bluuebunny/crossref_metadata_2025 huggingface dataset:
On cavity flow at high Reynolds numbers
Authors: Nallasamy M. , Prasad K. Krishna
Published: April 2006

The flow in a square cavity is studied by solving the full Navier–Stokes and energy equations numerically, employing finite-difference techniques. Solutions are obtained over a wide range of Reynolds numbers from 0 to 50000. The solutions show that only at very high Reynolds numbers (Re[ges ] 30000) does the flow in the cavity completely correspond to that assumed by Batchelor's model for separated flows. The flow and thermal fields at such high Reynolds numbers clearly exhibit a boundary-layer character. For the first time, it is demonstrated that the downstream secondary eddy grows and decays in a manner similar to the upstream one. The upstream and downstream secondary eddies remain completely viscous throughout the range of Reynolds numbers of their existence. It is suggested that the behaviour of the secondary eddies may be characteristic of internal separated flows.
The flow of a stratified fluid in a rotating annulus
Authors: Linden P. F.
Published: April 2006

The motion of a continuously stratified fluid in a rotating annulus is investigated experimentally. The flow is driven by the differential rotation of a lid on the annulus in contact with the fluid. For small enough Rossby numbers the basic flow is found to be axisymmetric, but in contrast to the unstratified case the zonal flow is not independent of the depth, and there is significant vertical shear in the interior. As the Rossby number of the flow is increased the axisymmetric flow becomes unstable to non-axisymmetric baroclinic disturbances. Some features of these disturbances as well as the time response to the motion of the lid are examined.
Energy stability of modulated circular Couette flow
Authors: Riley Peter J. , Laurence Robert L.
Published: April 2006

The stability of circular Couette flow when the outer cylinder is at rest and the inner is modulated both with and without a mean shear is examined in the narrow-gap limit. Disturbances are assumed to be axisymmetric. Two criteria are used to determine conditions for stability; the first requires that the motion be strongly stable, the second only that disturbances of arbitrary initial energy decay from cycle to cycle. The behaviour of critical parameters as a function of frequency is similar for the linear and the energy analysis. The range of Reynolds numbers bounded above by certain instability and below by conditional nonlinear stability is enlarged by modulation.
Intermittency in a thermal mixing layer
Authors: Keffer J. F. , Olsen G. J. , Kawall J. G.
Published: April 2006

An investigation of the existence of purely thermal intermittency has been undertaken for the flow produced by a step change in temperature in a decaying homogeneous turbulent field. The results show that a thermal interface can be defined and that it is a random function of space and time, having gross characteristics similar to the turbulent interface in a free shear flow. A technique for identifying the hot and cold regions of the fluid in a systematic way was developed and this permitted conditional averages of the mean and fluctuating temperature to be formed.
Prediction of the contributions to the Reynolds stress from bursting events in open-channel flows
Authors: Nakagawa Hiroji , Nezu Iehisa
Published: April 2006

In this paper we intend to predict the magnitude of the contribution to the Reynolds stress of bursting events: ‘ejections’, ‘sweeps’, ‘inward interactions’ and ‘outward interactions’. We shall do this by making use of the conditional probability distribution of the Reynolds stress −uv, which can be derived by applying the cumulant-discard method to the Gram-Charlier probability distribution of the two variablesuandv. The Reynolds-stress fluctuations in openchannel flows over smooth and rough beds are measured by dual-sensor hot-film anemometers, whose signals are conditionally sampled and sorted into the four quadrants of theu, vplane by using a high-speed digital data processing system.

We shall verify that even the third-order conditional probability distribution of the Reynolds stress shows fairly good agreement with the experimental results and that the sequence of events in the bursting process, i.e. ejections, sweeps and interactions, is directly related to the turbulent energy budget in the form of turbulent diffusion. Also, we shall show that the roughness effect is marked in the area from the wall to the middle of the equilibrium region, and that sweeps appear to be more important than ejections as the roughness increases and as the distance from the wall decreases.
The asymptotic stage of longitudinal turbulent dispersion within a tube
Authors: Dewey R. , Sullivan Paul J.
Published: April 2006

This paper describes an experimental investigation of the conditions for which the asymptotic description of longitudinal dispersion given by Taylor (1954) would apply. At non-dimensional times following the release of a dye pulse that are significantly larger than those previously investigated, the integrated concentration curves were observed to be skewed. At relatively short times from release the concentration curves appear to be well described by the models presented by Sullivan (1971) and by Chatwin (1973). Some features of the asymptotic behaviour, namely the translation of the modal value of the integrated concentration curve at the discharge velocity and the constant temporal growth rate of the variance, are observed at the longest times following release. On the basis of these observations it is estimated that a non-dimensional time interval oftu*/d=O(105/R*), whereR*=u*d/v,u*is the friction velocity,vthe kinematic viscosity anddthe tube diameter, is required for the Taylor result to become applicable. Thus application of Taylor's theory is significantly restricted in turbulent flows, especially those with irregular boundaries and those that are not stationary. There the variations in the flow must be small with respect to an equivalent ‘development time’ if a value of the ‘local’ longitudinal diffusion coefficient is to have meaning.
The stability of small amplitude Rossby waves in a channel
Authors: Plumb R. A.
Published: April 2006

The breakdown of Rossby waves in a bounded system is studied for the case in which the wave amplitude is small. In a very long, laterally bounded, channel all waves are unstable via second-order resonant interactions except those of wavenumber π/L in the cross-channel direction (where L is the channel width), which are stable if their longitudinal wavenumber is greater than 0·681π/L. These waves are, however, unstable to weaker side-band interactions, so that all waves with non-zero longitudinal wavenumber are unstable. The transition from sideband to triad instability occurs where the group velocity of the basic wave is equal to the velocity of long waves.
The separation of Stokes flows
Authors: Michael D. H. , O'Neill M. E.
Published: April 2006

A study is made of the extent to which local boundary geometry can influence separation in a two-dimensional or an axisymmetric Stokes flow. It is shown that a Stokes flow can separate from a point on a smooth body at an arbitrary angle, which can be determined only by reference to the global solution for the flow past the body, and the dominant mode in the stream function near a point of separation is O(r3) in the distance r from the separation point. When the body has a protruding cusped edge it is shown that separation can occur at an arbitrary inclination to the edge which must again be determined from the global solution. In this case the stream function is O(r3/2) near the edge. When the flow is locally within a wedge-shaped region of angle β, where β ≠ π or 2π, and β > 146·3°, it is shown that the dominant modes near the vertex of the wedge are non-separating modes. It follows that, in general, a Stokes flow around such a wedge cannot separate from the vertex. This conclusion is illustrated by reference to the global solution for uniform axisymmetric flow past a spherical lens, in which the structure of the flow near the rim is examined in detail. In the case of a body having a sharp edge of small but non-zero angle protruding into the flow, so that β is very close to 2π, it is shown that separation occurs exceedingly near to the edge. This happens, for example, in the flow past a thin concave-convex lens, for which separation occurs near the rim on the concave side. The analysis also suggests that a similar separation occurs very near the rim on the flatter side of a thin asymmetric biconvex lens. However, for the symmetric biconvex lens, and, as a special case, the circular disk, no separation occurs on either side near the rim. For β < 146·3·, streaming flow into the vertex of a wedge does not occur because of the presence of an infinite set of vortices, and the possibility of separation at the vertex in the sense discussed here does not arise.
Pleistocene variability of the Subtropical Convergence at East Tasman Plateau: Evidence from planktonic foraminiferal Mg/Ca (ODP Site 1172A)
Authors: Nürnberg Dirk , Groeneveld Jeroen
Published: April 2006

Combined measurements of Mg/Ca and stable oxygen isotopes in tests of the planktonic foraminifer G. bulloides from Ocean Drilling Program (ODP) Site 1172A (East Tasman Plateau) allowed us to reconstruct sea surface temperature (SSTMg/Ca), sea surface salinity (SSS), and hence variations in the Subtropical Convergence (STC) in the southwestern Tasman Sea over the last four major glacial‐interglacial changes. During interglacials the commonly enhanced SSTMg/Ca and SSS correspond to a lowered marine productivity and a lowered terrigenous flux, implying that the STC separating cool, high‐nutrient Subantarctic Surface Water from warm, saline, oligotrophic Subtropical Surface Water and hence the band of zonal westerlies responsible for the eolian dust flux were located south of East Tasman Plateau. The warm East Australian Current was well established during warm periods and propagated far south. During glacial times, SSTMg/Ca and SSS were lower, while both marine productivity and eolian flux increased. Such conditions prevailed during glacial Marine Isotope Stages MIS 12, MIS 10, and to a lesser degree MIS 6 and implied the extended northward influence of Subantarctic Surface Water and a shift of the STC to <44°S. The overall climatic signal at Site 1172A appears to be largely attenuated when compared to published climate records from comparable latitudes to the west and to the east. SSTMg/Ca amplitudes were more pronounced in the subantarctic Indian Ocean and at Chatham Rise. They exhibit a consistent pattern suggesting that latitudinal shifts of the STC occurred synchronously in the subantarctic Indian Ocean and at Chatham Rise but were largely damped at East Tasman Plateau due to the influence of the East Australian Current.
Evaluation of trends in derived snowfall and rainfall across Eurasia and linkages with discharge to the Arctic Ocean
Authors: Rawlins M. A. , Willmott C. J. , Shiklomanov A. , Linder E. , Frolking S. , Lammers R. B. , Vörösmarty C. J.
Published: April 2006

To more fully understand the role of precipitation in observed increases in freshwater discharge to the Arctic Ocean, data from a new archive of bias‐adjusted precipitation records for the former USSR (TD9813), along with the CRU and Willmott‐Matsuura data sets, were examined for the period 1936–1999. Across the six largest Eurasian river basins, snowfall derived from TD9813 exhibits a strongly significant increase until the late 1950s and a moderately significant decrease thereafter. A strongly significant decline in derived rainfall is also noted. Spatially, snowfall increases are found primarily across north‐central Eurasia, an area where the rainfall decreases are most prominent. Although no significant change is determined in Eurasian‐basin snowfall over the entire 64 year period, we note that interpolation from early, uneven station networks causes an overestimation of spatial precipitation, and that the local snowfall trends determined from gridded TD9813 data are likely underestimated. Yet, numerous uncertainties in historical Arctic climate data and the sparse, irregular nature of Arctic station networks preclude a confident assessment of precipitation‐discharge linkages during the period of reported discharge trends.
Nonlinear atmospheric teleconnections
Authors: Hsieh William W. , Wu Aiming , Shabbar Amir
Published: April 2006

Neural network models are used to reveal the nonlinear winter atmospheric teleconnection patterns associated with the El Niño‐Southern Oscillation (ENSO) and with the Arctic Oscillation (AO) over the N. Hemisphere. The nonlinear teleconnections (for surface air temperature, precipitation, sea level pressure and 500 hPa geopotential height) are found to relate quadratically to the ENSO and AO indices. Relative to linear teleconnections, nonlinear teleconections appear to propagate perturbations farther, into regions where classical linear teleconnections are insignificant.
Magnetic spectral signatures in the terrestrial plasma depletion layer: Hybrid simulations
Authors: Lu Q. M. , Guo F. , Wang S.
Published: April 2006

The electromagnetic ion cyclotron waves in the terrestrial plasma depletion layer (PDL) are characterized by three different spectral categories. They are LOW, where the ion cyclotron waves have a continuous spectrum with main power below 0.5Ωp (Ωp is the proton gyrofrequency); CON, where the main power in the continuous spectrum of the waves can extend from ∼0.1 up to 1.0Ωp; and BIF, where a diminution around 0.5Ωp occurs between two activity peaks in the spectrum. These magnetic fluctuations in the PDL are considered to be the combined effects of two types of ion cyclotron waves: proton cyclotron waves and helium cyclotron waves, which are excited by the H+ and He2+ temperature anisotropies, respectively. In this paper, with one‐dimensional (1‐D) hybrid simulations we investigate the nonlinear evolution of the ion cyclotron waves excited by the H+ and He2+ temperature anisotropies. The proton cyclotron waves with the dominant frequency (the amplitude at that frequency is largest in the spectrum) larger than 0.5Ωp are first excited, and then the helium cyclotron waves with the dominant frequency smaller than 0.5Ωp are excited. The frequencies of the proton cyclotron waves decrease in their corresponding nonlinear stage. For β∥p = 0.1 (where β∥p is the parallel proton plasma beta), the dominant frequency of the proton cyclotron waves remains around 0.62Ωp because of the He2+ absorption around the helium gyrofrequency. Therefore, after the helium cyclotron waves with the dominant frequency around 0.25Ωp are excited, there exist two activity peaks in the spectrum. At the quasi‐equilibrium stage, the amplitude of the proton cyclotron waves is very small because of the He2+ absorption, and a continuous spectrum with main power below 0.5Ωp is formed. When β∥p = 0.3, the effect of the He2+ absorption is very small and can be neglected. The frequencies of the proton cyclotron waves decrease in their nonlinear evolution. After the helium cyclotron waves are excited, their frequency band merges with that of the proton cyclotron waves and forms a continuous spectrum with main power extending above 0.5Ωp. At the quasi‐equilibrium stage, with the decrease of the frequencies of the ion cyclotron waves a continuous spectrum with main power below 0.5Ωp is formed. The relations between the three different spectral categories observed in the PDL and the spectra during the evolution of the ion cyclotron waves are also discussed. The results on the spectrum evolution of the ion cyclotron waves excited by the H+ and He2+ temperature anisotropies may help to explain the magnetic spectral signatures observed in the PDL.
Relationships among probability distributions of stream discharges in floods, climate, bed load transport, and river incision
Authors: Molnar Peter , Anderson Robert S. , Kier Grant , Rose John
Published: April 2006

Analyses of mean daily discharges and annual peak discharges for streams in 14 of the United States and spanning a wide range of climates show that frequency of occurrence relationships for the large‐discharge tails of both follow power laws. The number N(Q) of days on which the discharge exceeds Q, or the number of years in which the peak discharge exceeds Q, is related to Q by N(Q) Q−α. Values of the exponent α (1 < α < 6) decrease in magnitude with increasing aridity so that the ratio of the frequency of occurrence of very large discharges to that of smaller discharges is higher in arid than in humid environments of the United States. To examine the effect of climate change on bed load transport and river incision, we obtain a curve‐fit relating mean annual discharge per unit area of drainage basin (an effective precipitation rate ) to α: α − 1 n, where n ≈ 1.6. Using this relationship, we confirm that rivers in arid regions should incise less rapidly as climate becomes yet more arid. (If no water flows, the “river” transports no sediment.) Whether aridification of an initially humid environment leads to increased or decreased incision rates, however, depends on the minimum (threshold) discharge capable not only of transporting bed load but also sufficient to scour alluvium from the riverbed and then erode the bedrock. The curve fit relating to α implies that for aridification to accelerate incision, floods that recur only once or twice per millennium (or less frequently) must carry out most of the incision. An overestimate of n could permit smaller, more frequent floods to incise, but it appears that in only special circumstances will aridification accelerate steam incision.
Tree‐ring based drought reconstruction for the central Tien Shan area in northwest China
Authors: Li Jinbao , Gou Xiaohua , Cook Edward R. , Chen Fahu
Published: April 2006

A robust ring‐width chronology developed from two sites of Picea schrenkiana in the central Tien Shan area of northwest China was employed to study regional drought variability. Our analyses demonstrate both temperature and precipitation have significant effects on tree growth, thus both should be considered for climate reconstruction. Regional drought history (1675–2002 A.D.) was therefore reconstructed by calibrating with the Palmer Drought Severity Index (PDSI). Our reconstruction not only captured well those extreme drought events recorded in local historical archives, but also revealed the long‐term pattern of drought variability, especially the trend of increasing moisture during the 20th century. Multi‐taper method spectral analysis indicates the existence of some low‐ and high‐frequency cycles (146–171, 11.5, 10.6, 9.7, 6.1, 3.9, 3.4, 3.2, 2.4 and 2.1 yr). Overall, our study indicates the feasibility of combining tree‐rings and the PDSI to reconstruct large‐scale drought patterns over this area.
The conformational state of polyphenol oxidase from field bean (Dolichos lablab) upon SDS and acid-pH activation
Authors: Kanade Santosh R. , Paul Beena , Rao A. G. Appu , Gowda Lalitha R.
Published: April 2006

Field bean (Dolichos lablab) contains a single isoform of PPO (polyphenol oxidase) – a type III copper protein that catalyses the o-hydroxylation of monophenols and oxidation of o-diphenols using molecular oxygen – and is a homotetramer with a molecular mass of 120 kDa. The enzyme is activated manyfold either in the presence of the anionic detergent SDS below its critical micellar concentration or on exposure to acid-pH. The enhancement of kcat upon activation is accompanied by a marked shift in the pH optimum for the oxidation of t-butyl catechol from 4.5 to 6.0, an increased sensitivity to tropolone, altered susceptibility to proteolytic degradation and decreased thermostability. The Stokes radius of the native enzyme is found to increase from 49.1±2 to 75.9±0.6 Å (1 Å=0.1 nm). The activation by SDS and acid-pH results in a localized conformational change that is anchored around the catalytic site of PPO that alters the microenvironment of an essential glutamic residue. Chemical modification of field bean and sweet potato PPO with 1-ethyl-3-(3-dimethylaminopropyl)carbodi-imide followed by kinetic analysis leads to the conclusion that both the enzymes possess a core carboxylate essential to activity. This enhanced catalytic efficiency of PPO, considered as an inducible defence oxidative enzyme, is vital to the physiological defence strategy adapted by plants to insect herbivory and pathogen attack.
Crystal structure of a glycosylated Fab from an IgM cryoglobulin with properties of a natural proteolytic antibody
Authors: Ramsland Paul A. , Terzyan Simon S. , Cloud Gwendolyn , Bourne Christina R. , Farrugia William , Tribbick Gordon , Geysen H. Mario , Moomaw Carolyn R. , Slaughter Clive A. , Edmundson Allen B.
Published: April 2006

The 2.6 Å (1 Å=0.1 nm) resolution structure has been determined for the glycosylated Fab (fragment antigen binding) of an IgM (Yvo) obtained from a subject with Waldenström's macroglobulinaemia. Dynamic light scattering was used to estimate the gel point and monitor the formation of an ordered hydroscopic gel of Yvo IgM upon cooling. If a cryoglobulin forms gels in peripheral tissues and organs, the associated swelling and damage to microvasculature can result in considerable morbidity and mortality. The three-dimensional structure of the branched N-linked oligosaccharide associated with the CH1 domain (first constant domain of heavy chain) is reported. The carbohydrate may act to shield part of the lateral surface of the CH1 domain and crowd the junction between the CH1 and CH2 domains, thereby limiting the segmental flexibility of the Fab arms in intact Yvo IgM, especially at low temperatures. Recently, Yvo IgM was shown to have the properties of a naturally occurring proteolytic antibody [Paul, Karle, Planque, Taguchi, Salas, Nishiyama, Handy, Hunter, Edmundson and Hanson (2004) J. Biol. Chem. 279, 39611–39619; Planque, Bangale, Song, Karle, Taguchi, Poindexter, Bick, Edmundson, Nishiyama and Paul (2004) J. Biol Chem. 279, 14024–14032]. The Yvo protein displayed the ability to cleave, by a nucleophilic mechanism, the amide bonds of a variety of serine protease substrates and the gp120 coat protein of HIV. An atypical serine, arginine and glutamate motif is located in the middle of the Yvo antigen-binding site and displays an overall geometry that mimics the classical serine, histidine and aspartate catalytic triad of serine proteases. Our present findings indicate that pre-existing or natural antibodies can utilize at least one novel strategy for the cleavage of peptide bonds.
Yeast Hsl7 (histone synthetic lethal 7) catalyses the in vitro formation of ω-N
G-monomethylarginine in calf thymus histone H2A
Authors: Miranda Tina Branscombe , Sayegh Joyce , Frankel Adam , Katz Jonathan E. , Miranda Mark , Clarke Steven
Published: April 2006

The HSL7 (histone synthetic lethal 7) gene in the yeast Saccharomyces cerevisiae encodes a protein with close sequence similarity to the mammalian PRMT5 protein, a member of the class of protein arginine methyltransferases that catalyses the formation of ω-NG-monomethylarginine and symmetric ω-NG,N′G-dimethylarginine residues in a number of methyl-accepting species. A full-length HSL7 construct was expressed as a FLAG-tagged protein in Saccharomyces cerevisiae. We found that FLAG-tagged Hsl7 effectively catalyses the transfer of methyl groups from S-adenosyl-[methyl-3H]-L-methionine to calf thymus histone H2A. When the acid-hydrolysed radiolabelled protein products were separated by high-resolution cation-exchange chromatography, we were able to detect one tritiated species that co-migrated with an ω-NG-monomethylarginine standard. No radioactivity was observed that co-migrated with either the asymmetric or symmetric dimethylated derivatives. In control experiments, no methylation of histone H2A was found with two mutant constructs of Hsl7. Surprisingly, FLAG–Hsl7 does not appear to effectively catalyse the in vitro methylation of a GST (glutathione S-transferase)–GAR [glycine- and arginine-rich human fibrillarin-(1–148) peptide] fusion protein or bovine brain myelin basic protein, both good methyl-accepting substrates for the human homologue PRMT5. Additionally, FLAG–Hsl7 demonstrates no activity on purified calf thymus histones H1, H2B, H3 or H4. GST–Rmt1, the GST-fusion protein of the major yeast protein arginine methyltransferase, was also found to methylate calf thymus histone H2A. Although we detected Rmt1-dependent arginine methylation in vivo in purified yeast histones H2A, H2B, H3 and H4, we found no evidence for Hsl7-dependent methylation of endogenous yeast histones. The physiological substrates of the Hsl7 enzyme remain to be identified.
Akt phosphorylates and suppresses the transactivation of retinoic acid receptor α
Authors: Srinivas Harish , Xia Dianren , Moore Nicole L. , Uray Ivan P. , Kim Heetae , Ma Long , Weigel Nancy L. , Brown Powel H. , Kurie Jonathan M.
Published: April 2006

The transactivation of nuclear receptors is regulated by both ligand binding and phosphorylation. We previously showed that RARα (retinoic acid receptor α) phosphorylation by c-Jun N-terminal kinase contributes to retinoid resistance in a subset of NSCLC cells (non-small cell lung cancer cells), but the aetiology of this resistance in the remainder has not been fully elucidated [Srinivas, Juroske, Kalyankrishna, Cody, Price, Xu, Narayanan, Weigel and Kurie (2005) Mol. Cell. Biol. 25, 1054–1069]. In the present study, we report that Akt, which is constitutively activated in NSCLC cells, phosphorylates RARα and inhibits its transactivation. Biochemical and functional analyses showed that Akt interacts with RARα and phosphorylates the Ser96 residue of its DNA-binding domain. Mutation of Ser96 to alanine abrogated the suppressive effect of Akt. Overexpression of a dominant-negative form of Akt in an NSCLC cell line decreased RAR phosphorylation, increased RAR transactivation and enhanced the growth-inhibitory effects of an RAR ligand. The findings presented here show that Akt inhibits RAR transactivation and contributes to retinoid resistance in a subset of NSCLC cells.
Different mechanisms of mitochondrial proton leak in ischaemia/reperfusion injury and preconditioning: implications for pathology and cardioprotection
Authors: Nadtochiy Sergiy M. , Tompkins Andrew J. , Brookes Paul S.
Published: April 2006

The mechanisms of mitochondrial proton (H+) leak under various pathophysiological conditions are poorly understood. In the present study it was hypothesized that different mechanisms underlie H+ leak in cardiac IR (ischaemia/reperfusion) injury and IPC (ischaemic preconditioning). Potential H+ leak mechanisms examined were UCPs (uncoupling proteins), allosteric activation of the ANT (adenine nucleotide translocase) by AMP, or the PT (permeability transition) pore. Mitochondria isolated from perfused rat hearts that were subjected to IPC exhibited a greater H+ leak than did controls (202±27%, P<0.005), and this increased leakage was completely abolished by the UCP inhibitor, GDP, or the ANT inhibitor, CAT (carboxyattractyloside). Mitochondria from hearts subjected to IR injury exhibited a much greater amount of H+ leak than did controls (411±28%, P<0.001). The increased leakage after IR was weakly inhibited by GDP, but was inhibited, >50%, by carboxyattractyloside. In addition, it was inhibited by cardioprotective treatment strategies including pre-IR perfusion with the PT pore inhibitors cyclosporin A or sanglifehrin A, the adenylate kinase inhibitor, AP5A (diadenosine pentaphosphate), or IPC. Together these data suggest that the small increase in H+ leak in IPC is mediated by UCPs, while the large increase in H+ leak in IR is mediated by the ANT. Furthermore, under all conditions studied, in situ myocardial O2 efficiency was correlated with isolated mitochondrial H+ leak (r2=0.71). In conclusion, these data suggest that the modulation of H+ leak may have important implications for the outcome of IR injury.
Collagen binding by the mannose receptor mediated through the fibronectin type II domain
Authors: Napper Catherine E. , Drickamer Kurt , Taylor Maureen E.
Published: April 2006

The macrophage mannose receptor is the prototype for a family of receptors each having an extracellular region consisting of an N-terminal cysteine-rich domain related to the R-type carbohydrate-recognition domain of ricin, a fibronectin type II domain and eight to ten domains related to C-type carbohydrate-recognition domains. The mannose receptor acts as a molecular scavenger, clearing harmful glycoconjugates or micro-organisms through recognition of their defining carbohydrate structures. Cell-adhesion assays, as well as collagen-binding assays, have now been used to show that the mannose receptor can also bind collagen and that the fibronectin type II domain mediates this activity. Neither of the two types of sugar-binding domain in the receptor is involved in collagen binding. Fibroblasts expressing the mannose receptor adhere to type I, type III and type IV collagens, but not to type V collagen, and the adherence is inhibited by isolated mannose receptor fibronectin type II domain. The fibronectin type II domain shows the same specificity for collagen as the whole receptor, binding to type I, type III and type IV collagens. This is the first activity assigned to the fibronectin type II domain of the mannose receptor. The results suggest additional roles for this multifunctional receptor in mediating collagen clearance or cell–matrix adhesion.
Human papillomavirus in cervical screening and vaccination
Authors: Crosbie Emma J. , Kitchener Henry C.
Published: April 2006

Recent decades have witnessed a reduction in the incidence of cervical cancer in countries where screening programmes have achieved broad coverage. The recognized importance of high-risk HPV (human papillomavirus) infection in the aetiology of cervical cancer may introduce a role for HPV DNA testing in cervical screening programmes. Positive HPV DNA tests indicate women at risk of cervical cancer with greater sensitivity, but reduced specificity, compared with exfoliative cytology. Combining HPV testing with cytology may be useful in the triage of minor cytological abnormalities into those requiring referral to colposcopy (HPV positive) compared with those who can be safely managed by cytological surveillance (HPV negative). With its high sensitivity and high-negative-predictive value, HPV testing may also be useful for predicting treatment failure, since residual disease is very unlikely in the event of a negative HPV test. Ultimately, prevention is better than cure, and the advent of HPV prophylactic vaccines may obviate the need for population-based cervical screening programmes in the future. A multivalent vaccine administered to adolescents prior to the onset of sexual activity and boosted at regular intervals throughout their sexually active life may provide protection against type-specific HPV infection, malignant precursors and invasive cervical disease. Several large randomized placebo-controlled trials have been conducted with promising results. For those generations of women already exposed to high-risk HPV infection, therapeutic vaccines may offer advantages over conventional treatment, although much work still needs to be done.
Are retinal microvascular abnormalities associated with large artery endothelial dysfunction and intima-media thickness? The Hoorn Study
Authors: van Hecke Manon V. , Dekker Jacqueline M. , Nijpels Giel , Stolk Ronald P. , Henry Ronald M. A. , Heine Robert J. , Bouter Lex M. , Stehouwer Coen D. A. , Polak Bettine C. P.
Published: April 2006

It has been hypothesized that microvascular dysfunction affects endothelial dysfunction of the large arteries, which may explain the relationship of microvascular disease with macrovascular disease. The aim of the present study was to investigate the relationship of retinal microvascular disorders with endothelium-dependent FMD (flow-mediated vasodilatation) and carotid IMT (intima-media thickness). A total of 256 participants, aged 60–85 years, 70 with normal glucose metabolism, 69 with impaired glucose metabolism and 109 with Type II diabetes, were included in this study. All participants were ophthalmologically examined, including funduscopy and two field 45° fundus photography, and were graded for retinal sclerotic vessel abnormalities and retinopathy. Retinal arteriolar and venular diameters were measured with a computer-assisted method. Brachial artery, endothelium-dependent FMD and carotid IMT were assessed ultrasonically as measurements of endothelial function and early atherosclerosis respectively. After adjustment for age, sex and glucose tolerance status, retinal vessel diameters, retinal sclerotic vessel abnormalities and retinopathy were not significantly associated with FMD. In contrast with other retinal microvascular abnormalities, retinal venular dilatation was associated with increased IMT [standardized β value (95% confidence interval), 0.14 (0.005–0.25)]. This association was attenuated and lost statistical significance after adjustment for cardiovascular risk factors, in particular after correction for fasting insulin. In the present study, retinal microvascular disorders are not independently associated with impaired FMD. In addition, retinal venular dilatation is associated with increased IMT, although non-significantly after multivariable adjustment for cardiovascular risk factors. Therefore our data provide evidence that retinal microvascular disease is of limited value in risk stratification for future cardiovascular events.
Increased visfatin concentrations in women with gestational diabetes mellitus
Authors: Krzyzanowska Katarzyna , Krugluger Walter , Mittermayer Friedrich , Rahman Rupa , Haider Dominik , Shnawa Nadja , Schernthaner Guntram
Published: April 2006

The recently discovered adipocytokine visfatin has insulin-like properties. It lowers blood glucose and improves insulin sensitivity; however, clinical data on visfatin are limited. To evaluate the role of visfatin in GDM (gestational diabetes mellitus), we determined visfatin levels in women with GDM and in healthy pregnant controls. Furthermore, visfatin concentrations were investigated longitudinally during pregnancy and after delivery in a subgroup of women with GDM. Blood for measurement of visfatin and metabolic parameters was obtained from 64 women with GDM [median week of gestation, 34 (interquartile range, 27–36) weeks] and 30 healthy pregnant controls [median week of gestation, 34 (interquartile range, 28–36) weeks]. In a subgroup of 24 women with GDM, visfatin, leptin and metabolic parameters were investigated twice during pregnancy (28–30 and 38–40 weeks of gestation) and 2 weeks after delivery. In the cross-sectional analysis, median visfatin levels were significantly elevated in women with GDM [64.0 (interquartile range, 50.9–74.8) ng/ml] compared with controls [46.0 (interquartile range, 36.9–54.6) ng/ml; P<0.0001]. In women with GDM, visfatin correlated with week of gestation at the time of blood draw (R=0.35, P=0.005). No association with fasting glucose, insulin, homoeostasis model assessment-insulin resistance or body mass index was observed. According to the longitudinal analysis, visfatin increased during pregnancy (P=0.002) and rose further after delivery (P=0.014), whereas leptin and insulin levels decreased after parturition (both P<0.001). In conclusion, visfatin is elevated in women with GDM and increases during the course of pregnancy as well as after delivery. Furthermore, visfatin shows no association with insulin and leptin in women with GDM.
Molecular biology of human papillomavirus infection and cervical cancer
Authors: Doorbar John
Published: April 2006

HPVs (human papillomaviruses) infect epithelial cells and cause a variety of lesions ranging from common warts/verrucas to cervical neoplasia and cancer. Over 100 different HPV types have been identified so far, with a subset of these being classified as high risk. High-risk HPV DNA is found in almost all cervical cancers (>99.7%), with HPV16 being the most prevalent type in both low-grade disease and cervical neoplasia. Productive infection by high-risk HPV types is manifest as cervical flat warts or condyloma that shed infectious virions from their surface. Viral genomes are maintained as episomes in the basal layer, with viral gene expression being tightly controlled as the infected cells move towards the epithelial surface. The pattern of viral gene expression in low-grade cervical lesions resembles that seen in productive warts caused by other HPV types. High-grade neoplasia represents an abortive infection in which viral gene expression becomes deregulated, and the normal life cycle of the virus cannot be completed. Most cervical cancers arise within the cervical transformation zone at the squamous/columnar junction, and it has been suggested that this is a site where productive infection may be inefficiently supported. The high-risk E6 and E7 proteins drive cell proliferation through their association with PDZ domain proteins and Rb (retinoblastoma), and contribute to neoplastic progression, whereas E6-mediated p53 degradation prevents the normal repair of chance mutations in the cellular genome. Cancers usually arise in individuals who fail to resolve their infection and who retain oncogene expression for years or decades. In most individuals, immune regression eventually leads to clearance of the virus, or to its maintenance in a latent or asymptomatic state in the basal cells.
Use of growth-hormone-releasing peptide-6 (GHRP-6) for the prevention of multiple organ failure
Authors: Cibrián Danay , Ajamieh Hussam , Berlanga Jorge , León Olga S. , Alba Jose S. , Kim Micheal J.-T. , Marchbank Tania , Boyle Joseph J. , Freyre Freya , Garcia Del Barco Diana , Lopez-Saura Pedro , Guillen Gerardo , Ghosh Subrata , Goodlad Robert A. , Playford Raymond J.
Published: April 2006

Novel therapies for the treatment of MOF (multiple organ failure) are required. In the present study, we examined the effect of synthetic GHRP-6 (growth hormone-releasing peptide-6) on cell migration and proliferation using rat intestinal epithelial (IEC-6) and human colonic cancer (HT29) cells as in vitro models of injury. In addition, we examined its efficacy when given alone and in combination with the potent protective factor EGF (epidermal growth factor) in an in vivo model of MOF (using two hepatic vessel ischaemia/reperfusion protocols; 45 min of ischaemia and 45 min of reperfusion or 90 min of ischaemia and 120 min of reperfusion). In vitro studies showed that GHRP-6 directly influenced gut epithelial function as its addition caused a 3-fold increase in the rate of cell migration of IEC-6 and HT29 cells (P<0.01), but did not increase proliferation ([3H]thymidine incorporation). In vivo studies showed that, compared with baseline values, ischaemia/reperfusion caused marked hepatic and intestinal damage (histological scoring), neutrophilic infiltration (myeloperoxidase assay; 5-fold increase) and lipid peroxidation (malondialdehyde assay; 4-fold increase). Pre-treatment with GHRP-6 (120 μg/kg of body weight, intraperitoneally) alone truncated these effects by 50–85% (all P<0.05) and an additional benefit was seen when GHRP-6 was used in combination with EGF (1 mg/kg of body weight, intraperitoneally). Lung and renal injuries were also reduced by these pre-treatments. In conclusion, administration of GHRP-6, given alone or in combination with EGF to enhance its effects, may provide a novel simple approach for the prevention and treatment of MOF and other injuries of the gastrointestinal tract. In view of these findings, further studies appear justified.
Soft x-ray measurement of the toroidal pinch experiment RX reversed field pinch plasma using transition edge sensor calorimeter
Authors: Shinozaki Keisuke , Hoshino Akio , Ishisaki Yoshitaka , Morita Umeyo , Ohashi Takaya , Mihara Tatehiro , Mitsuda Kazuhisa , Tanaka Keiichi , Yagi Yasuyuki , Koguchi Haruhisa , Hirano Yoichi , Sakakita Hajime
Published: April 2006

A superconductive transition edge sensor (TES) calorimeter is for the first time applied for the diagnostics of the reversed field pinch plasma produced in the toroidal pinch experiment RX (TPE-RX), and the instrumental system is fully described. The first result from the soft x-ray spectroscopy in 0.2–3keV with an energy resolution ∼50eV are also presented. The TES calorimeter is made of a thin bilayer film of titanium and gold with a transition temperature of 151mK and its best energy resolution at our laboratory is 6.4eV, while it was significantly degraded by about a factor of eight during the plasma operation. The TES microcalorimeter was installed in a portable adiabatic demagnetization refrigerator (ADR), which is originally designed for a rocket experiment. The detector box is carefully designed to shield the strong magnetic field produced by the ADR and TPE-RX. The ADR was directly connected to TPE-RX with a vacuum duct in the sideway configuration, and cooled down to 125mK stabilized with an accuracy of 10μK rms using an improved proportional, integral, and derivative (PID) control method. Thin aluminized Toray Lumirror or Parylene-N films were used for the IR to UV blocking filters of the incident x-ray window to allow soft x-rays coming into the detector with good efficiency. TPE-RX was operated with the plasma current of Ip=220kA, and the wave forms of the TES output for every plasma shot lasting ∼80ms were obtained with a digital oscilloscope. The wave forms were analyzed with the optimal filtering method, and x-ray signals were extracted. A total of 3472 counts of x-ray signals were detected for 210 plasma shots during the flat-top phase of t=35–70ms. Combined with the data measured with a lithium drifted silicon detector in the 1.3–8keV range, spectral features are investigated using a spectral fitting package XSPEC. The obtained spectrum is well explained by thermal plasma emission, although an impurity iron-L line emissions at variously ionized states are dominant around 0.7–1.2keV. At least three different temperature components ranging T=350–900eV are required to account for the spectral shape, while the average temperature is consistent with the ruby laser Thomson scattering measurement.
High-efficiency target ion sources for radioactive ion beam generation
Authors: Alton G. D. , Liu Y. , Stracener D. W.
Published: April 2006

In this report, high-temperature ion sources are described, which have demonstrated the high ionization efficiency, species versatility, and operational reliability required at isotope-separator-online (ISOL) based radioactive ion beam facilities such as the Holifield Radioactive Ion Beam Facility (HRIBF). Specific attention is given to the ion optics, operational parameters, thermal transport properties, emittances, and ionization efficiencies of the HRIBF ion sources that have been carefully designed for safe handling in the high-level radiation fields incumbent at such facilities. Included in the article are descriptions and performance data for high-temperature, positive- (electron impact and surface ionization) and negative- (kinetic ejection and surface ionization) ion sources as well as low-temperature, batch-mode negative-ion sources, developed for processing long-lived isotopes that have been the principal contributors to recent successes held at the Holifield Radioactive Ion Beam Facility.
Phase behavior of polyampholytes from charged hard-sphere chain model
Authors: Jiang Jianwen , Feng Jian , Liu Honglai , Hu Ying
Published: April 2006

A molecular thermodynamic theory is developed for polyampholytes from the coarse-grained charged hard-sphere chain model. The phase behavior of polyampholytes with variations in sequence and chain length is satisfactorily predicted by the theory, consistent with simulation results and experimental observations. At a fixed chain length, the phase envelope expands as the sequence of charge distribution becomes less random. With increasing chain length, the phase envelope expands for diblock and random polyampholytes, but shrinks for zwitterionic polyampholytes. The predicted critical temperature, density, and pressure exhibit scaling relations with chain length for all the three (diblock, random, and zwitterionic) polyampholytes.
In search of the germanium halomethylidyne (GeC–X; X=F,Cl,Br) free radicals: Ab initio studies of their spectroscopic signatures
Authors: Tackett Brandon S. , Clouthier Dennis J.
Published: April 2006

A variety of ab initio methods have been used to calculate the X̃Π2 and ÃΣ+2 state spectroscopic parameters of the GeCX (X=F,Cl,Br) free radicals. The theoretical methods and basis sets were tested on GeCH, for which extensive experimental data are available, and found to give predictions sufficiently reliable to guide experimental searches for spectra. In all cases, the linear GeC–X species was found to be the global minimum on the potential energy surface, with the bent X–GeC (A′2) isomer as a local minimum much higher (62–36kcal∕mol) in energy. In both the ground and excited states, the GeC moiety is very similar to that of GeCH, with a double bond in the lower state and a triple bond in the excited state, indicating that halogenation does not radically perturb the energetics or structure of germanium methylidyne. Ground state GeCX radicals have suitable rotational constants for microwave studies, although they suffer from only modest dipole moments. Matrix infrared experiments are most likely to detect the ν1 fundamentals in the 1450–1100cm−1 region or the ν3 fundamentals at the transition between the mid- and far-infrared regions. We have used the ab initio values for the Renner-Teller parameter, the average bending frequency, and the spin-orbit coupling constant to calculate the ground state energy levels, which will be helpful in the interpretation of Ã-X̃ single vibronic level emission spectra, if they can be observed. The electronic absorption spectra of the Π3∕22 spin component of the 000 bands of all three radicals have been calculated assuming typical jet-expansion conditions and should be useful in future laser-induced fluorescence, resonance enhanced multiphoton ionization, or cavity ringdown searches for the electronic band systems.
Flow structure of water in carbon nanotubes: Poiseuille type or plug-like?
Authors: Hanasaki Itsuo , Nakatani Akihiro
Published: April 2006

We have conducted molecular dynamics simulations of water flow in carbon nanotubes (CNTs) for (6,6) to (20,20) CNTs at a streaming velocity of 100m∕s. The fluidized piston model (FPM) and the ice piston model (IPM) are employed to drive flow through the CNTs. The results show that the single-file water flow inside (6,6) CNT has a convex upward streaming velocity profile, whereas the velocity profiles in (10,10) to (20,20) CNTs are flat except near the tube wall. The flow structure of cylindrical water in the (8,8) CNT is intermediate between that for the (6,6) CNT and the larger CNTs. The flow parameters are found not to exhibit any dependence on streaming velocity at up to 300m∕s in the (12,12) CNT. The hydrogen bond lifetimes of water flowing in CNTs tend to be longer than for the corresponding equilibrium states, and nonzero flow does not reduce the microscopic structure or structural robustness (hydrogen bond lifetime). Although the atomic density profile varies with tube diameter, reflecting the change in static microscopic structure of flow from single file to cylindrical, tube diameter does not induce a clear transition in streaming velocity, temperature, or hydrogen bond lifetime over this diameter range. The results suggest that water flow in CNTs of this size is more pluglike than Poiseuille type, although the flow structure does not strictly accord with either definition.