bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of the primate area of high acuity. 2. Quantitative morphological changes associated with retinal and pars plana growth
Authors: SPRINGER A.D. , HENDRICKSON A.E.
Published: January 2005

Mechanisms underlying the development of the primate area of high acuity (AHA) remain poorly understood. Finite-element models have identified retinal stretch and intraocular pressure (IOP) as possible mechanical forces that can form a pit (Springer & Hendrickson, 2004). A series ofMacaca nemestrinamonkey retinas between 68 days postconception (dpc) and adult were used to quantify growth and morphological changes. Retinal and pars plana length, optic disc diameter, disc-pit distance, and inner and outer retinal laminar thickness were measured over development to identify when and where IOP or stretch might operate. Horizontal optic disc diameter increased 500 μm between 115 dpc and 2 months after birth when it reached adult diameter. Disc growth mainly influences the immediate surrounding retina, presumably displacing retinal tissue centrifugally. Pars plana elongation also began at 115 dpc and continued steadily to 3–4 years postnatal, so its influence would be relatively constant over retinal development. Unexpectedly, horizontal retinal length showed nonlinear growth, divided into distinct phases. Retinal length increased rapidly until 115 dpc and then remained unchanged (quiescent phase) between 115–180 dpc. After birth, the retina grew rapidly for 3 months and then very slowly into adulthood. The onset of pit development overlapped the late fetal quiescent phase, suggesting that the major mechanical factor initiating pit formation is IOP, not retinal growth-induced stretch. Developmental changes in the thickness of retinal layers were different for inner and outer retina at many, but not all, of the ten eccentricities examined. Peripheral inner and outer retinal layers thinned appreciably with age, consistent with retinal stretch having a larger effect on the retinal periphery. Central inner retina around the area of high acuity (AHA) changed tri-phasically. It increased in thickness prenatally, thinned transiently after birth, and then resumed thickening. Transient postnatal inner retinal thinning around the pit coincided with the resumption of retinal growth and with cone packing providing evidence that a small amount of growth-induced central retinal stretch may account for cone packing as previously hypothesized (Springer, 1999). Central outer retina around the AHA progressively thickened over the fetal period. It reached asymptotic thickness at birth and continued to thicken into adulthood at some temporal, but not nasal, central eccentricities. These data indicate that peripheral outer and inner retina progressively thin with age because of eye growth-induced stretch, while central retina is minimally affected by stretch. Outer and inner retinal laminar thickness at the same locus can change in different directions, suggesting that they shear with respect to one another. This shearing induces the elongation of Henle axons, while their angle reflects the direction of shear.
Gap junctional regulatory mechanisms in the AII amacrine cell of the rabbit retina
Authors: XIA XIAO-BO , MILLS STEPHEN L.
Published: January 2005

Gap junctions are commonplace in retina, often between cells of the same morphological type, but sometimes linking different cell types. The strength of coupling between cells derives from the properties of the connexins, but also is regulated by the intracellular environment of each cell. We measured the relative coupling of two different gap junctions made by AII amacrine cells of the rabbit retina. Permeability to the tracer Neurobiotin was measured at different concentrations of the neuromodulators dopamine, nitric oxide, or cyclic adenosine monophosphate (cAMP) analogs. Diffusion coefficients were calculated separately for the gap junctions between pairs of AII amacrine cells and for those connecting AII amacrine cells with ON cone bipolar cells. Increased dopamine caused diffusion rates to decline more rapidly across the AII–AII gap junctions than across the AII–bipolar cell gap junctions. The rate of decline at these sites was well fit by a model proposing that dopamine modulates two independent gates in AII–AII channels, but only a single gate on the AII side of the AII–bipolar channel. However, a membrane-permeant cAMP agonist modulated both types of channel equally. Therefore, the major regulator of channel closure in this network is the local cAMP concentration within each cell, as regulated by dopamine, rather than different cAMP sensitivity of their respective gates. In contrast, nitric oxide preferentially reduced AII–bipolar cell permeabilities. Coupling from AII amacrine cells to the different bipolar cell subtypes was differentially affected by dopamine, indicating that light adaptation actingviadopamine release alters network coupling properties in multiple ways.
The development of referential activities and clause-combining as aspects of the acquisition of discourse in French as L2
Authors: VÉRONIQUE DANIEL
Published: January 2005

This article describes the development of temporal reference and clause-combining in the acquisition of French L2 by adult Moroccan Arabic L1 speakers. The contribution of iconicity and of transfer from L1 in this development is discussed. The path towards grammaticalisation is less clearly marked in the domain of clause combining than in the domain of temporal reference, where after use of lexical and pragmatic means, inflection on the verb develops. Grammaticalised subordination is rarely used, except for circumstancial clauses. Paratactic devices such as clefting and NP copy tend to be used for discursive functions such as the introduction of background information in narratives, for instance.
Getting to know the city: the construction of spatial knowledge in London in the 1930s
Authors: POOLEY COLIN G.
Published: January 2005

This article explores the ways in which a young woman who migrated from Londonderry to London in the 1930s acquired and used spatial knowledge of the city. Using detailed diary evidence the article maps everyday action spaces, and examines themes such as the use of visual cues in the accumulation of spatial knowledge, the use of maps and signs, the influence of previous travel experiences and the organization of search and exploration strategies in the city.
Temporal evolution of summer convective activity over the Americas warm pools
Authors: Magaña Víctor , Caetano Ernesto
Published: January 2005

The present analysis describes the temporal evolution of various meteorological parameters over the Americas warm pools that are related to the occurrence of the Mid Summer Drought (MSD). Contrary to what has been suggested by some authors, the bimodal structure of precipitation over the Pacific side of Mesoamerica is not a form of intraseasonal variability in convective activity related to the Madden Julian Oscillation, but a characteristic of the annual cycle in precipitation. The MSD – sea surface temperature (SST) ‐ radiation relationship proposed by Magaña et al. [1999] partially hold during the summer of 2001, when the Climate Experiment over the Americas Warm Pools (ECAC) field campaigns were conducted, with the SST exhibiting a bimodal structure in the MSD region. The maximum in tropical convection over the Central America‐Caribbean coast appears to play an important role in modulating convective activity in the surrounding regions, through induced subsidence related to direct circulations. The Caribbean Low Level Jet (CLLJ) is in phase with maximum western Caribbean Sea convective activity, reaching maxima intensities in July.
On smoke suppression of clouds in Amazonia
Authors: Feingold Graham , Jiang Hongli , Harrington Jerry Y.
Published: January 2005

We use large eddy simulations of smoke‐cloud interactions to demonstrate the relative importance of various factors responsible for cloud suppression in the biomass burning regions of Amazonia. The model includes unprecedented treatment of coupled smoke aerosol‐cloud‐radiative feedbacks in a 3‐dimensional model that resolves scales of ∼100s m. It is shown that the vertical distribution of smoke aerosol in the convective boundary layer is crucial to determining whether cloudiness is reduced; Smoke aerosol emitted at the surface in a daytime convective boundary layer may reduce or increase cloudiness whereas smoke aerosol residing in the layer where clouds tend to form will reduce cloudiness. On the other hand, the reduction in surface latent and sensible heat fluxes associated with biomass burning is sufficient by itself to substantially reduce cloudiness.
Evidence of lightning NOx and convective transport of pollutants in satellite observations over North America
Authors: Choi Yunsoo , Wang Yuhang , Zeng Tao , Martin Randall V. , Kurosu Thomas P. , Chance Kelly
Published: January 2005

Column observations of NO2 by GOME and CO by MOPITT over North America and surrounding oceans for April 2000 are analyzed using a regional chemical transport model. Transient enhancements in these measurements due to lightning NOx production or convective transport are examined. Evidence is found for lightning enhancements of NO2 over the continent and western North Atlantic and for convective transport enhancements of CO over the ocean. The two independent satellite measurements show consistent enhancements related to convective events. Model results suggest that the enhancements are particularly large in the lower troposphere due to convective downdrafts of lightning NOx and shallow convection of CO, implying that low‐altitude aircraft in situ observations are potentially critical for evaluating the model simulations and validating satellite observations of these transient features.
Warming of the world ocean, 1955–2003
Authors: Levitus S. , Antonov J. , Boyer T.
Published: January 2005

We present new estimates of the variability of ocean heat content based on: a) additional data that extends the record to more recent years; b) additional historical data for earlier years. During 1955–1998 world ocean heat content (0–3000 m) increased 14.5 × 1022 J corresponding to a mean temperature increase of 0.037°C at a rate of 0.20 Wm−2 (per unit area of Earth's total surface area).
Cluster observations of electron holes in association with magnetotail reconnection and comparison to simulations
Authors: Cattell C. , Dombeck J. , Wygant J. , Drake J. F. , Swisdak M. , Goldstein M. L. , Keith W. , Fazakerley A. , André M. , Lucek E. , Balogh A.
Published: January 2005

Large‐amplitude (up to ∼50 mV/m) solitary waves, identified as electron holes, have been observed during waveform captures on two of the four Cluster satellites during several plasma sheet encounters that have been identified as the passage of a magnetotail reconnection x line. The electron holes were seen near the outer edge of the plasma sheet, within and on the edge of a density cavity, at distances on the order of a few ion inertial lengths from the center of the current sheet. The electron holes occur during intervals when there were narrow electron beams but not when the distributions were more isotropic or contained beams that were broad in pitch angle. The region containing the narrow beams (and therefore the electron holes) can extend over thousands of kilometers in the x and y directions, but is very narrow in the z direction. The association with electron beams and the density cavity and the location along the separatrices are consistent with simulations shown herein. The velocities and scale sizes of the electron holes are consistent with the predictions of Drake et al. [2003]. Particle simulations of magnetic reconnection reproduce the observed Cluster data only with the addition of a small (0.2 of the reversed field) ambient guide field. The results suggest that electron holes may sometimes be an intrinsic feature of magnetotail reconnection and that in such cases the traditional neglect of the guide field may not be justified. Very large amplitude lower hybrid waves (hundreds of millivolts per meter), as well as waves at frequencies up to the electron plasma frequency, were also observed during this interval.
Total electron content behavior over Japan during geomagnetic storms
Authors: Kutiev Ivan , Watanabe Shigeto , Otsuka Yoichi , Saito Akinori
Published: January 2005

The total electron content (TEC) obtained from GPS signals is used to study ionospheric dynamics over Japan during geomagnetically disturbed conditions. The numerous TEC measurements are averaged in cells with a size 1.5° × 1.5° geographic scale and formatted as time series within the years 2000–2002. To extract the storm time changes of TEC, the diurnal and 27‐day periodicities are subsequently removed. Diurnal variations are removed by replacing absolute TEC values in each cell with their relative deviations (RTEC) from medians. The hourly RTEC values from all cells within the central 4°‐wide band over Japan area are then approximated by a plane surface. This surface is represented by two parameters: its value at the center (rt) and the slope (b) along the main axis, taken as constants of the linear regression. The 27‐day periodicity was approximated by Fourier waves with main period of 640 hours and two harmonics separately for rt and b and subtracted from them. The analysis of rt and b behavior during a number of geomagnetic storms allowed us to reveal several repeatable features of average TEC behavior. It was found that TEC behavior during the storms is similar to that of foF2 at the F region and was local time–dependent. A marked poleward expansion of the equatorial ionosphere (crest region) at the end of recovery phase is persistently observed feature, produced probably by intensified eastward zonal winds. Such an expansion of equatorial ionosphere is observed also during isolated substorms, outside main geomagnetic storms. An oscillation‐like change of positive and negative disturbances with period of 24 hours is observed during a 4‐day period, following a moderate storm. In the absence of geomagnetic activity driver that effect is probably caused by the alternative expansion and contraction of equatorial ionosphere.
Annual and semiannual variations of the location and intensity of large‐scale field‐aligned currents
Authors: Ohtani S. , Ueno G. , Higuchi T. , Kawano H.
Published: January 2005

The present study examines seasonal variations of large‐scale field‐aligned current (FAC) systems in terms of the dipole tilt and clock angles. Magnetic field measurements from the DMSP F7 and F12‐F15 satellites are used. This data set consists of a total of ∼185,000 auroral oval crossings, out of which ∼121,000 crossings were selected for the present analysis. Focus is placed on the latitude at the demarcation between the region 2 (R2) and region 1 (R1) currents and the intensities of these currents. It is found that the dayside FAC moves poleward and equatorward in the summer and winter hemispheres, respectively, and the nightside FAC has the opposite seasonal dependence. In the midday sector the peak‐to‐peak variation of the FAC latitude over the entire range of the dipole tilt is ∼5°, whereas it is ∼4° around midnight. In the flank sectors the average FAC latitude is higher around the solstices than around the equinoxes irrespective of hemisphere. The corresponding dependence on the dipole clock angle can actually be found for almost all local time sectors, although the peak‐to‐peak variation of the expected semiannual variation, 2° around noon and <1° in other local time sectors, is smaller than that of the annual variation except for the flank sectors. A comparison with a model magnetic field strongly suggests that the dipole tilt effect on the magnetospheric configuration is the primary cause of the annual variation, whereas the semiannual variation is inferred to reflect the fact that geomagnetic activity tends to be higher around the equinoxes. The average dayside FAC intensity is larger in the summer hemisphere than in the winter hemisphere, which can be explained in terms of the seasonal variation of the ionospheric conductivity. The dayside R1 current intensity depends more strongly on the dipole tilt than the dayside R2 current intensity, and it changes by a factor of 2–3 over the entire range of the dipole tilt angle. In contrast, the annual variation of the nightside FAC intensity is more complicated, and the nightside R2 current seems to be more intense in the winter hemisphere than in the summer hemisphere. The dependence of the FAC intensity on the dipole clock angle is less significant especially for the R1 system. Nevertheless, the result suggests that the FAC tends to be more intense around the equinoxes, which is consistent with the semiannual variation of geomagnetic activity.
A comparative study of ozone production in five U.S. metropolitan areas
Authors: Kleinman L. I. , Daum P. H. , Lee Y.‐N. , Nunnermacker L. J. , Springston S. R. , Weinstein‐Lloyd J. , Rudolph J.
Published: January 2005

We present observations of O3 and O3 precursors measured at mid boundary layer altitude during field campaigns in Nashville, Tennessee (1995), New York City, New York (1996), Phoenix, Arizona (1998), Philadelphia, Pennsylvania (1999), and Houston, Texas (2000). Ozone production rates P(O3) and their sensitivity to NOx and volatile organic carbons (VOCs) are calculated using observed concentrations as inputs to a steady state box model. City to city comparisons are made to illustrate common features of urban photochemistry and features that are unique to specific cities. Ozone production rates vary from nearly zero to 155 ppb h−1. Differences in P(O3) depend on precursor concentrations, namely, radical sources, NOx and VOCs. Under conditions where P(O3) is greater than 25 ppb h−1, there is a potential to produce enough same‐day O3 to transform a typical regional background into a severe O3 episode. Six such cases were observed, in Nashville, Philadelphia, and Houston, with elevated O3 concentrations in the afternoon (130–211 ppb) following a morning in which P(O3) was 25–140 ppb h−1. High P(O3) occurs when NOx concentrations are 5–25 ppb and OH‐VOC reactivity is above 5 s−1. These conditions are infrequent, and aside from a common dependence on calm winds, reasons vary from city to city. In Nashville, high P(O3) was observed during a stagnation event over downtown and under the circumstance that an air mass with a high concentration of isoprene encountered a NOx source. In Houston, NOx and light olefins are coemitted from petrochemical facilities leading to the highest P(O3)s of the five cities studied. High values of P(O3) did not occur in Phoenix because of low radical production, caused mainly by a dry atmosphere, and a low VOC to NOx ratio. The sensitivity of P(O3) to its precursors varied from NOx limited in rural samples to VOC limited near emission sources. In Philadelphia, and especially Phoenix, the highest O3 production rates occurred under VOC‐limited conditions. In Nashville, New York City, and Houston the high‐P(O3) samples were near the ridge line where P(O3) responds somewhat to VOC reductions but is insensitive to NOx changes.
A k‐distribution technique for radiative transfer simulation in inhomogeneous atmosphere: 2. FKDM, fast k‐distribution model for the shortwave
Authors: Fomin Boris , Correa Marcelo de Paula
Published: January 2005

A new technique for developing k‐distributions applied to longwave radiation parameterization has been presented in a preceding paper. Now we discuss an extension of this technique to the shortwave spectral range. A fast k‐distribution model (FKDM) for gaseous absorption calculations suitable for use in weather and climate prediction is described. FKDM has been created using 15 k‐distribution terms only, less than in other comparable codes. The molecular species represented in the model are H2O, CO2, O3, and O2. In k‐distribution terms, characterized by strong absorption, representative absorption cross section is treated as a function of absorber amount along the direct solar radiation path, thus allowing improved fitting of solar fluxes and heating rates in upper troposphere and stratosphere. This technique has been applied to derive effective single‐scattering properties of clouds in each term for a more accurate treatment of cloud optical properties by taking into account correlation between water vapor and liquid water or ice absorption. It is shown that disregarding the above correlation in radiation models can essentially distort simulated fluxes and heating rates. FKDM has been developed and validated using a fast line‐by‐line model (FLBLM). Both FKDM and FLBLM used a Monte‐Carlo code. Validations have covered the tropical, midlatitude summer, midlatitude winter, subarctic summer, subarctic winter, and U.S. standard atmospheres, four atmospheres from the Spectral Radiance Experiment campaign, and a case of an observed tropical atmosphere. It is found that the FKDM heating rate accuracy for clear‐sky conditions is as follows: ∼0.1 and ∼0.2 K d−1 in the troposphere for standard and real atmospheres, respectively, and ∼0.5 K d−1 in all the cases at altitudes below 70 km. Downward flux errors are below 1%, upward flux errors are below 2% (usually ∼1.5 W m−2), and total atmospheric absorption errors are below 3% (usually 1.5–3 W m−2) in every case. The Intercomparison of Radiation Codes in Climate Models (ICRCCM) cloud models have also been used for the validations. It has been demonstrated that the usage of the technique to derive effective cloud optical properties halves maximal errors in calculated radiation fluxes absorbed by cloud.
Climate change and variability using European Centre for Medium‐Range Weather Forecasts reanalysis (ERA‐40) temperatures on the Tibetan Plateau
Authors: Frauenfeld Oliver W. , Zhang Tingjun , Serreze Mark C.
Published: January 2005

Surface air temperature measurements from meteorological stations on the Tibetan Plateau are compared to 2‐m temperatures from the European Centre for Medium‐Range Weather Forecasts (ECMWF) reanalysis (ERA‐40) to assess the accuracy of this reanalysis product. We focus on ERA‐40 grid cells containing at least four stations. The reanalysis temperatures are consistently lower, by as much as 7°C. However, temporal correlations are high, indicating that ERA‐40 captures the interannual variability very well. The temperature bias is almost exclusively due to differences between the grid cell and the station elevations. We conclude that the ERA‐40 temperatures provide better spatial fields of temperature than is possible with stations in this topographically complex, data‐sparse area. Using this spatially and temporally continuous data set, we provide a temperature climatology and assess long‐term climate trends. The high elevations of the western plateau are generally 10°C cooler than the eastern plateau. During winter, 2‐m temperatures are below 0°C on the entire plateau, with summer values of only 0°C in the west and 10°C in the east. While station records point to a long‐term climate warming trend, no trends are observed in ERA‐40. This could be due to inadequacies of the reanalysis data, although we see no evidence of anomalous nonclimatic shifts. The significant trends in station data may reflect the extensive land use change and industrialization that has occurred on the Tibetan Plateau. Reanalysis data are less influenced by these local effects.
Large Turnout for First‐Ever European Space Weather Week
Authors: Simpson Sarah
Published: January 2005

Space weather scientists and applications experts discuss the past, present, and future of space weather activities in Europe
Bone marrow as a source of circulating CXCR4+ tissue‐committed stem cells
Authors: Kucia Magda , Ratajczak Janina , Ratajczak Mariusz Z.
Published: January 2005

Several studies have suggested that adult haematopoietic stem cells (HSCs) may be capable of transdifferentiating across tissue‐lineage boundaries, giving rise to the concept that these stem cells are plastic in their differentiative capacity. This topic created much excitement in the scientific community, with the prospect of employing HSCs in tissue/organ regeneration (e.g. heart infarct, stroke, liver damage) as an alternative to multipotent embryonic stem cells. However, recent observations, and several alternative explanations of previously published data (e.g. cell fusion, epigenetic changes), do not support the concept of HSC plasticity. Our recent studies, in which we employed chemotactic isolation to a stromal‐cell‐derived‐factor‐1 (SDF‐1) gradient combined with real‐time reverse transcriptase (RT)‐PCR/immuno‐histochemical analyses, revealed that bone marrow (BM) contains a highly mobile population of CXCR4+ cells that express mRNA/proteins for various markers of early tissue‐committed stem cells (TCSCs). Based on this we postulate that the BM is not only a home for HSCs, but also a ‘hideout’ for non‐haematopoietic CXCR4+ TCSCs, and we suggest that their presence in BM tissue should be considered before experimental evidence is interpreted simply as transdifferentiation/plasticity of HSCs. Furthermore, our observation that the number of TCSCs is the highest in BM of young animals and decreases with age provides a novel insight into aging, and may explain why the regeneration process becomes less effective in older individuals.
The Protein Kinase Resource: everything you always wanted to know about protein kinases but were afraid to ask
Authors: Petretti Clotilde , Prigent Claude
Published: January 2005

Protein kinases and phosphatases play crucial roles in all the major cellular processes, such as signal transduction, cell differentiation, cell proliferation and cell cycle progression. Protein phosphorylation or dephosphorylation can form the basis of many critical processes, including enzyme activation or inactivation, protein localization and protein degradation. Given the importance of protein kinases to cellular development and function, it is critical that there are effective ways of disseminating information on protein kinases to the research community. This review describes such a web resource, ‘The Protein Kinase Resource’ (http:pkr.sdsc.eduhtmlindex.shtml), which serves as a repository for cellular and molecular data on protein kinases.
The Linderniaceae and Gratiolaceae are further Lineages Distinct from the Scrophulariaceae (Lamiales)
Authors: Rahmanzadeh R. , Müller K. , Fischer E. , Bartels D. , Borsch T.
Published: January 2005

Abstract:The Lamiales are one of the largest orders of angiosperms, with about 22 000 species. The Scrophulariaceae, as one of their most important families, has recently been shown to be polyphyletic. As a consequence, this family was re‐classified and several groups of former scrophulariaceous genera now belong to different families, such as the Calceolariaceae, Plantaginaceae, or Phrymaceae. In the present study, relationships of the generaCraterostigma, Linderniaand its allies, hitherto classified within the Scrophulariaceae, were analyzed. Sequences of the chloroplasttrnKintron and thematKgene (–2.5 kb) were generated for representatives of all major lineages of the Lamiales and the former Scrophulariaceae. Bayesian and parsimony analyses revealed two isolated lineages, one of which consists ofLinderniaand its allies, the other ofGratiolaand allies.Gratiolawas previously assumed to be related toLinderniaand was therefore included here. It is proposed to treat the two clades as separate families, Linderniaceae and Gratiolaceae. For the Linderniaceae, several morphological synapomorphies exist in addition to molecular data, such as conspicuous club‐shaped stamen appendages.
ESTs from the Fibre‐Bearing Stem Tissues of Flax (Linum usitatissimum L.): Expression Analyses of Sequences Related to Cell Wall Development
Authors: Day A. , Addi M. , Kim W. , David H. , Bert F. , Mesnage P. , Rolando C. , Chabbert B. , Neutelings G. , Hawkins S.
Published: January 2005

Abstract: In order to learn more about the diversity of genes expressed during flax fibre cell wall formation, expressed sequence tags (ESTs) were obtained from a cDNA library derived from the outer fibre‐bearing tissues of flax (Linum usitatissimum) stems (cv Hermes) harvested at the mid‐flowering stage. After elimination of vector and unreadable sequences, 927 ESTs were grouped into 67 clusters and 754 singletons. The flax ESTs have been submitted to the dbEST and GenBank databases with the accession numbers 25939634 ‐ 25940560 (dbEST) and CV478070 ‐ CV478996 (GenBank). Functional analysis allowed the grouping of ESTs into 13 functional categories and revealed that 62 % of ESTs were similar to known sequences, while 12.4 % of ESTs presented no similarity to any known sequences and 25.6 % of ESTs corresponded to proteins of unknown function. The most highly expressed transcripts belonged to four functional categories: protein maturation and metabolism (31 ESTs), signalling (22 ESTs), the cell wall (21 ESTs) and photosynthesis (19 ESTs). 4.4 % (41) of the total ESTs were potentially related to cell wall formation and maturation. The most highly expressed cell wall EST (15 ESTs) corresponded to a β‐xylosidase gene ‐ potentially involved in cell wall remodelling during growth and development. Other cell wall‐related ESTs corresponded to cellulose synthase, xyloglucan endotranglucosylase/hydrolase (XTH), β‐galactosidases, and peroxidases. The expression patterns of different cell wall‐related ESTs were determined at different developmental stages in flax plants grown under different field conditions. The potential roles of gene products associated with cell wall related ESTs in fibre cell wall development is discussed.
The Quantum Yield of CO2 Fixation is Reduced for Several Minutes after Prior Exposure to Darkness. Exploration of the Underlying Causes
Authors: Kirschbaum M. U. F. , Oja V. , Laisk A.
Published: January 2005

Abstract: Previous work has shown that the apparent quantum yield of CO2 fixation can be reduced for up to several minutes after prior exposure to darkness. In the work reported here, we investigated this phenomenon more fully and have deduced information about the underlying processes. This was done mainly by concurrent measurements of O2 and CO2 exchange in an oxygen‐free atmosphere. Measurements of O2 evolution indicated that photochemical efficiency was not lost through dark adaptation, and that O2 evolution could proceed immediately at high rates provided that there were reducible pools of photosynthetic intermediates. Part of the delay in reaching the full quantum yield of CO2 fixation could be attributed to the need to build up pools of photosynthetic intermediates to high enough levels to support steady rates of CO2 fixation. There was no evidence that Rubisco inactivation contributed towards delayed CO2 uptake (under measurement conditions of low light). However, we obtained evidence that an enzyme in the reaction path between triose phosphates and RuBP must become completely inactivated in the dark. As a consequence, in dark‐adapted leaves, a large amount of triose phosphates were exported from the chloroplast over the first minute of light rather than being converted to RuBP for CO2 fixation. That pattern was not observed if the pre‐incubation light level was increased to just 3 ‐ 5 μmol quanta m‐2 s‐1. The findings from this work underscore that there are fundamental differences in enzyme activation between complete darkness and even a very low light level of only 3 ‐ 5 μmol quanta m‐2 s‐1 which predispose leaves to different gas exchange patterns once leaves are transferred to higher light levels.
A scale-dependent Lagrangian dynamic model for large eddy simulation of complex turbulent flows
Authors: Bou-Zeid Elie , Meneveau Charles , Parlange Marc
Published: January 2005

A scale-dependent dynamic subgrid model based on Lagrangian time averaging is proposed and tested in large eddy simulations (LES) of high-Reynolds number boundary layer flows over homogeneous and heterogeneous rough surfaces. The model is based on the Lagrangian dynamic Smagorinsky model in which required averages are accumulated in time, following fluid trajectories of the resolved velocity field. The model allows for scale dependence of the coefficient by including a second test-filtering operation to determine how the coefficient changes as a function of scale. The model also uses the empirical observation that when scale dependence occurs (such as when the filter scale approaches the limits of the inertial range), the classic dynamic model yields the coefficient value appropriate for the test-filter scale. Validation tests in LES of high Reynolds number, rough wall, boundary layer flow are performed at various resolutions. Results are compared with other eddy-viscosity subgrid-scale models. Unlike the Smagorinsky–Lilly model with wall-damping (which is overdissipative) or the scale-invariant dynamic model (which is underdissipative), the scale-dependent Lagrangian dynamic model is shown to have good dissipation characteristics. The model is also tested against detailed atmospheric boundary layer data that include measurements of the response of the flow to abrupt transitions in wall roughness. For such flows over variable surfaces, the plane-averaged version of the dynamic model is not appropriate and the Lagrangian averaging is desirable. The simulated wall stress overshoot and relaxation after a jump in surface roughness and the velocity profiles at several downstream distances from the jump are compared to the experimental data. Results show that the dynamic Smagorinsky coefficient close to the wall is very sensitive to the underlying local surface roughness, thus justifying the use of the Lagrangian formulation. In addition, the Lagrangian formulation reproduces experimental data more accurately than the planar-averaged formulation in simulations over heterogeneous rough walls.
Manipulation and detection of single electrons for future information processing
Authors: Ono Yukinori , Fujiwara Akira , Nishiguchi Katsuhiko , Inokawa Hiroshi , Takahashi Yasuo
Published: January 2005

The ultimate goal of future information processing might be the realization of a circuit in which one bit is represented by a single electron. Such a challenging circuit would comprise elemental devices whose tasks are to drag, transfer, and detect single electrons. In achieving these tasks, the Coulomb blockade, which occurs in tiny conducting materials, plays an important role. This paper describes the current status of research on such single-charge-control devices from the viewpoints of circuit applications.
Conditions for self-assembly of quantum fortresses and analysis of their possible use as quantum cellular automata
Authors: Vandervelde T. E. , Kalas R. M. , Kumar P. , Kobayashi T. , Pernell T. L. , Bean J. C.
Published: January 2005

In this study, we detail the conditions that result in the generation of self-assembled quantum fortresses (QFs), in SiGe∕Si. A QF consists of four quantum dots (QDs) clustered around a central square pit, one QD per side. This structure strongly resembles the proposed quantum cellular automata (QCA) unit cell—the basis for a computer architecture. We map the growth conditions (epilayer thickness and Ge concentration) under which self-assembly of strain-stabilized QFs and their precursors occur. Additionally, we characterize how QFs change in height, width, and internal size scales within this parameter space. From this information, we develop a phenomenological model for why QFs form based upon changes in lattice spacing. We then calculate how QFs of the observed shapes and sizes would function as QCAs based on a Hubbard-type Hamiltonian model. This analysis reveals that self-assembled QFs grown at 550°C, a rate of 1Å∕s, a SiGe alloy composition of 37–40%, and a thickness of 15–35nm could be used as QCAs.
Few modes in infrared photonic crystal fibers
Authors: Rave E. , Sade S. , Millo A. , Katzir A.
Published: January 2005

Photonic crystal fibers guide light by trapping it in a periodic array of elements in the cladding area. We fabricated photonic crystal fibers by multiple extrusions of silver halide (AgClxBr1−x) crystals which are highly transparent in the middle infrared. The core of such a fiber consisted of pure silver bromide AgBr (n=2.16 at 10.6μm), and the cladding area consisted of concentric rings of fiber-optic elements made of pure silver chloride AgCl (n=1.98 at 10.6μm), which lowered the refractive index of the clad. Two types of photonic crystal fibers were fabricated, one with two concentric rings and one with five concentric rings of fiber-optic elements around the core. The characterization of the fibers, such as the power distribution, the attenuation, and the numerical aperture were measured. Both fibers behaved like regular core-clad structures. Simulations on these structures showed that each of these fibers guided a small number of modes and that adding rings to the structure lowered the number of bound modes in the core. This would pave the way for the fabrication of single-mode fibers. Photonic crystal fibers offer many advantages compared to conventional fibers, and they will be extremely useful for many applications in the middle and far infrared.
Bandstructure calculation using the k∙p method for arbitrary potentials with open boundary conditions
Authors: Odermatt Stefan , Luisier Mathieu , Witzigmann Bernd
Published: January 2005

We present a method to calculate the quantum-mechanical bandstructure of semiconductor heterostructures for open boundary conditions using k∙p theory. The method is efficient, numerically stable, and easy to implement. The open boundary conditions are derived from a perfectly matched layer (PML) formalism resulting in a complex coordinate stretching. Compared with previous methods like the transfer-matrix method and the quantum transmitting boundary method, the PML formalism reduces the computational costs several orders of magnitude without noticeable reduction of accuracy.
Two-photon resonance assisted huge nonlinear refraction and absorption in ZnO thin films
Authors: Lin Ja-Hon , Chen Yin-Jen , Lin Hung-Yu , Hsieh Wen-Feng
Published: January 2005

Optical nonlinearities of ZnO thin films, made by laser deposition, were investigated by the Z-scan method using a mode-locked femtosecond Ti:sapphire laser. The measured bound-electron nonlinear index of refraction γ and the two-photon absorption coefficient β at near-IR wavelengths show an enormous enhancement compared with measurements on bulk ZnO at 532 nm. The results reveal that two-photon resonance to the band edge and exciton energy level is responsible for the nonlinear absorption and that the free carrier induced the optical nonlinearity. With the excitation wavelength operated between 810 to 840 nm, a negative β value is measured due to the saturation of linear absorption of the defect states. Finally, we compared the values of β from the closed aperture Z-scan data (by considering the multi-photon absorption induced thermal nonlinearity) with those obtained from the open aperture Z-scan data. The results show that nonlinear refraction in the near-IR region is dominated by the bound-electron and free-carrier effect, although the thermal optical nonlinearity cannot be completely ignored.
Large eddy simulation of turbulent open-channel flow with free surface simulated by level set method
Authors: Yue Wusi , Lin Ching-Long , Patel Virendra C.
Published: January 2005

Turbulent open-channel flow over a two-dimensional laboratory-scale dune is studied using large eddy simulation. Free-surface motion is simulated using a level set method. Two subgrid scale models, namely, dynamic Smagorinsky and dynamic two-parameter models, are employed to assess model effects on the free surface. It is found that the two models have very similar performance in predicting the free-surface turbulence. Two flow depths are simulated to investigate the effects of water depth on flow coherent structures and turbulence statistics. In the deep-water flow, experimental data are used to assess for the numerical predictions of the mean flow field and turbulence statistics. They are found to be in good agreement. In the shallow-water flow, there is strong interaction between the free-surface and large-scale vortical structures emanating from the bed, increasing turbulence intensity and free-surface disturbance. The simulations predict streaky structures in the wall layer after flow reattachment in the deep-water flow, but not in the shallow-water case, suggesting that interaction between the free surface and the flow structures is significantly affected by the flow depth.
The effects of ion irradiation on porous silicon photoluminescence
Authors: Jacobsohn L. G. , Bennett B. L. , Cooke D. W. , Muenchausen R. E. , Nastasi M.
Published: January 2005

The effects of ion irradiation on porous Si (po-Si) photoluminescence (PL) are investigated to gain insight into the emission mechanism. Po-Si was obtained by standard electrochemical etching of p-doped Si(100) and the samples were aged for several weeks to achieve stability of the PL intensity. Specimens were progressively irradiated with H+, He+, or Ne++ ions followed by PL measurements. PL spectra were obtained as a function of the displacement per atom (DPA) parameter up to a DPA level of ∼10−2, which was sufficient to nearly extinguish PL. The quenching behavior showed a strong dependence on the chemical nature of the implanted species. Within experimental error, the quenching efficiency was equivalent for He+ and Ne++ irradiations, but was considerably higher for H+ irradiation. Channeling spectrometry showed the efficiency to be correlated with the self-recovery of defects generated during irradiation. The observed PL quenching is associated with the creation of nonradiative recombination sites within the band gap, but not with Si nanostructure amorphization and∕or surface oxygen removal. Significant recovery of quenched PL occurs over a period of 120days for specimens that are stored in air, but not for samples that are stored in vacuum. These results demonstrate the importance and complexity of surface oxidation on the po-Si luminescence mechanism.
Domain texture distributions in tetragonal lead zirconate titanate by x-ray and neutron diffraction
Authors: Jones Jacob L. , Slamovich Elliott B. , Bowman Keith J.
Published: January 2005

The domain structure of ferroelectric ceramics can be altered by the process of electrical poling. This paper develops quantitative approaches for reflection geometry and spherical harmonic texture analysis, both of which describe these changes at angles parallel to and tilted from the poling axis. The x-ray-diffraction approach uses the relative intensity ratio of ferroelectric poles in poled and unpoled lead zirconate titanate to calculate a domain switching fraction (η) or a multiple of a random distribution, which are shown to be linearly related. An x-ray area detector diffractometer was used for these measurements, although the technique applies to any x-ray reflection geometry. The neutron-diffraction approach employs a Rietveld refinement with a spherical harmonic texture model. Both approaches calculate similar domain textures for two poling fields and the small differences between the approaches can be attributed to surface domain texture. This paper shows that the March–Dollase pole distribution function can inadequately describe domain textures.
Enhanced peak-to-valley current ratio in InGaAs∕InAlAs trench-type quantum-wire negative differential resistance field-effect transistors
Authors: Sugaya Takeyoshi , Jang Kee-Youn , Hahn Cheol-Koo , Ogura Mutsuo , Komori Kazuhiro , Shinoda Akito , Yonei Kenji
Published: January 2005

Trench-type narrow InGaAs quantum-wire field-effect transistors (QWR-FETs) have been fabricated on (311)A InP V-groove substrates by hydrogen-assisted molecular-beam epitaxy. Enhanced negative differential resistance (NDR) effects with a peak-to-valley ratio (PVR) as high as 13.3 have been observed at an onset voltage of 0.16V in the QWR-FETs at 24K. The PVR increased with reductions in the InGaAs epitaxial layer thickness, which caused an enhanced mobility difference between the QWR and side quantum wells (QWs). This forms a velocity modulation transistor based on the real-space transfer of electrons from the high mobility QWR to the low mobility side QWs. The NDR effects were observed up to 230K as the gate length was decreased to 50nm. A unique feature of the QWR-FET is that NDR effects are controllable with the gate bias in a three-terminal configuration.
Mixing induced by Rayleigh–Taylor instability in a vortex
Authors: Coquart Laure , Sipp Denis , Jacquin Laurent
Published: January 2005

The direct numerical simulation (DNS) of a two-dimensional Lamb–Oseen vortex with a heavy internal core has been performed. Linear stability theory predicts the existence of Rayleigh–Taylor (RT) instabilities due to the destabilizing effect of the centrifugal force on the radial flow nonhomogeneities. The DNS first exhibits wavy azimuthal perturbations which are nonlinearly distorted into bubble-like patterns, characteristic of the standard development of the RT instabilities, i.e., instabilities obtained in a planar nonhomogeneous flow in the presence of gravity. Nevertheless, important differences may be observed in the late stage development of the instability: contrary to the standard case, the bubbles are then stretched in the azimuthal direction leading to a strong radial filamentation of the flow.
Occupational Structures in Service-Class Households: Comparisons of Rural, Suburban, and Inner-City Residential Environments
Authors: Hoggart Keith , Hiscock Chris
Published: January 2005

The authors explore the composition of service-class households in rural, suburban, and inner-city residential environments in terms of the occupations of household members. Focusing on single-adult and two-adult households, the authors use the Office for National Statistics (ONS) Longitudinal Study (LS) to examine the occupations of LS members and their partners. They find differences in the likelihood that service-class households are single-person households (with inner London standing apart in this regard). Findings contradict dominant messages in the literature that rural areas have fewer women with paid work and fewer with service-class jobs. Most evidently, provincial inner cities stand apart in these terms, with the position regarding paid work for adult couples in rural areas being more similar to paid work for adult couples in London than in suburban or provincial inner-city environments.
Inequity Measures for Evaluations of Environmental Justice: A Case Study of Close Proximity to Highways in New York City
Authors: Jacobson Jerry O , Hengartner Nicolas W , Louis Thomas A
Published: January 2005

Assessments of environmental and territorial justice are similar in that both assess whether empirical relations between the spatial arrangement of undesirable hazards (or desirable public goods and services) and sociodemographic groups are consistent with notions of social justice, evaluating the spatial distribution of benefits and burdens (outcome equity) and the process that produces observed differences (process equity). Using proximity to major highways in New York City as a case study, we review methodological issues pertinent to both fields and discuss choice and computation of exposure measures, but focus primarily on measures of inequity. We present inequity measures computed from the empirically estimated joint distribution of exposure and demographics and compare them with traditional measures such as linear regression, logistic regression, and Theil's entropy index. We find that measures computed from the full joint distribution provide more unified, transparent, and intuitive operational definitions of inequity and show how the approach can be used to structure siting and decommissioning decisions.