bluuebunny/crossref_metadata_2025 huggingface dataset:
Can synthetic aperture radars be used to estimate hurricane force winds?
Authors: Horstmann J. , Thompson D. R. , Monaldo F. , Iris S. , Graber H. C.
Published: November 2005

We compare wind fields retrieved from a RADARSAT‐I synthetic aperture radar (SAR) image acquired over Hurricane Ivan on September 10, 2004 using the C‐band geophysical model functions Cmod4 and its newest version Cmod5. Cmod4 has previously been shown to yield very good wind field estimates under low and moderate wind conditions. Wind directions obtained from streaks imaged by the SAR, that are well aligned with the mean surface wind direction are used to invert both algorithms to obtain estimates of the wind speed on scales of 1 km. These estimates are compared with predictions from a high‐resolution tropical cyclone model as well as local in situ data. It is found that the SAR wind speeds using Cmod5 agree reasonably well, while those from Cmod4 significantly under predict the measured wind speeds near the hurricane eye wall that reach values as high as 60 m s−1.
Examination of discontinuities in hourly surface relative humidity in Canada during 1953–2003
Authors: van Wijngaarden William A. , Vincent Lucie A.
Published: November 2005

Hourly values of relative humidity recorded at 75 stations across Canada were examined. Data were checked for possible discontinuities arising because of changes in procedures and instruments. It was found that the replacement of the psychrometer by the dewcel has produced a decreasing step in relative humidity at a number of stations. The historical records were closely examined to retrieve the dewcel installation date, and a procedure based on regression models was applied to determine if it corresponds to a significant step. Results show that there are more stations experiencing a dewcel step in the winter than in the summer. Examination of the trends also reveals that the step often accentuates the decreasing trends originally observed during winter and spring. However, significant steps taken into account, it appears that the relative humidity still decreased by several percent in the spring during 1953–2003 in western Canada. It seems that the southern and coastal stations are not as much affected by this change of instruments.
Modeling and measuring the nocturnal drainage flow in a high‐elevation, subalpine forest with complex terrain
Authors: Yi Chuixiang , Monson Russell K. , Zhai Zhiqiang , Anderson Dean E. , Lamb Brian , Allwine Gene , Turnipseed Andrew A. , Burns Sean P.
Published: November 2005

The nocturnal drainage flow of air causes significant uncertainty in ecosystem CO2, H2O, and energy budgets determined with the eddy covariance measurement approach. In this study, we examined the magnitude, nature, and dynamics of the nocturnal drainage flow in a subalpine forest ecosystem with complex terrain. We used an experimental approach involving four towers, each with vertical profiling of wind speed to measure the magnitude of drainage flows and dynamics in their occurrence. We developed an analytical drainage flow model, constrained with measurements of canopy structure and SF6 diffusion, to help us interpret the tower profile results. Model predictions were in good agreement with observed profiles of wind speed, leaf area density, and wind drag coefficient. Using theory, we showed that this one‐dimensional model is reduced to the widely used exponential wind profile model under conditions where vertical leaf area density and drag coefficient are uniformly distributed. We used the model for stability analysis, which predicted the presence of a very stable layer near the height of maximum leaf area density. This stable layer acts as a flow impediment, minimizing vertical dispersion between the subcanopy air space and the atmosphere above the canopy. The prediction is consistent with the results of SF6 diffusion observations that showed minimal vertical dispersion of nighttime, subcanopy drainage flows. The stable within‐canopy air layer coincided with the height of maximum wake‐to‐shear production ratio. We concluded that nighttime drainage flows are restricted to a relatively shallow layer of air beneath the canopy, with little vertical mixing across a relatively long horizontal fetch. Insight into the horizontal and vertical structure of the drainage flow is crucial for understanding the magnitude and dynamics of the mean advective CO2 flux that becomes significant during stable nighttime conditions and are typically missed during measurement of the turbulent CO2 flux. The model and interpretation provided in this study should lead to research strategies for the measurement of these advective fluxes and their inclusion in the overall mass balance for CO2 at this site with complex terrain.
Quasi‐steady centrifuge method for unsaturated hydraulic properties
Authors: Caputo Maria C. , Nimmo John R.
Published: November 2005

We have developed the quasi‐steady centrifuge (QSC) method as a variation of the steady state centrifuge method that can be implemented simply and inexpensively with greater versatility in terms of sample size and other features. It achieves these advantages by somewhat relaxing the criterion for steadiness of flow through the sample. This compromise entails an increase in measurement uncertainty but to a degree that is tolerable in most applications. We have tested this new approach with an easily constructed apparatus to establish a quasi‐steady flow of water in unsaturated porous rock samples spinning in a centrifuge, obtaining measurements of unsaturated hydraulic conductivity and water retention that agree with results of other methods. The QSC method is adaptable to essentially any centrifuge suitable for hydrogeologic applications, over a wide range of sizes and operating speeds. The simplified apparatus and greater adaptability of this method expands the potential for exploring situations that are common in nature but have been the subject of few laboratory investigations.
Investigation hydrologic scaling: Observed effects of heterogeneity and nonlocal processes across hillslope, watershed, and regional scales
Authors: Arrigo J. A. S. , Salvucci G. D.
Published: November 2005

The relationship between soil moisture and outflow is fundamental to land surface water and energy balance monitoring and modeling. However, characterizing it at levels above a point scale is complicated by factors including climate and surface heterogeneity, presence of lateral transports, and mismatches between spatial resolutions of measurements and models. We investigate the distinct roles of heterogeneity and nonlocal interactions in scaling this relationship from points to areas. Locations are modeled as independent columns, using measured soil moisture and precipitation data in a conditional averaging approach to estimate the local moisture outflow relationship. These estimates are aggregated using a distributional approach to account for the effect of heterogeneity. The locations are then treated as one large column; that is, the moisture outflow relationship is estimated directly from spatially aggregated data. We demonstrate that statistically significant differences between the two estimates indicate that the system is not well represented by the independence assumption; that is, local outflow is dependent on local moisture and is also independently influenced by large‐scale moisture. We applied these methods to data from a hillslope, a watershed, and the state of Illinois and found that heterogeneity and nonlocal processes significantly affected scaling in all three. The identified nonlocal effect is to decrease (increase) local outflow during large‐scale dry (wet) anomalies. A possible pathway is through decreased wind speed during dry anomalies. The combined effect increases the sensitivity of outflow to soil moisture as scale increases. These results could have implications for specifying parameters in large‐scale models, especially those calibrated with smaller‐scale field data.
Economies of scale and firm size optimum in rural water supply
Authors: Sauer Johannes
Published: November 2005

This article is focused on modeling and analyzing the cost structure of water‐supplying companies. A cross‐sectional data set was collected with respect to water firms in rural areas of former East and West Germany. The empirical data are analyzed by applying a symmetric generalized McFadden (SGM) functional form. This flexible functional form allows for testing the concavity required by microeconomic theory as well as the global imposition of such curvature restrictions without any loss of flexibility. The original specification of the SGM cost function is modified to incorporate fixed factors of water production and supply as, for example, groundwater intake or the number of connections supplied. The estimated flexible and global curvature correct cost function is then used to derive scale elasticities as well as the optimal firm size. The results show that no water supplier in the sample produces at constant returns to scale. The optimal firm size was found to be on average about three times larger than the existing one. These findings deliver evidence for the hypothesis that the legally set supplying areas, oriented at public administrative criteria as well as local characteristics of water resources, are economically inefficient. Hence structural inefficiency in the rural water sector is confirmed to be policy induced.
An interpolation between the wave and diffusion equations through the fractional evolution equations Dirac like
Authors: Pierantozzi T. , Vázquez L.
Published: November 2005

Through fractional calculus and following the method used by Dirac to obtain his well-known equation from the Klein-Gordon equation, we analyze a possible interpolation between the Dirac and the diffusion equations in one space dimension. We study the transition between the hyperbolic and parabolic behaviors by means of the generalization of the D’Alembert formula for the classical wave equation and the invariance under space and time inversions of the interpolating fractional evolution equations Dirac like. Such invariance depends on the values of the fractional index and is related to the nonlocal property of the time fractional differential operator. For this system of fractional evolution equations, we also find an associated conserved quantity analogous to the Hamiltonian for the classical Dirac case.
Thermal unfolding of proteins
Authors: Cieplak Marek , Sułkowska Joanna I.
Published: November 2005

Thermal unfolding of proteins is compared to folding and mechanical stretching in a simple topology-based dynamical model. We define the unfolding time and demonstrate its low-temperature divergence. Below a characteristic temperature, contacts break at separate time scales and unfolding proceeds approximately in a way reverse to folding. Features in these scenarios agree with experiments and atomic simulations on titin.
Determination of the helicity of oriented photofragments
Authors: Alexander Andrew J.
Published: November 2005

Equations to enable determination of the helicity (angular momentum orientation) of photofragments resulting from single-photon dissociation of an isotropic sample of molecules are presented. The symmetry of the photofragment distribution is illustrated by three-dimensional vector plots of the expectation values of projections of the fragment total angular momentum. Equations describing circular polarization of light in the spherical tensor basis are presented. Methods for the optical measurement of angular momentum orientation are discussed, including determination of the helicity of circularly polarized light by a quarter-wave plate or single Fresnel rhomb.
Adiabatic nanofocusing of plasmons by sharp metallic grooves: Geometrical optics approach
Authors: Gramotnev D. K.
Published: November 2005

In this paper, we demonstrate the possibility of efficient adiabatic nanofocusing of gap plasmons by sharp metallic V grooves or dielectric wedges covered with metal. The geometrical optics approach and the approximation of continuous electrodynamics are used for the analysis. In particular, it is demonstrated that both the phase and group velocities of an incident symmetric (with respect to the magnetic field) plasmon tend to zero at the tip of the groove, and the plasmon adiabatically slows down, eventually dissipating in the metal. The amplitude of the plasmon strongly increases near the tip of the groove. However, unlike nanofocusing by a sharp metal conical tip, even in the absence of dissipation, the amplitude of the plasmon near the tip of a V groove remains finite. The dependence of the maximal local-field enhancement on structural parameters, dissipation in the metal, angle of incidence, etc., is analyzed. It is also shown that a symmetric gap plasmon can effectively be guided by the groove, forming a channel plasmon-polariton—a special plasmon mode propagating along the tip of a metallic V groove. An existence condition for these strongly localized plasmon-polaritons is derived and discussed.
Mechanism of discharge development in SF6 with and without spacers under fast oscillating impulse condition
Authors: Zhang Q. , Jia J. , Yang L. , Tao F. , Qiu Y.
Published: November 2005

This paper describes the mechanism of leader discharge inception in SF6 gas with and without spacers exposed to fast oscillating impulse. A photomultiplier and a current probe are employed for the investigation of discharge development. The results show that the back discharge plays an important role in the initiation and the further development of the leader discharge along the spacer surface in the presence of fast oscillating impulses. In the case of SF6 gap, the steepness of impulse plays a notable role in the extension of the streamer from which the leader discharge is triggered.
Reduction of Curie temperature and saturation magnetization in Ba2−xNaxFeMoO6
Authors: Yoshida Koji , Fujii Yuki , Shimizu Hajime
Published: November 2005

We investigated the role of carrier electrons on ferromagnetism in a half-metallic double perovskite Ba2FeMoO6 by means of a partial substitution of Na+ for Ba2+. Single-phase samples of Ba2−xNaxFeMoO6 are synthesized up to x=0.6. The nonmetallic upturn in resistivity appears with the Na substitution, suggesting a reduction of the carrier doping level. Because of the observed decrease of both magnetoresistance and Curie temperature with x, the Na substitution negatively works for applicative performance. We will show, however, that the observed decrease of the saturation moment with x is of importance to advance understanding for the stabilization of ferromagnetism.
Diffuse mismatch model of thermal boundary conductance using exact phonon dispersion
Authors: Reddy Pramod , Castelino Kenneth , Majumdar Arun
Published: November 2005

The acoustic mismatch model (AMM) and the diffuse mismatch model (DMM) have been traditionally used to calculate the thermal boundary conductance of interfaces. In these calculations, the phonon dispersion relationship is usually approximated by a linear relationship (Debye approximation). This is accurate for wave vectors close to the zone center, but deviates significantly for wave vectors near the zone edges. Here, we present DMM calculations of the thermal conductance of Al–Si, Al–Ge, Cu–Si, and Cu–Ge interfaces by taking into account the full phonon dispersion relationship over the entire Brillouin zone obtained using the Born-von Karman model (BKM). The thermal boundary conductance thus calculated deviates significantly from DMM predictions obtained using the Debye model in all cases.
Nanopores of carbon nanotubes as practical hydrogen storage media
Authors: Han Sang Soo , Kim Hyun Seok , Han Kyu Sung , Lee Jai Young , Lee Hyuck Mo , Kang Jeung Ku , Woo Seong Ihl , van Duin Adri C. T. , Goddard William A.
Published: November 2005

We report on hydrogen desorption mechanisms in the nanopores of multiwalled carbon nanotubes (MWCNTs). The as-grown MWCNTs show continuous walls that do not provide sites for hydrogen storage under ambient conditions. However, after treating the nanotubes with oxygen plasma to create nanopores in the MWCNTs, we observed the appearance of a new hydrogen desorption peak in the 300–350 K range. Furthermore, the calculations of density functional theory and molecular dynamics simulations confirmed that this peak could be attributed to the hydrogen that is physically adsorbed inside nanopores whose diameter is approximately 1 nm. Thus, we demonstrated that 1 nm nanopores in MWCNTs offer a promising route to hydrogen storage media for onboard practical applications.
Contact-controlled sensing properties of flowerlike ZnO nanostructures
Authors: Feng P. , Wan Q. , Wang T. H.
Published: November 2005

Contact-controlled sensing is realized from flowerlike ZnO structures composed of rods. The rods are around 150 nm in diameter and up to a few micrometers in length. When they are exposed to air, a depletion region formed below the surface of the rods arising from the adsorption of oxygen. Surface depletion does not greatly reduce either the carrier density or the mobility in the rods but significantly modify the potential barrier of the contacts between the rods. Both the large diameter and the long length result in a low sensor resistance down to 104kΩ in air at 300 °C. The exponential increase of the tunneling rate with the thickness and height of the contact barrier leads to a high sensitivity up to 14.6 for 100 ppm ethanol. These results indicate that contact-controlled sensing can be used to fabricate high-performance sensors with both high sensitivity and low resistance.
Large photo-induced voltage in a ferroelectric thin film with in-plane polarization
Authors: Yao Kui , Gan Bee Keen , Chen Meima , Shannigrahi Santiranjan
Published: November 2005

A large photoinduced voltage of 7 V was obtained with an in-plane poled ferroelectric thin film having a composition of WO3 modified Pb0.97La0.03(Zr0.52Ti0.48)O3 (PLWZT), under ultraviolet (UV) illumination for about 80 s. By poling the ferroelectric film along the surface plane through pairs of interdigital electrodes, the interelectrode distance constraint on the voltage magnitude arising from the small film thickness was broken. Our experimental results showed that both the direction and magnitude of the photovoltaic output could be tuned with the poling electric field. The dependence of the photoinduced voltage on light wavelength, light intensity, and the gap of the interdigital electrode were investigated. The advantages of the photovoltaic configuration on the basis of an in-plane poled ferroelectric thin film were analyzed.
Seed yields in canola (Brassica napus cv. Karoo) depend on the distance of plants from honeybee apiaries
Authors: Manning Rob , Wallis Ian R.
Published: November 2005

This research examined the benefits of placing hives of honeybees (Apis mellifera L.) in canola (Brassica napus L.) at a density of approximately 1 hive/ha. We tested 3 main hypotheses. First, deploying honeybees increases the yield of seed. Second, that the benefits of honeybee pollination decline the further plants are from an apiary. Third, poorly pollinated plants should channel more resources into larger seeds, whereas plants benefiting from insect pollination should produce more but smaller seeds. The experiment confirmed all 3 hypotheses. Yields of seed increased by more than 20% or by 400 kg/ha, whereas the yield declined in plots located more than 200 m from the apiary. There are several explanations for the increased yield, including an enhanced production of fertile pods and, therefore, more seed, particularly small seed.
An investigation into the effects of closure type, light and pH on the development of shoots and roots and subsequent establishment of micropropagated cauliflower (Brassica oleracea var. botrytis) plants
Authors: Tsipouridis C. , Thomidis T. , Isaakidis A.
Published: November 2005

A cauliflower micropropagation protocol is described with emphasis on the environmental conditions used. The environmental conditions within the culture jars were modified by using 4 different cover methods. The best results were produced in cultures covered with cotton wool, and the worst results with tightly-closed aluminium caps. Light intensity also produced significant differences between cultured transplants. The dry and fresh weights were about 50 and 28% higher, respectively, in cultures grown under light. In contrast, cultures grown under dark had about 20% higher water content. Results also showed the most acidic medium used (pH 4.5) was the best as an initiation medium.
Resistance to Ascochyta rabiei (Pass.) Lab. in a wild Cicer germplasm collection
Authors: Nguyen T. T. , Taylor P. W. J. , Redden R. J. , Ford R.
Published: November 2005

Cultivated chickpea germplasm collections contain a low frequency of ascochyta blight resistant accessions. This might lead to limitations on the future progress of chickpea breeding worldwide. In an effort to identify novel sources of resistance to ascochyta blight, 56 unique accessions, comprising 8 annual wild Cicer species, were evaluated under a controlled environment that was optimal for infection with an aggressive Australian isolate of Ascochyta rabiei (Pass.) Labrousse. The majority of wild Cicer accessions were either susceptible or highly susceptible to A. rabiei 21 days after inoculation; however, 11 accessions, of which 7 were Cicer judaicum, were resistant. The most resistant accession detected in this study, ATC 46934, together with accessions ATC 46892 and ATC 46935, which were resistant in this and another study, should be targeted for use in future interspecific resistance breeding programs.
Zero catch criteria for declaring eradication of tephritid fruit flies: the probabilities
Authors: Meats A. , Clift A. D.
Published: November 2005

We examine procedures for declaring an area free of pest fruit flies following an eradication campaign. To date, the acceptable period of trapping zero flies has been calculated without an estimate of the probability of being wrong. The zero trapping periods are usually shorter when declaring local ‘area freedom’ from an endemic fly, than when claiming eradication of an exotic species. We use a model to calculate the probability of zero trap captures and therefore the probability of trapping further flies. The latter probability is always finite. A zero trapping result does not indicate the absence of flies. There must also be evidence of what constitutes a non-viable density, as indicated by the trapping rate. The non-viable densities of certain pest fruit fly species are known from decades of managing small incursions in fly-free zones. There is no need for implementation of eradication procedures if the trapping rate is sufficiently low, in these areas. For a given density of flies (defined in terms of expected mean catch per trap per week), the probability of zero trap captures reduces with time and the number of traps employed. If the model calculations use a non-sustainable density (inferred from trapping rate) then we may declare the actual density of flies to be less if the trapping result is zero for a given number of weeks with a given number of traps when the model predicts the probability of such a result to be sufficiently low, according to a criterion that is selected at a level suited to the purpose of the declaration.
Introduction of screening guidelines for men who have sex with men at an STD clinic, the Melbourne Sexual Health Centre, Australia
Authors: Lister Nichole A. , Smith Anthony , Fairley Christopher K.
Published: November 2005

Background: A recent audit indicated that a substantial proportion of men who have sex with men (MSM) were not screened for rectal gonorrhoea and chlamydia at the Melbourne Sexual Health Clinic, Melbourne, Australia. In response, screening guidelines for MSM were introduced at the clinic using a computer reminder. The aim of this study was to evaluate the impact of the guidelines and alert on screening MSM for gonorrhoea and chlamydia. Methods: The medical records of MSM were reviewed for gonorrhoea and chlamydia screening by site (pharyngeal, urethral and rectal), four months before the implementation of the guidelines and alert (July to October 2002), and one year thereafter (beginning November 2002). Results: After the introduction of the guidelines there was a significant increase in rectal chlamydia testing (55% to 67%, P < 0.001), and significant reduction in pharyngeal chlamydia and gonorrhoea testing (65% to 28%, P < 0.001, and 83% to 76%, P = 0.015 respectively). The proportion of tests that were positive by any site did not change (7% to 7%). Conclusions: The introduction of a computer reminder for new guidelines was temporally associated with screening that conformed more closely to clinical guidelines.
The stress-regulated protein M6a is a key modulator for neurite outgrowth and filopodium/spine formation
Authors: Alfonso Julieta , Fernández María E. , Cooper Benjamin , Flugge Gabriele , Frasch Alberto C.
Published: November 2005

Neuronal remodeling is a fundamental process by which the brain responds to environmental influences, e.g., during stress. In the hippocampus, chronic stress causes retraction of dendrites in CA3 pyramidal neurons. We have recently identified the glycoprotein M6a as a stress-responsive gene in the hippocampal formation. This gene is down-regulated in the hippocampus of both socially and physically stressed animals, and this effect can be reversed by antidepressant treatment. In the present work, we analyzed the biological function of the M6a protein. Immunohistochemistry showed that the M6a protein is abundant in all hippocampal subregions, and subcellular analysis in primary hippocampal neurons revealed its presence in membrane protrusions (filopodia/spines). Transfection experiments revealed that M6a overexpression induces neurite formation and increases filopodia density in hippocampal neurons. M6a knockdown with small interference RNA methodology showed that M6a low-expressing neurons display decreased filopodia number and a lower density of synaptophysin clusters. Taken together, our findings indicate that M6a plays an important role in neurite/filopodium outgrowth and synapse formation. Therefore, reduced M6a expression might be responsible for the morphological alterations found in the hippocampus of chronically stressed animals. Potential mechanisms that might explain the biological effects of M6a are discussed.
Evolutionary regulation of the blind subterranean mole rat,Spalax, revealed by genome-wide gene expression
Authors: Brodsky L. I. , Jacob-Hirsch J. , Avivi A. , Trakhtenbrot L. , Zeligson S. , Amariglio N. , Paz A. , Korol A. B. , Band M. , Rechavi G. , Nevo E.
Published: November 2005

We applied genome-wide gene expression analysis to the evolutionary processes of adaptive speciation of the Israeli blind subterranean mole rats of theSpalax ehrenbergisuperspecies. The four Israeli allospecies climatically and adaptively radiated into the cooler, mesic northern domain (N) and warmer, xeric southern domain (S). The kidney and brain mRNAs of two N and two S animals were examined through cross-species hybridizations with two types of Affymetrix arrays (mouse and rat) and muscle mRNA of six N and six S animals with spotted cDNA mouse arrays. The initial microarray analysis was hypothesis-free, i.e., conducted without reference to the origin of animals. Principal component analysis revealed that 20-30% of the expression signal variability could be explained by the differentiation of N-S species. Similar N-S effects were obtained for all tissues and types of arrays: two Affymetrix microarrays using probe oligomer signals and the spotted array. Likewise, ANOVA andttest statistics demonstrated significant N-S ecogeographic divergence and region-tissue specificity in gene expression. Analysis of differential gene expression between species corroborates previous results deduced by allozymes and DNA molecular polymorphisms. Functional categories show significant N-S ecologic putative adaptive divergent up-regulation of genes highlighting a higher metabolism in N, and potential adaptive brain activity and kidney urine cycle pathways in S. The present results confirm ecologic-genomic separation of blind mole rats into N and S. Gene expression regulation appears to be central to the evolution of blind mole rats.
Hypoxia inducible factor 1α regulates T cell receptor signal transduction
Authors: Neumann Aaron K. , Yang Jaeseok , Biju Mangat P. , Joseph Suresh K. , Johnson Randall S. , Haase Volker H. , Freedman Bruce D. , Turka Laurence A.
Published: November 2005

Low oxygen pressures exist in many solid tissues, including primary and secondary lymphoid organs. One key element in cellular adaptation to hypoxia is induced expression of hypoxia inducible factor (Hif) 1α. Here, we have examined the effect of Hif-1α, isolated from the myriad other effects of hypoxia, on T cell receptor (TCR) signaling in thymocytes. Because pVHL (von Hippel–Lindau protein) directs the proteolysis of Hif-1α under “normoxic” conditions, we achieved constitutive stabilization of Hif-1α through thymic deletion of
Vhlh
and reversed Hif-1α stabilization with double deletion of
Vhlh
and
Hif-1
α. We found that constitutive activity of Hif-1α resulted in diminished Ca
2+
response upon TCR crosslinking despite equivalent activation of phospholipase C
γ1
, normal intracellular Ca
2+
stores, and normal entry of Ca
2+
across the plasma membrane. Altered Ca
2+
response was instead due to accelerated removal of Ca
2+
from the cytoplasm into intracellular compartments, which occurred in association with Hif-1α-dependent overexpression of the calcium pump SERCA2 (sarcoplasmic/endoplasmic reticulum calcium ATPase 2). These data suggest a unique mechanism for control of TCR signaling through Hif-1α, which may be operative at the physiologic oxygen tensions seen in solid lymphoid organs.
The asialoglycoprotein receptor clears glycoconjugates terminating with sialic acidα2,6GalNAc
Authors: Park Eric I. , Mi Yiling , Unverzagt Carlo , Gabius Hans-Joachim , Baenziger Jacques U.
Published: November 2005

Endogenous ligands have not, to date, been identified for the asialoglycoprotein receptor (ASGP-R), which is abundantly expressed by parenchymal cells in the liver of mammals. On the basis of the rapid clearance of BSA bearing multiple chemically coupled sialic acid (Sia)α2,6GalNAcβ1,4GlcNAcβ1,2Man tetrasaccharides (SiaGGnM-BSA) from the circulation, and the ability of the ASGP-R hepatic lectin-1 subunit to bind SiaGGnM-BSA, we previously proposed that glycoproteins modified with structures terminating with Siaα2,6GalNAc may represent previously unrecognized examples of endogenous ligands for this receptor. Here, we have taken a genetic approach using wild-type and ASGP-R-deficient mice to determine that the ASGP-R
in vivo
does indeed account for the rapid clearance of glycoconjugates terminating with Siaα2,6GalNAc. We have also determined that the ASGP-R is able to bind core-substituted oligosaccharides with the terminal sequence Siaα2,6Galβ1,4GlcNAc but not those with the terminal Siaα2,3Galβ1,4GlcNAc. We propose that glycoproteins bearing terminals Siaα2,6GalNAc and Siaα2,6Gal are endogenous ligands for the ASGP-R, and that the ASGP-R helps to regulate the relative concentration of serum glycoproteins bearing α2,6-linked Sia.
An interpretation of size-scale plasticity in geometrically confined systems
Authors: Espinosa H. D. , Berbenni S. , Panico M. , Schwarz K. W.
Published: November 2005

The mesoscopic constitutive behavior of face-centered cubic metals as a function of the system characteristic dimension recently has been investigated experimentally. Strong size effects have been identified in both polycrystalline submicron thin films and single crystal micro pillars. The size effect is manifested as an increase in strength and hardening rate as the system dimensions are decreased. In this article, we provide a mechanistic interpretation for the observed mesoscopic behavior. By performing 3D discrete dislocation dynamics simulations of grains representative of the system microstructure and associated characteristic dimensions, we show that the experimentally observed size effects can be qualitatively described. In these simulations, a constant density of dislocation sources per unit of grain boundary area is modeled by sources randomly distributed at grain boundaries. The source length (strength) is modeled by a Gaussian distribution, in which average and standard deviation is independent of the system characteristic dimension. The simulations reveal that two key concepts are at the root of the observed plasticity size effect. First, the onset of plasticity is governed by a dislocation nucleation-controlled process (sources of various length, i.e., strengths, in our model). Second, the hardening rate is controlled by source exhaustion, i.e., sources are active only once as a result of the limited dislocation mobility arising from size and boundary effects. The model postulated here improves our understanding of why “smaller is stronger” and provides predictive capabilities that should enhance the reliable design of devices in applications such as microelectronics and micro/nano-electro-mechanical systems.
T-bet-dependent expression of osteopontin contributes to T cell polarization
Authors: Shinohara Mari L. , Jansson Marianne , Hwang Eun Sook , Werneck Miriam B. F. , Glimcher Laurie H. , Cantor Harvey
Published: November 2005

The osteopontin (Opn) glycoprotein has been implicated in diverse physiological processes, including vascularization, bone formation, and inflammatory responses. Studies of its role in immune responses has suggested that Opn can set the early stage of type-1 immune (cell-mediated) responses through differential regulation of IL-12 and IL-10 cytokine gene expression in macrophages. Although Opn has been suggested to play a role in the development of type-1 immunity, little is known about control of
Opn
gene expression. Here, we report that
Opn
gene expression in activated T cells, but not macrophages, is regulated by T-bet, a transcription factor that controls CD4
+
T helper (Th1) cell lineage commitment. We also find that T-bet-dependent expression of Opn in T cells is essential for efficient skewing of CD4
+
T and CD8
+
T cells toward the Th1 and type 1 CD8
+
T cells (Tc1) pathway, respectively. Taken together, these findings begin to delineate the genetic basis of Opn expression in T cells and further clarify the role of Opn in Th and Tc1 development.
Cell-free cloning using φ29 DNA polymerase
Authors: Hutchison Clyde A. , Smith Hamilton O. , Pfannkoch Cynthia , Venter J. Craig
Published: November 2005

We describe conditions for rolling-circle amplification (RCA) of individual DNA molecules 5–7 kb in size by >10
9
-fold, using φ29 DNA polymerase. The principal difficulty with amplification of small amounts of template by RCA using φ29 DNA polymerase is “background” DNA synthesis that usually occurs when template is omitted, or at low template concentrations. Reducing the reaction volume while keeping the amount of template fixed increases the template concentration, resulting in a suppression of background synthesis. Cell-free cloning of single circular molecules by using φ29 DNA polymerase was achieved by carrying out the amplification reactions in very small volumes, typically 600 nl. This procedure allows cell-free cloning of individual synthetic DNA molecules that cannot be cloned in
Escherichia coli
, for example synthetic phage genomes carrying lethal mutations. It also allows cell-free cloning of genomic DNA isolated from bacteria. This DNA can be sequenced directly from the φ29 DNA polymerase reaction without further amplification. In contrast to PCR amplification, RCA using φ29 DNA polymerase does not produce mutant jackpots, and the high processivity of the enzyme eliminates stuttering at homopolymer tracts. Cell-free cloning has many potential applications to both natural and synthetic DNA. These include environmental DNA samples that have proven difficult to clone and synthetic genes encoding toxic products. The method may also speed genome sequencing by eliminating the need for biological cloning.
Growth factor–induced shedding of syndecan-1 confers glypican-1 dependence on mitogenic responses of cancer cells
Authors: Ding Kan , Lopez-Burks Martha , Sánchez-Duran José Antonio , Korc Murray , Lander Arthur D.
Published: November 2005

The cell surface heparan sulfate proteoglycan (HSPG) glypican-1 is up-regulated by pancreatic and breast cancer cells, and its removal renders such cells insensitive to many growth factors. We sought to explain why the cell surface HSPG syndecan-1, which is also up-regulated by these cells and is a known growth factor coreceptor, does not compensate for glypican-1 loss. We show that the initial responses of these cells to the growth factor FGF2 are not glypican dependent, but they become so over time as FGF2 induces shedding of syndecan-1. Manipulations that retain syndecan-1 on the cell surface make long-term FGF2 responses glypican independent, whereas those that trigger syndecan-1 shedding make initial FGF2 responses glypican dependent. We further show that syndecan-1 shedding is mediated by matrix metalloproteinase-7 (MMP7), which, being anchored to cells by HSPGs, also causes its own release in a complex with syndecan-1 ectodomains. These results support a specific role for shed syndecan-1 or MMP7–syndecan-1 complexes in tumor progression and add to accumulating evidence that syndecans and glypicans have nonequivalent functions in vivo.
Sequential development of interleukin 2–dependent effector and regulatory T cells in response to endogenous systemic antigen
Authors: Knoechel Birgit , Lohr Jens , Kahn Estelle , Bluestone Jeffrey A. , Abbas Abul K.
Published: November 2005

Transfer of naive antigen-specific CD4+ T cells into lymphopenic mice that express an endogenous antigen as a systemic, secreted protein results in severe autoimmunity resembling graft-versus-host disease. T cells that respond to this endogenous antigen develop into effector cells that cause the disease. Recovery from this disease is associated with the subsequent generation of FoxP3+CD25+ regulatory cells in the periphery. Both pathogenic effector cells and protective regulatory cells develop from the same antigen-specific T cell population after activation, and their generation may occur in parallel or sequentially. Interleukin (IL)-2 plays a dual role in this systemic T cell reaction. In the absence of IL-2, the acute disease is mild because of reduced T cell effector function, but a chronic and progressive disease develops late and is associated with a failure to generate FoxP3+ regulatory T (T reg) cells in the periphery. Thus, a peripheral T cell reaction to a systemic antigen goes through a phase of effector cell–mediated pathology followed by T reg cell–mediated recovery, and both require the growth factor IL-2.
Avidity for antigen shapes clonal dominance in CD8+ T cell populations specific for persistent DNA viruses
Authors: Price David A. , Brenchley Jason M. , Ruff Laura E. , Betts Michael R. , Hill Brenna J. , Roederer Mario , Koup Richard A. , Migueles Steven A. , Gostick Emma , Wooldridge Linda , Sewell Andrew K. , Connors Mark , Douek Daniel C.
Published: November 2005

The forces that govern clonal selection during the genesis and maintenance of specific T cell responses are complex, but amenable to decryption by interrogation of constituent clonotypes within the antigen-experienced T cell pools. Here, we used point-mutated peptide–major histocompatibility complex class I (pMHCI) antigens, unbiased TCRB gene usage analysis, and polychromatic flow cytometry to probe directly ex vivo the clonal architecture of antigen-specific CD8+ T cell populations under conditions of persistent exposure to structurally stable virus-derived epitopes. During chronic infection with cytomegalovirus and Epstein-Barr virus, CD8+ T cell responses to immunodominant viral antigens were oligoclonal, highly skewed, and exhibited diverse clonotypic configurations; TCRB CDR3 sequence analysis indicated positive selection at the protein level. Dominant clonotypes demonstrated high intrinsic antigen avidity, defined strictly as a physical parameter, and were preferentially driven toward terminal differentiation in phenotypically heterogeneous populations. In contrast, subdominant clonotypes were characterized by lower intrinsic avidities and proportionately greater dependency on the pMHCI–CD8 interaction for antigen uptake and functional sensitivity. These findings provide evidence that interclonal competition for antigen operates in human T cell populations, while preferential CD8 coreceptor compensation mitigates this process to maintain clonotypic diversity. Vaccine strategies that reconstruct these biological processes could generate T cell populations that mediate optimal delivery of antiviral effector function.
‘Protein Peeling’: an approach for splitting a 3D protein structure into compact fragments
Authors: Gelly Jean-Christophe , de Brevern Alexandre G. , Hazout Serge
Published: November 2005

Motivation: The object of this study is to propose a new method to identify small compact units that compose protein three-dimensional structures. These fragments, called ‘protein units (PU)’, are a new level of description to well understand and analyze the organization of protein structures. The method only works from the contact probability matrix, i.e. the inter Cα-distances translated into probabilities. It uses the principle of conventional hierarchical clustering, leading to a series of nested partitions of the 3D structure. Every step aims at dividing optimally a unit into 2 or 3 subunits according to a criterion called ‘partition index’ assessing the structural independence of the subunits newly defined. Moreover, an entropy-derived squared correlation R is used for assessing globally the protein structure dissection. The method is compared to other splitting algorithms and shows relevant performance.

Availability: An Internet server with dedicated tools is available at

Contact:  debrevern@ebgm.jussieu.fr.
HTP-1-dependent constraints coordinate homolog pairing and synapsis and promote chiasma formation during C. elegans meiosis
Authors: Martinez-Perez Enrique , Villeneuve Anne M.
Published: November 2005

Synaptonemal complex (SC) assembly must occur between correctly paired homologous chromosomes to promote formation of chiasmata. Here, we identify the Caenorhabditis elegans HORMA-domain protein HTP-1 as a key player in coordinating establishment of homolog pairing and synapsis in C. elegans and provide evidence that checkpoint-like mechanisms couple these early meiotic prophase events. htp-1 mutants are defective in the establishment of pairing, but in contrast with the pairing-defective chk-2 mutant, SC assembly is not inhibited and generalized nonhomologous synapsis occurs. Extensive nonhomologous synapsis in htp-1; chk-2 double mutants indicates that HTP-1 is required for the inhibition of SC assembly observed in chk-2 gonads. htp-1 mutants show a decreased abundance of nuclei exhibiting a polarized organization that normally accompanies establishment of pairing; analysis of htp-1; syp-2 double mutants suggests that HTP-1 is needed to prevent premature exit from this polarized nuclear organization and that this exit stops homology search. Further, based on experiments monitoring the formation of recombination intermediates and crossover products, we suggest that htp-1 mutants are defective in preventing the use of sister chromatids as recombination partners. We propose a model in which HTP-1 functions to establish or maintain multiple constraints that operate to ensure coordination of events leading to chiasma formation.
The role of cuticular pheromones in courtship conditioning of
Drosophila males
Authors: Siwicki Kathleen K. , Riccio Paul , Ladewski Lisa , Marcillac Fabrice , Dartevelle Laurence , Cross Stephanie A. , Ferveur Jean-François
Published: November 2005

Courtship conditioning is an associative learning paradigm in
Drosophila melanogaster, wherein male courtship behavior is modified
by experience with unreceptive, previously mated females. While the training
experience with mated females involves multiple sensory and behavioral
interactions, we hypothesized that female cuticular hydrocarbons function as a
specific chemosensory conditioned stimulus in this learning paradigm. The
effects of training with mated females were determined in courtship tests with
either wild-type virgin females as courtship targets, or with target flies of
different genotypes that express distinct cuticular hydrocarbon (CH) profiles.
Results of tests with female targets that lacked the normal CH profile, and
with male targets that expressed typically female CH profiles, indicated that
components of this CH profile are both necessary and sufficient cues to elicit
the effects of conditioning. Results with additional targets indicated that
the female-specific 7,11-dienes, which induce naive males to court, are not
essential components of the conditioned stimulus. Rather, the learned response
was significantly correlated with the levels of 9-pentacosene (9-P), a
compound found in both males and females of many Drosophila strains
and species. Adding 9-P to target flies showed that it stimulates courting
males to attempt to copulate, and confirmed its role as a component of the
conditioned stimulus by demonstrating dose-dependent increases in the
expression of the learned response. Thus, 9-P can contribute significantly to
the conditioned suppression of male courtship toward targets that express this
pheromone.
Insulin receptor signaling in long-term memory consolidation following spatial learning
Authors: Dou Jing-Tao , Chen Min , Dufour Franck , Alkon Daniel L. , Zhao Wei-Qin
Published: November 2005

Evidence has shown that the insulin and insulin receptor (IR) play a role
in cognitive function. However, the detailed mechanisms underlying insulin's
action on learning and memory are not yet understood. Here we investigated
changes in long-term memory-associated expression of the IR and downstream
molecules in the rat hippocampus. After long-term memory consolidation
following a water maze learning experience, gene expression of IR showed an
up-regulation in the CA1, but a down-regulation in the CA3 region. These were
correlated with a significant reduction in hippocampal IR protein levels.
Learning-specific increases in levels of downstream molecules such as IRS-1
and Akt were detected in the synaptic membrane accompanied by decreases in Akt
phosphorylation. Translocation of Shc protein to the synaptic membrane and
activation of Erk1/2 were also observed after long-term memory formation.
Despite the clear memory-correlated alterations in IR signaling pathways,
insulin deficits in experimental diabetes mellitus (DM) rats induced by
intraperitoneal injections of streptozotocin resulted in only minor memory
impairments. This may be due to higher glucose levels in the DM brain, and to
compensatory mechanisms from other signaling pathways such as the insulin-like
growth factor-1 receptor (IGF-1R) system. Our results suggest that insulin/IR
signaling plays a modulatory role in learning and memory processing, which may
be compensated for by alternative pathways in the brain when an insulin
deficit occurs.