bluuebunny/crossref_metadata_2025 huggingface dataset:
Improved stabilization of conventional (brooke) ileostomies with the stapler technique
Authors: Ecker Karl W. , Schmid Thomas , Xu Han S. , Feifel Gernot
Published: September 2005

The rate of functional complications of conventional (Brooke) ileostomy is high and endangers the complete postoperative rehabilitation of the patients. About half of these complications (retraction with/without stenosis, intermittent recession, and prolapse) occur within the classical prominent stoma and are caused by displacement of the serosa surfaces. We have stabilized conventional ileostomies in 39 patients with rows of staples placed paramesenterially and longitudinally. The ileum was everted in the classical way in the primary construction of ileostomies in 19 patients. On the other hand, in 11 patients the prominence of the stoma was established by pulling the ileum out through the previously plane‐sutured stoma. In addition, 9 patients with ileostomies which were not primarily stabilized were corrected with the stapler technique to treat complications. With follow‐up ranging from 0.2 years to 4.2 years, there have been no complications due to sliding of the nipple in these 39 patients. In contrast, there were complications in 37% of 38 patients with non‐stabilized ileostomies with follow‐up to the second postoperative year. It was more easily reproducible, more exact, and less traumatic to create the stoma prominence by pulling the intestine out from a primarily plane stoma than with classical eversion. With use of the stapler in repairing complications, local ileostomy constructions were no longer required in every second patient. Consequently, a Brooke ileostomy can be constructed more easily with the stapler technique, ensuring long‐term function or restoration of function.
Molecular dynamics study of the metallochaperone Hah1 in its apo and Cu(I)‐loaded states: Role of the conserved residue M10
Authors: Poger David , Fuchs Jean-François , Nedev Hristo , Ferrand Michel , Crouzy Serge
Published: September 2005

Molecular dynamics simulations were performed on both apo and copper forms of the human copper chaperone, Hah1. Wild‐type Hah1 and a methionine (M10) to serine mutant were investigated. We have evidenced the central role of residue M10 in stabilizing the hydrophobic core of Hah1 as well as the internal structure of the metal‐binding site. When copper(I) is bound, the mobility of Hah1 is reduced whereas mutation of M10 implies a drastic increase of the mobility of apoHah1, stressing the importance of this highly conserved hydrophobic residue for copper sequestration by the apoprotein.
Riccardin C: A natural product that functions as a liver X receptor (LXR)α agonist and an LXRβ antagonist
Authors: Tamehiro Norimasa , Sato Yoji , Suzuki Takuo , Hashimoto Toshihiro , Asakawa Yoshinori , Yokoyama Shinji , Kawanishi Tohru , Ohno Yasuo , Inoue Kazuhide , Nagao Taku , Nishimaki-Mogami Tomoko
Published: September 2005

Liver X receptors (LXRs) α and β share considerable sequence homology and several functions, respond to the same endogenous and synthetic ligands, and play critical roles in maintaining lipid homeostasis. In this study, liverwort‐derived riccardin C (RC) and F (RF) were identified as an LXRα agonist/LXRβ antagonist and an LXRα antagonist, respectively. RC and RF bound to LXRs, but had different abilities to recruit a coactivator and thereby induce transactivation. Despite its unique subtype‐selective activity, RC enhanced ABCA1 and ABCG1 expression and cellular cholesterol efflux in THP‐1 cells. RC may provide a novel tool for identifying subtype‐function and drug development.
Differences between human proteinase 3 and neutrophil elastase and their murine homologues are relevant for murine model experiments
Authors: Wiesner Olaf , Litwiller Robert D. , Hummel Amber M. , Viss Margaret A. , McDonald Cari J. , Jenne Dieter E. , Fass David N. , Specks U.
Published: September 2005

Direct comparisons of human (h) and murine (m) neutrophil elastase (NE) and proteinase 3 (PR3) are important for the understanding and interpretation of inflammatory and PR3‐related autoimmune processes investigated in wild‐type‐, mNE‐ and mPR3/mNE knockout mice. To this end, we purified recombinant mPR3 and mNE expressed in HMC1 and 293 cells and compared their biophysical properties, proteolytic activities and susceptibility to inhibitors with those of their human homologues, hPR3 and hNE. Significant species differences in physico‐chemical properties, substrate specificities and enzyme kinetics towards synthetic peptide substrates, oxidized insulin B chain, and fibrinogen were detected. MeOSuc‐AAPV‐pNA and Suc‐AAPV‐pNA were hydrolyzed more efficiently by mPR3 than hPR3, but enzymatic activities of mNE and hNE were very similar. Fibrinogen was cleaved much more efficiently by mPR3 than by hPR3. All four proteases were inhibited by α1‐antitrypsin and elafin. Eglin C inihibited mNE, hNE, mPR3, but not hPR3. SLPI inhibited both NEs, but neither PR3. The custom‐designed hNE inhibitor, Val15‐aprotinin, is a poor inhibitor for mNE. In conclusion, appropriate interpretation of experiments in murine models requires individual species‐specific assessment of neutrophil protease function and inhibition.
Paleoproductivity evolution off central Chile from the Last Glacial Maximum to the Early Holocene
Authors: Romero Oscar E. , Kim Jung-Hyn , Hebbeln Dierk
Published: September 2005

A geochemical and paleontological reconstruction of paleoproductivity, upwelling intensity and sea surface temperature (SST) off central Chile at 35°S (GeoB3359-3) reveals marked changes from the Last Glacial Maximum (LGM) through the Early Holocene. Surface-water productivity was determined by the interaction between the atmospheric (the Southern Westerlies) and oceanographic (the Antarctic Circumpolar Current, ACC) systems from the LGM through early Termination I (TI). The northward shift of the climate zones during the LGM brought the ACC, as the main macronutrient source, closer to the GeoB3359-3, SST lowered, and surface water productivity and accumulation rates of biogenic components enhanced. With the poleward return of the Southern Westerlies and the ACC, the subtropical high-pressure system became the dominant atmospheric component southward till 35°S during the late TI and Early Holocene and caused surface water productivity to increase through enhanced upwelling.
Age and seasonal variation in the transition rates and detectability of Plasmodium falciparum malaria
Authors: SAMA W. , OWUSU-AGYEI S. , FELGER I. , DIETZ K. , SMITH T.
Published: September 2005

The effect of acquired immunity on the duration of Plasmodium falciparum infections is unclear, although this is an important term in models of malaria transmission. It is problematical to determine the duration of infections because of the difficulty of distinguishing persisting infections from new ones, and because parasite densities are often transiently below the limit of detection. We recently developed a dynamic model for infection incidence, clearance and detection of multiple genotype P. falciparum infections and fitted it to a panel dataset from a longitudinal study in Northern Ghana. We now extend this model to allow for seasonal and age variation in infection rates and also age dependence in clearance and in detectability of infections. These models indicate that there is seasonal variation in the infection rate, and age dependence in detectability. The best fitting models had no age dependence in infection or clearance rates, suggesting that acquired immunity mainly affects detectability.
advanced practice perspectives in radiation therapy
Authors: bolderston a.
Published: September 2005

roles for radiation therapists are currently in a period of rapid global change. technological advancement, increased entry-level education and the growing specialisation and professionalisation of many non-physician clinician groups are all significant drivers for change. there has been considerable interest in the province of ontario in “advanced practice” roles for therapists. this literature review identifies some of the background issues involved from a local and global perspective.
management issues in radiotherapy physics: a census of heads of radiotherapy physics in the nhs
Authors: thomas d. w.
Published: September 2005

an investigation of human resource issues in radiotherapy physics services in the nhs, including an evaluation of the extent to which the management of human resources was strategic, was undertaken as part of mba level research by a radiotherapy clinical scientist. the research incorporated a telephone census of heads, or acting heads, of radiotherapy physics services. this census looked at the establishment and scale of radiotherapy physics services, issues around recruitment and flexibility, business management, strategy and strategy formation and human resource management practices.

a 96% response rate was obtained with 55 out of a potential population of 57 subjects participating in the survey. it was found that at the time of the survey, 11.0% of all radiotherapy physicist posts were vacant. this was due predominantly to recruitment difficulties. furthermore, 42% of radiotherapy physicists in post were relatively inexperienced, having spent less than 6 years in the discipline. eighty-seven per cent of services had re-graded radiotherapy physicist posts in order to recruit. additionally, 53% of services had changed their skill mix by increasing the ratio of technologists to physicists. fifty-nine per cent of those services did so because of difficulties in recruiting radiotherapy physicists.

whereas 38 respondents (69% of total) said they had a human resource strategy linked to the service's business strategy, only 12 respondents (22% of total) claimed to undertake appraisal and training needs analyses coupled with personal development plans and continuing professional development. relatively little succession planning was undertaken, and only 14 services (26% of total) had well-developed succession plans.

recommendations are made as to how human resource management in nhs radiotherapy physics services could be more strategic.
Long‐term record of atmospheric CO2 and stable isotopic ratios at Waliguan Observatory: Background features and possible drivers, 1991–2002
Authors: Zhou Lingxi , Conway Thomas J. , White James W. C. , Mukai Hitoshi , Zhang Xiaochun , Wen Yupu , Li Jinlon , MacClune Kenneth
Published: September 2005

This paper describes background characteristics of atmospheric CO2 and stable isotopic ratios (δ13C and δ18O) as well as their possible drivers at Waliguan Baseline Observatory (WLG) (36°17′N, 100°54′E, 3816 m above sea level) in the inland plateau of western China. The study is based on observational CO2 data (NOAA Climate Monitoring and Diagnostics Laboratory discrete and WLG continuous measurements) obtained at WLG for the period from May 1991 to December 2002. Over this period the change in monthly means is ∼+16 ppm for CO2, ∼−0.2‰ for δ13C, and ∼−0.5‰ for δ18O. The overall increase of CO2 and subsequent decline of δ13C, with a Δδ13C/ΔCO2 ratio (−0.011 ± 0.105) ‰ ppm−1 at WLG, reflect the persistent worldwide influence of fossil fuel emissions. The negative secular trend of δ18O at WLG is probably due to vigorous 18O exchange with soils in the Northern Hemisphere (NH) and conversion from C3 to C4 plants via land use change. The CO2, δ13C, and δ18O mean annual cycles with peak‐to‐peak annual amplitudes of ∼10.5 ppm, ∼0.499 ‰, and ∼0.819‰, respectively, at WLG show typical middle‐to‐high NH continental features that correspond to the seasonal cycle of the terrestrial biosphere. The significant CO2 and δ13C interannual variability at WLG is very likely caused by worldwide climate anomalies and associated regional fluctuation in biospheric CO2 uptake in the Asian inland plateau as well as long‐range air mass transport. The results of this study help to provide a basic understanding of the individual sources and sinks of carbon in this area and help us to better address the role of the Asian inland terrestrial biosphere in the global carbon cycle.
A three‐dimensional seismic tomographic study of the gas hydrate stability zone, offshore Vancouver Island
Authors: Hobro J. W. D. , Minshull T. A. , Singh S. C. , Chand S.
Published: September 2005

Methane hydrate bottom‐simulating reflectors (BSRs) are widespread on the northern Cascadia margin offshore Vancouver Island. We conducted a three‐dimensional tomographic seismic study of the hydrate stability zone in an area around Ocean Drilling Program Site 889 using two deployments of five ocean bottom hydrophones and air gun shots along a series of closely spaced profiles in various orientations. Further constraints on reflector geometry come from coincident single‐channel reflection profiles. Travel times of reflected and refracted phases were inverted with a regularized three‐dimensional inversion using perturbation ray tracing through smooth isotropic media for the forward step. The seismic data allow us to constrain the velocity structure in a ∼6 km2 area around the drill site. Mean velocities range from 1.50 km s−1 at the seabed to 1.84 km s−1 at the BSR, and velocities at Site 889 match well those measured using a vertical seismic profile. At equivalent depths below the seafloor, velocities vary laterally by typically ∼0.15 km s−1. Close to the seafloor, velocities may be controlled primarily by lithology, but close to the BSR we infer hydrate contents of up to 15% of the pore space from effective medium modeling. The mean hydrate saturation in the well‐constrained volume of the velocity model is estimated to be 2.2%. There is no correlation between the seismic velocity above the BSR and the reflection coefficient at the BSR, so the latter is likely controlled primarily by the distribution of free gas beneath the hydrate stability zone.
Unaccounted role of Mediterranean Water in the drawdown of anthropogenic carbon
Authors: Álvarez Marta , Pérez Fiz F. , Shoosmith Deborah R. , Bryden Harry L.
Published: September 2005

A three‐sided box, MedBox, comprising the Strait of Gibraltar, 24°–41°N east of 22°W, was constructed using hydrographic and chemical data from three World Ocean Circulation Experiment cruises in 1997–1998. An extended optimum multiparameter (OMP) analysis resolves the water mass structure in the MedBox. The mass transport is estimated from data and models warranting mass conservation and no deep water formation within the region. Combining the mass transport, the OMP analysis, and the spatial distribution of anthropogenic carbon (CANT), some relevant questions about the Mediterranean Water (MW) formation, transport, and role in the global CO2 cycle are resolved. MW is produced at a rate of 2.7 ± 0.2 Sv in the eastern North Atlantic. It entrains 2.3 Sv of central waters during its formation, including also remnants of Antarctic Intermediate Water. The main advection route of MW is northward, close to the Iberian margin (2.2 Sv), while about 0.5 Sv are exported into the subtropical eastern North Atlantic. The eastern North Atlantic within the MedBox is a strong region of air‐sea CANT uptake, 0.7 ± 0.7 mmol m−2 d−1, where CANT is accumulated at a rate of 66 ± 21 kmol s−1 (0.025 GtC yr−1), 17% are taken up through the air‐sea interface, and the rest is advected into the area by the circulation. The entrainment of central waters to form MW drives a drawdown of 151 ± 14 kmol s−1 (0.06 GtC yr−1) from the surface to intermediate levels, and 88 ± 8 kmol s−1 (0.03 GtC yr−1) are exported with MW into the North Atlantic, mainly by the horizontal/eddy circulation.
Changes in wave climate off Hiratsuka, Japan, as affected by storm activity over the western North Pacific
Authors: Sasaki W. , Iwasaki S. I. , Matsuura T. , Iizuka S. , Watabe I.
Published: September 2005

Changes in wave climate off Hiratsuka during 1980–2003 are investigated on the basis of hourly observed wave and atmospheric data obtained at a tower 1 km off Hiratsuka in Sagami Bay, Japan. First, the interannual variability of significant wave heights (Hs) for the summer mean (June–August, SHs) is analyzed. A large difference between wave spectrum (E(f, t)) in high SHs years and that in low SHs years is found at the frequency of 0.09 Hz. It is revealed that the difference is related to the changes in enhanced tropical cyclone (with central air pressure below 980 hPa) activity in the western North Pacific. Second, the interannual variability of Hs for the winter mean (December–February, WHs) is investigated. It is found that there is a large difference between E(f, t) in high WHs years and that in low WHs years at the frequency of 0.11 Hz. It is revealed that the difference is related to the changes in southerly wind intensity (integral of southerly wind speed by hours) associated with extratropical cyclones. Third, the interdecadal variability of WHs is described. The time series of anomalies of WHs, smoothed by means of a 7‐year moving average, is divided into three periods: 1980–1985, 1986–1996, and 1997–2003. The first empirical orthogonal function of 10‐m meridional sea surface winds captures the interdecadal variability over the storm track. The smoothed WHs exhibits similar variation to that of the leading principal component of the winds.
Implementation of the asymptotic corrugation boundary condition in the finite difference time domain method
Authors: Simon Andrew E. , Kishk Ahmed A.
Published: September 2005

Geometry description in the finite difference time domain method is a tedious task if the geometry contains fine details, such as the case of corrugated objects. Such fine details constrain the cell size. The corrugated object can be modeled using the asymptotic corrugation boundary condition (ACBC) with a correction due to the width‐over‐period ratio. The ACBC forces certain field distributions inside the corrugation and allows for the removal of the corrugation teeth to have a homogeneous region with enforced field behavior that represents the actual corrugations. The ACBC approach is found to be accurate when the number of corrugations per wavelength is large (typically around 10 corrugations per wavelength). Computed results using ACBC are in good agreement with detailed simulations, which demonstrates the validity of the asymptotic approximations. Last, a major improvement in the computation time is achieved when using the ACBC to model structures that have a large number of corrugations per wavelength.
A probabilistic approach to wave propagation and scattering
Authors: Budaev Bair V. , Bogy David B.
Published: September 2005

The probabilistic approach to wave propagation starts in a way that is similar to ray theory, from the representation of the wave field as a product of the amplitude and of the exponent of the eikonal, which is computed by a canonical technique of analytical mechanics. However, an important difference is that the amplitude is not approximated but is represented by exact probabilistic formulas that admit efficient numerical evaluation, and that is a direct improvement of many asymptotic solutions. This approach is shown to be an effective tool for the analysis of numerous wave propagation problems, including those of wave diffraction by a screen occupying a plane angular sector and of electromagnetic diffraction by a wedge with anisotropic impedance boundary conditions.
Intermittent filtration of bacteria and colloids in porous media
Authors: Auset Maria , Keller Arturo A. , Brissaud François , Lazarova Valentina
Published: September 2005

Intermittent filtration through porous media used for water and wastewater treatment can achieve high pathogen and colloid removal efficiencies. To predict the removal of bacteria, the effects of cyclic infiltration and draining events (transient unsaturated flow) were investigated. Using physical micromodels, we visualized the intermittent transport of bacteria and other colloids in unsaturated porous media. Column experiments provided quantitative measurements of the phenomena observed at the pore scale. Tagged Escherichia coli and a conservative tracer (NaI) were introduced in an initial pulse into a 1.5 m sand column. Subsequent hydraulic flushes without tagged bacteria or tracer were repeated every 4 hours for the next 4 days, during which outflow concentrations were monitored. Breakthrough behavior between colloids and dissolved tracer differed significantly, reflecting the differences in transport processes. Advancement of the wetting front remobilized bacteria which were held in thin water films, attached to the air‐water interface (AWI), or entrapped in stagnant pore water between gas bubbles. In contrast, the tracer was only remobilized by diffusion from immobile to mobile water. Remobilization led to successive concentration peaks of bacteria and tracer in the effluent but with significant temporal differences. Observations at the pore‐scale indicated that the colloids were essentially irreversibly attached to the solid‐water interface, which explained to some extent the high removal efficiency of microbes in the porous media. Straining, cluster filtration, cell lysis, protozoa grazing, and bacteriophage parasitism could also contribute to the removal efficiency of bacteria.
Chemical and icosahedral short-range orders in liquid and undercooled Al80Mn20 and Al80Ni20 alloys: A first-principles-based approach
Authors: Jakse N. , Le Bacq O. , Pasturel A.
Published: September 2005

Atomic structures of stable liquid and undercooled liquid Al80Mn20 and Al80Ni20 alloys have been calculated by first-principles molecular-dynamics simulations. For both alloys, the local structure as defined by the Faber-Ziman pair-correlation functions is characterized by a strong Al–transition-metal affinity, which leads to a well-pronounced chemical short-range order which is more temperature dependent for Al80Mn20 than for Al80Ni20. In addition, a structural analysis using three-dimensional pair analysis techniques has been performed in details. More particularly, we find that the fivefold local symmetry around Mn atoms is predominant in both stable and undercooled Al80Mn20 alloys and displays no significant variation with temperatures. On the contrary, in Al80Ni20, a strong variation of the topological short-range order is observed since in the undercooled state, the local environment of Ni atoms is characterized by the predominance of the fivefold symmetry over the close-packed local symmetry which is opposed to what occurs in the stable liquid phase.
A comparative study between dissipative particle dynamics and molecular dynamics for simple- and complex-geometry flows
Authors: Keaveny Eric E. , Pivkin Igor V. , Maxey Martin , Em Karniadakis George
Published: September 2005

The purpose of this study is to compare the results from molecular-dynamics and dissipative particle dynamics (DPD) simulations of Lennard-Jones (LJ) fluid and determine the quantitative effects of DPD coarse graining on flow parameters. We illustrate how to select the conservative force coefficient, the cut-off radius, and the DPD time scale in order to simulate a LJ fluid. To show the effects of coarse graining and establish accuracy in the DPD simulations, we conduct equilibrium simulations, Couette flow simulations, Poiseuille flow simulations, and simulations of flow around a periodic array of square cylinders. For the last flow problem, additional comparisons are performed against continuum simulations based on the spectral/hp element method.
Demonstration of a visible laser on silicon using Eu-doped GaN thin films
Authors: Park J. H. , Steckl A. J.
Published: September 2005

We report the demonstration of visible laser action on silicon. We have utilized Eu-doped GaN for the active medium within a structure consisting of multiple AlGaN layers grown by molecular-beam epitaxy on a Si substrate. Stimulated emission was obtained at room temperature from Eu3+ at 620nm, with a threshold of ∼117kW∕cm2. Values of modal gain and loss of ∼100 and 46cm−1 were measured. This demonstration indicates that utilizing rare earths a range of lasers on Si can be obtained, covering the UV, visible, and IR regions, thus enabling a significant expansion of optoelectronic and microelectronic integrations.
Terahertz radiation from InAlAs and GaAs surface intrinsic-N+ structures and the critical electric fields of semiconductors
Authors: Hwang J. S. , Lin H. C. , Lin K. I. , Zhang X. C.
Published: September 2005

This study examines terahertz radiation from a series of In0.52Al0.48As and GaAs surface-intrinsic-N+ structures (SIN+) with surface-intrinsic layers of various thicknesses. The built-in electric fields in the SIN+ structures are used as the bias. Experimental results indicate that the amplitudes of the THz emission are independent of the built-in electric fields in the emitters when the built-in electric fields exceed the corresponding critical electric fields of the semiconductors. In contrast, the amplitudes of the THz emission are proportional to the thickness of the intrinsic layer and, therefore, the number of photo-excited charged carriers.
Growth of nominally undoped p-type ZnO on Si by pulsed-laser deposition
Authors: Oh Min-Suk , Kim Sang-Ho , Seong Tae-Yeon
Published: September 2005

We report on the growth of nominally undoped p-type ZnO films on Si(111) substrates by pulsed-laser deposition. Hall effect measurements show that the undoped ZnO films change from n-type to p-type material when the oxygen pressure changes from 6×10−5to3×10−4Torr during growth. Ti∕Au contacts produce ohmic behavior to n-type ZnO (∼1017cm−3), but leaky Schottky behavior to p-type ZnO (∼1018cm−3). Electrical and photoluminescence results indicate that native defects, such as oxygen and zinc vacancies, could play an important role in determining the conductivity of these nominally undoped ZnO films.
Wave propagation in nonlinear left-handed transmission line media
Authors: Kozyrev Alexander B. , Kim Hongjoon , Karbassi Abdolreza , van der Weide Daniel W.
Published: September 2005

Using a one-dimensional system, we demonstrate a wide variety of wave propagation phenomena possible in nonlinear left-handed media. These include effective second-harmonic generation where the fundamental wave and the second-harmonic wave are badly mismatched. We also observe parametric instabilities accompanying intensive harmonic generation.
Strengthening TiN diffusion barriers for Cu metallization by lightly doping Al
Authors: Yang L. C. , Hsu C. S. , Chen G. S. , Fu C. C. , Zuo J. M. , Lee B. Q.
Published: September 2005

Thin films of Ti1−xAlxN were deposited on (100) Si by ultrahigh-vacuum dual-target reactive sputtering, and the impact of lightly doping Al of x as small as 0.09 on altering the films’s microstructure upon thermal annealing, and hence the performance of the films (40nm thick) as diffusion barriers for Cu metallization was evaluated. The results of transmission electron microscopy, Rutherford backscattering spectroscopy, and grazing-incidence x-ray diffraction show that the TiN barrier layer gives the commonly observed voided, columnar grains composed of 5nm sized subgrains. Upon annealing, the subgrains tend to coalesce into 20nm sized equiaxed grains full of crystalline defects, initiating an inward penetration of Cu and a partial dissociation of TiN, transforming themselves, respectively, into pyramidal (or columnar) Cu3Si precipitates and a dendritic Ti5Si3 layer just after 550°C, 10min annealing. However, the lightly doped Al not only overrides the tendency to form intercolumnar voids inherent in sputter deposition by self-shadowing and statistical roughening, but also substantially enhances the microstructural and thermochemical stability, hence significantly improving barrier property, as evidenced from an annealing test at an elevated temperature (600°C) for a prolonged period of 30min.
Electric lithography by electrochemical polymerization
Authors: Shen W. , Chen Y. , Pei Q.
Published: September 2005

We demonstrate a lithographic technique, electric lithography, in which conductive patterns on a mask are transferred to a substrate by applying an electric field to locally configure a resist layer sandwiched between the patterns and the substrate. Proof-of-concept pattern transfer experiments were carried out through electrochemical polymerization of pyrrole monomers dissolved in an aqueous electrolyte and 2,2′’-bithiophene monomers dissolved in a solid polymer electrolyte. By controlling the intensity and duration of the applied electric field on different mask patterns, we have also demonstrated that the electric lithography can create on-demand three-dimensional patterns in the resist.
Forest fire causes and extent on United States Forest Service lands
Authors: Stephens Scott L.
Published: September 2005

Nationally, the causes and extent of fire on lands administrated by the United States Forest Service varied significantly from 1940 to 2000, with California experiencing the largest relative annual burned areas. The south-east and California experienced the largest relative area burned by fires from human ignitions. No significant differences were detected in the relative area burned by lightning in California, the upper and central Rocky Mountains, and the south-west, which all experienced the highest levels. The north-west and Rocky Mountains have experienced significant increases in the relative total area burned; the north-east, south-east, California, and coastal Alaska all remained unchanged. The northern Rocky Mountains, south-west, and north-east have all experienced significant increases in the amount of area burned by lightning without significant increases in lightning ignitions. Increasing fuel hazards in these areas probably contributed to the increasing area burned by lightning fires; changing climate could have also contributed to the increase in wildfire area from 1940 to 2000. To be effective across the diverse forest types and conditions in the USA, fire policy should better recognize and respond to the diversity of US forests and how they have burned in the past. This analysis determined that there is high geographical diversity on wildfire occurrence and causes. Local input is therefore important in designing diverse, ground-based solutions to address fire management challenges in the United States.
Influence of tree age on seed germination response to environmental factors and inhibitory substances in Pinus pinaster
Authors: Alvarez R. , Valbuena L. , Calvo L.
Published: September 2005

The present study analyses the reproductive behaviour of Pinus pinaster at different ages of the parent trees after subjecting the seeds to variations in environmental factors and inhibitory substances. An experiment was designed in which seeds from mature (43 years old) and young (13 years old) trees were subjected to different environmental factors: darkness, thermal shocks and the presence of inhibitory substances from the needles and the undergrowth humus of P. pinaster. A control treatment was also carried out for the seeds of each age. The results obtained indicate that the age of the parent trees has a significant effect on mean germination time after experimental treatments: shock temperatures, darkness, and leaf and humus exudates. Seeds from young populations have shorter mean germination times than those from adult populations. Similarly, mature P. pinaster populations show more diversity in the length of innate dormancy of their seeds than younger populations. However, age has no significant effect on total percentage germination. Significant reductions in germination were observed when seeds from mature and young trees were exposed to temperatures equal to or above 150°C for 5 min. Increased temperature also produces a delay in the onset of germination in both populations.
Estimating combustion of large downed woody debris from residual white ash
Authors: Smith Alistair M. S. , Hudak Andrew T.
Published: September 2005

The production of residual white ash patches within wildfires represents near-complete combustion of the available fuel and releases a considerable quantity of gases to the atmosphere. These patches are generally produced from combustion of large downed woody debris (LDWD) such as fallen trees and snags. However, LDWD are generally ignored in calculations of fuel combusted within environments where surface fires dominate (e.g. southern African savannas). To assess the potential of fractional white ash cover as a remotely sensed measure of LDWD combustion, both the proportion of the surface covered by white ash and the combustion completeness required to produce white ash must be quantified. An aerial photograph of woodland savanna fires in north-western Zimbabwe was analysed to estimate the proportion of white ash cover within a typical satellite sensor pixel. The proportion loss on ignition (LOI) of wood samples from the study area was measured and combined with previous estimates of mean tree biomass. The proportion of white ash within the aerial photographs was 0.2% (± 0.06), which corresponded to an additional 67 320 kg ha−1 of biomass combusted above that typically recorded as combusted from a surface fire in this environment (~7000 kg ha−1). This analysis should be repeated in other savannas and forests, where pre-fire fuel loads and post-fire fractional white ash cover may be higher.
Remote classification of head and backfire types from MODIS fire radiative power and smoke plume observations
Authors: Smith Alistair M. S. , Wooster Martin J.
Published: September 2005

The classification of savanna fires into headfire and backfire types can in theory help in assessing pollutant emissions to the atmosphere via relative apportionment of the amounts of smouldering and flaming combustion occurring, and is also important when assessing a fire’s ecological effects. This paper provides a preliminary assessment of whether a combination of visible and thermal satellite remote sensing can be used to classify fires into head and backfire categories. Remote determination of the fire radiative power, alongside assessments of the prevailing direction of the wind (through identification of the fire-related smoke plumes) and the fire front propagation (through its relation to the previously burned area) were used to infer the fire type category and to calculate ‘radiative’ fireline intensity (FLI). The ratio of radiative FLI for the head and backfire categories was found similar to that of in situ fireline intensity measurements, but the magnitudes of the radiative FLI values were around an order of magnitude lower. This agrees with other data suggesting that a fire’s radiative energy is around an order of magnitude lower than the fuel’s theoretical heat yield, and suggests that the remote measurement of radiative FLI and classification of headfire and backfire types is a realistic proposition for large wildfire activity.
Fire suppression impacts on postfire recovery of Sierra Nevada chaparral shrublands
Authors: Keeley Jon E. , Pfaff Anne H. , Safford Hugh D.
Published: September 2005

A substantial portion of chaparral shrublands in the southern part of California’s Sierra Nevada Mountain Range has never had a recorded fire since record keeping began in 1910. We hypothesised that such long periods without fire are outside the historical range of variability and that when such areas burn, postfire recovery is weaker than in younger stands. We predicted that long fire-free periods will result in loss of shrub species and deterioration of soil seed banks, which, coupled with higher fire intensities from the greater accumulation of dead biomass, will lead to poorer postfire regeneration. The 2002 McNally Fire burned ancient stands that were as much as 150 years old, as well as much younger (mature) stands. Based on shrub skeletons in the burned area as a surrogate for prefire density, we found that ancient stands change in structure, owing primarily to the loss of obligate seeding Ceanothus cuneatus; other species appear to have great longevity. Despite the reduction in C. cuneatus, postfire shrub–seedling recruitment remained strong in these ancient stands, although some seed bank deterioration is suggested by the three-quarters lower seedling recruitment than recorded from mature stands. Total diversity and the abundance of postfire endemic annuals are two other response variables that suggest that these ancient stands are recovering as well as mature stands. The one area of some concern is that non-native species richness and abundance increased in the ancient stands, suggesting that these are more open to alien colonisers. It is concluded that chaparral more than a century old is resilient to such long fire-free periods and fire severity impacts are indistinguishable from those in younger chaparral stands.
Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences
Authors: Xing Yi , Lee Christopher
Published: September 2005

Recently, it was proposed that alternative splicing may act as a mechanism for opening accelerated paths of evolution, by reducing negative selection pressure, but there has been little evidence so far that this mechanism could produce adaptive benefit. Here, we use metrics of very different types of selection pressures [e.g., against amino acid mutations (
Ka
/
Ks
), against mutations at synonymous sites (
Ks
), and for protein reading-frame preservation] to address this question by genomewide analyses of human, chimpanzee, mouse, and rat. These data show that alternative splicing relaxes
Ka
/
Ks
selection pressure up to 7-fold, but intriguingly this effect is accompanied by a strong increase in selection pressure against synonymous mutations, which propagates into the adjacent intron, and correlates strongly with the alternative splicing level observed for each exon. These effects are highly local to the alternatively spliced exon. Comparisons of these four genomes consistently show an increase in the density of amino acid mutations (
Ka
) in alternatively spliced exons and a decrease in the density of synonymous mutations (
Ks
). This selection pressure against synonymous mutations in alternatively spliced exons was accompanied in all four genomes by a striking increase in selection pressure for protein reading-frame preservation, and both increased markedly with increasing evolutionary age. Restricting our analysis to a subset of exons with strong evidence for biologically functional alternative splicing produced identical results. Thus alternative splicing apparently can create evolutionary “hotspots” within a protein sequence, and these events have evidently been selected for during mammalian evolution.
Characterization of a possible amyloidogenic precursor in glutamine-repeat neurodegenerative diseases
Authors: Armen Roger S. , Bernard Brady M. , Day Ryan , Alonso Darwin O. V. , Daggett Valerie
Published: September 2005

Several neurodegenerative diseases are linked to expanded repeats of glutamine residues, which lead to the formation of amyloid fibrils and neuronal death. The length of the repeats correlates with the onset of Huntington's disease, such that healthy individuals have <38 residues and individuals with >38 repeats exhibit symptoms. Because it is difficult to obtain atomic-resolution structural information for poly(
l
-glutamine) (polyQ) in aqueous solution experimentally, we performed molecular dynamics simulations to investigate the conformational behavior of this homopolymer. In simulations of 20-, 40-, and 80-mer polyQ, we observed the formation of the “α-extended chain” conformation, which is characterized by alternating residues in the α
L
and α
R
conformations to yield a sheet. The structural transition from disordered random-coil conformations to the α-extended chain conformation exhibits modest length and temperature dependence, in agreement with the experimental observation that aggregation depends on length and temperature. We propose that fibril formation in polyQ may occur through an α-sheet structure, which was proposed by Pauling and Corey [Pauling, L. & Corey, R. B. (1951)
Proc. Natl. Acad. Sci. USA
37, 251-256]. Also, we propose an atomic-resolution model of how the inhibitory peptide QBP1 (polyQ-binding peptide 1) may bind to polyQ in an α-extended chain conformation to inhibit fibril formation.
The putative high-affinity nitrate transporter NRT2.1 represses lateral root initiation in response to nutritional cues
Authors: Little Daniel Y. , Rao Hongyu , Oliva Sabrina , Daniel-Vedele Françoise , Krapp Anne , Malamy Jocelyn E.
Published: September 2005

Lateral root initiation is strongly repressed in
Arabidopsis
by the combination of high external sucrose and low external nitrate. A previously isolated mutant,
lin1
, can overcome this repression. Here, we show that
lin1
carries a missense mutation in the
NRT2.1
gene. Several allelic mutants, including one in which the
NRT2.1
gene is completely deleted, show similar phenotypes to
lin1
and fail to complement
lin1
.
NRT2.1
encodes a putative high-affinity nitrate transporter that functions at low external nitrate concentrations. Direct measurement of nitrate uptake and nitrate content in the
lin1
mutant seedlings established that both are indeed reduced. Because repression of lateral root initiation in WT plants can be relieved by increased concentrations of external nitrate, it is surprising to find that repression is also relieved by a defect in a component of the high-affinity nitrate uptake system. Furthermore, lateral root initiation is increased in
lin1
relative to WT even when seedlings are grown on nitrate-free media, suggesting that the mutant phenotype is nitrate-independent. These results indicate that NRT2.1 is a repressor of lateral root initiation and that this role is independent of nitrate uptake. We propose that
Arabidopsis
NRT2.1 acts either as a nitrate sensor or signal transducer to coordinate the development of the root system with nutritional cues.
UVA radiation is highly mutagenic in cells that are unable to repair 7,8-dihydro-8-oxoguanine in Saccharomyces cerevisiae
Authors: Kozmin S. , Slezak G. , Reynaud-Angelin A. , Elie C. , de Rycke Y. , Boiteux S. , Sage E.
Published: September 2005

UVA (320-400 nm) radiation constitutes >90% of the environmentally relevant solar UV radiation, and it has been proposed to have a role in skin cancer and aging. Because of the popularity of UVA tanning beds and prolonged periods of sunbathing, the potential deleterious effect of UVA has emerged as a source of concern for public health. Although generally accepted, the impact of DNA damage on the cytotoxic, mutagenic, and carcinogenic effect of UVA radiation remains unclear. In the present study, we investigated the sensitivity of a panel of yeast mutants affected in the processing of DNA damage to the lethal and mutagenic effect of UVA radiation. The data show that none of the major DNA repair pathways, such as base excision repair, nucleotide excision repair, homologous recombination, and postreplication repair, efficiently protect yeast from the lethal action of UVA radiation. In contrast, the results show that the Ogg1 DNA glycosylase efficiently prevents UVA-induced mutagenesis, suggesting the formation of oxidized guanine residues. Furthermore, sequence analysis of UVA-induced canavanine-resistant mutations reveals a bias in favor of GC→TA events when compared with spontaneous or H
2
O
2
-, UVC-, and γ-ray- induced canavanine-resistant mutations in the WT strain. Taken together, our data point out a major role of oxidative DNA damage, mostly 7,8-dihydro-8-oxoguanine, in the genotoxicity of UVA radiation in the yeast
Saccharomyces cerevisiae
. Therefore, the capacity of skin cells to repair 7,8-dihydro-8-oxoguanine may be a key parameter in the mutagenic and carcinogenic effect of UVA radiation in humans.
Rtt106p is a histone chaperone involved in heterochromatin-mediated silencing
Authors: Huang Shengbing , Zhou Hui , Katzmann David , Hochstrasser Mark , Atanasova Elena , Zhang Zhiguo
Published: September 2005

Epigenetic inheritance of heterochromatin structure is an important cellular process whose mechanism remains elusive. In this article, we describe the identification of nine enhancers of the silencing defect of a
Saccharomyces cerevisiae
-PCNA mutant by screening a library of ≈4,700 viable yeast deletion mutants. Of the nine mutants identified, six (
hir1
,
hir3
,
sas2
,
sas4
,
sas5
, and
sir1
) were previously known to reduce silencing synergistically with a mutation in Cac1p, the large subunit of chromatin assembly factor 1 (CAF-1). The predicted gene products that are affected in three other mutants (
nam7
,
msh2
, and
rtt106
) have not been implicated previously in silencing. Characterization of the
rtt106
Δ allele revealed that it synergistically reduced heterochromatin silencing when combined with a mutation in Cac1p but not with a mutation in Asf1p (a histone H3 and H4 chaperone). Moreover, Rtt106p interacted with histones H3 and H4 both
in vitro
and
in vivo
, and it displayed a nucleosome assembly activity
in vitro
. Furthermore, Rtt106p interacts with CAF-1 physically through Cac1p. These biochemical and genetic data indicate that Rtt106p is a previously uncharacterized histone chaperone connecting S phase to epigenetic inheritance.
A
Caenorhabditis elegans
nutrient response system partially dependent on nuclear receptor NHR-49
Authors: Van Gilst Marc R. , Hadjivassiliou Haralambos , Yamamoto Keith R.
Published: September 2005

Appropriate response to nutritional stress is critical for animal survival and metabolic health. To better understand regulatory networks that sense and respond to nutritional availability, we developed a quantitative RT-PCR strategy to monitor changes in metabolic gene expression resulting from short-term food deprivation (fasting) in
Caenorhabditis elegans
. Examining 97 fat and glucose metabolism genes in fed and fasted animals, we identified 18 genes significantly influenced by food withdrawal in all developmental stages. Fasting response genes fell into multiple kinetic classes, with some genes showing significant activation or repression just 1 h after food was removed. As expected, fasting stimulated the expression of genes involved in mobilizing fats for energy production, including mitochondrial β-oxidation genes. Surprisingly, however, we found that other mitochondrial β-oxidation genes were repressed by food deprivation. Fasting also affected genes involved in mono- and polyunsaturated fatty acid synthesis: four desaturases were induced, and one stearoyl-CoA desaturase (SCD) was strongly repressed. Accordingly, fasted animals displayed considerable changes in fatty acid composition. Finally, nuclear receptor
nhr-49
played a key role in nutritional response, enabling induction of β-oxidation genes upon food deprivation and facilitating activation of SCD in fed animals. Our characterization of a fasting response system and our finding that
nhr-49
regulates a sector within this system provide insight into the mechanisms by which animals respond to nutritional signals.
Reversible inhibition of copper amine oxidase activity by channel-blocking ruthenium(II) and rhenium(I) molecular wires
Authors: Contakes Stephen M. , Juda Gregory A. , Langley David B. , Halpern-Manners Nicholas W. , Duff Anthony P. , Dunn Alexander R. , Gray Harry B. , Dooley David M. , Guss J. Mitchell , Freeman Hans C.
Published: September 2005

Molecular wires comprising a Ru(II)- or Re(I)-complex head group, an aromatic tail group, and an alkane linker reversibly inhibit the activity of the copper amine oxidase from
Arthrobacter globiformis
(AGAO), with
K
i
values between 6 μM and 37 nM. In the crystal structure of a Ru(II)-wire:AGAO conjugate, the wire occupies the AGAO active-site substrate access channel, the trihydroxyphenylalanine quinone cofactor is ordered in the “off-Cu” position with its reactive carbonyl oriented toward the inhibitor, and the “gate” residue, Tyr-296, is in the “open” position. Head groups, tail-group substituents, and linker lengths all influence wire-binding interactions with the enzyme.