bluuebunny/crossref_metadata_2025 huggingface dataset:
Metrological sharp shooting for plasma proteins and peptides: The need for reference materials for accurate measurements in clinical proteomics and in vitro diagnostics to generate reliable results
Authors: Vitzthum Frank , Siest Gérard , Bunk David M. , Preckel Tobias , Wenz Christian , Hoerth Patric , Schulz‐Knappe Peter , Tammen Harald , Adamkiewicz Juergen , Merlini Giampaolo , Anderson N. Leigh
Published: August 2007

Reliable study results are necessary for the assessment of discoveries, including those from proteomics. Reliable study results are also crucial to increase the likelihood of making a successful choice of biomarker candidates for verification and subsequent validation studies, a current bottleneck for the transition to in vitro diagnostic (IVD). In this respect, a major need for improvement in proteomics appears to be accuracy of measurements, including both trueness and precision of measurement. Standardization and total quality management systems (TQMS) help to provide accurate measurements and reliable results. Reference materials are an essential part of standardization and TQMS in IVD and are crucial to provide metrological correct measurements and for the overall quality assurance process. In this article we give an overview on how reference materials are defined, prepared and what role they play in standardization and TQMS to support the generation of reliable results. We discuss how proteomics can support the establishment of reference materials and biomarker tests for IVD applications, how current reference materials used in IVD may be beneficially applied in proteomics, and we provide considerations on the establishment of reference materials specific for proteomics. For clarity, we solely focus on reference materials related to serum and plasma.
Effect of electron–electron interaction and plasmon excitation on the density‐of‐states for a two‐dimensional electron liquid
Authors: Gumbs Godfrey , Kogan Eugene
Published: August 2007

We calculate the Green's function for an interacting two‐dimensional electron liquid whose strength of interaction is characterized by the electron density parameter rs. The screened electron–electron interaction is expressed in terms of a frequency and wave vector‐dependent dielectric function ε (q, w). If this screening is neglected, the tunneling density of states (DOS) is strongly modified by the electron–electron interaction. This modification is seen as a dip near the Fermi energy. This dip becomes deeper and narrower as rs is increased. When screening is included, the DOS is considerably affected by the collective plasma excitations. In particular, the range of frequencies where the plasmon excitations contribute increases with rs. Also, the DOS near the Fermi energy for the screened electron liquid depends on the electron density. We treat ε (q, w) in the hydrodynamical approximation in order to investigate the way in which the tunneling DOS is modified at various electron densities. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Light–matter interaction in finite‐size plasma systems
Authors: Hoyer W. , Kira M. , Koch S. W. , Moloney J. V. , Wright E. M.
Published: August 2007

It is well known that electromagnetic waves with frequencies below the plasma frequency cannot propagate inside an electron plasma. For plasmas with infinite extensions, this property can be mathematically described by a Bogoliubov transformation of the photonic operators. More generally, the presence of finite‐size electron plasmas such as laser‐induced atmospheric light strings or metallic nano structures including metamaterials leads to a modification of the light–matter interaction. It is shown how this geometric property can be fully accounted for with the help of adapted mode functions used for the quantization of the electromagnetic field. In addition to the analytical derivations, numerical results for luminescence spectra out of quasi‐two‐dimensional, planar plasma sheets are presented. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Molecular piracy: manipulation of the ubiquitin system by Kaposi's sarcoma‐associated herpesvirus
Authors: Fujimuro Masahiro , Hayward S. Diane , Yokosawa Hideyoshi
Published: August 2007

Ubiquitination, one of several post‐translational protein modifications, plays a key role in the regulation of cellular events, including protein degradation, signal transduction, endocytosis, protein trafficking, apoptosis and immune responses. Ubiquitin attachment at the lysine residue of cellular factors acts as a signal for endocytosis and rapid degradation by the 26S proteasome. It has recently been observed that viruses, especially oncogenic herpesviruses, utilise molecular piracy by encoding their own proteins to interfere with regulation of cell signalling. Kaposi's sarcoma‐ associated herpesvirus (KSHV) manipulates the ubiquitin system to facilitate cell proliferation, anti‐apoptosis and evasion from immunity. In this review, we will describe the strategies used by KSHV at distinct stages of the viral life‐cycle to control the ubiquitin system and promote oncogenesis and viral persistence. Copyright © 2007 John Wiley & Sons, Ltd.
Attributable fractions with survival data
Authors: Samuelsen Sven Ove , Eide Geir Egil
Published: August 2007

Attributable fraction (AF) is an important concept in clinical and epidemiological studies. The concept has mainly been discussed in relation to case–control studies, cross‐sectional studies, and follow‐up studies of fixed length. Here, we propose and discuss several ways of defining and estimating AFs with right‐censored survival data, and thus with varying lengths of follow‐up. In particular, we define the attributable hazard fraction, the AF before timet, and the AF within study. These measures have different interpretations and may give different numerical values, as illustrated in an application to real data on time to the first receiving of cash benefits for hearing impairment in children. The results underline the need for careful selection of the type of measure and interpretation when reporting AFs for survival data. Copyright © 2007 John Wiley & Sons, Ltd.
Comparison of Methods for Colorimetric Amylose Determination in Cereal Grains
Authors: Mahmood Tariq , Turner Matthew A. , Stoddard Fred L.
Published: August 2007

Iodine‐based colorimetry remains the most widespread method for the determination of amylose content of starch. There are, however, many variants of this method, differing in solvent, temperature and method for converting absorbance to amylose content. Therefore, in thisstudy some of these methods were compared in order to identify which, if any, was most reliable. Australian commercial samples of wheat, rice, rye and oat were used. Flour was ground and starch was extracted. Half of the samples of flour and starch were defatted with n‐propanol. Defatted and full‐fat flours and starches were dissolved by six procedures: DMSO, urea‐DMSO, CaCl2‐DMSO, hot NaOH, cold NaOH and HCl. The solutions were diluted, coloured with iodine and the absorbances determined at 535 and 620 nm. Amylose content was determined by reference to standards using 620 nm as the single wavelength or by two calculations based on the ratio between the two absorbances. Reliability was tested by repeating all tests on three non‐consecutive days with three replicates on each day. Defatted starch provided more consistent results than flour or non‐defatted starch. The most reliable dissolution procedure, with both the lowest standard error and least day‐to‐day variation, was cold NaOH. One of the ratio‐based calculations provided adequate correction for the non‐starch content of flour of wheat and rice, but not of the other two cereals, and the other ratio‐based calculation seldom provided realistic results. It is concluded that a cold NaOH dissolution procedure is suitable for reliable amylose determination on defatted starch of a range of cereals from a single wavelength and that it is also suitable for use on defatted flour of some species.
A diffusion‐weighted template for gestational age‐related apparent diffusion coefficient values in the developing fetal brain
Authors: Cannie M. , De Keyzer F. , Meersschaert J. , Jani J. , Lewi L. , Deprest J. , Dymarkowski S. , Demaerel P.
Published: August 2007

Objective

To determine the pattern of apparent diffusion coefficient (ADC) values in the normal fetal brain obtained with diffusion‐weighted images (DWI) on magnetic resonance imaging (MRI) as a template for normal brain development throughout gestation.

Methods

This was a prospective study of 46 fetuses without suspicion of brain pathology undergoing a total of 66 ultrasound examinations between 17 and 37 weeks of gestation. At T2‐weighted MRI, four left and four right brain regions were delineated on transverse slices of the native DWI using a b‐value of 0 s/mm2 (b0 images). We examined native b‐value images and calculated ADCavg, ADClow and ADChigh in the basal ganglia, cerebellar hemisphere, frontal parenchyma and occipital parenchyma. Linear regression analysis was used to assess the relationship between gestational age and b0 values as well as the calculated ADC values.

Results

Delineations were successful in all fetuses for all regions except for the cerebellar hemispheres in four fetuses. There was a negative correlation between gestational age and b0 values in all examined anatomical regions (P<0.002). For ADCavg, there were no significant changes in the basal ganglia with increasing gestational age, a positive correlation in the frontal (P<0.0001) and occipital (P=0.03) parenchyma and a negative correlation in the cerebellar hemispheres (P=0.01). For ADClow, there was a negative correlation between gestational age and the cerebellum (P=0.0002) and basal ganglia (P=0.047), but no correlation for the frontal or occipital parenchyma. For ADChigh, there was a positive correlation with gestational age for the frontal parenchyma (P=0.004), occipital parenchyma (P=0.02) and basal ganglia (P=0.03) but there was no correlation for the cerebellum.

Conclusions

DWI b0 values decreased in the left and right basal ganglia, cerebellar hemisphere, frontal parenchyma and occipital parenchyma between 17 and 37 weeks of gestation and ADCavg values increased in two out of four cerebral regions. It remains to be determined to what extent these observations differ in fetuses with suspicion of brain anomalies and whether such measurements will be useful and more predictive of outcome compared with standard MRI sequences. Copyright © 2007 ISUOG. Published by John Wiley & Sons, Ltd.
Psychiatric manifestations revealing inborn errors of metabolism in adolescents and adults
Authors: Sedel F. , Baumann N. , Turpin J.‐C. , Lyon‐Caen O. , Saudubray J.‐M. , Cohen D.
Published: August 2007

Inborn errors of metabolism (IEMs) may present in adolescence or adulthood as a psychiatric disorder. In some instances, an IEM is suspected because of informative family history or because psychiatric symptoms form part of a more diffuse clinical picture with systemic, cognitive or motor neurological signs. However, in some cases, psychiatric signs may be apparently isolated. We propose a schematic classification of IEMs into three groups according to the type of psychiatric signs at onset. Group 1 represents emergencies, in which disorders can present with acute and recurrent attacks of confusion, sometimes misdiagnosed as acute psychosis. Diseases in this group include urea cycle defects, homocysteine remethylation defects and porphyrias. Group 2 includes diseases with chronic psychiatric symptoms arising in adolescence or adulthood. Catatonia, visual hallucinations, and aggravation with treatments are often observed. This group includes homocystinurias, Wilson disease, adrenoleukodystrophy and some lysosomal disorders. Group 3 is characterized by mild mental retardation and late‐onset behavioural or personality changes. This includes homocystinurias, cerebrotendinous xanthomatosis, nonketotic hyperglycinaemia, monoamine oxidase A deficiency, succinic semialdehyde dehydrogenase deficiency, creatine transporter deficiency, and α and β mannosidosis. Because specific treatments should be more effective at the ‘psychiatric stage’ before the occurrence of irreversible neurological lesions, clinicians should be aware of atypical psychiatric symptoms or subtle organic signs that are suggestive of an IEM. Here we present an overview of IEMs potentially revealed by psychiatric problems in adolescence or adulthood and provide a diagnostic strategy to guide metabolic investigations.
Consumption of c9,t11–18:2 or t10,c12–18:2 Enriched Dietary Supplements Does Not Influence Milk Macronutrients in Healthy, Lactating Women
Authors: Hasin Afroza , Griinari J. Mikko , Williams Janet E. , Shahin Alam M. , McGuire Mark A. , McGuire Michelle K.
Published: August 2007

Substantial research suggests that the t10,c12–18:2, but not the c9,t11–18:2, isomer of conjugated linoleic acid (CLA) reduces milk fat synthesis in lactating bovine and rodent species. Because fat is the major energy‐yielding component in human milk, we were interested in whether this is true for women as well. Thus, the effects of c9,t11–18:2 and t10,c12–18:2 on milk fat were examined in breast‐feeding women (n = 12) in a double‐blind, placebo‐controlled, crossover study with latin‐square design. The study was divided into six periods: baseline (3 days), three intervention periods (5 days each), and two washout periods (9 days each). During each intervention period, women consumed 750 mg/day of a supplement containing predominantly c9,t11–18:2, t10,c12–18:2, or 18:1 (olive oil placebo). Milk was collected by complete breast expression on the final day of each period. Infant milk consumption was estimated by 24 h weighing on the penultimate day of each intervention and washout period, and maternal adiposity (% body fat) was determined at baseline using dual energy X‐ray absorptiometry. Milk c9,t11–18:2 and t10,c12–18:2 concentrations were greater (P < 0.05) during the corresponding CLA treatment periods as compared to the placebo period, providing strong evidence of subject compliance. Both CLA isomers were transferred into milk fat at relatively high efficiency; average transfer efficiency was estimated to be 23.3%. Compared to the placebo treatment, milk fat content was not reduced during either CLA treatment. Data indicate that body fatness did not modify any putative effect of isomeric CLA consumption on milk fat concentration. The evidence from this study suggests that the sensitivity of lactating women's mammary tissue to an anti‐lipogenic effect of the t10,c12–18:2 isoform of CLA may be less than previously hypothesized.
The Diversity of Health Effects of Individual trans Fatty Acid Isomers
Authors: Gebauer Sarah K. , Psota Tricia L. , Kris‐Etherton Penny M.
Published: August 2007

There are multiple adverse effects of trans fatty acids (TFA) that are produced by partial hydrogenation (i.e., manufactured TFA), on CVD, blood lipids, inflammation, oxidative stress, endothelial health, body weight, insulin sensitivity, and cancer. It is not yet clear how specific TFA isomers vary in their biological activity and mechanisms of action. There is evidence of health benefits on some of the endpoints that have been studied for some animal TFA isomers, such as conjugated linoleic acid; however, these are not a major TFA source in the diet. Future research will bring clarity to our understanding of the biological effects of the individual TFA isomers. At this point, it is not possible to plan diets that emphasize individual TFA from animal sources at levels that would be expected to have significant health effects. Due to the multiple adverse effects of manufactured TFA, numerous agencies and governing bodies recommend limiting TFA in the diet and reducing TFA in the food supply. These initiatives and regulations, along with potential TFA alternatives, are presented herein.
Fatty Acid Composition of Selected Fresh Water Gammarids (Amphipoda, Crustacea): A Potentially Innovative Source of Omega‐3 LC PUFA
Authors: Kolanowski Wojciech , Stolyhwo Andrzej , Grabowski Michal
Published: August 2007

The aim of this work was to estimate the content and composition of n‐3 long chain polyunsaturated fatty acids in selected gammarid species commonly occurring in fresh waters of Central and Western Europe. Five gammarid species were investigated, two native, one old invader consider as semi‐native and two Ponto‐Caspian species invading the area in the last decade. Lipid content of evaluated species ranged from 75 to 130 g kg−1 of dry weight. Significant amounts of n‐3 LC PUFA were found in the lipid fraction of analyzed gammarids 11–23% of total fatty acids, especially in the Ponto‐Caspian species. The main n‐3 fatty acid was EPA—up to 16% of total fatty acids. The ratio of n‐6 to n‐3 was nutritionally desirable, especially in the case of the Ponto‐Caspian species. The results obtained and growing biomass of gammarids observed in fresh waters of Central and Western Europe, as well as the rapid depletion of sea fish communities leads us to the idea that these gammarids might be considered as a innovative source of n‐3 LC PUFA for nutritional, pharmaceutical and animal feeding purposes.
Determining heterogeneous bottom friction distributions using a numerical wave model
Authors: Keen T. R. , Rogers W. E. , Dykes J. , Kaihatu J. M. , Holland K. T.
Published: August 2007

This paper describes a method for estimating spatially variable bottom roughness lengths (kb) in friction‐dominated coastal regions where dense measurements of the significant wave height are available. The method utilizes a numerical wave model to calculate wavefields. The model‐predicted significant wave height is compared to a control simulation with a known kb field, which is a proxy for measured wave heights. The error is used in combination with an influence matrix to successively correct the bottom roughness field. This predictor‐corrector calculation is completed in a series of analysis cycles. The method is demonstrated in an idealized basin with different kb distributions. The test cases simulate swell propagating over a sloping beach. The original kb fields are recovered in a reasonable number of analysis cycles but the method is limited by the influence of bottom friction on the wave height. The inversion is shown to be robust in the presence of errors in the measured wavefield as well as random bathymetry errors. However, the inversion fails if bathymetry errors are large and/or systematic because the friction error is not substantially greater than the error from bathymetry, which is also a key parameter for calculating the wave height. Thus it is important to select parameters and variables that have well‐defined dependencies in the numerical wave model for this procedure to be effective.
Alkalinity of the Mediterranean Sea
Authors: Schneider Anke , Wallace Douglas W. R. , Körtzinger Arne
Published: August 2007

Total alkalinity (AT) was measured during the Meteor 51/2 cruise, crossing the Mediterranean Sea from west to east. AT concentrations were high (∼2600 μmol kg−1) and alkalinity‐salinity‐correlations had negative intercepts. These results are explained by evaporation coupled with high freshwater AT inputs into coastal areas. Salinity adjustment of AT revealed excess alkalinity throughout the water column compared to mid‐basin surface waters. Since Mediterranean waters are supersaturated with respect to calcite and aragonite, the excess alkalinity likely reflects alkalinity inputs to coastal areas close to regions of deep and intermediate water formation. An alkalinity budget shows that main alkalinity inputs come from the Black Sea and from rivers, whereas the Strait of Gibraltar is a net sink. The major sink appears to be carbonate sedimentation. The basin‐average net calcification rate and CaCO3 sedimentation was estimated to be 0.38 mol m−2 yr−1. The estimated residence time of AT is ∼160 yr.
The shallow velocity structure across the Dead Sea Transform fault, Arava Valley, from seismic data
Authors: Ryberg T. , Weber M. H. , Garfunkel Z. , Bartov Y.
Published: August 2007

Tomographic inversion techniques were applied to first‐arrival traveltimes of refracted P waves to study the shallowest part of the crust in the vicinity of the Arava Fault (AF), the Dead Sea Transform (DST) segment between the Dead Sea and the Red Sea; tomographic inversion techniques were applied to first‐arrival traveltimes of refracted P waves. A 100‐km‐long seismic line was centered on and oriented approximately perpendicular to the AF. A large number of P wave traveltimes from vibroseis and explosive shots (>280,000) were picked manually and used to invert for shallow P wave velocity structure. The regularized inversion approach (Zelt and Barton, 1998) was used for the tomographic inversion of the traveltimes. Extensive testing of model and inversion parameters was carried out to derive a reliable P wave velocity model. Complementary checker‐board tests indicate that depending on the size of velocity homogeneities, the velocity structure is well resolved down to a depth of several kilometers. This model represents the first shallow P wave velocity across the whole width of the DST system, showing features that correlate well with surface geology and also some buried structures. The model further suggests that the AF extends vertically downward to at least 3 km. The observed variation in upper‐crustal velocity implies the existence of a simple deformation compatible with a large lateral fault offset. From this model, a structural and dynamic interpretation of the DST system is then presented. The depth extension and geometry of several additional major faults and DST‐associated shallow sedimentary basins were successfully imaged through the integration of the well‐known surface geology and nearby boreholes. This work again confirms the DST as a typical transform fault system with a dominant strike‐slip motion confined to a narrow zone.
Subduction of the Philippine Sea plate beneath southwestern Japan: Slab geometry and its relationship to arc magmatism
Authors: Nakajima Junichi , Hasegawa Akira
Published: August 2007

We carry out high‐resolution three‐dimensional seismic tomography of the crust and upper mantle beneath southwestern (SW) Japan using arrival‐time data obtained from the nationwide seismograph network. The tomographic images provide new insights into the configuration of the Philippine Sea slab and arc magmatism. The results confirm the existence of an aseismic portion of the Philippine Sea slab at greater depths beyond the seismic portion. The Philippine Sea slab is subducting aseismically down to at least a depth of 200 km in Chubu, 60–80 km in Kinki, and 60 km in Chugoku and is subducting seismically to depths of 150–200 km in Kyushu. In the Chubu district, it is subducting seismically at a shallow dip and then bends downward beneath the volcanic area, whereas in the Kinki district, it is subducting subhorizontally as far as the Japan Sea. The differences in the slab geometry between adjacent regions correlate with the differences in volcanic activity, suggesting the importance of the geometry of the Philippine Sea slab on arc magmatism. Our tomographic images further imply subduction of the Philippine Sea slab down to a depth of around 70 km northwest of the Izu Peninsula. The Philippine Sea slab in that region might have split into western and eastern parts separated by a slab tear and collided with the Pacific slab at depths of 150–200 km.
On the speed of sound in the atmosphere as a function of altitude and frequency
Authors: Bass Henry E. , Hetzer Claus H. , Raspet Richard
Published: August 2007

Sutherland and Bass (2004) have developed a calculation of the speed of sound and attenuation at altitudes up to 160 km. Dispersion is included in their treatment though emphasis is placed on absorption. That theory is explored in more detail to describe dispersion in the thermosphere. In the lower atmosphere, variations in the speed of sound with altitude are dominated by temperature and wind speed changes; the vibrational and rotational relaxation frequencies, which depend on the ratio of frequency to pressure (f/P), are in the kilohertz to megahertz range. As altitude increases, f/P and the mean free path increase, relaxation frequencies drop significantly, and velocity dispersion due to rotational and translational relaxation intensifies. This relaxation and resulting dispersion cause sound speeds at fixed frequencies to increase significantly with altitude, and to lower the altitude at which sound is refracted downward. Although the most extreme effects of dispersion are masked by simultaneously increased attenuation, decreases in traveltime of several percent are predicted at frequencies slightly below 1 Hz, demonstrating that this dispersion must be taken into account in order to correctly predict atmospheric returns at low frequencies.
Prediction of radiative forcing values for hydrofluoroethers using density functional theory methods
Authors: Blowers Paul , Moline Dena Marie , Tetrault Kyle Franklin , Wheeler R'nld Ruth , Tuchawena Shane Lee
Published: August 2007

In this work, we use computational chemistry at the B3LYP/6–31g* level of theory combined with Pinnock's cloudy sky instantaneous radiative transfer model to predict radiative forcing for hydrofluoroether compounds. We validate our predictive ability using the 27 values of cloudy sky radiative forcing reported in the literature before populating a database of 25 other hydrofluoroethers where no radiative forcing data is available. These additional compounds were selected because kinetic data are available for them and one could predict global warming potentials using the work reported here.
Impact of El Niño–Southern Oscillation on European climate
Authors: Brönnimann S.
Published: August 2007

El Niño–Southern Oscillation (ENSO) is arguably the most important global climate pattern. While the effects in the Pacific–North American sector and the tropical regions are relatively well understood, the impacts on the circulation in the North Atlantic–European sector are discussed more controversially. Studies from the past 10 years demonstrate that ENSO does affect European climate. However, some of the effects undergo a seasonal modulation or are nonlinear. The signal can be modified by other factors and might be nonstationary on multidecadal scales, contributing to a large interevent variability. Here I review observational and model‐based evidence for ENSO's effect on European climate and discuss possible mechanisms, also including troposphere‐stratosphere coupling. The paper ends with a schematic depiction of the effects and a discussion of their relevance with respect to our scientific understanding of the climate system and of their relevance for seasonal climate forecasts.
A first approach to global runoff simulation using satellite rainfall estimation
Authors: Hong Yang , Adler Robert F. , Hossain Faisal , Curtis Scott , Huffman George J.
Published: August 2007

Motivated by the recent increasing availability of global remote sensing data for estimating precipitation and describing land surface characteristics, this note reports an approximate assessment of quasi‐global runoff computed by incorporating satellite rainfall data and other remote sensing products in a relatively simple rainfall‐runoff simulation approach: the Natural Resources Conservation Service (NRCS) runoff curve number (CN) method. Using an antecedent precipitation index (API) as a proxy of antecedent moisture conditions, this note estimates time‐varying NRCS‐CN values determined by the 5‐day normalized API. Driven by a multiyear (1998–2006) Tropical Rainfall Measuring Mission Multi‐satellite Precipitation Analysis, quasi‐global runoff was retrospectively simulated with the NRCS‐CN method and compared to Global Runoff Data Centre data at global and catchment scales. Results demonstrated the potential for using this simple method when diagnosing runoff values from satellite rainfall for the globe and for medium to large river basins. This work was done with the simple NRCS‐CN method as a first‐cut approach to understanding the challenges that lie ahead in advancing the satellite‐based inference of global runoff. We expect that the successes and limitations revealed in this study will lay the basis for applying more advanced methods to capture the dynamic variability of the global hydrologic process for global runoff monitoring in real time. The essential ingredient in this work is the use of global satellite‐based rainfall estimation.
Dunes, turbulent eddies, and interfacial exchange with permeable sediments
Authors: Cardenas M. Bayani , Wilson John L.
Published: August 2007

Interfaces between a water column and underlying porous media are ubiquitous in nature. Turbulent flow over an irregular interface separating a water column and underlying porous media drives advective‐fluid exchange between the two domains. We investigate the dynamics of this coupled system for unidirectional flow in the water column and a triangular interface modeled on dunes. Numerical simulations solve the Reynolds‐averaged Navier‐Stokes equations for the water column and then Darcy's Law and the continuity equation for the porous media. The two sets of equations are coupled via the pressure distribution along the interface. The pressure maximum and minimum along the interface, which are tied to the presence of an eddy, dominantly control the configuration of and flux through the interfacial exchange zone (IEZ) in the porous media. Since the length of eddies for fully developed turbulent flow is insensitive to the Reynolds numbers (Re), the configuration of the IEZ remains stable across a range ofRe, although flux through the IEZ is strongly dependent on theRe. The flux is a power function ofReand a linear function of the current‐topography induced pressure gradient along the interface. Mean residence times for fluids in the IEZ follow an inverse‐power relationship withResince the volume of the IEZ is insensitive toRe. The IEZ depths and fluxes can be predicted via equations fitted to the simulated IEZ depths and fluxes, scaled by the dune steepness, for differentRe, granted that other systems maintain close dynamic similitude with those studied here.
Surface wave tomography of the Gulf of California
Authors: Zhang X. , Paulssen H. , Lebedev S. , Meier T.
Published: August 2007

We measured interstation fundamental mode Rayleigh wave phase velocities using data from the NARS‐Baja seismic network located around the Gulf of California. A region‐average, shear velocity model and a set of azimuthally anisotropic phase velocity maps are obtained from these data. The average shear velocity structure shows a strong low‐velocity zone underlying a thin lid and the data are suggestive of low velocities down into the transition zone. The phase velocity maps display signatures of sedimentary layers, crustal thickness variations, upwelling under the plate boundary, and the presence of the subducted Farallon microplate remnants beneath the Gulf. The upper mantle features inferred from this study provide new seismic evidence on the tectonic evolution of the region.
Synergistic Induction of NR4A Orphan Nuclear Receptors by LPS and cAMP in Murine Macrophage Cells
Authors: Shandilya Harish , Morris Sidney
Published: August 2007

Although NR4A orphan nuclear receptors have been implicated in inflammatory gene expression and atherosclerosis, there is little information regarding their regulation by combinations of stimuli likely to be found in vivo, such as LPS and inducers of cAMP. LPS rapidly induced Nur77 and NOR1 mRNAs but had little effect on expression of Nurr1 mRNA. All three NR4As were rapidly induced by 8-bromo-cAMP and remained elevated for at least 8 h. Maximum induction of NOR1 by 8-bromo-cAMP was much greater than with LPS, but maximum induction of Nur77 was similar with both agents. Whereas Nurr1 mRNA had very little response to LPS, it was strongly induced by 8-bromo-cAMP, and Nurr1 mRNA levels remained elevated for at least 20 h. The combination of 8-bromo-cAMP and LPS acted synergistically to strongly induce NOR1 and Nur77, whereas LPS partially inhibited the induction of Nurr1 by 8-bromo-cAMP. Nurr1 protein levels correlated with Nurr1 mRNA levels but exhibited slower response kinetics. In summary, the NR4A receptors did not respond identically to individual stimuli or to combinations of stimuli. In particular, the magnitude of the responses to combinations of stimuli was quite different than to individual stimuli. Thus, NR4A receptor expression and the resulting functional consequences are more complex than appreciated from previous studies that evaluated regulation of NR4A expression by single stimuli.
Reconnection rates in driven magnetic reconnection
Authors: Birn J. , Hesse M.
Published: August 2007

Using resistive magnetohydrodynamic simulations, we investigate the influence of various parameters on the reconnection rate in two scenarios of magnetic reconnection. The first scenario consists of the “Newton Challenge” problem [Birn et al., Geophys. Res. Lett. 32, L06105 (2005)]. In this scenario, reconnection is initiated in a plane Harris-type current sheet by temporally limited, spatially varying, inflow of magnetic flux. The second scenario consists of the well-studied island coalescence problem. This scenario starts from an equilibrium containing periodic magnetic islands with parallel current filaments. Due to the attraction between parallel currents, pairs of islands may move toward each other, forming a current sheet in between. This leads to reconnection and ultimately the merging of islands. In either scenario, magnetic reconnection may be considered as being driven by external or internal forcing. Consistent with that interpretation we find that in either case the maximum reconnection rate (electric field) depends approximately linearly on the maximum driving electric field, when other parameters remain unchanged. However, this can be understood mostly from the change of characteristic background parameters; particularly, the increase of the magnetic field strength in the inflow region due to the added magnetic flux. This interpretation is consistent with the result that the maximum of the reconnection electric field is assumed significantly later (tens of Alfvén times) than the maximum driving and typically does not match the instantaneous driving electric field. Furthermore, the reconnection rate also depends on the resistivity and the time scale of the driving.
New theoretical considerations in polymer rheology: Elastic breakdown of chain entanglement network
Authors: Wang Shi-Qing , Ravindranath Sham , Wang Yangyang , Boukany Pouyan
Published: August 2007

Recent experimental evidence has motivated us to present a set of new theoretical considerations and to provide a rationale for interpreting the intriguing flow phenomena observed in entangled polymer solutions and melts [P. Tapadia and S. Q. Wang, Phys. Rev. Lett. 96, 016001 (2006); 96, 196001 (2006); S. Q. Wang et al., ibid. 97, 187801 (2006)]. Three forces have been recognized to play important roles in controlling the response of a strained entanglement network. During flow, an intermolecular locking force fiml arises and causes conformational deformation in each load-bearing strand between entanglements. The chain deformation builds up a retractive force fretract within each strand. Chain entanglement prevails in quiescence because a given chain prefers to stay interpenetrating into other chains within its pervaded volume so as to enjoy maximum conformational entropy. Since each strand of length lent has entropy equal to kBT, the disentanglement criterion is given by fretract>fent∼kBT∕lent in the case of interrupted deformation. This condition identifies fent as a cohesive force. Imbalance among these forces causes elastic breakdown of the entanglement network. For example, an entangled polymer yields during continuous deformation when the declining fiml cannot sustain the elevated fretract. This opposite trend of the two forces is at the core of the physics governing a “cohesive” breakdown at the yield point (i.e., the stress overshoot) in startup flow. Identifying the yield point as the point of force imbalance, we can also rationalize the recently observed striking scaling behavior associated with the yield point in continuous deformation of both shear and extension.
Interrelation between cluster formation time, cluster growth probability, and nucleation rate
Authors: Kashchiev Dimo
Published: August 2007

Approximate expressions are derived for the mean time τ for formation of a cluster of n molecules in nucleation of single-component phases. The derivation elucidates the interrelation between τ, the cluster growth probability P, and the stationary nucleation rate. The extraction of both τ(n) and P(n) data from individual cluster growth curves obtained in experiments or simulations is discussed. It is shown that the analysis of τ(n) data allows a model-independent determination of the nucleus size, the Zeldovich factor, the stationary nucleation rate, the frequency with which molecules are attached to the nucleus, and the difference between the works to form the nucleus and the smallest “cluster” of one molecule.
Nonadiabatic couplings from time-dependent density functional theory: Formulation in the Casida formalism and practical scheme within modified linear response
Authors: Hu Chunping , Hirai Hirotoshi , Sugino Osamu
Published: August 2007

We present an efficient method to compute nonadiabatic couplings (NACs) between the electronically ground and excited states of molecules, within the framework of time-dependent density functional theory (TDDFT) in frequency domain. Based on the comparison of dynamic polarizability formulated both in the many-body wave function form and the Casida formalism, a rigorous expression is established for NACs, which is similar to the calculation of oscillator strength in the Casida formalism. The adiabatic local density approximation (ALDA) gives results in reasonable accuracy as long as the conical intersection (ci) is not approached too closely, while its performance quickly degrades near the ci point. This behavior is consistent with the real-time TDDFT calculation. Through the use of modified linear response theory together with the ground-state-component separation scheme, the performance of ALDA can be greatly improved, not only in the vicinity of ci but also for Rydberg transitions and charge-transfer excitations. Several calculation examples, including the quantization of NACs from the Jahn-Teller effect in the H3 system, have been given to show that TDDFT can efficiently give NACs with an accuracy comparable to that of wave-function-based methods.
Optical phonons in InP1−xAsx revisited
Authors: Lockwood D. J. , Rowell N. L. , Yu G.
Published: August 2007

The transverse (TO) and longitudinal (LO) optical phonons in bulk alloys of InP1−xAsx at room temperature have been studied previously by Kekelidze et al. [J. Phys. Chem. Solids 34, 2117 (1973)] using infrared reflectance spectroscopy. Their analysis based on the classical model yielded results that indicated a linear dependence on composition for all four optical modes, but no actual mode frequencies were reported. We have reanalyzed their spectra using three different methods: the conventional Kramers-Kronig approach, the factorized model fitted to the differential of the reflectivity, and directly fitting the reflectivity. The results obtained for the mode frequencies are found to vary somewhat depending on the method used, but the two LO modes are seen to exhibit a slight nonlinear dependence on x. The results also provide information on the concentration dependence of the damping of the InP-like and InAs-like TO and LO phonons. The InP-like and InAs-like mode oscillator strengths have also been determined and are found to vary differently from that depicted schematically earlier by Kekelidze et al. Comparisons are made with infrared reflectivity results obtained earlier by Oswald [Z. Naturforsch. A 14A, 374 (1959)].
Optical power limiting in the femtosecond regime by silver nanoparticle–embedded polymer film
Authors: Porel S. , Venkatram N. , Rao D. Narayana , Radhakrishnan T. P.
Published: August 2007

A simple methodology is developed for the fabrication of freestanding polymer films with embedded silver nanoparticles grown in situ. Strong nonlinear absorption, positive nonlinear refraction, and efficient optical limiting in the femtosecond regime are demonstrated with these films. Additional investigations with supported films as well as parallel studies in the nanosecond regime are also presented. The freestanding nature of the films is not only of potential interest from the application perspective but also facilitates the unambiguous determination of the nonlinear coefficients of the metal nanoparticles embedded in polymer matrix without complications arising due to the contributions from the substrate.
Quantum mechanics with respect to different reference frames
Authors: Mangiarotti L. , Sardanashvily G.
Published: August 2007

Geometric (Schrödinger) quantization of nonrelativistic mechanics with respect to different reference frames is considered. In classical nonrelativistic mechanics, a reference frame is represented by a connection on a configuration space fibered over a time axis R. Under quantization, it yields a connection on the quantum algebra of Schrödinger operators. The operators of energy with respect to different reference frames are examined.
Innovation and robustness in complex regulatory gene networks
Authors: Ciliberti S. , Martin O. C. , Wagner A.
Published: August 2007

The history of life involves countless evolutionary innovations, a steady stream of ingenuity that has been flowing for more than 3 billion years. Very little is known about the principles of biological organization that allow such innovation. Here, we examine these principles for evolutionary innovation in gene expression patterns. To this end, we study a model for the transcriptional regulation networks that are at the heart of embryonic development. A genotype corresponds to a regulatory network of a given topology, and a phenotype corresponds to a steady-state gene expression pattern. Networks with the same phenotype form a connected graph in genotype space, where two networks are immediate neighbors if they differ by one regulatory interaction. We show that an evolutionary search on this graph can reach genotypes that are as different from each other as if they were chosen at random in genotype space, allowing evolutionary access to different kinds of innovation while staying close to a viable phenotype. Thus, although robustness to mutations may hinder innovation in the short term, we conclude that long-term innovation in gene expression patterns can only emerge in the presence of the robustness caused by connected genotype graphs.
Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation
Authors: Gupta Nitin , Tanner Stephen , Jaitly Navdeep , Adkins Joshua N. , Lipton Mary , Edwards Robert , Romine Margaret , Osterman Andrei , Bafna Vineet , Smith Richard D. , Pevzner Pavel A.
Published: August 2007

While bacterial genome annotations have significantly improved in recent years, techniques for bacterial proteome annotation (including post-translational chemical modifications, signal peptides, proteolytic events, etc.) are still in their infancy. At the same time, the number of sequenced bacterial genomes is rising sharply, far outpacing our ability to validate the predicted genes, let alone annotate bacterial proteomes. In this study, we use tandem mass spectrometry (MS/MS) to annotate the proteome of Shewanella oneidensis MR-1, an important microbe for bioremediation. In particular, we provide the first comprehensive map of post-translational modifications in a bacterial genome, including a large number of chemical modifications, signal peptide cleavages, and cleavages of N-terminal methionine residues. We also detect multiple genes that were missed or assigned incorrect start positions by gene prediction programs, and suggest corrections to improve the gene annotation. This study demonstrates that complementing every genome sequencing project by an MS/MS project would significantly improve both genome and proteome annotations for a reasonable cost.
Ketamine for emergency anaesthesia at very high altitude (4243 m above sea‐level)*
Authors: Grocott M. P. W. , Johannson L.
Published: August 2007

A 22‐year‐old woman presenting with postpartum haemorrhagic shock at 4243 m altitude required anaesthesia to identify and treat the source of bleeding. Slow intravenous administration of ketamine (0.5 mg.kg−1) resulted in deep anaesthesia and apnoea requiring hand ventilation for 5 min. Haemodynamic stability was maintained throughout the procedure. Haemostasis was achieved following uterine packing and suture of a second‐degree vaginal tear and small cervical tear. Confusion and visual hallucinations occurred upon awakening but recovery was otherwise uneventful. Ketamine can be used for emergency anaesthesia in a wilderness environment over 4000 m but it is probable that the benefits outweigh the risks only where life or limb are acutely threatened. Careful titration of the administered dose is strongly advised, particularly in patients where hypovolaemia and/or hypoxaemia are present. The availability of airway management equipment and the skills to use them may significantly reduce the risks associated with anaesthetic administration at very high altitude.
Torsades de pointes and self‐terminating ventricular fibrillation in a prescription methadone user
Authors: Atkinson D. , Dunne A. , Parker M.
Published: August 2007

Methadone is known to prolong the QT interval and precipitate torsades de pointes. A 54‐year‐old prescription methadone user with hypokalaemia was referred to Critical Care with acute confusion and respiratory distress. Alcohol withdrawal was the presumed precipitant. The real precipitant only became evident on analysis of a 24‐h ECG (Holter monitor) attached to the patient at the time. The patient had suffered prolonged (10 min) ventricular arrhythmias including torsades de pointes and self‐terminating ventricular fibrillation. The patient made a full recovery. Risk factors for acquired long QT syndrome and the treatment of torsades de pointes are discussed.
Pre‐operative high sensitivity C‐reactive protein and postoperative outcome in patients undergoing elective orthopaedic surgery
Authors: Ackland G. L. , Scollay J. M. , Parks R. W. , De Beaux I. , Mythen M. G.
Published: August 2007

High‐sensitivity C‐reactive protein (hsCRP) adds important prognostic information, not reflected by traditional risk factors, to the prediction of both the development and outcome of cardiovascular pathology. HsCRP levels also correlate inversely with cardiorespiratory fitness, an important determinant of peri‐operative outcome. We hypothesised that pre‐operative hsCRP should be associated with excess peri‐operative morbidity and longer length of stay. Pre‐operative hsCRP was measured blinded to standardised postoperative outcomes in 129 elective orthopaedic patients. HsCRP levels were divided into high (> 3 mg.l−1) or low (< 3 mg.l−1) groups (Center for Disease Control stratification). High‐CRP patients had significant cardiovascular history, received cardiac medication or steroid therapy (p < 0.05). Higher pre‐operative hsCRP was associated with longer length of stay: mean 7.5 days (95% CI: 6.2–8.8) vs 6.0 days (95% CI: 5.5–6.5; p = 0.03; log rank test). In 21 patients with > 8 days length of stay, high pre‐operative hsCRP patients were over‐represented (p = 0.04). Pre‐operative hsCRP is related to length of stay and delayed postoperative complications.