bluuebunny/crossref_metadata_2025 huggingface dataset:
Application of electronic structure and transition state theory: Reaction of hydrogen with silicon radicals
Authors: Crosby Lonnie D. , Kurtz Henry A.
Published: August 2006

The reaction of molecular hydrogen with silicon radicals is investigated through direct dynamics calculations. Previous studies of this reaction with E′ centers vary in their description of the reaction thermodynamics and kinetics. A survey of methods is conducted to illuminate the best method for describing these properties. This is achieved via a similar reaction with a silyl radical, in which both the forward and reverse directions are considered, discussed in terms of theory, basis, and the importance of tunneling corrections. The methods studied include Hartree–Fock (SCF), two density functionals (B3LYP and MPW1K), Møller–Plesset second‐order perturbation (MP2), and coupled‐cluster singles and doubles (CCSD) with a variety of all electron basis sets ranging from 6‐31G to aug‐cc‐pVTZ. Two methods are identified as good candidates: a density functional theory (DFT) method (MPW1K) and a dual‐level method including MP2, and CCSD theories. These methods yield rate constants that agree within one order of magnitude of experiment and activation energies within 1 kcal/mol over the 293–683 K temperature range. The B3LYP and SCF methods do not perform as well and are discounted early. Basis sets that perform well are found to include diffuse and polarizing functions on all atoms, including hydrogen. These include the 6‐31++G** and aug‐cc‐pVDZ basis sets. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Density functional theory studies of quantum transport in molecular systems
Authors: Meunier Vincent , Lu Wenchang , Sumpter Bobby G. , Bernholc Jerry
Published: August 2006

Conventional semiconducting devices are rapidly approaching their physical limits, encouraging an increasing number of researchers across multiple disciplines to attempt to devise innovative ways to decrease the size and increase the performance of critical features in microelectronic circuits. One possible route is based on the idea of using molecules and molecular structures as functional electronic devices. While impressive experimental progress toward the realization of molecular electronics has been achieved, full insight into the potential for molecular‐based electronics requires accurate theoretical investigations of the processes governing their functioning. In the present study, we show that large‐scale quantum electronic structure calculations coupled with nonequilibrium Green function theory can be employed to determine quantum conductance on practical length scales. The combination of state‐of‐the‐art quantum mechanical methods, efficient numerical algorithms, and high‐performance computing allows for realistic evaluation of properties at length scales that are routinely reached experimentally. Two illustrations of the method are presented. First, we investigate the electron transport properties of a Si/organic‐molecule/Si junction, using a numerically optimized basis. Second, quantum chemical calculations using up to 104 basis functions are carried out to investigate amphoteric doping of carbon nanotubes by encapsulation of organic molecules. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Portal hypertension in a patient with Hunter disease
Authors: Kato Tomomi , Isogai Koji , Orii Koji , Kuratsubo Izumi , Kondo Naomi , Orii Tadao , Suzuki Yasuyuki
Published: August 2006

Hepatosplenomegaly is one of the cardinal signs of Hunter disease; however, portal hypertension has not been described. We report portal hypertension in an adult Hunter patient with the attenuated phenotype.
Lipoprotein lipase gene analyses in one Turkish family and three different Chinese families with severe hypertriglyceridaemia: One novel and several established mutations
Authors: Nierman Melchior C. , Peter Jorge , Khoo Kah‐Lin , Defesche Joep C.
Published: August 2006

Lipoprotein lipase (LPL, triacylglycerol acylhydrolase; EC 3.1.1.3) deficiency (OMIM 238600) is an autosomal recessive inherited condition caused by mutations in the LPL gene, either in a homozygous or in a compound heterozygous state, leading to loss of lipolytic activity and resulting in severe hypertriglyceridaemia and subsequent risk for developing pancreatitis. Numerous LPL gene mutations leading to loss of catalytic function have been described. In this present study, we describe full clinical, biochemical and molecular analyses of severe hypertriglyceridaemic individuals in one Turkish and three Chinese families. We established one novel mutation (delCT1312–1313), a new combination of mutations (S193R and I194T) and four previously reported mutations (L252R, L252V, S193R and I194T) of the LPL gene and report phenotypes for these and four previously described mutations. Finally, we show that two patients homozygous for the LPL gene delCT1312–1313 mutations are characterized by absence of LPL activity that coincides with absence of LPL protein.
Fumaric aciduria: Mild phenotype in a 8‐year‐old girl with novel mutations
Authors: Maradin M. , Fumić K. , Hansikova H. , Tesarova M. , Wenchich L. , Dorner S. , Sarnavka V. , Zeman J. , Barić I.
Published: August 2006

Fumaric aciduria is a rare, autosomal recessive disorder caused by deficient acitivity of fumarate hydratase (FH). Common clinical features are hypotonia, failure to thrive, severe psychomotor retardation and seizures. Facial dysmorphism and brain malformations are frequent. Recently, some FH gene mutations have been associated with inherited cutaneous and uterine leiomyomas and papillary renal cell cancer. Our patient had a relatively mild phenotype, a previously not reported genotype and familial tumour predisposition. The mother and grandmother had uterine myomas. The paternal grandfather and his two brothers died from lung and laryngeal cancers. The pregnancy was complicated by bleeding and intrauterine growth retardation. Delivery was after 35 weeks, with normal Apgar score. The girl was hypotonic since birth. At age 2 months the parents noticed short apnoeic crises. She could sit at age 1.5 years, and walk with assistance at 4 years. At age 8 years highly increased excretion of fumaric acid was found twice (217 and 445 mmol/mol creatinine). Shortly before that the girl started to have leg and arm spasms. Grand mal seizures occurred twice. Facial dysmorphism included depressed nasal bridge, anteverted ears, hypertelorism and microcephaly. Speech was limited to few disyllables. She was atactic with spastic paraparesis. Brain MRI showed slight ventriculomegaly, white‐matter atrophy and hypoplasia of corpus callosum. Activity of FH in fibroblasts was 1.9 nmol/min/mg protein (controls 40–80). Analysis of the FH gene revealed the maternally derived c.1029_1031delAGT mutation, resulting in Val deletion and substitution of Gln by His, and paternally derived c.976C > T mutation, resulting in substitution of Pro by Ser.
Prolonged moderate‐intensity exercise without and with L‐carnitine supplementation in patients with MCAD deficiency
Authors: Huidekoper H. H. , Schneider J. , Westphal T. , Vaz F. M. , Duran M. , Wijburg F. A.
Published: August 2006

Medium‐chain acyl‐CoA dehydrogenase deficiency (MCADD) is probably the most common inborn error of fatty acid oxidation (FAO). Routine L‐carnitine supplementation in the treatment of MCADD is controversial. To establish the effects of L‐carnitine supplementation during prolonged moderate‐intensity exercise in MCADD, five patients and three control subjects were studied during 2 hours of moderate‐intensity exercise after a 12‐hour fast. Patients were studied twice, once with and once without L‐carnitine supplementation (50 mg/kg per day). Blood samples were collected before, during and after exercise, and analysed for routine parameters, acylcarnitines and carnitine biosynthesis intermediates. Urine was collected before and after exercise, and analysed for acylcarnitines. All patients were able to complete the exercise test without any apparent clinical or biochemical adverse effects, even without L‐carnitine supplementation. A significant rise in plasma free fatty acids and octanoylcarnitine levels during exercise was seen in all patients, indicating a substantial increase in FAO during exercise. Octanoylcarnitine levels in plasma were significantly higher in patients with L‐carnitine supplementation, suggesting increased clearance of accumulating acylcarnitines. A statistically significant increase of plasma and urinary free carnitine levels, as well as of plasma γ‐butyrobetaine was seen in MCADD patients without L‐carnitine supplementation. These data suggest an increase in carnitine biosynthesis. In conclusion, although L‐carnitine supplementation may promote clearance of accumulating acylcarnitines during moderate‐intensity exercise, no apparent beneficial effect of this supplementation on clinical and biochemical parameters was observed in MCADD patients. Our results suggest that MCADD patients are able to increase carnitine biosynthesis during exercise to compensate for carnitine losses.
Needs assessment and review of services for people with inherited metabolic disease in the United Kingdom
Authors: Burton Hilary , Sanderson Simon , Shortland Graham , Lee Philip
Published: August 2006

Patients with inherited metabolic diseases need to be viewed as a specialist care group because of the range of expertise required for their diagnosis and management. In the UK, professional concerns have been expressed that existing services would struggle to meet needs resulting from new diagnostic and screening techniques, new treatments and increased survival. This needs assessment and service review was therefore undertaken at the request of the Joint Committee on Medical Genetics, guided by a national multidisciplinary stakeholder group. All 24 specialist centres identified in the UK provided evidence for the review. Approximately 10 000 patients are known to services and their annual number of referrals is increasing. Possible shortfalls in the number of patients attending specialist services were estimated for the UK as a whole by extrapolating the results from the region with the most comprehensive service and comparing this with known patient numbers. This analysis suggests that a further 5600 children and 3300 adults are not looked after by specialist services or have been lost to follow‐up. The comprehensiveness of services was assessed using a new scoring system for clinical and organizational criteria. There are major regional disparities in the comprehensiveness of service provision across the country, with some regions having little or no specialist service. Unmet need will increase as a result of new diagnostic technologies, more effective treatments and new neonatal screening programmes; specialist services need to be developed and expanded to provide a comprehensive and more equitable service to the UK population.
FOLIAR SCLEREIDS IN DIONYSIA (PRIMULACEAE) FROM A PHYLOGENETIC PERSPECTIVE
Authors: TRIFT I. , ANDERBERG A. A.
Published: August 2006

Sclereid presence and distribution were studied in leaves from 50 species of Dionysia (Primulaceae). Of 16 species not previously investigated, 11 were shown to possess sclereids. The sclereids are dermal, terminal or diffused (according to the position in the leaf) and develop from different tissues, and hence are not homologous structures. The presence of different types of sclereids in different species is discussed. Sclereid characters are optimized on a cladogram based on an analysis of three DNA regions. Some clades are associated with certain types of sclereids. Terminal sclereids are most common in Iran, and diffused sclereids in Afghanistan. The evolution of sclereids in the genus is discussed, and a redefinition of what can be called a sclereid in Dionysia is presented.
Water mass analysis and alongshore variation in upwelling intensity in the eastern Great Australian Bight
Authors: McClatchie Sam , Middleton John F. , Ward Tim M.
Published: August 2006

A study of climatological and conductivity‐temperature‐depth (CTD) data for 2004 is made to provide a conceptual model of upwelling for the eastern region of the Great Australian Bight. In particular, the data and other studies provide strong evidence that shelf break upwelling is confined to the southwest Kangaroo Island region and does not occur farther to the west off the Eyre Peninsula. Rather, the upwelled water is likely to remain in a Kangaroo Island “pool” until subsequent upwelling events draw the water to the shallower and surface coastal regions of the eastern Bight. In this manner the surface upwelling apparent off the Bonney Coast, Kangaroo Island, and the eastern Great Australian Bight (GAB) can appear to be simultaneous. Moreover, it appears likely that the water within the Kangaroo Island pool remains nutrient rich. Support for this model comes from CTD sections collected in 2004 that show that the upwelled signal (cool, <17°C; fresher, <35.6; dense, σt > 26 kg m−3) diminishes in width and intensity with increasing distance from Kangaroo Island. The pattern of fluorescence is similar to that for temperature in the upwelled plume and indicates that the Kangaroo Island pool remains nutrient rich. Relatively low oxygen concentrations may indicate a previous bloom. The warmest water is found near the shelf break along with very low values of fluorescence and relatively higher levels of oxygen suggesting nutrient‐limited growth of phytoplankton. These data also support the notion that the upwelled nutrient‐rich water is supplied from the Kangaroo Island pool and not by shelf break upwelling in the eastern GAB. Anomalously salty and fresh water is identified as resulting from evaporation in coastal bays and groundwater aquifer discharge.
Increased net CO2 outgassing in the upwelling region of the southern Bering Sea in a period of variable marine climate between 1995 and 2001
Authors: Fransson A. , Chierici M. , Nojiri Y.
Published: August 2006

We investigated seasonality and interannual variability of the surface water pCO2 (pCO2sw) and sea‐air CO2 fluxes in the upwelling region of the southern Bering Sea (53°N to 55°N, 174°E to 194°E). Data of surface water and atmospheric pCO2, sea surface temperature and salinity were based on automated measurements on board cargo ships for 6 years (1995–2001). We observed a significant interannual trend towards more CO2 supersaturated surface water relative to the atmosphere. From linear regression of seasonally detrended data we obtained an annual pCO2sw increase of 6.5 ± 1.4 μatm yr−1 and 11 ± 1.9 μatm yr−1 in the basin and shelf slope, respectively. This was higher than the observed pCO2air increase (between 0.47 ± 0.28 and 0.96 ± 0.62 μatm yr−1), indicating the importance of other processes than oceanic CO2 uptake from the atmosphere to explain the pCO2sw increase. Sea surface temperature and salinity showed a trend towards cooler and more saline conditions. We estimated large interannual variability of net annual oceanic CO2 outgassing, with low CO2 outgassing in years before 1998 (<1 mol m−2 yr−1), increasing to a maximum of 4.5 mol m−2 yr−1 in 2000. Highest net CO2 outgassing was observed in the relatively cold years of 1999 and 2000, whereas the exceedingly warm year 1997 showed four times lower CO2 flux to the atmosphere. Interestingly, we found close coupling between the net CO2 outgassing and biological production; years with less net CO2 outgassing coincided with high biological CO2 drawdown, especially evident in 1997.
Detection of water quality trends at high, median, and low flow in a Catskill Mountain stream, New York, through a new statistical method
Authors: Murdoch Peter S. , Shanley James B.
Published: August 2006

The effects of changes in acid deposition rates resulting from the Clean Air Act Amendments of 1990 should first appear in stream waters during rainstorms and snowmelt, when the surface of the watershed is most hydrologically connected to the stream. Early detection of improved stream water quality is possible if trends at high flow could be separately determined. Trends in concentrations of sulfate (SO42−), nitrate (NO3−), calcium plus magnesium (Ca2++Mg2+), and acid‐neutralizing capacity (ANC) in Biscuit Brook, Catskill Mountains, New York, were assessed through segmented regression analysis (SRA). The method uses annual concentration‐to‐discharge relations to predict concentrations for specific discharges, then compares those annual values to determine trends at specific discharge levels. Median‐flow trends using SRA were comparable to those predicted by the seasonal Kendall tau test and a multiple regression residual analysis. All of these methods show that stream water SO42− concentrations have decreased significantly since 1983; Ca2++Mg2+ concentrations have decreased at a steady but slower rate than SO42−; and ANC shows no trend. The new SRA method, however, reveals trends that differ at specified flow levels. ANC has increased, and NO3− concentrations have decreased at high flows, but neither has changed as significantly at low flows. The general downward trend in SO42− flattened at median flow and reversed at high flow between 1997 and 2002. The reversal of the high‐flow SO42− trend is consistent with increases in SO42− concentrations in both precipitation and soil solutions at Biscuit Brook. Separate calculation of high‐flow trends provides resource managers with an early detection system for assessing changes in water quality resulting from changes in acidic deposition.
Winter‐spring fronts in Taiwan Strait
Authors: Li Chunyan , Hu Jianyu , Jan Sen , Wei Zexun , Fang Guohong , Zheng Quanan
Published: August 2006

Fine structures of surface fronts during winter‐spring in the Taiwan Strait and their evolution over time are studied using satellite and in situ data. At times, different water masses are interleaved into each other. The northward intruding warm water bifurcates into several branches, causing complicated multiple cross strait fronts with maximum surface temperature gradients at the fronts to be greater than 2°C/km. The mean surface velocity of the fronts estimated from a sequence of satellite images is between 0.15 and 0.3 m/s during the February–March 2001 frontal event. The speed appears to have accelerated during the latter stages from 0.2 m/s during March 2–4 to 0.3 m/s during March 4–6. The total northward transport associated with the passage of the fronts is estimated to be 0.6–1 Sv between February 16 and March 6, 2001. The timescale of the passage of the fronts through the entire Taiwan Strait is therefore at least four weeks. Hydrographic observations in February–March of 1998 and 2000 also demonstrate similar frontal events with strong vertical gradients of water temperature and salinity on the western side of the strait. The 1998 data also show clearly that the low temperature and low salinity Zhemin Coastal Current separates from the coast and enters into the middle of the strait, a feature consistent with the satellite observations.
Analysis of instability and mesoscale motion off southern Norway
Authors: Fossum I.
Published: August 2006

Instability and mesoscale motion in the Norwegian Coastal Current are investigated, with particular reference to explaining why recurrent anticyclonic eddies are observed in the area off the southern tip of Norway. A numerical simulation is performed for the year 2001 with a continuously stratified, σ coordinate ocean model. The model results are analyzed by combining energy diagnostics with potential vorticity analysis. The model produces recurrent anticyclonic eddies in the area of observed eddy activity. Both barotropic and baroclinic instabilities are found along the coast east of the recurring eddy region, i.e., upstream in the Norwegian Coastal Current. Very few signs of instability are seen in the eddy region itself. This indicates that the origin of the eddies is farther east and that both barotropic and baroclinic instabilities contribute to the generation of the eddies. The instability vary considerably throughout the year, with most instability in the autumn and winter and least instability in the summer. A correspondence between this seasonal dependency of the instability and outbreak events of low‐salinity water from the Skagerrak is found. In the aftermath of every simulated outbreak event an anticyclonic eddy is seen off the southern tip of Norway, reflecting that the outbreak events initiate stronger instability and thereby are responsible for the generation of the anticyclonic eddies.
Mesoscale fluvial erosion parameters deduced from modeling the Mediterranean sea level drop during the Messinian (late Miocene)
Authors: Loget N. , Davy P. , Van Den Driessche J.
Published: August 2006

After a base level drop, rivers are the first components of the landscape to respond by incising into topography. A base level drop results in a knickpoint in the downstream part of river longitudinal profiles. Whether knickpoints are preserved or erased during the upstream propagation of incision is still debated. Preservation and erasure of knickpoints are two end‐member processes that work in natural systems at different timescales, different length scales, and different places. The huge (1500 m) and fast (tens of kiloyears) sea level drop in the Mediterranean during the Messinian resulted in the fast propagation of incision far inland. This is especially the case in the Rhone Valley (southern France) where the knickpoint is 300 km from the Mediterranean coast. Numerical modeling of this event has been performed using the ros model, which simulates both erosional and depositional processes in rivers. The best fit between numerical results and geological data is obtained for a nonlinear relation between incision and drainage area and for a small transport length of sediment. This small transport length, at least 2 orders of magnitude lower than the length of the Rhone, suggests that the longitudinal profile relaxed in a diffusive way, so that the initial knickpoint was not preserved. Finally, after a base level fall, the propagation of fluvial incision is very fast at geological timescales (hundreds of kiloyears). Despite this, the diffusive response implies that the time required for restoration of an equilibrium profile is very long.
Relative contributions of transient and steady state infiltration during ephemeral streamflow
Authors: Blasch Kyle W. , Ferré Ty P. A. , Hoffmann John P. , Fleming John B.
Published: August 2006

Simulations of infiltration during three ephemeral streamflow events in a coarse‐grained alluvial channel overlying a less permeable basin‐fill layer were conducted to determine the relative contribution of transient infiltration at the onset of streamflow to cumulative infiltration for the event. Water content, temperature, and piezometric measurements from 2.5‐m vertical profiles within the alluvial sediments were used to constrain a variably saturated water flow and heat transport model. Simulated and measured transient infiltration rates at the onset of streamflow were about two to three orders of magnitude greater than steady state infiltration rates. The duration of simulated transient infiltration ranged from 1.8 to 20 hours, compared with steady state flow periods of 231 to 307 hours. Cumulative infiltration during the transient period represented 10 to 26% of the total cumulative infiltration, with an average contribution of approximately 18%. Cumulative infiltration error for the simulated streamflow events ranged from 9 to 25%. Cumulative infiltration error for typical streamflow events of about 8 hours in duration in is about 90%. This analysis indicates that when estimating total cumulative infiltration in coarse‐grained ephemeral stream channels, consideration of the transient infiltration at the onset of streamflow will improve predictions of the total volume of infiltration that may become groundwater recharge.
Optimization of environmental water purchases with uncertainty
Authors: Hollinshead Sarah P. , Lund Jay R.
Published: August 2006

Water managers are turning increasingly to market solutions to meet new environmental demands for water in fully allocated systems. This paper presents a three‐stage probabilistic optimization model that identifies least cost strategies for staged seasonal water purchases for an environmental water acquisition program given hydrologic, operational, and biological uncertainties. Multistage linear programming is used to minimize the expected cost of long‐term, spot, and option water purchases used to meet uncertain environmental demands. Results prescribe the location, timing, and type of optimal water purchases and illustrate how least cost strategies change as information becomes available during the year. Results also provide sensitivity analysis, including shadow values that estimate the expected cost of additional dedicated environmental water. The model's application to California's Environmental Water Account is presented with a discussion of its utility for planning and policy purposes. Model limitations and sensitivity analysis are discussed, as are operational and research recommendations.
Water source dynamics in a glacierized alpine river basin (Taillon‐Gabiétous, French Pyrénées)
Authors: Brown Lee E. , Hannah David M. , Milner Alexander M. , Soulsby Chris , Hodson Andrew J. , Brewer Mark J.
Published: August 2006

Currently, there is minimal information relating to temporal variability of water source contributions in alpine glacierized basins or the influence of glacier meltwater in a basin‐wide context. This study adopts an end‐member mixing approach to understand basin‐scale water source dynamics in a French Pyrenean, alpine glacierized river system (Taillon‐Gabiétous). Major ion and Si data were collected for snow, groundwater tributaries, and four mainstream sites during the 2002/2003 melt seasons. Three conceptual water sources were identified: “quick flow” (dilute, rapidly routed meltwater), “distributed” (SO42− enriched, slow routed subglacial waters), and “groundwater” (Si‐enriched groundwater). Water source contributions at nested spatial and temporal scales were determined using end‐member mixing and uncertainty analysis. Changes in stream hydrochemistry indicated marked meltwater‐groundwater mixing. Quick flow contributions typically decreased over the melt season; groundwater contributions were highest at the beginning of the melt seasons following recharge by snowmelt but also later in the 2002 melt season following prolonged precipitation. Overall, the results suggest an alternative alpine basin melt season hydrological progression compared with previous models (i.e., simple snowmelt to glacier melt to groundwater domination) and emphasize the need to understand water source dynamics to inform related water resource availability, water quality, and stream ecology studies within alpine basins.
Influence of errors in radar rainfall estimates on hydrological modeling prediction uncertainty
Authors: Borga Marco , Degli Esposti Silvia , Norbiato Daniele
Published: August 2006

This study aims to assess the impact of a class of radar rainfall errors on prediction uncertainty of a conceptual water balance model. Uncertainty assessment is carried out by means of the Generalized Likelihood Uncertainty Estimation procedure (GLUE). The effects of model input and structural error are separated, and the potential for compensating errors between them is investigated. It is shown that the radar rainfall bias term operates in a multiplicative sense on the model structural uncertainty, by either magnifying or reducing it according to the sign of the bias. The results show also that adjustment of radar rainfall, aimed to remove local biases and to reduce random errors, allows ensuring that a larger percentage of the observed flows are enclosed by the uncertainty bounds, with respect to nonadjusted radar input. However, this is obtained at the price of increasing the wideness of the uncertainty bounds. This effect is emphasized with increasing the radar beam elevation. As a second step, the issue of the impact of radar rainfall estimation error on model parameter distribution and parameter transferability across sites under the radar umbrella is examined. Radar data at different radar beam elevations are used to simulate radar estimation errors at different distances from the radar site and to analyze the impact of these errors on prediction uncertainty. The results show that distortion of parameter distribution due to radar error may be considerable and that adjustment of radar rainfall estimates improves the regionalization potential of radar‐based precipitation estimates (at least for ranges less than 70 km).
A comparison of new and existing equations for estimating sensible heat flux using surface renewal and similarity concepts
Authors: Castellví F. , Snyder R. L. , Baldocchi D. D. , Martínez‐Cob A.
Published: August 2006

This paper describes two approaches for estimating sensible heat flux, using surface renewal and similarity concepts. One approach depends on a temperature structure function parameter and is valid in the inertial sublayer. The other approach depends on the temperature standard deviation and operates when measurements are made above the canopy top, either in the roughness or inertial sublayer. The approaches were tested over grass, rangeland grass, wheat, grape vineyard, and nectarine and olive orchards. It is shown that the free convection limit expression for the standard deviation method holds for slightly unstable conditions. When surface homogeneity and fetch requirements are not fully met in the field, the results show that the equations based on surface renewal principles are more robust and accurate than equations exclusively based on similarity backgrounds. It is likely that the two methods are less sensitive to site‐specific adjustment of the similarity relationships unless the canopy is rather heterogeneous. Under unstable conditions, the free convection limit equation, which depends on the temperature standard deviation, can provide online sensible heat flux estimates using affordable battery‐powered data logger with temperature data as the only input. The approach performed well when measuring above the canopy in the roughness and inertial sublayers, thus suggesting that the method is useful for long‐term monitoring over growing vegetation.
Influence of Indian Ocean sea surface temperature variability on southwest Western Australian winter rainfall
Authors: Samuel Jos M. , Verdon Danielle C. , Sivapalan Murugesu , Franks Stewart W.
Published: August 2006

Southwest Western Australia (SWWA) has experienced a significant drop in winter rainfall during the past three decades, the cause of which is still subject to considerable speculation and debate. This prolonged drought has heavily impacted on water resources in the state, the predicted continuation of which is of major concern to the people of Western Australia. In this paper, the possible influence of sea surface temperature (SST) variability occurring over parts of the Indian Ocean on SWWA rainfall variability is explored. The results of our statistical analyses show that winter rainfall (May to October) in SWWA is lower in years when warm SSTs dominate the southern and tropical western Indian Ocean, compared to years when cool anomalies are present in the same region. In addition, a step change that can be detected in the SST anomalies in the southern and tropical western Indian Ocean occurring around 1970 happens to coincide with a similar sharp reduction in SWWA rainfall. It is suggested that the possible association between the Indian Ocean SST anomalies and observed variability of SWWA rainfall may be utilized, at a minimum, as possible diagnostic tools in the evaluation of global climate model outputs, in this way constraining the uncertainties in their predictions.
The influence of subgrid surface‐layer variability on vertical transport of a chemical species in a convective environment
Authors: Devine G. M. , Carslaw K. S. , Parker D. J. , Petch J. C.
Published: August 2006

We use a 2‐D cloud‐resolving model over a 256 km domain to examine the influence of subgrid‐scale processes on the concentration and vertical transport of a chemical species (dimethyl sulphide, or DMS) in a deep convective marine environment. Two issues are highlighted. Firstly, deriving fluxes using a spatially averaged surface wind representative of a global model reduces the domain‐mean DMS concentration by approximately 50%. Emission of DMS from the surface is greater in the CRM because it resolves the localized intense winds embedded in the dynamical structure of convective systems. Secondly, we find that the spatial pattern of DMS concentration in the boundary layer is positively correlated with the pattern of convective updraughts. Using a mean concentration field reduces transport to the upper troposphere by more than 50%. The explanation is that secondary convection occurs preferentially on the edges of cold pools, where DMS concentrations are higher than the domain mean.
Comparison of Odin‐OSIRIS OH A2Σ+‐X2Π 0‐0 mesospheric observations and ACE‐FTS water vapor observations
Authors: Gattinger R. L. , Boone C. D. , Walker K. A. , Degenstein D. A. , Bernath P. F. , Llewellyn E. J.
Published: August 2006

As the production of hydroxyl (OH) in the mesosphere is driven by solar photodissociation of water vapor, the OH vertical profile is thus influenced by the water vapor profile. The details of this coupling are investigated by using experimental water vapor profiles observed by the Atmospheric Chemistry Experiment Fourier Transform Spectrometer (ACE‐FTS) instrument as input to a photochemical model to predict OH profiles for comparison with experimental OH profiles observed by the Optical Spectrograph and Infra‐Red Imager System (OSIRIS) instrument. We show that the model OH profiles in the 60 km to 80 km altitude region employing standard reaction rates are in agreement within 15% with the experimental OH profiles over a range of longitudes and local times, whereas the MAHRSI observations indicate the model OH densities in the middle mesosphere are approximately 30% too large. The quality of the OSIRIS OH observations and the ACE‐FTS water vapor observations are both sufficiently accurate in the upper mesosphere to yield satisfactory agreement for individual profile comparisons. An example of the hemispheric maps of OH density measured by OSIRIS is shown for an altitude of 80 km.
Assembly of transcription factor IIB at a promoter in vivo requires contact with RNA polymerase II
Authors: Elsby Laura M , O'Donnell Amanda J M , Green Laura M , Sharrocks Andrew D , Roberts Stefan G E
Published: August 2006

The general transcription factor TFIIB has a central role in the assembly of the preinitiation complex at the promoter, providing a platform for the entry of RNA polymerase II/TFIIF. We used an RNA interference (RNAi)‐based system in which TFIIB expression is ablated in vivo and replaced with a TFIIB derivative that contains a silent mutation and is refractory to the RNAi. Using this approach, we found that transcriptionally defective TFIIB amino‐terminal mutants showed distinct effects on the basis of their ability to compete with wild‐type TFIIB in vivo. Moreover, analysis of the TFIIB mutant derivatives by chromatin immunoprecipitation showed that promoter occupancy by TFIIB is dependent on the association with RNA polymerase II. Together, our results support a mode of preinitiation complex assembly in which TFIIB/RNA polymerase II recruitment to the promoter occurs in vivo.
RAD18‐independent ubiquitination of proliferating‐cell nuclear antigen in the avian cell line DT40
Authors: Simpson Laura J , Ross Anna‐Laura , Szüts Dávid , Alviani Cherry A , Oestergaard Vibe H , Patel Ketan J , Sale Julian E
Published: August 2006

Ubiquitination of proliferating‐cell nuclear antigen (PCNA) at K164 by RAD6/RAD18 has a key role in DNA damage tolerance in yeast. Here, we report on the first genetic study of this modification in a vertebrate cell. As in yeast, mutation of K164 of PCNA to arginine in the avian cell line DT40 results in sensitivity to DNA damage but, by contrast, the DT40 pcnaK164R mutant is more sensitive than the rad18 mutant. Consistent with this, we show the presence of residual ubiquitination of PCNA at K164 in the absence of functional RAD18, suggesting the presence of an alternate PCNA ubiquitinating enzyme in DT40. Furthermore, RAD18 and PCNA K164 have non‐overlapping roles in the suppression of sister chromatid exchange in DT40, showing that RAD18 has other functions that do not involve the ubiquitination of PCNA.
High-resolution infrared studies in slit supersonic discharges: CH2 stretch excitation of jet-cooled CH2Cl radical
Authors: Whitney Erin S. , Haeber Thomas , Schuder Michael D. , Blair Andrew C. , Nesbitt David J.
Published: August 2006

First high-resolution infrared spectra are presented for jet-cooled CH2Cl35 and CH2Cl37 radicals in the symmetric (ν1)CH2 stretching mode. A detailed spectral assignment yields refined lower and upper state rotational constants, as well as fine structure spin-rotation parameters from least-squares fits to the sub-Doppler line shapes for individual transitions. The rotational constants are consistent with a nearly planar structure, but do not exclude substantial large amplitude bending motion over a small barrier to planarity accessible with zero-point excitation. High level coupled cluster (singles/doubles/triples) calculations, extrapolated to the complete basis set limit, predict a slightly nonplanar equilibrium structure (θ∼11°), with a vibrationally adiabatic treatment of the bend coordinate yielding a v=1←0 anharmonic frequency (393cm−1) in excellent agreement with matrix studies (νbend∼400cm−1). The antisymmetric CH2 stretch vibration is not observed despite high sensitivity detection (signal to noise ratio >20:1) in the symmetric stretch band. This is consistent with density functional theory intensity calculations indicating a >35-fold smaller antisymmetric stretch transition moment for CH2Cl, and yet contrasts dramatically with high-resolution infrared studies of CH2F radical, for which both symmetric and antisymmetric CH2 stretches are observed in a nearly 2:1 intensity ratio. A simple physical model is presented based on a competition between bond-dipole and “charge-sloshing” contributions to the transition moment, which nicely explains the trends in CH2X symmetric versus asymmetric stretch intensities as a function of electron withdrawing group (X=D,Br,Cl,F).
Jet-cooled infrared spectroscopy in slit supersonic discharges: Symmetric and antisymmetric CH2 stretching modes of fluoromethyl (CH2F) radical
Authors: Whitney Erin S. , Dong Feng , Nesbitt David J.
Published: August 2006

The combination of shot noise-limited direct absorption spectroscopy with long-path-length slit supersonic discharges has been used to obtain first high-resolution infrared spectra for jet-cooled CH2F radicals in the symmetric (ν1) and antisymmetric (ν5) CH2 stretching modes. Spectral assignment has yielded refined lower- and upper-state rotational constants and fine-structure parameters from least-squares fits to the sub-Doppler line shapes for individual transitions. The rotational constants provide indications of large amplitude vibrational averaging over a low-barrier double minimum inversion-bending potential. This behavior is confirmed by high-level coupled cluster singles/doubles/triples calculations extrapolated to the complete basis set limit and adiabatically corrected for zero point energy. The calculations predict a nonplanar equilibrium structure (θ≈29°, where θ is defined to be 180° minus the angle between the C–F bond and the CH2 plane) with a 132cm−1 barrier to planarity and a vibrational bend frequency (νbend≈276cm−1), in good agreement with previous microwave estimates (νbend=300(30)cm−1) by Hirota and co-workers [Y. Endo et al., J. Chem. Phys. 79, 1605 (1983)]. The nearly 2:1 ratio of absorption intensities for the symmetric versus antisymmetric bands is in good agreement with density functional theory calculations, but in sixfold contrast with simple local mode CH2 bond dipole predictions of 1:3. This discrepancy arises from a surprisingly strong dependence of the symmetric stretch intensity on the inversion bend angle and provides further experimental support for a nonplanar equilibrium structure.
Water on extended and point defects at MgO surfaces
Authors: Costa D. , Chizallet C. , Ealet B. , Goniakowski J. , Finocchi F.
Published: August 2006

The interaction of water with extended defects such as mono- and diatomic steps at the MgO(100) surface is investigated through first-principles simulations, as a function of water coverage. At variance with flat MgO(100) terraces, water adsorption is always dissociative on mono- and diatomic steps, as well as on MgO(110) surfaces. In most of the equilibrium configurations, the oxygen of the hydroxyl groups is two- or fourfold coordinated, but single-coordinated OH groups can be stabilized at diatomic step edges. The structural properties of the hydroxyl groups are discussed as a function of their coordination numbers and mutual interactions, as well as the surface defect morphology. It is shown that characteristics of water adsorption are primarily driven by the coordination number of the surface acid-base pair where the dissociation occurs. However, the OH groups resulting from water dissociation are also considerably stabilized by the electrostatic interaction with coadsorbed protons. At low coverage such an interaction, considerably stronger than hydrogen bonding, practically hinders any proton diffusion away from its neighboring hydroxyl. The computed adsorption energies allow us to discuss the onset of water desorption from flat MgO(100) terraces, diatomic and monoatomic steps, and from Mg–O divacancy.
Site-selected Auger electron spectroscopy of N2O
Authors: Bolognesi Paola , Coreno Marcello , Avaldi Lorenzo , Storchi Loriano , Tarantelli Francesco
Published: August 2006

The N 1s Auger spectra for the two nonequivalent N atoms in N2O have been measured via Auger electron-photoelectron coincidence spectroscopy. The site-selected Auger spectra are compared with the normal Auger spectrum and with accurate theoretical calculations accounting for the effects of the dynamics of the nuclei on the energy and linewidth of the Auger bands. Such effects are found to be crucial factors in determining the different band shapes in the site-selected spectra.
The microwave spectrum of the 1,1-difluoroprop-2-ynyl radical, F2Ċ–CCH
Authors: Kang Lu , Novick Stewart E.
Published: August 2006

The rotational spectrum of the 1,1-difluoroprop-2-ynyl radical, F2Ċ–CCH, a partially fluorinated variant of the propargyl radical, has been recorded in the ground electronic, B12, state using pulsed discharge, pulsed-jet, Fabry-Pérot Fourier transform microwave spectroscopy. Five successive a-type rotational transitions, from N=1-0 to N=5-4, and Ka=0, 1, and 2, were measured between 6.5 and 32.5GHz with an uncertainty of 5kHz. The molecular constants, including fine and hyperfine constants, were precisely determined. These constants are compared with our predictions based on a density functional theory level ab initio calculations and with the fine and hyperfine constants of the propargyl radical. The measured electron spin densities suggest that both the difluoropropargyl and the difluoroallenyl resonance forms [F2Ċ–CCH↔F2CCĊH] make major contributions to the electronic structure of the radical.
Melting curve and fluid equation of state of carbon dioxide at high pressure and high temperature
Authors: Giordano Valentina M. , Datchi Frédéric , Dewaele Agnès
Published: August 2006

The melting curve and fluid equation of state of carbon dioxide have been determined under high pressure in a resistively heated diamond anvil cell. The melting line was determined from room temperature up to 11.1±0.1GPa and 800±5K by visual observation of the solid-fluid equilibrium and in situ measurements of pressure and temperature. Raman spectroscopy was used to identify the solid phase in equilibrium with the melt, showing that solid I is the stable phase along the melting curve in the probed range. Interferometric and Brillouin scattering experiments were conducted to determine the refractive index and sound velocity of the fluid phase. A dispersion of the sound velocity between ultrasonic and Brillouin frequencies is evidenced and could be reproduced by postulating the presence of a thermal relaxation process. The Brillouin sound velocities were then transformed to thermodynamic values in order to calculate the equation of state of fluid CO2. An analytic formulation of the density with respect to pressure and temperature is proposed, suitable in the P-T range of 0.1–8GPa and 300–700K and accurate within 2%. Our results show that the fluid above 500K is less compressible than predicted from various phenomenological models.
Optimized effective potential from a correlated wave function: Optimized effective potential-generalized valence bond (OEP-GVB)
Authors: Muller Richard P. , Desjarlais Michael P.
Published: August 2006

The optimized effective potential (OEP) method allows orbital-dependent functionals to be used in density functional theory. Traditionally the orbital-dependent functional of interest has been the Hartree-Fock energy, leading to exact exchange density functional theory. Here we present results that use a generalized valence-bond (GVB) wave function, a multiconfigurational wave function that includes static correlation and dissociates to the proper limits. We demonstrate the effectiveness of the OEP-GVB method by showing the dissociation of H2 and the excitation spectrum of He.
Debye equation of state for fluid helium-3
Authors: Huang Yonghua , Chen Guobang , Arp Vincent
Published: August 2006

An equation of state for He3 using the Helmholtz potential function has been developed. The lower limit of the equation of 0.01K is safely above the superfluid transition at 0.0026K. The upper limit of 60K is approximately the upper limit of available He3 property measurements. The new state equation form is based on Debye function which goes smoothly to zero in the limit of zero temperature and reduces to the ideal gas in the limit of zero density and/or very high temperature. The equation combines (a) necessary temperature-independent compressibility terms at the lowest temperatures, (b) terms describing the linear specific heat of a Fermi fluid below 1K, (c) terms describing the phonon excitations which begin above about 1K, and (d) terms which attempt to fit the conventional critical point thermodynamics at 3.3157K and 114604Pa. State properties, e.g., p-V-T relations, specific heats, thermal expansion, sound velocity, etc., are determined from the Helmholtz energy by standard thermodynamics. Transport properties, e.g., thermal conductivity and viscosity, are not obtained in this work.
Electrical characteristics and reliability properties of metal-oxide-semiconductor field-effect transistors with Dy2O3 gate dielectric
Authors: Chang Sheng-Chih , Deng Shao-You , Lee Joseph Ya-Min
Published: August 2006

Dy 2 O 3 is a promising candidate for future metal-oxide-semiconductor (MOS) gate dielectric applications. In this work, MOS capacitors and field-effect transistors with Dy2O3 gate dielectric were fabricated. The maximum electron mobility was 339cm2∕Vs. The time dependent dielectric breakdown (TDDB) of Dy2O3 as a function of electric field and temperature was studied. It was observed that the Weibull slopes were independent of capacitor area and the Weibull slope increased with increasing Dy2O3 thickness. The TDDB of Dy2O3 followed the E model. The activation energy Ea was linearly dependent on the electric field and the field acceleration parameter γ is independent of temperature.