bluuebunny/crossref_metadata_2025 huggingface dataset:
Potassium channels involved in human sperm volume regulation—quantitative studies at the protein and mRNA levels
Authors: Yeung C.H. , Cooper T.G.
Published: December 2007

KCNE1, KCNA5 and KCNK5 have been identified, by using specific blockers, as K+‐channels involved in sperm volume regulation under physiological conditions. All three channels were localised on the cytoplasmic droplets and tail of human ejaculated spermatozoa by fluorescence microscopy. Using flow cytometric quantification, KCNE1 was found to be present in 80% or more spermatozoa and KCNK5 in only about 20%, with KCNA5 expressed by 20–90% of cells. Whereas the extents of such protein expression did not differ statistically between semen donors and subfertile patients, the former group exhibited higher capacities for sperm volume regulation which were correlated with other sperm qualities including normal morphology and motile sperm number in the ejaculate. Channel identification was further confirmed at the protein level using Western blotting. RT‐PCR analysis of testicular and sperm RNA of proven quality indicated the presence of Kcne1, Kcna5 and Kcnk5 transcripts. Subsequent sequencing of PCR products demonstrated that the nucleotide sequences of the entire encoding regions of Kcne1 and Kcnk5 were identical to those published in the database, whereas that of Kcna5 mRNA showed a single nucleotide synonymous deviation that agrees with the published genomic sequence. Quantitative real‐time PCR analysis of sperm RNA revealed the amounts of Kcne1 > Kcna5 > Kcnk5, in the same order as for protein expression. Thus, KCNE1 is probably the major K+‐channel involved in regulatory volume decrease in human spermatozoa, and channel activity is regulated beyond the extent of protein expression. Mol. Reprod. Dev. 75: 659–668, 2008. © 2007 Wiley‐Liss, Inc.
BRAF provides proliferation and survival signals in MSI colorectal carcinoma cells displaying BRAFV600E but not KRAS mutations
Authors: Preto A , Figueiredo J , Velho S , Ribeiro AS , Soares P , Oliveira C , Seruca R
Published: December 2007

BRAF kinase is a downstream target of KRAS and activates the MAPK pathway. These two molecules are prone to mutations in sporadic microsatellite unstable (MSI) colorectal carcinomas (CRC) and BRAFV600E mutations are inversely associated with oncogenic KRAS mutations. The biological significance of BRAFV600E oncogenic activation is not well established in this type of tumour. We aimed to study proliferation and survival effects induced by BRAF inhibition in MSI CRC cell lines harbouring distinct genetic backgrounds (BRAFV600E or KRASG13D). Suppression of BRAF in BRAFV600E MSI CRC cell lines by RNA interference significantly inhibited proliferation and induced apoptosis, as demonstrated by BrdU incorporation and TUNEL assay, respectively. No significant differences were seen in proliferation and apoptosis, in cell lines harbouring KRASG13D, after BRAF inhibition. We further analysed proliferation‐associated molecules (pERK1/2, cyclin D1, p27Kip1) and apoptosis‐associated molecules (Bcl‐2, Bax, pAkt, pBad, XIAP) in all cell lines. After BRAF down‐regulation, we found a more pronounced decrease in ERK1/2 phosphorylation and cyclin D1 expression levels in BRAF‐mutated cell lines in comparison to KRAS mutated cells. Upon BRAF inhibition, we also found an increase in p27Kip1 levels and a more pronounced decrease in the levels of anti‐apoptotic protein Bcl‐2, specifically in cell lines with BRAFV600E. In conclusion, we have shown that MSI KRAS and BRAF mutant CRC cell lines respond differently to BRAF knockdown. This report provides evidence supporting BRAF as a good target for therapeutic intervention in patients with sporadic MSI CRC harbouring activating mutations in BRAF but not in KRAS. Copyright © 2007 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
One‐step preparation of solution processable conducting polyaniline by inverted emulsion polymerization using didecyl ester of 4‐sulfophthalic acid as multifunctional dopant
Authors: John Amalraj , Palaniappan Srinivasan , Djurado David , Pron Adam
Published: December 2007

A new one‐step method of preparation of solution processable conductive polyaniline (PANI) is reported using didecyl ester of 4‐sulfophthalic acid (DESPA) as multifunctional material. It consists of inversed emulsion polymerization of aniline in water/chloroform mixture with benzoyl peroxide initiator, maleic acid (MA) as a codopant and DESPA as protonating agent, surfactant, and plasticizer. The resulting product combines reasonable conductivity (ca.0.03 S/cm) with solubility in common solvents such as tetrahydrofuran and chloroform. Elemental analysis together with spectroscopic studies show that the protonation level of emulsion polymerized PANI (0.47 per mer involving one ring and one nitrogen) is very close to that predicted for PANI in the oxidation state of emeraldine (0.5). MA is incorporated into the polymer matrix as a co‐dopant in the ratio 1:4 with respect to the DESPA dopant. PANI‐DESPA‐MA three components system shows a highly ordered, layer‐type supramolecular structure, in which planes of regularly π‐stacked PANI chains are separated by a double layer of dopants. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 1051–1057, 2008
Modelling issues for tall reinforced concrete core wall buildings
Authors: Wallace John W.
Published: December 2007

Reinforced concrete walls are commonly used as the primary lateral force‐resisting system for tall buildings. As the tools for conducting nonlinear response history analysis have improved and with the advent of performance‐based seismic design, reinforced concrete walls and core walls are often employed as the only lateral force‐resisting system. Proper modelling of the load versus deformation behaviour of reinforced concrete walls and link beams is essential to accurately predict important response quantities. Given this critical need, an overview of modelling approaches appropriate to capture the lateral load responses of both slender and stout reinforced concrete walls, as well as link beams, is presented. Modelling of both flexural and shear responses is addressed, as well as the potential impact of coupled flexure–shear behaviour. Model results are compared with experimental results to assess the ability of common modelling approaches to accurately predict both global and local experimental responses. Based on the findings, specific recommendations are made for general modelling issues, limiting material strains for combined bending and axial load, and shear backbone relations. Copyright © 2007 John Wiley & Sons, Ltd.
Crystal Structures of Alkali Metal Peroxodiphosphates
Authors: Oeckler Oliver , Montbrun Lydia
Published: December 2007

Peroxodiphosphates of alkali metals can be prepared from K4P2O8, which is synthesized by electrolysis, in metathesis reactions with the corresponding perchlorates. Single crystals have been obtained by diffusion of methanol into aqueous solutions of the peroxodiphosphates. The crystal structures of Li4P2O8·4H2O (P21/n;a= 8.057(2) Å,b= 5.074(1) Å,c= 12.288(3) Å, β = 100.53(2)°;V= 493.9(2) Å3;Z= 2), Na4P2O8·18H2O (at 130 K:P61;a= 9.0984(14) Å,c= 49.926(13) Å;V= 3579.2(12) Å3;Z= 6) and K4P2O8(P21/c;a= 5.9041(15) Å,b= 10.254(2) Å,c= 7.356(2) Å, β = 99.05(3)°;V= 439.79(18) Å3;Z= 2) have been determined by X‐ray diffraction. In the Li salt the cations are tetrahedrally coordinated by one water molecule and three oxygen atoms of the anions, whereas the Na salt is characterized by binuclear [Na2(H2O)9]2+complexes. At low temperatures, the latter undergoes a phase transition from a structure with disordered anions to a completely ordered phase. K4P2O8is solvent‐free and exhibits irregular cation coordination. The structure of the peroxodiphosphate anion is very similar in all compounds; the mean O–O distance is 1.49(1) Å. In addition, the structure determination of K4(HPO4)2·3H2O2(P21/n;a= 6.076(1) Å,b= 6.579(1) Å,c= 17.215(2) Å, β = 99.73(1)°;V= 678.26(17) Å3;Z= 2), which can be mistaken for K4P2O8, is presented.
Syntheses and X‐ray Structure Analyses of the First Bis(chelated) Copper and Iron Bisguanidine Complexes
Authors: Herres‐Pawlis Sonja , Haase Roxana , Akin Enver , Flörke Ulrich , Henkel Gerald
Published: December 2007

The synthesis of N1,N2‐bis(1,3‐dimethylimidazolidin‐2‐ylidene)ethane‐1,2‐diamine and the synthesis and structure determination of bis{N1,N2‐bis(1,3‐dimethylimidazolidin‐2‐ylidene)ethane‐1,2‐diamine}copper(II)‐tetraiododicuprate(I) ([Cu(DMEG2e)2][Cu2I4]) and bis{N1,N2‐bis(1,3‐dimethylimidazolidin‐2‐ylidene)ethane‐1,2‐diamine}iron(II)‐octacarbonyl‐diferrate(‐I) ([Fe(DMEG2e)2][Fe2(CO)8]) which represent the first bis(chelated) bisguanidine complexes are described. The dicationic [M(DMEG2e)2]2+ molecules with M = Cu, Fe follow the same structural principles and thus differ in their coordination geometries from ideal‐typical expectations.
Syntheses, Structures, and Properties of Mono‐ and Tetranuclear Nickel(II) Complexes Derived from a Tridentate Schiff Base Ligand
Authors: Zhao Zhen‐Guo , Wu Xiao‐Yuan , Zhai Quan‐Guo , Chen Li‐Juan , Zhang Quan‐Zheng , Li Wei , Xie Yi‐Ming , Lu Can‐Zhong
Published: December 2007

Three new nickel(II) complexes constructed with N‐(2‐hydroxybenzyl)‐β‐alanine (H2L), namely [NiL(phen)H2O]·H2O (1) (phen = 1.10‐phenanthroline), [Ni4L4(H2O)4]·5H2O (2) and K[Ni4L4(NCS)(H2O)5]·5.42H2O (3) have been synthesized and characterized by single‐crystal X‐ray diffraction analysis. Complex 1 exhibits a discrete structure, and the structures are bound together through hydrogen bonding to a one‐dimensional chain in ladder‐like fashion. Complexes 2 and 3 contain similar [Ni4(μ2‐O)6] cores with “zig‐zig” arrangement. In complex 3, the tetranuclear nickel units [Ni4L4(H2O)4] and [Ni4L4(NCS)(H2O)] are alternately bridged by potassium atoms to a one‐dimensional chain. The neighboring chains are further linked up by {K2O2} units to a two‐dimensional layer structure. Moreover, the IR, XRD, TGA and the temperature‐dependent magnetic susceptibility for 2 and 3 have also been studied.
Influence of a chronic myositis on rat spinal field potentials evoked by TTX‐resistant unmyelinated skin and muscle afferents
Authors: Lambertz D. , Hoheisel U. , Mense S.
Published: December 2007

A recent study of our group has shown that in the segments L4 and L5 of the rat, the synaptic field potentials (SFPs) evoked by tetrodotoxin‐resistant (TTX‐r, presumably nociceptive) muscle afferents differ in size and peak location from those of cutaneous afferents from the same body region [Lambertz D, Hoheisel U, Mense S. Distribution of synaptic field potentials induced by TTX‐resistant skin and muscle afferents in rat segment L4 and L5. Neurosci Lett 2006;409:14–8]. Here, we investigated the influence of a muscle inflammation on the distribution of SFPs of TTX‐r afferent fibres from muscle and skin in the thoracic and lumbar spinal cord. During a TTX block of the dorsal roots L3–L6, a skin nerve (sural, SU) or a muscle nerve (gastrocnemius‐soleus, GS) were electrically stimulated at an intensity supramaximal for unmyelinated afferents and the SFPs recorded with tungsten microelectrodes. In control (non‐inflamed) rats, the largest SFPs evoked by TTX‐r GS afferents were recorded in laminae IV–VI with a maximum in segment L4, whereas the largest SU‐induced SFPs were more superficially located with a maximum in L3. In chronic myositis animals, SFPs induced by GS TTX‐r fibres exhibited significant decreases in lamina IV–VI of Th 12 and L5 as well as in lamina VII of L5. In contrast, SFPs evoked by SU TTX‐r afferents showed significant increases in lamina IV–VI in L1 and in lamina VII in L4. The results demonstrate that a chronic myositis has a strong influence also on the synaptic effects of nociceptive afferents from the skin, which may explain the subjective cutaneous sensations during a pathological alteration of muscle.
Vitamin D status in Sri Lankans living in Sri Lanka and Norway
Authors: Meyer Haakon E. , Holvik Kristin , Lofthus Cathrine M. , Tennakoon Sampath U. B.
Published: December 2007

Vitamin D deficiency is common in non-Western immigrant groups living in Western countries. A comparison of vitamin D status in individuals who have emigrated and individuals who remain in their country of origin is needed in order to provide information about the effect of moving to northern latitudes. A total of 196 participants aged 30–60 years in a cross-sectional population-based study in Kandy, Sri Lanka (latitude 7° north) and 242 Sri Lankans aged 31–60 years participating in a cross-sectional population-based study in Oslo, Norway (latitude 60° north) were included in the analysis. All serum samples were analysed for serum 25-hydroxyvitamin D (s-25(OH)D) in the same laboratory. Sri Lankans living in Norway had substantially lower s-25(OH)D (mean 31·5 nmol/l) compared with those living in Sri Lanka (mean 54·2 nmol/l), and the prevalence of s-25(OH)D <  25 nmol/l was 9·3 times higher (95 % CI 4·4, 19·6) in Norway compared with Sri Lanka. In Sri Lanka there was a clear seasonal variation with the lowest s-25(OH)D levels in August–September and the highest levels in November–December. We conclude that vitamin D status among Sri Lankans living in Kandy, Sri Lanka was considerably higher than that among Sri Lankans living in Oslo, Norway. The low vitamin D status commonly observed in non-Western immigrant groups living at northern latitudes should not be regarded as normal levels for these groups. However, also in Sri Lanka we found a profound seasonal variation with the lowest levels in August and September after the Monsoon.
Relationship between energy from added sugars and frequency of added sugars intake in Irish children, teenagers and adults
Authors: Joyce Triona , McCarthy Sinead N. , Gibney Michael J.
Published: December 2007

A WHO report on diet, nutrition and the prevention of chronic diseases recommended that frequency of consumption of foods and/or drinks containing free sugars should be limited to a maximum of four times per d. In addition, they recommended a reduction in the intake of free sugars to a maximum of no more than 10 % of energy intake. These recommendations were developed with the aim of reducing the prevalence of dental caries. The aim of the present study was to establish if there is a quantitative relationship between energy from added sugars and frequency of added sugars intakes in Irish children, teenagers and adults. In addition, the intake of added and total sugars and main contributors to added sugar intakes were examined. Data for the present analysis were based on the North/South Ireland Food Consumption Survey (n1379; aged 18–64 years), the National Children's Food Survey (n594; aged 5–12 years) and the National Teen Food Survey (n441; aged 13–17 years) which used 7 d food diaries to collect food and beverage intake data in representative samples of Irish adults, children and teenagers respectively. Results showed that in adults, frequency of intake of added sugar intake of four times per d corresponded to a mean added sugar intake of 9 %, which was similar to the WHO recommendation. In children and teenagers, a frequency of intake of four times per d corresponded to a mean added sugar intake of 14·6 and 12·4 % respectively and was therefore not in agreement with the WHO recommendation.
Imaging Modes for Scanning Confocal Electron Microscopy in a Double Aberration-Corrected Transmission Electron Microscope
Authors: Nellist P.D. , Cosgriff E.C. , Behan G. , Kirkland A.I.
Published: December 2007

Aberration correction leads to reduced focal depth of field in the electron microscope. This reduced depth of field can be exploited to probe specific depths within a sample, a process known as optical sectioning. An electron microscope fitted with aberration correctors for both the pre- and postspecimen optics can be used in a confocal mode that provides improved depth resolution and selectivity over optical sectioning in the scanning transmission electron microscope (STEM). In this article we survey the coherent and incoherent imaging modes that are likely to be used in scanning confocal electron microscopy (SCEM) and provide simple expressions to describe the images that result. Calculations compare the depth response of SCEM to optical sectioning in the STEM. The depth resolution in a crystalline matrix is also explored by performing a Bloch wave calculation for the SCEM geometry in which the pre- and postspecimen optics are defocused away from their confocal conditions.
Predictive model for permeability reduction by small wetting phase saturations
Authors: Motealleh Siyavash , Bryant Steven L.
Published: December 2007

Laboratory experiments show that the rate of decrease in gas phase permeability as a function of water saturation can be large at small saturations. Drying out the water saturation during gas injection has been observed to reduce absolute permeability. This paper proposes a quantitative grain‐scale explanation for these observations. We also show why the effect is magnified in rocks having lower porosity. To compute phase geometry and permeability, we use a physically representative network model. The network is extracted from a model rock, built from a dense random packing of spheres modified geometrically to simulate rock‐forming processes. At small saturations the wetting phase exists largely in the form of pendular rings held at grain contacts. The rings decrease the void area available for flowing nonwetting phase. Because the hydraulic conductance of the throat varies with the square of the void area (other factors being equal), the effect on permeability is disproportionate to the volume occupied by the rings. The same approach quantifies the reduction in permeability by salt precipitation during drying.
Inertial effects in dispersion in porous media
Authors: Wood Brian D.
Published: December 2007

In this work we develop the macroscale transport equation for dispersion of a nonreactive chemical species, with a particular focus on the influence of inertial contributions at moderate Reynolds numbers. Our starting point is the continuum level description of transport written at the subpore scale. Volume averaging is used to upscale these equations to develop the macroscale solute balance that applies at the Darcy scale. We develop a fully transient version of the ancillary closure problem that predicts the total dispersion tensor, and we solve the closure using finite Fourier transforms. The result of this effort is a nonlocal macroscale transport equation, where the nonlocal dispersion depends upon the microscale geometry of the pore space and the physical characteristics of the fluid. Both the longitudinal and transverse components of the total dispersion tensor are computed for a simple three‐dimensional unit cell. The computational results indicate that a simple three‐dimensional periodic unit cell is able to capture the correct behavior for the longitudinal dispersion in the range 101 < Pep < 2.5 × 105, although the magnitude of the longitudinal dispersion coefficient is underpredicted by up to a factor of about 4. For the transverse dispersion coefficient, the simple unit cell provides much less satisfactory results when compared with experimental data. The inertial effects for the longitudinal dispersion coefficient were relatively small, but for the transverse dispersion coefficient, inertial effects were predicted to increase the transverse dispersion coefficient up to 40 times that which would be predicted for Stokes flow.
Rapid transitions in the Atlantic thermohaline circulation triggered by global warming and meltwater during the last deglaciation
Authors: Knorr Gregor , Lohmann Gerrit
Published: December 2007

In a series of sensitivity experiments, using a three‐dimensional ocean general circulation model, rapid climate shifts during the last deglaciation are interpreted in terms of gradual temperature changes and freshwater perturbations, which impact on the Atlantic thermohaline circulation (THC). We show that increasing global temperature leads to a rapid intensification of the THC. The transition to an interglacial THC mode is preconditioned by a decrease of the subsurface temperatures due to an increase in ventilation of the subsurface water in the northern North Atlantic, which enhances the merdional transport of salt to the northern high latitudes and gradually erodes the halocline. This process enables the remaining temperature inversion to overcome the salinity stratification in the northern North Atlantic, which causes a kick start of vigorous convection and a rapid intensification of the Atlantic THC. As a result of the abrupt THC amplification and the deglacial warming and sea ice retreat in the Southern Ocean, enhanced transport of relatively salty surface and intermediate‐depth waters from the Indian Ocean provides an additional source of salt to the North Atlantic, which changes the stability behavior of the THC with respect to freshwater perturbations. A warming‐induced transition from a weak glacial THC to a stronger THC state, with different North Atlantic freshwater hysteresis characteristics, provides a concept that might explain the sequence of events, characterizing the last glacial termination as recorded in proxy data.
Impact of correlated observation errors on inverted CO2 surface fluxes from OCO measurements
Authors: Chevallier Frédéric
Published: December 2007

Proper assignment of error statistics is essential in the field of Bayesian inference. This paper studies the impact of correlated observation errors in the case of the estimation of CO2 surface fluxes from NASA's forthcoming Orbiting Carbon Observatory (OCO). Using a series of observation simulation system experiments, it is shown that hypothetical observation error correlations of 0.5 in neighbouring observations have a rather limited impact on the accuracy of the inverted fluxes when they are correctly taken into account. The information loss induced by commonly‐used approximate treatments of the observation error correlations (neglecting, observation thinning and error inflating), that are computationally more efficient, is quantified. Error inflation has the least detrimental impact among the suboptimal set‐ups and limits the loss in uncertainty reduction to a few per cent, in spite of its very low reduced chi‐squared.
A high resolution satellite‐only GRACE‐based mean dynamic topography of the South Atlantic Ocean
Authors: Vianna Marcio L. , Menezes Viviane V. , Chambers Don P.
Published: December 2007

A new filtering method based on Singular Spectrum Analysis has been devised to extract high resolution (0.25° × 0.25° grid) satellite‐only Mean Dynamic Ocean Topography(MDT) constructed by differencing of the GGM02 GRACE Gravity Model from the GSFCMSS00 Mean Sea Surface. This data‐adaptive interpolation‐type filter is adequate for the finite domain MDT processing since it minimizes smoothing and does not lose boundary points. It is applied to the computation of two new MDTs and MDT‐derived mean geostrophic circulation maps of the South Atlantic region from 15°N to 50°S. Advantages of these new maps are clarified when contrasted with the Rio‐2005, Chambers‐Zlotnicki‐2004 and ADCP cruise transect data.
A younger, thinner Arctic ice cover: Increased potential for rapid, extensive sea‐ice loss
Authors: Maslanik J. A. , Fowler C. , Stroeve J. , Drobot S. , Zwally J. , Yi D. , Emery W.
Published: December 2007

Satellite‐derived estimates of sea‐ice age and thickness are combined to produce a proxy ice thickness record for 1982 to the present. These data show that in addition to the well‐documented loss of perennial ice cover as a whole, the amount of oldest and thickest ice within the remaining multiyear ice pack has declined significantly. The oldest ice types have essentially disappeared, and 58% of the multiyear ice now consists of relatively young 2‐ and 3‐year‐old ice compared to 35% in the mid‐1980s. Ice coverage in summer 2007 reached a record minimum, with ice extent declining by 42% compared to conditions in the 1980s. The much‐reduced extent of the oldest and thickest ice, in combination with other factors such as ice transport that assist the ice‐albedo feedback by exposing more open water, help explain this large and abrupt ice loss.
Small‐scale temperature fluctuations associated with gravity waves cause additional radiative cooling of mesopause the region
Authors: Kutepov Alexander A. , Feofilov Artem G. , Medvedev Alexander S. , Pauldrach Adalbert W. A. , Hartogh Paul
Published: December 2007

We present a study of the radiative cooling of the mesosphere and lower thermosphere in the infrared bands of CO2, O3 and H2O due to small‐scale irregular temperature fluctuations caused by gravity waves. These persistent fluctuations are presently not well represented by general circulation models. A statistical model of gravity wave‐induced temperature variations was applied to large‐scale temperature profiles, and the corresponding direct radiative calculations were performed. We show that temperature fluctuations can cause an additional cooling up to 3 K day−1 near the mesopause. The effect is produced mainly by the fundamental 15 μm band of the main CO2 isotope. We found a simple correction depending on the temperature fluctuations variance, which should be added in radiative calculations to the mean temperature profile to account for the additional cooling associated with the unresolved disturbances.
Longitudinal structure of the equatorial ionosphere: Time evolution of the four‐peaked EIA structure
Authors: Lin C. H. , Hsiao C. C. , Liu J. Y. , Liu C. H.
Published: December 2007

Longitudinal structure of the equatorial ionosphere during the 24 h local time period is observed by the FORMOSAT‐3/COSMIC (F3/C) satellite constellation. By binning the F3/C radio occultation observations during September and October 2006, global ionospheric total electron content (TEC) maps at a constant local time map (local time TEC map, referred as LT map) can be obtained to monitor the development and subsidence of the four‐peaked longitudinal structure of the equatorial ionosphere. From LT maps, the four‐peaked structure starts to develop at 0800–1000 LT and becomes most prominent at 1200–1600 LT. The longitudinal structure starts to subside after 2200–2400 LT and becomes indiscernible after 0400–0600 LT. In addition to TEC, ionospheric peak altitude also shows a four‐peaked longitudinal structure with variation very similar to TEC during daytime. The four‐peaked structure of the ionospheric peak altitude is indiscernible at night. With global local time maps of ionospheric TEC and peak altitude, we compare temporal variations of the longitudinal structure with variations of E × B drift from the empirical model. Our results indicate that the observations are consistent with the hypothesis that the four‐peaked longitudinal structure is caused by the equatorial plasma fountain modulated by the E3 nonmigrating tide. Additionally, the four maximum regions show a tendency of moving eastward with propagation velocity of several 10 s m/s.
Gas hydrate concentration and characteristics within Hydrate Ridge inferred from multicomponent seismic reflection data
Authors: Kumar Dhananjay , Sen Mrinal K. , Bangs Nathan L.
Published: December 2007

A seismic experiment composed of streamer and ocean bottom seismometer (OBS) surveys was conducted in the summer of 2002 at southern Hydrate Ridge, offshore Oregon, to map the gas hydrate distribution within the hydrate stability zone. Gas hydrate concentrations within the reservoir can be estimated with P wave velocity (Vp); however, we can further constrain gas hydrate concentrations using S wave velocity (Vs), and use Vs through its relationship to Vp (Vp/Vs) to reveal additional details such as gas hydrate form within the matrix (i.e., hydrate cements the grains, becomes part of the matrix frame or floats in pore space). Both Vp and Vs can be derived simultaneously by inverting multicomponent seismic data. In this study, we use OBS data to estimate seismic velocities where both gas hydrate and free gas are present in the shallow sediments. Once Vp and Vs are estimated, they are simultaneously matched with modeled velocities to estimate the gas hydrate concentration. We model Vp using an equation based on a modification of Wood's equation that incorporates an appropriate rock physics model and Vs using an empirical relation. The gas hydrate concentration is estimated to be up to 7% of the rock volume, or 12% of the pore space. However, Vp and Vs do not always fit the model simultaneously. Vp can vary substantially more than Vs. Thus we conclude that a model, in which higher concentrations of hydrate do not affect shear stiffness, is more appropriate. Results suggest gas hydrates form within the pore space of the sediments and become part of the rock framework in our survey area.
Coupling of water and carbon fluxes via the terrestrial biosphere and its significance to the Earth's climate system
Authors: Ferguson Paul R. , Veizer Ján
Published: December 2007

Terrestrial water vapor fluxes represent one of the largest movements of mass and energy in the Earth's outer spheres, yet the relative contributions of abiotic water vapor fluxes and those that are regulated solely by the physiology of plants remain poorly constrained. By interpreting differences in the oxygen‐18 and deuterium content of precipitation and river water, a methodology was developed to partition plant transpiration (T) from the evaporative flux that occurs directly from soils and water bodies (Ed) and plant surfaces (In). The methodology was applied to fifteen large watersheds in North America, South America, Africa, Australia, and New Guinea, and results indicated that approximately two thirds of the annual water flux from the “water‐limited” ecosystems that are typical of higher‐latitude regions could be attributed toT. In contrast to “water‐limited” watersheds, whereTcomprised 55% of annual precipitation,Tin high‐rainfall, densely vegetated regions of the tropics represented a smaller proportion of precipitation and was relatively constant, defining a plateau beyond which additional water input by precipitation did not correspond to higherTvalues. In response to variable water input by precipitation, estimates ofTbehaved similarly to net primary productivity, suggesting that in conformity with small‐scale measurements, the terrestrial water and carbon cycles are inherently coupled via the biosphere. Although the estimates ofTare admittedly first‐order, they offer a conceptual perspective on the dynamics of energy exchange between terrestrial systems and the atmosphere, where the carbon cycle is essentially driven by solar energy via the water cycle intermediary.
Ice properties of single‐layer stratocumulus during the Mixed‐Phase Arctic Cloud Experiment: 1. Observations
Authors: McFarquhar Greg M. , Zhang Gong , Poellot Michael R. , Kok Gregory L. , McCoy Robert , Tooman Tim , Fridlind Ann , Heymsfield Andrew J.
Published: December 2007

During the Department of Energy's Atmospheric Radiation Measurement Program's Mixed‐Phase Arctic Cloud Experiment (M‐PACE) in fall 2004, the University of North Dakota Citation measured 53 profiles within single‐layer stratus clouds by executing spiral ascents and descents over Barrow and Oliktok Point, Alaska, and by flying ramped ascents and descents between. Cloud phase was identified from an algorithm that uses voltage change from the Rosemount ice detector, the size distribution (SD) shape measured by the Forward Scattering Spectrometer Probe (FSSP), and manual identification of particles imaged by the Cloud Particle Imager, the two‐dimensional cloud probe (2DC) and the high‐volume precipitation sampler (HVPS). Size and mass distribution functions were derived using data from the FSSP, one‐dimensional cloud probe, 2DC and HVPS in conjunction with total water content (TWC) measured by the Counterflow Virtual Impactor. With clouds defined as locations where TWC > 0.001 g m−3, there were a total of 513 30‐s averaged SDs in single‐layer clouds, of which 71% were in mixed‐phase parcels, 23% in ice‐phase and 6% in liquid‐phase. The mixed‐phase parcels were dominated by contributions from liquid drops, with the liquid mass fraction fl having averages and standard deviations of 0.89 ± 0.18 with 75% of cases having fl > 0.9. For these single‐layer clouds, fl increased with normalized cloud altitude zn, defined as linearly increasing from 0 at cloud base to 1 at cloud top with fl averaging 0.96 ± 0.13 near zn = 1 and 0.70 ± 0.30 near zn = 0. The effective radius of water droplets rew increased with zn, from an average of 6.9 ± 1.8 μm near zn = 0 to 11.4 ± 2.4 μm near zn = 1, whereas the effective radius of ice crystals rei (25.2 ± 3.9 μm) was nearly independent of zn. The averaged cloud droplet number concentration and concentrations of ice crystals with maximum dimensions greater than 53 μm were 43.6 ± 30.5 × 103 L−1 and 2.8 ± 6.9 L−1, respectively, and nearly independent of zn. In contrast to past measurements in mixed‐phase clouds combined from many geographical locations where fl increased with temperature, fl decreased from −12° to −3°C as clouds typically consisted of a liquid topped layer with precipitating ice below.
Evaluation of the applicability of the dual‐domain mass transfer model in porous media containing connected high‐conductivity channels
Authors: Liu Gaisheng , Zheng Chunmiao , Gorelick Steven M.
Published: December 2007

This paper evaluates the dual‐domain mass transfer (DDMT) model to represent transport processes when small‐scale high‐conductivity (K) preferential flow paths (PFPs) are present in a homogenous porous media matrix. The effects of PFPs upon solute transport were examined through detailed numerical experiments involving different realizations of PFP networks, PFP/matrix conductivity contrasts varying from 10:1 to 200:1, different magnitudes of effective conductivities, and a range of molecular diffusion coefficients. Results suggest that the DDMT model can reproduce both the near‐source peak and the downstream low‐concentration spreading observed in the embedded dendritic network when there are large conductivity contrasts between high‐K PFPs and the low‐K matrix. The accuracy of the DDMT model is also affected by the geometry of PFP networks and by the relative significance of the diffusion process in the network‐matrix system.
Simulating the dissolution of a complex dense nonaqueous phase liquid source zone: 1. Model to predict interfacial area
Authors: Grant G. P. , Gerhard J. I.
Published: December 2007

A thermodynamically based model for predicting two‐fluid interfacial area (IFA) within a porous medium as a function of wetting phase saturation (SW) and saturation history is presented. The model considers consistency with multiphase flow constitutive relationships, the conversion of total to effective specific interfacial area, energy losses, and the change of interfacial area as residual nonwetting phase dissolves. The model requires as input only the capillary pressure–saturation relationships and porosity. Published, high‐resolution interfacial area‐saturation data sets were adequately reproduced when independent measures of these parameters were employed by the model. In particular, the model is found to reproduce key IFA(SW) features including the IFA magnitude and SW value corresponding to the function's maximum, negligible IFA at residual SW and the observed hysteresis of IFA(SW). Varying key model parameters reveals that the magnitude of the IFA(SW) relationship is predicted to be linearly related to the porosity and entry pressure of the porous medium and is unaffected by interfacial tension. Interfacial area is a parameter in the single boundary layer expression of mass transfer between two immiscible liquids in porous media. The model's ability to predict local‐scale IFA for a wide variety of fluid‐fluid‐porous media systems while accounting for saturation and saturation history thus provides an avenue for simulating the dissolution of complex source zones containing both pooled and residual dense nonaqueous phase liquids.
Exchange anisotropy in polycrystalline FeNi∕FeMn films with hysteresis loop asymmetry
Authors: Merenkov D. N. , Bludov A. N. , Gnatchenko S. L. , Baran M. , Szymczak R. , Novosad V. A.
Published: December 2007

The process of magnetization reversal of a FeNi(50Å)∕FeMn(50Å) polycrystalline film prepared in a magnetic field has been investigated at temperatures ranging from 25to300K. The external field was oriented in the film plane along the easy or difficult axis of the ferromagnetic layer. In the process of magnetization reversal of the film along the easy axis, strong asymmetry of the hysteresis loop is observed together with an exchange shift. As temperature decreases, the asymmetry becomes more pronounced and the shift increases. The field dependences of the magnetization of the film are symmetric and are not shifted when the external field is applied along the difficult axis. The magnetization reversal process is examined on the basis of a model that takes account of the appearance of high-order exchange anisotropy in polycrystalline films. It is shown that the observed strong asymmetry of the hysteresis loop is associated with the formation of a canted phase and the existence of a metastable state. As the film temperature decreases, the interval of fields where the canted phase can exist becomes wider as a result of an increase of the exchange anisotropy constants.
Andreev reflection study of the new magnetic superconductor Mo3Sb7 in magnetic field
Authors: Dmitriev V. M. , Rybaltchenko L. F. , Ishchenko L. A. , Khristenko E. V. , Bukowski Z. , Troć R.
Published: December 2007

Andreev reflection in contacts based on the magnetic superconductor Mo3Sb7 in a magnetic field is investigated by the point-contact method. It is found that the behavior of the order parameter in the magnetic field Δ(H) is essentially dependent on the value of Δ, which varies widely (Δ(0,0)≈0.01–0.31meV) for different contacts at practically invariant Tc. At high Δ the dependence Δmax(H) deviates slightly from the theoretical prediction applicable under point-contact conditions. As the order parameter decreases, the deviation starts to increase and becomes very large when Δ approaches its minimum. Proceeding from the results obtained in this study and from the temperature measurements on Mo3Sb7 performed previously, we are inclined as before to assign the compound to the class of superconductors with an anisotropic gap function. Therefore, in no way can it be considered as a conventional BCS-type superconductor. The upper critical field Hc2≃16.5kOe found here is close to that obtained from magnetization measurements in other studies. According to an estimate made, the pair-breaking effect of the Pauli paramagnetism is rather weak in Mo3Sb7.
Anomalous magnetism of YbPb3: the effect of pressure
Authors: Baranovskiy A. E. , Grechnev G. E. , Panfilov A. S. , Svechkarev I. V. , Żogal O. , Czopnik A. , Hackemer A.
Published: December 2007

In the compound YbPb3, the anomalous diamagnetism of which is due to the presence of a point of degeneracy of the energy bands near the Fermi level, the influence of hydrostatic pressure of up to 2kbar on the magnetic susceptibility at fixed temperatures of 78 and 300K. A theoretical analysis of the experimental data shows that appreciable growth of the diamagnetism under pressure comes about because a point of band degeneracy is approaching the Fermi level. The initial position of the band with respect to the Fermi level is refined, and its dependence on the atomic volume is determined.
Bidirectional tornado modes on the Joint European Torus
Authors: Sandquist P. , Sharapov S. E. , Lisak M. , Johnson T. ,   JET-EFDA contributors
Published: December 2007

In discharges on the Joint European Torus [P. H. Rebut and B. E. Keen, Fusion Technol. 11, 13 (1987)] with safety factor q(0)<1 and high-power ion cyclotron resonance heating (ICRH), monster sawtooth crashes are preceded by frequency sweeping “tornado modes” in the toroidal Alfvén eigenmode frequency range. A suite of equilibrium and spectral magnetohydrodynamical codes is used for explaining the observed evolution of the tornado mode frequency and for identifying temporal evolution of the safety factor inside the q=1 radius just before sawtooth crashes. In some cases, the tornado modes are observed simultaneously with both positive and negative toroidal mode numbers. Hence, a free energy source other than the radial gradient of the energetic ion pressure exciting these modes is sought. The distribution function of the ICRH-accelerated ions is assessed with the SELFO code [J. Hedin et al., Nucl. Fusion 42, 527 (2002)] and energetic particle drive due to the velocity space anisotropy of ICRH-accelerated ions is considered analytically as the possible source for excitation of bidirectional tornado modes.
Oscillator strengths of the Mulliken, Swan, Ballik-Ramsay, Phillips, and dΠg3←cΣu+3 systems of C2 calculated by MRCI methods utilizing a biorthogonal transformation of CASSCF orbitals
Authors: Schmidt Timothy W. , Bacskay George B.
Published: December 2007

Ab initio oscillator strengths and lifetimes for the DΣu+1←XΣg+1 Mulliken system of C2 are reported. The calculations were carried out at the MRCI level of theory with Davidson’s correction using aug-cc-pV6Z basis sets and include core and core-valence correlation as well as relativistic corrections, computed with aug-cc-pCVQZ and cc-pVQZ bases, respectively. The MRCI calculations of transition moments utilize a biorthogonal transformation of the CASSCF orbitals. This approach was also employed to recompute the transition moments of the Swan, Ballik-Ramsay, Phillips, and dΠg3←cΣu+3 systems of C2, which were the subject of our previous study [D. L. Kokkin et al., J. Chem. Phys. 126, 084302 (2007)], resulting in an improved set of oscillator strengths for the latter systems as well. The oscillator strength of the Mulliken origin band, f00DA, was calculated to be 0.0535, in excellent agreement with the accepted astronomical value of 0.054.
Geometry optimization for peptides and proteins: Comparison of Cartesian and internal coordinates
Authors: Koslover Elena F. , Wales David J.
Published: December 2007

We present the results of several benchmarks comparing the relative efficiency of different coordinate systems in optimizing polypeptide geometries. Cartesian, natural internal, and primitive internal coordinates are employed in quasi-Newton minimization for a variety of biomolecules. The peptides and proteins used in these benchmarks range in size from 16 to 999 residues. They vary in complexity from polyalanine helices to a β-barrel enzyme. We find that the relative performance of the different coordinate systems depends on the parameters of the optimization method, the starting point for the optimization, and the size of the system studied. In general, internal coordinates were found to be advantageous for small peptides. For larger structures, Cartesians appear to be more efficient for empirical potentials where the energy and gradient can be evaluated relatively quickly compared to the cost of the coordinate transformations.
Interface structure and strain relaxation in BaTiO3 thin films grown on GdScO3 and DyScO3 substrates with buried coherent SrRuO3 layer
Authors: Chen Y. B. , Sun H. P. , Katz M. B. , Pan X. Q. , Choi K. J. , Jang H. W. , Eom C. B.
Published: December 2007

To obtain the electrical properties of strained ferroelectric thin films, bottom electrodes with lattice constants and thermal coefficients matched to both films and substrates are needed. The interface structure, strain configuration, and strain relaxation in such bilayer systems are different from those in single layer systems. Here, we report transmission electron microscopy studies of epitaxial BaTiO3 films grown on GdScO3 and DyScO3 substrates with buried SrRuO3 layers. We found that the different strain relaxation behaviors observed in the bilayer are mainly dependent on lattice mismatch of each layer to the substrate and the thicknesses of each layer.
Resistance switching in BaTiO3−δ∕Si p-n heterostructure
Authors: Liu Guo-zhen , Jin Kui-juan , Qiu Jie , He Meng , Lu Hui-bin , Xing Jie , Zhou Yue-liang , Yang Guo-zhen
Published: December 2007

The resistance switching characteristic and electric displacement-voltage hysteresis loop have been observed in BaTiO3−δ∕Si p-n heterostructures fabricated by laser molecular beam epitaxy. The ferroelectric response of BaTiO3−δ can be enhanced by the interface polarization of the junction. The resistance switching property observed in the BaTiO3−δ∕Si p-n junction can be attributed to the irreversibility of polarization in the polarization and depolarization processes. The present results indicate a potential application of resistance switching in the heterostructures consisting of oxides and Si.
Oblique modulation of electron-acoustic waves in a Fermi electron-ion plasma
Authors: Bhowmik C. , Misra A. P. , Shukla P. K.
Published: December 2007

The oblique modulational instability (MI) of electron-acoustic waves (EAWs) in a quantum plasma whose components are two distinct groups of electrons (one inertial cold electrons and other inertialess hot electrons) and immobile ions is investigated, by using a quantum hydrodynamic model. The analysis is carried out through the derivation of the nonlinear Schrödinger equation for the modulated EAW packets. The effects of obliqueness, the quantum diffraction (H), and the equilibrium density ratio of the cold to hot electron component (δ) on the MI of EAWs are numerically examined. At quantum scales, these parameters are found to significantly modify the MI domain in the plane of wave number and the angle (θ) between the modulation and the propagation direction. The relevance of our results in astrophysical environments, as well as in intense laser-solid density plasma interaction experiments is discussed.
Diffusion of an annular plasma in positron acceleration
Authors: Chen Francis F.
Published: December 2007

Electron acceleration to multi-GeV energies has been demonstrated using plasma wakefields in a tunnel-ionized plasma. However, coherent wakefields for positron acceleration may require hollow plasmas pre-ionized by a laser beam. The lifetime of such a plasma is determined by an unusual diffusion problem in which the diffusion rate varies by an order of magnitude inside the hole. The problem is solved by numerical differentiation without using a particle-in-cell code. The densities assumed in this work match those in existing positron experiments and are low compared with those in electron experiments. Future positron experiments at higher densities will not exhibit the nonlinear diffusion treated here because they will be dominated by recombination and tunneling ionization by the beam.
Anisotropic spin-dependent electron tunneling in a triple-barrier resonant tunneling diode
Authors: Isić Goran , Radovanović Jelena , Milanović Vitomir
Published: December 2007

The one-band envelope function approximation is used to investigate the spin-dependent tunneling of conduction band electrons in semiconductor heterostructures when both the bulk inversion asymmetry (BIA) and structure inversion asymmetry (SIA) are present. It is shown that under certain conditions the interplay between BIA and SIA may be used to induce a strong dependence of transmission probabilities on the direction of electrons lateral momenta thus offering means to improve the existing designs of nonmagnetic semiconductor spin filters.
Microstadium single-nanowire laser
Authors: Park Hong-Gyu , Qian Fang , Barrelet Carl J. , Li Yat
Published: December 2007

We report room-temperature lasing in an optically pumped single-nanowire stadium microresonator. The photoluminescence from a chemically synthesized GaN nanowire is coupled and confined in a silicon-nitride stadium microcavity. Photoluminescence spectroscopy exhibits lasing at 372nm with a lasing threshold of 1536kW∕cm2. We compute a Q factor of ∼3500 for the microstadium single-nanowire structure using finite-difference time-domain simulation. The successful demonstration of this hybrid structure using bottom-up and top-down approaches represents a significant step toward high-density integration of functional building blocks for an ultracompact nanophotonic circuit.