use a combination of two-photon intravital microscopy and immunofluorescence on ordered sequential sections to analyze the infiltration and destruction of solid tumors by CTLs. We show that in the periphery of a thymoma growing subcutaneously, activated CTLs migrate with high instantaneous velocities. The CTLs arrest in close contact to tumor cells expressing their cognate antigen. In regions where most tumor cells are dead, CTLs resume migration, sometimes following collagen fibers or blood vessels. CTLs migrating along blood vessels preferentially adopt an elongated morphology. CTLs also infiltrate tumors in depth, but only when the tumor cells express the cognate CTL antigen. In tumors that do not express the cognate antigen, CTL infiltration is restricted to peripheral regions, and lymphocytes neither stop moving nor kill tumor cells. Antigen expression by tumor cells therefore determines both CTL motility within the tumor and profound tumor infiltration.
Characterizations of positive selfadjoint extensions
Authors: Sebestyén Zoltán , Stochel Jan
Published: February 2007

The set of all positive selfadjoint extensions of a positive operator

T
T

(which is not assumed to be densely defined) is described with the help of the partial order which is relevant to the theory of quadratic forms. This enables us to improve and extend a result of M. G. Krein to the case of not necessarily densely defined operators

T
T

.