bluuebunny/crossref_metadata_2025 huggingface dataset:
A global assessment of deep-sea basalt sites for carbon sequestration
Authors: Goldberg David , Slagle Angela
Published: December 2008

In recent years, the debate over the most effective means to stabilize greenhouse gas concentrations in the atmosphere has endorsed multiple approaches and a variety of technologies. Assuring secure storage of anthropogenic carbon dioxide is one of our most pressing global scientific challenges that may contribute to achieving a stable solution over the next several decades. Geological sequestration by injection into deep-sea basalt formations provides unique and significant advantages over other potential storage options, including: (a) vast reservoir capacities with high porosity and permeability, sufficient to accommodate centuries-long U.S. production of fossil fuel CO~2~ at locations within a few hundreds of kilometers of populated areas; (b) chemical reactivity of CO~2~ with basalt and in situ fluids to produce stable, non-toxic carbonates; and (c) significant risk reduction for post-injection leakage by geological, gravitational, and mineral trapping mechanisms. We compare independent trapping mechanisms available in deep-sea basalts to those in saline aquifers, which have also been proposed as potential storage environments for anthropogenic carbon dioxide. We suggest that deep-sea basalts offer significant advantages over saline aquifers, in terms of reduced risk of post-injection leakage and storage capacity. Using a global site assessment strategy to highlight the most secure oceanic basalt sites that provide all trapping mechanisms, we initially identify potential target regions that occur in deep-sea basalt and calculate the potential injection volume for each. The largest volumes and most secure basalt sites occur in regions adjacent to intermediate- to fast-spreading seismic ridges as well as deep aseismic ridges. We then use site-specific criteria, such as abundance of ODP and IODP drill sites with basement penetration, permeability and/or porosity data, to refine volume calculations and to prioritize these target regions as promising locations to securely accommodate carbon dioxide injection. Pilot injection studies in deep-sea basalts are necessary to establish the viability of these reservoirs for future CO~2~ sequestration. We suggest that basaltic crust at deep ocean sites offers vast capacity and potential for permanent sequestration of carbon dioxide to mitigate atmospheric build-up of this greenhouse gas.
Membrane remodelling during vaccinia virus morphogenesis
Authors: Chichón Francisco Javier , Rodríguez María Josefa , Risco Cristina , Fraile‐Ramos Alberto , Fernández José Jesús , Esteban Mariano , Carrascosa José L.
Published: December 2008

Background information. VACV (vaccinia virus) is one of the most complex viruses, with a size exceeding 300 nm and more than 100 structural proteins. Its assembly involves sequential interactions and important rearrangements of its structural components.

Results. We have used electron tomography of sections of VACV‐infected cells to follow, in three dimensions, the remodelling of the membrane components of the virus during envelope maturation. The tomograms obtained suggest that a number of independent ‘crescents’ interact with each other to enclose the volume of an incomplete ellipsoid in the viral factory area, attaining the overall shape and size characteristic of the first immature form of the virus [IV (immature virus)]. The incorporation of the DNA into these forms leads to particles with a nucleoid [IVN (IV with nucleoid)] that results in local disorganization of the envelope in regions near the condensed DNA. These particles suffer the progressive disappearance of the membrane outer spikes with a change in the shape of the membrane, becoming locally curled. The transformation of the IVN into the mature virus involves an extreme rearrangement of the particle envelope, which becomes fragmented and undulated. During this process, we also observed connections between the outer membranes with internal ones, suggesting that the latter originate from internalization of the IV envelope.

Conclusions. The main features observed for VACV membrane maturation during morphogenesis resemble the breakdown and reassembly of cellular endomembranes.
TGF-β regulates the expression of transcription factor KLF6 and its splice variants and promotes co-operative transactivation of common target genes through a Smad3–Sp1–KLF6 interaction
Authors: Botella Luisa M. , Sanz-Rodriguez Francisco , Komi Yusuke , Fernandez-L Africa , Varela Elisa , Garrido-Martin Eva M. , Narla Goutham , Friedman Scott L. , Kojima Soichi
Published: December 2008

KLF6 (Krüppel-like factor 6) is a transcription factor and tumour suppressor with a growing range of biological activities and transcriptional targets. Among these, KLF6 suppresses growth through transactivation of TGF-β1 (transforming growth factor-β1). KLF6 can be alternatively spliced, generating lower-molecular-mass isoforms that antagonize the full-length WT (wild-type) protein and promote growth. A key target gene of full-length KLF6 is endoglin, which is induced in vascular injury. Endoglin, a homodimeric cell membrane glycoprotein and TGF-β auxiliary receptor, has a pro-angiogenic role in endothelial cells and is also involved in malignant progression. The aim of the present work was to explore the effect of TGF-β on KLF6 expression and splicing, and to define the contribution of TGF-β on promoters regulated by co-operation between KLF6 and Sp1 (specificity protein 1). Using co-transfection, co-immunoprecipitation and fluorescence resonance energy transfer, our data demonstrate that KLF6 co-operates with Sp1 in transcriptionally regulating KLF6-responsive genes and that this co-operation is further enhanced by TGF-β1 through at least two mechanisms. First, in specific cell types, TGF-β1 may decrease KLF6 alternative splicing, resulting in a net increase in full-length, growth-suppressive KLF6 activity. Secondly, KLF6–Sp1 co-operation is further enhanced by the TGF-β–Smad (similar to mothers against decapentaplegic) pathway via the likely formation of a tripartite KLF6–Sp1–Smad3 complex in which KLF6 interacts indirectly with Smad3 through Sp1, which may serve as a bridging molecule to co-ordinate this interaction. These findings unveil a finely tuned network of interactions between KLF6, Sp1 and TGF-β to regulate target genes.
QT interval prolongation and decreased heart rate variability in cirrhotic patients: relevance of hepatic venous pressure gradient and serum calcium
Authors: Genovesi Simonetta , Prata Pizzala Daniela M. , Pozzi Massimo , Ratti Laura , Milanese Maria , Pieruzzi Federico , Vincenti Antonio , Stella Andrea , Mancia Giuseppe , Stramba-Badiale Marco
Published: December 2008

A prolongation of QT interval has been shown in patients with cirrhosis and it is considered as part of the definition of the so-called ‘cirrhotic cardiomyopathy’. The aim of the present study was to assess the determinants of QT interval prolongation in cirrhotic patients. Forty-eight male patients with different stages of liver disease were divided into three subgroups according to the Child–Pugh classification. All patients underwent a 24-h ECG Holter recording. The 24-h mean of QT intervals corrected for heart rate (termed QTc) and the slope of the regression line QT/RR were calculated. HRV (heart rate variability), plasma calcium and potassium concentration and HVPG (hepatic venous pressure gradient) were measured. QTc was progressively prolonged from Child A to Child C patients (P=0.001). A significant correlation between QTc and HVPG was found (P=0.003). Patients with alcohol-related cirrhosis presented QTc prolongation more frequently than patients with post-viral cirrhosis (P<0.001). The QT/RR slope was steeper in subjects with alcoholic aetiology as compared with viral aetiology (P=0.02), suggesting that these patients have a further QTc prolongation when heart rate decreases. The plasma calcium concentration was inversely correlated with QTc (P<0.001). The presence of severe portal hypertension was associated with decreased HRV (P<0.001). Cirrhotic patients with a more severe disease, especially of alcoholic aetiology, who have greater HVPG and lower calcium plasma levels, have an altered ventricular repolarization and a reduced vagal activity to the heart, which may predispose to life-threatening arrhythmias.
Interval exercise is a path to good health, but how much, how often and for whom?
Authors: MacDonald Maureen J. , Currie Katharine D.
Published: December 2008

Interval exercise training has now been examined in a wide variety of individuals, ranging from elite athletes to patients with severe cardiovascular disease. The advantages of interval exercise training programmes in comparison with constant intensity exercise programmes are that they appear to deliver superior improvements in several cardiovascular risk factors, fitness and performance. Depending on the design, some interval exercise programmes result in a range of benefits, even though the time commitment may be dramatically less than more traditional continuous intensity programmes. In the present issue of Clinical Science, a study by Tjønna and co-workers demonstrates that aerobic interval training may also be a powerful tool in combating the increased cardiovascular risk observed in overweight adolescents.
Ab initio characterization of the conical intersections involved in the photochemistry of phenol
Authors: Vieuxmaire Olivier P. J. , Lan Zhenggang , Sobolewski Andrzej L. , Domcke Wolfgang
Published: December 2008

The nature of the vibronic interactions between the π1π∗ (A′), the π1σ∗ (A″), and the S0 (A′) states at the CIππ∗/πσ∗ and CIπσ∗/ππ conical intersections has been investigated by accurate ab initio calculations. Potential energy surfaces have been constructed at the complete-active-space self-consistent-field and multireference configuration-interaction (MRCI) levels of theory along each of the ten normal coordinates of A″ symmetry that potentially can be coupling modes at these conical intersections. The OH torsion was found to be by far the strongest coupling mode in each case. As for benzene, a “channel three” radiationless decay mechanism associated with a prefulvenic conical intersection, CIpref, was found to exist in phenol. The reaction path connecting the prefulvenic form of phenol with the minimum-energy structure of the S1 state was computed at different levels of theory. The barrier to be overcome for the opening of the prefulvenic decay channel is estimated as 6370 cm−1 at the MRCI level, that is, about 2300 cm−1 above the energy of CIππ∗/πσ∗. With sufficient excess energy in the S1 state, the prefulvenic decay mechanism can be in competition with the hydrogen detachment process.
Numerical experiments on the drift wave–zonal flow paradigm for nonlinear saturation
Authors: Waltz R. E. , Holland C.
Published: December 2008

This paper confirms that E×B shearing from toroidally symmetric (toroidal mode number n=0) “radial modes” provides the dominant nonlinear saturation mechanism for drift wave (n≠0) turbulence, which in turn nonlinearly drives the modes. In common usage, this is loosely referred to as the “drift wave–zonal flow paradigm” for nonlinear saturation despite the fact that radial modes have several components distinguished in this paper: a residual or zero mean frequency “zonal flow” part and an oscillatory “geodesic acoustic mode” (GAM) part. Linearly, the zonal flows (and GAMs) are weakly damped only by ion-ion collisions, while the GAMs are strongly Landau damped only at low safety factor q. At high q the Hinton–Rosenbluth residual flow from an impulse vanishes and only the weakly damped GAMs remain. With the linear physics and driving rates of the finite-n transport modes unchanged, this paper argues that GAMs are only somewhat less effective than the residual zonal flows in providing the nonlinear saturation, and in some cases E×B shearing from GAMs (or at least the GAM physics) appears to dominate: transport appears to be nearly linear in the GAM frequency. By deleting the drift wave–drift wave nonlinear coupling, it is found that drift wave–radial mode nonlinear coupling triads account for most of the nonlinear saturation. Furthermore, the E×B shear components of the radial modes nonlinearly stabilize the finite-n modes, while the diamagnetic components nonlinearly destabilize them. Finally, from wave number spectral contour plots of the time average nonlinear entropy transfer function (and rates), it is shown that the peak in entropy generation coincides with the peak in transport production, while entropy dissipation (like Landau damping) is spread equally over all n modes (including n=0). Most of these conclusions appear to hold about equally well for all types of drift wave turbulence.
Formation of even-numbered hydrogen cluster cations in ultracold helium droplets
Authors: Jaksch S. , Mauracher A. , Bacher A. , Denifl S. , Ferreira da Silva F. , Schöbel H. , Echt O. , Märk T. D. , Probst M. , Bohme D. K. , Scheier P.
Published: December 2008

Neutral hydrogen clusters are grown in ultracold helium nanodroplets by successive pickup of hydrogen molecules. Even-numbered hydrogen cluster cations are observed upon electron-impact ionization with and without attached helium atoms and in addition to the familiar odd-numbered Hn+. The helium matrix affects the fragmentation dynamics that usually lead to the formation of overwhelmingly odd-numbered Hn+. The use of high-resolution mass spectrometry allows the unambiguous identification of even-numbered Hn+ up to n≅120 by their mass excess that distinguishes them from Hen+, mixed HemHn+, and background ions. The large range in size of these hydrogen cluster ions is unprecedented, as is the accuracy of their definition. Apart from the previously observed magic number n=6, pronounced drops in the abundance of even-numbered cluster ions are seen at n=30 and 114, which suggest icosahedral shell closures at H6+(H2)12 and H6+(H2)54. Possible isomers of H6+ are identified at the quadratic configuration interaction with inclusion of single and double excitations (QCISD)/aug-cc-pVTZ level of theory
Acceleration insensitive encapsulated silicon microresonator
Authors: Jha C. M. , Salvia J. , Chandorkar S. A. , Melamud R. , Kuhl E. , Kenny T. W.
Published: December 2008

This paper presents the acceleration sensitivity and the resulting vibration-induced phase noise of an electrostatically coupled encapsulated silicon microresonator. External vibrations can produce phase noise in microresonators by generating time-varying stress in the resonant beams. A spring mounted resonator design that reduces the induced axial stress is presented here. Measurements and simulations show that the acceleration sensitivity and the vibration-induced phase noise of this device can be reduced 1000 times smaller than that of the previously published silicon microresonator and 10 times smaller than the commercially used high end SC (stress compensated)-cut quartz resonator.
Limitations of a simplified dangling bond recombination model for a-Si:H
Authors: Li Tsu-Tsung Andrew , McIntosh Keith R. , Cuevas Andres
Published: December 2008

The validity of a widely used simple closed-form expression for the recombination associated with dangling bonds in hydrogenated amorphous silicon (a-Si:H) is linked to the relative position of the distribution of the dangling bond states with respect to the quasi-Fermi levels for trapped electrons and holes. However, these quasi-Fermi levels for traps have not been derived before. In this work, we derive the four relevant quasi-Fermi levels for traps associated with dangling bonds in a-Si:H and clarify the limitations of the simple model.
Directing the transportation of a water droplet on a patterned superhydrophobic surface
Authors: Xu Qian Feng , Wang Jian Nong , Smith Ian H. , Sanderson Kevin D.
Published: December 2008

Directional transportation of a ball-like water droplet on a superhydrophobic (SH) surface has been experimentally demonstrated. A SH surface with a water contact angle of as high as 160° and a sliding angle close to 0° is prepared by a sol-gel method based on removable polymeric nanospheres. A designed path line is then created on the prepared SH surface. The contact angle possesses anisotropy on the patterned SH surface. When the tilted angle of the patterned SH surface and the volume of the water droplet are proper, the sliding of a ball-like water droplet follows the designed line precisely.
Fiske steps and hysteresis in YBa2Cu3O7 grain boundary Josephson junctions: Structural information of the barrier by means of a nondestructive approach
Authors: Navacerrada M. A. , Lucía M. L. , Sánchez-Quesada F. , Sarnelli E.
Published: December 2008

A deep analysis of the current-voltage (I-V) characteristics of YBa2Cu3O7 grain boundary Josephson junctions (GBJJs) allows us to go much farther than the usual calculus of the transport parameters. It is possible to construct a structural image of the barrier by an exhaustive and complementary analysis of both transport and electromagnetic parameters obtained from I-V curves. For such an approach, we have chosen the following three representative bicrystalline geometries: 24° [001] asymmetric, 45° [100] asymmetric, and 24° [001] symmetric +45° [100] asymmetric. The dependence of the product ICRN on the junction normal resistance is of the ICRN−1 type pointing to a SNINS model (S denotes superconductor, I denotes insulator, and N denotes normal metal) for all our GBJJs. A satisfactory explanation of the discrepancy of the capacitance of the barrier estimated from Fiske resonance positions and hysteresis in the I-V curves needs of such a model. Moreover an estimation of the length of the normal regions adjacent to the crystallographic barrier can be made. This comparative analysis is presented in order to extract interesting information about the particular transport mechanisms involved in these GBJJs.
The accelerated formation of MgB2 phase with high critical current density by Cu and SiC multidoping during the low-temperature sintering process
Authors: Ma Zongqing , Liu Yongchang , Yu Liming , Zhao Qian
Published: December 2008

Combined with the thermal analysis and phase identification, it is found that during the low-temperature sintering process of the SiC-doped MgB2 samples, the Cu addition can improve both the reaction between Mg and B and the reaction between Mg and SiC and thus accelerate the formation of the MgB2 phase with effective C substitution for B. Accordingly, we successfully synthesize MgB2 bulks with excellent critical current density (Jc) by proper amount of Cu and SiC multidoping sintered at 575 °C for only 5 h.
Semicircular bend testing with split Hopkinson pressure bar for measuring dynamic tensile strength of brittle solids
Authors: Dai F. , Xia K. , Luo S. N.
Published: December 2008

We propose and validate an indirect tensile testing method to measure the dynamic tensile strength of rocks and other brittle solids: semicircular bend (SCB) testing with a modified split Hopkinson pressure bar (SHPB) system. A strain gauge is mounted near the failure spot on the specimen to determine the rupture time. The momentum trap technique is utilized to ensure single pulse loading for postmortem examination. Tests without and with pulse shaping are conducted on rock specimens. The evolution of tensile stress at the failure spot is determined via dynamic and quasistatic finite element analyses with the dynamic loads measured from SHPB as inputs. Given properly shaped incident pulse, far-field dynamic force balance is achieved and the peak of the loading matches in time with the rupture onset of the specimen. In addition, the dynamic tensile stress history at the failure spot obtained from the full dynamic finite element analysis agrees with the quasistatic analysis. The opposite occurs for the test without pulse shaping. These results demonstrate that when the far-field dynamic force balance is satisfied, the inertial effects associated with stress wave loading are minimized and thus one can apply the simple quasistatic analysis to obtain the tensile strength in the SCB-SHPB testing. This method provides a useful and cost effective way to measure indirectly the dynamic tensile strength of rocks and other brittle materials.
An in situ electrical study on primary hydrogen spillover from nanocatalysts to amorphous carbon support
Authors: Lin Chikai , Yang Zhenzhen , Xu Tao , Zhao Yufeng
Published: December 2008

Primary hydrogen spillover has been studied using a unique electrical method. We observed that at ambient temperature, when a discontinuous nanogranular Pd film is on the top of an amorphous carbon film, the electrical conductance of the carbon film decreases in pressurized hydrogen. In comparison, in the absence of this Pd layer, the conductance of the carbon film remains unchanged in pressurized hydrogen. The observed decrease in the current in the Pd/carbon structure is ascribed to the hydrogenation of the dangling carbon bonds and sp2-sp3 transition in the amorphous carbon by the primary spillover hydrogen atoms from Pd nanoclusters.
Terahertz electromagnetic interference shielding using single-walled carbon nanotube flexible films
Authors: Seo M. A. , Yim J. H. , Ahn Y. H. , Rotermund F. , Kim D. S. , Lee S. , Lim H.
Published: December 2008

We performed time-domain terahertz spectroscopy on thin layers of single-walled carbon nanotubes (SWCNTs) coated on flexible films. The SWCNT layers demonstrate good shielding of electromagnetic waves in the terahertz range while maintaining good transparency for visible light. The shielding efficiency can be engineered through the thickness control and/or chemical treatment of SWCNT layers. The frequency-dependent dielectric constants of SWCNT layers are in good agreement with the Drude free-electron model.
Directional light extraction from thin-film resonant cavity light-emitting diodes with a photonic crystal
Authors: Bergenek K. , Wiesmann Ch. , Zull H. , Wirth R. , Sundgren P. , Linder N. , Streubel K. , Krauss T. F.
Published: December 2008

We report directional light extraction from AlGaInP thin-film resonant cavity light emitting diodes (RCLEDs) with shallow photonic crystals (PhCs). Diffraction of guided modes into the light extraction cone enhances the light extraction by a factor of 2.6 compared to unstructured RCLEDs, where the farfields still show higher directionality than Lambertian emitters. The external quantum efficiency is 15.5% to air and 26% with encapsulation, respectively. The PhC-RCLEDs are also more stable to a temperature induced wavelength shift than unstructured RCLEDs.
Growth-rate-dependent partitioning of RNA polymerases in bacteria
Authors: Klumpp Stefan , Hwa Terence
Published: December 2008

Physiological changes that result in changes in bacterial gene expression are often accompanied by changes in the growth rate for fast adapting enteric bacteria. Because the availability of RNA polymerase (RNAP) in cells depends on the growth rate, transcriptional control involves not only the regulation of promoters, but also depends on the available (or free) RNAP concentration, which is difficult to quantify directly. Here, we develop a simple physical model describing the partitioning of cellular RNAP into different classes: RNAPs transcribing mRNA and ribosomal RNA (rRNA), RNAPs nonspecifically bound to DNA, free RNAP, and immature RNAP. Available experimental data for
Escherichia coli
allow us to determine the 2 unknown parameters of the model and hence deduce the free RNAP concentration at different growth rates. The results allow us to predict the growth-rate dependence of the activities of constitutive (unregulated) promoters, and to disentangle the growth-rate-dependent regulation of promoters (e.g., the promoters of rRNA operons) from changes in transcription due to changes in the free RNAP concentration at different growth rates. Our model can quantitatively account for the observed changes in gene expression patterns in mutant
E. coli
strains with altered levels of RNAP expression without invoking additional parameters. Applying our model to the case of the stringent response after amino acid starvation, we can evaluate the plausibility of various scenarios of passive transcriptional control proposed to account for the observed changes in the expression of rRNA and biosynthetic operons.
Retinoic acid-gated sequence-specific translational control by RARα
Authors: Poon Michael M. , Chen Lu
Published: December 2008

Retinoic acid (RA) plays important roles in development by modulating gene transcription through nuclear receptor activation. Increasing evidence supports a role for RA and RA receptors (RARs) in synaptic plasticity in the brain. We have recently reported that RA mediates a type of homeostatic synaptic plasticity through activation of dendritic protein synthesis, a process that requires dendritically localized RARα and is independent of transcriptional regulation. The molecular basis of this translational regulation by RA/RARα signaling, however, is unknown. Here we show that RARα is actively exported from the nucleus. Cytoplasmic RARα acts as an RNA-binding protein that associates with a subset of mRNAs, including dendritically localized glutamate receptor 1 (GluR1) mRNA. This binding is mediated by the RARα carboxyl terminal F-domain and specific sequence motifs in the 5′UTR of the GluR1 mRNA. Moreover, RARα association with the GluR1 mRNA directly underlies the translational control of GluR1 by RA: RARα represses GluR1 translation, while RA binding to RARα reduces its association with the GluR1 mRNA and relieves translational repression. Taken together, our results demonstrate a ligand-gated translational regulation mechanism mediated by a non-genomic function of RA/RARα signaling.
Crystal structure of a near-full-length archaeal MCM: Functional insights for an AAA+ hexameric helicase
Authors: Brewster Aaron S. , Wang Ganggang , Yu Xian , Greenleaf William B. , Carazo José María , Tjajadi Matthew , Klein Michael G. , Chen Xiaojiang S.
Published: December 2008

The minichromosome maintenance protein (MCM) complex is an essential replicative helicase for DNA replication in Archaea and Eukaryotes. Whereas the eukaryotic complex consists of 6 homologous proteins (MCM2–7), the archaeon
Sulfolobus solfataricus
has only 1 MCM protein (ssoMCM), 6 subunits of which form a homohexamer. Here, we report a 4.35-Å crystal structure of the near-full-length ssoMCM. The structure shows an elongated fold, with 5 subdomains that are organized into 2 large N- and C-terminal domains. A near-full-length ssoMCM hexamer generated based on the 6-fold symmetry of the N-terminal
Methanothermobacter thermautotrophicus
(mtMCM) hexamer shows intersubunit distances suitable for bonding contacts, including the interface around the ATP pocket. Four unusual β-hairpins of each subunit are located inside the central channel or around the side channels in the hexamer. Additionally, the hexamer fits well into the double-hexamer EM map of mtMCM. Our mutational analysis of residues at the intersubunit interfaces and around the side channels demonstrates their critical roles for hexamerization and helicase function. These structural and biochemical results provide a basis for future study of the helicase mechanisms of the archaeal and eukaryotic MCM complexes in DNA replication.
Dendritic cells in the thymus contribute to T-regulatory cell induction
Authors: Proietto Anna I. , van Dommelen Serani , Zhou Penghui , Rizzitelli Alexandra , D'Amico Angela , Steptoe Raymond J. , Naik Shalin H. , Lahoud Mireille H. , Liu Yang , Zheng Pan , Shortman Ken , Wu Li
Published: December 2008

Central tolerance is established through negative selection of self-reactive thymocytes and the induction of T-regulatory cells (TRs). The role of thymic dendritic cells (TDCs) in these processes has not been clearly determined. In this study, we demonstrate thatin vivo, TDCs not only play a role in negative selection but in the induction of TRs. TDCs include two conventional dendritic cell (DC) subtypes, CD8loSirpαhi/+(CD8loSirpα+) and CD8hiSirpαlo/−(CD8loSirpα−), which have different origins. We found that the CD8hiSirpα+DCs represent a conventional DC subset that originates from the blood and migrates into the thymus. Moreover, we show that the CD8loSirpα+DCs demonstrate a superior capacity to induce TRsin vitro. Finally, using a thymic transplantation system, we demonstrate that the DCs in the periphery can migrate into the thymus, where they efficiently induce TRgeneration and negative selection.
How main-chains of proteins explore the free-energy landscape in native states
Authors: Senet Patrick , Maisuradze Gia G. , Foulie Colette , Delarue Patrice , Scheraga Harold A.
Published: December 2008

Understanding how a single native protein diffuses on its free-energy landscape is essential to understand protein kinetics and function. The dynamics of a protein is complex, with multiple relaxation times reflecting a hierarchical free-energy landscape. Using all-atom molecular dynamics simulations of an α/β protein (crambin) and a β-sheet polypeptide (BS2) in their “native” states, we demonstrate that the mean-square displacement of dihedral angles, defined by 4 successive C
α
atoms, increases as a power law of time,
t
α
, with an exponent α between 0.08 and 0.39 (α = 1 corresponds to Brownian diffusion), at 300 K. Residues with low exponents are located mainly in well-defined secondary elements and adopt 1 conformational substate. Residues with high exponents are found in loops/turns and chain ends and exist in multiple conformational substates, i.e., they move on multiple-minima free-energy profiles.
TRPV6 is not required for 1α,25-dihydroxyvitamin D
3
-induced intestinal calcium absorption in vivo
Authors: Kutuzova Galina D. , Sundersingh Flora , Vaughan Jennifer , Tadi Bulli Padmaja , Ansay Susan E. , Christakos Sylvia , DeLuca Hector F.
Published: December 2008

The requirement for TRPV6 for vitamin D-dependent intestinal calcium absorption in vivo has been examined by using vitamin D-deficient TRPV6 null mice and littermate wild-type mice. Each of the vitamin D-deficient animals received each day for 4 days 50 ng of 1,25-dihydroyvitamin D
3
in 0.1 ml of 95% propylene glycol:5% ethanol vehicle or vehicle only. Both the wild-type and TRPV6 null mice responded equally well to 1,25-dihydroxyvitamin D
3
in increasing intestinal calcium absorption. These results, along with our microarray data, demonstrate that TRPV6 is not required for vitamin D-induced intestinal calcium absorption and may not carry out a significant role in this process. These and previous results using calbindin D9k null mutant mice illustrate that molecular events in the intestinal calcium absorption process in response to the active form of vitamin D remain to be defined.
The Nore1B/Mst1 complex restrains antigen receptor-induced proliferation of naïve T cells
Authors: Zhou Dawang , Medoff Benjamin D. , Chen Lanfen , Li Lequn , Zhang Xian-feng , Praskova Maria , Liu Matthew , Landry Aimee , Blumberg Richard S. , Boussiotis Vassiliki A. , Xavier Ramnik , Avruch Joseph
Published: December 2008

The Mst1 and Mst2 protein kinases are the mammalian homologs of hippo, a major inhibitor of cell proliferation in Drosophila. Mst1 is most abundant in lymphoid tissues. Mice lacking Mst1 exhibit markedly reduced levels of the Mst1 regulatory protein Nore1B/RAPL in lymphoid cells, whereas Mst2 abundance is unaltered. Mst1-null mice exhibit normal T cell development but low numbers of mature naïve T cells with relatively normal numbers of effector/memory T cells.
In vitro
, the Mst1-deficient naïve T cells exhibit markedly greater proliferation in response to stimulation of the T cell receptor whereas the proliferative responses of the Mst1-null effector/memory T cell cohort is similar to wild type. Thus, elimination of Mst1 removes a barrier to the activation and proliferative response of naïve T cells. The levels of Mst1 and Nore1B/RAPL in wild-type effector/memory T cells are approximately 10% those seen in wild-type naïve T cells, which may contribute to the enhanced proliferative responses of the former. Freshly isolated Mst1-null T cells exhibit high rates of ongoing apoptosis, a likely basis for their low numbers
in vivo
; they also exhibit defective clustering of LFA-1, as previously observed for Nore1B/RAPL-deficient T cells. Among known Mst1 substrates, only the phosphorylation of the cell cycle inhibitory proteins MOBKL1A/B is lost entirely in TCR-stimulated, Mst1-deficient T cells. Mst1/2-catalyzed MOBKL1A/B phosphorylation slows proliferation and is therefore a likely contributor to the anti-proliferative action of Mst1 in naïve T cells. The Nore1B/RAPL-Mst1 complex is a negative regulator of naïve T cell proliferation.
Some reflections on the relationship between ‘gesture’ and ‘sign’
Authors: Kendon Adam
Published: December 2008

In recent discussions there has been a tendency to refer to ‘gesture’ and ‘sign’ as if these are distinct categories, sometimes even as if they are in opposition to one another. Here I trace the historical origins of this distinction. I suggest that it is a product of the application to the analysis of sign languages of a formalist model of language derived from structural linguistics, on the one hand, and, on the other, of a cognitive-psychological view of ‘gesture’ that emerged in the latter half of the twentieth century. I suggest that this division between ‘gesture’ and ‘sign’ tends to exaggerate differences and obscure areas of overlap. It should be replaced by a comparative semiotics of the utterance uses of visible bodily action. This will be better able to articulate the similarities and differences between how kinesics is used, according to whether and how it is employed in relation to other communicative modalities such as speech.
Variation of residual stresses during cross-rolling
Authors: Wierzbanowski K. , Wroński S. , Baczmański A. , Wróbel M. , Fitzpatrick M. , Braham CH. , Lodini A.
Published: December 2008

Residual stresses in cross-rolled polycrystalline copper and low carbon steel are studied. Cross-rolling modifies both residual stresses and crystallographic texture. Consequently, it can be used in order to improve the final properties of a material by introducing a given state of internal stress and by imposing more symmetry to the texture.
Residual stress and texture evaluation by diffraction techniques in nano-HA coated implants
Authors: Citterio Hélène , Benmarouane Abdel , Jakani Saad , Millet Pierre , Lodini Alain
Published: December 2008

In order to reduce the delay for implant osseointegration, hydroxyapatite coatings sprayed on titanium substrate are proposed for commercial implants. Clinical failures of these coatings have been reported several months or years after the surgery due to resorption or mechanical failures. Our objectives were to improve the quality of the coating using a plasma thermal spraying process with nanosized powder as feedstock to generate partially nanostructured coatings. In order to be thermally sprayed, the individual nanoparticles are agglomerated into spherical micrometer-sized granules. The main goal of using nanostructured feedstock is to preserve the nanostructure of deposited HA in the morphology of the layers. The behaviour of agglomerated particles before the impact is of crucial importance, especially if they leave the plasma jet axis. The texture of bone crystallites is investigated after implantation near the interface. The preferred orientation is expected to change close to the interface due to reorganization of the bone’s constituents. Our texture study with neutron diffraction of sheep tibia at the interface with implant revealed the great interest to cover implants with a high quality HAp coating.
Characterization of residual stresses in IN 718 turbine discs by neutron diffraction and finite element modeling
Authors: Staron P. , Cihak U. , Stockinger M. , Clemens H.
Published: December 2008

Residual stresses in a commercially produced forged and water-quenched turbine disc made of the nickel-based superalloy IN 718 have been studied using neutron diffraction. The aim of this experimental study was to verify the residual stress predictions of a finite element simulation that is used to model forging and cooling of the discs. In addition to the disc, a thin plate of the same material was also studied. The residual stress predictions of the simulation for the disc agree quite well with the residual stress results obtained from neutron diffraction measurements. However, the heat transfer rate during water quenching was found to be a crucial parameter in the simulation. The stress distributions in the thin plate could only be predicted satisfactorily by using a temperature dependent heat transfer coefficient that was derived from temperature measurements in a disc during quenching.
Measurements of textures and stresses in Ni2MnGa ferromagnetic shape-memory alloys
Authors: Wang Y.D. , Ren Y. , Li H. , Cong D.Y. , Choo H. , Liaw P.K. , Lin Peng R. , Zuo L.
Published: December 2008

The neutron diffraction method and the synchrotron high-energy X-ray diffraction technique provide global and local measurements of textures and residual stresses in both structural and functional materials under various environments. In this paper, we present the in situ measurements in ferromagnetic shape-memory alloys during phase transformation, which reveal the good “memory” of textures and stresses.
Residual stresses in and around electromagnetically installed rivets measured using synchrotron and neutron diffraction
Authors: Fox M.E. , Withers P.J.
Published: December 2008

The residual stresses in and around riveted joints, formed with an electromagnetic riveter (as used in production of the Airbus A380 wing) have been investigated. Synchrotron X-ray and neutron diffraction were used to assess the stresses introduced into skin panel sections by installation of the fasteners. The stress profiles thus obtained exhibited an annular compressive zone, peaking around 400 MPa, around the fastener hole, balanced by tensile residual stresses (at a maximum of approximately 150 MPa) in the bulk material. The in-plane stress field was found to resemble that expected around a cold expanded hole. An analytical solution for the residual stresses in an autofrettaged tube was compared with the stresses around the rivet, allowing estimation of the pressures applied by the rivet to the fastener hole during rivet placement. These pressures were related to the yield stress of the skin material being riveted. This pressure produces a plastic misfit around the hole that places the rivet/hole interface under significant hoop compression. This compressive region is expected to confer significant advantages in terms of the fatigue lifetime of the riveted joints.
Neutron diffraction study of nano-hydroxyapatite coatings on titanium substrates
Authors: Jakani S. , Mathon M.-H. , Benmarouane A. , Lodini A.
Published: December 2008

Nanosized hydroxyapatite (HAP Ca10(PO4)6(OH)2) powders were characterized before and after depositing on the (Ti–6Al–4V) substrate using neutron diffraction and scanning electron microscopy (SEM). The crystallite size of nano-hydroxyapatite powder is 90 nm. After depositing via plasma thermal spraying (PTS), followed by 2 h heat treatment to reduce the amorphous fraction, the deposited coating shows retension of the nanometre crystallite sizes (about 120 nm). The SEM observations reveal a spherical geometry of agglomerated particles.
The effects of restraint and post-weld heat treatment on residual stress distribution in a bead-on-plate weld
Authors: Paradowska A.M. , Price J.W.H. , Ibrahim R. , Finlayson T.R. , Ripley M.I. , Blevins R.
Published: December 2008

Welding residual stresses have important consequences for the performance of engineering components and high residual stresses can lead to loss of performance in corrosion, fatigue and fracture. Despite their importance, they are often the single largest unknown in industrial damage situations due to the difficulty of their measurement. In this paper, the neutron diffraction technique is used to investigate residual strains and stresses due to repair welding. The aim of this research was to characterize the residual stress distribution which arises in a welded component as a result of restraint and how it is reduced by subsequent post-weld heat treatment (PWHT). Three-dimensional residual strain/stress distributions are presented. The test results show that restraint during welding increases the levels of residual stress in all three directions. A significant stress relaxation due to PWHT has been observed. Results are also compared with values specified by the structural integrity assessment standard, BS7910.
Crystallographic characterization of pseudoelastic phase transformation in Cu–13.1Al–4.0Ni (wt.%) single crystal high temperature shape memory alloy using neutron diffraction
Authors: Kannarpady Ganesh K. , Brown Don , Bhattacharyya Abhijit , Vogel Sven , Pulnev Sergei
Published: December 2008

This paper reports neutron diffraction experiments on high temperature Cu–13.1Al–4.0Ni (wt.%) shape memory alloy single crystals. The Cu–13.1%Al–4%Ni (wt.%) single crystal wires having nominal dimensions of 2.0 mm (diameter) and 100 mm (length) were subjected to tensile load at room temperature and at 175°C (well above the austenitic finish temperature). Diffraction patterns were acquired at various stress levels. The growth and decay of different variants during the (β11 18R monoclinic martensite reorientation under load were identified. Neutron diffraction results at 175 and 200°C were used to study the biased martensitic variant formation during the (β1) cubic austenite to (β11) 18R monoclinic martensite transformation under load. The observed results are correlated with stress-overall strain data obtained from experiments carried out at different test temperatures in an Instron machine with a high temperature environmental chamber.
The NatA Acetyltransferase Couples Sup35 Prion Complexes to the [PSI+] Phenotype
Authors: Pezza John A. , Langseth Sara X. , Raupp Yamamoto Rochele , Doris Stephen M. , Ulin Samuel P. , Salomon Arthur R. , Serio Tricia R.
Published: December 2008

Protein-only (prion) epigenetic elements confer unique phenotypes by adopting alternate conformations that specify new traits. Given the conformational flexibility of prion proteins, protein-only inheritance requires efficient self-replication of the underlying conformation. To explore the cellular regulation of conformational self-replication and its phenotypic effects, we analyzed genetic interactions between [PSI+], a prion form of the S. cerevisiae Sup35 protein (Sup35[PSI+]), and the three Nα-acetyltransferases, NatA, NatB, and NatC, which collectively modify ∼50% of yeast proteins. Although prion propagation proceeds normally in the absence of NatB or NatC, the [PSI+] phenotype is reversed in strains lacking NatA. Despite this change in phenotype, [PSI+] NatA mutants continue to propagate heritable Sup35[PSI+]. This uncoupling of protein state and phenotype does not arise through a decrease in the number or activity of prion templates (propagons) or through an increase in soluble Sup35. Rather, NatA null strains are specifically impaired in establishing the translation termination defect that normally accompanies Sup35 incorporation into prion complexes. The NatA effect cannot be explained by the modification of known components of the [PSI+] prion cycle including Sup35; thus, novel acetylated cellular factors must act to establish and maintain the tight link between Sup35[PSI+]complexes and their phenotypic effects.
Regulation of Renal Epithelial Tight Junctions by the von Hippel-Lindau Tumor Suppressor Gene Involves Occludin and Claudin 1 and Is Independent of E-Cadherin
Authors: Harten Sarah K. , Shukla Deepa , Barod Ravi , Hergovich Alexander , Balda Maria S. , Matter Karl , Esteban Miguel A. , Maxwell Patrick H.
Published: December 2008

Epithelial-to-mesenchymal transitions (EMT) are important in renal development, fibrosis, and cancer. Loss of function of the tumor suppressor VHL leads to many features of EMT, and it has been hypothesized that the pivotal mediator is down-regulation of the adherens junction (AJ) protein E-cadherin. Here we show that VHL loss-of-function also has striking effects on the expression of the tight junction (TJ) components occludin and claudin 1 in vitro in VHL-defective clear cell renal cell carcinoma (CCRCC) cells and in vivo in VHL-defective sporadic CCRCCs (compared with normal kidney). Occludin is also down-regulated in premalignant foci in kidneys from patients with germline VHL mutations, consistent with a contribution to CCRCC initiation. Reexpression of E-cadherin was sufficient to restore AJ but not TJ assembly, indicating that the TJ defect is independent of E-cadherin down-regulation. Additional experiments show that activation of hypoxia inducible factor (HIF) contributes to both TJ and AJ abnormalities, thus the VHL/HIF pathway contributes to multiple aspects of the EMT phenotype that are not interdependent. Despite the independent nature of the defects, we show that treatment with the histone deacetylase inhibitor sodium butyrate, which suppresses HIF activation, provides a method for reversing EMT in the context of VHL inactivation.
Detecting glycan cancer biomarkers in serum samples using MALDI FT-ICR mass spectrometry data
Authors: Barkauskas Donald A. , An Hyun Joo , Kronewitter Scott R. , de Leoz Maria Lorna , Chew Helen K. , de Vere White Ralph W. , Leiserowitz Gary S. , Miyamoto Suzanne , Lebrilla Carlito B. , Rocke David M.
Published: December 2008

Motivation: The development of better tests to detect cancer in its earliest stages is one of the most sought-after goals in medicine. Especially important are minimally invasive tests that require only blood or urine samples. By profiling oligosaccharides cleaved from glycosylated proteins shed by tumor cells into the blood stream, we hope to determine glycan profiles that will help identify cancer patients using a simple blood test. The data in this article were generated using matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry (MALDI FT-ICR MS). We have developed novel methods for analyzing this type of mass spectrometry data and applied it to eight datasets from three different types of cancer (breast, ovarian and prostate).

Results: The techniques we have developed appear to be effective in the analysis of MALDI FT-ICR MS data. We found significant differences between control and cancer groups in all eight datasets, including two structurally related compounds that were found to be significantly different between control and cancer groups in all three types of cancer studied.

Availability: The software used to perform the analysis described in this article is available in the form of an R package called fticrms, version 0.6, either from the Comprehensive R Archive Network (http://www.r-project.org/) or from the first author.

Contact:  barkda@wald.ucdavis.edu