Science.gov

Sample records for large regional domain

  1. Regional Climate Model Sensitivity to Domain Size

    NASA Astrophysics Data System (ADS)

    Leduc, M.; Laprise, R.

    2006-05-01

    Regional Climate Models are increasingly used to add small-scale features that are not present in their lateral boundary conditions (LBCs). It is well known that the limited area over which a model integrates must be large enough to allow the full development of small scales features (Jones et al., 1995). On the other hand, integrations on very large domains have shown important departures from the driving data, unless large-scale nudging is applied (e.g., Castro and Pielke, 2005). Here the effects of domain size on the development of small-scales are examined using the "Big-Brother" approach developed by Denis et al. (2002). This method consists of generating a high-resolution simulation over a large domain (the Big-Brother). The next step is to degrade this dataset with a low-pass filter based on discrete cosine transform (DCT; Denis et al., 2002) to emulate coarse-resolution LBCs that are usually taken from GCMs or reanalyses. A second simulation (the Little-Brother) is driven by the coarse-resolution LBCs and generates its own small-scale features inside the new smaller domain. Nested and added scales of the Little- Brother can then be compared with the Big-Brother (unfiltered) ones by using the DCT-filter again. Three February months (1990,1991 and 1992) were integrated over a continental grid (Big-Brother: 196x196 gridpoints) with a spatial resolution of 45 km covering almost the entire North-America. After filtering, this dataset is used to drive five simulations with varying domain size (48x48, 72x72, 96x96, 120x120 and 144x144) centred on the same geographic location; all other parameters are kept constant. Monthly statistics of the five Little-Brothers are compared with the virtual reference (Big-Brother) over the common domain (28x28) corresponding to the smallest Little-Brother but without its sponge zone. Results show that temporal correlation of large-scale events increases when the domain size is reduced from 144x144 to 48x48. For the same domain

  2. Large domain motions in Ago protein controlled by the guide DNA-strand seed region determine the Ago-DNA-mRNA complex recognition process.

    PubMed

    Xia, Zhen; Huynh, Tien; Ren, Pengyu; Zhou, Ruhong

    2013-01-01

    The recognition mechanism and cleavage activity of argonaute (Ago), miRNA, and mRNA complexes are the core processes to the small non-coding RNA world. The 5' nucleation at the 'seed' region (position 2-8) of miRNA was believed to play a significant role in guiding the recognition of target mRNAs to the given miRNA family. In this paper, we have performed all-atom molecular dynamics simulations of the related and recently revealed Ago-DNA:mRNA ternary complexes to study the dynamics of the guide-target recognition and the effect of mutations by introducing "damaging" C·C mismatches at different positions in the seed region of the DNA-RNA duplex. Our simulations show that the A-form-like helix duplex gradually distorts as the number of seed mismatches increases and the complex can survive no more than two such mismatches. Severe distortions of the guide-target heteroduplex are observed in the ruinous 4-sites mismatch mutant, which give rise to a bending motion of the PAZ domain along the L1/L2 "hinge-like" connection segment, resulting in the opening of the nucleic-acid-binding channel. These long-range interactions between the seed region and PAZ domain, moderated by the L1/L2 segments, reveal the central role of the seed region in the guide-target strands recognition: it not only determines the guide-target heteroduplex's nucleation and propagation, but also regulates the dynamic motions of Ago domains around the nucleic-acid-binding channel.

  3. Domain regulation of imprinting cluster in Kip2/Lit1 subdomain on mouse chromosome 7F4/F5: large-scale DNA methylation analysis reveals that DMR-Lit1 is a putative imprinting control region.

    PubMed

    Yatsuki, Hitomi; Joh, Keiichiro; Higashimoto, Ken; Soejima, Hidenobu; Arai, Yuji; Wang, Youdong; Hatada, Izuho; Obata, Yayoi; Morisaki, Hiroko; Zhang, Zhongming; Nakagawachi, Tetsuji; Satoh, Yuji; Mukai, Tsunehiro

    2002-12-01

    Mouse chromosome 7F4/F5, where the imprinting domain is located, is syntenic to human 11p15.5, the locus for Beckwith-Wiedemann syndrome. The domain is thought to consist of the two subdomains Kip2 (p57(kip2))/Lit1 and Igf2/H19. Because DNA methylation is believed to be a key factor in genomic imprinting, we performed large-scale DNA methylation analysis to identify the cis-element crucial for the regulation of the Kip2/Lit1 subdomain. Ten CpG islands (CGIs) were found, and these were located at the promoter sites, upstream of genes, and within intergenic regions. Bisulphite sequencing revealed that CGIs 4, 5, 8, and 10 were differentially methylated regions (DMRs). CGIs 4, 5, and 10 were methylated paternally in somatic tissues but not in germ cells. CGI8 was methylated in oocyte and maternally in somatic tissues during development. Parental-specific DNase I hypersensitive sites (HSSs) were found near CGI8. These data indicate that CGI8, called DMR-Lit1, is not only the region for gametic methylation but might also be the imprinting control region (ICR) of the subdomain.

  4. Site-specific mutations in a loop region of the C-terminal domain of the large subunit of ribulose bisphosphate carboxylase/oxygenase that influence substrate partitioning.

    PubMed

    Gutteridge, S; Rhoades, D F; Herrmann, C

    1993-04-15

    Amino acids composing a flexible loop (loop 6) of the eight-stranded barrel domain of the L-subunit of Synechococcus ribulose bisphosphate carboxylase/oxygenase (EC 4.1.1.39) involved in reaction intermediate stabilization have been modified by site-specific mutagenesis. Changes at positions both distant and within the active site affect overall catalysis and substrate partitioning. Most significantly, replacement of the active site Lys (Lys-334) with Arg at the apex of the loop almost completely suppressed the carboxylase activity of the enzyme relative to oxygenation, with only a modest reduction in overall catalysis. Val-331 and Thr-342, more distant from the active site but with interacting side chains, were changed to larger and smaller residues with differential effects on both turnover and substrate partitioning. Substitution of the loop with the sequence found in more efficient carboxylases only increased partitioning marginally when accompanied by alterations in the C-terminal tail of the L-subunit that interacts with the loop. Generally, modifications to the loop composition also affected enediol formation, the first step of catalysis, suggesting that the geometry and hence flexibility of this segment affect more than just stabilization of the intermediates immediately following reaction with CO2 or O2.

  5. Atomic structure of the sweet-tasting protein thaumatin I at pH 8.0 reveals the large disulfide-rich region in domain II to be sensitive to a pH change

    SciTech Connect

    Masuda, Tetsuya; Ohta, Keisuke; Mikami, Bunzo; Kitabatake, Naofumi; Tani, Fumito

    2012-03-02

    Highlights: Black-Right-Pointing-Pointer Structure of a recombinant thaumatin at pH 8.0 determined at a resolution of 1.0 A. Black-Right-Pointing-Pointer Substantial fluctuations of a loop in domain II was found in the structure at pH 8.0. Black-Right-Pointing-Pointer B-factors for Lys137, Lys163, and Lys187 were significantly affected by pH change. Black-Right-Pointing-Pointer An increase in mobility might play an important role in the heat-induced aggregation. -- Abstract: Thaumatin, an intensely sweet-tasting plant protein, elicits a sweet taste at 50 nM. Although the sweetness remains when thaumatin is heated at 80 Degree-Sign C for 4 h under acid conditions, it rapidly declines when heating at a pH above 6.5. To clarify the structural difference at high pH, the atomic structure of a recombinant thaumatin I at pH 8.0 was determined at a resolution of 1.0 A. Comparison to the crystal structure of thaumatin at pH 7.3 and 7.0 revealed the root-mean square deviation value of a C{alpha} atom to be substantially greater in the large disulfide-rich region of domain II, especially residues 154-164, suggesting that a loop region in domain II to be affected by solvent conditions. Furthermore, B-factors of Lys137, Lys163, and Lys187 were significantly affected by pH change, suggesting that a striking increase in the mobility of these lysine residues, which could facilitate a reaction with a free sulfhydryl residue produced via the {beta}-elimination of disulfide bonds by heating at a pH above 7.0. The increase in mobility of lysine residues as well as a loop region in domain II might play an important role in the heat-induced aggregation of thaumatin above pH 7.0.

  6. Functional regions of the mouse interleukin-10 receptor cytoplasmic domain.

    PubMed Central

    Ho, A S; Wei, S H; Mui, A L; Miyajima, A; Moore, K W

    1995-01-01

    The functions of wild-type and mutant mouse interleukin-10 receptors (mIL-10R) expressed in murine Ba/F3 cells were studied. As observed previously, IL-10 stimulates proliferation of IL-10R-expressing Ba/F3 cells. Accumulation of viable cells in the proliferation assay is to a significant extent balanced by concomitant cell death. Moreover, growth in IL-10 also induces a previously unrecognized response, differentiation of the cells, as evidenced both by formation of large clusters of cells in cultures with IL-10 and by induction or enhancement of expression of several cell surface antigens, including CD32/16, CD2, LECAM-1 (v-selectin), and heat-stable antigen. Two distinct functional regions near the C terminus of the mIL-10R cytoplasmic domain which mediate proliferation were identified; one of these regions also mediates the differentiation response. A third region proximal to the transmembrane domain was identified; removal of this region renders the cell 10- to 100-fold more sensitive to IL-10 in the proliferation assay. In cells expressing both wild-type and mutant IL-10R, stimulation with IL-10 leads to tyrosine phosphorylation of the kinases JAK1 and TYK2 but not JAK2 or JAK3 under the conditions tested. PMID:7544437

  7. Domain nesting for multi-scale large eddy simulation

    NASA Astrophysics Data System (ADS)

    Fuka, Vladimir; Xie, Zheng-Tong

    2016-04-01

    The need to simulate city scale areas (O(10 km)) with high resolution within street canyons in certain areas of interests necessitates different grid resolutions in different part of the simulated area. General purpose computational fluid dynamics codes typically employ unstructured refined grids while mesoscale meteorological models more often employ nesting of computational domains. ELMM is a large eddy simulation model for the atmospheric boundary layer. It employs orthogonal uniform grids and for this reason domain nesting was chosen as the approach for simulations in multiple scales. Domains are implemented as sets of MPI processes which communicate with each other as in a normal non-nested run, but also with processes from another (outer/inner) domain. It should stressed that the duration of solution of time-steps in the outer and in the inner domain must be synchronized, so that the processes do not have to wait for the completion of their boundary conditions. This can achieved by assigning an appropriate number of CPUs to each domain, and to gain high efficiency. When nesting is applied for large eddy simulation, the inner domain receives inflow boundary conditions which lack turbulent motions not represented by the outer grid. ELMM remedies this by optional adding of turbulent fluctuations to the inflow using the efficient method of Xie and Castro (2008). The spatial scale of these fluctuations is in the subgrid-scale of the outer grid and their intensity will be estimated from the subgrid turbulent kinetic energy in the outer grid.

  8. Observation of large nematic domains of discotic liquid crystals

    NASA Astrophysics Data System (ADS)

    Shinde, Abhijeet; Wang, Xuezhen; Cheng, Zhengdong

    2015-03-01

    Discotic liquid crystals are commonly found in nature in the form of clay, nacre. They are technologically important in applications such as conductive polymers, semiconductors and photovoltaics. Size and its distribution play an important role in their self-assemblies. Here we observed large nematic domains of discotic liquid crystals grown on a time scale of months. The development of such domains is observed to be faster for nanodisks that relatively smaller in size. The orientation of nanodisks is affected by gravity and inter-particle interactions which are yet to be fully understood.

  9. Large-scale regions of antimatter

    SciTech Connect

    Grobov, A. V. Rubin, S. G.

    2015-07-15

    Amodified mechanism of the formation of large-scale antimatter regions is proposed. Antimatter appears owing to fluctuations of a complex scalar field that carries a baryon charge in the inflation era.

  10. Time-Domain Filtering for Spatial Large-Eddy Simulation

    NASA Technical Reports Server (NTRS)

    Pruett, C. David

    1997-01-01

    An approach to large-eddy simulation (LES) is developed whose subgrid-scale model incorporates filtering in the time domain, in contrast to conventional approaches, which exploit spatial filtering. The method is demonstrated in the simulation of a heated, compressible, axisymmetric jet, and results are compared with those obtained from fully resolved direct numerical simulation. The present approach was, in fact, motivated by the jet-flow problem and the desire to manipulate the flow by localized (point) sources for the purposes of noise suppression. Time-domain filtering appears to be more consistent with the modeling of point sources; moreover, time-domain filtering may resolve some fundamental inconsistencies associated with conventional space-filtered LES approaches.

  11. Multi-Robot FastSLAM for Large Domains

    DTIC Science & Technology

    2007-03-01

    LARGE DOMAINS THESIS Presented to the Faculty Department of Electrical and Computer Engineering Graduate School of Engineering and Management...Air Force Institute of Technology Air University Air Education and Training Command In Partial Fulfillment of the Requirements for the Degree of...in our offices and homes . Like humans, robots rely on sensor measurements to interpret theirs environment and subsequently build maps using the

  12. Frequency domain multiplexing for large-scale bolometer arrays

    SciTech Connect

    Spieler, Helmuth

    2002-05-31

    The development of planar fabrication techniques for superconducting transition-edge sensors has brought large-scale arrays of 1000 pixels or more to the realm of practicality. This raises the problem of reading out a large number of sensors with a tractable number of connections. A possible solution is frequency-domain multiplexing. I summarize basic principles, present various circuit topologies, and discuss design trade-offs, noise performance, cross-talk and dynamic range. The design of a practical device and its readout system is described with a discussion of fabrication issues, practical limits and future prospects.

  13. Spectral domain of large nonsymmetric correlated Wishart matrices.

    PubMed

    Vinayak; Benet, Luis

    2014-10-01

    We study complex eigenvalues of the Wishart model for nonsymmetric correlation matrices. The model is defined for two statistically equivalent but different Gaussian real matrices, as C=AB(t)/T, where B(t) is the transpose of B and both matrices A and B are of dimensions N×T. If A and B are uncorrelated, or equivalently if C vanishes on average, it is known that at large matrix dimension the domain of the eigenvalues of C is a circle centered-at-origin and the eigenvalue density depends only on the radial distances. We consider actual correlation in A and B and derive a result for the contour describing the domain of the bulk of the eigenvalues of C in the limit of large N and T where the ratio N/T is finite. In particular, we show that the eigenvalue domain is sensitive to the correlations. For example, when C is diagonal on average with the same element c≠0, the contour is no longer a circle centered at origin but a shifted ellipse. In this case we explicitly derive a result for the spectral density which again depends only on the radial distances. For more general cases, we show that the contour depends on the symmetric and antisymmetric parts of the correlation matrix resulting from the ensemble-averaged C. If the correlation matrix is normal, then the contour depends only on its spectrum. We also provide numerics to justify our analytics.

  14. Spectral domain of large nonsymmetric correlated Wishart matrices

    NASA Astrophysics Data System (ADS)

    Vinayak, Benet, Luis

    2014-10-01

    We study complex eigenvalues of the Wishart model for nonsymmetric correlation matrices. The model is defined for two statistically equivalent but different Gaussian real matrices, as C =ABt/T, where Bt is the transpose of B and both matrices A and B are of dimensions N ×T. If A and B are uncorrelated, or equivalently if C vanishes on average, it is known that at large matrix dimension the domain of the eigenvalues of C is a circle centered-at-origin and the eigenvalue density depends only on the radial distances. We consider actual correlation in A and B and derive a result for the contour describing the domain of the bulk of the eigenvalues of C in the limit of large N and T where the ratio N /T is finite. In particular, we show that the eigenvalue domain is sensitive to the correlations. For example, when C is diagonal on average with the same element c ≠0, the contour is no longer a circle centered at origin but a shifted ellipse. In this case we explicitly derive a result for the spectral density which again depends only on the radial distances. For more general cases, we show that the contour depends on the symmetric and antisymmetric parts of the correlation matrix resulting from the ensemble-averaged C. If the correlation matrix is normal, then the contour depends only on its spectrum. We also provide numerics to justify our analytics.

  15. Identification of structural domains within the large subunit of herpes simplex virus ribonucleotide reductase.

    PubMed

    Conner, J; Cross, A; Murray, J; Marsden, H

    1994-12-01

    The large subunit (R1) of herpes simplex virus (HSV) ribonucleotide reductase is a bifunctional protein consisting of a unique N-terminal protein kinase domain and a ribonucleotide reductase domain. Previous studies showed that the two functional domains are linked by a protease sensitive site. Here we provide evidence for two subdomains, of 30K and 53K, within the reductase domain. The two fragments, which were produced by limited proteolysis and were resistant to further degradation, remained tightly associated in a complex containing two molecules of each. They were capable of binding the R2 subunit of HSV ribonucleotide reductase with approximately the same affinity as the intact protein but the complex did not complement the small subunit (R2) to give an active enzyme. At low concentrations (0.4 micrograms/ml) of trypsin or V8 protease, cleavage between the subdomains was prevented by the presence of the N-terminal protein kinase domain. At higher protease concentrations (1 micrograms/ml) the N-terminal domain is extensively proteolysed and the 30K and 53K domains were generated. Identical results were obtained using purified R1 isolated from infected cell extracts or following expression in Escherichia coli. The origin of the two domains was investigated by N-terminal sequencing of the 53K fragment and by examining their reactivity with a panel of R1-specific monoclonal antibodies which we isolated and epitope mapped for that purpose. The trypsin cleavage site was found to lie between arginine 575 and asparagine 576, and proteolysis in this region was not prevented by the presence of R2 or the nonapeptide YAGAVVNDL. We propose that the ribonucleotide reductase region of HSV R1 exists in a two domain structure, and that the interdomain linking region is protected by the unique N terminus.

  16. The Smad3 linker region contains a transcriptional activation domain.

    PubMed

    Wang, Guannan; Long, Jianyin; Matsuura, Isao; He, Dongming; Liu, Fang

    2005-02-15

    Transforming growth factor-beta (TGF-beta)/Smads regulate a wide variety of biological responses through transcriptional regulation of target genes. Smad3 plays a key role in TGF-beta/Smad-mediated transcriptional responses. Here, we show that the proline-rich linker region of Smad3 contains a transcriptional activation domain. When the linker region is fused to a heterologous DNA-binding domain, it activates transcription. We show that the linker region physically interacts with p300. The adenovirus E1a protein, which binds to p300, inhibits the transcriptional activity of the linker region, and overexpression of p300 can rescue the linker-mediated transcriptional activation. In contrast, an adenovirus E1a mutant, which cannot bind to p300, does not inhibit the linker-mediated transcription. The native Smad3 protein lacking the linker region is unable to mediate TGF-beta transcriptional activation responses, although it can be phosphorylated by the TGF-beta receptor at the C-terminal tail and has a significantly increased ability to form a heteromeric complex with Smad4. We show further that the linker region and the C-terminal domain of Smad3 synergize for transcriptional activation in the presence of TGF-beta. Thus our findings uncover an important function of the Smad3 linker region in Smad-mediated transcriptional control.

  17. Chapter 4: Regional magnetic domains of the Circum-Arctic: A framework for geodynamic interpretation

    USGS Publications Warehouse

    Saltus, R.W.; Miller, E.L.; Gaina, C.; Brown, P.J.

    2011-01-01

    We identify and discuss 57 magnetic anomaly pattern domains spanning the Circum-Arctic. The domains are based on analysis of a new Circum-Arctic data compilation. The magnetic anomaly patterns can be broadly related to general geodynamic classification of the crust into stable, deformed (magnetic and nonmagnetic), deep magnetic high, oceanic and large igneous province domains. We compare the magnetic domains with topography/bathymetry, regional geology, regional free air gravity anomalies and estimates of the relative magnetic 'thickness' of the crust. Most of the domains and their geodynamic classification assignments are consistent with their topographic/bathymetric and geological expression. A few of the domains are potentially controversial. For example, the extent of the Iceland Faroe large igneous province as identified by magnetic anomalies may disagree with other definitions for this feature. Also the lack of definitive magnetic expression of oceanic crust in Baffin Bay, the Norwegian-Greenland Sea and the Amerasian Basin is at odds with some previous interpretations. The magnetic domains and their boundaries provide clues for tectonic models and boundaries within this poorly understood portion of the globe. ?? 2011 The Geological Society of London.

  18. A domain decomposition algorithm for solving large elliptic problems

    SciTech Connect

    Nolan, M.P.

    1991-01-01

    AN algorithm which efficiently solves large systems of equations arising from the discretization of a single second-order elliptic partial differential equation is discussed. The global domain is partitioned into not necessarily disjoint subdomains which are traversed using the Schwarz Alternating Procedure. On each subdomain the multigrid method is used to advance the solution. The algorithm has the potential to decrease solution time when data is stored across multiple levels of a memory hierarchy. Results are presented for a virtual memory, vector multiprocessor architecture. A study of choice of inner iteration procedure and subdomain overlap is presented for a model problem, solved with two and four subdomains, sequentially and in parallel. Microtasking multiprocessing results are reported for multigrid on the Alliant FX-8 vector-multiprocessor. A convergence proof for a class of matrix splittings for the two-dimensional Helmholtz equation is given. 70 refs., 3 figs., 20 tabs.

  19. Frequency domain identification for robust large space structure control design

    NASA Technical Reports Server (NTRS)

    Yam, Y.; Bayard, D. S.; Scheid, R. E.

    1991-01-01

    A methodology is demonstrated for frequency domain identification of large space structures which systematically transforms experimental raw data into a form required for synthesizing H(infinity) controllers using modern robust control design software (e.g., Matlab Toolboxes). A unique feature of this approach is that the additive uncertainty is characterized to a specified statistic confidence rather than with hard bounds. In this study, the difference in robust performance is minimal between the two levels of confidence. In general cases, the present methodology provides a tool for performance/confidence level tradeoff studies. For simplicity, the additive uncertainty on a frequency grid is considered and the interpolation error in between grid points is neglected.

  20. Connections between large-domain Newtonian turbulence and minimal-channel exact coherent states

    NASA Astrophysics Data System (ADS)

    Kushwaha, Anubhav; Graham, Michael

    2016-11-01

    Direct numerical simulations (DNS) of plane Poiseuille flow of a Newtonian fluid are performed in a large domain at transitional Reynolds numbers. In this Reynolds number regime, turbulent trajectories in minimal channels move chaotically between lower and upper branch invariant solutions known as exact coherent states (ECS). It is found that while they spend most of the time in a core region of the state space, fluctuating about the upper branch ECS, they occasionally escape the core region and pass through the vicinity of lower branch solutions. One particular set of the lower branch solutions form the lower bound of the turbulent trajectory with regard to flow properties like wall shear stress, energy dissipation rate and turbulent kinetic energy. We compare the evolution of wall shear stress in minimal channels with those in patches the size of minimal channels in a large domain and find that they are not only indistinguishable but also bounded on the lower end by the same set of lower branch ECS. This suggests that localised regions in a large box approach the travelling wave solutions in a way similar to minimal channels. We also show that low and high drag regions occur spatiotemporally when the turbulence trajectory approaches the lower and upper branch ECS, respectively. The work was supported by AFOSR Grant FA9550-15-1-0062.

  1. Assessing the effect of domain size over the Caribbean region using the PRECIS regional climate model

    NASA Astrophysics Data System (ADS)

    Centella-Artola, Abel; Taylor, Michael A.; Bezanilla-Morlot, Arnoldo; Martinez-Castro, Daniel; Campbell, Jayaka D.; Stephenson, Tannecia S.; Vichot, Alejandro

    2015-04-01

    This study investigates the sensitivity of the one-way nested PRECIS regional climate model (RCM) to domain size for the Caribbean region. Simulated regional rainfall patterns from experiments using three domains with horizontal resolution of 50 km are compared with ERA reanalysis and observed datasets to determine if there is an optimal RCM configuration with respect to domain size and the ability to reproduce important observed climate features in the Caribbean. Results are presented for the early wet season (May-July) and late wet season (August-October). There is a relative insensitivity to domain size for simulating some important features of the regional circulation and key rainfall characteristics e.g. the Caribbean low level jet and the mid summer drought (MSD). The downscaled precipitation has a systematically negative precipitation bias, even when the domain was extended to the African coast to better represent circulation associated with easterly waves and tropical cyclones. The implications for optimizing modelling efforts within resource-limited regions like the Caribbean are discussed especially in the context of the region's participation in global initiatives such as CORDEX.

  2. Robust All-quad Meshing of Domains with Connected Regions

    PubMed Central

    Rushdi, Ahmad A.; Mitchell, Scott A.; Bajaj, Chandrajit L.; Ebeida, Mohamed S.

    2016-01-01

    In this paper, we present a new algorithm for all-quad meshing of non-convex domains, with connected regions. Our method starts with a strongly balanced quadtree. In contrast to snapping the grid points onto the geometric boundaries, we move points a slight distance away from the common boundaries. Then we intersect the moved grid with the geometry. This allows us to avoid creating any flat quads, and we are able to handle two-sided regions and more complex topologies than prior methods. The algorithm is provably correct, robust, and cleanup-free; meaning we have angle and edge length bounds, without the use of any pillowing, swapping, or smoothing. Thus, our simple algorithm is also more predictable than prior art. PMID:27570571

  3. ENDLESS: An extended nonperiodic domain large-eddy simulation approach for scalar plumes

    NASA Astrophysics Data System (ADS)

    Chen, Bicheng; Yang, Di; Meneveau, Charles; Chamecki, Marcelo

    2016-05-01

    Large-eddy simulation (LES) has proven to be a valuable tool for high-fidelity modeling of environmental and geophysical turbulent flows. An important application of LES is to study the transport of effluents (e.g. oils from a subsea blowout) in the ocean mixed layer (OML). Oil plumes being transported in the OML experience the action of shear-generated turbulence, Langmuir circulations, Ekman transport and submesoscale quasi-geostrophic eddies. To resolve such turbulent processes, grid sizes of a few meters are desirable while horizontal domain sizes of LES are typically restricted from hundreds of meters to a few kilometers, for LES to remain practically affordable. Yet transported oil plumes evolve to large scales extending to tens or even hundreds of kilometers. In this study, the Extended Nonperiodic Domain LES for Scalar transport (ENDLESS) is proposed as a multi-scale approach to tackle this challenge while being computationally affordable. The basic idea is to simulate the shear turbulence and Langmuir circulations on a small horizontal domain with periodic boundary conditions while the resulting transport velocity field is replicated periodically following adaptively the large-scale plume as it evolves spatially towards much larger scales. This approach also permits the superposition of larger-scale quasi two-dimensional flow motions on the oil advection, allowing for coupling with regional circulation models. A validation case and two sample applications to oil plume evolution in the OML are presented in order to demonstrate key features and computational speedup associated with the ENDLESS method.

  4. Kininogen domain 3 contains regions recognized by antiphosphatidylethanolamine antibodies.

    PubMed

    Katsunuma, J; Sugi, T; Inomo, A; Matsubayashi, H; Izumi, S-I; Makino, T

    2003-01-01

    Antiphosphatidylethanolamine antibodies (APE) have been described in patients with thrombotic diseases and recurrent pregnancy loss (RPL). It has been reported that certain APE are not specific for phosphatidylethanolamine (PE) per se, but are directed to PE-binding plasma proteins, called kininogens. Our recent in vitro data suggest that APE may recognize the domain 3 (D3) region of kininogens. In this study, we have used synthetic peptides that span the D3 of kininogens in inhibition and direct binding studies to identify epitopes that are sites for binding APE. Our present data demonstrate that among 24 RPL patients who were positive for kininogen-dependent immunoglobulin (IgG) APE, 17 patients (70.8%) recognized the LDC27 peptide. We mapped the APE-binding region on D3 using plasma from a RPL patient (X) who had a high titer of IgG APE that recognized LDC27. APE of patient X recognized a 13-residue segment in LDC27, named CNA13. Leu331-Met357 (LDC27) and Cys333-Lys345 (CNA13) are located on the carboxyl-terminal portion of kininogen D3, which is known as the major kininogen heavy chain cell attachment site where it overlaps its cysteine protease inhibitory region. Because APE interferes with the balance of hemostasis in vitro, APE may therefore induce a similar condition in patients thereby causing thrombosis and RPL.

  5. Binding to retinoblastoma pocket domain does not alter the inter-domain flexibility of the J domain of SV40 large T antigen.

    PubMed

    Williams, Christina K; Vaithiyalingam, Sivaraja; Hammel, Michal; Pipas, James; Chazin, Walter J

    2012-02-15

    Simian Virus 40 uses the large T antigen (Tag) to bind and inactivate retinoblastoma tumor suppressor proteins (Rb), which can result in cellular transformation. Tag is a modular protein with four domains connected by flexible linkers. The N-terminal J domain of Tag is necessary for Rb inactivation. Binding of Rb is mediated by an LXCXE consensus motif immediately C-terminal to the J domain. Nuclear magnetic resonance (NMR) and small angle X-ray scattering (SAXS) were used to study the structural dynamics and interaction of Rb with the LXCXE motif, the J domain and a construct (N(260)) extending from the J domain through the origin binding domain (OBD). NMR and SAXS data revealed substantial flexibility between the domains in N(260). Binding of pRb to a construct containing the LXCXE motif and the J domain revealed weak interactions between pRb and the J domain. Analysis of the complex of pRb and N(260) indicated that the OBD is not involved and retains its dynamic independence from the remainder of Tag. These results support a 'chaperone' model in which the J domain of Tag changes its orientation as it acts upon different protein complexes.

  6. Packaging of a large capacity magnetic bubble domain spacecraft recorder

    NASA Technical Reports Server (NTRS)

    Becker, F. J.; Stermer, R. L.

    1977-01-01

    A Solid State Spacecraft Data Recorder (SSDR), based on bubble domain technology, having a storage capacity of 10 to the 8th power bits, was designed and is being tested. The recorder consists of two memory modules each having 32 cells, each cell containing sixteen 100 kilobit serial bubble memory chips. The memory modules are interconnected to a Drive and Control Unit (DCU) module containing four microprocessors, 500 integrated circuits, a RAM core memory and two PROM's. The two memory modules and DCU are housed in individual machined aluminum frames, are stacked in brick fashion and through bolted to a base plate assembly which also houses the power supply.

  7. Single SQUID frequency-domain multiplexer for large bolometer arrays

    SciTech Connect

    Yoon, Jongsoo; Clarke, John; Gildemeister, J.M.; Lee, Adrian T.; Myers, M.J.; Skidmore, J.T.; Richards, P.L.; Spieler, H.G.

    2001-08-20

    We describe the development of a frequency-domain superconducting quantum interference device (SQUID) multiplexer which monitors a row of low-temperature sensors simultaneously with a single SQUID. Each sensor is ac biased with a unique frequency and all the sensor currents are added in a superconducting summing loop. A single SQUID measures the current in the summing loop, and the individual signals are lock-in detected after the room temperature SQUID electronics. The current in the summing loop is nulled by feedback to eliminate direct crosstalk. We have built an eight-channel prototype and demonstrated channel separation and signal recovery.

  8. The large terminase DNA packaging motor grips DNA with its ATPase domain for cleavage by the flexible nuclease domain.

    PubMed

    Hilbert, Brendan J; Hayes, Janelle A; Stone, Nicholas P; Xu, Rui-Gang; Kelch, Brian A

    2017-01-12

    Many viruses use a powerful terminase motor to pump their genome inside an empty procapsid shell during virus maturation. The large terminase (TerL) protein contains both enzymatic activities necessary for packaging in such viruses: the adenosine triphosphatase (ATPase) that powers DNA translocation and an endonuclease that cleaves the concatemeric genome at both initiation and completion of genome packaging. However, how TerL binds DNA during translocation and cleavage remains mysterious. Here we investigate DNA binding and cleavage using TerL from the thermophilic phage P74-26. We report the structure of the P74-26 TerL nuclease domain, which allows us to model DNA binding in the nuclease active site. We screened a large panel of TerL variants for defects in binding and DNA cleavage, revealing that the ATPase domain is the primary site for DNA binding, and is required for nuclease activity. The nuclease domain is dispensable for DNA binding but residues lining the active site guide DNA for cleavage. Kinetic analysis of DNA cleavage suggests flexible tethering of the nuclease domains during DNA cleavage. We propose that interactions with the procapsid during DNA translocation conformationally restrict the nuclease domain, inhibiting cleavage; TerL release from the capsid upon completion of packaging unlocks the nuclease domains to cleave DNA.

  9. Fabrication of Large Domain YBa2Cu3O(x) for Magnetic Suspension Applications

    NASA Technical Reports Server (NTRS)

    Sengupta, S.; Corpus, J.; Gaines, J. R., Jr.; Todt, V. R.; Zhang, X.; Miller, D. J.

    1996-01-01

    Large domain YBa2Cu3O(x) levitators have been fabricated using a seeded melt processing technique. Depending upon the seed, either a single or five domained sample can be obtained. The grain boundaries separating each domains in the five domain levitator are found to be 90 degrees. Similar levitation forces can be observed for single and five domained samples. After thermal cycling, however, a small decrease in the levitation force of the five domain levitator was observed as a function of thermal cycles while nearly no change in force was observed in the single domain levitator. Finally, it is shown that both, single and five domain YBCO, behave similarly as a function of sample thickness.

  10. Frequency domain identification experiment on a large flexible structure

    NASA Technical Reports Server (NTRS)

    Bayard, D. S.; Hadaegh, F. Y.; Yam, Y.; Scheid, R. E.; Mettler, E.; Milman, M. H.

    1989-01-01

    Recent experiences in the field of flexible structure control in space have indicated a need for on-orbit system identification to support robust control redesign to avoid in-flight instabilities and maintain high spacecraft performance. The authors highlight an automated frequency domain system identification methodology recently developed to fill this need. The methodology supports (1) the estimation of system quantities useful for robust control analysis and design, (2) experiment design tailored to performing system identification in a typically constrained on-orbit environment, and (3) the automation of operations to reduce human-in-the-loop requirements. A basic overview of the methodology is presented first, followed by an experimental verification of the approach performed on the JPL/AFAL testbed facility.

  11. Characterization of Arctic Highly Magnetic Domains - the Geophysical Expression of Inferred Large Igneous Province(s)

    NASA Astrophysics Data System (ADS)

    Saltus, R. W.; Oakey, G.; Miller, E. L.; Jackson, R.

    2012-12-01

    The magnetic anomalies of the high arctic are dominated by a large domain (1000 x 1700 km; the High Arctic Magnetic High, HAMH) consisting of numerous high-amplitude magnetic high ridges with a complex set of orientations and by other smaller, but still fundamentally highly magnetic, domains. The magnetic potential anomaly field (also known as pseudogravity) of the HAMH shows a single large intensity high and underscores the crustal-scale thickness of this geophysical feature (which also forms a prominent anomaly on satellite magnetic maps). The seafloor morphology of this region includes the complex linear trends of the Alpha and Mendeleev ridges, but the magnetic expression of this domain extends beyond the complex bathymetry to include areas where Canada Basin sediments have covered the complex basement topography. The calculated magnetic effect of the bathymetric ridges matches some of the observed magnetic anomalies, but not others. We have analyzed and modeled the distinctive HAMH and other smaller magnetic high domains to generate estimates of their volume and to characterize the directionality of their component features. Complimentary processing and modeling of high arctic gravity anomalies allows characterization of the density component of these geophysical features. Spatially, the HAMH encompasses the Alpha and Mendeleev "ridges," that are considered to represent a major mafic igneous province. The term "Alpha-Mendeleev Large Igneous Province" is given to a domain mapped by tracing magnetic anomalies in a recent map published by AAPG (Grantz and others, 2009). On this map the province is described as "alkali basalt with ages between 120 and 90 Ma". New seismic and bathymetric data, collected as part of on-going research efforts for definition of extended continental shelf, are revealing new details about the Alpha ridge. One interesting development is the possible identification of a supervolcano that may represent a major locus of igneous activity. In

  12. Automated frequency domain system identification of a large space structure

    NASA Technical Reports Server (NTRS)

    Yam, Y.; Bayard, D. S.; Hadaegh, F. Y.; Mettler, E.; Milman, M. H.

    1989-01-01

    This paper presents the development and experimental results of an automated on-orbit system identification method for large flexible spacecraft that yields estimated quantities to support on-line design and tuning of robust high performance control systems. The procedure consists of applying an input to the plant, obtaining an output, and then conducting nonparametric identification to yield the spectral estimate of the system transfer function. A parametric model is determined by curve fitting the spectral estimate to a rational transfer function. The identification method has been demonstrated experimentally on the Large Spacecraft Control Laboratory in JPL.

  13. The Invariance Hypothesis Implies Domain-Specific Regions in Visual Cortex

    PubMed Central

    Leibo, Joel Z.; Liao, Qianli; Anselmi, Fabio; Poggio, Tomaso

    2015-01-01

    Is visual cortex made up of general-purpose information processing machinery, or does it consist of a collection of specialized modules? If prior knowledge, acquired from learning a set of objects is only transferable to new objects that share properties with the old, then the recognition system’s optimal organization must be one containing specialized modules for different object classes. Our analysis starts from a premise we call the invariance hypothesis: that the computational goal of the ventral stream is to compute an invariant-to-transformations and discriminative signature for recognition. The key condition enabling approximate transfer of invariance without sacrificing discriminability turns out to be that the learned and novel objects transform similarly. This implies that the optimal recognition system must contain subsystems trained only with data from similarly-transforming objects and suggests a novel interpretation of domain-specific regions like the fusiform face area (FFA). Furthermore, we can define an index of transformation-compatibility, computable from videos, that can be combined with information about the statistics of natural vision to yield predictions for which object categories ought to have domain-specific regions in agreement with the available data. The result is a unifying account linking the large literature on view-based recognition with the wealth of experimental evidence concerning domain-specific regions. PMID:26496457

  14. Sonic hedgehog lineage in the mouse hypothalamus: from progenitor domains to hypothalamic regions

    PubMed Central

    2012-01-01

    Background The hypothalamus is a brain region with essential functions for homeostasis and energy metabolism, and alterations of its development can contribute to pathological conditions in the adult, like hypertension, diabetes or obesity. However, due to the anatomical complexity of the hypothalamus, its development is not well understood. Sonic hedgehog (Shh) is a key developmental regulator gene expressed in a dynamic pattern in hypothalamic progenitor cells. To obtain insight into hypothalamic organization, we used genetic inducible fate mapping (GIFM) to map the lineages derived from Shh-expressing progenitor domains onto the four rostrocaudally arranged hypothalamic regions: preoptic, anterior, tuberal and mammillary. Results Shh-expressing progenitors labeled at an early stage (before embryonic day (E)9.5) contribute neurons and astrocytes to a large caudal area including the mammillary and posterior tuberal regions as well as tanycytes (specialized median eminence glia). Progenitors labeled at later stages (after E9.5) give rise to neurons and astrocytes of the entire tuberal region and in particular the ventromedial nucleus, but not to cells in the mammillary region and median eminence. At this stage, an additional Shh-expressing domain appears in the preoptic area and contributes mostly astrocytes to the hypothalamus. Shh-expressing progenitors do not contribute to the anterior region at any stage. Finally, we show a gradual shift from neurogenesis to gliogenesis, so that progenitors expressing Shh after E12.5 generate almost exclusively hypothalamic astrocytes. Conclusions We define a fate map of the hypothalamus, based on the dynamic expression of Shh in the hypothalamic progenitor zones. We provide evidence that the large neurogenic Shh-expressing progenitor domains of the ventral diencephalon are continuous with those of the midbrain. We demonstrate that the four classical transverse zones of the hypothalamus have clearly defined progenitor domains

  15. Insights into Hox protein function from a large scale combinatorial analysis of protein domains.

    PubMed

    Merabet, Samir; Litim-Mecheri, Isma; Karlsson, Daniel; Dixit, Richa; Saadaoui, Mehdi; Monier, Bruno; Brun, Christine; Thor, Stefan; Vijayraghavan, K; Perrin, Laurent; Pradel, Jacques; Graba, Yacine

    2011-10-01

    Protein function is encoded within protein sequence and protein domains. However, how protein domains cooperate within a protein to modulate overall activity and how this impacts functional diversification at the molecular and organism levels remains largely unaddressed. Focusing on three domains of the central class Drosophila Hox transcription factor AbdominalA (AbdA), we used combinatorial domain mutations and most known AbdA developmental functions as biological readouts to investigate how protein domains collectively shape protein activity. The results uncover redundancy, interactivity, and multifunctionality of protein domains as salient features underlying overall AbdA protein activity, providing means to apprehend functional diversity and accounting for the robustness of Hox-controlled developmental programs. Importantly, the results highlight context-dependency in protein domain usage and interaction, allowing major modifications in domains to be tolerated without general functional loss. The non-pleoitropic effect of domain mutation suggests that protein modification may contribute more broadly to molecular changes underlying morphological diversification during evolution, so far thought to rely largely on modification in gene cis-regulatory sequences.

  16. The human insulin gene is part of a large open chromatin domain specific for human islets.

    PubMed

    Mutskov, Vesco; Felsenfeld, Gary

    2009-10-13

    Knowledge of how insulin (INS) gene expression is regulated will lead to better understanding of normal and abnormal pancreatic beta cell function. We have mapped histone modifications over the INS region, coupled with an expression profile, in freshly isolated islets from multiple human donors. Unlike many other human genes, in which active modifications tend to be concentrated within 1 kb around the transcription start site, these marks are distributed over the entire coding region of INS as well. Moreover, a region of approximately 80 kb around the INS gene, which contains the {tyrosine hydroxylase (TH)-(INS)-insulin-like growth factor 2 antisense (IGF2AS)-insulin-like growth factor 2 (IGF2)} gene cluster, unusually is marked by almost uniformly elevated levels of histone acetylation and H3K4 dimethylation, extending both downstream into IGF2 and upstream beyond the TH gene. This is accompanied by islet specific coordinate expression with INS of the neighboring TH and IGF2 genes. The presence of islet specific intergenic transcripts suggests their possible function in the maintenance of this unusual large open chromatin domain.

  17. Highly heterologous region in the N-terminal extracellular domain of reptilian follitropin receptors.

    PubMed

    Akazome, Y; Ogasawara, O; Park, M K; Mori, T

    1996-12-01

    The primary structure of the N-terminal extracellular region of the follitropin receptor (FSH-R), which is thought to be responsible for hormone binding specificity, was determined in three reptilian species (tortoise, gecko, and lizard). Remarkably low sequence homologies were detected in the C-terminal part of the extracellular domain. This region was estimated to be a part of exon 10, which is the last exon of the FSH-R gene. In this region, not only were low homologies detected among the three reptilian species, but also specific deletions and/or insertions were found. In particular, large deletions were detected in squamate (gecko and lizard) FSH-Rs. Phylogenetic analysis indicated that these large deletions occurred recently, i.e., after the Triassic period. In another region characterized, sequence homologies were high, with tortoise-rat homology 78.4%, gecko-rat 64.7%, and lizard-rat 69.1%. In this highly conserved region, however, some reptile-specific alterations were detected, such as the loss of a cysteine residue in putative exon 7 and the existence of potential N-linked glycosylation sites in putative exon 9.

  18. Insights into interphase large-scale chromatin structure from analysis of engineered chromosome regions.

    PubMed

    Belmont, A S; Hu, Y; Sinclair, P B; Wu, W; Bian, Q; Kireev, I

    2010-01-01

    How chromatin folds into mitotic and interphase chromosomes has remained a difficult question for many years. We have used three generations of engineered chromosome regions as a means of visualizing specific chromosome regions in live cells and cells fixed under conditions that preserve large-scale chromatin structure. Our results confirm the existence of large-scale chromatin domains and fibers formed by the folding of 10-nm and 30-nm chromatin fibers into larger, spatially distinct domains. Transcription at levels within severalfold of the levels measured for endogenous loci occur within these large-scale chromatin structures on a condensed template linearly compacted several hundred fold to 1000-fold relative to B-form DNA. However, transcriptional induction is accompanied by a severalfold decondensation of this large-scale chromatin structure that propagates hundreds of kilobases beyond the induced gene. Examination of engineered chromosome regions in mouse embryonic stem cells (ESCs) and differentiated cells suggests a surprising degree of plasticity in this large-scale chromatin structure, allowing long-range DNA interactions within the context of large-scale chromatin fibers. Recapitulation of gene-specific differences in large-scale chromatin conformation and nuclear positioning using these engineered chromosome regions will facilitate identification of cis and trans determinants of interphase chromosome architecture.

  19. Insights into interphase large-scale chromatin structure from analysis of engineered chromosome regions

    PubMed Central

    Belmont, Andrew S.; Hu, Yan; Sinclair, Paul; Wu, Wei; Bian, Qian; Kireev, Igor

    2012-01-01

    How chromatin folds into mitotic and interphase chromosomes has remained a difficult question for many years. We have used three generations of engineered chromosome regions as a means of visualizing specific chromosome regions in live cells and cells fixed under conditions which preserve large-scale chromatin structure. Our results confirm the existence of large-scale chromatin domains and fibers formed by the folding of 10 and 30 nm chromatin fibers into larger, spatially distinct domains. Transcription at levels within several fold of the levels measured for endogenous loci occur within these large-scale chromatin structures on a condensed template linearly compacted several hundred fold to one thousand fold relative to B-form DNA. However, transcriptional induction is accompanied by a several fold decondensation of this large-scale chromatin structure that propagates hundreds of kb beyond the induced gene. Examination of engineered chromosome regions in mouse ES and differentiated cells suggests a surprising degree of plasticity in this large-scale chromatin structure, allowing long-range DNA interactions within the context of large-scale chromatin fibers. Recapitulation of gene specific differences in large-scale chromatin conformation and nuclear positioning using these engineered chromosome regions will facilitate identification of cis and trans determinants of interphase chromosome architecture. PMID:21467143

  20. Functional analysis of the NH{sub 2}-terminal hydrophobic region and BRICHOS domain of GKN1

    SciTech Connect

    Yoon, Jung Hwan; Choi, Yoo Jin; Choi, Won Suk; Nam, Suk Woo; Lee, Jung Young; Park, Won Sang

    2013-11-01

    Highlights: •NH{sub 2}-terminal and BRICHOS domain of GKN1 inhibited tumor cell growth. •NH{sub 2}-terminal and BRICHOS domain of GKN1 regulated cell cycle. •NH{sub 2}-terminal and BRICHOS domain of GKN1 inhibited epigenetic regulators. -- Abstract: Gastrokine 1 (GKN1) protects the gastric antral mucosa and promotes healing by facilitating restitution and proliferation after injury. GKN1 is down-regulated in Helicobacter pylori-infected gastric epithelial cells and loss of GKN1 expression is tightly associated with gastric carcinogenesis. However, the underlying mechanisms as a tumor suppressor are largely unknown. Presently, the hydrophobic region and BRICHOS domain of GKN1, pGKN1{sup D13N}, pGKN1{sup Δ68–199}, and pGKN1{sup Δ1–67,165–199} were shown to suppress gastric cancer cell growth and recapitulate GKN1 functions. As well, the hydrophobic region and BRICHOS domain of GKN1 had a synergistic anti-cancer effect with 5-FU on tumor cell growth, implying that the NH{sub 2}-terminal hydrophobic region and BRICHOS domain of GKN1 are sufficient for tumor suppression, thereby suggesting a therapeutic intervention for gastric cancer. Also, its domain inducing endogenous miR-185 directly targeted the epigenetic effectors DNMT1 and EZH2 in gastric cancer cells. Our results suggest that the NH{sub 2}-terminal hydrophobic region and BRICHOS domain of GKN1 are sufficient for its tumor suppressor activities.

  1. Investigating the Role of Large-Scale Domain Dynamics in Protein-Protein Interactions

    PubMed Central

    Delaforge, Elise; Milles, Sigrid; Huang, Jie-rong; Bouvier, Denis; Jensen, Malene Ringkjøbing; Sattler, Michael; Hart, Darren J.; Blackledge, Martin

    2016-01-01

    Intrinsically disordered linkers provide multi-domain proteins with degrees of conformational freedom that are often essential for function. These highly dynamic assemblies represent a significant fraction of all proteomes, and deciphering the physical basis of their interactions represents a considerable challenge. Here we describe the difficulties associated with mapping the large-scale domain dynamics and describe two recent examples where solution state methods, in particular NMR spectroscopy, are used to investigate conformational exchange on very different timescales. PMID:27679800

  2. Development of a regional macroinvertebrate index for large river bioassessment

    EPA Science Inventory

    Large river bioassessment protocols lag far behind those of wadeable streams and often rely on fish assemblages of individual rivers. We developed a regional macroinvertebrate index and assessed relative condition of six large river tributaries to the upper Mississippi and Ohio r...

  3. Large-area formation of self-aligned crystalline domains of organic semiconductors on transistor channels using CONNECT.

    PubMed

    Park, Steve; Giri, Gaurav; Shaw, Leo; Pitner, Gregory; Ha, Jewook; Koo, Ja Hoon; Gu, Xiaodan; Park, Joonsuk; Lee, Tae Hoon; Nam, Ji Hyun; Hong, Yongtaek; Bao, Zhenan

    2015-05-05

    The electronic properties of solution-processable small-molecule organic semiconductors (OSCs) have rapidly improved in recent years, rendering them highly promising for various low-cost large-area electronic applications. However, practical applications of organic electronics require patterned and precisely registered OSC films within the transistor channel region with uniform electrical properties over a large area, a task that remains a significant challenge. Here, we present a technique termed "controlled OSC nucleation and extension for circuits" (CONNECT), which uses differential surface energy and solution shearing to simultaneously generate patterned and precisely registered OSC thin films within the channel region and with aligned crystalline domains, resulting in low device-to-device variability. We have fabricated transistor density as high as 840 dpi, with a yield of 99%. We have successfully built various logic gates and a 2-bit half-adder circuit, demonstrating the practical applicability of our technique for large-scale circuit fabrication.

  4. Allosteric role of the large-scale domain opening in biological catch-binding

    NASA Astrophysics Data System (ADS)

    Pereverzev, Yuriy V.; Prezhdo, Oleg V.; Sokurenko, Evgeni V.

    2009-05-01

    The proposed model demonstrates the allosteric role of the two-domain region of the receptor protein in the increased lifetimes of biological receptor/ligand bonds subjected to an external force. The interaction between the domains is represented by a bounded potential, containing two minima corresponding to the attached and separated conformations of the two protein domains. The dissociative potential with a single minimum describing receptor/ligand binding fluctuates between deep and shallow states, depending on whether the domains are attached or separated. A number of valuable analytic expressions are derived and are used to interpret experimental data for two catch bonds. The P-selectin/P-selectin-glycoprotein-ligand-1 (PSGL-1) bond is controlled by the interface between the epidermal growth factor (EGF) and lectin domains of P-selectin, and the type 1 fimbrial adhesive protein (FimH)/mannose bond is governed by the interface between the lectin and pilin domains of FimH. Catch-binding occurs in these systems when the external force stretches the receptor proteins and increases the interdomain distance. The allosteric effect is supported by independent measurements, in which the domains are kept separated by attachment of another ligand. The proposed model accurately describes the experimentally observed anomalous behavior of the lifetimes of the P-selectin/PSGL-1 and FimH/mannose complexes as a function of applied force and provides valuable insights into the mechanism of catch-binding.

  5. Epitaxial Growth and Electronic Properties of Large Hexagonal Graphene Domains on Cu(111) Thin Film

    NASA Astrophysics Data System (ADS)

    Ago, Hiroki; Kawahara, Kenji; Ogawa, Yui; Tanoue, Shota; Bissett, Mark A.; Tsuji, Masaharu; Sakaguchi, Hidetsugu; Koch, Roland J.; Fromm, Felix; Seyller, Thomas; Komatsu, Katsuyoshi; Tsukagoshi, Kazuhito

    2013-07-01

    Large hexagonal single-crystalline domains of single-layer graphene are epitaxially grown by ambient-pressure chemical vapor deposition over a thin Cu(111) film deposited on c-plane sapphire. The hexagonal graphene domains with a maximum size of 100 µm are oriented in the same direction due to the epitaxial growth. Reflecting high crystallinity, a clear band structure with the Dirac cone is observed by angle-resolved photoelectron spectroscopy (ARPES), and a high carrier mobility exceeding 4,000 cm2 V-1 s-1 is obtained on SiO2/Si at room temperature. Our epitaxial approach combined with large domain growth is expected to contribute to future electronic applications.

  6. How do disordered regions achieve comparable functions to structured domains?

    PubMed

    Latysheva, Natasha S; Flock, Tilman; Weatheritt, Robert J; Chavali, Sreenivas; Babu, M Madan

    2015-06-01

    The traditional structure to function paradigm conceives of a protein's function as emerging from its structure. In recent years, it has been established that unstructured, intrinsically disordered regions (IDRs) in proteins are equally crucial elements for protein function, regulation and homeostasis. In this review, we provide a brief overview of how IDRs can perform similar functions to structured proteins, focusing especially on the formation of protein complexes and assemblies and the mediation of regulated conformational changes. In addition to highlighting instances of such functional equivalence, we explain how differences in the biological and physicochemical properties of IDRs allow them to expand the functional and regulatory repertoire of proteins. We also discuss studies that provide insights into how mutations within functional regions of IDRs can lead to human diseases.

  7. Domain wall dynamics in ultrathin Pt/Co/AlOx microstrips under large combined magnetic fields

    NASA Astrophysics Data System (ADS)

    Jué, E.; Thiaville, A.; Pizzini, S.; Miltat, J.; Sampaio, J.; Buda-Prejbeanu, L. D.; Rohart, S.; Vogel, J.; Bonfim, M.; Boulle, O.; Auffret, S.; Miron, I. M.; Gaudin, G.

    2016-01-01

    The dynamics of magnetic domain walls in ultrathin strip-patterned Pt/Co/AlOx samples with perpendicular easy axis has been studied experimentally under an easy-axis field, superposed to a hard-axis field oriented along the strip. The easy-axis field is large so that the domain walls move well beyond the creep regime. A chiral effect is observed where the domain wall velocity shows a monotonous and surprisingly large variation with an in-plane field. A micromagnetic analysis, combining analytic, one-dimensional, and two-dimensional simulations with structural disorder, shows that this behavior can be reproduced with a Dzyaloshinskii-Moriya interaction of the interfacial type, with due consideration of the dynamics of the tilt degree of freedom of the domain wall. The estimated effective value of this interaction (D ≈-2.2 mJ /m2 for a 0.6 nm Co thickness) is consistent with values obtained by other techniques. It is also shown, by micromagnetic analysis, that several modes and characteristic times occur in the dynamics of the tilt of such domain walls.

  8. Large- to small-scale dynamo in domains of large aspect ratio: kinematic regime

    NASA Astrophysics Data System (ADS)

    Shumaylova, Valeria; Teed, Robert J.; Proctor, Michael R. E.

    2017-04-01

    The Sun's magnetic field exhibits coherence in space and time on much larger scales than the turbulent convection that ultimately powers the dynamo. In this work, we look for numerical evidence of a large-scale magnetic field as the magnetic Reynolds number, Rm, is increased. The investigation is based on the simulations of the induction equation in elongated periodic boxes. The imposed flows considered are the standard ABC flow (named after Arnold, Beltrami & Childress) with wavenumber ku = 1 (small-scale) and a modulated ABC flow with wavenumbers ku = m, 1, 1 ± m, where m is the wavenumber corresponding to the long-wavelength perturbation on the scale of the box. The critical magnetic Reynolds number R_m^{crit} decreases as the permitted scale separation in the system increases, such that R_m^{crit} ∝ [L_x/L_z]^{-1/2}. The results show that the α-effect derived from the mean-field theory ansatz is valid for a small range of Rm after which small scale dynamo instability occurs and the mean-field approximation is no longer valid. The transition from large- to small-scale dynamo is smooth and takes place in two stages: a fast transition into a predominantly small-scale magnetic energy state and a slower transition into even smaller scales. In the range of Rm considered, the most energetic Fourier component corresponding to the structure in the long x-direction has twice the length-scale of the forcing scale. The long-wavelength perturbation imposed on the ABC flow in the modulated case is not preserved in the eigenmodes of the magnetic field.

  9. Free-decay time-domain modal identification for large space structures

    NASA Technical Reports Server (NTRS)

    Kim, Hyoung M.; Vanhorn, David A.; Doiron, Harold H.

    1992-01-01

    Concept definition studies for the Modal Identification Experiment (MIE), a proposed space flight experiment for the Space Station Freedom (SSF), have demonstrated advantages and compatibility of free-decay time-domain modal identification techniques with the on-orbit operational constraints of large space structures. Since practical experience with modal identification using actual free-decay responses of large space structures is very limited, several numerical and test data reduction studies were conducted. Major issues and solutions were addressed, including closely-spaced modes, wide frequency range of interest, data acquisition errors, sampling delay, excitation limitations, nonlinearities, and unknown disturbances during free-decay data acquisition. The data processing strategies developed in these studies were applied to numerical simulations of the MIE, test data from a deployable truss, and launch vehicle flight data. Results of these studies indicate free-decay time-domain modal identification methods can provide accurate modal parameters necessary to characterize the structural dynamics of large space structures.

  10. Probabilistic flood risk assessment over large geographical regions

    NASA Astrophysics Data System (ADS)

    Dyck, Jozef; Willems, Patrick

    2013-06-01

    We develop a probabilistic model to estimate the rate of flood-induced losses for a set of properties distributed over a large geographical region (e.g., a portfolio of insured properties within a country). The use of detailed physically based models over large areas becomes difficult due to the vast amount of data needed and the high implementation cost. The proposed model allows one to incorporate results from such detailed models but can also be used in regions that have not been studied in much detail. Minimal required information includes the rate and spatial extent of severe precipitation, the topography and river network from which regions at risk of flooding can be identified, and information on historical floods with an approximate delineation of the flooded area, and associated aggregate losses for at least a few major events. An application to river flood loss from residential buildings in Belgium is presented.

  11. Sensitivity of Domain Size of a Regional Climate Model on the Indian Summer Monsoon Simulations

    NASA Astrophysics Data System (ADS)

    Pattnayak, K. C.; Panda, S. K.; Vaddi, D.; Mamgain, A.; Dash, S. K.

    2013-12-01

    The characteristics of Indian Summer Monsoon circulation and rainfall simulated by Regional Climate Model version 4.2 (RegCM4.2) using two domains: the smaller domain over India and the larger one over South Asia (SA) domain have been examined. The larger domain over the South Asia has been identified in the framework of World Climate Research Programme (WCRP) coordinated experiment known as the COordinated Regional climate Downscaling Experiment (CORDEX). This study is made over a period of 36 years starting from 1st January 1970 to 31st December 2005 at 50 km horizontal resolution of the model over both the domains using RegCM version 4.2. The UK Met Office Hadley Centre Global Circulation Model Version 2.0 (HadGEM2) outputs obtained from the Coupled Model Inter-comparison Project Phase 5 (CMIP5) for IPCC AR5 have been used as the initial and lateral boundary conditions. The model simulated precipitation has been compared with the IMD 0.5°x0.5° gridded rainfall which is available over the Indian land mass. Results show that the total precipitation is reduced significantly when the domain size is reduced from South Asia to smaller Indian domain. The simulated Indian precipitation obtained in the South Asian domain has a good agreement with the corresponding IMD observations. It is also seen that the domain size has dominant impact on the convective precipitation simulated by the model whereas there is no significant change in the non-convective precipitation. The wind field at 850hPa over the Arabian Sea is close to the NCEP/NCAR reanalysis in SA domain as compared against that obtained in the Indian domain. The cross-equatorial flow and the Somali Jet are better simulated in the SA than the Indian domain. Thus both the wind and rainfall fields' simulated by RegCM4 over India in case of SA domain are closer to the respective observations as compared to those obtained using the Indian domain. Since, the vertically integrated moisture flux over the Arabian Sea is

  12. Crystal structure of the simian virus 40 large T-antigen origin-binding domain.

    PubMed

    Meinke, Gretchen; Bullock, Peter A; Bohm, Andrew

    2006-05-01

    The origins of replication of DNA tumor viruses have a highly conserved feature, namely, multiple binding sites for their respective initiator proteins arranged as inverted repeats. In the 1.45-angstroms crystal structure of the simian virus 40 large T-antigen (T-ag) origin-binding domain (obd) reported herein, T-ag obd monomers form a left-handed spiral with an inner channel of 30 angstroms having six monomers per turn. The inner surface of the spiral is positively charged and includes residues known to bind DNA. Residues implicated in hexamerization of full-length T-ag are located at the interface between adjacent T-ag obd monomers. These data provide a high-resolution model of the hexamer of origin-binding domains observed in electron microscopy studies and allow the obd's to be oriented relative to the hexamer of T-ag helicase domains to which they are connected.

  13. Computational modelling of a large dimension wind farm cluster using domain coupling

    NASA Astrophysics Data System (ADS)

    da Costa Gomes, V. M. M. G.; Palma, J. M. L. M.

    2016-09-01

    The accuracy of Computational Fluid Dynamics (CFD) models for Atmospheric Boundary Layer (ABL) flows relies largely on the placement of the domain boundaries and the quality of the imposed flow conditions, the inlet boundary in particular. Exploiting the parabolic nature of many ABL flows and of CFD modelled ABL flow in particular, a precursor simulation is used as source of flow data to improve the target domain's inlet flow description over the standard synthetic boundary conditions, one-directionally coupling the solutions to the two simulations. Using the approach, a case of flow over a two wind farm offshore cluster is modelled using two small coupled simulations, matching the results of a single simulation including the full cluster at a significant computational time saving, in the order of 70%. Further savings were shown to be possible by reducing the resolution of the precursor simulation, with negligible impact on the results at the target domain.

  14. Crystal Structure of the Simian Virus 40 Large T-Antigen Origin-Binding Domain

    SciTech Connect

    Meinke,G.; Bullock, P.; Bohm, A.

    2006-01-01

    The origins of replication of DNA tumor viruses have a highly conserved feature, namely, multiple binding sites for their respective initiator proteins arranged as inverted repeats. In the 1.45- Angstroms crystal structure of the simian virus 40 large T-antigen (T-ag) origin-binding domain (obd) reported herein, T-ag obd monomers form a left-handed spiral with an inner channel of 30 Angstroms having six monomers per turn. The inner surface of the spiral is positively charged and includes residues known to bind DNA. Residues implicated in hexamerization of full-length T-ag are located at the interface between adjacent T-ag obd monomers. These data provide a high-resolution model of the hexamer of origin-binding domains observed in electron microscopy studies and allow the obd's to be oriented relative to the hexamer of T-ag helicase domains to which they are connected.

  15. Crystal structure of a conserved domain in the intermembrane space region of the plastid division protein ARC6.

    PubMed

    Kumar, Nitin; Radhakrishnan, Abhijith; Su, Chih-Chia; Osteryoung, Katherine W; Yu, Edward W

    2016-02-01

    The chloroplast division machinery is composed of numerous proteins that assemble as a large complex to divide double-membraned chloroplasts through binary fission. A key mediator of division-complex formation is ARC6, a chloroplast inner envelope protein and evolutionary descendant of the cyanobacterial cell division protein Ftn2. ARC6 connects stromal and cytosolic contractile rings across the two membranes through interaction with an outer envelope protein within the intermembrane space (IMS). The ARC6 IMS region bears a structurally uncharacterized domain of unknown function, DUF4101, that is highly conserved among ARC6 and Ftn2 proteins. Here we report the crystal structure of this domain from Arabidopsis thaliana ARC6. The domain forms an α/β barrel open towards the outer envelope membrane but closed towards the inner envelope membrane. These findings provide new clues into how ARC6 and its homologs contribute to chloroplast and cyanobacterial cell division.

  16. Investigation of multilayer domains in large-scale CVD monolayer graphene by optical imaging

    NASA Astrophysics Data System (ADS)

    Yu, Yuanfang; Li, Zhenzhen; Wang, Wenhui; Guo, Xitao; Jiang, Jie; Nan, Haiyan; Ni, Zhenhua

    2017-03-01

    CVD graphene is a promising candidate for optoelectronic applications due to its high quality and high yield. However, multi-layer domains could inevitably form at the nucleation centers during the growth. Here, we propose an optical imaging technique to precisely identify the multilayer domains and also the ratio of their coverage in large-scale CVD monolayer graphene. We have also shown that the stacking disorder in twisted bilayer graphene as well as the impurities on the graphene surface could be distinguished by optical imaging. Finally, we investigated the effects of bilayer domains on the optical and electrical properties of CVD graphene, and found that the carrier mobility of CVD graphene is seriously limited by scattering from bilayer domains. Our results could be useful for guiding future optoelectronic applications of large-scale CVD graphene. Project supported by the National Natural Science Foundation of China (Nos. 61422503, 61376104), the Open Research Funds of Key Laboratory of MEMS of Ministry of Education (SEU, China), and the Fundamental Research Funds for the Central Universities.

  17. Crystal structure of a shark single-domain antibody V region in complex with lysozyme.

    PubMed

    Stanfield, Robyn L; Dooley, Helen; Flajnik, Martin F; Wilson, Ian A

    2004-09-17

    Cartilaginous fish are the phylogenetically oldest living organisms known to possess components of the vertebrate adaptive immune system. Key to their immune response are heavy-chain, homodimeric immunoglobulins called new antigen receptors (IgNARs), in which the variable (V) domains recognize antigens with only a single immunoglobulin domain, akin to camelid heavy-chain V domains. The 1.45 angstrom resolution crystal structure of the type I IgNAR V domain in complex with hen egg-white lysozyme (HEL) reveals a minimal antigen-binding domain that contains only two of the three conventional complementarity-determining regions but still binds HEL with nanomolar affinity by means of a binding interface comparable in size to conventional antibodies.

  18. Local and Regional Impacts of Large Scale Wind Energy Deployment

    NASA Astrophysics Data System (ADS)

    Michalakes, J.; Hammond, S.; Lundquist, J. K.; Moriarty, P.; Robinson, M.

    2010-12-01

    The U.S. is currently on a path to produce 20% of its electricity from wind energy by 2030, almost a 10-fold increase over present levels of electricity generated from wind. Such high-penetration wind energy deployment will entail extracting elevated energy levels from the planetary boundary layer and preliminary studies indicate that this will have significant but uncertain impacts on the local and regional environment. State and federal regulators have raised serious concerns regarding potential agricultural impacts from large farms deployed throughout the Midwest where agriculture is the basis of the local economy. The effects of large wind farms have been proposed to be both beneficial (drying crops to reduce occurrences of fungal diseases, avoiding late spring freezes, enhancing pollen viability, reducing dew duration) and detrimental (accelerating moisture loss during drought) with no conclusive investigations thus far. As both wind and solar technologies are deployed at scales required to replace conventional technologies, there must be reasonable certainty that the potential environmental impacts at the micro, macro, regional and global scale do not exceed those anticipated from carbon emissions. Largely because of computational limits, the role of large wind farms in affecting regional-scale weather patterns has only been investigated in coarse simulations and modeling tools do not yet exist which are capable of assessing the downwind affects of large wind farms may have on microclimatology. In this presentation, we will outline the vision for and discuss technical and scientific challenges in developing a multi-model high-performance simulation capability covering the range of mesoscale to sub-millimeter scales appropriate for assessing local, regional, and ultimately global environmental impacts and quantifying uncertainties of large scale wind energy deployment scenarios. Such a system will allow continuous downscaling of atmospheric processes on wind

  19. On the domain-specificity of the visual and non-visual face-selective regions.

    PubMed

    Axelrod, Vadim

    2016-08-01

    What happens in our brains when we see a face? The neural mechanisms of face processing - namely, the face-selective regions - have been extensively explored. Research has traditionally focused on visual cortex face-regions; more recently, the role of face-regions outside the visual cortex (i.e., non-visual-cortex face-regions) has been acknowledged as well. The major quest today is to reveal the functional role of each this region in face processing. To make progress in this direction, it is essential to understand the extent to which the face-regions, and particularly the non-visual-cortex face-regions, process only faces (i.e., face-specific, domain-specific processing) or rather are involved in a more domain-general cognitive processing. In the current functional MRI study, we systematically examined the activity of the whole face-network during face-unrelated reading task (i.e., written meaningful sentences with content unrelated to faces/people and non-words). We found that the non-visual-cortex (i.e., right lateral prefrontal cortex and posterior superior temporal sulcus), but not the visual cortex face-regions, responded significantly stronger to sentences than to non-words. In general, some degree of sentence selectivity was found in all non-visual-cortex cortex. Present result highlights the possibility that the processing in the non-visual-cortex face-selective regions might not be exclusively face-specific, but rather more or even fully domain-general. In this paper, we illustrate how the knowledge about domain-general processing in face-regions can help to advance our general understanding of face processing mechanisms. Our results therefore suggest that the problem of face processing should be approached in the broader scope of cognition in general.

  20. A fast algorithm based on the domain decomposition method for scattering analysis of electrically large objects

    NASA Astrophysics Data System (ADS)

    Yin, Lei; Hong, Wei

    2002-01-01

    By combining the finite difference (FD) method with the domain decomposition method (DDM), a fast and rigorous algorithm is presented in this paper for the scattering analysis of extremely large objects. Unlike conventional methods, such as the method of moments (MOM) and FD method, etc., the new algorithm decomposes an original large domain into small subdomains and chooses the most efficient method to solve the electromagnetic (EM) equations on each subdomain individually. Therefore the computational complexity and scale are substantially reduced. The iterative procedure of the algorithm and the implementation of virtual boundary conditions are discussed in detail. During scattering analysis of an electrically large cylinder, the conformal band computational domain along the circumference of the cylinder is decomposed into sections, which results in a series of band matrices with very narrow band. Compared with the traditional FD method, it decreases the consumption of computer memory and CPU time from O(N2) to O(N/m) and O(N), respectively, where m is the number of subdomains and Nis the number of nodes or unknowns. Furthermore, this method can be easily applied for the analysis of arbitrary shaped cylinders because the subdomains can be divided into any possible form. On the other hand, increasing the number of subdomains will hardly increase the computing time, which makes it possible to analyze the EM scattering problems of extremely large cylinders only on a PC. The EM scattering by two-dimensional cylinders with maximum perimeter of 100,000 wavelengths is analyzed. Moreover, this method is very suitable for parallel computation, which can further promote the computational efficiency.

  1. Fabrication of large domain YBa{sub 2}Cu{sub 3}O{sub x} for magnetic suspension applications

    SciTech Connect

    Todt, V.R.; Zhang, X.; Miller, D.J.; Sengupta, S.; Corpus, J.; Gains, J.R. Jr.

    1995-12-31

    Large domain YBa{sub 2}Cu{sub 3}O{sub x} levitators have been fabricated using a seeded melt processing technique. Depending upon the seed, either a single or five domained sample can be obtained. The grain boundaries separating each domains in the five domain levitator are found to be 90 degrees. Similar levitation forces can be observed for single and five domained samples. After thermal cycling, however, a small decrease in the levitation force of the five domain levitator was observed as a function of thermal cycles while nearly no change in force was observed in the single domain levitator. Finally it is shown that both, single and five domain YBCO, behave similarly as a function of sample thickness.

  2. The CHAP domain: a large family of amidases including GSP amidase and peptidoglycan hydrolases.

    PubMed

    Bateman, Alex; Rawlings, Neil D

    2003-05-01

    Cleavage of peptidoglycan plays an important role in bacterial cell division, cell growth and cell lysis. Here, we reveal that several known peptidoglycan amidases fall into a family, which includes many proteins of previously unknown function. The family includes two different peptidoglycan cleavage activities: L-muramoyl-L-alanine amidase and D-alanyl-glycyl endopeptidase activity. The family includes the amidase portion of the bifunctional glutathionylspermidine synthase/amidase enzyme from bacteria and pathogenic trypanosomes. The glutathionylspermidine synthase is thought to be a key component of the alternative pathway in trypanosomes for protection from oxygen-radical damage and has been proposed as a potential drug target. The CHAP (cysteine, histidine-dependent amidohydrolases/peptidases) domain is often found in association with other domains that cleave peptidoglycan. The large number of multifunctional hydrolases suggests that they might act in a cooperative manner to cleave specialized substrates.

  3. Parallel Domain Decomposition Formulation and Software for Large-Scale Sparse Symmetrical/Unsymmetrical Aeroacoustic Applications

    NASA Technical Reports Server (NTRS)

    Nguyen, D. T.; Watson, Willie R. (Technical Monitor)

    2005-01-01

    The overall objectives of this research work are to formulate and validate efficient parallel algorithms, and to efficiently design/implement computer software for solving large-scale acoustic problems, arised from the unified frameworks of the finite element procedures. The adopted parallel Finite Element (FE) Domain Decomposition (DD) procedures should fully take advantages of multiple processing capabilities offered by most modern high performance computing platforms for efficient parallel computation. To achieve this objective. the formulation needs to integrate efficient sparse (and dense) assembly techniques, hybrid (or mixed) direct and iterative equation solvers, proper pre-conditioned strategies, unrolling strategies, and effective processors' communicating schemes. Finally, the numerical performance of the developed parallel finite element procedures will be evaluated by solving series of structural, and acoustic (symmetrical and un-symmetrical) problems (in different computing platforms). Comparisons with existing "commercialized" and/or "public domain" software are also included, whenever possible.

  4. Rayleigh-Bénard convection in large-aspect-ratio domains.

    PubMed

    Paul, M R; Chiam, K-H; Cross, M C; Fischer, P F

    2004-08-06

    The coarsening and wave number selection of striped states growing from random initial conditions are studied in a nonrelaxational, spatially extended, and far-from-equilibrium system by performing large-scale numerical simulations of Rayleigh-Bénard convection in a large-aspect-ratio cylindrical domain with experimentally realistic boundaries. We find evidence that various measures of the coarsening dynamics scale in time with different power-law exponents, indicating that multiple length scales are required in describing the time dependent pattern evolution. The translational correlation length scales with time as t0.12, the orientational correlation length scales as t0.54, and the density of defects scale as t(-0.45). The final pattern evolves toward the wave number where isolated dislocations become motionless, suggesting a possible wave number selection mechanism for large-aspect-ratio convection.

  5. Absence of remotely triggered large earthquakes beyond the mainshock region

    USGS Publications Warehouse

    Parsons, T.; Velasco, A.A.

    2011-01-01

    Large earthquakes are known to trigger earthquakes elsewhere. Damaging large aftershocks occur close to the mainshock and microearthquakes are triggered by passing seismic waves at significant distances from the mainshock. It is unclear, however, whether bigger, more damaging earthquakes are routinely triggered at distances far from the mainshock, heightening the global seismic hazard after every large earthquake. Here we assemble a catalogue of all possible earthquakes greater than M 5 that might have been triggered by every M 7 or larger mainshock during the past 30 years. We compare the timing of earthquakes greater than M 5 with the temporal and spatial passage of surface waves generated by large earthquakes using a complete worldwide catalogue. Whereas small earthquakes are triggered immediately during the passage of surface waves at all spatial ranges, we find no significant temporal association between surface-wave arrivals and larger earthquakes. We observe a significant increase in the rate of seismic activity at distances confined to within two to three rupture lengths of the mainshock. Thus, we conclude that the regional hazard of larger earthquakes is increased after a mainshock, but the global hazard is not.

  6. Light domain walls, massive neutrinos and the large scale structure of the Universe

    NASA Technical Reports Server (NTRS)

    Massarotti, Alessandro

    1991-01-01

    Domain walls generated through a cosmological phase transition are considered, which interact nongravitationally with light neutrinos. At a redshift z greater than or equal to 10(exp 4), the network grows rapidly and is virtually decoupled from the matter. As the friction with the matter becomes dominant, a comoving network scale close to that of the comoving horizon scale at z of approximately 10(exp 4) gets frozen. During the later phases, the walls produce matter wakes of a thickness d of approximately 10h(exp -1)Mpc, that may become seeds for the formation of the large scale structure observed in the Universe.

  7. The EBNA-2 arginine-glycine domain is critical but not essential for B-lymphocyte growth transformation; the rest of region 3 lacks essential interactive domains.

    PubMed Central

    Tong, X; Yalamanchili, R; Harada, S; Kieff, E

    1994-01-01

    Since deletion of region 3 (amino acids [aa] 333 to 425) of Epstein-Barr virus nuclear protein 2 (EBNA-2) results in EBV recombinants which cannot transform primary B lymphocytes (J. I. Cohen, F. Wang, and E. Kieff, J. Virol. 65:2545-2554, 1991), the role of domains of region 3 was investigated. Deletion of the Arg-Gly repeat domain, R-337GQSRGRGRGRGRGRGKG354, results in EBV recombinants that transform primary B lymphocytes with modestly decreased activity. The transformed cells grow slowly and are difficult to expand. EBNA-2 deleted for the Arg-Gly domain does not associate with the nuclear chromatin fraction. The Arg-Gly repeat has an intrinsic ability to bind to histone H1, to other proteins, including EBNA-1, and to nucleic acids, especially poly(G). Two independent deletions of each part of the rest of region 3 (aa 359 to 383 and 385 to 430) have little effect on transformation, while deletion of the rest of region 3 (aa 361 to 425) as a single segment substantially reduces transformation efficiency. EBNA-2 deleted for all of region 3 can still transactivate the LMP1 promoter in transient expression assays but is less active than EBNA-2 in transactivating the BamHI-C promoter. EBNA-2 deleted for the Arg-Gly domain is better than EBNA-2 at transactivating the LMP1 promoter and is as active as EBNA-2 in transactivating the BamHI-C promoter. These data are most compatible with a model in which the Arg-Gly domain of region 3 is a modulator of EBNA-2 interactions and activities, while the rest of region 3 is important in positioning the region 2 J kappa binding domain relative to the region 4 acidic transactivating domain. Despite the null phenotype of the region 3 deletion, region 3 is unlikely to mediate essential interactions with other proteins. Images PMID:8083959

  8. Design of the large hadron electron collider interaction region

    NASA Astrophysics Data System (ADS)

    Cruz-Alaniz, E.; Newton, D.; Tomás, R.; Korostelev, M.

    2015-11-01

    The large hadron electron collider (LHeC) is a proposed upgrade of the Large Hadron Collider (LHC) within the high luminosity LHC (HL-LHC) project, to provide electron-nucleon collisions and explore a new regime of energy and luminosity for deep inelastic scattering. The design of an interaction region for any collider is always a challenging task given that the beams are brought into crossing with the smallest beam sizes in a region where there are tight detector constraints. In this case integrating the LHeC into the existing HL-LHC lattice, to allow simultaneous proton-proton and electron-proton collisions, increases the difficulty of the task. A nominal design was presented in the the LHeC conceptual design report in 2012 featuring an optical configuration that focuses one of the proton beams of the LHC to β*=10 cm in the LHeC interaction point to reach the desired luminosity of L =1033 cm-2 s-1 . This value is achieved with the aid of a new inner triplet of quadrupoles at a distance L*=10 m from the interaction point. However the chromatic beta beating was found intolerable regarding machine protection issues. An advanced chromatic correction scheme was required. This paper explores the feasibility of the extension of a novel optical technique called the achromatic telescopic squeezing scheme and the flexibility of the interaction region design, in order to find the optimal solution that would produce the highest luminosity while controlling the chromaticity, minimizing the synchrotron radiation power and maintaining the dynamic aperture required for stability.

  9. Large scale arrays of four-state vortex domains in BiFeO3 thin film

    NASA Astrophysics Data System (ADS)

    Wang, W. Y.; Zhu, Y. L.; Tang, Y. L.; Xu, Y. B.; Liu, Y.; Li, S.; Zhang, S. R.; Wang, Y. J.; Ma, X. L.

    2016-11-01

    Exotic domain states, like vortex, offer the promise of superior properties and the potential disclination strain is a key factor for their formation in ferroelectrics. Here we show that large scale arrays of four-state vortex domains can be obtained in rhombohedral BiFeO3 thin films grown on PrScO3 substrates by pulsed laser deposition. Cs-corrected scanning transmission electron microscopy demonstrates that each vortex domain is comprised of four ferroelectric variants with two 180° domain walls and two 109° domain walls. Atomic mappings of the lattice distortions unit cell by unit cell reveal that the cores of the vortex might be charged. The strains are mainly concentrated on domain walls. The formation mechanism of such large scale vortex-like states was discussed.

  10. Classical convective energy transport in large gradient regions

    SciTech Connect

    Hinton, F.L.

    1996-12-31

    Large gradients in density and temperature occur near the edge in H-mode plasmas and in the core of tokamak plasmas with negative central shear. Transport in these regions may be comparable to neoclassical. Standard neoclassical theory does not apply when the gradient lengths are comparable to an ion orbit excursion, or banana width. A basic question for neoclassical transport in large gradient regions is: do ion-ion collisions drive particle transport? Near the plasma edge in H-mode, where ion orbit loss requires that the ion energy transport be convective, neoclassical particle transport due to ion-ion collisions may play an important role. In negative central shear plasmas, where transport is inferred to be near neoclassical, it is important to have accurate predictions for the neoclassical rate of energy and particle transport. A simple 2-D slab model has been used, with a momentum-conserving collision operator, to show that ion-ion collisions do drive particle transport. When the gradients are large, the {open_quotes}field particle{close_quotes} contribution to the particle flux is non-local, and does not cancel the {open_quotes}test particle{close_quotes} contribution, which is local. Solutions of the kinetic equation are found which show that the steepness of the density profile, for increasing particle flux, is limited by orbit averaging. The gradient length is limited by the thermal gyroradius, and the convective energy flux is independent of ion temperature. This will allow an ion thermal runaway to occur, if there are no other ion energy loss mechanisms.

  11. Importance of the Linker Region in Matrix Metalloproteinase-1 Domain Interactions

    PubMed Central

    Singh, Warispreet; Fields, Gregg B.; Christov, Christo Z.; Karabencheva-Christova, Tatyana G.

    2016-01-01

    Collagenolysis is catalyzed by enzymes from the matrix metalloproteinase (MMP) family, where one of the most studied is MMP-1. The X-ray crystallographic structure of MMP-1 complexed with a collagen-model triple-helical peptide (THP) provided important atomistic information, but few details on the effects of the conformational flexibility on catalysis. In addition, the role of the linker region between the catalytic (CAT) and hemopexin-like (HPX) domains was not defined. In order to reveal the dynamics and correlations of MMP-1 comprehensive atomistic molecular dynamics simulations of an MMP-1•THP complex was performed. To examine the role of the linker region for MMP-1 function simulations with linker regions from MT1-MMP/MMP-14 and MMP-13 replacing the MMP-1 linker region were performed. The MD studies were in good agreement with the experimental observation that in the MMP-1•THP X-ray crystallographic structure MMP-1 is in a “closed” conformation. MD revealed that the interactions of the THP with the both the CAT and HPX domains of MMP-1 are dynamic in nature, and the linker region of MMP-1 influences the interactions and dynamics of both the CAT and HPX domains and collagen binding to MMP-1. PMID:26998255

  12. Regional climate projections for the MENA-CORDEX domain: analysis of projected temperature and precipitation changes

    NASA Astrophysics Data System (ADS)

    Hänsler, Andreas; Weber, Torsten; Eggert, Bastian; Saeed, Fahad; Jacob, Daniela

    2014-05-01

    Within the CORDEX initiative a multi-model suite of regionalized climate change information will be made available for several regions of the world. The German Climate Service Center (CSC) is taking part in this initiative by applying the regional climate model REMO to downscale global climate projections of different coupled general circulation models (GCMs) for several CORDEX domains. Also for the MENA-CORDEX domain, a set of regional climate change projections has been established at the CSC by downscaling CMIP5 projections of the Max-Planck-Institute Earth System Model (MPI-ESM) for the scenarios RCP4.5 and RCP8.5 with the regional model REMO for the time period from 1950 to 2100 to a horizontal resolution of 0.44 degree. In this study we investigate projected changes in future climate conditions over the domain towards the end of the 21st century. Focus in the analysis is given to projected changes in the temperature and rainfall characteristics and their differences for the two scenarios will be highlighted.

  13. More Than 1,001 Problems with Protein Domain Databases: Transmembrane Regions, Signal Peptides and the Issue of Sequence Homology

    PubMed Central

    Wong, Wing-Cheong; Maurer-Stroh, Sebastian; Eisenhaber, Frank

    2010-01-01

    Large-scale genome sequencing gained general importance for life science because functional annotation of otherwise experimentally uncharacterized sequences is made possible by the theory of biomolecular sequence homology. Historically, the paradigm of similarity of protein sequences implying common structure, function and ancestry was generalized based on studies of globular domains. Having the same fold imposes strict conditions over the packing in the hydrophobic core requiring similarity of hydrophobic patterns. The implications of sequence similarity among non-globular protein segments have not been studied to the same extent; nevertheless, homology considerations are silently extended for them. This appears especially detrimental in the case of transmembrane helices (TMs) and signal peptides (SPs) where sequence similarity is necessarily a consequence of physical requirements rather than common ancestry. Thus, matching of SPs/TMs creates the illusion of matching hydrophobic cores. Therefore, inclusion of SPs/TMs into domain models can give rise to wrong annotations. More than 1001 domains among the 10,340 models of Pfam release 23 and 18 domains of SMART version 6 (out of 809) contain SP/TM regions. As expected, fragment-mode HMM searches generate promiscuous hits limited to solely the SP/TM part among clearly unrelated proteins. More worryingly, we show explicit examples that the scores of clearly false-positive hits, even in global-mode searches, can be elevated into the significance range just by matching the hydrophobic runs. In the PIR iProClass database v3.74 using conservative criteria, we find that at least between 2.1% and 13.6% of its annotated Pfam hits appear unjustified for a set of validated domain models. Thus, false-positive domain hits enforced by SP/TM regions can lead to dramatic annotation errors where the hit has nothing in common with the problematic domain model except the SP/TM region itself. We suggest a workflow of flagging

  14. Improved precipitation extremes and climatology in a regional coupled model simulation over CORDEX south Asia domain

    NASA Astrophysics Data System (ADS)

    Kumar, P.; Sein, D.; Cabos, W.; Jacob, D.

    2014-12-01

    The South Asian continents are densely populated and their economy is largely dependent on agriculture which primarily depends on the summer monsoon (June-September). The region is highly vulnerable to climate variability and change. It has been well established that the SST anomalies in the Indian and the Pacific Ocean attributes to the monsoon interannual as well as intraseasonal variability. Most of the CMIP3 and CMIP5 climate models have difficulty in simulating the mean climate over South Asia. Regional Climate Models (RCMs) however simulate orographic induced precipitation better, but show limited ability to simulate mean precipitation over land and an overestimation over ocean more generally. These systematic differences between climate models and observation's may be related to poorly represented ocean dynamics and SST.For the first time a regional coupled atmosphere-ocean model is developed to study the monsoon climatology over the CORDEX South Asia domain. The REgional atmosphere MOdel REMO with 50km horizontal resolution is coupled via Oasis coupler to the Max Planck Institute for Meteorology global ocean - sea ice model MPIOM with increased resolution over the Indian Ocean (up to 20 km). Hereafter this coupled system will be called as ROM. For this study, four simulations for the period 1958-2001 are performed (i) REMO forced with ECMWF ERA40 reanalysis (ii) ROM forced with ECMWF ERA40 reanalysis (iii) REMO forced with MPI-ESM-LR CMIP5 historical simulation (iv) ROM forced with MPI-ESM-LR CMIP5 historical simulation. Differences in coupled and un-coupled RCM simulations are analyzed to investigate the effect of coupling on simulated climate, especially precipitation daily annual cycles and monthly spatial patterns. It has been observed that simulated feedback of ocean SST has positive influence on precipitation simulation of ROM both over land and ocean. The intensity of tropical cyclone is well simulated by the model ROM which improves the monsoon

  15. Solution coating of large-area organic semiconductor thin films with aligned single-crystalline domains

    NASA Astrophysics Data System (ADS)

    Diao, Ying; Tee, Benjamin C.-K.; Giri, Gaurav; Xu, Jie; Kim, Do Hwan; Becerril, Hector A.; Stoltenberg, Randall M.; Lee, Tae Hoon; Xue, Gi; Mannsfeld, Stefan C. B.; Bao, Zhenan

    2013-07-01

    Solution coating of organic semiconductors offers great potential for achieving low-cost manufacturing of large-area and flexible electronics. However, the rapid coating speed needed for industrial-scale production poses challenges to the control of thin-film morphology. Here, we report an approach—termed fluid-enhanced crystal engineering (FLUENCE)—that allows for a high degree of morphological control of solution-printed thin films. We designed a micropillar-patterned printing blade to induce recirculation in the ink for enhancing crystal growth, and engineered the curvature of the ink meniscus to control crystal nucleation. Using FLUENCE, we demonstrate the fast coating and patterning of millimetre-wide, centimetre-long, highly aligned single-crystalline organic semiconductor thin films. In particular, we fabricated thin films of 6,13-bis(triisopropylsilylethynyl) pentacene having non-equilibrium single-crystalline domains and an unprecedented average and maximum mobilities of 8.1±1.2 cm2 V-1 s-1 and 11 cm2 V-1 s-1. FLUENCE of organic semiconductors with non-equilibrium single-crystalline domains may find use in the fabrication of high-performance, large-area printed electronics.

  16. Solution coating of large-area organic semiconductor thin films with aligned single-crystalline domains.

    PubMed

    Diao, Ying; Tee, Benjamin C-K; Giri, Gaurav; Xu, Jie; Kim, Do Hwan; Becerril, Hector A; Stoltenberg, Randall M; Lee, Tae Hoon; Xue, Gi; Mannsfeld, Stefan C B; Bao, Zhenan

    2013-07-01

    Solution coating of organic semiconductors offers great potential for achieving low-cost manufacturing of large-area and flexible electronics. However, the rapid coating speed needed for industrial-scale production poses challenges to the control of thin-film morphology. Here, we report an approach--termed fluid-enhanced crystal engineering (FLUENCE)--that allows for a high degree of morphological control of solution-printed thin films. We designed a micropillar-patterned printing blade to induce recirculation in the ink for enhancing crystal growth, and engineered the curvature of the ink meniscus to control crystal nucleation. Using FLUENCE, we demonstrate the fast coating and patterning of millimetre-wide, centimetre-long, highly aligned single-crystalline organic semiconductor thin films. In particular, we fabricated thin films of 6,13-bis(triisopropylsilylethynyl) pentacene having non-equilibrium single-crystalline domains and an unprecedented average and maximum mobilities of 8.1±1.2 cm(2) V(-1) s(-1) and 11 cm(2) V(-1) s(-1). FLUENCE of organic semiconductors with non-equilibrium single-crystalline domains may find use in the fabrication of high-performance, large-area printed electronics.

  17. Regional Bowen ratio controls on afternoon moist convection: A large eddy simulation study

    NASA Astrophysics Data System (ADS)

    Kang, Song-Lak

    2016-12-01

    This study examines the effect of the regional Bowen ratio β, the ratio of the domain-averaged surface sensible heat flux (SHF) to latent heat flux (LHF), on afternoon moist convection. With a temporally evolving but spatially uniform surface available energy over a mesoscale domain under a weak capping inversion, we run large eddy simulation of the afternoon convective boundary layer (CBL). We first prescribe a small β of 0.56 (a wet surface) and then the reversed large β of 1.80 (a dry surface) by switching the SHF and LHF fields. The perturbation fields of the fluxes are prescribed with the Fourier spectra of κ- 3 (κ is horizontal wave number; strong mesoscale heterogeneity) and κ0 (homogeneity). The large β cases have strong vertical buoyancy fluxes and produce more vigorous updrafts. In the heterogeneous, large β surface case, with the removal of convective inhibition over a mesoscale subdomain of large SHF, deep convection develops. In the heterogeneous, small β surface case, convective clouds develop but do not progress into precipitating convection. In the homogeneous surface cases, randomly distributed shallow clouds develop with significantly more and thicker clouds in the large β case. (Co)spectral analyses confirm the more vigorous turbulent thermals in the large β cases and reveal that the moisture advection by the surface heterogeneity-induced mesoscale flows makes the correlation between mesoscale temperature and moisture perturbations change from negative to positive, which facilitates the mesoscale pool of high relative humidity air just above the CBL top, a necessary condition for deep convection.

  18. A case study of the intraseasonal oscillation traversing the TOGA-COARE LSD. [large-scale domain

    NASA Technical Reports Server (NTRS)

    Vincent, Dayton G.; Schrage, Jon M.; Sliwinski, L. D.

    1993-01-01

    The paper presents examination of tree intraseasonal (30-60 day) oscillations (ISOs) that occurred during the southern summer season (December 1, 1985 - February 28, 1986) traversing the Large-Scale Domain (LSD) TOGA-COARE, the region which also plays an important role in ENSO, Australian monsoon, and extratropical circulations. Data presented include Hovmoeller diagrams of 5-day running means of 250-mb velocity potential anomalies and OLR anomalies; graphs of five-day running means of OLR in precipitable water (W) per sq m, averaged over 10 x 10 deg boxes centered on 5 S and (1) 145 E, (2) 155 E, (3) 165 E, and (4) 165 D, indicating the midpoint of each ISO; and vertical profiles of zonal wind in m/s averaged over the time period that each ISO spends in the 10 x 10 deg box centered at 5 S, and 175 E and 145 E.

  19. Asymmetric assembly of Merkel cell polyomavirus large T-antigen origin binding domains at the viral origin.

    PubMed

    Harrison, Celia J; Meinke, Gretchen; Kwun, Hyun Jin; Rogalin, Henry; Phelan, Paul J; Bullock, Peter A; Chang, Yuan; Moore, Patrick S; Bohm, Andrew

    2011-06-17

    The double-stranded DNA polyomavirus Merkel cell polyomavirus (MCV) causes Merkel cell carcinoma, an aggressive but rare human skin cancer that most often affects immunosuppressed and elderly persons. As in other polyomaviruses, the large T-antigen of MCV recognizes the viral origin of replication by binding repeating G(A/G)GGC pentamers. The spacing, number, orientation, and necessity of repeats for viral replication differ, however, from other family members such as SV40 and murine polyomavirus. We report here the 2.9 Å crystal structure of the MCV large T-antigen origin binding domain (OBD) in complex with a DNA fragment from the MCV origin of replication. Consistent with replication data showing that three of the G(A/G)GGC-like binding sites near the center of the origin are required for replication, the crystal structure contains three copies of the OBD. This stoichiometry was verified using isothermal titration calorimetry. The affinity for G(A/G)GGC-containing double-stranded DNA was found to be ~740 nM, approximately 8-fold weaker than the equivalent domain in SV40 for the analogous region of the SV40 origin. The difference in affinity is partially attributable to DNA-binding residue Lys331 (Arg154 in SV40). In contrast to SV40, a small protein-protein interface is observed between MCV OBDs when bound to the central region of the origin. This protein-protein interface is reminiscent of that seen in bovine papilloma virus E1 protein. Mutational analysis indicates, however, that this interface contributes little to DNA binding energy.

  20. Asymmetric Assembly of Merkel Cell Polyomavirus Large T-Antigen Origin Binding Domains at the Viral Origin

    SciTech Connect

    C Harrison; G Meinke; H Kwun; H Rogalin; P Phelan; P Bullock; Y Chang; P Moore; A Bohm

    2011-12-31

    The double-stranded DNA polyomavirus Merkel cell polyomavirus (MCV) causes Merkel cell carcinoma, an aggressive but rare human skin cancer that most often affects immunosuppressed and elderly persons. As in other polyomaviruses, the large T-antigen of MCV recognizes the viral origin of replication by binding repeating G(A/G)GGC pentamers. The spacing, number, orientation, and necessity of repeats for viral replication differ, however, from other family members such as SV40 and murine polyomavirus. We report here the 2.9 {angstrom} crystal structure of the MCV large T-antigen origin binding domain (OBD) in complex with a DNA fragment from the MCV origin of replication. Consistent with replication data showing that three of the G(A/G)GGC-like binding sites near the center of the origin are required for replication, the crystal structure contains three copies of the OBD. This stoichiometry was verified using isothermal titration calorimetry. The affinity for G(A/G)GGC-containing double-stranded DNA was found to be {approx} 740 nM, approximately 8-fold weaker than the equivalent domain in SV40 for the analogous region of the SV40 origin. The difference in affinity is partially attributable to DNA-binding residue Lys331 (Arg154 in SV40). In contrast to SV40, a small protein-protein interface is observed between MCV OBDs when bound to the central region of the origin. This protein-protein interface is reminiscent of that seen in bovine papilloma virus E1 protein. Mutational analysis indicates, however, that this interface contributes little to DNA binding energy.

  1. Large cutting tools in the Danjiangkou Reservoir Region, central China.

    PubMed

    Kuman, Kathleen; Li, Chaorong; Li, Hao

    2014-11-01

    Handaxe-bearing sites in China are currently known to occur in a number of alluvial basins, the best known being Dingcun, Bose and Luonan. Bose in the south and Luonan in central China on the northern margin of the Qinling Mountains are most familiar to English-speaking researchers. Here we document the Danjiangkou Reservoir Region (DRR) as another major area for large cutting tools (LCTs), located in central China on the southeastern edge of the Qinling Mountains. Large cutting tools are preserved in three terraces of the Han and Dan Rivers in Hubei and Henan Provinces, with dates from ca. 0.8 Ma (millions of years ago) (Terrace 4) to the first half of the Middle Pleistocene (Terrace 3), and possibly to the Late Pleistocene (Terrace 2). This paper reports on LCTs discovered in Terraces 3 and 2, with a majority from the older terrace (and one specimen from Terrace 4). Regional environments during the Middle Pleistocene were relatively warm, humid and stable. Despite the poor quality of raw materials (predominantly quartz phyllite and trachyte for the LCTs), good examples of both handaxes and cleavers are present, plus two types of picks. The LCT technology is compared and contrasted with other Asian industries and with the Acheulean. Overall the DRR LCTs show both technological and morphological similarities with Acheulean LCTs, with some differences that are mainly attributed to raw material properties, subsistence ecology, and 'cultural drift.' The DRR LCTs expand the range of morphological variability of the East Asian material and highlight the need for greater reliance on technological analysis and raw material evaluation for best comparison of Chinese assemblages with the Acheulean tradition.

  2. Flood Hazard Mapping over Large Regions using Geomorphic Approaches

    NASA Astrophysics Data System (ADS)

    Samela, Caterina; Troy, Tara J.; Manfreda, Salvatore

    2016-04-01

    Historically, man has always preferred to settle and live near the water. This tendency has not changed throughout time, and today nineteen of the twenty most populated agglomerations of the world (Demographia World Urban Areas, 2015) are located along watercourses or at the mouth of a river. On one hand, these locations are advantageous from many points of view. On the other hand, they expose significant populations and economic assets to a certain degree of flood hazard. Knowing the location and the extent of the areas exposed to flood hazards is essential to any strategy for minimizing the risk. Unfortunately, in data-scarce regions the use of traditional floodplain mapping techniques is prevented by the lack of the extensive data required, and this scarcity is generally most pronounced in developing countries. The present work aims to overcome this limitation by defining an alternative simplified procedure for a preliminary, but efficient, floodplain delineation. To validate the method in a data-rich environment, eleven flood-related morphological descriptors derived from DEMs have been used as linear binary classifiers over the Ohio River basin and its sub-catchments, measuring their performances in identifying the floodplains at the change of the topography and the size of the calibration area. The best performing classifiers among those analysed have been applied and validated across the continental U.S. The results suggest that the classifier based on the index ln(hr/H), named the Geomorphic Flood Index (GFI), is the most suitable to detect the flood-prone areas in data-scarce environments and for large-scale applications, providing good accuracy with low requirements in terms of data and computational costs. Keywords: flood hazard, data-scarce regions, large-scale studies, binary classifiers, DEM, USA.

  3. Functional regions of the N-terminal domain of the antiterminator RfaH

    PubMed Central

    Belogurov, Georgiy A; Sevostyanova, Anastasia; Svetlov, Vladimir; Artsimovitch, Irina

    2010-01-01

    RfaH is a bacterial elongation factor that increases expression of distal genes in several long, horizontally acquired operons. RfaH is recruited to the transcription complex during RNA chain elongation through specific interactions with a DNA element called ops. Following recruitment, RfaH remains bound to RNA polymerase (RNAP) and acts as an antiterminator by reducing RNAP pausing and termination at some factor-independent and Rho-dependent signals. RfaH consists of two domains connected by a flexible linker. The N-terminal RfaH domain (RfaHN) recognizes the ops element, binds to the RNAP and reduces pausing and termination in vitro. Functional analysis of single substitutions in this domain reported here suggests that three separate RfaHN regions mediate these functions. We propose that a polar patch on one side of RfaHN interacts with the non-template DNA strand during recruitment, whereas a hydrophobic surface on the opposite side of RfaHN remains bound to the β′ subunit clamp helices domain throughout transcription of the entire operon. The third region is apparently dispensable for RfaH binding to the transcription complex but is required for the antitermination modification of RNAP. PMID:20132437

  4. Synthesis of Large-Sized Single-Crystal Hexagonal Boron Nitride Domains on Nickel Foils by Ion Beam Sputtering Deposition.

    PubMed

    Wang, Haolin; Zhang, Xingwang; Liu, Heng; Yin, Zhigang; Meng, Junhua; Xia, Jing; Meng, Xiang-Min; Wu, Jinliang; You, Jingbi

    2015-12-22

    Large-sized single-crystal h-BN domains with a lateral size up to 100 μm are synthesized on Ni foils by ion-beam sputtering deposition. The nucleation density of h-BN is dramatically decreased by reducing the concentrations of both active sites and species on the Ni surface through a brief in situ pretreatment of the substrate and optimization of the growth parameters, enabling the growth of large-sized domains.

  5. Sarcocystis neurona: molecular characterization of enolase domain I region and a comparison to other protozoa.

    PubMed

    Bolten, K E; Marsh, A E; Reed, S M; Dubey, J P; Toribio, R E; Saville, W J A

    2008-09-01

    Sarcocystis neurona causes protozoal myeloencephalitis and has the ability to infect a wide host range in contrast to other Sarcocystis species. In the current study, five S. neurona isolates from a variety of sources, three Sarcocystis falcatula, one Sarcocystis dasypi/S. neurona-like isolate, and one Besnoitia darlingi isolate were used to compare the enolase 2 gene segment containing the domain I region to previously sequenced enolase genes from Neospora caninum, Neospora hughesi, Toxoplasma gondii, Plasmodium falciparum, and Trypanosoma cruzi; enolase 2 segment containing domain I region is highly conserved amongst these parasites of veterinary and medical importance. Immunohistochemistry results indicates reactivity of T. gondii enolase 1 and 2 antibodies to S. neurona merozoites and metrocytes, but no reactivity of anti-enolase 1 to the S. neurona bradyzoite stage despite reactivity to T. gondii bradyzoites, suggesting expression differences between organisms.

  6. A regional paleomagnetic study of lithotectonic domains in the Central Gneiss Belt, Grenville Province, Ontario

    NASA Astrophysics Data System (ADS)

    Constanzo Alvarez, Vincenzo; Dunlop, David J.

    1998-04-01

    We have made a regional paleomagnetic study of lithotectonic domains in the Central Gneiss Belt of the Grenville Province in Ontario along ten N-S and E-W traverses up to 200 km in length. Although originally intended to clarify the tectonic mechanism by which these exotic terranes were assembled and welded to the Archean Superior craton during the ˜1150-Ma Grenvillian orogeny, we actually learned much more about the timing of post-orogenic uplift of the various domains around 1000-900 Ma as they stabilized and became part of the Rodinia supercontinent. The normal (N) and reverse (R) natural remanent magnetizations (NRMs) of all domains, as well as those of reactivated regions flanking the Grenville Front (GF, the Superior-Grenville boundary) to the north and south, have paleomagnetic poles falling on the 980-920-Ma ( 40Ar/ 39Ar calibrated) portion of the Grenville apparent polar wander track for Laurentia. There is a general tendency for paleopoles to young with increasing distance of domains from the GF, implying that more southerly domains were uplifted and magnetized later, but two of the domains do not fit this pattern. Previously reported younging trends away from the GF, based on K/Ar thermochron maps and paleomagnetic 'zone poles', are untrustworthy because of hydrothermal alteration, which causes chemical remagnetization and anomalously old K/Ar ages near the GF. Another trend in our data is a regular increase in the R/N ratio with increasing distance south of the GF. In the reactivated zones flanking the GF, NRMs are overwhelmingly of N polarity, whereas well away from the GF, R/N is close to 50:50. Also, NRM intensities and susceptibility values increase 100-fold away from the GF, peaking ≈10 km south of the front, with a pulse-like pattern similar to that documented in anomalously high 40Ar/ 39Ar dates in the same region. Both the magnetic and Ar/Ar results are likely due to a 'wave' of hydrothermal alteration and remagnetization during which fluids

  7. Leveraging domain knowledge to facilitate visual exploration of large population datasets.

    PubMed

    Hsu, William; Bui, Alex A T

    2013-01-01

    Observational patient data provides an unprecedented opportunity to gleam new insights into diseases and assess patient quality of care, but a challenge lies in matching our ability to collect data with a comparable ability to understand and apply this information. Visual analytic techniques are promising as they permit the exploration and manipulation of complex datasets through a graphical user interface. Nevertheless, current visualization tools rely on users to manually configure which aspects of the dataset are shown and how they are presented. In this paper, we describe an approach that utilizes characteristics of the data and domain knowledge to assist users with summarizing the information space of a large population. We present a representation that captures contextual information about the data and constructs that operate on this information to tailor the data's presentation. We describe a use case of this approach in exploring a claims dataset of individuals with spinal dysraphism.

  8. Wavefront reconstruction for extremely large telescopes via CuRe with domain decomposition.

    PubMed

    Rosensteiner, Matthias

    2012-11-01

    The Cumulative Reconstructor is an accurate, extremely fast reconstruction algorithm for Shack-Hartmann wavefront sensor data. But it has shown an unacceptable high noise propagation for large apertures. Therefore, in this paper we describe a domain decomposition approach to deal with this drawback. We show that this adaptation of the algorithm gives the same reconstruction quality as the original algorithm and leads to a significant improvement with respect to noise propagation. The method is combined with an integral control and compared to the classical matrix vector multiplication algorithm on an end-to-end simulation of a single conjugate adaptive optics system. The reconstruction time is 20n (number of subapertures), and the method is parallelizable.

  9. A bifurcation analysis of boiling water reactor on large domain of parametric spaces

    NASA Astrophysics Data System (ADS)

    Pandey, Vikas; Singh, Suneet

    2016-09-01

    The boiling water reactors (BWRs) are inherently nonlinear physical system, as any other physical system. The reactivity feedback, which is caused by both moderator density and temperature, allows several effects reflecting the nonlinear behavior of the system. Stability analyses of BWR is done with a simplified, reduced order model, which couples point reactor kinetics with thermal hydraulics of the reactor core. The linear stability analysis of the BWR for steady states shows that at a critical value of bifurcation parameter (i.e. feedback gain), Hopf bifurcation occurs. These stable and unstable domains of parametric spaces cannot be predicted by linear stability analysis because the stability of system does not include only stability of the steady states. The stability of other dynamics of the system such as limit cycles must be included in study of stability. The nonlinear stability analysis (i.e. bifurcation analysis) becomes an indispensable component of stability analysis in this scenario. Hopf bifurcation, which occur with one free parameter, is studied here and it formulates birth of limit cycles. The excitation of these limit cycles makes the system bistable in the case of subcritical bifurcation whereas stable limit cycles continues in an unstable region for supercritical bifurcation. The distinction between subcritical and supercritical Hopf is done by two parameter analysis (i.e. codimension-2 bifurcation). In this scenario, Generalized Hopf bifurcation (GH) takes place, which separates sub and supercritical Hopf bifurcation. The various types of bifurcation such as limit point bifurcation of limit cycle (LPC), period doubling bifurcation of limit cycles (PD) and Neimark-Sacker bifurcation of limit cycles (NS) have been identified with the Floquet multipliers. The LPC manifests itself as the region of bistability whereas chaotic region exist because of cascading of PD. This region of bistability and chaotic solutions are drawn on the various

  10. River Seepage Conductance in Large-Scale Regional Studies.

    PubMed

    Morel-Seytoux, Hubert J; Miller, Calvin D; Miracapillo, Cinzia; Mehl, Steffen

    2016-12-20

    Flow exchange between surface and groundwater is of great importance be it for beneficial allocation and use of water resources or for the proper exercise of water rights. In large-scale regional studies, most numerical models use coarse grid sizes, which make it difficult to provide an accurate depiction of the phenomenon. In particular, a somewhat arbitrary leakance coefficient in a third type (i.e., Cauchy, General Head) boundary condition is used to calculate the seepage discharge as a function of the difference of head in the river and in the aquifer, whose value is often found by calibration. A different approach is presented to analytically estimate that leakance coefficient. It is shown that a simple equivalence can be deduced from the analytical solution for the empirical coefficient, so that it provides the accuracy of the analytical solution while the model maintains a very coarse grid, treating the water-table aquifer as a single calculation layer. Relating the empirical leakance coefficient to the exact conductance, derived from physical principles, provides a physical basis for the leakance coefficient. Factors such as normalized wetted perimeter, degree of penetration of the river, presence of a clogging layer, and anisotropy can be included with little computational demand. In addition the river coefficient in models such as MODFLOW, for example, can be easily modified when grid size is changed without need for recalibration.

  11. Rendering Future Vegetation Change across Large Regions of the US

    NASA Astrophysics Data System (ADS)

    Sant'Anna Dias, Felipe; Gu, Yuting; Agarwalla, Yashika; Cheng, Yiwei; Patil, Sopan; Stieglitz, Marc; Turk, Greg

    2015-04-01

    We use two Machine Learning techniques, Decision Trees (DT) and Neural Networks (NN), to provide classified images and photorealistic renderings of future vegetation cover at three large regions in the US. The training data used to generate current vegetation cover include Landsat surface reflectance images, USGS Land Cover maps, 50 years of mean annual temperature and precipitation for the period 1950 - 2000, elevation, aspect and slope data. Present vegetation cover was generated on a 100m grid. Future vegetation cover for the period 2061- 2080 was predicted using the 1 km resolution bias corrected data from the NASA Goddard Institute for Space Studies Global Climate Model E simulation. The three test regions encompass a wide range of climatic gradients, topographic variation, and vegetation cover. The central Oregon site covers 19,182 square km and includes the Ochoco and Malheur National Forest. Vegetation cover is 50% evergreen forest and 50% shrubs and scrubland. The northwest Washington site covers 14,182 square km. Vegetation cover is 60% evergreen forest, 14% scrubs, 7% grassland, and 7% barren land. The remainder of the area includes deciduous forest, perennial snow cover, and wetlands. The third site, the Jemez mountain region of north central New Mexico, covers 5,500 square km. Vegetation cover is 47% evergreen forest, 31% shrubs, 13% grasses, and 3% deciduous forest. The remainder of the area includes developed and cultivated areas and wetlands. Using the above mentioned data sets we first trained our DT and NN models to reproduce current vegetation. The land cover classified images were compared directly to the USGS land cover data. The photorealistic generated vegetation images were compared directly to the remotely sensed surface reflectance maps. For all three sites, similarity between generated and observed vegetation cover was quite remarkable. The three trained models were then used to explore what the equilibrium vegetation would look like for

  12. Angular dependence of the reflectance from an isotropic polydomain medium: effect of large domain size on total reflection.

    PubMed

    Mayerhöfer, Thomas G; Popp, Jürgen

    2005-03-01

    We investigate the angular dependence of the reflectance from an isotropic medium consisting of optically large and anisotropic, randomly oriented domains, assuming a highly refractive, isotropic, and homogeneous incidence medium, which is presumed to have a higher refractive index than any of the domains' principal indices of refraction. By employing average reflectance and transmittance theory, we are able to show that the onset of total reflection is considerably shifted to higher angles of incidence compared with an isotropic medium with domains that are small compared with the wavelength. The onset of total reflection for a random medium with large domains is found to be dependent only on the largest principal index of refraction of the domains, assuming that all domains have the same optical properties. Therefore the shift of the onset depends on the magnitude of the optical anisotropy of the domains. Even in the case of a small optical anisotropy, large cross-polarization terms are predicted in the vicinity of the onset of total reflection. These terms show a pronounced maximum near that onset and extend beyond it.

  13. The neck region of the myosin motor domain acts as a lever arm to generate movement.

    PubMed Central

    Uyeda, T Q; Abramson, P D; Spudich, J A

    1996-01-01

    The myosin head consists of a globular catalytic domain that binds actin and hydrolyzes ATP and a neck domain that consists of essential and regulatory light chains bound to a long alpha-helical portion of the heavy chain. The swinging neck-level model assumes that a swinging motion of the neck relative to the catalytic domain is the origin of movement. This model predicts that the step size, and consequently the sliding velocity, are linearly related to the length of the neck. We have tested this point by characterizing a series of mutant Dictyostelium myosins that have different neck lengths. The 2xELCBS mutant has an extra binding site for essential light chain. The delta RLCBS mutant myosin has an internal deletion that removes the regulatory light chain binding site. The delta BLCBS mutant lacks both light chain binding sites. Wild-type myosin and these mutant myosins were subjected to the sliding filament in vitro motility assay. As expected, mutants with shorter necks move slower than wild-type myosin in vitro. Most significantly, a mutant with a longer neck moves faster than the wild type, and the sliding velocities of these myosins are linearly related to the neck length, as predicted by the swinging neck-lever model. A simple extrapolation to zero speed predicts that the fulcrum point is in the vicinity of the SH1-SH2 region in the catalytic domain. Images Fig. 1 Fig. 2 Fig. 3 PMID:8633089

  14. Structure of the dimerization domain of DiGeorge critical region 8

    SciTech Connect

    Senturia, R.; Faller, M.; Yin, S.; Loo, J.A.; Cascio, D.; Sawaya, M.R.; Hwang, D.; Clubb, R.T.; Guo, F.

    2010-09-27

    Maturation of microRNAs (miRNAs, {approx}22nt) from long primary transcripts [primary miRNAs (pri-miRNAs)] is regulated during development and is altered in diseases such as cancer. The first processing step is a cleavage mediated by the Microprocessor complex containing the Drosha nuclease and the RNA-binding protein DiGeorge critical region 8 (DGCR8). We previously reported that dimeric DGCR8 binds heme and that the heme-bound DGCR8 is more active than the heme-free form. Here, we identified a conserved dimerization domain in DGCR8. Our crystal structure of this domain (residues 298-352) at 1.7 {angstrom} resolution demonstrates a previously unknown use of a WW motif as a platform for extensive dimerization interactions. The dimerization domain of DGCR8 is embedded in an independently folded heme-binding domain and directly contributes to association with heme. Heme-binding-deficient DGCR8 mutants have reduced pri-miRNA processing activity in vitro. Our study provides structural and biochemical bases for understanding how dimerization and heme binding of DGCR8 may contribute to regulation of miRNA biogenesis.

  15. Structure of the dimerization domain of DiGeorge critical region 8.

    PubMed

    Senturia, Rachel; Faller, Michael; Yin, Sheng; Loo, Joseph A; Cascio, Duilio; Sawaya, Michael R; Hwang, Daniel; Clubb, Robert T; Guo, Feng

    2010-07-01

    Maturation of microRNAs (miRNAs, approximately 22nt) from long primary transcripts [primary miRNAs (pri-miRNAs)] is regulated during development and is altered in diseases such as cancer. The first processing step is a cleavage mediated by the Microprocessor complex containing the Drosha nuclease and the RNA-binding protein DiGeorge critical region 8 (DGCR8). We previously reported that dimeric DGCR8 binds heme and that the heme-bound DGCR8 is more active than the heme-free form. Here, we identified a conserved dimerization domain in DGCR8. Our crystal structure of this domain (residues 298-352) at 1.7 A resolution demonstrates a previously unknown use of a WW motif as a platform for extensive dimerization interactions. The dimerization domain of DGCR8 is embedded in an independently folded heme-binding domain and directly contributes to association with heme. Heme-binding-deficient DGCR8 mutants have reduced pri-miRNA processing activity in vitro. Our study provides structural and biochemical bases for understanding how dimerization and heme binding of DGCR8 may contribute to regulation of miRNA biogenesis.

  16. Evidences of SNPs in the variable region of hemocyanin Ig-like domain in shrimp Litopenaeus vannamei.

    PubMed

    Guo, Lingling; Zhao, Xianliang; Zhang, Yueling; Wang, Zehuan; Zhong, Mingqi; Li, Shengkang; Lun, Jingsheng

    2013-11-01

    Single nucleotide polymorphisms (SNPs) are the commonest mode of genetic variation in invertebrate immune-related genes. Hemocyanin presents in the hemolymph of both mollusks and arthropods and functions as an important antigen non-specific immune protein. But people know very little about its gene polymorphism so far. In current study, bioinformatics, molecular biology and environmental challenge approaches were used to identify the SNPs within hemocyanin Ig-like domain in shrimp Litopenaeus vannamei. A total of 11 SNPs were found in a variable region of Ig-like domain from L. vannamei hemocyanin large subunit (1258-1460 bp, HcLV1), 5 of which (1272, 1315, 1380, 1410 and 1450) were confirmed present in both genomic DNA and cDNA by clone sequencing. Furthermore, HcLV1 showed 3, 5 and 5 SSCP bands, respectively, in 16, 25 and 30 °C-treated shrimps, suggesting that the SSCP pattern of HcLV1 could be modulated by environmental stress. In addition, HcLV1 displayed two extra bands with different mobility when shrimps treated with Vibrio parahaemolyticus for 6-24 h, which was not observed in the control group. In conclusion, our data suggest that shrimp L. vannamei hemocyanin Ig-like domain possesses SNPs, which may be associated with environmental stress or pathogenic challenge.

  17. Time Domain Science and Fundamental Physics with the Next-generation Very Large Array

    NASA Astrophysics Data System (ADS)

    Demorest, Paul; Bower, Geoffrey C.; ngVLA Time Domain/Physics Science Working Group

    2017-01-01

    The Next-generation Very Large Array (ngVLA) is a design concept for a future large-area radio telescope under development by the NRAO and interested members of the scientific community. The approximate ngVLA specifications call for a frequency range of ~1--116 GHz, ten times the effective collecting area and moderately increased field of view versus the current VLA, and an array configuration consisting of a dense (~km-scale) array core with some baselines extending out to hundreds of km. This instrument will enable new discoveries in many diverse areas of research relevant to modern astronomy; our group has explored the impact the ngVLA will have in time domain astronomy and fundamental physics.Here we present several key science topics considered as part of this work. These include: Searching for and timing radio pulsars at the galactic center -- the frequency coverage and sensitivity of the ngVLA will allow detection of highly-scattered pulsars near Sgr A*. Monitoring these sources will permit unprecedented tests of general relativity. Detecting and characterizing explosive transient sources -- electromagnetic observations of gravitational-wave sources provide complementary information to the GW signals themselves. Observations across the wide frequency range spanned by the ngVLA are critical for energy calorimetry of these events. Finally, with sufficient long-baseline coverage, novel astrometric approaches to cosmology become possible, by watching the expansion of the universe in real time through correlated proper motions of many extragalactic radio sources.

  18. The SV40 large T-antigen origin binding domain directly participates in DNA unwinding.

    PubMed

    Foster, Erin C; Simmons, Daniel T

    2010-03-16

    The origin binding domain (OBD) of SV40 large T-ag serves a critical role during initiation of DNA replication to position T-ag on the origin. After origin recognition, T-ag forms a double hexamer over the origin. Within each hexamer, the OBD adopts a lock washer structure where the origin recognizing A1 and B2 loops face toward the helicase domain and likely become unavailable for binding DNA. In this study, we investigated the role of the central channel of the OBD hexamer in DNA replication by analyzing the effects of mutations of residues lining the channel. All mutants showed binding defects with origin DNA and ssDNA especially at low protein concentrations, but only half were defective at supporting DNA replication in vitro. All mutants were normal in unwinding linear origin DNA fragments. However, replication defective mutants failed to unwind a small origin containing circular DNA whereas replication competent mutants did so normally. The presence of RPA and/or pol/prim restored circular DNA unwinding activity of compromised mutants probably by interacting with the separated DNA strands on the T-ag surface. We interpret these results to indicate a role for the OBD central channel in binding and threading ssDNA during unwinding of circular SV40 DNA. Mixing experiments suggested that only one monomer in an OBD hexamer was necessary for DNA unwinding. We present a model of DNA threading through the T-ag complex illustrating how single-stranded DNA could pass close to a trough generated by key residues in one monomer of the OBD hexamer.

  19. Novel structure of an N-terminal domain that is crucial for the dimeric assembly and DNA-binding of an archaeal DNA polymerase D large subunit from Pyrococcus horikoshii.

    PubMed

    Matsui, Ikuo; Urushibata, Yuji; Shen, Yulong; Matsui, Eriko; Yokoyama, Hideshi

    2011-02-04

    Archaea-specific D-family DNA polymerase forms a heterotetramer consisting of two large polymerase subunits and two small exonuclease subunits. The N-terminal (1-300) domain structure of the large subunit was determined by X-ray crystallography, although ∼50 N-terminal residues were disordered. The determined structure consists of nine alpha helices and three beta strands. We also identified the DNA-binding ability of the domain by SPR measurement. The N-terminal (1-100) region plays crucial roles in the folding of the large subunit dimer by connecting the ∼50 N-terminal residues with their own catalytic region (792-1163).

  20. Atmospheric Impact of Large Methane Emission in the Arctic Region

    NASA Astrophysics Data System (ADS)

    Bhattacharyya, S.; Cameron-Smith, P. J.; Bergmann, D.; Reagan, M. T.; Collins, W.; Elliott, S. M.; Maltrud, M. E.

    2011-12-01

    A highly potent greenhouse gas, methane, is locked in the solid phase as ice-like deposits containing a mixture of water and gas (mostly methane) called clathrates, in ocean sediments and underneath permafrost regions. Clathrates are stable under high pressure and low temperatures. Recent estimates suggest that about 1600 - 2000GtC of clathrates are present in oceans and 400GtC in Arctic permafrost (Archer et al.2009) which is about 4000 times that of current annual emissions. In a warming climate, increase in ocean temperatures could alter the geothermal gradient, which in turn could lead to dissociation of the clathrates and release of methane into the ocean and subsequently into the atmosphere as well. This could be of particular importance in the shallow part of the Arctic Ocean where the clathrates are found in depths of only 300m. In this presentation, we shall show results from our ongoing simulation of a scenario of large scale methane outgassing from clathrate dissociation due to warming ocean temperatures in the Arctic based on ocean sediment modeling. To that end we use the CESM (Community Earth System Model) version 1 with fully active coupled atmosphere-ocean-land model together with fast atmospheric chemistry module to simulate the response to increasing methane emissions in the Barents Sea, Canadian Archipelago and the Sea of Okhotsk. The simulation shows the effect these methane emissions could have on global surface methane, surface ozone, surface air temperature and other related indices. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. LLNL-ABS-491764

  1. Coordinated Multi-layer Multi-domain Optical Network (COMMON) for Large-Scale Science Applications (COMMON)

    SciTech Connect

    Vokkarane, Vinod

    2013-09-01

    We intend to implement a Coordinated Multi-layer Multi-domain Optical Network (COMMON) Framework for Large-scale Science Applications. In the COMMON project, specific problems to be addressed include 1) anycast/multicast/manycast request provisioning, 2) deployable OSCARS enhancements, 3) multi-layer, multi-domain quality of service (QoS), and 4) multi-layer, multidomain path survivability. In what follows, we outline the progress in the above categories (Year 1, 2, and 3 deliverables).

  2. Implementation Strategies for Large-Scale Transport Simulations Using Time Domain Particle Tracking

    NASA Astrophysics Data System (ADS)

    Painter, S.; Cvetkovic, V.; Mancillas, J.; Selroos, J.

    2008-12-01

    Time domain particle tracking is an emerging alternative to the conventional random walk particle tracking algorithm. With time domain particle tracking, particles are moved from node to node on one-dimensional pathways defined by streamlines of the groundwater flow field or by discrete subsurface features. The time to complete each deterministic segment is sampled from residence time distributions that include the effects of advection, longitudinal dispersion, a variety of kinetically controlled retention (sorption) processes, linear transformation, and temporal changes in groundwater velocities and sorption parameters. The simulation results in a set of arrival times at a monitoring location that can be post-processed with a kernel method to construct mass discharge (breakthrough) versus time. Implementation strategies differ for discrete flow (fractured media) systems and continuous porous media systems. The implementation strategy also depends on the scale at which hydraulic property heterogeneity is represented in the supporting flow model. For flow models that explicitly represent discrete features (e.g., discrete fracture networks), the sampling of residence times along segments is conceptually straightforward. For continuous porous media, such sampling needs to be related to the Lagrangian velocity field. Analytical or semi-analytical methods may be used to approximate the Lagrangian segment velocity distributions in aquifers with low-to-moderate variability, thereby capturing transport effects of subgrid velocity variability. If variability in hydraulic properties is large, however, Lagrangian velocity distributions are difficult to characterize and numerical simulations are required; in particular, numerical simulations are likely to be required for estimating the velocity integral scale as a basis for advective segment distributions. Aquifers with evolving heterogeneity scales present additional challenges. Large-scale simulations of radionuclide

  3. Calculus of variations in the large, existence of trajectories in a domain with boundary, and Whitney's inverted pendulum problem

    NASA Astrophysics Data System (ADS)

    Bolotin, S. V.; Kozlov, V. V.

    2015-10-01

    For non-autonomous Lagrangian systems we introduce the notion of a dynamically convex domain with respect to the Lagrangian. We establish the solubility of boundary-value problems in compact dynamically convex domains. If the Lagrangian is time-periodic, then such a domain contains a periodic trajectory. The proofs use the Hamilton principle and known tools of the calculus of variations in the large. Our general results are applied to Whitney's problem on the existence of motions of an inverted pendulum without falls.

  4. Simultaneous Solar Maximum Mission (SMM) and Very Large Array (VLA) observations of solar active regions

    NASA Technical Reports Server (NTRS)

    Willson, Robert F.

    1991-01-01

    Very Large Array observations at 20 cm wavelength can detect the hot coronal plasma previously observed at soft x ray wavelengths. Thermal cyclotron line emission was detected at the apex of coronal loops where the magnetic field strength is relatively constant. Detailed comparison of simultaneous Solar Maximum Mission (SMM) Satellite and VLA data indicate that physical parameters such as electron temperature, electron density, and magnetic field strength can be obtained, but that some coronal loops remain invisible in either spectral domain. The unprecedent spatial resolution of the VLA at 20 cm wavelength showed that the precursor, impulsive, and post-flare components of solar bursts originate in nearby, but separate loops or systems of loops.. In some cases preburst heating and magnetic changes are observed from loops tens of minutes prior to the impulsive phase. Comparisons with soft x ray images and spectra and with hard x ray data specify the magnetic field strength and emission mechanism of flaring coronal loops. At the longer 91 cm wavelength, the VLA detected extensive emission interpreted as a hot 10(exp 5) K interface between cool, dense H alpha filaments and the surrounding hotter, rarefield corona. Observations at 91 cm also provide evidence for time-correlated bursts in active regions on opposite sides of the solar equator; they are attributed to flare triggering by relativistic particles that move along large-scale, otherwise-invisible, magnetic conduits that link active regions in opposite hemispheres of the Sun.

  5. Building Large-Domain Twisted Bilayer Graphene with van Hove Singularity.

    PubMed

    Tan, Zhenjun; Yin, Jianbo; Chen, Cheng; Wang, Huan; Lin, Li; Sun, Luzhao; Wu, Jinxiong; Sun, Xiao; Yang, Haifeng; Chen, Yulin; Peng, Hailin; Liu, Zhongfan

    2016-07-26

    Twisted bilayer graphene (tBLG) with van Hove Singularity (VHS) has exhibited novel twist-angle-dependent chemical and physical phenomena. However, scalable production of high-quality tBLG is still in its infancy, especially lacking the angle controlled preparation methods. Here, we report a facile approach to prepare tBLG with large domain sizes (>100 μm) and controlled twist angles by a clean layer-by-layer transfer of two constituent graphene monolayers. The whole process without interfacial polymer contamination in two monolayers guarantees the interlayer interaction of the π-bond electrons, which gives rise to the existence of minigaps in electronic structures and the consequent formation of VHSs in density of state. Such perturbation on band structure was directly observed by angle-resolved photoemission spectroscopy with submicrometer spatial resolution (micro-ARPES). The VHSs lead to a strong light-matter interaction and thus introduce ∼20-fold enhanced intensity of Raman G-band, which is a characteristic of high-quality tBLG. The as-prepared tBLG with strong light-matter interaction was further fabricated into high-performance photodetectors with selectively enhanced photocurrent generation (up to ∼6 times compared with monolayer in our device).

  6. The generation and selection of single-domain, v region libraries from nurse sharks.

    PubMed

    Flajnik, Martin F; Dooley, Helen

    2009-01-01

    The cartilaginous fish (sharks, skates, and rays) are the oldest phylogenetic group in which a human-type adaptive immune system and immunoglobulins (Igs) have been found. In addition to their conventional (heavy-light chain heterodimeric) isotypes, IgM and IgW, sharks produce the novel isotype, IgNAR, a heavy chain homodimer that does not associate with light chains. Instead, its variable (V) regions act as independent, soluble units in order to bind antigen. In this chapter, we detail our immunization protocol in order to raise a humoral IgNAR response in the nurse shark (Ginglymostoma cirratum) and the subsequent cloning of the single-domain V regions from this isotype in order to select antigen-specific binders by phage display.

  7. Structural basis of empathy and the domain general region in the anterior insular cortex

    PubMed Central

    Mutschler, Isabella; Reinbold, Céline; Wankerl, Johanna; Seifritz, Erich; Ball, Tonio

    2013-01-01

    Empathy is key for healthy social functioning and individual differences in empathy have strong implications for manifold domains of social behavior. Empathy comprises of emotional and cognitive components and may also be closely linked to sensorimotor processes, which go along with the motivation and behavior to respond compassionately to another person's feelings. There is growing evidence for local plastic change in the structure of the healthy adult human brain in response to environmental demands or intrinsic factors. Here we have investigated changes in brain structure resulting from or predisposing to empathy. Structural MRI data of 101 healthy adult females was analyzed. Empathy in fictitious as well as real-life situations was assessed using a validated self-evaluation measure. Furthermore, empathy-related structural effects were also put into the context of a functional map of the anterior insular cortex (AIC) determined by activation likelihood estimate (ALE) meta-analysis of previous functional imaging studies. We found that gray matter (GM) density in the left dorsal AIC correlates with empathy and that this area overlaps with the domain general region (DGR) of the anterior insula that is situated in-between functional systems involved in emotion–cognition, pain, and motor tasks as determined by our meta-analysis. Thus, we propose that this insular region where we find structural differences depending on individual empathy may play a crucial role in modulating the efficiency of neural integration underlying emotional, cognitive, and sensorimotor information which is essential for global empathy. PMID:23675334

  8. First steps of the regional climate model MAR over the Euro-CORDEX domain

    NASA Astrophysics Data System (ADS)

    Scholzen, Chloé; Fettweis, Xavier

    2016-04-01

    In the framework of the Euro-CORDEX initiative, the Laboratory of Climatology of the University of Liège, Belgium, is currently using the regional climate model MAR (for "Modèle Atmosphérique Régional") to simulate the past, present and future climate over Europe. Simulations are being performed for both available resolutions over the Euro-CORDEX domain, namely 0.11 deg. (12.5 km) and 0.44 deg. (50 km). Historical and present-day runs (1979-2015) use the ERA-Interim and the NCEP/NCAR-v1 reanalyses as boundary conditions, whereas future projections are driven by two selected GCMs from the CMIP5 database: NorESM1-M and MIROC5. All CMIP5-GCMs were previously compared against ERA-Interim reanalysis data in terms of their ability to represent the current mean climate over Europe. The GCMs also underwent a statistical classification based on the calculation of skill-scores evaluating for instance 850 hPa temperature and 500 hPa geopotential height. Several settings and parameters were tested in order to calibrate the regional climate model MAR over the Euro-CORDEX domain. MAR was validated with respect to observations from the European Climate Assessment & Dataset (ECA&D). The aim of this study is to assess the performance of MAR in comparing its results to other RCMs used within the Euro-CORDEX initiative.

  9. The J-domain proteins of Arabidopsis thaliana: an unexpectedly large and diverse family of chaperones.

    PubMed

    Miernyk, J A

    2001-07-01

    A total of 89 J-domain proteins were identified in the genome of the model flowering plant Arabidopsis thaliana. The deduced amino acid sequences of the J-domain proteins were analyzed for an assortment of structural features and motifs. Based on the results of sequence comparisons and structure and function predictions, 51 distinct families were identified. The families ranged in size from 1 to 6 members. Subcellular localizations of the A thaliana J-domain proteins were predicted; species were found in both the soluble and membrane compartments of all cellular organelles. Based on digital Northern analysis, the J-domain proteins could be separated into groups of low, medium, and moderate expression levels. This genomics-based analysis of the A thaliana J-domain proteins establishes a framework for detailed studies of biological function and specificity. It additionally provides a comprehensive basis for evolutionary comparisons.

  10. Identification of a Receptor-Binding Region within Domain 4 of the Protective Antigen Component of Anthrax Toxin

    PubMed Central

    Varughese, Mini; Teixeira, Avelino V.; Liu, Shihui; Leppla, Stephen H.

    1999-01-01

    Anthrax toxin from Bacillus anthracis is a three-component toxin consisting of lethal factor (LF), edema factor (EF), and protective antigen (PA). LF and EF are the catalytic components of the toxin, whereas PA is the receptor-binding component. To identify residues of PA that are involved in interaction with the cellular receptor, two solvent-exposed loops of domain 4 of PA (amino acids [aa] 679 to 693 and 704 to 723) were mutagenized, and the altered proteins purified and tested for toxicity in the presence of LF. In addition to the intended substitutions, novel mutations were introduced by errors that occurred during PCR. Substitutions within the large loop (aa 704 to 723) had no effect on PA activity. A mutated protein, LST-35, with three substitutions in the small loop (aa 679 to 693), bound weakly to the receptor and was nontoxic. A mutated protein, LST-8, with changes in three separate regions did not bind to receptor and was nontoxic. Toxicity was greatly decreased by truncation of the C-terminal 3 to 5 aa, but not by their substitution with nonnative residues or the extension of the terminus with nonnative sequences. Comparison of the 28 mutant proteins described here showed that the large loop (aa 704 to 722) is not involved in receptor binding, whereas residues in and near the small loop (aa 679 to 693) play an important role in receptor interaction. Other regions of domain 4, in particular residues at the extreme C terminus, appear to play a role in stabilizing a conformation needed for receptor-binding activity. PMID:10085028

  11. Large-scale phase separation with nano-twin domains in manganite spinel (Co,Fe,Mn)3O4

    NASA Astrophysics Data System (ADS)

    Horibe, Y.; Takeyama, S.; Mori, S.

    2016-08-01

    The effect of Mn concentration on the formation of nano-domain structures in the spinel oxide (Co,Fe,Mn)3O4 was investigated by electron diffraction, bright-, and dark-field imaging technique with transmission electron microscopy. Large scale phase separation with nano-twin domains was observed in Co0.6Fe1.0Mn1.4O4, in contrast to the highly aligned checkerboard nano-domains in Co0.6Fe0.9Mn1.5O4. Diffusion of the Mn3+ ions with the Jahn-Teller distortions is suggested to play an important role in the formation of checkerboard nano-domain structure.

  12. Conservation voltage reduction: Estimating methodology for a large regional application

    SciTech Connect

    De Steese, J.G. ); Kennedy, B.W. ); Merrick, S.B. )

    1992-04-01

    Conservation Voltage Reduction (CVR) is an established and cost-effective practice that has motivated many utilities to investigate its application on individual systems. This paper describes a supply-curve methodology that can determine the conservation value of CVR applied to many distribution systems in a region. In the area served by Bonneville Power Administration involving approximately 150 utilities, the systematic implementations of CVR could conserve between 170 and 268 Average Megawatts at a cost of 5 cents/kWh. This was shown to be a larger resource than might be achievable by applying more conventional efficiency improvements to transmission and distribution (T D) systems in the region.

  13. Conservation voltage reduction: Estimating methodology for a large regional application

    SciTech Connect

    De Steese, J.G.; Kennedy, B.W.; Merrick, S.B.

    1992-04-01

    Conservation Voltage Reduction (CVR) is an established and cost-effective practice that has motivated many utilities to investigate its application on individual systems. This paper describes a supply-curve methodology that can determine the conservation value of CVR applied to many distribution systems in a region. In the area served by Bonneville Power Administration involving approximately 150 utilities, the systematic implementations of CVR could conserve between 170 and 268 Average Megawatts at a cost of 5 cents/kWh. This was shown to be a larger resource than might be achievable by applying more conventional efficiency improvements to transmission and distribution (T&D) systems in the region.

  14. Structure-based design of a disulfide-linked oligomeric form of the simian virus 40 (SV40) large T antigen DNA-binding domain

    SciTech Connect

    Meinke, Gretchen; Phelan, Paul; Fradet-Turcotte, Amélie; Archambault, Jacques; Bullock, Peter A.

    2011-06-01

    With the aim of forming the ‘lock-washer’ conformation of the origin-binding domain of SV40 large T antigen in solution, using structure-based analysis an intermolecular disulfide bridge was engineered into the origin-binding domain to generate higher order oligomers in solution. The 1.7 Å resolution structure shows that the mutant forms a spiral in the crystal and has the de novo disulfide bond at the protein interface, although structural rearrangements at the interface are observed relative to the wild type. The modular multifunctional protein large T antigen (T-ag) from simian virus 40 orchestrates many of the events needed for replication of the viral double-stranded DNA genome. This protein assembles into single and double hexamers on specific DNA sequences located at the origin of replication. This complicated process begins when the origin-binding domain of large T antigen (T-ag ODB) binds the GAGGC sequences in the central region (site II) of the viral origin of replication. While many of the functions of purified T-ag OBD can be studied in isolation, it is primarily monomeric in solution and cannot assemble into hexamers. To overcome this limitation, the possibility of engineering intermolecular disulfide bonds in the origin-binding domain which could oligomerize in solution was investigated. A recent crystal structure of the wild-type T-ag OBD showed that this domain forms a left-handed spiral in the crystal with six subunits per turn. Therefore, we analyzed the protein interface of this structure and identified two residues that could potentially support an intermolecular disulfide bond if changed to cysteines. SDS–PAGE analysis established that the mutant T-ag OBD formed higher oligomeric products in a redox-dependent manner. In addition, the 1.7 Å resolution crystal structure of the engineered disulfide-linked T-ag OBD is reported, which establishes that oligomerization took place in the expected manner.

  15. Layer resolved magnetic domain imaging of epitaxial heterostructures in large applied magnetic fields

    NASA Astrophysics Data System (ADS)

    Zohar, S.; Choi, Y.; Love, D. M.; Mansell, R.; Barnes, C. H. W.; Keavney, D. J.; Rosenberg, R. A.

    2015-02-01

    We use X-ray Excited Luminescence Microscopy to investigate the elemental and layer resolved magnetic reversal in an interlayer exchange coupled (IEC) epitaxial Fe/Cr wedge/Co heterostructure. The transition from strongly coupled parallel Co-Fe reversal for Cr thickness tCr < 0.34 nm to weakly coupled layer independent reversal for tCr > 1.5 nm is punctuated at 0.34 < tCr < 1.5 nm by a combination of IEC guided domain wall motion and stationary zig zag domain walls. Domain walls nucleated at switching field minima are guided by IEC spatial gradients and collapse at switching field maxima.

  16. Application of Spectral Filtering scheme for Spherical Limited-Area domain to Regional forecast model

    NASA Astrophysics Data System (ADS)

    Park, J.-R.; Cheong, H.-. B.; Kang, H.-. G.

    2012-04-01

    The spectral filter for spherical limited-area domain was applied to time integration procedure of regional model as a numerical scheme to remove small scale noises, which cannot be properly resolved in numerical models. This filter is designed to provide the sharp filter response, selective scale decomposition, and the isotropy on the limited-area domain by using the filter equation with high-order spherical Laplacian operator. The high-order filter equation is solved by low-order elliptic equations with the first or the second spherical Laplacian operator. It is controlled by the order of the spherical Laplacian operator and wave cutoff scale parameter. For the application to the regional weather forecast model, the filter is reconstructed into the regional map projection, e.g., Mercator map projection. The weather research and forecasting (WRF) model is used and the spectral filter works on the vertical velocity field in which the unresolved kinematic features appear prominently. The filter parameters are set to damp the amplitude of wave component with wavelength of two times the grid interval by half in every time step. The effect of the filter on the removal of small-scale waves was evaluated through the tropical cyclone (TC) track and intensity prediction. For the accurate prediction of typhoon, the TC initialization scheme, named the structure adjustable balanced vortex (SABV) scheme, is used for all test cases. In comparison with the simulated result using the diffusion scheme provided in the model for the same purpose, the model performance was improved, especially in track prediction. The 1-day accumulated precipitation of the test simulation using the spectral filter exhibits the most similar pattern to the observation. The spectra analysis of vertical velocity field showed that the spectral filtering scheme restrains the undesirable small upturned spectral energy usually produced in limited-area models.

  17. The cardiac-specific N-terminal region of troponin I positions the regulatory domain of troponin C.

    PubMed

    Hwang, Peter M; Cai, Fangze; Pineda-Sanabria, Sandra E; Corson, David C; Sykes, Brian D

    2014-10-07

    The cardiac isoform of troponin I (cTnI) has a unique 31-residue N-terminal region that binds cardiac troponin C (cTnC) to increase the calcium sensitivity of the sarcomere. The interaction can be abolished by cTnI phosphorylation at Ser22 and Ser23, an important mechanism for regulating cardiac contractility. cTnC contains two EF-hand domains (the N and C domain of cTnC, cNTnC and cCTnC) connected by a flexible linker. Calcium binding to either domain favors an "open" conformation, exposing a large hydrophobic surface that is stabilized by target binding, cTnI[148-158] for cNTnC and cTnI[39-60] for cCTnC. We used multinuclear multidimensional solution NMR spectroscopy to study cTnI[1-73] in complex with cTnC. cTnI[39-60] binds to the hydrophobic face of cCTnC, stabilizing an alpha helix in cTnI[41-67] and a type VIII turn in cTnI[38-41]. In contrast, cTnI[1-37] remains disordered, although cTnI[19-37] is electrostatically tethered to the negatively charged surface of cNTnC (opposite its hydrophobic surface). The interaction does not directly affect the calcium binding affinity of cNTnC. However, it does fix the positioning of cNTnC relative to the rest of the troponin complex, similar to what was previously observed in an X-ray structure [Takeda S, et al. (2003) Nature 424(6944):35-41]. Domain positioning impacts the effective concentration of cTnI[148-158] presented to cNTnC, and this is how cTnI[19-37] indirectly modulates the calcium affinity of cNTnC within the context of the cardiac thin filament. Phosphorylation of cTnI at Ser22/23 disrupts domain positioning, explaining how it impacts many other cardiac regulatory mechanisms, like the Frank-Starling law of the heart.

  18. The cardiac-specific N-terminal region of troponin I positions the regulatory domain of troponin C

    PubMed Central

    Hwang, Peter M.; Cai, Fangze; Pineda-Sanabria, Sandra E.; Corson, David C.; Sykes, Brian D.

    2014-01-01

    The cardiac isoform of troponin I (cTnI) has a unique 31-residue N-terminal region that binds cardiac troponin C (cTnC) to increase the calcium sensitivity of the sarcomere. The interaction can be abolished by cTnI phosphorylation at Ser22 and Ser23, an important mechanism for regulating cardiac contractility. cTnC contains two EF–hand domains (the N and C domain of cTnC, cNTnC and cCTnC) connected by a flexible linker. Calcium binding to either domain favors an “open” conformation, exposing a large hydrophobic surface that is stabilized by target binding, cTnI[148–158] for cNTnC and cTnI[39–60] for cCTnC. We used multinuclear multidimensional solution NMR spectroscopy to study cTnI[1–73] in complex with cTnC. cTnI[39–60] binds to the hydrophobic face of cCTnC, stabilizing an alpha helix in cTnI[41–67] and a type VIII turn in cTnI[38–41]. In contrast, cTnI[1–37] remains disordered, although cTnI[19–37] is electrostatically tethered to the negatively charged surface of cNTnC (opposite its hydrophobic surface). The interaction does not directly affect the calcium binding affinity of cNTnC. However, it does fix the positioning of cNTnC relative to the rest of the troponin complex, similar to what was previously observed in an X-ray structure [Takeda S, et al. (2003) Nature 424(6944):35–41]. Domain positioning impacts the effective concentration of cTnI[148–158] presented to cNTnC, and this is how cTnI[19–37] indirectly modulates the calcium affinity of cNTnC within the context of the cardiac thin filament. Phosphorylation of cTnI at Ser22/23 disrupts domain positioning, explaining how it impacts many other cardiac regulatory mechanisms, like the Frank–Starling law of the heart. PMID:25246568

  19. Appearance of large crystalline domains in VO{sub 2} films grown on sapphire (001) and their phase transition characteristics

    SciTech Connect

    Azhan, Nurul Hanis; Su, Kui; Okimura, Kunio; Zaghrioui, Mustapha; Sakai, Joe

    2015-06-28

    We report the first observation of large crystalline domains of several μm-size in VO{sub 2} films deposited on Al{sub 2}O{sub 3} (001) substrates by rf-biased reactive sputtering technique. The large crystalline domains, dominated with random in-plane oriented growth of (011){sub M1}-orientation, appear only under adequate substrate biasing, such as 10 W, while most biasing conditions result in conventional nanosized grains of highly oriented (010){sub M1}-orientation. Two temperature-controlled analyses, x-ray diffraction and micro-Raman spectroscopy, have revealed that some parts of large crystalline domains undergo intermediate monoclinic (M2) phase during the thermally-induced structural phase transition from monoclinic (M1) to rutile-tetragonal (R) phase. As an effect of the appearance of large crystalline domains, the film showed in-plane tensile stress, resulting in high T{sub IMT} of 69 °C due to the elongation of the V-V distance in its low-temperature monoclinic phase.

  20. Regions of very low H3K27me3 partition the Drosophila genome into topological domains

    PubMed Central

    Flower, Rosalyn; Choo, Siew Woh

    2017-01-01

    It is now well established that eukaryote genomes have a common architectural organization into topologically associated domains (TADs) and evidence is accumulating that this organization plays an important role in gene regulation. However, the mechanisms that partition the genome into TADs and the nature of domain boundaries are still poorly understood. We have investigated boundary regions in the Drosophila genome and find that they can be identified as domains of very low H3K27me3. The genome-wide H3K27me3 profile partitions into two states; very low H3K27me3 identifies Depleted (D) domains that contain housekeeping genes and their regulators such as the histone acetyltransferase-containing NSL complex, whereas domains containing moderate-to-high levels of H3K27me3 (Enriched or E domains) are associated with regulated genes, irrespective of whether they are active or inactive. The D domains correlate with the boundaries of TADs and are enriched in a subset of architectural proteins, particularly Chromator, BEAF-32, and Z4/Putzig. However, rather than being clustered at the borders of these domains, these proteins bind throughout the H3K27me3-depleted regions and are much more strongly associated with the transcription start sites of housekeeping genes than with the H3K27me3 domain boundaries. While we have not demonstrated causality, we suggest that the D domain chromatin state, characterised by very low or absent H3K27me3 and established by housekeeping gene regulators, acts to separate topological domains thereby setting up the domain architecture of the genome. PMID:28282436

  1. A new functional motif in Hox domain-containing ceramide synthases: identification of a novel region flanking the Hox and TLC domains essential for activity.

    PubMed

    Mesika, Adi; Ben-Dor, Shifra; Laviad, Elad L; Futerman, Anthony H

    2007-09-14

    Ceramide is synthesized in mammals by a family of ceramide synthases (CerS) each of which uses a relatively restricted set of fatty acyl-CoAs for N-acylation of the sphingoid long chain base (Pewzner-Jung, Y., Ben-Dor, S., and Futerman, A. H. (2006) J. Biol. Chem. 281, 25001-25005). CerS are characterized by two functional domains, the Tram-Lag-CLN8 (TLC) domain and the homeobox (Hox) domain, which is found in all mammalian CerS except CerS1. We now demonstrate that the majority of the Hox domain is not required for CerS activity since its deletion in CerS5 does not affect activity. Subsequently, we define a highly conserved new motif of 12 amino acid residues that flanks the Hox and TLC domains but is not part of the TLC domain, which is essential for CerS5 and CerS6 activity. Two positively charged residues in this domain, one of which is conserved in all putative CerS in all organisms, are essential for activity since site-directed mutagenesis of either (Lys-134 and Lys-140 in CerS5) results in an approximately 50% loss of activity, whereas mutation of both leads to a complete loss of activity. Because this region is conserved across species, we propose that it plays a previously unidentified and essential role in CerS activity and can be used as a new motif to define Hox domain-containing CerS.

  2. The ICTP Regional System Model (RESM) to simulate the monsoon in the South Asia CORDEX domain

    NASA Astrophysics Data System (ADS)

    Di Sante, Fabio; Coppola, Erika; Farneti, Riccardo; Giorgi, Filippo

    2016-04-01

    South Asian climate is characterized mainly by the wet and dry dipole that divides the annual cycle in two seasons: the monsoon season and the dry season. The life and the economy of those regions is very much influenced by the climate variability and the monsoon variability therefore is crucial to understand the physical mechanism associated with them. The spatial and temporal representation of the monsoons over the South Asian region is one of the main challenge of global and regional climate models principally because they fail to represent the SST (sea surface temperature) induced rainfall when forced with observed SST resulting in a poor representation of the monsoon cycle (Fu et al. 2002). The coupling with the ocean is essential to be able to simulate the correct air-sea interaction; the results are in general much improved and the monsoon patterns and the time representation (like the onset for example) are closer to the observations (Fu et al. 2002; Fu et al. 2007; Ratnam et Al. 2008; Seo et Al. 2009). Here we present a Regional Earth System Model (RESM) composed by a regional climate model RegCM4 (Giorgi et al, 2012) coupled with the regional oceanic model MITgcm (Marshall et al, 1997) and two hydrological model: ChyM (Cetemps Hydrological Model, Coppola et al, 2007) and HD model (Max-Planck's HD model; Hagemann and Dümenil, 1998). We simulate the Southern Asian Climate taking into account the whole hydrological cycle. Wind stress, water fluxes and heat fluxes are exchanged from the atmosphere to the ocean, SST are exchanged from ocean to the atmosphere and in order to conserve mass, the river discharge is calculated from the Hydrological model and sent to the ocean. The main goal of this work is to evaluate the impacts of local air-sea interaction in the simulation of the interannual variability, over the Indian CORDEX (Giorgi et al, 2009) domain through regionally ocean-atmosphere-river coupled and uncoupled simulations, with a focus on monsoon season

  3. Regional climate simulations with COSMO-CLM over MENA-CORDEX domain

    NASA Astrophysics Data System (ADS)

    Galluccio, Salvatore; Bucchignani, Edoardo; Mercogliano, Paola; Montesarchio, Myriam

    2014-05-01

    In the frame of WCRP Coordinated Regional Downscaling Experiment (CORDEX), a set of common Regional Climate Downscaling (RCD) domains has been defined, as a prerequisite for the development of model evaluation and climate projection frameworks. CORDEX domains encompass the majority of land areas of the world. In this work, climate simulations have been performed over MENA-CORDEX domain, which includes North-Africa, southern Europe and the whole Arabian peninsula. The non-hydrostatic regional climate model COSMO-CLM has been used. At CMCC, regional climate modelling is a part of an integrated simulation system and it has been used in different European and African projects to provide qualitative and quantitative evaluation of the hydrogeological and public health risks. A series of simulations has been conducted over the MENA-CORDEX area at spatial resolution of 0.44°. A sensitivity analysis was conducted to adjust the model configuration to better reproduce the observed climate data. The numerical simulations were driven by ERA-Interim reanalysis (horizontal resolution of 0.703°) for the period 1979-1984; the first year, was considered as a spin up period. The validation was performed by using several data sets: CRU data set was used to validate temperature, precipitation and cloud cover; MERRA data set was used to validate temperature and precipitation and GPCP for precipitation. The model sensitivity to the external parameters was tested considering two different configurations for the surface albedo. In the first one, albedo is only function of soil-type whereas in the second configuration it is prescribed by two external fields for dry and saturated soil based on MODIS data. Moreover, we tested two aerosol distributions as well, namely the default Tanre aerosol distribution and aerosol maps according to Tegen (NASA/GISS). We found, as expected, a significant sensitivity, in particular on the African region. We also varied tuning and physical parameters, such

  4. Disease Mutations in the Ryanodine Receptor Central Region: Crystal Structures of a Phosphorylation Hot Spot Domain

    SciTech Connect

    Yuchi, Zhiguang; Lau, Kelvin; Van Petegem, Filip

    2015-02-09

    Ryanodine Receptors (RyRs) are huge Ca{sup 2+} release channels in the endoplasmic reticulum membrane and form targets for phosphorylation and disease mutations. We present crystal structures of a domain in three RyR isoforms, containing the Ser2843 (RyR1) and Ser2808/Ser2814 (RyR2) phosphorylation sites. The RyR1 domain is the target for 11 disease mutations. Several of these are clustered near the phosphorylation sites, suggesting that phosphorylation and disease mutations may affect the same interface. The L2867G mutation causes a drastic thermal destabilization and aggregation at room temperature. Crystal structures for other disease mutants show that they affect surface properties and intradomain salt bridges. In vitro phosphorylation experiments show that up to five residues in one long loop of RyR2 can be phosphorylated by PKA or CaMKII. Docking into cryo-electron microscopy maps suggests a putative location in the clamp region, implying that mutations and phosphorylation may affect the allosteric motions within this area.

  5. Anisotropic aberration correction using region of interest based digital adaptive optics in Fourier domain OCT.

    PubMed

    Kumar, Abhishek; Kamali, Tschackad; Platzer, René; Unterhuber, Angelika; Drexler, Wolfgang; Leitgeb, Rainer A

    2015-04-01

    In this paper a numerical technique is presented to compensate for anisotropic optical aberrations, which are usually present across the lateral field of view in the out of focus regions, in high resolution optical coherence tomography and microscopy (OCT/OCM) setups. The recorded enface image field at different depths in the tomogram is digitally divided into smaller sub-regions or the regions of interest (ROIs), processed individually using subaperture based digital adaptive optics (DAO), and finally stitched together to yield a final image with a uniform diffraction limited resolution across the entire field of view (FOV). Using this method, a sub-micron lateral resolution is achieved over a depth range of 218 [Formula: see text]for a nano-particle phantom sample imaged using a fiber based point scanning spectral domain (SD) OCM system with a limited depth of focus (DOF) of ~7 [Formula: see text]at a numerical aperture (NA) of 0.6. Thus, an increase in DOF by ~30x is demonstrated in this case. The application of this method is also shown in ex vivo mouse adipose tissue.

  6. Anisotropic aberration correction using region of interest based digital adaptive optics in Fourier domain OCT

    PubMed Central

    Kumar, Abhishek; Kamali, Tschackad; Platzer, René; Unterhuber, Angelika; Drexler, Wolfgang; Leitgeb, Rainer A.

    2015-01-01

    In this paper a numerical technique is presented to compensate for anisotropic optical aberrations, which are usually present across the lateral field of view in the out of focus regions, in high resolution optical coherence tomography and microscopy (OCT/OCM) setups. The recorded enface image field at different depths in the tomogram is digitally divided into smaller sub-regions or the regions of interest (ROIs), processed individually using subaperture based digital adaptive optics (DAO), and finally stitched together to yield a final image with a uniform diffraction limited resolution across the entire field of view (FOV). Using this method, a sub-micron lateral resolution is achieved over a depth range of 218 μmfor a nano-particle phantom sample imaged using a fiber based point scanning spectral domain (SD) OCM system with a limited depth of focus (DOF) of ~7 μmat a numerical aperture (NA) of 0.6. Thus, an increase in DOF by ~30x is demonstrated in this case. The application of this method is also shown in ex vivo mouse adipose tissue. PMID:25908999

  7. Age-associated hyper-methylated regions in the human brain overlap with bivalent chromatin domains.

    PubMed

    Watson, Corey T; Disanto, Giulio; Sandve, Geir Kjetil; Breden, Felix; Giovannoni, Gavin; Ramagopalan, Sreeram V

    2012-01-01

    Recent associations between age-related differentially methylated sites and bivalently marked chromatin domains have implicated a role for these genomic regions in aging and age-related diseases. However, the overlap between such epigenetic modifications has so far only been identified with respect to age-associated hyper-methylated sites in blood. In this study, we observed that age-associated differentially methylated sites characterized in the human brain were also highly enriched in bivalent domains. Analysis of hyper- vs. hypo-methylated sites partitioned by age (fetal, child, and adult) revealed that enrichment was significant for hyper-methylated sites identified in children and adults (child, fold difference = 2.28, P = 0.0016; adult, fold difference = 4.73, P = 4.00 × 10(-5)); this trend was markedly more pronounced in adults when only the top 100 most significantly hypo- and hyper-methylated sites were considered (adult, fold difference = 10.7, P = 2.00 × 10(-5)). Interestingly, we found that bivalently marked genes overlapped by age-associated hyper-methylation in the adult brain had strong involvement in biological functions related to developmental processes, including neuronal differentiation. Our findings provide evidence that the accumulation of methylation in bivalent gene regions with age is likely to be a common process that occurs across tissue types. Furthermore, particularly with respect to the aging brain, this accumulation might be targeted to loci with important roles in cell differentiation and development, and the closing off of these developmental pathways. Further study of these genes is warranted to assess their potential impact upon the development of age-related neurological disorders.

  8. Interaction of the GTP-binding and GTPase-activating domains of ARD1 involves the effector region of the ADP-ribosylation factor domain.

    PubMed

    Vitale, N; Moss, J; Vaughan, M

    1997-02-14

    ADP-ribosylation factors (ARFs) are a family of approximately 20-kDa guanine nucleotide-binding proteins and members of the Ras superfamily, originally identified and purified by their ability to enhance the ADP-ribosyltransferase activity of cholera toxin and more recently recognized as critical participants in vesicular trafficking pathways and phospholipase D activation. ARD1 is a 64-kDa protein with an 18-kDa carboxyl-terminal ARF domain (p3) and a 46-kDa amino-terminal extension (p5) that is widely expressed in mammalian tissues. Using recombinant proteins, we showed that p5, the amino-terminal domain of ARD1, stimulates the GTPase activity of p3, the ARF domain, and appears to be the GTPase-activating protein (GAP) component of this bifunctional protein, whereas in other members of the Ras superfamily a separate GAP molecule interacts with the effector region of the GTP-binding protein. p5 stimulated the GTPase activity of p3 but not of ARF1, which differs from p3 in several amino acids in the effector domain. After substitution of 7 amino acids from p3 in the appropriate position in ARF1, the chimeric protein ARF1(39-45p3) bound to p5, which increased its GTPase activity. Specifically, after Gly40 and Thr45 in the putative effector domain of ARF1 were replaced with the equivalent Asp and Pro, respectively, from p3, functional interaction of the chimeric ARF1 with p5 was increased. Thus, Asp25 and Pro30 of the ARF domain (p3) of ARD1 are involved in its functional and physical interaction with the GTPase-activating (p5) domain of ARD1. After deletion of the amino-terminal 15 amino acids from ARF1(39-45p3), its interaction with p5 was essentially equivalent to that of p3, suggesting that the amino terminus of ARF1(39-45p3) may interfere with binding to p5. These results are consistent with the conclusion that the GAP domain of ARD1 interacts with the effector region of the ARF domain and thereby stimulates GTP hydrolysis.

  9. 77 FR 35357 - Atlantic Highly Migratory Species; Commercial Atlantic Region Non-Sandbar Large Coastal Shark...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-06-13

    ...; Commercial Atlantic Region Non-Sandbar Large Coastal Shark Fishery Opening Date AGENCY: National Marine...-sandbar large coastal shark fishery. This action is necessary to inform fishermen and dealers about the fishery opening date. DATES: The commercial Atlantic region non-sandbar large coastal shark fishery...

  10. Interlocked chiral/polar domain walls and large optical rotation in Ni{sub 3}TeO{sub 6}

    SciTech Connect

    Wang, Xueyun; Huang, Fei-Ting; Yang, Junjie; Oh, Yoon Seok; Cheong, Sang-Wook

    2015-07-01

    Chirality, i.e., handedness, pervades much of modern science from elementary particles, DNA-based biology to molecular chemistry; however, most of the chirality-relevant materials have been based on complex molecules. Here, we report inorganic single-crystalline Ni{sub 3}TeO{sub 6}, forming in a corundum-related R3 structure with both chirality and polarity. These chiral Ni{sub 3}TeO{sub 6} single crystals exhibit a large optical specific rotation (α)—1355° dm{sup −1} cm{sup 3} g{sup −1}. We demonstrate, for the first time, that in Ni{sub 3}TeO{sub 6}, chiral and polar domains form an intriguing domain pattern, resembling a radiation warning sign, which stems from interlocked chiral and polar domain walls through lowering of the wall energy.

  11. Non-Linear and Flexible Regions of the Human Notch1 Extracellular Domain Revealed by High-Resolution Structural Studies

    PubMed Central

    Weisshuhn, Philip C.; Sheppard, Devon; Taylor, Paul; Whiteman, Pat; Lea, Susan M.; Handford, Penny A.; Redfield, Christina

    2016-01-01

    Summary The Notch receptor is a key component of a core metazoan signaling pathway activated by Delta/Serrate/Lag-2 ligands expressed on an adjacent cell. This results in a short-range signal with profound effects on cell-fate determination, cell proliferation, and cell death. Key to understanding receptor function is structural knowledge of the large extracellular portion of Notch which contains multiple repeats of epidermal growth factor (EGF)-like domains. Here we investigate the EGF4-13 region of human Notch1 (hN1) using a multidisciplinary approach. Ca2+-binding measurements, X-ray crystallography, {1H}-15N heteronuclear nuclear Overhauser effects, and residual dipolar couplings support a non-linear organization for the EGF4-13 region with a rigid, bent conformation for EGF4-7 and a single flexible linkage between EGF9 and EGF10. These data allow us to construct an informed model for EGF10-13 which, in conjunction with comparative binding studies, demonstrates that EGF10 has an important role in determining Notch receptor sensitivity to Dll-4. PMID:26996961

  12. Effective crop evapotranspiration measurement using time-domain reflectometry technique in a sub-humid region

    NASA Astrophysics Data System (ADS)

    Srivastava, R. K.; Panda, R. K.; Halder, Debjani

    2016-06-01

    The primary objective of this study was to evaluate the performance of the time-domain reflectometry (TDR) technique for daily evapotranspiration estimation of peanut and maize crop in a sub-humid region. Four independent methods were used to estimate crop evapotranspiration (ETc), namely, soil water balance budgeting approach, energy balance approach—(Bowen ratio), empirical methods approach, and Pan evaporation method. The soil water balance budgeting approach utilized the soil moisture measurement by gravimetric and TDR method. The empirical evapotranspiration methods such as combination approach (FAO-56 Penman-Monteith and Penman), temperature-based approach (Hargreaves-Samani), and radiation-based approach (Priestley-Taylor, Turc, Abetw) were used to estimate the reference evapotranspiration (ET0). The daily ETc determined by the FAO-56 Penman-Monteith, Priestley-Taylor, Turc, Pan evaporation, and Bowen ratio were found to be at par with the ET values derived from the soil water balance budget; while the methods Abetw, Penman, and Hargreaves-Samani were not found to be ideal for the determination of ETc. The study illustrates the in situ applicability of the TDR method in order to make it possible for a user to choose the best way for the optimum water consumption for a given crop in a sub-humid region. The study suggests that the FAO-56 Penman-Monteith, Turc, and Priestley-Taylor can be used for the determination of crop ETc using TDR in comparison to soil water balance budget.

  13. A new regional climate simulation using RegCM4 over the CORDEX South Asia domain

    NASA Astrophysics Data System (ADS)

    Mariotti, Laura; Bacer, Sara; Coppola, Erika; Giorgi, Filippo

    2014-05-01

    We present a new high-resolution regional climate simulation over the CORDEX South Asia made with the latest version of the Regional Climate Model RegCM4. The simulation has been performed at 25 km of resolution using the ERA-Interim boundary conditions. The simulated results are compared with the monthly mean surface observations for temperature and precipitation over the entire domain. The rainy season during the June-July-August-September (JJAS) over India shows a bigger improvement using a different parameterization of the MIT-Emanuel convection scheme for land and ocean. Another big improvement has been found with the UW PBL scheme (Bretherton and McCaa, 2004). The model shows in JJAS season a slight cold bias over the mountain compared with CRU dataset, instead in Indian land area the pattern of the temperature is well represented. The monsoon precipitation over the Indian continent is reasonably represented. A good agreement was found from the comparison between RegCM4 with the IMD dataset by studying the area weighted average values time series of monthly accumulated rainfall (cm) in Indian land area.

  14. Sensitivity analysis with the regional climate model COSMO-CLM over the CORDEX-MENA domain

    NASA Astrophysics Data System (ADS)

    Bucchignani, E.; Cattaneo, L.; Panitz, H.-J.; Mercogliano, P.

    2016-02-01

    The results of a sensitivity work based on ERA-Interim driven COSMO-CLM simulations over the Middle East-North Africa (CORDEX-MENA) domain are presented. All simulations were performed at 0.44° spatial resolution. The purpose of this study was to ascertain model performances with respect to changes in physical and tuning parameters which are mainly related to surface, convection, radiation and cloud parameterizations. Evaluation was performed for the whole CORDEX-MENA region and six sub-regions, comparing a set of 26 COSMO-CLM runs against a combination of available ground observations, satellite products and reanalysis data to assess temperature, precipitation, cloud cover and mean sea level pressure. The model proved to be very sensitive to changes in physical parameters. The optimized configuration allows COSMO-CLM to improve the simulated main climate features of this area. Its main characteristics consist in the new parameterization of albedo, based on Moderate Resolution Imaging Spectroradiometer data, and the new parameterization of aerosol, based on NASA-GISS AOD distributions. When applying this configuration, Mean Absolute Error values for the considered variables are as follows: about 1.2 °C for temperature, about 15 mm/month for precipitation, about 9 % for total cloud cover, and about 0.6 hPa for mean sea level pressure.

  15. Structure-based design of a disulfide-linked oligomeric form of the simian virus 40 (SV40) large T antigen DNA-binding domain.

    PubMed

    Meinke, Gretchen; Phelan, Paul; Fradet-Turcotte, Amélie; Archambault, Jacques; Bullock, Peter A

    2011-06-01

    The modular multifunctional protein large T antigen (T-ag) from simian virus 40 orchestrates many of the events needed for replication of the viral double-stranded DNA genome. This protein assembles into single and double hexamers on specific DNA sequences located at the origin of replication. This complicated process begins when the origin-binding domain of large T antigen (T-ag ODB) binds the GAGGC sequences in the central region (site II) of the viral origin of replication. While many of the functions of purified T-ag OBD can be studied in isolation, it is primarily monomeric in solution and cannot assemble into hexamers. To overcome this limitation, the possibility of engineering intermolecular disulfide bonds in the origin-binding domain which could oligomerize in solution was investigated. A recent crystal structure of the wild-type T-ag OBD showed that this domain forms a left-handed spiral in the crystal with six subunits per turn. Therefore, we analyzed the protein interface of this structure and identified two residues that could potentially support an intermolecular disulfide bond if changed to cysteines. SDS-PAGE analysis established that the mutant T-ag OBD formed higher oligomeric products in a redox-dependent manner. In addition, the 1.7 Å resolution crystal structure of the engineered disulfide-linked T-ag OBD is reported, which establishes that oligomerization took place in the expected manner.

  16. Structure-based Design of a Disulfide-lined Oligomeric Form of the Simian Virus 40 (SV40) Large T Antigen DNA-Binding Domain

    SciTech Connect

    G Meinke; P Phelan; A Fradet-Turcotte; J Archambault; P Bullock

    2011-12-31

    The modular multifunctional protein large T antigen (T-ag) from simian virus 40 orchestrates many of the events needed for replication of the viral double-stranded DNA genome. This protein assembles into single and double hexamers on specific DNA sequences located at the origin of replication. This complicated process begins when the origin-binding domain of large T antigen (T-ag ODB) binds the GAGGC sequences in the central region (site II) of the viral origin of replication. While many of the functions of purified T-ag OBD can be studied in isolation, it is primarily monomeric in solution and cannot assemble into hexamers. To overcome this limitation, the possibility of engineering intermolecular disulfide bonds in the origin-binding domain which could oligomerize in solution was investigated. A recent crystal structure of the wild-type T-ag OBD showed that this domain forms a left-handed spiral in the crystal with six subunits per turn. Therefore, we analyzed the protein interface of this structure and identified two residues that could potentially support an intermolecular disulfide bond if changed to cysteines. SDS-PAGE analysis established that the mutant T-ag OBD formed higher oligomeric products in a redox-dependent manner. In addition, the 1.7 {angstrom} resolution crystal structure of the engineered disulfide-linked T-ag OBD is reported, which establishes that oligomerization took place in the expected manner.

  17. Large mining blasts from the Kursk Mining Region, Russia

    SciTech Connect

    Leith, W. Adushkin, V.; Spivak, A.

    1997-01-01

    Monitoring the Comprehensive Nuclear Test Ban Treaty (CTBT) by seismic means will require identification of seismic sources at magnitude levels where industrial explosions (primarily, mining blasts) may comprise a significant fraction of the total number of events recorded, and may for some countries dominate the seismicity. Thus, data on blasting practice have both political significance for the negotiation of treaties involving seismic monitoring of nuclear tests, and operational applications in terms of establishing monitoring and inspection needs on a mine-by-mine basis. While it is generally accepted that mining explosions contribute to seismicity at lower seismic magnitudes (less than about magnitude 3.5), the rate of mining seismicity as a function of seismic magnitude is unknown for most countries outside the U.S. This results in a large uncertainty when estimating the task of discriminating nuclear explosions from chemical explosions and earthquakes, by seismic means, under a comprehensive nuclear test ban. This uncertainty directly affects estimates of seismic network enhancements required to achieve treaty verification requirements at magnitudes less than about 3.5. 24 refs., 64 figs., 11 tabs.

  18. Physical Environmental Correlates of Domain-Specific Sedentary Behaviours across Five European Regions (the SPOTLIGHT Project)

    PubMed Central

    De Cocker, Katrien; Roda, Célina; Oppert, Jean-Michel; Mackenbach, Joreintje D.; Lakerveld, Jeroen; Glonti, Ketevan; Bardos, Helga; Rutter, Harry; Cardon, Greet; De Bourdeaudhuij, Ilse

    2016-01-01

    Background The relation between neighbourhood environmental factors and domain-specific sedentary behaviours among adults remains unclear. This study firstly aims to examine the association of perceived and objectively measured neighbourhood safety, aesthetics, destinations and functionality with transport-related, work-related and leisure-time sedentary behaviour. Secondly, the study aims to assess whether these associations are moderated by age, gender or educational level. Methods In 60 randomly sampled neighbourhoods from 5 urban regions in Europe (Ghent and suburbs, Paris and inner suburbs, Budapest and suburbs, the Randstad, and Greater London), a virtual audit with Google Street View was performed to assess environmental characteristics. A total of 5,205 adult inhabitants of these neighbourhoods reported socio-demographic characteristics, sedentary behaviours, and neighbourhood perceptions in an online survey. Generalized linear mixed models were conducted to examine associations between physical environmental neighbourhood factors and sedentary behaviours. Interaction terms were added to test the moderating role of individual-level socio-demographic variables. Results Lower levels of leisure-time sedentary behaviour (i.e. all leisure activities except television viewing and computer use) were observed among adults who perceived greater numbers of destinations such as supermarkets, recreational facilities, or restaurants in their neighbourhood, and among adults who lived in a neighbourhood with more objectively measured aesthetic features, such as trees, water areas or public parks. Lower levels of work-related sedentary behaviour were observed among adults who perceived less aesthetic features in their neighbourhood, and among adults who lived in a neighbourhood with less objectively measured destinations. Both age, gender and educational level moderated the associations between neighbourhood environmental factors and sedentary behaviours. Conclusion

  19. Terahertz-Field-Induced Large Macroscopic Polarization and Domain-Wall Dynamics in an Organic Molecular Dielectric

    NASA Astrophysics Data System (ADS)

    Morimoto, T.; Miyamoto, T.; Yamakawa, H.; Terashige, T.; Ono, T.; Kida, N.; Okamoto, H.

    2017-03-01

    A rapid polarization control in paraelectric materials is important for an ultrafast optical switching useful in the future optical communication. In this study, we applied terahertz-pump second-harmonic-generation-probe and optical-reflectivity-probe spectroscopies to the paraelectric neutral phase of an organic molecular dielectric, tetrathiafulvalene-p -chloranil and revealed that a terahertz pulse with the electric-field amplitude of ˜400 kV /cm produces in the subpicosecond time scale a large macroscopic polarization whose magnitude reaches ˜20 % of that in the ferroelectric ionic phase. Such a large polarization generation is attributed to the intermolecular charge transfers and breathing motions of domain walls between microscopic neutral and ionic domains induced by the terahertz electric field.

  20. RNA helicase domain of tobamovirus replicase executes cell-to-cell movement possibly through collaboration with its nonconserved region.

    PubMed

    Hirashima, Kyotaro; Watanabe, Yuichiro

    2003-11-01

    UR-hel, a chimeric virus obtained by replacement of the RNA helicase domain of tobacco mosaic virus (TMV)-U1 replicase with that from the TMV-R strain, could replicate similarly to TMV-U1 in protoplasts but could not move from cell to cell (K. Hirashima and Y. Watanabe, J. Virol. 75:8831-8836, 2001). It was suggested that TMV recruited both the movement protein (MP) and replicase for cell-to-cell movement by unknown mechanisms. Here, we found that a recombinant, UR-hel/V, in which the nonconserved region was derived from TMV-R in addition to the RNA helicase domain of replicase, could move from cell to cell. We also analyzed revertants isolated from UR-hel, which recovered cell-to-cell movement by their own abilities. We found amino acid substitutions responsible for phenotypic reversion only in the nonconserved region and/or RNA helicase domain but never in MP. Together, these data show that both the nonconserved region and the RNA helicase domain of replicase are involved in cell-to-cell movement. The RNA helicase domain of tobamovirus replicase possibly does not interact directly with MP but interacts with its nonconserved region to execute cell-to-cell movement.

  1. Sub-terahertz frequency-domain spectroscopy reveals single-grain mobility and scatter influence of large-area graphene.

    PubMed

    Cervetti, Christian; Heintze, Eric; Gorshunov, Boris; Zhukova, Elena; Lobanov, Svyatoslav; Hoyer, Alexander; Burghard, Marko; Kern, Klaus; Dressel, Martin; Bogani, Lapo

    2015-04-24

    The response of individual domains in wafer-sized chemical vapor deposition graphene is measured by contactless sub-terahertz interferometry, observing the intrinsic optical conductance and reaching very high mobility values. It is shown that charged scatterers limit the mobility, validating previous theoretical predictions, and sub-terahertz quality assessment is demonstrated, as necessary for large-scale applications in touchscreens, as well as wearable and optoelectronic devices.

  2. Structural insights into the specific binding of huntingtin proline-rich region with the SH3 and WW domains.

    PubMed

    Gao, Yong-Guang; Yan, Xian-Zhong; Song, Ai-Xin; Chang, Yong-Gang; Gao, Xue-Chao; Jiang, Nan; Zhang, Qi; Hu, Hong-Yu

    2006-12-01

    The interactions of huntingtin (Htt) with the SH3 domain- or WW domain-containing proteins have been implicated in the pathogenesis of Huntington's disease (HD). We report the specific interactions of Htt proline-rich region (PRR) with the SH3GL3-SH3 domain and HYPA-WW1-2 domain pair by NMR. The results show that Htt PRR binds with the SH3 domain through nearly its entire chain, and that the binding region on the domain includes the canonical PxxP-binding site and the specificity pocket. The C terminus of PRR orients to the specificity pocket, whereas the N terminus orients to the PxxP-binding site. Htt PRR can also specifically bind to WW1-2; the N-terminal portion preferentially binds to WW1, while the C-terminal portion binds to WW2. This study provides structural insights into the specific interactions between Htt PRR and its binding partners as well as the alteration of these interactions that involve PRR, which may have implications for the understanding of HD.

  3. Multiscale method for modeling binding phenomena involving large objects: application to kinesin motor domains motion along microtubules

    NASA Astrophysics Data System (ADS)

    Li, Lin; Alper, Joshua; Alexov, Emil

    2016-03-01

    Many biological phenomena involve the binding of proteins to a large object. Because the electrostatic forces that guide binding act over large distances, truncating the size of the system to facilitate computational modeling frequently yields inaccurate results. Our multiscale approach implements a computational focusing method that permits computation of large systems without truncating the electrostatic potential and achieves the high resolution required for modeling macromolecular interactions, all while keeping the computational time reasonable. We tested our approach on the motility of various kinesin motor domains. We found that electrostatics help guide kinesins as they walk: N-kinesins towards the plus-end, and C-kinesins towards the minus-end of microtubules. Our methodology enables computation in similar, large systems including protein binding to DNA, viruses, and membranes.

  4. Multiscale method for modeling binding phenomena involving large objects: application to kinesin motor domains motion along microtubules.

    PubMed

    Li, Lin; Alper, Joshua; Alexov, Emil

    2016-03-18

    Many biological phenomena involve the binding of proteins to a large object. Because the electrostatic forces that guide binding act over large distances, truncating the size of the system to facilitate computational modeling frequently yields inaccurate results. Our multiscale approach implements a computational focusing method that permits computation of large systems without truncating the electrostatic potential and achieves the high resolution required for modeling macromolecular interactions, all while keeping the computational time reasonable. We tested our approach on the motility of various kinesin motor domains. We found that electrostatics help guide kinesins as they walk: N-kinesins towards the plus-end, and C-kinesins towards the minus-end of microtubules. Our methodology enables computation in similar, large systems including protein binding to DNA, viruses, and membranes.

  5. An amphiphilic region in the cytoplasmic domain of KdpD is recognized by the signal recognition particle and targeted to the Escherichia coli membrane

    PubMed Central

    Maier, Katja S; Hubich, Stefanie; Liebhart, Helga; Krauss, Susanne; Kuhn, Andreas; Facey, Sandra J

    2008-01-01

    The sensor protein KdpD of Escherichia coli is composed of a large N-terminal hydrophilic region (aa 1–400), four transmembrane regions (aa 401–498) and a large hydrophilic region (aa 499–894) at the C-terminus. KdpD requires the signal recognition particle (SRP) for its targeting to the membrane. Deletions within KdpD show that the first 50 residues are required for SRP-driven membrane insertion. A fusion protein of the green fluorescent protein (GFP) with KdpD is found localized at the membrane only when SRP is present. The membrane targeting of GFP was not observed when the first 50 KdpD residues were deleted. A truncated mutant of KdpD containing only the first 25 amino acids fused to GFP lost its ability to specifically interact with SRP, whereas a specific interaction between SRP and the first 48 amino acids of KdpD fused to GFP was confirmed by pull-down experiments. Conclusively, a small amphiphilic region of 27 residues within the amino-terminal domain of KdpD (aa 22–48) is recognized by SRP and targets the protein to the membrane. This shows that membrane proteins with a large N-terminal region in the cytoplasm can be membrane-targeted early on to allow co-translational membrane insertion of their distant transmembrane regions. PMID:18433452

  6. Development and use of domain-specific antibodies in a characterization of the large subunits of soybean photosystem 1

    NASA Technical Reports Server (NTRS)

    Henry, R. L.; Takemoto, L. J.; Murphy, J.; Gallegos, G. L.; Guikema, J. A.; Spooner, B. S. (Principal Investigator)

    1992-01-01

    The molecular architecture of the soybean photosystem 1 reaction center complex was examined using a combination of surface labeling and immunological methodology on isolated thylakoid membranes. Synthetic peptides (12 to 14 amino acids in length) were prepared which correspond to the N-terminal regions of the 83 and 82.4 kDa subunits of photosystem 1 (the PsaA and PsaB proteins, respectively). Similarly, a synthetic peptide was prepared corresponding to the C-terminal region of the PsaB subunit. These peptides were conjugated to a carrier protein, and were used for the production of polyclonal antibodies in rabbits. The resulting sera could distinguish between the PsaA and PsaB photosystem 1 subunits by Western blot analysis, and could identify appropriate size classes of cyanogen bromide cleavage fragments as predicted from the primary sequences of these two subunits. When soybean thylakoid membranes were surface-labeled with N-hydroxysuccinimidobiotin, several subunits of the complete photosystem 1 lipid/protein complex incorporated label. These included the light harvesting chlorophyll proteins of photosystem 1, and peptides thought to aid in the docking of ferredoxin to the complex during photosynthetic electron transport. However, the PsaA and PsaB subunits showed very little biotinylation. When these subunits were examined for the domains to which biotin did attach, most of the observed label was associated with the N-terminal domain of the PsaA subunit, as identified using a domain-specific polyclonal antisera.

  7. Automated on-orbit frequency domain identification for large space structures

    NASA Technical Reports Server (NTRS)

    Bayard, D. S.; Hadaegh, F. Y.; Yam, Y.; Scheid, R. E.; Mettler, E.; Milman, M. H.

    1991-01-01

    Recent experiences in the field of flexible structure control in space have indicated a need for on-orbit system identification to support robust control redesign to avoid in-flight instabilities and maintain high spacecraft performance. This paper highlights an automated frequency domain system identification methodology recently developed to fulfill this need. The methodology is focused to support (1) the estimation of system quantities useful for robust control analysis and design; (2) experiment design tailored to performing system identification in a typically constrained on-orbit environment; and (3) the automation of operations to reduce 'human in the loop' requirements.

  8. Fast analysis of wide-band scattering from electrically large targets with time-domain parabolic equation method

    NASA Astrophysics Data System (ADS)

    He, Zi; Chen, Ru-Shan

    2016-03-01

    An efficient three-dimensional time domain parabolic equation (TDPE) method is proposed to fast analyze the narrow-angle wideband EM scattering properties of electrically large targets. The finite difference (FD) of Crank-Nicolson (CN) scheme is used as the traditional tool to solve the time-domain parabolic equation. However, a huge computational resource is required when the meshes become dense. Therefore, the alternating direction implicit (ADI) scheme is introduced to discretize the time-domain parabolic equation. In this way, the reduced transient scattered fields can be calculated line by line in each transverse plane for any time step with unconditional stability. As a result, less computational resources are required for the proposed ADI-based TDPE method when compared with both the traditional CN-based TDPE method and the finite-different time-domain (FDTD) method. By employing the rotating TDPE method, the complete bistatic RCS can be obtained with encouraging accuracy for any observed angle. Numerical examples are given to demonstrate the accuracy and efficiency of the proposed method.

  9. [Domain organization of the ORF2 C-terminal region of the German cockroach retroposon R1].

    PubMed

    Kagramanova, A S; Kapelinskaia, T V; Korolev, A L; Mukha, D V

    2010-08-01

    Using cosmid vector, a gene library of German cockroach Blattella germanica was constructed. From this library, clones containing full-length copies of two subfamilies of R1 retroposons were selected. Retroposons R1 of German cockroach belonging to different subfamilies were shown to be different in domain organization of the ORF2 C-terminal region. For the first time, retroposons transmembrane domains were identified in the sequences of R1. It was demonstrated that two retroposon R1 subfamilies of German cockroach arose as a result of intragenomic divergence rather than via horizontal transfer of alien mobile element into cockroach genome. The differences in domain organization appeared not as a result of saltatory recombination processes, but as a consequence of gradual mutation accumulation, which led to either degeneration, or to domain formation.

  10. Validation of the regional climate model MAR over the CORDEX Africa domain and comparison with other regional models using unpublished data set

    NASA Astrophysics Data System (ADS)

    Prignon, Maxime; Agosta, Cécile; Kittel, Christoph; Fettweis, Xavier; Michel, Erpicum

    2016-04-01

    In the framework of the CORDEX project, we have applied the regional model MAR over the Africa domain at a resolution of 50 km. ERA-Interim and NCEP-NCAR reanalysis have been used as 6 hourly forcing at the MAR boundaries over 1950-2015. While MAR was already been validated over the West Africa, it is the first time that MAR simulations are carried out at the scale of the whole continent. Unpublished daily measurements, covering the Sahel and more areas up South, with a large set of variables, are used as validation of MAR, other CORDEX-Africa RCMs and both reanalyses. Comparisons with the CRU and the ECA&D databases are also performed. The unpublished daily data set covers the period 1884-2006 and comes from 1460 stations. The measured variables are wind, evapotranspiration, relative humidity, insolation, rain, surface pressure, temperature, vapour pressure and visibility. It covers 23 countries: Algeria, Benin, Burkina, Canary Islands, Cap Verde, Central Africa, Chad, Congo, Ivory Coast, Gabon, Gambia, Ghana, Guinea, Guinea-Bissau, Mali, Mauritania, Morocco, Niger, Nigeria, Senegal, Sudan and Togo.

  11. Mutations in the ligand-binding domain of the androgen receptor gene cluster in two regions of the gene.

    PubMed

    McPhaul, M J; Marcelli, M; Zoppi, S; Wilson, C M; Griffin, J E; Wilson, J D

    1992-11-01

    We have analyzed the nucleotide sequence of the androgen receptor from 22 unrelated subjects with substitution mutations of the hormone-binding domain. Eleven had the phenotype of complete testicular feminization, four had incomplete testicular feminization, and seven had Reifenstein syndrome. The underlying functional defect in cultured skin fibroblasts included individuals with absent, qualitative, or quantitative defects in ligand binding. 19 of the 21 substitution mutations (90%) cluster in two regions that account for approximately 35% of the hormone-binding domain, namely, between amino acids 726 and 772 and between amino acids 826 and 864. The fact that one of these regions is homologous to a region of the human thyroid hormone receptor (hTR-beta) which is a known cluster site for mutations that cause thyroid hormone resistance implies that this localization of mutations is not a coincidence. These regions of the androgen receptor may be of particular importance for the formation and function of the hormone-receptor complex.

  12. Multipactor radiation analysis within a waveguide region based on a frequency-domain representation of the dynamics of charged particles.

    PubMed

    Gimeno, B; Sorolla, E; Anza, S; Vicente, C; Gil, J; Pérez, A M; Boria, V E; Pérez-Soler, F J; Quesada, F; Alvarez, A; Raboso, D

    2009-04-01

    A technique for the accurate computation of the electromagnetic fields radiated by a charged particle moving within a parallel-plate waveguide is presented. Based on a transformation of the time-varying current density of the particle into a time-harmonic current density, this technique allows the evaluation of the radiated electromagnetic fields both in the frequency and time domains, as well as in the near- and far-field regions. For this purpose, several accelerated versions of the parallel-plate Green's function in the frequency domain have been considered. The theory has been successfully applied to the multipactor discharge occurring within a two metal-plates region. The proposed formulation has been tested with a particle-in-cell code based on the finite-difference time-domain method, obtaining good agreement.

  13. Mapping of the high affinity Fc epsilon receptor binding site to the third constant region domain of IgE.

    PubMed Central

    Nissim, A; Jouvin, M H; Eshhar, Z

    1991-01-01

    Identification of the precise region(s) on the IgE molecule that take part in the binding of IgE to its high affinity receptor (Fc epsilon RI) may lead to the design of IgE analogues able to block the allergic response. To localize the Fc epsilon RI-binding domain of mouse IgE, we attempted to confer on human IgE, which normally does not bind to the rodent receptor, the ability to bind to the rat Fc epsilon RI. Employing exon shuffling, we have expressed chimeric epsilon-heavy chain genes composed of a mouse (4-hydroxy-3-nitrophenyl)acetic acid (NP)-binding VH domain, and human C epsilon in which various domains were replaced by their murine counterparts. This has enabled us to test the Fc epsilon RI-binding of each mouse IgE domain while maintaining the overall conformation of the molecule. All of the chimeric IgE molecules which contain the murine C epsilon 3, bound equally to both the rodent and human receptor, as well as to monoclonal antibodies recognizing a site on IgE which is identical or very close to the Fc epsilon RI binding site. Deletion of the second constant region domain did not impair either the binding capacity of the mutated IgE or its ability to mediate mast cell degradation. These results assign the third epsilon domain of IgE as the principal region involved in the interaction with the Fc epsilon RI. Images PMID:1824934

  14. Large-eddy simulation in complex domains using the finite element method

    SciTech Connect

    McCallen, R.C.; Kornblum, B.T.; Kollman, W.

    1996-11-12

    Finite element methods (FEM) are demonstrated in combination with large-eddy simulations (LES) as a valuable tool for the study of turbulent, separating channel flows, specifically the flow over a backward facing step.

  15. Peculiar long-range supercurrent in superconductor-ferromagnet-superconductor junction containing a noncollinear magnetic domain in the ferromagnetic region

    SciTech Connect

    Meng, Hao; Wu, Xiuqiang; Ren, Yajie

    2015-01-14

    We study the supercurrent in clean superconductor-ferromagnet-superconductor heterostructure containing a noncollinear magnetic domain in the ferromagnetic region. It is demonstrated that the magnetic domain can lead to a spin-flip scattering process, which reverses the spin orientations of the singlet Cooper pair and simultaneously changes the sign of the corresponding electronic momentum. If the ferromagnetic layers on both sides of magnetic domain have the same features, the long-range proximity effect will take place. That is because the singlet Cooper pair will create an exact phase-cancellation effect and gets an additional π phase shift as it passes through the entire ferromagnetic region. Then, the equal spin triplet pair only exists in the magnetic domain region and can not diffuse into the other two ferromagnetic layers. So, the supercurrent mostly arises from the singlet Cooper pairs, and the equal spin triplet pairs are not involved. This result can provide a approach for generating the long-range supercurrent.

  16. CnaA domains in bacterial pili are efficient dissipaters of large mechanical shocks.

    PubMed

    Echelman, Daniel J; Alegre-Cebollada, Jorge; Badilla, Carmen L; Chang, Chungyu; Ton-That, Hung; Fernández, Julio M

    2016-03-01

    Pathogenic bacteria adhere despite severe mechanical perturbations induced by the host, such as coughing. In Gram-positive bacteria, extracellular protein appendages termed pili are necessary for adherence under mechanical stress. However, little is known about the behavior of Gram-positive pili under force. Here, we demonstrate a mechanism by which Gram-positive pili are able to dissipate mechanical energy through mechanical unfolding and refolding of isopeptide bond-delimited polypeptide loops present in Ig-type CnaA domains. Using single-molecule force spectroscopy, we find that these loops of the pilus subunit SpaA of the SpaA-type pilus from Corynebacterium diphtheriae and FimA of the type 2 pilus from Actinomyces oris unfold and extend at forces that are the highest yet reported for globular proteins. Loop refolding is limited by the hydrophobic collapse of the polypeptide and occurs in milliseconds. Remarkably, both SpaA and FimA initially refold to mechanically weaker intermediates that recover strength with time or ligand binding. Based on the high force extensibility, CnaA-containing pili can dissipate ∼28-fold as much energy compared with their inextensible counterparts before reaching forces sufficient to cleave covalent bonds. We propose that efficient mechanical energy dissipation is key for sustained bacterial attachment against mechanical perturbations.

  17. Exploring Symmetry as an Avenue to the Computational Design of Large Protein Domains

    SciTech Connect

    Fortenberry, Carie; Bowman, Elizabeth Anne; Proffitt, Will; Dorr, Brent; Combs, Steven; Harp, Joel; Mizoue, Laura; Meiler, Jens

    2012-03-15

    It has been demonstrated previously that symmetric, homodimeric proteins are energetically favored, which explains their abundance in nature. It has been proposed that such symmetric homodimers underwent gene duplication and fusion to evolve into protein topologies that have a symmetric arrangement of secondary structure elements - 'symmetric superfolds'. Here, the ROSETTA protein design software was used to computationally engineer a perfectly symmetric variant of imidazole glycerol phosphate synthase and its corresponding symmetric homodimer. The new protein, termed FLR, adopts the symmetric ({beta}{alpha}){sub 8} TIM-barrel superfold. The protein is soluble and monomeric and exhibits two-fold symmetry not only in the arrangement of secondary structure elements but also in sequence and at atomic detail, as verified by crystallography. When cut in half, FLR dimerizes readily to form the symmetric homodimer. The successful computational design of FLR demonstrates progress in our understanding of the underlying principles of protein stability and presents an attractive strategy for the in silico construction of larger protein domains from smaller pieces.

  18. Exploring symmetry as an avenue to the computational design of large protein domains.

    PubMed

    Fortenberry, Carie; Bowman, Elizabeth Anne; Proffitt, Will; Dorr, Brent; Combs, Steven; Harp, Joel; Mizoue, Laura; Meiler, Jens

    2011-11-16

    It has been demonstrated previously that symmetric, homodimeric proteins are energetically favored, which explains their abundance in nature. It has been proposed that such symmetric homodimers underwent gene duplication and fusion to evolve into protein topologies that have a symmetric arrangement of secondary structure elements--"symmetric superfolds". Here, the ROSETTA protein design software was used to computationally engineer a perfectly symmetric variant of imidazole glycerol phosphate synthase and its corresponding symmetric homodimer. The new protein, termed FLR, adopts the symmetric (βα)(8) TIM-barrel superfold. The protein is soluble and monomeric and exhibits two-fold symmetry not only in the arrangement of secondary structure elements but also in sequence and at atomic detail, as verified by crystallography. When cut in half, FLR dimerizes readily to form the symmetric homodimer. The successful computational design of FLR demonstrates progress in our understanding of the underlying principles of protein stability and presents an attractive strategy for the in silico construction of larger protein domains from smaller pieces.

  19. CnaA domains in bacterial pili are efficient dissipaters of large mechanical shocks

    PubMed Central

    Echelman, Daniel J.; Alegre-Cebollada, Jorge; Badilla, Carmen L.; Chang, Chungyu; Ton-That, Hung; Fernández, Julio M.

    2016-01-01

    Pathogenic bacteria adhere despite severe mechanical perturbations induced by the host, such as coughing. In Gram-positive bacteria, extracellular protein appendages termed pili are necessary for adherence under mechanical stress. However, little is known about the behavior of Gram-positive pili under force. Here, we demonstrate a mechanism by which Gram-positive pili are able to dissipate mechanical energy through mechanical unfolding and refolding of isopeptide bond-delimited polypeptide loops present in Ig-type CnaA domains. Using single-molecule force spectroscopy, we find that these loops of the pilus subunit SpaA of the SpaA-type pilus from Corynebacterium diphtheriae and FimA of the type 2 pilus from Actinomyces oris unfold and extend at forces that are the highest yet reported for globular proteins. Loop refolding is limited by the hydrophobic collapse of the polypeptide and occurs in milliseconds. Remarkably, both SpaA and FimA initially refold to mechanically weaker intermediates that recover strength with time or ligand binding. Based on the high force extensibility, CnaA-containing pili can dissipate ∼28-fold as much energy compared with their inextensible counterparts before reaching forces sufficient to cleave covalent bonds. We propose that efficient mechanical energy dissipation is key for sustained bacterial attachment against mechanical perturbations. PMID:26884173

  20. Gating of the MlotiK1 potassium channel involves large rearrangements of the cyclic nucleotide-binding domains

    PubMed Central

    Mari, Stefania A.; Pessoa, João; Altieri, Stephen; Hensen, Ulf; Thomas, Lise; Morais-Cabral, João H.; Müller, Daniel J.

    2011-01-01

    Cyclic nucleotide-regulated ion channels are present in bacteria, plants, vertebrates, and humans. In higher organisms, they are closely involved in signaling networks of vision and olfaction. Binding of cAMP or cGMP favors the activation of these ion channels. Despite a wealth of structural and studies, there is a lack of structural data describing the gating process in a full-length cyclic nucleotide-regulated channel. We used high-resolution atomic force microscopy (AFM) to directly observe the conformational change of the membrane embedded bacterial cyclic nucleotide-regulated channel MlotiK1. In the nucleotide-bound conformation, the cytoplasmic cyclic nucleotide-binding (CNB) domains of MlotiK1 are disposed in a fourfold symmetric arrangement forming a pore-like vestibule. Upon nucleotide-unbinding, the four CNB domains undergo a large rearrangement, stand up by ∼1.7 nm, and adopt a structurally variable grouped conformation that closes the cytoplasmic vestibule. This fully reversible conformational change provides insight into how CNB domains rearrange when regulating the potassium channel. PMID:22135457

  1. A non-overlapping domain decomposition method with non-matching grids for modeling large finite antenna arrays

    NASA Astrophysics Data System (ADS)

    Lee, Seung-Cheol; Vouvakis, Marinos N.; Lee, Jin-Fa

    2005-02-01

    A non-overlapping domain decomposition method (DDM) is proposed herein to solve Maxwell equations in R3. In this work, the Maxwell equations are discretized using a vector finite element method with hierarchical H(curl) vector basis functions. There are two major ingredients in the proposed non-overlapping DDM: (a) A proper 1st order transmission condition to enforce field continuity across domain boundaries and (b) A cement technique to allow non-matching grids for neighboring domains. Moreover, a detail Fourier analysis of the transmission condition for a canonical half-space example is presented. The analysis provides significant insights into the convergence behavior of the proposed non-overlapping DDM for solving electromagnetic radiation problems, such as the large finite antenna arrays. Particularly for the antenna arrays, the proposed non-overlapping DDM is extremely efficient since the formulation can easily incorporate geometrical repetitions. Exponentially tapered notch (Vivaldi) antenna arrays with size up to 100 × 100 elements are solved on a common PC to validate the proposed non-overlapping DDM.

  2. An Anomaly in the Domain Chaos State of Rayleigh-B'enard Convection with Large Aspect Ratio

    NASA Astrophysics Data System (ADS)

    Becker, Nathan

    2005-03-01

    Rayleigh-B'enard convection-patterns exhibit a type of spatio-temporal chaos known as domain chaos (DC) at the onset of convection when the sample rotates fast enough about the vertical axis. DC is characterized by domains of straight rolls that chaotically change their orientation and size due to the Küppers-Lortz instability.ootnotetextG. Küppers and D. Lortz, J. Fluid Mech. 35, 609 (1969). However, in a large aspect ratio γ≡r/d=82 cylindrical sample, where r is the radius of the cell and d is the cell thickness, we observed DC in the sample center, surrounded by an annulus of radial rolls populated by occasional defects reminiscent of undulation chaos.ootnotetextK. E. Daniels, B.B. Plapp, and E. Bodenschatz, Phys. Rev. Lett. 84, 5320 (2000). This was unexpected because smaller samples do exhibit domain chaos throughout and the weakly-nonlinear theory that describes the supercritical bifurcation to chaos is expected to be more applicable as γ increases. One possible explanation is that the centrifugal force, which is neglected in the theory, plays an important role.ootnotetextA. Jayaraman and H. Greenside (private communication).

  3. A comparison of different inverse carbon flux estimation approaches for application on a regional domain

    NASA Astrophysics Data System (ADS)

    Tolk, L. F.; Dolman, A. J.; Meesters, A. G. C. A.; Peters, W.

    2011-10-01

    We have implemented six different inverse carbon flux estimation methods in a regional carbon dioxide (CO2) flux modeling system for the Netherlands. The system consists of the Regional Atmospheric Mesoscale Modeling System (RAMS) coupled to a simple carbon flux scheme which is run in a coupled fashion on relatively high resolution (10 km). Using an Ensemble Kalman filter approach we try to estimate spatiotemporal carbon exchange patterns from atmospheric CO2 mole fractions over the Netherlands for a two week period in spring 2008. The focus of this work is the different strategies that can be employed to turn first-guess fluxes into optimal ones, which is known as a fundamental design choice that can affect the outcome of an inversion significantly. Different state-of-the-art approaches with respect to the estimation of net ecosystem exchange (NEE) are compared quantitatively: (1) where NEE is scaled by one linear multiplication factor per land-use type, (2) where the same is done for photosynthesis (GPP) and respiration (R) separately with varying assumptions for the correlation structure, (3) where we solve for those same multiplication factors but now for each grid box, and (4) where we optimize physical parameters of the underlying biosphere model for each land-use type. The pattern to be retrieved in this pseudo-data experiment is different in nearly all aspects from the first-guess fluxes, including the structure of the underlying flux model, reflecting the difference between the modeled fluxes and the fluxes in the real world. This makes our study a stringent test of the performance of these methods, which are currently widely used in carbon cycle inverse studies. Our results show that all methods struggle to retrieve the spatiotemporal NEE distribution, and none of them succeeds in finding accurate domain averaged NEE with correct spatial and temporal behavior. The main cause is the difference between the structures of the first-guess and true CO2 flux

  4. A comparison of different inverse carbon flux estimation approaches for application on a regional domain

    NASA Astrophysics Data System (ADS)

    Tolk, L. F.; Dolman, A. J.; Meesters, A. G. C. A.; Peters, W.

    2011-01-01

    We have implemented six different inverse carbon flux estimation methods in a regional carbon dioxide (CO2) flux modeling system for The Netherlands. The system consists of the Regional Atmospheric Mesoscale Modeling System (RAMS) coupled to a simple carbon flux scheme which is run in a coupled fashion on relatively high resolution (10 km). Using an Ensemble Kalman filter approach we try to estimate spatiotemporal carbon exchange patterns from atmospheric CO2 mole fractions over The Netherlands for a two week period in spring 2008. The focus of this work is the different strategies that can be employed to turn first-guess fluxes into optimal ones, which is known as a fundamental design choice that can affect the outcome of an inversion significantly. Different state-of-the-art approaches with respect to the estimation of net ecosystem exchange (NEE) are compared quantitatively: (1) where NEE is scaled by one linear multiplication factor per land-use type, (2) where the same is done for photosynthesis (GPP) and respiration (R) separately with varying assumptions for the correlation structure, (3) where we solve for those same multiplication factors but now for each grid box, and (4) where we optimize physical parameters of the underlying biosphere model for each land-use type. The pattern to be retrieved in this pseudo-data experiment is different in nearly all aspects from the first-guess fluxes, including the structure of the underlying flux model, reflecting the difference between the modeled fluxes and the fluxes in the real world. This makes our study a stringent test of the performance of these methods, which are currently widely used in carbon cycle inverse studies. Our results show that all methods struggle to retrieve the spatiotemporal NEE distribution, and none of them succeeds in finding accurate domain averaged NEE with correct spatial and temporal behavior. The main cause is the difference between the structures of the first-guess and true CO2 flux

  5. Lineament Domain of Regional Strike-Slip Corridor: Insight from the Neogene Transtensional De Geer Transform Fault in NW Spitsbergen

    NASA Astrophysics Data System (ADS)

    Cianfarra, P.; Salvini, F.

    2015-05-01

    Lineaments on regional scale images represent controversial features in tectonic studies. Published models explain the presence of the lineament domains in most geodynamic environments as resulting from the enhanced erosion along strikes normal to the upper crustal regional extension. Despite their success in many tectonic frameworks, these models fail to explain the existing lineament domains in the regional strike-slip corridors that separate regional blocks, including the transform faults. The present paper investigates the lineament distribution in such environments, and specifically presents the results from a study along the shear corridor of the De Geer Transform Fault in the North Atlantic, responsible for the separation and drifting away between Northern Greenland and the Svalbard Archipelago since Oligocene times. The study spans from satellite image analysis and outcrop scale investigations to a more regional analysis on a digital bathymetric model of the North Atlantic-Arctic Ocean. Lineaments were automatically detected in the spectral band 8 (0.52-0.9 μm) of a Landsat 7 image (15 m/pixel resolution). A total of 320 image lineaments were extracted from both the regional and the local scale investigations and statistically analyzed. Results from the multi-scalar lineament analyses revealed the existence of a main N-S lineament domain regionally persistent from the De Geer corridor to the western margin of northern Spitsbergen where it relates to the youngest, post-Oligocene, tectonics observed onshore. This is confirmed by field observations showing that the N-S faults represent the youngest brittle deformation system and systematically cut the deformations associated with the building of the Tertiary West Spitsbergen fold and thrust belt. The N-S lineament domain is the result of the activity of a larger, regional scale tectonic feature, NW-SE oriented and responsible for the localized extension within its deformation corridor, the De Geer Transform

  6. Nature and distribution of geological domains at the Africa-Eurasia plate boundary off SW Iberia and regional geodynamic implications

    NASA Astrophysics Data System (ADS)

    Martínez-Loriente, Sara; Sallarès, Valentí; Gràcia, Eulàlia; Bartolome, Rafael

    2014-05-01

    We present a new classification of geological domains at the Africa-Eurasia plate boundary off SW Iberia, together with a regional geodynamic reconstruction spanning from the Mesozoic extension to the Neogene-to-present-day convergence. It is based on seismic velocity and density models along two regional wide-angle seismic transects, one running NW-SE from the Horseshoe to the Seine abyssal plains, and the other running N-S from S Portugal to the Seine Abyssal Plain, combined with previously available information. The seismic velocity and density structure at the Seine Abyssal Plain and the internal Gulf of Cadiz indicates the presence of a highly heterogeneous oceanic crust, similar to that described in ultra-slow spreading centers, whereas in the Horseshoe and Tagus abyssal plains, the basement structure resembles that of exhumed mantle sections identified in the Northern Atlantic margin. The integration of all this new information allows defining the presence of three oceanic domains offshore SW Iberia: (1) the Seine Abyssal Plain domain, generated during the first stages of slow seafloor spreading in the NE Central Atlantic (Early Jurassic); (2) the Gulf of Cadiz domain, made of oceanic crust generated in the Alpine-Tethys spreading system between Iberia and Africa, which was coeval with the formation of the Seine Abyssal Plain domain and lasted up to the North Atlantic continental break-up (Late Jurassic); and (3) the Gorringe Bank domain, mainly made of rocks exhumed from the mantle with little synchronous magmatism, which formed during the first stages of North Atlantic opening. Our models suggest that the Seine Abyssal Plain and Gulf of Cadiz domains are separated by the Lineament South strike-slip fault, whereas the Gulf of Cadiz and Gorringe Bank domains appear to be limited by a deep thrust fault located at the center of the Horseshoe Abyssal Plain. The formation and evolution of these three domains during the Mesozoic is key to understand the sequence

  7. A large-domain approach for calculating ship boundary layers and wakes and wave fields for nonzero Froude number

    SciTech Connect

    Tahara, Y.; Stern, F.

    1996-09-01

    A large-domain approach is developed for calculating ship boundary layers and wakes and wave fields for nonzero Froude number. The Reynolds-averaged Navier-Stokes and continuity equations are solved with the Baldwin-Lomax turbulence model, exact nonlinear kinematic and approximate dynamic free-surface boundary conditions, and a body/free-surface conforming grid. The results are validated through comparisons with data for the Series 60 C{sub B} = 0.6 ship model at low and high Froude numbers and results of a precursory interactive approach. Both approaches yield satisfactory results; however, the large-domain results indicate improved resolution of the flow close to the hull and wake centerplane and of the Froucle number differences due to near-wall turbulence modeling and non-linear free-surface boundary conditions. Additional evaluation is provided through discussion of the recent CFD Workshop Tokyo 1994, where both methods were among the best. Last, some concluding remarks are made. 20 refs., 7 figs.

  8. Analysis and modeling of the variable region of camelid single-domain antibodies.

    PubMed

    Sircar, Aroop; Sanni, Kayode A; Shi, Jiye; Gray, Jeffrey J

    2011-06-01

    Camelids have a special type of Ab, known as heavy chain Abs, which are devoid of classical Ab light chains. Relative to classical Abs, camelid heavy chain Abs (cAbs) have comparable immunogenicity, Ag recognition diversity and binding affinities, higher stability and solubility, and better manufacturability, making them promising candidates for alternate therapeutic scaffolds. Rational engineering of cAbs to improve therapeutic function requires knowledge of the differences of sequence and structural features between cAbs and classical Abs. In this study, amino acid sequences of 27 cAb variable regions (V(H)H) were aligned with the respective regions of 54 classical Abs to detect amino acid differences, enabling automatic identification of cAb V(H)H CDRs. CDR analysis revealed that the H1 often (and sometimes the H2) adopts diverse conformations not classifiable by established canonical rules. Also, although the cAb H3 is much longer than classical H3 loops, it often contains common structural motifs and sometimes a disulfide bond to the H1. Leveraging these observations, we created a Monte Carlo-based cAb V(H)H structural modeling tool, where the CDR H1 and H2 loops exhibited a median root-mean-square deviation to natives of 3.1 and 1.5 Å, respectively. The protocol generated 8-12, 14-16, and 16-24 residue H3 loops with a median root-mean-square deviation to natives of 5.7, 4.5, and 6.8 Å, respectively. The large deviation of the predicted loops underscores the challenge in modeling such long loops. cAb V(H)H homology models can provide structural insights into interaction mechanisms to enable development of novel Abs for therapeutic and biotechnological use.

  9. Identification of Regions in the Receiver Domain of the ETHYLENE RESPONSE1 Ethylene Receptor of Arabidopsis Important for Functional Divergence.

    PubMed

    Bakshi, Arkadipta; Wilson, Rebecca L; Lacey, Randy F; Kim, Heejung; Wuppalapati, Sai Keerthana; Binder, Brad M

    2015-09-01

    Ethylene influences the growth and development of Arabidopsis (Arabidopsis thaliana) via five receptor isoforms. However, the ETHYLENE RESPONSE1 (ETR1) ethylene receptor has unique, and sometimes contrasting, roles from the other receptor isoforms. Prior research indicates that the receiver domain of ETR1 is important for some of these noncanonical roles. We determined that the ETR1 receiver domain is not needed for ETR1's predominant role in mediating responses to the ethylene antagonist, silver. To understand the structure-function relationship underlying the unique roles of the ETR1 receiver domain in the control of specific traits, we performed alanine-scanning mutagenesis. We chose amino acids that are poorly conserved and are in regions predicted to have altered tertiary structure compared with the receiver domains of the other two receptors that contain a receiver domain, ETR2 and ETHYLENE INSENSITIVE4. The effects of these mutants on various phenotypes were examined in transgenic, receptor-deficient Arabidopsis plants. Some traits, such as growth in air and growth recovery after the removal of ethylene, were unaffected by these mutations. By contrast, three mutations on one surface of the receiver domain rendered the transgene unable to rescue ethylene-stimulated nutations. Additionally, several mutations on another surface altered germination on salt. Some of these mutations conferred hyperfunctionality to ETR1 in the context of seed germination on salt, but not for other traits, that correlated with increased responsiveness to abscisic acid. Thus, the ETR1 receiver domain has multiple functions where different surfaces are involved in the control of different traits. Models are discussed for these observations.

  10. Women Workers in Regional Areas and in Large States and Metropolitan Areas, 1971.

    ERIC Educational Resources Information Center

    Employment Standards Administration (DOL), Washington, DC. Women's Bureau.

    Data from the Bureau of Labor Statistics has been summarized on labor force participation and unemployment rates in 1971, of women 16 years of age and over, in the various census regions of the United States and in 10 large States and 20 large Standard Metropolitan Statistical Areas (SMSA's); separate data also have been summarized for women of…

  11. Molecular insights into the binding of phosphoinositides to the TH domain region of TIPE proteins.

    PubMed

    Antony, Priya; Baby, Bincy; Vijayan, Ranjit

    2016-11-01

    Phosphatidylinositols and their phosphorylated derivatives, phosphoinositides, play a central role in regulating diverse cellular functions. These phospholipids have been shown to interact with the hydrophobic TH domain of the tumor necrosis factor (TNF)-α-induced protein 8 (TIPE) family of proteins. However, the precise mechanism of interaction of these lipids is unclear. Here we report the binding mode and interactions of these phospholipids in the TH domain, as elucidated using molecular docking and simulations. Results indicate that phosphoinositides bind to the TH domain in a similar way by inserting their lipid tails in the hydrophobic cavity. The exposed head group is stabilized by interactions with critical positively charged residues on the surface of these proteins. Further MD simulations confirmed the dynamic stability of these lipids in the TH domain. This computational analysis thus provides insight into the binding mode of phospholipids in the TH domain of the TIPE family of proteins. Graphical abstract A phosphoinositide (phosphatidylinositol 4-phosphate; PtdIns4P) docked to TIPE2.

  12. Simulation of Electron Diffusion Region processes in magnetospheric current layers with the new semi-implicit adaptive Multi Level Multi Domain method

    NASA Astrophysics Data System (ADS)

    Innocenti, M. E.; Beck, A.; Markidis, S.; Lapenta, G.

    2014-12-01

    Magnetic reconnection is the magnetosphere is characterized by the complex interplay of microscopic and macroscopic scale: processes originating at the electron scales may eventually produce noticeable effects at the macroscopic scales also. A suitable example is the acceleration of electron jets to electron Alfvén speed in the inner Electron Diffusion Region (EDR) (Drake08): the accelerated electrons then evolve into an outer EDR with length of the order of the ion skin depth (Karimabadi07).This same example highlights the challenges entailed in numerical simulations of magnetic reconnection. Large domains have to be simulated to appreciate the large scale reconnection dynamics, but at the same time electron scale resolution has to be used, at least locally, to allow microscale processes to develop. This dramatically increases the computational costs of simulations, especially if a realistic mass ratio between the particle species is used. We show here simulations of large domain magnetic reconnection processes with electron scale resolution. These simulations are made possible at a moderate computational cost by the use of the newly developed semi-implicit Multi Level Multi Domain method (Innocenti13, Beck13), which combines the advantages of implicit algorithms (Vu92) and adaptivity. With the MLMD method, a domain larger than the Ion Diffusion Region is simulated with realistic mass ratio and with ion scale resolution. The EDR is then simulated also with higher spatial and temporal resolution, to allow electron scale, faster processes to develop there. Since electron scale resolution is used only in a small part of the total domain, the computational cost of MLMD simulations is dramatically lowered with respect to fully resolved simulations. Comparable levels of physical details is delivered (Innocenti14, submitted). To prove this, we show here that the MLMD method can capture characteristic EDR electron scale processes such as the formation of an inversion

  13. Interfacial Partitioning of a Loop Hinge Residue Contributes to Diacylglycerol Affinity of Conserved Region 1 Domains*

    PubMed Central

    Stewart, Mikaela D.; Cole, Taylor R.; Igumenova, Tatyana I.

    2014-01-01

    Conventional and novel isoenzymes of PKC are activated by the membrane-embedded second messenger diacylglycerol (DAG) through its interactions with the C1 regulatory domain. The affinity of C1 domains to DAG varies considerably among PKCs. To gain insight into the origin of differential DAG affinities, we conducted high-resolution NMR studies of C1B domain from PKCδ (C1Bδ) and its W252Y variant. The W252Y mutation was previously shown to render C1Bδ less responsive to DAG (Dries, D. R., Gallegos, L. L., and Newton, A. C. (2007) A single residue in the C1 domain sensitizes novel protein kinase C isoforms to cellular diacylglycerol production. J. Biol. Chem. 282, 826–830) and thereby emulate the behavior of C1B domains from conventional PKCs that have a conserved Tyr at the equivalent position. Our data revealed that W252Y mutation did not perturb the conformation of C1Bδ in solution but significantly reduced its propensity to partition into a membrane-mimicking environment in the absence of DAG. Using detergent micelles doped with a paramagnetic lipid, we determined that both the residue identity at position 252 and complexation with diacylglycerol influence the geometry of C1Bδ-micelle interactions. In addition, we identified the C-terminal helix α1 of C1Bδ as an interaction site with the head groups of phosphatidylserine, a known activator of PKCδ. Taken together, our studies (i) reveal the identities of C1Bδ residues involved in interactions with membrane-mimicking environment, DAG, and phosphatidylserine, as well as the affinities associated with each event and (ii) suggest that the initial ligand-independent membrane recruitment of C1B domains, which is greatly facilitated by the interfacial partitioning of Trp-252, is responsible, at least in part, for the differential DAG affinities. PMID:25124034

  14. Effects of large-scale deforestation on precipitation in the monsoon regions: remote versus local effects.

    PubMed

    Devaraju, N; Bala, Govindasamy; Modak, Angshuman

    2015-03-17

    In this paper, using idealized climate model simulations, we investigate the biogeophysical effects of large-scale deforestation on monsoon regions. We find that the remote forcing from large-scale deforestation in the northern middle and high latitudes shifts the Intertropical Convergence Zone southward. This results in a significant decrease in precipitation in the Northern Hemisphere monsoon regions (East Asia, North America, North Africa, and South Asia) and moderate precipitation increases in the Southern Hemisphere monsoon regions (South Africa, South America, and Australia). The magnitude of the monsoonal precipitation changes depends on the location of deforestation, with remote effects showing a larger influence than local effects. The South Asian Monsoon region is affected the most, with 18% decline in precipitation over India. Our results indicate that any comprehensive assessment of afforestation/reforestation as climate change mitigation strategies should carefully evaluate the remote effects on monsoonal precipitation alongside the large local impacts on temperatures.

  15. Effects of large-scale deforestation on precipitation in the monsoon regions: Remote versus local effects

    PubMed Central

    Devaraju, N.; Bala, Govindasamy; Modak, Angshuman

    2015-01-01

    In this paper, using idealized climate model simulations, we investigate the biogeophysical effects of large-scale deforestation on monsoon regions. We find that the remote forcing from large-scale deforestation in the northern middle and high latitudes shifts the Intertropical Convergence Zone southward. This results in a significant decrease in precipitation in the Northern Hemisphere monsoon regions (East Asia, North America, North Africa, and South Asia) and moderate precipitation increases in the Southern Hemisphere monsoon regions (South Africa, South America, and Australia). The magnitude of the monsoonal precipitation changes depends on the location of deforestation, with remote effects showing a larger influence than local effects. The South Asian Monsoon region is affected the most, with 18% decline in precipitation over India. Our results indicate that any comprehensive assessment of afforestation/reforestation as climate change mitigation strategies should carefully evaluate the remote effects on monsoonal precipitation alongside the large local impacts on temperatures. PMID:25733889

  16. Role of the Outer Pore Domain in Transient Receptor Potential Vanilloid 1 Dynamic Permeability to Large Cations*

    PubMed Central

    Munns, Clare H.; Chung, Man-Kyo; Sanchez, Yuly E.; Amzel, L. Mario; Caterina, Michael J.

    2015-01-01

    Transient receptor potential vanilloid 1 (TRPV1) has been shown to alter its ionic selectivity profile in a time- and agonist-dependent manner. One hallmark of this dynamic process is an increased permeability to large cations such as N-methyl-d-glucamine (NMDG). In this study, we mutated residues throughout the TRPV1 pore domain to identify loci that contribute to dynamic large cation permeability. Using resiniferatoxin (RTX) as the agonist, we identified multiple gain-of-function substitutions within the TRPV1 pore turret (N628P and S629A), pore helix (F638A), and selectivity filter (M644A) domains. In all of these mutants, maximum NMDG permeability was substantially greater than that recorded in wild type TRPV1, despite similar or even reduced sodium current density. Two additional mutants, located in the pore turret (G618W) and selectivity filter (M644I), resulted in significantly reduced maximum NMDG permeability. M644A and M644I also showed increased and decreased minimum NMDG permeability, respectively. The phenotypes of this panel of mutants were confirmed by imaging the RTX-evoked uptake of the large cationic fluorescent dye YO-PRO1. Whereas none of the mutations selectively altered capsaicin-induced changes in NMDG permeability, the loss-of-function phenotypes seen with RTX stimulation of G618W and M644I were recapitulated in the capsaicin-evoked YO-PRO1 uptake assay. Curiously, the M644A substitution resulted in a loss, rather than a gain, in capsaicin-evoked YO-PRO1 uptake. Modeling of our mutations onto the recently determined TRPV1 structure revealed several plausible mechanisms for the phenotypes observed. We conclude that side chain interactions at a few specific loci within the TRPV1 pore contribute to the dynamic process of ionic selectivity. PMID:25568328

  17. Real-time display with large field of view on fourier domain optical coherence tomography at 1310 nm wavelength for dermatology

    NASA Astrophysics Data System (ADS)

    Xiao, Qing; Hou, Jue; Fu, Ling

    2012-06-01

    A Fourier domain optical coherence tomography (OCT) system with 1310 nm light was demonstrated to study inflammatory human skin and the skin coated with a moisturizer in vivo. By using a graphics processing unit (GPU), the display rate could reach 20 frames/s with 1000 A-scans contained in one image. The field of view (FOV) of the cross-sectional image is 7 mm in the lateral direction and the penetration depth is ˜1 mm in skin. The result shows that, in inflammatory skin, the epidermis became thicker and had a decreased scattering; furthermore, the region of the severe lesion present an uneven thickness of the epidermis compared with the peripheral area. For the result of a finger tip coated with the moisturizer, the antireflection effect was significant and the stratum corneum became more transparent. In this letter, we demonstrated that real-time display with a large FOV could enable screening of a large tissue area; thereby increasing the dermatologic diagnostic potential of the method by permitting a comparison of the lesion and the normal peripheral region.

  18. Different regional climatic drivers of Holocene large wildfires in boreal forests of northeastern America

    NASA Astrophysics Data System (ADS)

    Remy, Cécile C.; Hély, Christelle; Blarquez, Olivier; Magnan, Gabriel; Bergeron, Yves; Lavoie, Martin; Ali, Adam A.

    2017-03-01

    Global warming could increase climatic instability and large wildfire activity in circumboreal regions, potentially impairing both ecosystem functioning and human health. However, links between large wildfire events and climatic and/or meteorological conditions are still poorly understood, partly because few studies have covered a wide range of past climate-fire interactions. We compared palaeofire and simulated climatic data over the last 7000 years to assess causes of large wildfire events in three coniferous boreal forest regions in north-eastern Canada. These regions span an east-west cline, from a hilly region influenced by the Atlantic Ocean currently dominated by Picea mariana and Abies balsamea to a flatter continental region dominated by Picea mariana and Pinus banksiana. The largest wildfires occurred across the entire study zone between 3000 and 1000 cal. BP. In western and central continental regions these events were triggered by increases in both the fire-season length and summer/spring temperatures, while in the eastern region close to the ocean they were likely responses to hydrological (precipitation/evapotranspiration) variability. The impact of climatic drivers on fire size varied spatially across the study zone, confirming that regional climate dynamics could modulate effects of global climate change on wildfire regimes.

  19. Phage Display Derived IgNAR V Region Binding Domains for Therapeutic Development.

    PubMed

    Ubah, Obinna C; Barelle, Caroline J; Buschhaus, Magdalena J; Porter, Andrew J

    2016-01-01

    Phage display technology has revolutionized the science of drug discovery by transforming the generation and manipulation of ligands, such as antibody fragments, enzymes, and peptides. The basis of this technology is the expression of recombinant proteins or peptides fused to a phage coat protein, and subsequent isolation of ligands based on a variety of catalytic, physicochemical/binding kinetic and/or biological characteristics. An incredible number of diagnostic and therapeutic domains have been successfully isolated using phage display technology. The variable domain of the New Antigen Receptors (VNAR) found in cartilaginous fish, is also amenable to phage display selection. Whilst not an antibody, VNARs are unquestionable the oldest (450 million years), and smallest antigen binding, single-domains so far identified in the vertebrate kingdom. Their role as an integral part of the adaptive immune system of sharks has been well established, enhancing our understanding of the evolutionary origins of humoral immunity and the unusual but divergent ancestry of the VNARs themselves. VNARs exhibit remarkable physicochemical properties, such as small size, stability in extreme conditions, solubility, molecular flexibility, high affinity and selectivity for target. The purpose of this review is to illustrate the important role phage display has played in the isolation and characterization of potent therapeutic and diagnostic VNAR domains.

  20. Existence domains of large amplitude dust-acoustic solitons in non-thermal plasmas with positive and negative dust

    SciTech Connect

    Maharaj, S. K.; Bharuthram, R.; Singh, S. V.; Lakhina, G. S.; Pillay, S. R.

    2011-11-29

    Using the traditional Sagdeev pseudopotential approach, the existence of large amplitude solitons is investigated for a plasma composed of cold negative dust, adiabatic positive dust, non-thermal ions and Boltzmann electrons. The lower and upper soliton Mach number limitations are determined as a function of various parameters and physical reasons are provided as to why these Mach number limits occur. Some regions in parameter space have been identified where only negative or positive solitons occur, whereas, other regions support the coexistence of both positive and negative potential solitons.

  1. Existence domains of large amplitude dust-acoustic solitons in non-thermal plasmas with positive and negative dust

    NASA Astrophysics Data System (ADS)

    Maharaj, S. K.; Bharuthram, R.; Singh, S. V.; Pillay, S. R.; Lakhina, G. S.

    2011-11-01

    Using the traditional Sagdeev pseudopotential approach, the existence of large amplitude solitons is investigated for a plasma composed of cold negative dust, adiabatic positive dust, non-thermal ions and Boltzmann electrons. The lower and upper soliton Mach number limitations are determined as a function of various parameters and physical reasons are provided as to why these Mach number limits occur. Some regions in parameter space have been identified where only negative or positive solitons occur, whereas, other regions support the coexistence of both positive and negative potential solitons.

  2. Generating extreme weather event sets from very large ensembles of regional climate models

    NASA Astrophysics Data System (ADS)

    Massey, Neil; Guillod, Benoit; Otto, Friederike; Allen, Myles; Jones, Richard; Hall, Jim

    2015-04-01

    Generating extreme weather event sets from very large ensembles of regional climate models Neil Massey, Benoit P. Guillod, Friederike E. L. Otto, Myles R. Allen, Richard Jones, Jim W. Hall Environmental Change Institute, University of Oxford, Oxford, UK Extreme events can have large impacts on societies and are therefore being increasingly studied. In particular, climate change is expected to impact the frequency and intensity of these events. However, a major limitation when investigating extreme weather events is that, by definition, only few events are present in observations. A way to overcome this issue it to use large ensembles of model simulations. Using the volunteer distributed computing (VDC) infrastructure of weather@home [1], we run a very large number (10'000s) of RCM simulations over the European domain at a resolution of 25km, with an improved land-surface scheme, nested within a free-running GCM. Using VDC allows many thousands of climate model runs to be computed. Using observations for the GCM boundary forcings we can run historical "hindcast" simulations over the past 100 to 150 years. This allows us, due to the chaotic variability of the atmosphere, to ascertain how likely an extreme event was, given the boundary forcings, and to derive synthetic event sets. The events in these sets did not actually occur in the observed record but could have occurred given the boundary forcings, with an associated probability. The event sets contain time-series of fields of meteorological variables that allow impact modellers to assess the loss the event would incur. Projections of events into the future are achieved by modelling projections of the sea-surface temperature (SST) and sea-ice boundary forcings, by combining the variability of the SST in the observed record with a range of warming signals derived from the varying responses of SSTs in the CMIP5 ensemble to elevated greenhouse gas (GHG) emissions in three RCP scenarios. Simulating the future with a

  3. Large-region acoustic source mapping using a movable array and sparse covariance fitting.

    PubMed

    Zhao, Shengkui; Tuna, Cagdas; Nguyen, Thi Ngoc Tho; Jones, Douglas L

    2017-01-01

    Large-region acoustic source mapping is important for city-scale noise monitoring. Approaches using a single-position measurement scheme to scan large regions using small arrays cannot provide clean acoustic source maps, while deploying large arrays spanning the entire region of interest is prohibitively expensive. A multiple-position measurement scheme is applied to scan large regions at multiple spatial positions using a movable array of small size. Based on the multiple-position measurement scheme, a sparse-constrained multiple-position vectorized covariance matrix fitting approach is presented. In the proposed approach, the overall sample covariance matrix of the incoherent virtual array is first estimated using the multiple-position array data and then vectorized using the Khatri-Rao (KR) product. A linear model is then constructed for fitting the vectorized covariance matrix and a sparse-constrained reconstruction algorithm is proposed for recovering source powers from the model. The user parameter settings are discussed. The proposed approach is tested on a 30 m × 40 m region and a 60 m × 40 m region using simulated and measured data. Much cleaner acoustic source maps and lower sound pressure level errors are obtained compared to the beamforming approaches and the previous sparse approach [Zhao, Tuna, Nguyen, and Jones, Proc. IEEE Intl. Conf. on Acoustics, Speech and Signal Processing (ICASSP) (2016)].

  4. Analysis of the large (L) protein gene of the porcine rubulavirus LPMV: identification of possible functional domains.

    PubMed

    Svenda, M; Berg, M; Moreno-López, J; Linné, T

    1997-04-01

    The complete nucleotide sequence of the porcine rubulavirus LPMV (La Piedad Michoacan virus) large (L) protein gene was determined and analysed. The L mRNA was found to span 6,786 nucleotides, containing one single large open reading frame (ORF), putatively encoding a polypeptide of 2,251 amino acids. By aligning the amino acid sequence of the LPMV L-protein with L-protein of a number of viruses belonging to the order mononegavirale, a high degree of similarity between the LPMV L-protein and other rubula virus L-proteins was demonstrated, extending through almost the whole protein. Additionally we could identify several regions as being highly conserved among all studied viruses of the order mononegavirale. The significance of these regions are discussed.

  5. Pectin Homogalacturonans: Nanostructural Characterization of Methylesterified Domains

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Functionality of pectic hydrocolloids is largely dependent on the two major domains commonly found in their homogalacturonan (HG) regions, i.e., methylester protected domains (MPDs)and non methylesterified domains (NMDs). MPDs can participate in hydrogen bonding and hydrophobic interactions but unli...

  6. Nucleation Control for Large, Single Crystalline Domains of Monolayer Hexagonal Boron Nitride via Si-Doped Fe Catalysts

    PubMed Central

    2015-01-01

    The scalable chemical vapor deposition of monolayer hexagonal boron nitride (h-BN) single crystals, with lateral dimensions of ∼0.3 mm, and of continuous h-BN monolayer films with large domain sizes (>25 μm) is demonstrated via an admixture of Si to Fe catalyst films. A simple thin-film Fe/SiO2/Si catalyst system is used to show that controlled Si diffusion into the Fe catalyst allows exclusive nucleation of monolayer h-BN with very low nucleation densities upon exposure to undiluted borazine. Our systematic in situ and ex situ characterization of this catalyst system establishes a basis for further rational catalyst design for compound 2D materials. PMID:25664483

  7. Entropy-driven binding of opioid peptides induces a large domain motion in human dipeptidyl peptidase III.

    PubMed

    Bezerra, Gustavo A; Dobrovetsky, Elena; Viertlmayr, Roland; Dong, Aiping; Binter, Alexandra; Abramic, Marija; Macheroux, Peter; Dhe-Paganon, Sirano; Gruber, Karl

    2012-04-24

    Opioid peptides are involved in various essential physiological processes, most notably nociception. Dipeptidyl peptidase III (DPP III) is one of the most important enkephalin-degrading enzymes associated with the mammalian pain modulatory system. Here we describe the X-ray structures of human DPP III and its complex with the opioid peptide tynorphin, which rationalize the enzyme's substrate specificity and reveal an exceptionally large domain motion upon ligand binding. Microcalorimetric analyses point at an entropy-dominated process, with the release of water molecules from the binding cleft ("entropy reservoir") as the major thermodynamic driving force. Our results provide the basis for the design of specific inhibitors that enable the elucidation of the exact role of DPP III and the exploration of its potential as a target of pain intervention strategies.

  8. Entropy-driven binding of opioid peptides induces a large domain motion in human dipeptidyl peptidase III

    PubMed Central

    Bezerra, Gustavo A.; Dobrovetsky, Elena; Viertlmayr, Roland; Dong, Aiping; Binter, Alexandra; Abramić, Marija; Macheroux, Peter; Dhe-Paganon, Sirano; Gruber, Karl

    2012-01-01

    Opioid peptides are involved in various essential physiological processes, most notably nociception. Dipeptidyl peptidase III (DPP III) is one of the most important enkephalin-degrading enzymes associated with the mammalian pain modulatory system. Here we describe the X-ray structures of human DPP III and its complex with the opioid peptide tynorphin, which rationalize the enzyme's substrate specificity and reveal an exceptionally large domain motion upon ligand binding. Microcalorimetric analyses point at an entropy-dominated process, with the release of water molecules from the binding cleft (“entropy reservoir”) as the major thermodynamic driving force. Our results provide the basis for the design of specific inhibitors that enable the elucidation of the exact role of DPP III and the exploration of its potential as a target of pain intervention strategies. PMID:22493238

  9. High-precision, large-domain three-dimensional manipulation of nano-materials for fabrication nanodevices

    PubMed Central

    2011-01-01

    Nanoscaled materials are attractive building blocks for hierarchical assembly of functional nanodevices, which exhibit diverse performances and simultaneous functions. We innovatively fabricated semiconductor nano-probes of tapered ZnS nanowires through melting and solidifying by electro-thermal process; and then, as-prepared nano-probes can manipulate nanomaterials including semiconductor/metal nanowires and nanoparticles through sufficiently electrostatic force to the desired location without structurally and functionally damage. With some advantages of high precision and large domain, we can move and position and interconnect individual nanowires for contracting nanodevices. Interestingly, by the manipulating technique, the nanodevice made of three vertically interconnecting nanowires, i.e., diode, was realized and showed an excellent electrical property. This technique may be useful to fabricate electronic devices based on the nanowires' moving, positioning, and interconnecting and may overcome fundamental limitations of conventional mechanical fabrication. PMID:21794151

  10. The use of regional coordinating centers in large clinical trials: the DIG trial.

    PubMed

    Collins, Joseph F; Martin, Sylvia; Kent, Eleanor; Liuni, Connie; Garg, Rekha; Egan, Debra

    2003-12-01

    The Digitalis Investigation Group (DIG) trial was a large simple clinical trial that involved 302 participating centers in the United States and Canada. In order to encourage participation by Canadian investigators, to provide additional help to what were expected to be largely research-inexperienced investigators in Canada, and to provide the study's data coordinating center with resources in Canada to deal with potentially different rules, regulations, and cultural differences, regional coordinating centers were established in four regions of Canada: the maritime provinces, Quebec, Ontario, and western Canada. Canadian centers recruited significantly better than their U.S. counterparts and had slightly better retention and follow-up. While it is not possible to declare that the regional coordinating centers were responsible for this improvement, it is believed that these regional centers did play a role. This role included being able to identify investigators who could be expected to do well, providing one-on-one training and instruction to investigators, and being able to solve problems and implement change in the relatively fewer centers in their regions. The regional coordinating center also reduced the intensity of the workload on the data coordinating center by serving as the primary point of contact for Canadian investigators. The use of regional coordinating centers in studies with a large number of participating centers is highly recommended.

  11. eHealth vision towards cooperative patient care--domain fields and architectural challenges of regional health care networks.

    PubMed

    Gusew, Nathalie; Gerlach, Annekatrin; Bartkiewicz, Thomas; Goldapp, Michael; Haux, Reinhold; Heller, Ulrich; Hellrung, Nils; Kierdorf, Horst-P; Kleinschmidt, Thorsten; Markurth, Ulrich; Marschollek, Michael; Plischke, Maik; Schubert, Rainer; Seidel, Christoph; Wiegmann, Holger

    2010-01-01

    Numerous eHealth projects and efforts to establish inter-organizational communication and to build up regional health care networks could be observed in the last ten years. Nevertheless the success of such efforts is profoundly different. The aim of this paper is to introduce the lately started regional initiative eHealth.Braunschweig compounding of the major health care players (hospitals, physician offices, nursing services and nursing homes) in the region of Braunschweig, participants from research institutions and industry. We propose in this paper the main goals of the regional initiative eHealth.Braunschweig, its constitution and major approaches. Based on respective literature and our former projects as well as experiences in this field we discuss our vision of a patient-oriented cooperative health care by depicting regional distinctions, identifying the major domain fields in this context and discussing the architectural challenges for the regional health care network eHealth.Braunschweig. In our view this work can be considered as a systematical approach to the establishment of regional health care networks with lasting and sustainable effects on patient-centered health care in a region.

  12. Identification of a positively evolving putative binding region with increased variability in posttranslational motifs in zonadhesin MAM domain 2.

    PubMed

    Herlyn, Holger; Zischler, Hans

    2005-10-01

    Positive selection has been shown to be pervasive in sex-related proteins of many metazoan taxa. However, we are only beginning to understand molecular evolutionary processes on the lineage to humans. To elucidate the evolution of proteins involved in human reproduction, we studied the sequence evolution of MAM domains of the sperm-ligand zonadhesin in respect to single amino acid sites, solvent accessibility, and posttranslational modification. GenBank-data were supplemented by new cDNA-sequences of a representative non-human primate panel. Solvent accessibility predictions identified a probably exposed fragment of 30 amino acids belonging to MAM domain 2 (i.e., MAM domain 3 in mouse). The fragment is characterized by significantly increased rate of positively selected amino acid sites and exhibits high variability in predicted posttranslational modification, and, thus, might represent a binding region in the mature protein. At the same time, there is a significant coincidence of positively selected amino acid sites and non-conserved posttranslational motifs. We conclude that the binding specificity of zonadhesin MAM domains, especially of the presumed epitope, is achieved by positive selection at the level of single amino acid sites and posttranslational modifications, respectively.

  13. Defining Lipid Interacting Domains in the N-terminal Region of Apolipoprotein B

    PubMed Central

    Jiang, Zhenghui Gordon; Gantz, Donald; Bullitt, Esther; McKnight, C. James

    2008-01-01

    Apolipoprotein B (ApoB) is a nonexchangeable apolipoprotein that dictates the synthesis of chylomicrons and very low density lipoproteins. ApoB is the major protein in low density lipoprotein, also known as the “bad cholesterol” that is directly implicated in atherosclerosis. It has been suggested that the N-terminal domain of apoB plays a critical role in the formation of apoB-containing lipoproteins through the initial recruitment of phospholipids in the endoplasmic reticulum. However, very little is known about the mechanism of lipoprotein nucleation by apoB. Here we demonstrate that a strong phospholipid remodeling function is associated with the predicted α-helical and C-sheet domains in the N-terminal 17% of apoB (B17). Using dimyristoylphosphatidylcholine (DMPC) as a model lipid, these domains can convert multilamellar DMPC vesicles into discoidal-shaped particles. The nascent particles reconstituted from different apoB domains are distinctive and compositionally homogenous. This phospholipid remodeling activity is also observed with egg phosphatidylcholine (egg PC) and is therefore not DMPC dependent. Using kinetic analysis of the DMPC clearance assay, we show that the identified phospholipid binding sequences all map to the surface of the lipid binding pocket in the B17 model based on the homologous protein, lipovitellin. Since both B17 and microsomal triglyceride transfer protein (MTP), a critical chaperone during lipoprotein assembly, are homologous to lipovitellin, the identification of these phospholipid remodeling sequences in B17 provides important insights into the potential mechanism that initiates the assembly of apoB-containing lipoproteins. PMID:17002280

  14. Dynamic Triggering of Earthquakes in the Salton Sea Region of Southern California from Large Regional and Teleseismic Earthquakes

    NASA Astrophysics Data System (ADS)

    Doran, A.; Meng, X.; Peng, Z.; Wu, C.; Kilb, D. L.

    2010-12-01

    We perform a systematic survey of dynamically triggered earthquakes in the Salton Sea region of southern California using borehole seismic data recordings (2007 to present). We define triggered events as high-frequency seismic energy during large-amplitude seismic waves of distant earthquakes. Our mainshock database includes 26 teleseismic events (epicentral distances > 1000 km; Mw ≥ 7.5), and 8 regional events (epicentral distances 100 - 1000 km; Mw ≥ 5.5). Of these, 1 teleseismic and 7 regional events produce triggered seismic activity within our study region. The triggering mainshocks are not limited to specific azimuths. For example, triggering is observed following the 2008 Mw 6.0 Nevada earthquake to the north and the 2010 Mw7.2 Northern Baja California earthquake to the south. The peak ground velocities in our study region generated by the triggering mainshocks exceed 0.03 cm/s, which corresponds to a dynamic stress of ~2 kPa. This apparent triggering threshold is consistent with thresholds found in the Long Valley Caldera (Brodsky and Prejean, 2005), the Parkfield section of San Andreas Fault (Peng et al., 2009), and near the San Jacinto Fault (Kane et al., 2007). The triggered events occur almost instantaneously with the arrival of large amplitude seismic waves and appear to be modulated by the passing surface waves, similar to recent observations of triggered deep “non-volcanic” tremor along major plate boundary faults in California, Cascadia, Japan, and Taiwan (Peng and Gomberg, 2010). However, unlike these deep ‘tremor’ events, the triggered signals we find in this study have very short P- to S-arrival times, suggesting that they likely originate from brittle failure in the shallow crust. Confirming this, spectra of the triggered signals mimic spectra of typical shallow events in the region. Extending our observation time window to ~1 month following the mainshock event we find that for the 2010 Mw 7.2 Northern Baja California mainshock

  15. Tilt Angle and Footpoint Separation of Small and Large Bipolar Sunspot Regions Observed with HMI

    NASA Astrophysics Data System (ADS)

    McClintock, B. H.; Norton, A. A.

    2016-02-01

    We investigate bipolar sunspot regions and how tilt angle and footpoint separation vary during emergence and decay. The Helioseismic and Magnetic Imager on board the Solar Dynamic Observatory collects data at a higher cadence than historical records and allows for a detailed analysis of regions over their lifetimes. We sample the umbral tilt angle, footpoint separation, and umbral area of 235 bipolar sunspot regions in Helioseismic and Magnetic Imager—Debrecen Data with an hourly cadence. We use the time when the umbral area peaks as time zero to distinguish between the emergence and decay periods of each region and we limit our analysis of tilt and separation behavior over time to within ±96 hr of time zero. Tilt angle evolution is distinctly different for regions with small (≈30 MSH), midsize (≈50 MSH), and large (≈110 MSH) maximum umbral areas, with 45 and 90 MSH being useful divisions for separating the groups. At the peak umbral area, we determine median tilt angles for small (7.°6), midsize (5.°9), and large (9.°3) regions. Within ±48 hr of the time of peak umbral area, large regions steadily increase in tilt angle, midsize regions are nearly constant, and small regions show evidence of negative tilt during emergence. A period of growth in footpoint separation occurs over a 72-hr period for all of the regions from roughly 40 to 70 Mm. The smallest bipoles (<9 MSH) are outliers in that they do not obey Joy's law and have a much smaller footpoint separation. We confirm the Muñoz-Jaramillo et al. (2015) results that the sunspots appear to be two distinct populations.

  16. TILT ANGLE AND FOOTPOINT SEPARATION OF SMALL AND LARGE BIPOLAR SUNSPOT REGIONS OBSERVED WITH HMI

    SciTech Connect

    McClintock, B. H.; Norton, A. A. E-mail: aanorton@stanford.edu

    2016-02-10

    We investigate bipolar sunspot regions and how tilt angle and footpoint separation vary during emergence and decay. The Helioseismic and Magnetic Imager on board the Solar Dynamic Observatory collects data at a higher cadence than historical records and allows for a detailed analysis of regions over their lifetimes. We sample the umbral tilt angle, footpoint separation, and umbral area of 235 bipolar sunspot regions in Helioseismic and Magnetic Imager—Debrecen Data with an hourly cadence. We use the time when the umbral area peaks as time zero to distinguish between the emergence and decay periods of each region and we limit our analysis of tilt and separation behavior over time to within ±96 hr of time zero. Tilt angle evolution is distinctly different for regions with small (≈30 MSH), midsize (≈50 MSH), and large (≈110 MSH) maximum umbral areas, with 45 and 90 MSH being useful divisions for separating the groups. At the peak umbral area, we determine median tilt angles for small (7.°6), midsize (5.°9), and large (9.°3) regions. Within ±48 hr of the time of peak umbral area, large regions steadily increase in tilt angle, midsize regions are nearly constant, and small regions show evidence of negative tilt during emergence. A period of growth in footpoint separation occurs over a 72-hr period for all of the regions from roughly 40 to 70 Mm. The smallest bipoles (<9 MSH) are outliers in that they do not obey Joy's law and have a much smaller footpoint separation. We confirm the Muñoz-Jaramillo et al. results that the sunspots appear to be two distinct populations.

  17. Amplicon structure in multidrug-resistant murine cells: a nonrearranged region of genomic DNA corresponding to large circular DNA.

    PubMed Central

    Ståhl, F; Wettergren, Y; Levan, G

    1992-01-01

    Multidrug resistance (MDR) in tumor cell lines is frequently correlated with amplification of one or more mdr genes. Usually the amplified domain also includes several neighboring genes. Using pulsed-field gel electrophoresis, we have established a restriction map covering approximately 2,200 kb in the drug-sensitive mouse tumor cell line TC13K. The mapped region is located on mouse chromosome 5 and includes the three mdr genes, the gene for the calcium-binding sorcin protein, and a gene with unknown function designated class 5. Long-range maps of the amplified DNA sequences in five of six MDR sublines that had been independently derived from TC13K generally displayed the same pattern as did the parental cell line. All six MDR sublines exhibited numerous double minutes, and one of them displayed a homogeneously staining region in a subpopulation. Large circular molecules, most likely identical to one chromatid of the double minutes, were detected in four of the sublines by linearization with gamma irradiation. The size of the circles was about 2,500 kb, which correlated to a single unit of the amplified domain. We therefore propose that in four independent instances of MDR development, a single unit of about 2,500 kb has been amplified in the form of circular DNA molecules. The restriction enzyme map of the amplified unit is unchanged compared with that of the parental cell line, whereas the joining sites of the circular DNA molecules are not identical but are in the same region. Images PMID:1545798

  18. Structural Rearrangements of the Central Region of the Morbillivirus Attachment Protein Stalk Domain Trigger F Protein Refolding for Membrane Fusion*

    PubMed Central

    Ader, Nadine; Brindley, Melinda A.; Avila, Mislay; Origgi, Francesco C.; Langedijk, Johannes P. M.; Örvell, Claes; Vandevelde, Marc; Zurbriggen, Andreas; Plemper, Richard K.; Plattet, Philippe

    2012-01-01

    It is unknown how receptor binding by the paramyxovirus attachment proteins (HN, H, or G) triggers the fusion (F) protein to fuse with the plasma membrane for cell entry. H-proteins of the morbillivirus genus consist of a stalk ectodomain supporting a cuboidal head; physiological oligomers consist of non-covalent dimer-of-dimers. We report here the successful engineering of intermolecular disulfide bonds within the central region (residues 91–115) of the morbillivirus H-stalk; a sub-domain that also encompasses the putative F-contacting section (residues 111–118). Remarkably, several intersubunit crosslinks abrogated membrane fusion, but bioactivity was restored under reducing conditions. This phenotype extended equally to H proteins derived from virulent and attenuated morbillivirus strains and was independent of the nature of the contacted receptor. Our data reveal that the morbillivirus H-stalk domain is composed of four tightly-packed subunits. Upon receptor binding, these subunits structurally rearrange, possibly inducing conformational changes within the central region of the stalk, which, in turn, promote fusion. Given that the fundamental architecture appears conserved among paramyxovirus attachment protein stalk domains, we predict that these motions may act as a universal paramyxovirus F-triggering mechanism. PMID:22431728

  19. Regional cerebral abnormalities measured by frequency-domain near-infrared spectroscopy in pediatric patients during extracorporeal membrane oxygenation.

    PubMed

    Tian, Fenghua; Jenks, Christopher; Potter, Donald; Miles, Darryl; Raman, Lakshmi

    2016-12-02

    Extracorporeal membrane oxygenation (ECMO) is a form of advanced cardio-respiratory support provided to critically ill patients with severe respiratory and/or cardiovascular failure. While children undergoing ECMO therapy have significant risk for neurological morbidity, currently there is a lack of reliable bedside tool to detect the neurologic events for patients on ECMO. This study assessed the feasibility of frequency-domain near-infrared spectroscopy (NIRS) for detection of intracranial complications during ECMO therapy. The frequency-domain NIRS device measured the absorption coefficient (µa) and reduced scattering coefficient (µs') at six cranial positions from seven pediatric patients (0-16 years) during ECMO support and five healthy controls (2-14 years). Regional abnormalities in both absorption and scattering were identified among ECMO patients. A main finding in this study is that the abnormalities in scattering appear to be associated with lower-than-normal µs' values in regional areas of the brain. Since light scattering originates from the intracellular structures (such as nuclei and mitochondria), a reduction in scattering primarily reflects loss or decreased density of the brain matter. The results from this study indicate a potential to use the frequency-domain NIRS as a safe and complementary technology for detection of intracranial complications during ECMO therapy.

  20. Evidence that the large noncoding sequence is the main control region of maternally and paternally transmitted mitochondrial genomes of the marine mussel (Mytilus spp.).

    PubMed Central

    Cao, Liqin; Kenchington, Ellen; Zouros, Eleftherios; Rodakis, George C

    2004-01-01

    Both the maternal (F-type) and paternal (M-type) mitochondrial genomes of the Mytilus species complex M. edulis/galloprovincialis contain a noncoding sequence between the l-rRNA and the tRNA(Tyr) genes, here called the large unassigned region (LUR). The LUR, which is shorter in M genomes, is capable of forming secondary structures and contains motifs of significant sequence similarity with elements known to have specific functions in the sea urchin and the mammalian control region. Such features are not present in other noncoding regions of the F or M Mytilus mtDNA. The LUR can be divided on the basis of indels and nucleotide variation in three domains, which is reminiscent of the tripartite structure of the mammalian control region. These features suggest that the LUR is the main control region of the Mytilus mitochondrial genome. The middle domain has diverged by only 1.5% between F and M genomes, while the average divergence over the whole molecule is approximately 20%. In contrast, the first domain is among the most divergent parts of the genome. This suggests that different parts of the LUR are under different selection constraints that are also different from those acting on the coding parts of the molecule. PMID:15238532

  1. Multiple interactions of the intrinsically disordered region between the helicase and nuclease domains of the archaeal Hef protein.

    PubMed

    Ishino, Sonoko; Yamagami, Takeshi; Kitamura, Makoto; Kodera, Noriyuki; Mori, Tetsuya; Sugiyama, Shyogo; Ando, Toshio; Goda, Natsuko; Tenno, Takeshi; Hiroaki, Hidekazu; Ishino, Yoshizumi

    2014-08-01

    Hef is an archaeal protein that probably functions mainly in stalled replication fork repair. The presence of an unstructured region was predicted between the two distinct domains of the Hef protein. We analyzed the interdomain region of Thermococcus kodakarensis Hef and demonstrated its disordered structure by CD, NMR, and high speed atomic force microscopy (AFM). To investigate the functions of this intrinsically disordered region (IDR), we screened for proteins interacting with the IDR of Hef by a yeast two-hybrid method, and 10 candidate proteins were obtained. We found that PCNA1 and a RecJ-like protein specifically bind to the IDR in vitro. These results suggested that the Hef protein interacts with several different proteins that work together in the pathways downstream from stalled replication fork repair by converting the IDR structure depending on the partner protein.

  2. Improving Teaching and Learning in a Regional University Campus through a Focus on the Affective Domain

    ERIC Educational Resources Information Center

    Sawyer, Janet; Zianian, Tahereh; Evans, Nina; Gillham, David

    2012-01-01

    This paper describes the research process undertaken in a pilot study conducted at the University of South Australia's Centre for Regional Engagement (CRE), and reports the feedback collected in relation to this process and the project overall. Academic staff and students from CRE's two sites located in the rural and regional cities of Whyalla and…

  3. Importance of Hypervariable Region 2 for Stability and Affinity of a Shark Single-Domain Antibody Specific for Ebola Virus Nucleoprotein

    PubMed Central

    Anderson, George P.; Teichler, Daniel D.; Zabetakis, Dan; Shriver-Lake, Lisa C.; Liu, Jinny L.; Lonsdale, Stephen G.; Goodchild, Sarah A.; Goldman, Ellen R.

    2016-01-01

    Single-domain antibodies derived from the unique New Antigen Receptor found in sharks have numerous potential applications, ranging from diagnostic reagents to therapeutics. Shark-derived single-domain antibodies possess the same characteristic ability to refold after heat denaturation found in single-domain antibodies derived from camelid heavy-chain-only antibodies. Recently, two shark derived single-domain antibodies specific for the nucleoprotein of Ebola virus were described. Our evaluation confirmed their high affinity for the nucleoprotein, but found their melting temperatures to be low relative to most single-domain antibodies. Our first approach towards improving their stability was grafting antigen-binding regions (complementarity determining regions) of one of these single-domain antibodies onto a high melting temperature shark single-domain antibody. This resulted in two variants: one that displayed excellent affinity with a low melting temperature, while the other had poor affinity but a higher melting temperature. These new proteins, however, differed in only 3 amino acids within the complementarity determining region 2 sequence. In shark single-domain antibodies, the complementarity determining region 2 is often referred to as hypervariable region 2, as this segment of the antibody domain is truncated compared to the sequence in camelid single-domain antibodies and conventional heavy chain variable domains. To elucidate which of the three amino acids or combinations thereof were responsible for the affinity and stability we made the 6 double and single point mutants that covered the intermediates between these two clones. We found a single amino acid change that achieved a 10°C higher melting temperature while maintaining sub nM affinity. This research gives insights into the impact of the shark sdAb hypervariable 2 region on both stability and affinity. PMID:27494523

  4. Variations of the crustal thickness in the Betic-Rif domain and their foreland regions, by P-Receiver Functions

    NASA Astrophysics Data System (ADS)

    Stich, D.; Mancilla, F.; Morales, J.; Martin, R.; Diaz, J.; Pazos, A.; Cordoba, D.; Pulgar, J. A.; Ibarra, P.; Harnafi, M.; Gonzalez-Lodeiro, F.

    2012-12-01

    To image the crustal structure of the Betic-Rif Range and the surrounding area we perform a P-receiver function study (PRF). We calculate PRFs at 110 broadband stations located in South Iberia Peninsula and North Morocco to obtain thickness and average Vp/Vs ratio for the Crust. The Crustal thickness values show strong lateral variations throughout the region. Crustal thicknesses vary between ~19 km and ~46 km. The Betic and Rif ranges are underlined by a thickened crust with crustal thicknesses between ~35 km and ~46 km, reaching the highest values in the contact between the Alboran Domain and External Zones. Southeast Iberia and Northeast Morocco are affected by significant crustal thinning, with crustal thicknesses ranging from ~19 km to ~30 km, with the shallowest Moho along the Mediterranean coast. The transition from thick to thin crust is coincident with the faults system of the Trans-Alboran Shear Zone. Toward the North, the Iberian Massif is an homogeneous domain of average 30-31 km crustal thickness and flat Moho discontinuity with low average Vp/Vs ratios ~1.72. Further south an extended domain, which includes the Atlas domain and its foreland regions, presents crustal thickness of 27-34km. Vp/Vs ratios in north Morocco show normal values of ~1.75 for most stations except for the Atlas domain, where several stations present low Vp/Vs ratios around 1.71. The obtained PRFs are migrated to depth building cross-section images to delineate the crustal mantle discontinuity (Moho) along the study area. In the migrated images, we include altogether ~11.200 PFRs to follow the Moho discontinuity from the Iberian Massif, in the North, along the Gribraltar arc towards the Moroccan Massif in the South. These images show how, in the North, the Iberian crust underthrust the Alboran domain along their contact with the observation of a slab, from the western limit until the 3°W longitude, reaching the maximum depth of ~70 km under the coast coincide with the

  5. An analytical model of the large neutral regions during the late stage of reionization

    SciTech Connect

    Xu, Yidong; Yue, Bin; Chen, Xuelei; Su, Meng; Fan, Zuhui

    2014-02-01

    In this paper, we investigate the nature and distribution of large neutral regions during the late epoch of reionization. In the 'bubble model' of reionization, the mass distribution of large ionized regions ('bubbles') during the early stage of reionization is obtained by using the excursion set model, where the ionization of a region corresponds to the first up-crossing of a barrier by random trajectories. We generalize this idea and develop a method to predict the distribution of large-scale neutral regions during the late stage of reionization, taking into account the ionizing background after the percolation of H II regions. The large-scale neutral regions, which we call 'neutral islands', are not individual galaxies or minihalos, but larger regions where fewer galaxies formed and hence ionized later and they are identified in the excursion set model with the first down-crossings of the island barrier. Assuming that the consumption rate of ionizing background photons is proportional to the surface area of the neutral islands, we obtained the size distribution of the neutral islands. We also take the 'bubbles-in-island' effect into account by considering the conditional probability of up-crossing a bubble barrier after down-crossing the island barrier. We find that this effect is very important. An additional barrier is set to avoid islands being percolated through. We find that there is a characteristic scale for the neutral islands, while the small islands are rapidly swallowed up by the ionizing background; this characteristic scale does not change much as the reionization proceeds.

  6. Dipole plasmon resonance induced large third-order optical nonlinearity of Au triangular nanoprism in infrared region.

    PubMed

    Chen, Ziyu; Dai, Hongwei; Liu, Jiaming; Xu, Hui; Li, Zixuan; Zhou, Zhang-Kai; Han, Jun-Bo

    2013-07-29

    Au triangular nanoprisms with strong dipole plasmon absorption peak at 1240 nm were prepared by wet chemical methods. Both numerical calculations and experiments were carried out to investigate the optical properties of the samples. Finite difference time domain (FDTD) and Local Density of States (LDOS) calculations demonstrate that strong electric field enhancement and large LDOS can be obtained at tip areas of the Au triangular nanoprisms. Z scan techniques were used to characterize the nonlinear absorption, nonlinear refraction, as well as one- and two-photon figures of merit (W and T, respectively) of the sample. The results show that maximum nonlinear refractive index can be obtained around the resonance absorption wavelength of 1240 nm, detuning the wavelength from the absorption peak will lead to the decrease of the nonlinear refractive index n(2), while the nonlinear absorption coefficient β doesn't change much with the wavelength. This large wavelength dependence of n(2) and small change of β enable the sample to satisfy the all-optical switching demand of W> 1 and T< 1 easily in a large wavelength range of 1200-1300 nm. These significant nonlinear properties of the sample imply that Au triangular nanoprism is a good candidate for future optical switches in infrared optical communication wavelength region.

  7. Solution structure of the region 51–160 of human KIN17 reveals an atypical winged helix domain

    PubMed Central

    Carlier, Ludovic; Couprie, Joël; le Maire, Albane; Guilhaudis, Laure; Milazzo-Segalas, Isabelle; Courçon, Marie; Moutiez, Mireille; Gondry, Muriel; Davoust, Daniel; Gilquin, Bernard; Zinn-Justin, Sophie

    2007-01-01

    Human KIN17 is a 45-kDa eukaryotic DNA- and RNA-binding protein that plays an important role in nuclear metabolism and in particular in the general response to genotoxics. Its amino acids sequence contains a zinc finger motif (residues 28–50) within a 30-kDa N-terminal region conserved from yeast to human, and a 15-kDa C-terminal tandem of SH3-like subdomains (residues 268–393) only found in higher eukaryotes. Here we report the solution structure of the region 51–160 of human KIN17. We show that this fragment folds into a three-α-helix bundle packed against a three-stranded β-sheet. It belongs to the winged helix (WH) family. Structural comparison with analogous WH domains reveals that KIN17 WH module presents an additional and highly conserved 310-helix. Moreover, KIN17 WH helix H3 is not positively charged as in classical DNA-binding WH domains. Thus, human KIN17 region 51–160 might rather be involved in protein–protein interaction through its conserved surface centered on the 310-helix. PMID:18029424

  8. On the need for long-term, on the order of a decade, hydro-climatic forecasts over large domains

    NASA Astrophysics Data System (ADS)

    Burges, S. J.

    2012-12-01

    All problems of hydrology have been influenced to some extent by the need to describe delivery of water to, and its movement through, the critical zone. The nature of the questions and the level of required quantitative description have changed with time, but all involve accurate accounting of all components of the hydrologic cycle. The broadest issues involve the temporal and spatial distributions of excess (floods) or too little (droughts) water. The spatial domains can range from small catchments to major fractions of continents. The temporal domains range from relatively short-term, on the order of hours to days to a few months, to multiple decades. Hydrologic engineers have long recognized the need to offer designs for human occupied catchments that accommodate hydrologic extremes (principally floods and droughts) that affect human and animal safety, for example, through disruptions to infrastructure and supply chains, food supplies, and water supplies. As more has been learned about the criticality of ecosystems to the well-being of the planet, water allocation issues have become those of "water for people" and "water for ecology". These latter requirements have emphasized the need for increased accuracy of estimating water budgets, and how water (and pollutants) moves through the associated critical domain. Given the now large physical demand for societal water use (it exceeds 50% of the mean annual river flow in most conterminous US river basins) hydrologic balances that include the operation of water resource infrastructure (flood damage mitigation dams and levees, storage reservoirs for municipal and industrial water, irrigation and ecological preservation) have become the norm. In most basins the storage reservoirs are relatively small (few store more than the mean annual flow of rivers) and long-term hydrological forecasting has become a major issue. Whether the issue is floods or droughts, there is now a pressing need for societally useful forecasts

  9. Replacement and deletion mutations in the catalytic domain and belt region of Aspergillus awamori glucoamylase to enhance thermostability.

    PubMed

    Liu, H L; Doleyres, Y; Coutinho, P M; Ford, C; Reilly, P J

    2000-09-01

    Three single-residue mutations, Asp71-->Asn, Gln409-->Pro and Gly447-->Ser, two long-to-short loop replacement mutations, Gly23-Ala24-Asp25-Gly26-Ala27-Trp28- Val29-Ser30-->Asn-Pro-Pro (23-30 replacement) and Asp297-Ser298-Glu299-Ala300-Val301-->Ala-G ly-Ala (297-301 replacement) and one deletion mutation removing Glu439, Thr440 and Ser441 (Delta439-441), all based on amino acid sequence alignments, were made to improve Aspergillus awamori glucoamylase thermostability. The first and second single-residue mutations were designed to introduce a potential N:-glycosylation site and to restrict backbone bond rotation, respectively, and therefore to decrease entropy during protein unfolding. The third single-residue mutation was made to decrease flexibility and increase O:-glycosylation in the already highly O:-glycosylated belt region that extends around the globular catalytic domain. The 23-30 replacement mutation was designed to eliminate a very thermolabile extended loop on the catalytic domain surface and to bring the remainder of this region closer to the rest of the catalytic domain, therefore preventing it from unfolding. The 297-301 replacement mutant GA was made to understand the function of the random coil region between alpha-helices 9 and 10. Delta439-441 was constructed to decrease belt flexibility. All six mutations increased glucoamylase thermostability without significantly changing enzyme kinetic properties, with the 23-30 replacement mutation increasing the activation free energy for thermoinactivation by about 4 kJ/mol, which leads to a 4 degrees C increase in operating temperature at constant thermostability.

  10. Bayesian WLS/GLS regression for regional skewness analysis for regions with large crest stage gage networks

    USGS Publications Warehouse

    Veilleux, Andrea G.; Stedinger, Jery R.; Eash, David A.

    2012-01-01

    This paper summarizes methodological advances in regional log-space skewness analyses that support flood-frequency analysis with the log Pearson Type III (LP3) distribution. A Bayesian Weighted Least Squares/Generalized Least Squares (B-WLS/B-GLS) methodology that relates observed skewness coefficient estimators to basin characteristics in conjunction with diagnostic statistics represents an extension of the previously developed B-GLS methodology. B-WLS/B-GLS has been shown to be effective in two California studies. B-WLS/B-GLS uses B-WLS to generate stable estimators of model parameters and B-GLS to estimate the precision of those B-WLS regression parameters, as well as the precision of the model. The study described here employs this methodology to develop a regional skewness model for the State of Iowa. To provide cost effective peak-flow data for smaller drainage basins in Iowa, the U.S. Geological Survey operates a large network of crest stage gages (CSGs) that only record flow values above an identified recording threshold (thus producing a censored data record). CSGs are different from continuous-record gages, which record almost all flow values and have been used in previous B-GLS and B-WLS/B-GLS regional skewness studies. The complexity of analyzing a large CSG network is addressed by using the B-WLS/B-GLS framework along with the Expected Moments Algorithm (EMA). Because EMA allows for the censoring of low outliers, as well as the use of estimated interval discharges for missing, censored, and historic data, it complicates the calculations of effective record length (and effective concurrent record length) used to describe the precision of sample estimators because the peak discharges are no longer solely represented by single values. Thus new record length calculations were developed. The regional skewness analysis for the State of Iowa illustrates the value of the new B-WLS/BGLS methodology with these new extensions.

  11. Regional modeling of large wildfires under current and potential future climates in Colorado and Wyoming, USA

    USGS Publications Warehouse

    West, Amanda; Kumar, Sunil; Jarnevich, Catherine S.

    2016-01-01

    Regional analysis of large wildfire potential given climate change scenarios is crucial to understanding areas most at risk in the future, yet wildfire models are not often developed and tested at this spatial scale. We fit three historical climate suitability models for large wildfires (i.e. ≥ 400 ha) in Colorado andWyoming using topography and decadal climate averages corresponding to wildfire occurrence at the same temporal scale. The historical models classified points of known large wildfire occurrence with high accuracies. Using a novel approach in wildfire modeling, we applied the historical models to independent climate and wildfire datasets, and the resulting sensitivities were 0.75, 0.81, and 0.83 for Maxent, Generalized Linear, and Multivariate Adaptive Regression Splines, respectively. We projected the historic models into future climate space using data from 15 global circulation models and two representative concentration pathway scenarios. Maps from these geospatial analyses can be used to evaluate the changing spatial distribution of climate suitability of large wildfires in these states. April relative humidity was the most important covariate in all models, providing insight to the climate space of large wildfires in this region. These methods incorporate monthly and seasonal climate averages at a spatial resolution relevant to land management (i.e. 1 km2) and provide a tool that can be modified for other regions of North America, or adapted for other parts of the world.

  12. Large-Scale Covariability Between Aerosol and Precipitation Over the 7-SEAS Region: Observations and Simulations

    NASA Technical Reports Server (NTRS)

    Huang, Jingfeng; Hsu, N. Christina; Tsay, Si-Chee; Zhang, Chidong; Jeong, Myeong Jae; Gautam, Ritesh; Bettenhausen, Corey; Sayer, Andrew M.; Hansell, Richard A.; Liu, Xiaohong; Jiang, Jonathan H.

    2012-01-01

    One of the seven scientific areas of interests of the 7-SEAS field campaign is to evaluate the impact of aerosol on cloud and precipitation (http://7-seas.gsfc.nasa.gov). However, large-scale covariability between aerosol, cloud and precipitation is complicated not only by ambient environment and a variety of aerosol effects, but also by effects from rain washout and climate factors. This study characterizes large-scale aerosol-cloud-precipitation covariability through synergy of long-term multi ]sensor satellite observations with model simulations over the 7-SEAS region [10S-30N, 95E-130E]. Results show that climate factors such as ENSO significantly modulate aerosol and precipitation over the region simultaneously. After removal of climate factor effects, aerosol and precipitation are significantly anti-correlated over the southern part of the region, where high aerosols loading is associated with overall reduced total precipitation with intensified rain rates and decreased rain frequency, decreased tropospheric latent heating, suppressed cloud top height and increased outgoing longwave radiation, enhanced clear-sky shortwave TOA flux but reduced all-sky shortwave TOA flux in deep convective regimes; but such covariability becomes less notable over the northern counterpart of the region where low ]level stratus are found. Using CO as a proxy of biomass burning aerosols to minimize the washout effect, large-scale covariability between CO and precipitation was also investigated and similar large-scale covariability observed. Model simulations with NCAR CAM5 were found to show similar effects to observations in the spatio-temporal patterns. Results from both observations and simulations are valuable for improving our understanding of this region's meteorological system and the roles of aerosol within it. Key words: aerosol; precipitation; large-scale covariability; aerosol effects; washout; climate factors; 7- SEAS; CO; CAM5

  13. Identification and analysis of genomic regions with large between-population differentiation in humans.

    PubMed

    Myles, S; Tang, K; Somel, M; Green, R E; Kelso, J; Stoneking, M

    2008-01-01

    The primary aim of genetic association and linkage studies is to identify genetic variants that contribute to phenotypic variation within human populations. Since the overwhelming majority of human genetic variation is found within populations, these methods are expected to be effective and can likely be extrapolated from one human population to another. However, they may lack power in detecting the genetic variants that contribute to phenotypes that differ greatly between human populations. Phenotypes that show large differences between populations are expected to be associated with genomic regions exhibiting large allele frequency differences between populations. Thus, from genome-wide polymorphism data genomic regions with large allele frequency differences between populations can be identified, and evaluated as candidates for large between-population phenotypic differences. Here we use allele frequency data from approximately 1.5 million SNPs from three human populations, and present an algorithm that identifies genomic regions containing SNPs with extreme Fst. We demonstrate that our candidate regions have reduced heterozygosity in Europeans and Chinese relative to African-Americans, and are likely enriched with genes that have experienced positive natural selection. We identify genes that are likely responsible for phenotypes known to differ dramatically between human populations and present several candidates worthy of future investigation. Our list of high Fst genomic regions is a first step in identifying the genetic variants that contribute to large phenotypic differences between populations, many of which have likely experienced positive natural selection. Our approach based on between population differences can compliment traditional within population linkage and association studies to uncover novel genotype-phenotype relationships.

  14. THEMIS Observations of the Magnetopause Electron Diffusion Region: Large Amplitude Waves and Heated Electrons

    NASA Technical Reports Server (NTRS)

    Tang, Xiangwei; Cattell, Cynthia; Dombeck, John; Dai, Lei; Wilson, Lynn B. III; Breneman, Aaron; Hupack, Adam

    2013-01-01

    We present the first observations of large amplitude waves in a well-defined electron diffusion region based on the criteria described by Scudder et al at the subsolar magnetopause using data from one Time History of Events and Macroscale Interactions during Substorms (THEMIS) satellite. These waves identified as whistler mode waves, electrostatic solitary waves, lower hybrid waves, and electrostatic electron cyclotron waves, are observed in the same 12 s waveform capture and in association with signatures of active magnetic reconnection. The large amplitude waves in the electron diffusion region are coincident with abrupt increases in electron parallel temperature suggesting strong wave heating. The whistler mode waves, which are at the electron scale and which enable us to probe electron dynamics in the diffusion region were analyzed in detail. The energetic electrons (approx. 30 keV) within the electron diffusion region have anisotropic distributions with T(sub e(right angle))/T(sub e(parallel)) > 1 that may provide the free energy for the whistler mode waves. The energetic anisotropic electrons may be produced during the reconnection process. The whistler mode waves propagate away from the center of the "X-line" along magnetic field lines, suggesting that the electron diffusion region is a possible source region of the whistler mode waves.

  15. Applying the Time-Domain Moment Tensor Inversion technique to Regional Earthquake Data in the Puerto Rico-Virgin Island Region

    NASA Astrophysics Data System (ADS)

    Martinez-Torres, F. A.; Lopez, A. M.

    2015-12-01

    The quick determination of an earthquake's moment tensor, whose description relate to centroid depth, faulting geometry and size, is crucial for tsunami warning systems. Whether an event possesses the critical parameters to produce a devastating tsunami, tsunami warning centers must knowThis research project seeks to test, well-formulated time-domain moment tensor inversion code in order to obtain in quasi real-time faulting parameters of significant regional earthquakes in the Puerto Rico-Virgin Islands region. The inversion code has been developed by researchers at the Berkeley Seismological Laboratory, whose main attractive is to decrease the time it takes to have an estimate calculation of a moment tensor for any major earthquake using regional data, approximately less than 7 minutes of an earthquake's origin time. Four seismic events in the region have been used as testbed to the inversion code configured for this area. In order to compare our results, previously computed and published moment tensor inversions from the Global CMT and USGS for the same events were used to assess the deviations from results obtained in this study. Our results indicate the inversion method is capable of reproducing the regional and teleseismic solutions, and thus can be incorporated into daily earthquake location operations at the Puerto Rico Seismic Network (PRSN) for quick estimation of faulting mechanisms and tsunami warning purposes.

  16. The large N-terminal region of the Brr2 RNA helicase guides productive spliceosome activation

    PubMed Central

    Absmeier, Eva; Wollenhaupt, Jan; Mozaffari-Jovin, Sina; Becke, Christian; Lee, Chung-Tien; Preussner, Marco; Heyd, Florian; Urlaub, Henning; Lührmann, Reinhard; Santos, Karine F.; Wahl, Markus C.

    2015-01-01

    The Brr2 helicase provides the key remodeling activity for spliceosome catalytic activation, during which it disrupts the U4/U6 di-snRNP (small nuclear RNA protein), and its activity has to be tightly regulated. Brr2 exhibits an unusual architecture, including an ∼500-residue N-terminal region, whose functions and molecular mechanisms are presently unknown, followed by a tandem array of structurally similar helicase units (cassettes), only the first of which is catalytically active. Here, we show by crystal structure analysis of full-length Brr2 in complex with a regulatory Jab1/MPN domain of the Prp8 protein and by cross-linking/mass spectrometry of isolated Brr2 that the Brr2 N-terminal region encompasses two folded domains and adjacent linear elements that clamp and interconnect the helicase cassettes. Stepwise N-terminal truncations led to yeast growth and splicing defects, reduced Brr2 association with U4/U6•U5 tri-snRNPs, and increased ATP-dependent disruption of the tri-snRNP, yielding U4/U6 di-snRNP and U5 snRNP. Trends in the RNA-binding, ATPase, and helicase activities of the Brr2 truncation variants are fully rationalized by the crystal structure, demonstrating that the N-terminal region autoinhibits Brr2 via substrate competition and conformational clamping. Our results reveal molecular mechanisms that prevent premature and unproductive tri-snRNP disruption and suggest novel principles of Brr2-dependent splicing regulation. PMID:26637280

  17. The AtMYB12 activation domain maps to a short C-terminal region of the transcription factor.

    PubMed

    Stracke, Ralf; Turgut-Kara, Neslihan; Weisshaar, Bernd

    2017-03-11

    The Arabidopsis thaliana R2R3-MYB transcription factor MYB12 is a light-inducible, flavonol-specific activator of flavonoid biosynthesis. The transactivation activity of the AtMYB12 protein was analyzed using a C-terminal deletion series in a transient A. thaliana protoplast assay with the goal of mapping the activation domain (AD). Although the deletion of the last 46 C-terminal amino acids did not affect the activation capacity, the deletion of the last 98 amino acids almost totally abolished transactivation of two different target promoters. A domain swap experiment using the yeast GAL4 DNA-binding domain revealed that the region from positions 282 to 328 of AtMYB12 was sufficient for transactivation. In contrast to the R2R3-MYB ADs known thus far, that of AtMYB12 is not located at the rearmost C-terminal end of the protein. The AtMYB12 AD is conserved in other experimentally proven R2R3-MYB flavonol regulators from different species.

  18. An adaptive subspace trust-region method for frequency-domain seismic full waveform inversion

    NASA Astrophysics Data System (ADS)

    Zhang, Huan; Li, Xiaofan; Song, Hanjie; Liu, Shaolin

    2015-05-01

    Full waveform inversion is currently considered as a promising seismic imaging method to obtain high-resolution and quantitative images of the subsurface. It is a nonlinear ill-posed inverse problem, the main difficulty of which that prevents the full waveform inversion from widespread applying to real data is the sensitivity to incorrect initial models and noisy data. Local optimization theories including Newton's method and gradient method always lead the convergence to local minima, while global optimization algorithms such as simulated annealing are computationally costly. To confront this issue, in this paper we investigate the possibility of applying the trust-region method to the full waveform inversion problem. Different from line search methods, trust-region methods force the new trial step within a certain neighborhood of the current iterate point. Theoretically, the trust-region methods are reliable and robust, and they have very strong convergence properties. The capability of this inversion technique is tested with the synthetic Marmousi velocity model and the SEG/EAGE Salt model. Numerical examples demonstrate that the adaptive subspace trust-region method can provide solutions closer to the global minima compared to the conventional Approximate Hessian approach and the L-BFGS method with a higher convergence rate. In addition, the match between the inverted model and the true model is still excellent even when the initial model deviates far from the true model. Inversion results with noisy data also exhibit the remarkable capability of the adaptive subspace trust-region method for low signal-to-noise data inversions. Promising numerical results suggest this adaptive subspace trust-region method is suitable for full waveform inversion, as it has stronger convergence and higher convergence rate.

  19. The flagellin hypervariable region is a potential flagella display domain in probiotic Escherichia coli strain Nissle 1917.

    PubMed

    Yang, Ying; Yang, Yi; Ou, Bingming; Xia, Pengpeng; Zhou, Mingxu; Li, Luan; Zhu, Guoqiang

    2016-09-01

    The most studied probiotic, Escherichia coli strain Nissle 1917 (EcN) possesses flagella of serotype H1. To explore the potential to use EcN flagellin in flagella display applications, we investigated the effect of deleting amino acids in the hypervariable region of flagellin on EcNc (EcN cured of its two cryptic plasmids pMUT1 and pMUT2). Two EcNc flagellin isogenic mutants with deletions of amino acid residual from 277 to 286 and from 287 to 296 in the hypervariable domain were constructed. Both mutants were flagellated, adherent to IPEC-J2 cells, and colonized BALB/c mice. These hypervariable regions may have future utility in the display of heterologous epitopes.

  20. New Features of Time Domain Electric-Field Structures in the Auroral Acceleration Region

    SciTech Connect

    Mozer, F.S.; Ergun, R.; Temerin, M.; Cattell, C.; Dombeck, J.; Wygant, J.

    1997-08-01

    The Polar Satellite carries the first three-axis electric field detector flown in the magnetosphere. Its direct measurement of electric field components perpendicular and parallel to the local magnetic field has revealed new classes and features of electric field structures associated with the plasma acceleration that produces discrete auroras and that populates the magnetosphere with plasma of ionospheric origin. These structures, associated with the hydrogen ion cyclotron mode, include very large solitary waves, spiky field structures, wave envelopes of parallel electric fields, and very large amplitude, nonlinear, coherent ion cyclotron waves. {copyright} {ital 1997} {ital The American Physical Society}

  1. Constraint satisfaction techniques for modeling large complexes: Application to the central domain of 16S ribosomal RNA

    SciTech Connect

    Altman, R.B.; Weiser, B.; Noller, H.F.

    1994-12-31

    Standard experimental techniques for determining the structure of small to moderately-sized molecules are difficult to apply to large macromolecular complexes. These complexes, consisting of multiple protein and/or nucleic acid components, can contain many thousands of atoms and the experimental techniques used to study them provide relatively sparse structural information with significant measurement uncertainty. Computational technologies are required to reduce the conformational search space and synthesize the data in order to produce the structures or (more usually) sets of structures compatible with the data. In this paper, we show that a method based on the constraint satisfaction paradigm produces a three-dimensional topology for the central domain of the 16S ribosomal RNA that is generally consistent with interactively built models, although differing in significant ways. The modeling incorporates information about secondary structure of the nucleic acid, neutron diffraction data about the relative positions and uncertainties of the proteins, and protection experiments indicating proximities of segments of RNA to specific protein subunits. Unlike previously proposed models, our model contains explicit information about the range of positions for each subunit that are compatible with the data. The system uses a grid search, checks distances in a direction-dependent manner, uses disjunctive distance constraints, and checks for volume overlap violations.

  2. Wavelength dependence of linear polarization in the visible and near infrared domain for large levitating grains (PROGRA2 instruments)

    NASA Astrophysics Data System (ADS)

    Renard, J.-B.; Hadamcik, E.; Couté, B.; Jeannot, M.; Levasseur-Regourd, A. C.

    2014-10-01

    Remote sensing measurements of light scattered by dust in solar system objects can provide clues on their physical properties. Databases obtained in the laboratory with numerous samples are necessary to interpret these measurements. We present here first studies of the wavelength dependence of the linear polarization between 545 nm and 1.5 μm, using the imaging polarimeters PROGRA2 for large levitating compact grains (PROGRA2-VIS in the visible domain, and the new instrument PROGRA2-IR in the near infrared). The measurements are conducted in microgravity conditions during parabolic flights for glass beads, quartz, sands, silicon carbides, anthracite, and lunar and Martian simulants. Comparison between measurements on glass beads and Mie calculations with glass spheres provides an assessment of the quality of the instruments. The dependence of the polarization on the wavelength is related to the complex refractive index of the particles, i.e. to their composition and to the size of the grains. More laboratory measurements will be necessary, in particular with smaller grains in aggregates, to better reproduce the remote sensing observations of solar system bodies.

  3. Structure of the origin-binding domain of simian virus 40 large T antigen bound to DNA.

    PubMed

    Bochkareva, Elena; Martynowski, Dariusz; Seitova, Almagoul; Bochkarev, Alexey

    2006-12-13

    The large T antigen (T-ag) protein binds to and activates DNA replication from the origin of DNA replication (ori) in simian virus 40 (SV40). Here, we determined the crystal structures of the T-ag origin-binding domain (OBD) in apo form, and bound to either a 17 bp palindrome (sites 1 and 3) or a 23 bp ori DNA palindrome comprising all four GAGGC binding sites for OBD. The T-ag OBDs were shown to interact with the DNA through a loop comprising Ser147-Thr155 (A1 loop), a combination of a DNA-binding helix and loop (His203-Asn210), and Asn227. The A1 loop traveled back-and-forth along the major groove and accounted for most of the sequence-determining contacts with the DNA. Unexpectedly, in both T-ag-DNA structures, the T-ag OBDs bound DNA independently and did not make direct protein-protein contacts. The T-ag OBD was also captured bound to a non-consensus site ATGGC even in the presence of its canonical site GAGGC. Our observations taken together with the known biochemical and structural features of the T-ag-origin interaction suggest a model for origin unwinding.

  4. MASK, a large ankyrin repeat and KH domain-containing protein involved in Drosophila receptor tyrosine kinase signaling.

    PubMed

    Smith, Rachel K; Carroll, Pamela M; Allard, John D; Simon, Michael A

    2002-01-01

    The receptor tyrosine kinases Sevenless (SEV) and the Epidermal growth factor receptor (EGFR) are required for the proper development of the Drosophila eye. The protein tyrosine phosphatase Corkscrew (CSW) is a common component of many RTK signaling pathways, and is required for signaling downstream of SEV and EGFR. In order to identify additional components of these signaling pathways, mutations that enhanced the phenotype of a dominant negative form of Corkscrew were isolated. This genetic screen identified the novel signaling molecule MASK, a large protein that contains two blocks of ankyrin repeats as well as a KH domain. MASK genetically interacts with known components of these RTK signaling pathways. In the developing eye imaginal disc, loss of MASK function generates phenotypes similar to those generated by loss of other components of the SEV and EGFR pathways. These phenotypes include compromised photoreceptor differentiation, cell survival and proliferation. Although MASK is localized predominantly in the cellular cytoplasm, it is not absolutely required for MAPK activation or nuclear translocation. Based on our results, we propose that MASK is a novel mediator of RTK signaling, and may act either downstream of MAPK or transduce signaling through a parallel branch of the RTK pathway.

  5. Identification of a Major Dimorphic Region in the Functionally Critical N-Terminal ID1 Domain of VAR2CSA

    PubMed Central

    Doritchamou, Justin; Sabbagh, Audrey; Jespersen, Jakob S.; Renard, Emmanuelle; Salanti, Ali; Nielsen, Morten A.; Deloron, Philippe; Tuikue Ndam, Nicaise

    2015-01-01

    The VAR2CSA protein of Plasmodium falciparum is transported to and expressed on the infected erythrocyte surface where it plays a key role in placental malaria (PM). It is the current leading candidate for a vaccine to prevent PM. However, the antigenic polymorphism integral to VAR2CSA poses a challenge for vaccine development. Based on detailed analysis of polymorphisms in the sequence of its ligand-binding N-terminal region, currently the main focus for vaccine development, we assessed var2csa from parasite isolates infecting pregnant women. The results reveal for the first time the presence of a major dimorphic region in the functionally critical N-terminal ID1 domain. Parasite isolates expressing VAR2CSA with particular motifs present within this domain are associated with gravidity- and parasite density-related effects. These observations are of particular interest in guiding efforts with respect to optimization of the VAR2CSA-based vaccines currently under development. PMID:26393516

  6. New Evidences for Preserved Segmentation of the Alpine-Tethyan Domain in the Iberia-Africa Plate Boundary Region

    NASA Astrophysics Data System (ADS)

    Fernandez, M.; Torne, M.; Verges, J.; Buffett, G. G.

    2015-12-01

    Based on gravity analysis and previous integrated studies combining potential fields and seismic data, we demonstrate that the Iberia-Africa plate boundary region is characterized by several tectonically inverted transtensional domains inherited from the Jurassic. Gravity data, when filtered for short wavelengths, show conspicuous positive Bouguer anomalies associated with the Gorringe Bank, the Guadalquivir Bank and the Ronda/Beni-Bousera peridotitic massifs. Gravity modelling combined with seismic and geological data shows that the filtered Bouguer anomalies are compatible with relatively high-density and shallow-buried bodies, which correspond to partly serpentinized peridotitic slices with similar densities and geometries as those proved for the Gorringe Bank. The study indicates that the Alpine convergence between Africa and Iberia since Late Cretaceous times reactivated these transtensional domains, which were less deformed westwards and thus preserved their segmentation. The interpretation of these Bouguer anomalies and their distribution substantiates the double-polarity subduction model proposed for the region, and agrees with the present-day seismically diffuse character of the Iberia-Africa plate boundary.

  7. Large-scale data analysis of power grid resilience across multiple US service regions

    NASA Astrophysics Data System (ADS)

    Ji, Chuanyi; Wei, Yun; Mei, Henry; Calzada, Jorge; Carey, Matthew; Church, Steve; Hayes, Timothy; Nugent, Brian; Stella, Gregory; Wallace, Matthew; White, Joe; Wilcox, Robert

    2016-05-01

    Severe weather events frequently result in large-scale power failures, affecting millions of people for extended durations. However, the lack of comprehensive, detailed failure and recovery data has impeded large-scale resilience studies. Here, we analyse data from four major service regions representing Upstate New York during Super Storm Sandy and daily operations. Using non-stationary spatiotemporal random processes that relate infrastructural failures to recoveries and cost, our data analysis shows that local power failures have a disproportionally large non-local impact on people (that is, the top 20% of failures interrupted 84% of services to customers). A large number (89%) of small failures, represented by the bottom 34% of customers and commonplace devices, resulted in 56% of the total cost of 28 million customer interruption hours. Our study shows that extreme weather does not cause, but rather exacerbates, existing vulnerabilities, which are obscured in daily operations.

  8. Large irreversible non-180° domain switching after poling treatment in Pb(Zr, Ti)O3 films

    NASA Astrophysics Data System (ADS)

    Ehara, Yoshitaka; Yasui, Shintaro; Oikawa, Takahiro; Shiraishi, Takahisa; Oshima, Naoya; Yamada, Tomoaki; Imai, Yasuhiko; Sakata, Osami; Funakubo, Hiroshi

    2016-05-01

    (11 1 ¯ )/(111)-oriented rhombohedral Pb(Zr0.65Ti0.35)O3 films with different domain fractions were epitaxially grown on various single crystals. The volume fraction of (111)-polar-axis oriented domains in as-deposited films, Vpol.(as-depo.), was controlled by selecting a single crystal substrate with a different thermal expansion coefficient. Applying an electric field, referred to as "poling treatment", resulted in irreversible non-180° domain switching from the (11 1 ¯ )-oriented domain (non-polar-axis) to the (111)-oriented domain (polar-axis), which was observed by synchrotron X-ray diffraction. Remanent polarization (Pr) values were higher than those estimated using the proportional relationship with Vpol.(as-depo.). However, the experimental Pr values were in good agreement with the values estimated using the volume fraction of (111)-oriented domains after applying the poling treatment. In rhombohedral Pb(Zr0.65Ti0.35)O3 films, 30%-50% of the (11 1 ¯ )-oriented domains switched irreversibly to (111)-oriented domains as a result of the poling treatment. The present results show that the domain structures of films may change dramatically after the poling process, and both before and after the poling state should be characterized in order to interpret polarization and piezoelectric behaviors. This study helps to clarify the ferroelectric and piezoelectric properties of Pb(Zr, Ti)O3 films after poling treatment.

  9. Carbohydrate-binding module 74 is a novel starch-binding domain associated with large and multidomain α-amylase enzymes.

    PubMed

    Valk, Vincent; Lammerts van Bueren, Alicia; van der Kaaij, Rachel M; Dijkhuizen, Lubbert

    2016-06-01

    Microbacterium aurum B8.A is a bacterium that originates from a potato starch-processing plant and employs a GH13 α-amylase (MaAmyA) enzyme that forms pores in potato starch granules. MaAmyA is a large and multi-modular protein that contains a novel domain at its C terminus (Domain 2). Deletion of Domain 2 from MaAmyA did not affect its ability to degrade starch granules but resulted in a strong reduction in granular pore size. Here, we separately expressed and purified this Domain 2 in Escherichia coli and determined its likely function in starch pore formation. Domain 2 independently binds amylose, amylopectin, and granular starch but does not have any detectable catalytic (hydrolytic or oxidizing) activity on α-glucan substrates. Therefore, we propose that this novel starch-binding domain is a new carbohydrate-binding module (CBM), the first representative of family CBM74 that assists MaAmyA in efficient pore formation in starch granules. Protein sequence-based BLAST searches revealed that CBM74 occurs widespread, but in bacteria only, and is often associated with large and multi-domain α-amylases containing family CBM25 or CBM26 domains. CBM74 may specifically function in binding to granular starches to enhance the capability of α-amylase enzymes to degrade resistant starches (RSs). Interestingly, the majority of family CBM74 representatives are found in α-amylases originating from human gut-associated Bifidobacteria, where they may assist in resistant starch degradation. The CBM74 domain thus may have a strong impact on the efficiency of RS digestion in the mammalian gastrointestinal tract.

  10. Mapping regional patterns of large forest fires in Wildland-Urban Interface areas in Europe.

    PubMed

    Modugno, Sirio; Balzter, Heiko; Cole, Beth; Borrelli, Pasquale

    2016-05-01

    Over recent decades, Land Use and Cover Change (LUCC) trends in many regions of Europe have reconfigured the landscape structures around many urban areas. In these areas, the proximity to landscape elements with high forest fuels has increased the fire risk to people and property. These Wildland-Urban Interface areas (WUI) can be defined as landscapes where anthropogenic urban land use and forest fuel mass come into contact. Mapping their extent is needed to prioritize fire risk control and inform local forest fire risk management strategies. This study proposes a method to map the extent and spatial patterns of the European WUI areas at continental scale. Using the European map of WUI areas, the hypothesis is tested that the distance from the nearest WUI area is related to the forest fire probability. Statistical relationships between the distance from the nearest WUI area, and large forest fire incidents from satellite remote sensing were subsequently modelled by logistic regression analysis. The first European scale map of the WUI extent and locations is presented. Country-specific positive and negative relationships of large fires and the proximity to the nearest WUI area are found. A regional-scale analysis shows a strong influence of the WUI zones on large fires in parts of the Mediterranean regions. Results indicate that the probability of large burned surfaces increases with diminishing WUI distance in touristic regions like Sardinia, Provence-Alpes-Côte d'Azur, or in regions with a strong peri-urban component as Catalunya, Comunidad de Madrid, Comunidad Valenciana. For the above regions, probability curves of large burned surfaces show statistical relationships (ROC value > 0.5) inside a 5000 m buffer of the nearest WUI. Wise land management can provide a valuable ecosystem service of fire risk reduction that is currently not explicitly included in ecosystem service valuations. The results re-emphasise the importance of including this ecosystem service

  11. Effects of large scale deforestation on precipitation in the monsoon regions: Remote versus local effects

    NASA Astrophysics Data System (ADS)

    Bala, G.; N, D.; Modak, A.

    2015-12-01

    In this study, we investigate the bio-geophysical effects of large-scale deforestation on monsoon regions using idealized deforestation simulations. The simulations are performed using the NCAR CAM5 atmospheric model coupled to a mixed layer ocean model. The four deforestation experiments are named Global, Boreal, Temperate and Tropical, respectively. In these deforestation experiments, trees are replaced by grasses around the globe, between 20oS and 20oN, between 20oN and 50oN and poleward of 50oN, respectively. We find that the remote forcing from large-scale deforestation in the Temperate and Boreal cases shift the Inter-tropical Convergence Zone (ITCZ) southward. This results in a significant decrease in precipitation in the Northern Hemisphere monsoon regions (East Asia, North America, North Africa, South Asia) and moderate precipitation increases in the Southern Hemisphere monsoon regions (South Africa, South America and Australia). The magnitude of the monsoonal precipitation changes depend on the location of deforestation with remote effects showing a larger influence than local effects. The South Asian Monsoon region is affected the most with 18% decline in precipitation over India in the Global deforestation case. Our results indicate that any comprehensive assessment of afforestation/reforestation as climate change mitigation strategies should carefully evaluate the remote effects on monsoonal precipitation besides the large local impacts on temperatures and carbon sequestration benefits. Our results also demonstrate the linkages between any large scale forcing that causes large warming/cooling in the high latitudes and rainfall changes in tropical monsoonal regions via ITCZ shifts. Figure Caption: Changes in annual mean precipitation (mm/day) between the deforestation experiments and the control simulation. Hatched areas are regions where changes are statistically significant at the 95% confidence level. Shading in line plots represents the ±1 standard

  12. A computational approach identifies two regions of Hepatitis C Virus E1 protein as interacting domains involved in viral fusion process

    PubMed Central

    Bruni, Roberto; Costantino, Angela; Tritarelli, Elena; Marcantonio, Cinzia; Ciccozzi, Massimo; Rapicetta, Maria; El Sawaf, Gamal; Giuliani, Alessandro; Ciccaglione, Anna Rita

    2009-01-01

    Background The E1 protein of Hepatitis C Virus (HCV) can be dissected into two distinct hydrophobic regions: a central domain containing an hypothetical fusion peptide (FP), and a C-terminal domain (CT) comprising two segments, a pre-anchor and a trans-membrane (TM) region. In the currently accepted model of the viral fusion process, the FP and the TM regions are considered to be closely juxtaposed in the post-fusion structure and their physical interaction cannot be excluded. In the present study, we took advantage of the natural sequence variability present among HCV strains to test, by purely sequence-based computational tools, the hypothesis that in this virus the fusion process involves the physical interaction of the FP and CT regions of E1. Results Two computational approaches were applied. The first one is based on the co-evolution paradigm of interacting peptides and consequently on the correlation between the distance matrices generated by the sequence alignment method applied to FP and CT primary structures, respectively. In spite of the relatively low random genetic drift between genotypes, co-evolution analysis of sequences from five HCV genotypes revealed a greater correlation between the FP and CT domains than respect to a control HCV sequence from Core protein, so giving a clear, albeit still inconclusive, support to the physical interaction hypothesis. The second approach relies upon a non-linear signal analysis method widely used in protein science called Recurrence Quantification Analysis (RQA). This method allows for a direct comparison of domains for the presence of common hydrophobicity patterns, on which the physical interaction is based upon. RQA greatly strengthened the reliability of the hypothesis by the scoring of a lot of cross-recurrences between FP and CT peptides hydrophobicity patterning largely outnumbering chance expectations and pointing to putative interaction sites. Intriguingly, mutations in the CT region of E1, reducing the

  13. Combining resources, combining forces: regionalizing hospital library services in a large statewide health system*

    PubMed Central

    Martin, Heather J.; Delawska-Elliott, Basia

    2015-01-01

    After a reduction in full-time equivalents, 2 libraries in large teaching hospitals and 2 libraries in small community hospitals in a western US statewide health system saw opportunity for expansion through a regional reorganization. Despite a loss of 2/3 of the professional staff and a budgetary decrease of 27% over the previous 3 years, the libraries were able to grow business, usage, awareness, and collections through organizational innovation and improved efficiency. This paper describes the experience—including process, challenges, and lessons learned—of an organizational shift to regionalized services, collections, and staffing. Insights from this process may help similar organizations going through restructuring. PMID:25552945

  14. Combining resources, combining forces: regionalizing hospital library services in a large statewide health system.

    PubMed

    Martin, Heather J; Delawska-Elliott, Basia

    2015-01-01

    After a reduction in full-time equivalents, 2 libraries in large teaching hospitals and 2 libraries in small community hospitals in a western US statewide health system saw opportunity for expansion through a regional reorganization. Despite a loss of 2/3 of the professional staff and a budgetary decrease of 27% over the previous 3 years, the libraries were able to grow business, usage, awareness, and collections through organizational innovation and improved efficiency. This paper describes the experience--including process, challenges, and lessons learned--of an organizational shift to regionalized services, collections, and staffing. Insights from this process may help similar organizations going through restructuring.

  15. Regionalization of local geomorphometric derivations for geological mapping in the sedimentary domain of central Amazônia

    NASA Astrophysics Data System (ADS)

    Valeriano, Márcio de Morisson; Rossetti, Dilce de Fátima

    2017-03-01

    regionalization process improved the potential of local geomorphometric data for updating and revision of geological maps and for guiding future surveys in the sedimentary domain of Amazônia.

  16. Characterization of the {alpha}-helix region in domain 3 of the haemolytic lectin CEL-III: implications for self-oligomerization and haemolytic processes.

    PubMed

    Hisamatsu, Keigo; Tsuda, Nobuaki; Goda, Shuichiro; Hatakeyama, Tomomitsu

    2008-01-01

    CEL-III is a haemolytic lectin, which has two beta-trefoil domains (domains 1 and 2) and a beta-sheet-rich domain (domain 3). In domain 3 (residues 284-432), there is a hydrophobic region containing two alpha-helices (H8 and H9, residues 317-357) and a loop between them, in which alternate hydrophobic residues, especially Val residues, are present. To elucidate the role of the alpha-helix region in the haemolytic process, peptides corresponding to different parts of this region were synthesized and characterized. The peptides containing the sequence that corresponded to the loop and second alpha-helix (H9) showed the strongest antibacterial activity for Staphylococcus aureus and Bacillus subtilis through a marked permeabilization of the bacterial cell membrane. The recombinant glutathione S-transferase (GST)-fusion proteins containing domain 3 or the alpha-helix region peptide formed self-oligomers, whereas mutations in the alternate Val residues in the alpha-helix region lead to decreased oligomerization ability of the fusion proteins. These results suggest that the alpha-helix region, particularly its alternate Val residues are important for oligomerization of CEL-III in target cell membranes, which is also required for a subsequent haemolytic action.

  17. Process Domains in Synthetic Landscapes: Slope-Area Relationships in the Mountaintop Mining Region of Central Appalachia.

    NASA Astrophysics Data System (ADS)

    Jaeger, K. L.; Ross, M. R.

    2014-12-01

    Landscapes and the governing geomorphic processes that shape them have been described in a conceptual framework of process domains. At a coarse scale, process domains are segregated between hillslope, colluvial, and alluvial processes, which can be distinguished by governing erosional processes and partitioned by local slope-drainage area relationships. In landscapes that have experienced dramatic topographic alteration such as the mountaintop coal-mining (MTM) region of central Appalachia, the resulting modified environment may be considered a synthetic landscape. Such a landscape has process domains that are decoupled from prior landscape evolution trajectories. In particular, landslide and debris flow processes, which are a predominant geomorphic agent in these steep mountain systems and a primary sediment delivery mechanism to the downstream fluvial network, may be eliminated from this landscape and detectable through changes in slope-area relationships. We evaluate differences in slope-area relationships using 10-m DEMs between two time periods, pre-mined and post-mined. At five study site located within the MTM region in the central Appalachian Mountains, US, we compare slope-area changes to adjacent unmined landscapes over the same time periods. Distinct differences exist in the character of slope-area relationships between unmined and MTM sites and local slopes are systematically and considerably reduced in all process zones of mined sites. In particular, there is an expansion of the unchanneled valley zone through either an individual or simultaneous upslope shift into the hillslope region and downslope shift into the debris flow region. In addition, local slopes are markedly reduced (33% to 44%) in the post-mined period relative to the pre-mined period at all sites and are generally below the threshold required to trigger landslides and debris flows. The consequence of altered erosion processes in this upper portion of the catchment, particularly the

  18. Preferential binding of the methyl-CpG binding domain protein 2 at methylated transcriptional start site regions.

    PubMed

    Chatagnon, Amandine; Perriaud, Laury; Nazaret, Nicolas; Croze, Séverine; Benhattar, Jean; Lachuer, Joël; Dante, Robert

    2011-11-01

    Methyl-CpG Binding Domain (MBD) proteins are thought to be key molecules in the interpretation of DNA methylation signals leading to gene silencing through recruitment of chromatin remodeling complexes. In cancer, the MBD-family member, MBD2, may be primarily involved in the repression of genes exhibiting methylated CpG at their 5' end. Here we ask whether MBD2 randomly associates methylated sequences, producing chance effects on transcription, or exhibits a more specific recognition of some methylated regions. Using chromatin and DNA immunoprecipitation, we analyzed MBD2 and RNA polymerase II deposition and DNA methylation in HeLa cells on arrays representing 25,500 promoter regions. This first whole-genome mapping revealed the preferential localization of MBD2 near transcription start sites (TSSs), within the region analyzed, 7.5 kb upstream through 2.45 kb downstream of 5' transcription start sites. Probe by probe analysis correlated MBD2 deposition and DNA methylation. Motif analysis did not reveal specific sequence motifs; however, CCG and CGC sequences seem to be overrepresented. Nonrandom association (multiple correspondence analysis, p < 0.0001) between silent genes, DNA methylation and MBD2 binding was observed. The association between MBD2 binding and transcriptional repression weakened as the distance between binding site and TSS increased, suggesting that MBD2 represses transcriptional initiation. This hypothesis may represent a functional explanation for the preferential binding of MBD2 at methyl-CpG in TSS regions.

  19. Spitzer observations of dust emission from H II regions in the Large Magellanic Cloud

    SciTech Connect

    Stephens, Ian W.; Evans, Jessica Marie; Xue, Rui; Chu, You-Hua; Gruendl, Robert A.; Segura-Cox, Dominique M.

    2014-04-01

    Massive stars can alter physical conditions and properties of their ambient interstellar dust grains via radiative heating and shocks. The H II regions in the Large Magellanic Cloud (LMC) offer ideal sites to study the stellar energy feedback effects on dust because stars can be resolved, and the galaxy's nearly face-on orientation allows us to unambiguously associate H II regions with their ionizing massive stars. The Spitzer Space Telescope survey of the LMC provides multi-wavelength (3.6-160 μm) photometric data of all H II regions. To investigate the evolution of dust properties around massive stars, we have analyzed spatially resolved IR dust emission from two classical H II regions (N63 and N180) and two simple superbubbles (N70 and N144) in the LMC. We produce photometric spectral energy distributions (SEDs) of numerous small subregions for each region based on its stellar distributions and nebular morphologies. We use DustEM dust emission model fits to characterize the dust properties. Color-color diagrams and model fits are compared with the radiation field (estimated from photometric and spectroscopic surveys). Strong radial variations of SEDs can be seen throughout the regions, reflecting the available radiative heating. Emission from very small grains drastically increases at locations where the radiation field is the highest, while polycyclic aromatic hydrocarbons (PAHs) appear to be destroyed. PAH emission is the strongest in the presence of molecular clouds, provided that the radiation field is low.

  20. Crystal structure of the functional region of Uro-adherence factor A from Staphylococcus saprophyticus reveals participation of the B domain in ligand binding.

    PubMed

    Matsuoka, Eriko; Tanaka, Yoshikazu; Kuroda, Makoto; Shouji, Yuko; Ohta, Toshiko; Tanaka, Isao; Yao, Min

    2011-02-01

    Staphylococci use cell wall-anchored proteins as adhesins to attach to host tissues. Staphylococcus saprophyticus, a uropathogenic species, has a unique cell wall-anchored protein, uro-adherence factor A (UafA), which shows erythrocyte binding activity. To investigate the mechanism of adhesion by UafA, we determined the crystal structure of the functional region of UafA at 1.5 Å resolution. The structure was composed of three domains, designated as the N2, N3, and B domains, arranged in a triangular relative configuration. Hemagglutination inhibition assay with domain-truncated mutants indicated that both N and B domains were necessary for erythrocyte binding. Based on these results, a novel manner of ligand binding in which the B domain acts as a functional domain was proposed as the adhesion mechanism of S. saprophyticus.

  1. Crystal structure of the functional region of Uro-adherence factor A from Staphylococcus saprophyticus reveals participation of the B domain in ligand binding

    PubMed Central

    Matsuoka, Eriko; Tanaka, Yoshikazu; Kuroda, Makoto; Shouji, Yuko; Ohta, Toshiko; Tanaka, Isao; Yao, Min

    2011-01-01

    Staphylococci use cell wall-anchored proteins as adhesins to attach to host tissues. Staphylococcus saprophyticus, a uropathogenic species, has a unique cell wall-anchored protein, uro-adherence factor A (UafA), which shows erythrocyte binding activity. To investigate the mechanism of adhesion by UafA, we determined the crystal structure of the functional region of UafA at 1.5 Å resolution. The structure was composed of three domains, designated as the N2, N3, and B domains, arranged in a triangular relative configuration. Hemagglutination inhibition assay with domain-truncated mutants indicated that both N and B domains were necessary for erythrocyte binding. Based on these results, a novel manner of ligand binding in which the B domain acts as a functional domain was proposed as the adhesion mechanism of S. saprophyticus. PMID:21280131

  2. Molecular genetic analysis of the heterodimeric splicing factor U2AF: the RS domain on either the large or small Drosophila subunit is dispensable in vivo

    PubMed Central

    Rudner, David Z.; Breger, Kevin S.; Rio, Donald C.

    1998-01-01

    The pre-mRNA splicing factor U2AF (U2 snRNP auxiliary factor) has an essential role in 3′ splice site selection. U2AF binds the intron pyrimidine tract between the branchpoint and the 3′ splice site and recruits U2 snRNP to the branch site at an early step in spliceosome assembly. Human U2AF is a heterodimer composed of large (hU2AF65) and small (hU2AF35) subunits. Both subunits contain a domain enriched in arginine–serine dipeptide repeats termed an RS domain. The two U2AF RS domains have been assigned essential and independent roles in spliceosome assembly in vitro—the hU2AF65 RS domain is required to target U2 snRNP to the branch site and the hU2AF35 RS domain is necessary for protein–protein interactions with constitutive and alternative splicing factors. We have investigated the functional requirements for the RS domains on the Drosophila U2AF homolog in vivo. In sharp contrast to its essential role in U2 snRNP recruitment in vitro, the RS domain on the Drosophila large subunit homolog (dU2AF50) was completely dispensable in vivo. Prompted by this unexpected result, we analyzed the RS domain on the Drosophila small subunit homolog (dU2AF38). Despite its requirement for enhancer-dependent splicing activity in vitro, the dU2AF38 RS domain was also inessential in vivo. Finally, we have tested whether the Drosophila U2AF heterodimer requires any RS domain. Flies mutant for both the small and large subunits could not be rescued by dU2AF50ΔRS and dU2AF38ΔRS transgenes. Therefore, in contrast to the separate roles assigned to the U2AF RS domains in vitro, our genetic data suggest that they may have redundant functions in vivo. PMID:9531538

  3. Use of sequence analysis of the P2 domain for characterization of norovirus strains causing a large multistate outbreak of norovirus gastroenteritis in Germany 2012.

    PubMed

    Höhne, Marina; Niendorf, Sandra; Mas Marques, Andreas; Bock, C-Thomas

    2015-10-01

    Human norovirus is the main cause of non-bacterial gastroenteritis worldwide. It is transmitted from person to person, by fecally contaminated food or water or through virus containing aerosols originating during vomiting of infected persons. In September and October 2012, the largest foodborne norovirus outbreak in Germany so far spread over 5 Federal States (Berlin, Brandenburg, Saxony, Saxony-Anhalt, and Thuringia) affecting nearly 11,000 people mainly in schools and child care facilities. Epidemiological and trace-back investigations supported the assumption that a batch of frozen strawberries imported from China was the likely source of the outbreak. Sequence analysis of the capsid region encoding the P2 domain was used successfully for identification of transmission routes and epidemiologic relationship but was hampered by a lack of universal primers for all known genotypes so far. In the present study, a molecular approach was designed to track outbreak-related samples from the affected states of the large foodborne outbreak in Germany. Therefore, sequence analysis within the highly variable P2 domain of the capsid gene using newly developed universal P2 primers for genogroup I and genogroup II strains in combination with sequencing of the polymerase gene (region A) and the orf1/orf2 junction (region c) was used. The sequence analysis of 138 norovirus positive stool samples suspected to be outbreak-related revealed a considerable genomic diversity. At least 3 strains of genogroup I (I.3, I.4, and I.9) and 5 strains of genogroup II (II.6, II.7, II. 8, and recombinants II.P7_II.6, and II.P16_II.13) as well as 19 samples containing mixtures of these strains were detected. Six samples were considered as not linked to the outbreak. The most prevalent genotype was GI.4 (48/132; 36%). Genotype I.9 and the recombinant strain II.P16_II.13 were detected for the first time in Germany. Notably, the genotype II.P16_II.13 could also be determined in one of the samples of

  4. A conserved proline-rich region of the Saccharomyces cerevisiae cyclase-associated protein binds SH3 domains and modulates cytoskeletal localization.

    PubMed Central

    Freeman, N L; Lila, T; Mintzer, K A; Chen, Z; Pahk, A J; Ren, R; Drubin, D G; Field, J

    1996-01-01

    Saccharomyces cerevisiae cyclase-associated protein (CAP or Srv2p) is multifunctional. The N-terminal third of CAP binds to adenylyl cyclase and has been implicated in adenylyl cyclase activation in vivo. The widely conserved C-terminal domain of CAP binds to monomeric actin and serves an important cytoskeletal regulatory function in vivo. In addition, all CAP homologs contain a centrally located proline-rich region which has no previously identified function. Recently, SH3 (Src homology 3) domains were shown to bind to proline-rich regions of proteins. Here we report that the proline-rich region of CAP is recognized by the SH3 domains of several proteins, including the yeast actin-associated protein Abp1p. Immunolocalization experiments demonstrate that CAP colocalizes with cortical actin-containing structures in vivo and that a region of CAP containing the SH3 domain binding site is required for this localization. We also demonstrate that the SH3 domain of yeast Abp1p and that of the yeast RAS protein guanine nucleotide exchange factor Cdc25p complex with adenylyl cyclase in vitro. Interestingly, the binding of the Cdc25p SH3 domain is not mediated by CAP and therefore may involve direct binding to adenylyl cyclase or to an unidentified protein which complexes with adenylyl cyclase. We also found that CAP homologous from Schizosaccharomyces pombe and humans bind SH3 domains. The human protein binds most strongly to the SH3 domain from the abl proto-oncogene. These observations identify CAP as an SH3 domain-binding protein and suggest that CAP mediates interactions between SH3 domain proteins and monomeric actin. PMID:8552082

  5. A conserved proline-rich region of the Saccharomyces cerevisiae cyclase-associated protein binds SH3 domains and modulates cytoskeletal localization.

    PubMed

    Freeman, N L; Lila, T; Mintzer, K A; Chen, Z; Pahk, A J; Ren, R; Drubin, D G; Field, J

    1996-02-01

    Saccharomyces cerevisiae cyclase-associated protein (CAP or Srv2p) is multifunctional. The N-terminal third of CAP binds to adenylyl cyclase and has been implicated in adenylyl cyclase activation in vivo. The widely conserved C-terminal domain of CAP binds to monomeric actin and serves an important cytoskeletal regulatory function in vivo. In addition, all CAP homologs contain a centrally located proline-rich region which has no previously identified function. Recently, SH3 (Src homology 3) domains were shown to bind to proline-rich regions of proteins. Here we report that the proline-rich region of CAP is recognized by the SH3 domains of several proteins, including the yeast actin-associated protein Abp1p. Immunolocalization experiments demonstrate that CAP colocalizes with cortical actin-containing structures in vivo and that a region of CAP containing the SH3 domain binding site is required for this localization. We also demonstrate that the SH3 domain of yeast Abp1p and that of the yeast RAS protein guanine nucleotide exchange factor Cdc25p complex with adenylyl cyclase in vitro. Interestingly, the binding of the Cdc25p SH3 domain is not mediated by CAP and therefore may involve direct binding to adenylyl cyclase or to an unidentified protein which complexes with adenylyl cyclase. We also found that CAP homologous from Schizosaccharomyces pombe and humans bind SH3 domains. The human protein binds most strongly to the SH3 domain from the abl proto-oncogene. These observations identify CAP as an SH3 domain-binding protein and suggest that CAP mediates interactions between SH3 domain proteins and monomeric actin.

  6. Amino Terminal Region of Dengue Virus NS4A Cytosolic Domain Binds to Highly Curved Liposomes.

    PubMed

    Hung, Yu-Fu; Schwarten, Melanie; Hoffmann, Silke; Willbold, Dieter; Sklan, Ella H; Koenig, BerndW

    2015-07-21

    Dengue virus (DENV) is an important human pathogen causing millions of disease cases and thousands of deaths worldwide. Non-structural protein 4A (NS4A) is a vital component of the viral replication complex (RC) and plays a major role in the formation of host cell membrane-derived structures that provide a scaffold for replication. The N-terminal cytoplasmic region of NS4A(1-48) is known to preferentially interact with highly curved membranes. Here, we provide experimental evidence for the stable binding of NS4A(1-48) to small liposomes using a liposome floatation assay and identify the lipid binding sequence by NMR spectroscopy. Mutations L6E;M10E were previously shown to inhibit DENV replication and to interfere with the binding of NS4A(1-48) to small liposomes. Our results provide new details on the interaction of the N-terminal region of NS4A with membranes and will prompt studies of the functional relevance of the curvature sensitive membrane anchor at the N-terminus of NS4A.

  7. CURRENT HELICITY OF ACTIVE REGIONS AS A TRACER OF LARGE-SCALE SOLAR MAGNETIC HELICITY

    SciTech Connect

    Zhang, H.; Gao, Y.; Xu, H.; Moss, D.; Kleeorin, N.; Rogachevskii, I.; Kuzanyan, K.; Sokoloff, D.

    2012-05-20

    We demonstrate that the current helicity observed in solar active regions traces the magnetic helicity of the large-scale dynamo generated field. We use an advanced two-dimensional mean-field dynamo model with dynamo saturation based on the evolution of the magnetic helicity and algebraic quenching. For comparison, we also studied a more basic two-dimensional mean-field dynamo model with simple algebraic alpha-quenching only. Using these numerical models we obtained butterfly diagrams both for the small-scale current helicity and also for the large-scale magnetic helicity, and compared them with the butterfly diagram for the current helicity in active regions obtained from observations. This comparison shows that the current helicity of active regions, as estimated by -A {center_dot} B evaluated at the depth from which the active region arises, resembles the observational data much better than the small-scale current helicity calculated directly from the helicity evolution equation. Here B and A are, respectively, the dynamo generated mean magnetic field and its vector potential. A theoretical interpretation of these results is given.

  8. The Compact Body Plan of Tardigrades Evolved by the Loss of a Large Body Region.

    PubMed

    Smith, Frank W; Boothby, Thomas C; Giovannini, Ilaria; Rebecchi, Lorena; Jockusch, Elizabeth L; Goldstein, Bob

    2016-01-25

    The superphylum Panarthropoda (Arthropoda, Onychophora, and Tardigrada) exhibits a remarkable diversity of segment morphologies, enabling these animals to occupy diverse ecological niches. The molecular identities of these segments are specified by Hox genes and other axis patterning genes during development [1, 2]. Comparisons of molecular segment identities between arthropod and onychophoran species have yielded important insights into the origins and diversification of their body plans [3-9]. However, the relationship of the segments of tardigrades to those of arthropods and onychophorans has remained enigmatic [10, 11], limiting our understanding of early panarthropod body plan diversification. Here, we reveal molecular identities for all of the segments of a tardigrade. Based on our analysis, we conclude that tardigrades have lost a large intermediate region of the body axis-a region corresponding to the entire thorax and most of the abdomen of insects-and that they have lost the Hox genes that originally specified this region. Our data suggest that nearly the entire tardigrade body axis is homologous to just the head region of arthropods. Based on our results, we reconstruct a last common ancestor of Panarthropoda that had a relatively elongate body plan like most arthropods and onychophorans, rather than a compact, tardigrade-like body plan. These results demonstrate that the body plan of an animal phylum can originate by the loss of a large part of the body.

  9. The intrinsically disordered amino-terminal region of human RecQL4: multiple DNA-binding domains confer annealing, strand exchange and G4 DNA binding

    PubMed Central

    Keller, Heidi; Kiosze, Kristin; Sachsenweger, Juliane; Haumann, Sebastian; Ohlenschläger, Oliver; Nuutinen, Tarmo; Syväoja, Juhani E.; Görlach, Matthias; Grosse, Frank; Pospiech, Helmut

    2014-01-01

    Human RecQL4 belongs to the ubiquitous RecQ helicase family. Its N-terminal region represents the only homologue of the essential DNA replication initiation factor Sld2 of Saccharomyces cerevisiae, and also participates in the vertebrate initiation of DNA replication. Here, we utilized a random screen to identify N-terminal fragments of human RecQL4 that could be stably expressed in and purified from Escherichia coli. Biophysical characterization of these fragments revealed that the Sld2 homologous RecQL4 N-terminal domain carries large intrinsically disordered regions. The N-terminal fragments were sufficient for the strong annealing activity of RecQL4. Moreover, this activity appeared to be the basis for an ATP-independent strand exchange activity. Both activities relied on multiple DNA-binding sites with affinities to single-stranded, double-stranded and Y-structured DNA. Finally, we found a remarkable affinity of the N-terminus for guanine quadruplex (G4) DNA, exceeding the affinities for other DNA structures by at least 60-fold. Together, these findings suggest that the DNA interactions mediated by the N-terminal region of human RecQL4 represent a central function at the replication fork. The presented data may also provide a mechanistic explanation for the role of elements with a G4-forming propensity identified in the vicinity of vertebrate origins of DNA replication. PMID:25336622

  10. Functional Anthology of Intrinsic Disorder. II. Cellular Components, Domains, Technical Terms, Developmental Processes and Coding Sequence Diversities Correlated with Long Disordered Regions

    PubMed Central

    Vucetic, Slobodan; Xie, Hongbo; Iakoucheva, Lilia M.; Oldfield, Christopher J.; Dunker, A. Keith; Obradovic, Zoran; Uversky, Vladimir N.

    2008-01-01

    Biologically active proteins without stable ordered structure (i.e., intrinsically disordered proteins) are attracting increased attention. Functional repertoires of ordered and disordered proteins are very different, and the ability to differentiate whether a given function is associated with intrinsic disorder or with a well-folded protein is crucial for modern protein science. However, there is a large gap between the number of proteins experimentally confirmed to be disordered and their actual number in nature. As a result, studies of functional properties of confirmed disordered proteins, while helpful in revealing the functional diversity of protein disorder, provide only a limited view. To overcome this problem, a bioinformatics approach for comprehensive study of functional roles of protein disorder was proposed in the first paper of this series (Xie H., Vucetic S., Iakoucheva L.M., Oldfield C.J., Dunker A.K., Obradovic Z., Uversky V.N. (2006) Functional anthology of intrinsic disorder. I. Biological processes and functions of proteins with long disordered regions. J. Proteome Res.). Applying this novel approach to Swiss-Prot sequences and functional keywords, we found over 238 and 302 keywords to be strongly positively or negatively correlated, respectively, with long intrinsically disordered regions. This paper describes ~90 Swiss-Prot keywords attributed to the cellular components, domains, technical terms, developmental processes and coding sequence diversities possessing strong positive and negative correlation with long disordered regions. PMID:17391015

  11. W phase source inversion using high-rate regional GPS data for large earthquakes

    NASA Astrophysics Data System (ADS)

    Riquelme, S.; Bravo, F.; Melgar, D.; Benavente, R.; Geng, J.; Barrientos, S.; Campos, J.

    2016-04-01

    W phase moment tensor inversion has proven to be a reliable method for rapid characterization of large earthquakes. For global purposes it is used at the United States Geological Survey, Pacific Tsunami Warning Center, and Institut de Physique du Globe de Strasbourg. These implementations provide moment tensors within 30-60 min after the origin time of moderate and large worldwide earthquakes. Currently, the method relies on broadband seismometers, which clip in the near field. To ameliorate this, we extend the algorithm to regional records from high-rate GPS data and retrospectively apply it to six large earthquakes that occurred in the past 5 years in areas with relatively dense station coverage. These events show that the solutions could potentially be available 4-5 min from origin time. Continuously improving GPS station availability and real-time positioning solutions will provide significant enhancements to the algorithm.

  12. The Effector Domain Region of the Vibrio vulnificus MARTX Toxin Confers Biphasic Epithelial Barrier Disruption and Is Essential for Systemic Spread from the Intestine

    PubMed Central

    Gavin, Hannah E.; Beubier, Nike T.

    2017-01-01

    Vibrio vulnificus causes highly lethal bacterial infections in which the Multifunctional Autoprocessing Repeats-in-Toxins (MARTX) toxin product of the rtxA1 gene is a key virulence factor. MARTX toxins are secreted proteins up to 5208 amino acids in size. Conserved MARTX N- and C-terminal repeat regions work in concert to form pores in eukaryotic cell membranes, through which the toxin’s central region of modular effector domains is translocated. Upon inositol hexakisphosphate-induced activation of the of the MARTX cysteine protease domain (CPD) in the eukaryotic cytosol, effector domains are released from the holotoxin by autoproteolytic activity. We previously reported that the native MARTX toxin effector domain repertoire is dispensable for epithelial cellular necrosis in vitro, but essential for cell rounding and apoptosis prior to necrotic cell death. Here we use an intragastric mouse model to demonstrate that the effector domain region is required for bacterial virulence during intragastric infection. The MARTX effector domain region is essential for bacterial dissemination from the intestine, but dissemination occurs in the absence of overt intestinal tissue pathology. We employ an in vitro model of V. vulnificus interaction with polarized colonic epithelial cells to show that the MARTX effector domain region induces rapid intestinal barrier dysfunction and increased paracellular permeability prior to onset of cell lysis. Together, these results negate the inherent assumption that observations of necrosis in vitro directly predict bacterial virulence, and indicate a paradigm shift in our conceptual understanding of MARTX toxin function during intestinal infection. Results implicate the MARTX effector domain region in mediating early bacterial dissemination from the intestine to distal organs–a key step in V. vulnificus foodborne pathogenesis–even before onset of overt intestinal pathology. PMID:28060924

  13. Regionalized PM2.5 Community Multiscale Air Quality model performance evaluation across a continuous spatiotemporal domain

    NASA Astrophysics Data System (ADS)

    Reyes, Jeanette M.; Xu, Yadong; Vizuete, William; Serre, Marc L.

    2017-01-01

    The regulatory Community Multiscale Air Quality (CMAQ) model is a means to understanding the sources, concentrations and regulatory attainment of air pollutants within a model's domain. Substantial resources are allocated to the evaluation of model performance. The Regionalized Air quality Model Performance (RAMP) method introduced here explores novel ways of visualizing and evaluating CMAQ model performance and errors for daily Particulate Matter ≤ 2.5 μm (PM2.5) concentrations across the continental United States. The RAMP method performs a non-homogenous, non-linear, non-homoscedastic model performance evaluation at each CMAQ grid. This work demonstrates that CMAQ model performance, for a well-documented 2001 regulatory episode, is non-homogeneous across space/time. The RAMP correction of systematic errors outperforms other model evaluation methods as demonstrated by a 22.1% reduction in Mean Square Error compared to a constant domain wide correction. The RAMP method is able to accurately reproduce simulated performance with a correlation of r = 76.1%. Most of the error coming from CMAQ is random error with only a minority of error being systematic. Areas of high systematic error are collocated with areas of high random error, implying both error types originate from similar sources. Therefore, addressing underlying causes of systematic error will have the added benefit of also addressing underlying causes of random error.

  14. Statistical and Scaling Properties of Remotely-Sensed Soil Moisture in Two Contrasting Domains in the North American Monsoon Region

    NASA Technical Reports Server (NTRS)

    Mascaro, Giuseppe; Vivoni, Enrique

    2009-01-01

    Characterizing soil moisture (theta) variability is important for inferring high-resolution information from coarse estimates provided by remote sensors. In this study, we analyze the spatial variability and scale invariance of high-resolution theta estimates collected in two contrasting semiarid areas, Arizona (AZ) and Sonora (SON), during the Soil Moisture Experiment - North American Monsoon in 2004 (SMEX04- NAME). Results reveal that as the mean theta condition () becomes drier, the spatial standard deviation becomes smaller in both domains. The coefficient of variation of theta decreases with in SON, but does not display a clear tendency with in AZ. We also found the presence of scale invariance and multifractality in the range of support scales from 51.2 km to 0.8 km for all soil moisture fields in the two regions. The multifractal properties of theta are clearly linked to in SON, while the relation is affected by more dispersion in AZ. We argue this is due to differences in the dynamic (rainfall) and static (vegetation) controls on theta in the two domains.

  15. Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains.

    PubMed

    Brackley, Chris A; Johnson, James; Kelly, Steven; Cook, Peter R; Marenduzzo, Davide

    2016-05-05

    Biophysicists are modeling conformations of interphase chromosomes, often basing the strengths of interactions between segments distant on the genetic map on contact frequencies determined experimentally. Here, instead, we develop a fitting-free, minimal model: bivalent or multivalent red and green 'transcription factors' bind to cognate sites in strings of beads ('chromatin') to form molecular bridges stabilizing loops. In the absence of additional explicit forces, molecular dynamic simulations reveal that bound factors spontaneously cluster-red with red, green with green, but rarely red with green-to give structures reminiscent of transcription factories. Binding of just two transcription factors (or proteins) to active and inactive regions of human chromosomes yields rosettes, topological domains and contact maps much like those seen experimentally. This emergent 'bridging-induced attraction' proves to be a robust, simple and generic force able to organize interphase chromosomes at all scales.

  16. Distinct Roles of the Repeat-Containing Regions and Effector Domains of the Vibrio vulnificus Multifunctional-Autoprocessing Repeats-in-Toxin (MARTX) Toxin

    PubMed Central

    Kim, Byoung Sik; Gavin, Hannah E.

    2015-01-01

    ABSTRACT Vibrio vulnificus is a seafood-borne pathogen that destroys the intestinal epithelium, leading to rapid bacterial dissemination and death. The most important virulence factor is the multifunctional-autoprocessing repeats-in-toxin (MARTX) toxin comprised of effector domains in the center region flanked by long repeat-containing regions which are well conserved among MARTX toxins and predicted to translocate effector domains. Here, we examined the role of the repeat-containing regions using a modified V. vulnificus MARTX (MARTXVv) toxin generated by replacing all the internal effector domains with β-lactamase (Bla). Bla activity was detected in secretions from the bacterium and also in the cytosol of intoxicated epithelial cells. The modified MARTXVv toxin without effector domains retained its necrotic activity but lost its cell-rounding activity. Further, deletion of the carboxyl-terminal repeat-containing region blocked toxin secretion from the bacterium. Deletion of the amino-terminal repeat-containing region had no effect on secretion but completely abolished translocation and necrosis. Neither secretion nor translocation was affected by enzymatically inactivating the cysteine protease domain of the toxin. These data demonstrate that the amino-terminal and carboxyl-terminal repeat-containing regions of the MARTXVv toxin are necessary and sufficient for the delivery of effector domains and epithelial cell lysis in vitro but that effector domains are required for other cytopathic functions. Furthermore, Ca2+-dependent secretion of the modified MARTXVv toxin suggests that nonclassical RTX-like repeats found in the carboxyl-terminal repeat-containing region are functionally similar to classical RTX repeats found in other RTX proteins. PMID:25827415

  17. Time and Frequency Domain Synthesis in the Optimal Design of Shock and Vibration Isolation for Large Structural Systems

    DTIC Science & Technology

    1997-06-01

    DOMAIN SYNTHESIS COMPUTER CODE The computer language used for the frequency domain synthesis and all other computer coding in this thesis is MATLAB V.4.2c... method is really not restrictive in its application, but rather in what information it can provide. D. STATIC DISPLACEMENT SYNTHESIS COMPUTER CODE The...synthesis, and perform a comparative analysis of the synthesis versus classical Guyan reduction methods . The programs presented in Appendix B can be

  18. LARGE SOLAR ENERGETIC PARTICLE EVENTS ASSOCIATED WITH FILAMENT ERUPTIONS OUTSIDE ACTIVE REGIONS

    SciTech Connect

    Gopalswamy, N.; Mäkelä, P.; Akiyama, S.; Yashiro, S.; Xie, H.; Thakur, N.; Kahler, S. W.

    2015-06-10

    We report on four large filament eruptions (FEs) from solar cycles 23 and 24 that were associated with large solar energetic particle (SEP) events and interplanetary type II radio bursts. The post-eruption arcades corresponded mostly to C-class soft X-ray enhancements, but an M1.0 flare was associated with one event. However, the associated coronal mass ejections (CMEs) were fast (speeds ∼ 1000 km s{sup −1}) and appeared as halo CMEs in the coronagraph field of view. The interplanetary type II radio bursts occurred over a wide wavelength range, indicating the existence of strong shocks throughout the inner heliosphere. No metric type II bursts were present in three events, indicating that the shocks formed beyond 2–3 Rs. In one case, there was a metric type II burst with low starting frequency, indicating a shock formation height of ∼2 Rs. The FE-associated SEP events did have softer spectra (spectral index >4) in the 10–100 MeV range, but there were other low-intensity SEP events with spectral indices ≥4. Some of these events are likely FE-SEP events, but were not classified as such in the literature because they occurred close to active regions. Some were definitely associated with large active region flares, but the shock formation height was large. We definitely find a diminished role for flares and complex type III burst durations in these large SEP events. Fast CMEs and shock formation at larger distances from the Sun seem to be the primary characteristics of the FE-associated SEP events.

  19. Large Solar Energetic Particle Events Associated With Filament Eruptions Outside Active Regions

    NASA Technical Reports Server (NTRS)

    Gopalswamy, N.; Makela, P.; Akiyama, S.; Yashiro, S.; Xie, H.; Thakur, N.; Kahler, S. W.

    2015-01-01

    We report on four large filament eruptions (FEs) from solar cycles 23 and 24 that were associated with large solar energetic particle (SEP) events and interplanetary type II radio bursts. The post-eruption arcades corresponded mostly to C-class soft X-ray enhancements, but an M1.0 flare was associated with one event. However, the associated coronal mass ejections (CMEs) were fast (speeds approx. 1000 km/s) and appeared as halo CMEs in the coronagraph field of view. The interplanetary type II radio bursts occurred over a wide wavelength range, indicating the existence of strong shocks throughout the inner heliosphere. No metric type II bursts were present in three events, indicating that the shocks formed beyond 2-3 Rs. In one case, there was a metric type II burst with low starting frequency, indicating a shock formation height of approx.2 Rs. The FE-associated SEP events did have softer spectra (spectral index >4) in the 10-100 MeV range, but there were other low-intensity SEP events with spectral indices ?4. Some of these events are likely FE-SEP events, but were not classified as such in the literature because they occurred close to active regions. Some were definitely associated with large active region flares, but the shock formation height was large. We definitely find a diminished role for flares and complex type III burst durations in these large SEP events. Fast CMEs and shock formation at larger distances from the Sun seem to be the primary characteristics of the FE-associated SEP events.

  20. Saliency region selection in large aerial imagery using multiscale SLIC segmentation

    NASA Astrophysics Data System (ADS)

    Sahli, Samir; Lavigne, Daniel A.; Sheng, Yunlong

    2012-06-01

    Advents in new sensing hardwares like GigE-cameras and fast growing data transmission capability create an imbalance between the amount of large scale aerial imagery and the means at disposal for treating them. Selection of saliency regions can reduce significantly the prospecting time and computation cost for the detection of objects in large scale aerial imagery. We propose a new approach using multiscale Simple Linear Iterative Clustering (SLIC) technique to compute the saliency regions. The SLIC is fast to create compact and uniform superpixels, based on the distances in both color and geometric spaces. When a salient structure of the object is over-segmented by the SLIC, a number of superpixels will follow the edges in the structure and therefore acquires irregular shapes. Thus, the superpixels deformation betrays presence of salient structures. We quantify the non-compactness of the superpixels as a salience measure, which is computed using the distance transform and the shape factor. To treat objects or object details of various sizes in an image, or the multiscale images, we compute the SLIC segmentations and the salient measures at multiple scales with a set of predetermined sizes of the superpixels. The final saliency map is a sum of the salience measures obtained at multiple scales. The proposed approach is fast, requires no input of user-defined parameter, produces well defined salient regions at full resolution and adapted to multi-scale image processing.

  1. Aspect angle dependence of the E region irregularity velocity at large flow angles

    NASA Astrophysics Data System (ADS)

    Makarevich, R. A.; Koustov, A. V.; Senior, A.; Uspensky, M.; Honary, F.; Dyson, P. L.

    2007-11-01

    We present the Doppler velocity observations of 1-m plasma waves in the auroral E region by the Scandinavian Twin Auroral Radar Experiment (STARE) Norway VHF coherent radar in the context of simultaneous and coincident measurements of electron and ion drift velocities determined by the European Incoherent Scatter (EISCAT) tristatic radar facility. The measurements were performed in the afternoon sector (1500-2000 MLT) at seven locations along the STARE radar beam 2 with different values of the magnetic off-perpendicular (aspect) angle α between 0.48° and 2.63° and at large angles with respect to the electron background drift (θ = 55°-90°). It is demonstrated that the STARE line-of-sight velocity, normalized to the EISCAT-derived electron drift speed at large flow angles, exhibits a decrease with increasing aspect angle, and the rate of decrease is investigated as a function of the flow angle. We also compare the STARE velocity with the electron and ion drift velocity components along the STARE radar beam look direction and show that, at large aspect angles, the E region velocity is correlated (anticorrelated) with the ion (electron) drift velocity component. The results are discussed in the contexts of the linear fluid theory of the modified two-stream plasma instability and the theory of anomalous collisions.

  2. Past, present and future of Tropical Cyclone climatology over CORDEX South-Asia domain: A coupled regional climate model study

    NASA Astrophysics Data System (ADS)

    Kumar, P.; Sein, D.; Koldunov, N.; Hodges, K.; Haensler, A.; Daniela, J.

    2015-12-01

    Tropical cyclones (TC) in the Indian Ocean arise from cyclonic disturbances that naturally form in the inter-tropical convergence zone between 5N and 20N latitudes when sea surface temperatures (SST) are at 27C or above. This relationship between SST and TC formation and intensification implies that rising SST in the climate change era will increase the probability of tropical cyclone formation and that therefore as global temperatures rise so will the frequency and intensity of tropical cyclones. However horizontal resolution of the global general circulation models used in IPCC simulations are usually too coarse to reproduce many smaller scale processes like TC. We present a novel approach to downscale climate change scenarios, which could be also used to investigate the generation and propagation of tropical cyclones over the northern Indian Ocean. The REgional atmosphere MOdel REMO is coupled to the global ocean - sea ice model MPIOM with increased resolution over the Indian Ocean (~20km). The resulting coupled system called ROM. The coupled domain is standard CORDEX south Asia domain (0.44 deg). The models are coupled via the OASIS coupler. Exchange between ocean and atmosphere was made every three hours. Lateral atmospheric and upper oceanic boundary conditions outside the coupled domain were prescribed using ERA40, MPIESM-LR historical and MPIESM-LR RCP85 data. Here we present the results of the dynamical downscaling approach both coupled (ROM) and uncoupled (REMO) simulations for the same period. The validation period (ERA40 and Historical) is 1958-2001. While comparing with observations mean (1958-2001) annual frequency of 8 TC/year, ROM simulated with ERA40 (Historical) TCs are 12 (10), whereas with REMO they are 21 (18). Therefore ROM simulated TC frequency is much more realistic than REMO. REMO has simulated two times more TCs than ROM, hence leading to strong overestimation of TC tracks densities over the region. Scenario simulations (RCP85) showed

  3. Architecture of the Nitric-oxide Synthase Holoenzyme Reveals Large Conformational Changes and a Calmodulin-driven Release of the FMN Domain*♦

    PubMed Central

    Yokom, Adam L.; Morishima, Yoshihiro; Lau, Miranda; Su, Min; Glukhova, Alisa; Osawa, Yoichi; Southworth, Daniel R.

    2014-01-01

    Nitric-oxide synthase (NOS) is required in mammals to generate NO for regulating blood pressure, synaptic response, and immune defense. NOS is a large homodimer with well characterized reductase and oxygenase domains that coordinate a multistep, interdomain electron transfer mechanism to oxidize l-arginine and generate NO. Ca2+-calmodulin (CaM) binds between the reductase and oxygenase domains to activate NO synthesis. Although NOS has long been proposed to adopt distinct conformations that alternate between interflavin and FMN-heme electron transfer steps, structures of the holoenzyme have remained elusive and the CaM-bound arrangement is unknown. Here we have applied single particle electron microscopy (EM) methods to characterize the full-length of the neuronal isoform (nNOS) complex and determine the structural mechanism of CaM activation. We have identified that nNOS adopts an ensemble of open and closed conformational states and that CaM binding induces a dramatic rearrangement of the reductase domain. Our three-dimensional reconstruction of the intact nNOS-CaM complex reveals a closed conformation and a cross-monomer arrangement with the FMN domain rotated away from the NADPH-FAD center, toward the oxygenase dimer. This work captures, for the first time, the reductase-oxygenase structural arrangement and the CaM-dependent release of the FMN domain that coordinates to drive electron transfer across the domains during catalysis. PMID:24737326

  4. Severe deep convection events in the Andes region (Mendoza, Argentina) and their relation with large amplitude mountain waves

    NASA Astrophysics Data System (ADS)

    de la Torre, Alejandro; Hierro, Lic. R.; Llamedo, Lic. P.; Rolla, Lic. A.; Alexander, Peter

    In addition to an environmental lapse rate conditionally unstable and sufficient available mois-ture, some process by which a parcel is lifted to its LFC is required for the occurrence of deep convection. Since rising motions associated with synoptic scale processes are too weak to lift a moist parcel to its LFC, some strong sub-synoptic mechanism such us upward motion over a frontal zone, anabatic/katabatic winds or mountain waves are required to supply the necessary energy to trigger deep convection. We analyze here, two selected recent severe storms developed in the absence of fronts and registered at the south of Mendoza, Argentina, a semiarid region situated at midlatitudes (roughly between 32S and 36S) at the east of the highest Andes tops. The storms were initiated at the same local time. In both cases, large amplitude stationary mountain waves with similar wavelengths were generated through the forcing of the NW wind by the Andes Range, just before the first cell was detected in the S-band radar. Mesoscale model simulatons (WRF3V, three domains, inner at 4 km) were conducted. The wave pat-tern was analyzed at several constant pressure levels with a Morlet wavelet. This wavelet has proven to be a useful technique for this purpose, as propagating mountain waves are well local-ized within a horizontal domain of some hundred kilometers. The simulated evolution in space and time of vertical wind oscillations (even better than reflectivity) reveal their influence in the genesis zone of both storms. The synoptic conditions observed (low-pressure system over the NW of Argentina, slow displacement of anticyclones in Pacific and Atlantic oceans, a low level jet carrying warm and moist air from the N and geopotential distribution at 1000, 500 and 300 hPa) are consistent with earlier works. We describe and discuss, in both cases, i) the vertical and horizontal wavelengths, ii) the direction of propagation of the main wave modes, iii) their lineal polarization and phase

  5. DUST EMISSION FROM EVOLVED AND UNEVOLVED H II REGIONS IN THE LARGE MAGELLANIC CLOUD

    SciTech Connect

    Slater, C. T.; Oey, M. S.; Li, A.; Bernard, J.-Ph.; Paradis, D.; Churchwell, E.; Gordon, K. D.; Lawton, B.; Meixner, M.; Indebetouw, R.; Reach, W.T.

    2011-05-10

    We present a study of the dust properties of 12 classical and superbubble H II regions in the Large Magellanic Cloud. We use infrared photometry from Spitzer (8, 24, 70, and 160 {mu} m bands), obtained as part of the Surveying the Agents of a Galaxy's Evolution (SAGE) program, along with archival spectroscopic classifications of the ionizing stars to examine the role of stellar sources on dust heating and processing. Our infrared observations show surprisingly little correlation between the emission properties of the dust and the effective temperatures or bolometric magnitudes of stars in the H II regions, suggesting that the H II region evolutionary timescale is not on the order of the dust processing timescale. We find that the infrared emission of superbubbles and classical H II regions shows little differentiation between the two classes, despite the significant differences in age and morphology. We do detect a correlation of the 24 {mu} m emission from hot dust with the ratio of 70-160 {mu} m flux. This correlation can be modeled as a trend in the temperature of a minority hot dust component, while a majority of the dust remains significantly cooler.

  6. A large outbreak of Japanese encephalitis predominantly among adults in northern region of West Bengal, India.

    PubMed

    Gurav, Yogesh K; Bondre, Vijay P; Tandale, Babasaheb V; Damle, Rekha G; Mallick, Sanjay; Ghosh, Uday S; Nag, Shankha S

    2016-11-01

    Unusual rise of acute encephalitis syndrome cases (AES) were reported in July 2014 in the northern region of West Bengal, India. Investigations were carried out to characterize the outbreak and to identify the associated virus etiology. This observational study is based on 398 line listed AES cases, mostly (70.8%, 282/398) adults, with case fatality ratio of 28.9% (115/398). Japanese encephalitis virus infection was detected in 134 (49.4%) among 271 AES cases tested and most of them (79.1%, 106/134) were adults. The study reports a large outbreak of genotype III Japanese encephalitis among adults in northern region of West Bengal, India. J. Med. Virol. 88:2004-2011, 2016. © 2016 Wiley Periodicals, Inc.

  7. Ages of calderas, large explosive craters and active volcanoes in the Kuril-Kamchatka region, Russia

    NASA Astrophysics Data System (ADS)

    Braitseva, O. A.; Melekestsev, I. V.; Ponomareva, V. V.; Sulerzhitsky, L. D.

    1995-12-01

    The ages of most of calderas, large explosive craters and active volcanoes in the Kuril-Kamchatka region have been determined by extensive geological, geomorphological, tephrochronological and isotopic geochronological studies, including more than 600 14C dates. Eight ‘Krakatoa-type’ and three ‘Hawaiian-type’ calderas and no less than three large explosive craters formed here during the Holocene. Most of the Late Pleistocene Krakatoa-type calderas were established around 30 000 40 000 years ago. The active volcanoes are geologically very young, with maximum ages of about 40 000 50 000 years. The overwhelming majority of recently active volcanic cones originated at the very end of the Late Pleistocene or in the Holocene. These studies show that all Holocene stratovolcanoes in Kamchatka were emplaced in the Holocene only in the Eastern volcanic belt. Periods of synchronous, intensified Holocene volcanic activity occurred within the time intervals of 7500 7800 and 1300 1800 14C years BP.

  8. The Gould's Belt very large array survey. III. The Orion region

    SciTech Connect

    Kounkel, Marina; Hartmann, Lee; Loinard, Laurent; Ortiz-León, Gisela N.; Rodríguez, Luis F.; Pech, Gerardo; Rivera, Juana L.; Mioduszewski, Amy J.; Dzib, Sergio A.; Torres, Rosa M.; Boden, Andrew F.; Evans, Neal J. II; Briceño, Cesar; Tobin, John

    2014-07-20

    We present results from a high-sensitivity (60 μJy), large-scale (2.26 deg{sup 2}) survey obtained with the Karl G. Jansky Very Large Array as part of the Gould's Belt Survey program. We detected 374 and 354 sources at 4.5 and 7.5 GHz, respectively. Of these, 148 are associated with previously known young stellar objects (YSOs). Another 86 sources previously unclassified at either optical or infrared wavelengths exhibit radio properties that are consistent with those of young stars. The overall properties of our sources at radio wavelengths such as their variability and radio to X-ray luminosity relation are consistent with previous results from the Gould's Belt Survey. Our detections provide target lists for follow-up Very Long Baseline Array radio observations to determine their distances as YSOs are located in regions of high nebulosity and extinction, making it difficult to measure optical parallaxes.

  9. Generation of large-scale equatorial F-region plasma depletions during geomagnetic storms: A review

    NASA Astrophysics Data System (ADS)

    Sahai, Y.; Fagundes, P.; Bittencourt, J.; Pimenta, A.

    All-sky imaging observations of the F-region OI 630 nm nightglow emission allow us to visualize large - scale equatorial plasma depletions, generally known as transequatorial plasma bubbles. These quasi north south direction aligned- ionospheric plasma depletions are o tical signatures of strong range type equatorialp spread-F. An extensive data base of the OI 630 nm emission all-sky imaging- observations has been obtained at Cachoeira Paulista (22.7o S, 45.0 o W; dip latitude ~16o S), Brazil, between the years 1987 and 2000. An analysis of these observations revealed that normally large-scale ionospheric plasma depletions do not occur during the months of May to August (southern winter) in the Brazilian sector. However, large-scale ionospheric plasma depletions during thes e months have been observed on several occasions in association with geomagnetic storms. In this paper, a detailed analysis of the events when large - scale ionospheric plasma depletions were initiated and evolved during magnetic disturbances will be present ed and discussed.

  10. Measured Response of Local, Mid-range and Far-range Discontinuities of Large Metal Groundplanes using Time Domain Techniques

    NASA Astrophysics Data System (ADS)

    Schrader, T.; Münter, K.; Battermann, S.; Garbe, H.

    2005-05-01

    This work describes a method to detect and to quantify any local or mid-range discontinuity on extended flat metal planes. Often these planes are used for antenna calibration (open area test site - OATS) or the plane could be the ground of a semi-anechoic chamber used in Electromagnetic Compatibility (EMC) testing. The measurement uncertainty of antenna calibration or EMC testing depends on the groundplane's quality, which can be accessed using this method. A vector network analyzer with time-domain option is used to determine the complex-valued input scattering parameter S11,F of an aperture antenna in a monostatic setup. S;11,F contains the information desired about the discontinuities and is measured in the frequency domain with high dynamic range. But only after a linear filtering utilizing the Chirp-Z-Transform the obtained time-domain signal S11,T evidence of local and mid-range discontinuities.

  11. Self-association of isolated large cytoplasmic domain of plasma membrane H+ -ATPase from Saccharomyces cerevisiae: role of the phosphorylation domain in a general dimeric model for P-ATPases.

    PubMed

    Almeida, W I; Martins, O B; Carvalho-Alves, P C

    2006-11-01

    Large cytoplasmic domain (LCD) plasma membrane H+ -ATPase from S. cerevisiae was expressed as two fusion polypeptides in E. coli: a DNA sequence coding for Leu353-Ileu674 (LCDh), comprising both nucleotide (N) and phosphorylation (P) domains, and a DNA sequence coding for Leu353-Thr543 (LCDDeltah, lacking the C-terminus of P domain), were inserted in expression vectors pDEST-17, yielding the respective recombinant plasmids. Overexpressed fusion polypeptides were solubilized with 6 M urea and purified on affinity columns, and urea was removed by dialysis. Their predicted secondary structure contents were confirmed by CD spectra. In addition, both recombinant polypeptides exhibited high-affinity 2',3'-O-(2,4,6-trinitrophenyl)adenosine-5'-triphosphate (TNP-ATP) binding (Kd = 1.9 microM and 2.9 microM for LCDh and LCDDeltah, respectively), suggesting that they have native-like folding. The gel filtration profile (HPLC) of purified LCDh showed two main peaks, with molecular weights of 95 kDa and 39 kDa, compatible with dimeric and monomeric forms, respectively. However, a single elution peak was observed for purified LCDDeltah, with an estimated molecular weight of 29 kDa, as expected for a monomer. Together, these data suggest that LCDh exist in monomer-dimer equilibrium, and that the C-terminus of P domain is necessary for self-association. We propose that such association is due to interaction between vicinal P domains, which may be of functional relevance for H+ -ATPase in native membranes. We discuss a general dimeric model for P-ATPases with interacting P domains, based on published crystallography and cryo-electron microscopy evidence.

  12. The Status of Large-Scale Assessment in the Pacific Region. REL Technical Brief. REL 2008-No. 003

    ERIC Educational Resources Information Center

    Ryan, Jennifer; Keir, Scott

    2008-01-01

    This technical brief describes the large-scale assessment measures and practices used in the jurisdictions served by the Pacific Regional Educational Laboratory. The need for effective large-scale assessment was identified as a major priority for improving student achievement in the Pacific Region jurisdictions: American Samoa, Guam, Hawaii, the…

  13. Mutational analysis of the Acropora millepora PaxD paired domain highlights the importance of the linker region for DNA binding.

    PubMed

    Nordström, Karin; Scholten, Ingo; Nordström, Johanna; Larhammar, Dan; Miller, David

    2003-11-27

    Pax transcription factors are found in animals, from simple sponges to insects and vertebrates. The defining feature of Pax proteins is the DNA-binding paired domain (PD), which consists of two helix-turn-helix subdomains, joined with a linker region. Despite high specificity in vivo, the paired domains of different Pax proteins bind similar consensus DNA sequences in vitro. Using bandshift techniques, we show here that the paired domain of the Acropora millepora PaxD protein, which unambiguously belongs to the Pax3/7 group, does not bind to three defined paired domain-binding sites. Domain swapping experiments and site-directed mutagenesis identified two amino acid residues in the linker region of the paired domain as critical to DNA binding; G70 and S71 are highly conserved in Pax proteins, but differ in PaxD (L70 and N71). The PaxD data thus highlight the importance of the linker region, and particularly G70 and S71, in DNA binding by Pax proteins.

  14. Computational analysis of the extracellular domain of the Ca²⁺-sensing receptor: an alternate model for the Ca²⁺ sensing region.

    PubMed

    Morrill, Gene A; Kostellow, Adele B; Gupta, Raj K

    2015-03-27

    The extracellular Ca(2+) sensing receptor (CaSR) belongs to Class C G-protein-coupled receptors (GPCRs) which include receptors for amino acids, γ-aminobutyric acid and glutamate neurotransmitters. CaSR has been described as having an extended sequence containing a Ca(2+) binding pocket within an extracellular amino (N)-terminal domain, called a Venus Fly Trap (VFT) module. CaSR is thought to consist of three domains: 1) a Ca(2+-)sensory domain, 2) a region containing 7 transmembrane (TM) helices, and 3) a carboxy (C)-terminal tail. We find that SPOCTOPUS (a combination of hidden Markov models and artificial neural networks) predicts that Homo sapiens CaSR contains two additional TM helices ((190)D - G(210); (262)S-E(282)), with the second TM helix containing a pore-lining region ((265)K - I(280)). This predicts that the putative Ca(2+) sensory domain is within an extracellular loop, N-terminal to the highly conserved heptahelical bundle. This loop contains both the cysteine-rich domain ((537)V - C(598)) and a 14 residue "linker" sequence ((599)I - F(612)) thought to support signal transmission to the heptahelical bundle. Thus domain 1 may contain a 189 residue N-terminal extracellular region followed successively by TM-1, a short intracellular loop, TM-2 and a 329 residue extracellular loop; rather than the proposed 620 residue VFT module based on crystallography of the N-terminal region of mGluR1. Since the topologies of the two proteins differ, the published CaSR VFT model is questionable. CaSR also contains multiple caveolin-binding motifs and cholesterol-binding (CRAC/CARC) domains, facilitating localization to plasma membrane lipid rafts. Ion sensing may involve combination of pore-lining regions from CaSR dimers and CaSR-bound caveolins to form ion channels capable of monitoring ionized Ca(2+) levels.

  15. Regional and stress drop effects on aftershock productivity of large megathrust earthquakes

    NASA Astrophysics Data System (ADS)

    Wetzler, Nadav; Brodsky, Emily E.; Lay, Thorne

    2016-12-01

    The total number of aftershocks increases with main shock magnitude, resulting in an overall well-defined relationship. Observed variations from this trend prompt questions regarding influences of regional environment and individual main shock rupture characteristics. We investigate how aftershock productivity varies regionally and with main shock source parameters for large (Mw ≥ 7.0) circum-Pacific megathrust earthquakes within the past 25 years, drawing on extant finite-fault rupture models. Aftershock productivity is found to be higher for subduction zones of the western circum-Pacific than for subduction zones in the eastern circum-Pacific. This appears to be a manifestation of differences in faulting susceptibility between island arcs and continental arcs. Surprisingly, events with relatively large static stress drop tend to produce fewer aftershocks than comparable magnitude events with lower stress drop; however, for events with similar coseismic rupture area, aftershock productivity increases with stress drop and radiated energy, indicating a significant impact of source rupture process on productivity.

  16. A variably spliced region in the type 1 ryanodine receptor may participate in an inter-domain interaction.

    PubMed

    Kimura, Takashi; Pace, Suzy M; Wei, Lan; Beard, Nicole A; Dirksen, Robert T; Dulhunty, Angela F

    2007-01-01

    The aim of the present study was to examine residues that are variably spliced in the juvenile and adult isoforms of the skeletal-muscle RyR1 (type 1 ryanodine receptor). The juvenile ASI(-) splice variant is less active than the adult ASI(+) variant and is overexpressed in patients with DM (myotonic dystrophy) [Kimura, Nakamori, Lueck, Pouliquin, Aoike, Fujimura, Dirksen, Takahashi, Dulhunty and Sakoda (2005) Hum. Mol. Genet. 14, 2189-2200]. In the present study, we explore the ASI region using synthetic peptides corresponding to rabbit RyR1 residues Thr3471-Gly3500 either containing [PASI(+)] or lacking [PASI(-)] the ASI residues. Both peptides increased [3H]ryanodine binding to rabbit RyR1s, increased Ca2+ release from sarcoplasmic reti-culum vesicles and increased single RyR1 channel activity. The peptide PASI(-) was more active in each case than PASI(+). [3H]Ryanodine binding to recombinant ASI(+)RyR1 or ASI(-)-RyR1 was enhanced more by PASI(-) than PASI(+), with the greatest increase seen when PASI(-) was added to ASI(-)RyR1. The activation of the RyR channels is consistent with the hypo-thesis that the peptides interrupt an inhibitory inter-domain inter-action and that PASI(-) is more effective at interrupting this interaction than PASI(+). We therefore suggest that the ASI(-) sequence interacts more tightly than the ASI(+) sequence with its binding partner, so that the ASI(-)RyR1 is more strongly inhibited (less active) than the ASI(+)RyR1. Thus the affinity of the binding partners in this inter-domain interaction may deter-mine the activities of the mature and juvenile isoforms of RyR1 and the stronger inhibition in the juvenile isoform may contribute to the myopathy in DM.

  17. Extraordinary boundary morphologies of large-scale ordered domains of spheres in thin films of a narrowly dispersed diblock copolymer via thermodynamic control

    NASA Astrophysics Data System (ADS)

    Shi, Ling-Ying; Li, Hang; Lei, Wei-Wei; Ni, Wei; Ran, Rong; Pan, Yu; Fan, Xing-He; Shen, Zhihao

    2015-10-01

    Long-range ordering of body centered cubic (BCC) spheres and various extraordinary morphologies at the boundaries of the adjacent orderly oriented domains are observed in thermally annealed thin films of a series of specific narrowly dispersed diblock copolymers, poly(dimethylsiloxane)-b-poly{2,5-bis[(4-butoxyphenyl)oxycarbonylstyrene} (PDMS-b-PBPCS, DB). The series of asymmetrical DB block copolymers (BCPs) with volume fractions of PDMS (fPDMS's) from 10% to 23% self-assemble into thermodynamically stable body centered cubic (BCC) nanostructures in bulk at ambient temperature after thermal annealing. The thin films of these BCPs with a relatively large film thickness on a carbon-film coated substrate are annealed in a vacuum at 180 °C for 3 days and are characterized by transmission electron microscopy (TEM) and X-ray photoelectron spectroscopy (XPS). For all thin films of these BCPs, micrometer-scale domains with a rectangular unit cell similar to the projection of the BCC lattice along the [110] direction to the substrate are observed. And the XPS results indicate that the surface layers of the thin films are composed of both PDMS and PBPCS blocks. For the thin films of the BCPs with fPDMS values of 10% and 13%, the neighboring [110]-oriented BCC domains match well with each other, and the boundaries are defect-free. For the thin film of the BCP with a fPDMS value of 23%, the PDMS spheres in the [110]-oriented BCC domains in the TEM micrograph are overlapped with each other, and interesting morphologies including defect-free interfaces, interfaces with line defects, and domains with defects and local ordering are observed at the boundaries of the neighboring [110]-oriented domains.Long-range ordering of body centered cubic (BCC) spheres and various extraordinary morphologies at the boundaries of the adjacent orderly oriented domains are observed in thermally annealed thin films of a series of specific narrowly dispersed diblock copolymers, poly

  18. Hydrologic effects of large southwestern USA wildfires significantly increase regional water supply: fact or fiction?

    NASA Astrophysics Data System (ADS)

    Wine, M. L.; Cadol, D.

    2016-08-01

    In recent years climate change and historic fire suppression have increased the frequency of large wildfires in the southwestern USA, motivating study of the hydrological consequences of these wildfires at point and watershed scales, typically over short periods of time. These studies have revealed that reduced soil infiltration capacity and reduced transpiration due to tree canopy combustion increase streamflow at the watershed scale. However, the degree to which these local increases in runoff propagate to larger scales—relevant to urban and agricultural water supply—remains largely unknown, particularly in semi-arid mountainous watersheds co-dominated by winter snowmelt and the North American monsoon. To address this question, we selected three New Mexico watersheds—the Jemez (1223 km2), Mogollon (191 km2), and Gila (4807 km2)—that together have been affected by over 100 wildfires since 1982. We then applied climate-driven linear models to test for effects of fire on streamflow metrics after controlling for climatic variability. Here we show that, after controlling for climatic and snowpack variability, significantly more streamflow discharged from the Gila watershed for three to five years following wildfires, consistent with increased regional water yield due to enhanced infiltration-excess overland flow and groundwater recharge at the large watershed scale. In contrast, we observed no such increase in discharge from the Jemez watershed following wildfires. Fire regimes represent a key difference between the contrasting responses of the Jemez and Gila watersheds with the latter experiencing more frequent wildfires, many caused by lightning strikes. While hydrologic dynamics at the scale of large watersheds were previously thought to be climatically dominated, these results suggest that if one fifth or more of a large watershed has been burned in the previous three to five years, significant increases in water yield can be expected.

  19. Physical Properties of Large and Small Granules in Solar Quiet Regions

    NASA Astrophysics Data System (ADS)

    Yu, Daren; Xie, Zongxia; Hu, Qinghua; Yang, Shuhong; Zhang, Jun; Wang, Jingxiu

    2011-12-01

    The normal mode observations of seven quiet regions obtained by the Hinode spacecraft are analyzed to study the physical properties of granules. An artificial intelligence technique is introduced to automatically find the spatial distribution of granules in feature spaces. In this work, we investigate the dependence of granular continuum intensity, mean Doppler velocity, and magnetic fields on granular diameter. We recognized 71,538 granules by an automatic segmentation technique and then extracted five properties: diameter, continuum intensity, Doppler velocity, and longitudinal and transverse magnetic flux density to describe the granules. To automatically explore the intrinsic structures of the granules in the five-dimensional parameter space, the X-means clustering algorithm and one-rule classifier are introduced to define the rules for classifying the granules. It is found that diameter is a dominating parameter in classifying the granules and two families of granules are derived: small granules with diameters smaller than 1farcs44, and large granules with diameters larger than 1farcs44. Based on statistical analysis of the detected granules, the following results are derived: (1) the averages of diameter, continuum intensity, and Doppler velocity in the upward direction of large granules are larger than those of small granules; (2) the averages of absolute longitudinal, transverse, and unsigned flux density of large granules are smaller than those of small granules; (3) for small granules, the average of continuum intensity increases with their diameters, while the averages of Doppler velocity, transverse, absolute longitudinal, and unsigned magnetic flux density decrease with their diameters. However, the mean properties of large granules are stable; (4) the intensity distributions of all granules and small granules do not satisfy Gaussian distribution, while that of large granules almost agrees with normal distribution with a peak at 1.04 I 0.

  20. PHYSICAL PROPERTIES OF LARGE AND SMALL GRANULES IN SOLAR QUIET REGIONS

    SciTech Connect

    Yu Daren; Xie Zongxia; Hu Qinghua; Yang Shuhong; Zhang Jun; Wang Jingxiu E-mail: zjun@ourstar.bao.ac.cn

    2011-12-10

    The normal mode observations of seven quiet regions obtained by the Hinode spacecraft are analyzed to study the physical properties of granules. An artificial intelligence technique is introduced to automatically find the spatial distribution of granules in feature spaces. In this work, we investigate the dependence of granular continuum intensity, mean Doppler velocity, and magnetic fields on granular diameter. We recognized 71,538 granules by an automatic segmentation technique and then extracted five properties: diameter, continuum intensity, Doppler velocity, and longitudinal and transverse magnetic flux density to describe the granules. To automatically explore the intrinsic structures of the granules in the five-dimensional parameter space, the X-means clustering algorithm and one-rule classifier are introduced to define the rules for classifying the granules. It is found that diameter is a dominating parameter in classifying the granules and two families of granules are derived: small granules with diameters smaller than 1.''44, and large granules with diameters larger than 1.''44. Based on statistical analysis of the detected granules, the following results are derived: (1) the averages of diameter, continuum intensity, and Doppler velocity in the upward direction of large granules are larger than those of small granules; (2) the averages of absolute longitudinal, transverse, and unsigned flux density of large granules are smaller than those of small granules; (3) for small granules, the average of continuum intensity increases with their diameters, while the averages of Doppler velocity, transverse, absolute longitudinal, and unsigned magnetic flux density decrease with their diameters. However, the mean properties of large granules are stable; (4) the intensity distributions of all granules and small granules do not satisfy Gaussian distribution, while that of large granules almost agrees with normal distribution with a peak at 1.04 I{sub 0}.

  1. Four large-scale field-aligned current systmes in the dayside high-latitude region

    NASA Technical Reports Server (NTRS)

    Ohtani, S.; Potemra, T. A.; Newell, P.T.; Zanetti, L. J.; Iijima, T.; Watanabe, M.; Blomberg, L. G.; Elphinstone, R. D.; Murphree, J. S.; Yamauchi, M.

    1995-01-01

    A system of four current sheets of large-scale field-aligned currents (FACs) was discovered in the data set of simultaneous Viking and Defense Meteorological Satellire Program-F7 (DMSP-F7) crossing of the dayside high-latitude region. This paper reports four examples of this system that were observed in the prenoon sector. The flow polarities of FACs are upward, downward, upward, and downward, from equatorward to poleward. The lowest-latitude upward current is flowing mostly in the central plasma sheet (CPS) precipitation region, often overlapping with the boundary plasma sheet (BPS) at its poleward edge, andis interpreted as a region 2 current. The pair of downward and upward FACs in the middle of te structure are collocated with structured electron precipitation. The precipitation of high-energy (greater than 1 keV) electrons is more intense in the lower-latitude downward current sheet. The highest-latitude downward flowing current sheet is located in a weak, low-energy particle precipitation region, suggesting that this current is flowing on open field lines. Simulaneous observations in the postnoon local time sector reveal the standard three-sheet structure of FACs, sometimes described as region 2, region 1, and mantle (referred to the midday region O) currents. A high correlation was found between the occurrence of the four FAC sheet structure and negative interplanetary magnetic field (IMF) B(sub Y). We discuss the FAC structurein terms of three types of convection cells: the merging, viscous, andlobe cells. During strongly negative IMF B(sub Y), two convection reversals exist in the prenoon sector; one is inside the viscous cell, and the other is between the viscous cell and the lobe cell. This structure of convection flow is supported by the Viking electric field and auroral UV image data. Based on the convection pattern, the four FAC sheet structure is interpreted as the latitude overlap of midday and morning FAC systems. We suggest that the for

  2. Large methane emission upon spring thaw from natural wetlands in the northern permafrost region

    SciTech Connect

    Song, Changchun; Xu, Xiaofeng; Sun, Xiaoxin; Tian, Hanqin; Sun, Li; Miao, Yuqing; Wang, Xianwei; Guo, Yuedong

    2012-01-01

    The permafrost carbon climate feedback is one of the major mechanisms in controlling the climate ecosystem interactions in northern high latitudes. Of this feedback, methane (CH4) emission from natural wetlands is critically important due to its high warming potential. The freeze thaw transition has been confirmed to play an important role in annual CH4 budget, yet the magnitude of this effect is uncertain. An intensive field campaign was carried out in the Sanjiang Plain, Northeast China to estimate the CH4 emission in the spring freeze thaw transition period. The observation concluded that a large CH4 source was caused by spring thaw; the maximum hourly emission rate was 48.6 g C m 2 h 1, more than three orders of the regularly observed CH4 emission rate in the growing season. In some sporadically observed 'hot spots', the spring thawing effect contributed to a large CH4 source of 31.3 10.1 g C m 2, which is approximately 80% of the previously calculated annual CH4 emission in the same study area. If our results are typical for natural wetlands in the Northern Hemisphere permafrost region, we estimate a global CH4 source strength of 0.5 1.0 Tg C (1 Tg =1012 g) caused by spring thaw in the Northern Hemisphere permafrost region in the year 2011. Combining with available satellite and flask data, a regional extrapolation reaches a temporal pattern of CH4 emission during 2003 2009 which is consistent with recently observed changes in atmospheric CH4 concentration in the high latitudes. This suggests that the CH4 emission upon spring thaw in the high latitudes might be enhanced by the projected climate warming. These findings indicate that the spring thawing effect is an important mechanism in the permafrost carbon climate feedback and needs to be incorporated in Earth system models.

  3. Origin of Strong Lunar Magnetic Anomalies: More Detailed Mapping in Regions Antipodal to Young Large Basins

    NASA Astrophysics Data System (ADS)

    Hood, L. L.; Richmond, N.; Spudis, P.

    2012-12-01

    Previous work has found evidence that the largest concentrations of strong lunar crustal magnetic fields are in regions antipodal to four young large lunar basins: Orientale, Imbrium, Crisium, and Serenitatis (Mitchell et al., Icarus, 2008; and references therein). A preliminary model for the production of lunar basin antipodal magnetic signatures has been developed (Hood and Artemieva, Icarus, 2008; Gattacceca et al., EPSL, 2010). The model involves shock magnetization of crustal materials in the presence of a transient magnetic field amplified by the expanding ionized vapor-melt cloud as it converges in the antipodal region. The model does not exclude a core dynamo; any ambient magnetic field (external solar wind or internal core dynamo) can be amplified in the antipodal zone. In this paper, we report further efforts to map in more detail Lunar Prospector magnetometer data in regions antipodal to young lunar basins. In addition to the four basins identified above, we also consider the polar Schrodinger basin, which is one of the three youngest lunar basins and which has not been previously considered in this context. We apply a direct mapping method (see Hood, Icarus, 2011 for details) to produce more complete maps of lunar magnetic anomalies at low altitudes over the central far side and over the north polar region. We also consider geologic data and spacecraft imagery to identify unusual modified terrain, which may be indicative of shock modification in the same basin antipodal zones. Previous work indicates the existence of such terrain antipodal to Imbrium, Orientale, and Serenitatis, as well as antipodal to the Caloris basin on Mercury. Results first confirm the concentrations of anomalies antipodal to Orientale, Imbrium, Crisium, and Orientale, and the occurrence of modified terrain in three of the four basin antipode zones (see, e.g., Richmond et al., JGR, 2005). In addition, we report here evidence for a large concentration of anomalies that is centered

  4. THE GOULD’S BELT VERY LARGE ARRAY SURVEY. II. THE SERPENS REGION

    SciTech Connect

    Ortiz-León, Gisela N.; Loinard, Laurent; Rodríguez, Luis F.; Pech, Gerardo; Rivera, Juana L.; González-Lópezlira, Rosa A.; Mioduszewski, Amy J.; Dzib, Sergio A.; Torres, Rosa M.; Boden, Andrew F.; Hartmann, Lee; Kounkel, Marina A.; II, Neal J. Evans; Briceño, Cesar; Tobin, John

    2015-05-20

    We present deep (∼17 μJy) radio continuum observations of the Serpens molecular cloud, the Serpens south cluster, and the W40 region obtained using the Very Large Array in its A configuration. We detect a total of 146 sources, 29 of which are young stellar objects (YSOs), 2 of which are BV stars, and 5 more of which are associated with phenomena related to YSOs. Based on their radio variability and spectral index, we propose that about 16 of the remaining 110 unclassified sources are also YSOs. For approximately 65% of the known YSOs detected here as radio sources, the emission is most likely non-thermal and related to stellar coronal activity. As also recently observed in Ophiuchus, our sample of YSOs with X-ray counterparts lies below the fiducial Güdel and Benz relation. Finally, we analyze the proper motions of nine sources in the W40 region. This allows us to better constrain the membership of the radio sources in the region.

  5. Future changes in daily snowfall intensity projected by large ensemble regional climate experiments

    NASA Astrophysics Data System (ADS)

    Kawase, H.

    2015-12-01

    We investigate the future changes in daily snowfall intensity in Japan analyzing the large ensemble regional climate experiments. Dynamical downscalings are conducted by Non-Hydrostatic Regional Climate Model (NHRCM) with 20 km from the global climate projections using Meteorological Research Institute-Atmospheric General Circulation Model (MRI-AGCM). Fifty ensemble experiments are performed in the present climate. For the future climate projections, 90 ensemble experiments are performed based on the six patterns of SST changes in the periods when 4 K rise in global-mean surface air temperature is projected. The accumulated snowfall in winter decreases in Japan except for the northern parts of Japan. Especially, the inland areas in the Sea of Japan side, which is famous for the heaviest snowfall region in the world, shows the remarkable decrease in snowfall in the future climate. The experiments also show increased number of days without snowfall and decreased number of days with weak snowfall due to significant warming in the most parts of Japan. On the other hand, the extreme daily snowfall, which occurs once ten years, would increase at higher elevations in the Sea of Japan side. This means that extreme daily snowfall in the present climate would occur more frequently in the future climate. The warmer atmosphere can contain more water vapor and warmer ocean can supply more water vapor to the low atmosphere. The surface air temperature at higher elevations is still lower than 0 degree Celsius, which could result in the increased extreme daily snowfall.

  6. Amino acids in the COOH-terminal region of the oxytocin receptor third intracellular domain are important for receptor function.

    PubMed

    Zhong, Miao; Parish, Bridgette; Murtazina, Dilyara A; Ku, Chun-Ying; Sanborn, Barbara M

    2007-04-01

    Previously, residue K6.30 in the COOH-terminal region of the third intracellular domain (3iC) of the oxytocin (OT) receptor (OTR) was identified as important for receptor function leading to phospholipase C activation in both OTR and the vasopressin V(2) receptor (V(2)R) chimera V(2)ROTR3iC. Substitution of either A6.28K or V6.30K in wild-type V(2)R did not recapitulate the increase in phosphatidylinositide (PI) turnover observed in V(2)ROTR3iC. Hence, the role of K6.30 may be context-specific. Deletion of two NH(2)-terminal OTR3iC segments in the V(2)ROTR3iC chimera did not diminish vasopressin-stimulated PI turnover, whereas deletion of RVSSVKL (residues 6.19-6.25) reduced receptor expression. Deletion of this sequence in wild-type OTR reduced expression by 50% without affecting affinity for [(3)H]OT. This OTR mutant was unable to activate PI turnover or extracellular signal-regulated kinase 1/2 phosphorylation. The effects of alanine substitution for individual residues in RVSSVKL indicated differential importance for OTR function. The R6.19A substitution lost high-affinity sites for [(3)H]OT and the ability to stimulate PI turnover. Affinity for [(3)H]OT and membrane expression was not affected by any other substitutions. OTR-V6.20A and OTR-K6.24A mutants functioned as well as wild-type OTR, whereas OTR S6.21A, S6.22A, and V6.23A mutants exhibited impaired abilities to activate PI turnover (20-40% of OTR), and the OTR-L6.25A mutant exhibited constitutive activity. In conclusion, specific amino acids in the RVSSVKL segment in the COOH-terminal region of the third intracellular domain of OTR influence the ability of OTR to activate G protein-mediated actions.

  7. Characteristics of very large aspect angle E-region coherent echoes at 933 MHz

    NASA Astrophysics Data System (ADS)

    Jackel, B. J.; Moorcroft, D. R.; Schlegel, K.

    1997-01-01

    The EISCAT UHF radar system was used to study the characteristics of E-region coherent backscatter at very large magnetic aspect angles (5-11°). Data taken using 60 s pulses during elevation scans through horizontally uniform backscatter permitted the use of inversion techniques to determine height profiles of the scattering layer. The layer was always singly peaked, with a mean height of 104 km, and mean thickness (full width at half maximum) of 10 km, both independent of aspect angle. Aspect sensitivities were also estimated, with the Sodankylä-Tromsø link observing 5 dB/degree at aspect angles near 5°, decreasing to 3 dB/degree at 10° aspect angle. Observed coherent phase velocities from all three stations were found to be roughly consistent with LOS measurements of a common E-region phase velocity vector. The E-region phase velocity had the same orientation as the F-region ion drift velocity, but was approximately 50% smaller in magnitude. Spectra were narrow with skewness of about +1 (for negative velocities), increasing slightly with aspect angle. Acknowledgements. The authors are grateful to Prof. D. J. Southwood (Imperial College, London), J. C. Samson (University of Alberta, Edmonton), L. J. Lanzerotti (AT&T Bell Laboratories), A. Wolfe (New York City Technical College) and to Dr. M. Vellante (University of LÁquila) for helpful discussions. They also thank Dr. A. Meloni (Istituto Nazionale di Geofisica, Roma) who made available geomagnetic field observations from LÁquila Geomagnetic Observatory. This research activity at LÁquila is supported by MURST (40% and 60% contracts) and by GIFCO/CNR. Topical Editor K.-H. Glaßmeier thanks C. Waters and S. Fujita for their help in evaluating this paper.-> Correspondence to :P. Francia->

  8. A Survey of Large Molecules of Biological Interest toward Selected High Mass Star Forming Regions

    NASA Technical Reports Server (NTRS)

    Remijan, A.; Shiao, Y.-S.; Friedel, D. N.; Meier, D. S.; Snyder, L. E.

    2004-01-01

    We have surveyed three high mass Galactic star forming regions for interstellar methanol (CH3OH), formic acid (HCOOH), acetic acid (CH3COOH), methyl formate (HCOOCH3), methyl cyanide (CH3CN), and ethyl cyanide (CH3CH2CN) with the BIMA Array. From our observations, we have detected two new sources of interstellar HCOOH toward the hot core regions G19.61-0.23 and W75N. We have also made the first detections of CH3CH2CN and HCOOCH3 toward G19.61-0.23. The relative HCOOH/HCOOCH3 abundance ratio toward G19.61-0.23 is 0.18 which is comparable to the abundance ratios found by Liu and colleagues toward Sgr B2(N-LMH), Orion and W51(approximately 0.10). We have made the first detection of HCOOCH3 toward W75N. The relative HCOOH/HCOOCH3 abundance ratio toward W75N is 0.26 which is more than twice as large as the abundance ratios found by Liu and colleagues. Furthermore, the hot core regions around W75N show a chemical differentiation between the O and N cores similar to what is seen toward the Orion Hot Core and Compact Ridge and W3(OH) and W3(H2O). It is also apparent from our observations that the high mass star forming region G45.47+0.05 does not contain any compact hot molecular core and as a consequence its chemistry may be similar to cold dark clouds. Finally, the formation of CH3COOH appears to favor HMCs with well mixed N and O, despite the fact that CH3COOH does not contain a N atom. If proved to be true, this is an important constraint on CH3COOH formation and possibly other structurally similar biomolecules.

  9. Two-dimensional characterization of 3C-SiC layers using scanning internal photoemission microscopy: Mapping of electrical characteristics and crystal quality in domain boundary regions

    NASA Astrophysics Data System (ADS)

    Shiojima, Kenji; Shingo, Masato; Ichikawa, Naoto; Kato, Masashi

    2017-04-01

    3C-SiC layers epitaxially grown on 4H-SiC substrates have been characterized by forming Ni Schottky contacts by scanning internal photoemission microscopy. The sample surface consists of 3C-SiC domains with a flat top. By focusing and scanning a laser beam over the contacts, the domain pattern was clearly visualized in a photoyield map. By combining photoyield maps measured with red and green lasers, we found that the Schottky barrier height is smaller and larger recombination occurs in the boundary regions than in the flat regions.

  10. Regional analgesia for improvement of long-term functional outcome after elective large joint replacement

    PubMed Central

    Atchabahian, Arthur; Schwartz, Gary; Hall, Charles B; Lajam, Claudette M; Andreae, Michael H

    2015-01-01

    Background Regional analgesia is more effective than conventional analgesia for controlling pain and may facilitate rehabilitation after large joint replacement in the short term. It remains unclear if regional anaesthesia improves functional outcomes after joint replacement beyond three months after surgery. Objectives To assess the effects of regional anaesthesia and analgesia on long-term functional outcomes 3, 6 and 12 months after elective major joint (knee, shoulder and hip) replacement surgery. Search methods We performed an electronic search of several databases (CENTRAL, MEDLINE, EMBASE, CINAHL), and handsearched reference lists and conference abstracts. We updated our search in June 2015. Selection criteria We included randomized controlled trials (RCTs) comparing regional analgesia versus conventional analgesia in patients undergoing total shoulder, hip or knee replacement. We included studies that reported a functional outcome with a follow-up of at least three months after surgery. Data collection and analysis We used standard methodological procedures expected by Cochrane. We contacted study authors for additional information. Main results We included six studies with 350 participants followed for at least three months. All of these studies enrolled participants undergoing total knee replacement. Studies were at least partially blinded. Three studies had a high risk of performance bias and one a high risk of attrition bias, but the risk of bias was otherwise unclear or low. Only one study assessed joint function using a global score. Due to heterogeneity in outcome and reporting, we could only pool three out of six RCTs, with range of motion assessed at three months after surgery used as a surrogate for joint function. All studies had a high risk of detection bias. Using the random-effects model, there was no statistically significant difference between the experimental and control groups (mean difference 3.99 degrees, 95% confidence interval (CI)

  11. Signaling activity of transforming growth factor beta type II receptors lacking specific domains in the cytoplasmic region.

    PubMed Central

    Wieser, R; Attisano, L; Wrana, J L; Massagué, J

    1993-01-01

    The transforming growth factor beta (TGF-beta) type II receptor (T beta R-II) is a transmembrane serine/threonine kinase that contains two inserts in the kinase region and a serine/threonine-rich C-terminal extension. T beta R-II is required for TGF-beta binding to the type I receptor, with which it forms a heteromeric receptor complex, and its kinase activity is required for signaling by this complex. We investigated the role of various cytoplasmic regions in T beta R-II by altering or deleting these regions and determining the signaling activity of the resulting products in cell lines made resistant to TGF-beta by inactivation of the endogenous T beta R-II. TGF-beta binding to receptor I and responsiveness to TGF-beta in these cells can be restored by transfection of wild-type T beta R-II. Using this system, we show that the kinase insert 1 and the C-terminal tail of T beta R-II, in contrast to the corresponding regions in most tyrosine kinase receptors, are not essential to specify ligand-induced responses. Insert 2 is necessary to support the catalytic activity of the receptor kinase, and its deletion yields a receptor that is unable to mediate any of the responses tested. However, substitution of this insert with insert 2 from the activin receptor, ActR-IIB, does not diminish the ability of T beta R-II to elicit these responses. A truncated T beta R-II lacking the cytoplasmic domain still binds TGF-beta, supports ligand binding to receptor I, and forms a complex with this receptor. However, TGF-beta binding to receptor I facilitated by this truncated T beta R-II fails to inhibit cell proliferation, activate extracellular matrix protein production, or activate transcription from a promoter containing TGF-beta-responsive elements. We conclude that the transcriptional and antiproliferative responses to TGF-beta require both components of a heteromeric receptor complex that differs from tyrosine kinase receptors in its mode of signaling. Images PMID:8246946

  12. Large-Scale Structures in the Zone of Avoidance: The Galactic Anticenter Region

    NASA Technical Reports Server (NTRS)

    Lu, Nanyao Y.; Freudling, Wolfram

    1995-01-01

    We have selected a sample of 876 galaxy candidates from the IRAS Point Source Catalog in the region of 2(exp h) < alpha < 10(exp h) and 0 deg < delta < 36 deg, which crosses the Galactic anticenter part of the Zone of Avoidance (ZOA) and includes most of the highly obscured Orion-Taurus complex region. We have identified galaxies among the candidate sources by attempting to detect the 21 cm H I line of those sources which were not known to be galaxies at the beginning of the survey. In this manner, we constructed a galaxy sample which is largely free from Galactic reddening. Of the 272 observed candidates, 89 were detected in the H I line up to a heliocentric velocity of v(sub h) approximately 16,000 km/s. The resulting galaxy sample of 717 galaxies is fairly complete (within about 10%) and uniform (within about 4%) in the part of the survey area 10 deg away from the Galactic plane and for velocities up to at least 9000 km/s. This provides, for the first time, a largely unbiased view on the large-scale structures in much of the survey area. Our main results are the following: (1) Several large voids are identified. In particular, a void between alpha approximately equals 3(sup h) and 4(sup h), up to v(sub h) approximately 6000 km/s, separates the Pisces-Perseus supercluster at alpha < 3(sup h) from structures at alpha > 4(sup h); and a "nearby void" occupies most of our survey area and reaches out to a redshift of nearly 3000 km/s. (2) We found no nearby galaxy concentration that could significantly contribute to the "Local Velocity Anomoly" (LVA), but a general excess of galaxies around v(sub h) approximately 5000 km/s in the survey area. (3) The contrast between the "Great Wall" at v(sub h) approximately 8500 km/s and the void in front of it appears to gradually diffuse out after it enters the Zone of Avoidance from the northern Galactic hemisphere. (4) Our data combined with other galaxy surveys in or near the Galactic anticenter part of the ZOA suggest that the

  13. Large single domain 123 material produced by seeding with single crystal rare earth barium copper oxide single crystals

    DOEpatents

    Todt, Volker; Miller, Dean J.; Shi, Donglu; Sengupta, Suvankar

    1998-01-01

    A method of fabricating bulk YBa.sub.2 Cu.sub.3 O.sub.x where compressed powder oxides and/or carbonates of Y and Ba and Cu present in mole ratios to form YBa.sub.2 Cu.sub.3 O.sub.x are heated in the presence of a Nd.sub.1+x Ba.sub.2-x Cu.sub.3 O.sub.y seed crystal to a temperature sufficient to form a liquid phase in the YBa.sub.2 Cu.sub.3 O.sub.x while maintaining the seed crystal solid. The materials are slowly cooled to provide a YBa.sub.2 Cu.sub.3 O.sub.x material having a predetermined number of domains between 1 and 5. Crack-free single domain materials can be formed using either plate shaped seed crystals or cube shaped seed crystals with a pedestal of preferential orientation material.

  14. SISGR -- Domain Microstructures and Mechanisms for Large, Reversible and Anhysteretic Strain Behaviors in Phase Transforming Ferroelectric Materials

    SciTech Connect

    Wang, Yu U.

    2013-12-06

    This four-year project (including one-year no-cost extension) aimed to advance fundamental understanding of field-induced strain behaviors of phase transforming ferroelectrics. We performed meso-scale phase field modeling and computer simulation to study domain evolutions, mechanisms and engineering techniques, and developed computational techniques for nanodomain diffraction analysis; to further support above originally planned tasks, we also carried out preliminary first-principles density functional theory calculations of point defects and domain walls to complement meso-scale computations as well as performed in-situ high-energy synchrotron X-ray single crystal diffraction experiments to guide theoretical development (both without extra cost to the project thanks to XSEDE supercomputers and DOE user facility Advanced Photon Source).

  15. Systematics of basidiomycetous yeasts: a comparison of large subunit D1/D2 and internal transcribed spacer rDNA regions.

    PubMed

    Scorzetti, Gloria; Fell, J W; Fonseca, A; Statzell-Tallman, Adele

    2002-12-01

    Basidiomycetous yeasts in the Urediniomycetes and Hymenomycetes were examined by sequence analysis in two ribosomal DNA regions: the D1/D2 variable domains at the 5' end of the large subunit rRNA gene (D1/D2) and the internal transcribed spacers (ITS) 1 and 2. Four major lineages were recognized in each class: Microbotryum, Sporidiobolus, Erythrobasidium and Agaricostilbum in the Urediniomycetes; Tremellales, Trichosporonales, Filobasidiales and Cystofilobasidiales in the Hymenomycetes. Bootstrap support for many of the clades within those lineages is weak; however, phylogenetic analysis provides a focal point for in-depth study of biological relationships. Combined sequence analysis of the D1/D2 and ITS regions is recommended for species identification, while species definition requires classical biological information such as life cycles and phenotypic characterization.

  16. Coupled Soil Water and Heat Transport Near the Land Surface in Arid and Semiarid Regions - Multi-Domain Modeling

    NASA Astrophysics Data System (ADS)

    Mohanty, Binayak; Yang, Zhenlei

    2016-04-01

    Understanding and simulating coupled water and heat transfer appropriately in the shallow subsurface is of vital significance for accurate prediction of soil evaporation that would improve the coupling between land surface and atmosphere, which consequently could enhance the reliability of weather as well as climate forecast. The theory of Philip and de Vries (1957), accounting for water vapor diffusion only, was considered physically incomplete and consequently extended and improved by several researchers by explicitly taking water vapor convection, dispersion or air flow into account. It is generally believed that the soil moisture is usually low in the near surface layer under highly transient field conditions, particularly in arid and semiarid regions, and that accurate characterization of water vapor transport is critical when modeling simultaneous water and heat transport in the shallow field soils. The first objective of this study is thus mainly to test existing coupled water and heat transport theories and to develop reasonable and simplified numerical models using field experimental data collected under semi-arid and arid hydro-climatic conditions. In addition, more complex multi-domain models are developed for ubiquitous heterogeneous terrestrial surfaces such as horizontal textural contrasts or structured heterogeneity including macropores (fractures, cracks, root channels, etc.). This would make coupled water and heat transfer models applicable in such non-homogeneous soils more meaningful and enhance the skill of land-atmosphere interaction models at a larger context.

  17. Characterization of Two Monoclonal Antibodies That Recognize Linker Region and Carboxyl Terminal Domain of Coronavirus Nucleocapsid Protein

    PubMed Central

    Zhu, Yunnuan; Shi, Hongyan; Chen, Jianfei; Shi, Da; Feng, Li

    2016-01-01

    The transmissible gastroenteritis virus (TGEV) nucleocapsid (N) protein plays important roles in the replication and translation of viral RNA. The present study provides the first description of two monoclonal antibodies (mAbs) (5E8 and 3D7) directed against the TGEV N protein linker region (LKR) and carboxyl terminal domain (CTD). The mAbs 5E8 and 3D7 reacted with native N protein in western blotting and immunofluorescence assay (IFA). Two linear epitopes, 189SVEQAVLAALKKLG202 and 246VTRFYGARSSSA257, located in the LKR and CTD of TGEV N protein, respectively, were identified after truncating the protein and applying a peptide scanning technique. Using mAb 5E8, we observed that the N protein was expressed in the cytoplasm during TGEV replication and that the protein could be immunoprecipitated from TGEV-infected PK-15 cells. The mAb 5E8 can be applied for different approaches to diagnosis of TGEV infection. In addition, the antibodies represent useful tools for investigating the antigenic properties of the N protein. PMID:27689694

  18. Simultaneous Solar Maximum Mission (SMM) and very large array observations of solar active regions

    NASA Technical Reports Server (NTRS)

    Lang, K. R.

    1986-01-01

    The research deals mainly with Very Large Array and Solar Maximum Mission observations of the ubiquitous coronal loops that dominate the structure of the low corona. As illustrated, the observations of thermal cyclotron lines at microwave wavelengths provide a powerful new method of accurately specifying the coronal magnetic field strength. Processes are delineated that trigger solar eruptions from coronal loops, including preburst heating and the magnetic interaction of coronal loops. Evidence for coherent burst mechanisms is provided for both the Sun and nearby stars, while other observations suggest the presence of currents that may amplify the coronal magnetic field to unexpectedly high levels. The existence is reported of a new class of compact, variable moving sources in regions of apparently weak photospheric field.

  19. Lipid domains in intact fiber-cell plasma membranes isolated from cortical and nuclear regions of human eye lenses of donors from different age groups.

    PubMed

    Raguz, Marija; Mainali, Laxman; O'Brien, William J; Subczynski, Witold K

    2015-03-01

    The results reported here clearly document changes in the properties and the organization of fiber-cell membrane lipids that occur with age, based on electron paramagnetic resonance (EPR) analysis of lens membranes of clear lenses from donors of age groups from 0 to 20, 21 to 40, and 61 to 80 years. The physical properties, including profiles of the alkyl chain order, fluidity, hydrophobicity, and oxygen transport parameter, were investigated using EPR spin-labeling methods, which also provide an opportunity to discriminate coexisting lipid domains and to evaluate the relative amounts of lipids in these domains. Fiber-cell membranes were found to contain three distinct lipid environments: bulk lipid domain, which appears minimally affected by membrane proteins, and two domains that appear due to the presence of membrane proteins, namely boundary and trapped lipid domains. In nuclear membranes the amount of boundary and trapped phospholipids as well as the amount of cholesterol in trapped lipid domains increased with the donors' age and was greater than that in cortical membranes. The difference between the amounts of lipids in domains uniquely formed due to the presence of membrane proteins in nuclear and cortical membranes increased with the donors' age. It was also shown that cholesterol was to a large degree excluded from trapped lipid domains in cortical membranes. It is evident that the rigidity of nuclear membranes was greater than that of cortical membranes for all age groups. The amount of lipids in domains of low oxygen permeability, mainly in trapped lipid domains, were greater in nuclear than cortical membranes and increased with the age of donors. These results indicate that the nuclear fiber cell plasma membranes were less permeable to oxygen than cortical membranes and become less permeable to oxygen with age. In clear lenses, age-related changes in the lens lipid and protein composition and organization appear to occur in ways that increase fiber

  20. Lipid Domains in Intact Fiber-Cell Plasma Membranes Isolated from Cortical and Nuclear Regions of Human Eye Lenses of Donors from Different Age Groups

    PubMed Central

    Raguz, Marija; Mainali, Laxman; O’Brien, William J.; Subczynski, Witold K.

    2015-01-01

    The results reported here clearly document changes in the properties and the organization of fiber-cell membrane lipids that occur with age, based on electron paramagnetic resonance (EPR) analysis of lens membranes of clear lenses from donors of age groups from 0 to 20, 21 to 40, and 61 to 80 years. The physical properties, including profiles of the alkyl chain order, fluidity, hydrophobicity, and oxygen transport parameter, were investigated using EPR spin-labeling methods, which also provide an opportunity to discriminate coexisting lipid domains and to evaluate the relative amounts of lipids in these domains. Fiber-cell membranes were found to contain three distinct lipid environments: bulk lipid domain, which appears minimally affected by membrane proteins, and two domains that appear due to the presence of membrane proteins, namely boundary and trapped lipid domains. In nuclear membranes the amount of boundary and trapped phospholipids as well as the amount of cholesterol in trapped lipid domains increased with the donors’ age and was greater than that in cortical membranes. The difference between the amounts of lipids in domains uniquely formed due to the presence of membrane proteins in nuclear and cortical membranes increased with the donors’ age. It was also shown that cholesterol was to a large degree excluded from trapped lipid domains in cortical membranes. It is evident that the rigidity of nuclear membranes was greater than that of cortical membranes for all age groups. The amount of lipids in domains of low oxygen permeability, mainly in trapped lipid domains, were greater in nuclear than cortical membranes and increased with the age of donors. These results indicate that the nuclear fiber cell plasma membranes were less permeable to oxygen than cortical membranes and become less permeable to oxygen with age. In clear lenses, age-related changes in the lens lipid and protein composition and organization appear to occur in ways that increase fiber

  1. Involvement of the heterodimeric interface region of the nucleotide binding domain-2 (NBD2) in the CFTR quaternary structure and membrane stability.

    PubMed

    Micoud, Julien; Chauvet, Sylvain; Scheckenbach, Klaus Ernst Ludwig; Alfaidy, Nadia; Chanson, Marc; Benharouga, Mohamed

    2015-10-01

    The cystic fibrosis transmembrane conductance regulator (CFTR) is the only member of the ATP-binding cassette (ABC) superfamily that functions as a chloride channel. The predicted structure of CFTR protein contains two membrane-spanning domains (MSDs), each followed by a nucleotide binding domain (NBD1 and NBD2). The opening of the Cl- channel is directly linked to ATP-driven tight dimerization of CFTR's NBD1 and NBD2 domains. The presence of a heterodimeric interfaces (HI) region in NBD1 and NBD2 generated a head to tail orientation necessary for channel activity. This process was also suggested to promote important conformational changes in the associated transmembrane domains of CFTR, which may impact the CFTR plasma membrane stability. To better understand the role of the individual HI region in this process, we generated recombinant CFTR protein with suppressed HI-NBD1 and HI-NBD2. Our results indicate that HI-NBD2 deletion leads to the loss of the dimerization profile of CFTR that affect its plasma membrane stability. We conclude that, in addition to its role in Cl- transport, HI-NBD2 domain confers membrane stability of CFTR by consolidating its quaternary structure through interactions with HI-NBD1 region.

  2. Autoantibodies from patients with primary biliary cirrhosis recognize a region within the nucleoplasmic domain of inner nuclear membrane protein LBR.

    PubMed

    Lin, F; Noyer, C M; Ye, Q; Courvalin, J C; Worman, H J

    1996-01-01

    Autoantibodies from rare patients with primary biliary cirrhosis (PBC) recognize LBR, or lamin B receptor, an integral membrane protein of the inner nuclear membrane. Human LBR has a nucleoplasmic, amino-terminal domain of 208 amino acids followed by a carboxyl-terminal domain with eight putative transmembrane segments. Autoantibodies against LBR from four patients with PBC recognized the nucleoplasmic, amino-terminal domain but not the carboxyl-terminal domain. Immunoblotting of smaller fusion proteins demonstrated that these autoantibodies recognized a conformational epitope(s) contained within the stretch of amino acids from 1 to 60. These results, combined with those of previous studies, show that autoepitopes of nuclear membrane proteins are located within their nucleocytoplasmic domains and that autoantibodies from patients with PBC predominantly react with one domain of a protein antigen. This work also provides further characterization of anti-LBR antibodies that have found utility as reagents in cell biology research.

  3. 2.0 A crystal structure of a four-domain segment of human fibronectin encompassing the RGD loop and synergy region.

    PubMed

    Leahy, D J; Aukhil, I; Erickson, H P

    1996-01-12

    We have determined the 2.0 A crystal structure of a fragment of human fibronectin encompassing the seventh through the RGD-containing tenth type III repeats (FN7-10). The structure reveals an extended rod-like molecule with a long axis of approximately 140 A and highly variable relationships between adjacent domains. An unusually small rotation between domains 9 and 10 creates a distinctive binding site, in which the RGD loop from domain 10 and the "synergy" region from domain 9 are on the same face of FN7-10 and thus easily accessible to a single integrin molecule. The cell-binding RGD loop is well-ordered in this structure and extends approximately 10 A away from the FN7-10 core.

  4. Extraordinary boundary morphologies of large-scale ordered domains of spheres in thin films of a narrowly dispersed diblock copolymer via thermodynamic control.

    PubMed

    Shi, Ling-Ying; Li, Hang; Lei, Wei-Wei; Ni, Wei; Ran, Rong; Pan, Yu; Fan, Xing-He; Shen, Zhihao

    2015-11-14

    Long-range ordering of body centered cubic (BCC) spheres and various extraordinary morphologies at the boundaries of the adjacent orderly oriented domains are observed in thermally annealed thin films of a series of specific narrowly dispersed diblock copolymers, poly(dimethylsiloxane)-b-poly{2,5-bis[(4-butoxyphenyl)oxycarbonylstyrene} (PDMS-b-PBPCS, DB). The series of asymmetrical DB block copolymers (BCPs) with volume fractions of PDMS (f(PDMS)'s) from 10% to 23% self-assemble into thermodynamically stable body centered cubic (BCC) nanostructures in bulk at ambient temperature after thermal annealing. The thin films of these BCPs with a relatively large film thickness on a carbon-film coated substrate are annealed in a vacuum at 180 °C for 3 days and are characterized by transmission electron microscopy (TEM) and X-ray photoelectron spectroscopy (XPS). For all thin films of these BCPs, micrometer-scale domains with a rectangular unit cell similar to the projection of the BCC lattice along the [110] direction to the substrate are observed. And the XPS results indicate that the surface layers of the thin films are composed of both PDMS and PBPCS blocks. For the thin films of the BCPs with f(PDMS) values of 10% and 13%, the neighboring [110]-oriented BCC domains match well with each other, and the boundaries are defect-free. For the thin film of the BCP with a f(PDMS) value of 23%, the PDMS spheres in the [110]-oriented BCC domains in the TEM micrograph are overlapped with each other, and interesting morphologies including defect-free interfaces, interfaces with line defects, and domains with defects and local ordering are observed at the boundaries of the neighboring [110]-oriented domains.

  5. Study of the Seismic Cycle of large Earthquakes in central Peru: Lima Region

    NASA Astrophysics Data System (ADS)

    Norabuena, E. O.; Quiroz, W.; Dixon, T. H.

    2009-12-01

    Since historical times, the Peruvian subduction zone has been source of large and destructive earthquakes. The more damaging one occurred on May 30 1970 offshore Peru’s northern city of Chimbote with a death toll of 70,000 people and several hundred US million dollars in property damage. More recently, three contiguous plate interface segments in southern Peru completed their seismic cycle generating the 1996 Nazca (Mw 7.1), the 2001 Atico-Arequipa (Mw 8.4) and the 2007 Pisco (Mw 7.9) earthquakes. GPS measurements obtained between 1994-2001 by IGP-CIW an University of Miami-RSMAS on the central Andes of Peru and Bolivia were used to estimate their coseismic displacements and late stage of interseismic strain accumulation. However, we focus our interest in central Peru-Lima region, which with its about 9’000,000 inhabitants is located over a locked plate interface that has not broken with magnitude Mw 8 earthquakes since May 1940, September 1966 and October 1974. We use a network of 11 GPS monuments to estimate the interseismic velocity field, infer spatial variations of interplate coupling and its relation with the background seismicity of the region.

  6. Forcing the statistical regionalization method WETTREG with large scale models of different resolution: A sensitivity study

    NASA Astrophysics Data System (ADS)

    Spekat, A.; Baumgart, S.; Kreienkamp, F.; Enke, W.

    2010-09-01

    The statistical regionalization method WETTREG is making use of the assumption that future climate changes are linked to changes in large scale atmospheric patterns. The frequency distributions of those patterns and their time-dependency are identified in the output fields of dynamical climate models and applied to force WETTREG. Thus, the magnitude and the time evolution of high-resolution climate signals for time horizons far into the 21st century can be computed. The model results employed to force WETTREG include the GCMS ECHAM5C, HadCM3C and CNRM. Additionally results from the dynamical regional models CLM, DMI, HadRM, RACMO and REMO, nested into one or more of these global models, are used in their pattern-generating capacity to force WETTREG. The study yield insight concerning the forcing-dependent sensitivity of WETTREG as well as the bandwidth of climate change signals. Recent results for the German State of Hesse will be presented in an intercomparison study.

  7. The D1-D2 region of the large subunit ribosomal DNA as barcode for ciliates.

    PubMed

    Stoeck, T; Przybos, E; Dunthorn, M

    2014-05-01

    Ciliates are a major evolutionary lineage within the alveolates, which are distributed in nearly all habitats on our planet and are an essential component for ecosystem function, processes and stability. Accurate identification of these unicellular eukaryotes through, for example, microscopy or mating type reactions is reserved to few specialists. To satisfy the demand for a DNA barcode for ciliates, which meets the standard criteria for DNA barcodes defined by the Consortium for the Barcode of Life (CBOL), we here evaluated the D1-D2 region of the ribosomal DNA large subunit (LSU-rDNA). Primer universality for the phylum Ciliophora was tested in silico with available database sequences as well as in the laboratory with 73 ciliate species, which represented nine of 12 ciliate classes. Primers tested in this study were successful for all tested classes. To test the ability of the D1-D2 region to resolve conspecific and congeneric sequence divergence, 63 Paramecium strains were sampled from 24 mating species. The average conspecific D1-D2 variation was 0.18%, whereas congeneric sequence divergence averaged 4.83%. In pairwise genetic distance analyses, we identified a D1-D2 sequence divergence of <0.6% as an ideal threshold to discriminate Paramecium species. Using this definition, only 3.8% of all conspecific and 3.9% of all congeneric sequence comparisons had the potential of false assignments. Neighbour-joining analyses inferred monophyly for all taxa but for two Paramecium octaurelia strains. Here, we present a protocol for easy DNA amplification of single cells and voucher deposition. In conclusion, the presented data pinpoint the D1-D2 region as an excellent candidate for an official CBOL barcode for ciliated protists.

  8. VERY LARGE ARRAY OH ZEEMAN OBSERVATIONS OF THE STAR-FORMING REGION S88B

    SciTech Connect

    Sarma, A. P.; Eftimova, M.; Brogan, C. L.; Bourke, T. L.; Troland, T. H.

    2013-04-10

    We present observations of the Zeeman effect in OH thermal absorption main lines at 1665 and 1667 MHz taken with the Very Large Array toward the star-forming region S88B. The OH absorption profiles toward this source are complicated, and contain several blended components toward a number of positions. Almost all of the OH absorbing gas is located in the eastern parts of S88B, toward the compact continuum source S88B-2 and the eastern parts of the extended continuum source S88B-1. The ratio of 1665/1667 MHz OH line intensities indicates the gas is likely highly clumped, in agreement with other molecular emission line observations in the literature. S88-B appears to present a similar geometry to the well-known star-forming region M17, in that there is an edge-on eastward progression from ionized to molecular gas. The detected magnetic fields appear to mirror this eastward transition; we detected line-of-sight magnetic fields ranging from 90 to 400 {mu}G, with the lowest values of the field to the southwest of the S88B-1 continuum peak, and the highest values to its northeast. We used the detected fields to assess the importance of the magnetic field in S88B by a number of methods; we calculated the ratio of thermal to magnetic pressures, we calculated the critical field necessary to completely support the cloud against self-gravity and compared it to the observed field, and we calculated the ratio of mass to magnetic flux in terms of the critical value of this parameter. All these methods indicated that the magnetic field in S88B is dynamically significant, and should provide an important source of support against gravity. Moreover, the magnetic energy density is in approximate equipartition with the turbulent energy density, again pointing to the importance of the magnetic field in this region.

  9. THE GOULD’S BELT VERY LARGE ARRAY SURVEY. V. THE PERSEUS REGION

    SciTech Connect

    Pech, Gerardo; Loinard, Laurent; Rodríguez, Luis F.; Ortiz-León, Gisela N.; Rivera, Juana L.; Zapata, Luis A.; Dzib, Sergio A.; Mioduszewski, Amy J.; Torres, Rosa M.; Boden, Andrew F.; Hartman, Lee; Kounkel, Marina A.; Evans II, Neal J.; Briceño, Cesar; Tobin, John

    2016-02-20

    We present multiepoch, large-scale (∼2000 arcmin{sup 2}), fairly deep (∼16 μJy), high-resolution (∼1″) radio observations of the Perseus star-forming complex obtained with the Karl G. Jansky Very Large Array at frequencies of 4.5 and 7.5 GHz. These observations were mainly focused on the clouds NGC 1333 and IC 348, although we also observed several fields in other parts of the Perseus complex. We detect a total of 206 sources, 42 of which are associated with young stellar objects (YSOs). The radio properties of about 60% of the YSOs are compatible with a nonthermal radio emission origin. Based on our sample, we find a fairly clear relation between the prevalence of nonthermal radio emission and evolutionary status of the YSOs. By comparing our results with previously reported X-ray observations, we show that YSOs in Perseus follow a Güdel–Benz relation with κ = 0.03, consistent with other regions of star formation. We argue that most of the sources detected in our observations but not associated with known YSOs are extragalactic, but provide a list of 20 unidentified radio sources whose radio properties are consistent with being YSO candidates. Finally, we also detect five sources with extended emission features that can clearly be associated with radio galaxies.

  10. In Silico Prediction of Scaffold/Matrix Attachment Regions in Large Genomic Sequences

    PubMed Central

    Frisch, Matthias; Frech, Kornelie; Klingenhoff, Andreas; Cartharius, Kerstin; Liebich, Ines; Werner, Thomas

    2002-01-01

    Scaffold/matrix attachment regions (S/MARs) are essential regulatory DNA elements of eukaryotic cells. They are major determinants of locus control of gene expression and can shield gene expression from position effects. Experimental detection of S/MARs requires substantial effort and is not suitable for large-scale screening of genomic sequences. In silico prediction of S/MARs can provide a crucial first selection step to reduce the number of candidates. We used experimentally defined S/MAR sequences as the training set and generated a library of new S/MAR-associated, AT-rich patterns described as weight matrices. A new tool called SMARTest was developed that identifies potential S/MARs by performing a density analysis based on the S/MAR matrix library (http://www.genomatix.de/cgi-bin/smartest_pd/smartest.pl). S/MAR predictions were evaluated by using six genomic sequences from animal and plant for which S/MARs and non-S/MARs were experimentally mapped. SMARTest reached a sensitivity of 38% and a specificity of 68%. In contrast to previous algorithms, the SMARTest approach does not depend on the sequence context and is suitable to analyze long genomic sequences up to the size of whole chromosomes. To demonstrate the feasibility of large-scale S/MAR prediction, we analyzed the recently published chromosome 22 sequence and found 1198 S/MAR candidates. PMID:11827955

  11. NEAR-INFRARED POLARIZATION SOURCE CATALOG OF THE NORTHEASTERN REGIONS OF THE LARGE MAGELLANIC CLOUD

    SciTech Connect

    Kim, Jaeyeong; Pak, Soojong; Jeong, Woong-Seob; Park, Won-Kee; Tamura, Motohide E-mail: jeongws@kasi.re.kr

    2016-01-15

    We present a near-infrared band-merged photometric and polarimetric catalog for the 39′ × 69′ fields in the northeastern part of the Large Magellanic Cloud (LMC), which were observed using SIRPOL, an imaging polarimeter of the InfraRed Survey Facility. This catalog lists 1858 sources brighter than 14 mag in the H band with a polarization signal-to-noise ratio greater than three in the J, H, or K{sub s} bands. Based on the relationship between the extinction and the polarization degree, we argue that the polarization mostly arises from dichroic extinctions caused by local interstellar dust in the LMC. This catalog allows us to map polarization structures to examine the global geometry of the local magnetic field, and to show a statistical analysis of the polarization of each field to understand its polarization properties. In the selected fields with coherent polarization position angles, we estimate magnetic field strengths in the range of 3−25 μG using the Chandrasekhar–Fermi method. This implies the presence of large-scale magnetic fields on a scale of around 100 parsecs. When comparing mid- and far-infrared dust emission maps, we confirmed that the polarization patterns are well aligned with molecular clouds around the star-forming regions.

  12. Occurrences of large-magnitude earthquakes in the Kachchh region, Gujarat, western India: Tectonic implications

    NASA Astrophysics Data System (ADS)

    Khan, Prosanta Kumar; Mohanty, Sarada Prasad; Sinha, Sushmita; Singh, Dhananjay

    2016-06-01

    Moderate-to-large damaging earthquakes in the peninsular part of the Indian plate do not support the long-standing belief of the seismic stability of this region. The historical record shows that about 15 damaging earthquakes with magnitudes from 5.5 to ~ 8.0 occurred in the Indian peninsula. Most of these events were associated with the old rift systems. Our analysis of the 2001 Bhuj earthquake and its 12-year aftershock sequence indicates a seismic zone bound by two linear trends (NNW and NNE) that intersect an E-W-trending graben. The Bouguer gravity values near the epicentre of the Bhuj earthquake are relatively low (~ 2 mgal). The gravity anomaly maps, the distribution of earthquake epicentres, and the crustal strain-rate patterns indicate that the 2001 Bhuj earthquake occurred along a fault within strain-hardened mid-crustal rocks. The collision resistance between the Indian plate and the Eurasian plate along the Himalayas and anticlockwise rotation of the Indian plate provide the far-field stresses that concentrate within a fault-bounded block close to the western margin of the Indian plate and is periodically released during earthquakes, such as the 2001 MW 7.7 Bhuj earthquake. We propose that the moderate-to-large magnitude earthquakes in the deeper crust in this area occur along faults associated with old rift systems that are reactivated in a strain-hardened environment.

  13. Surface Forcing of the Infrared Cooling Profile over the Tibetan Plateau. Part II: Cooling-Rate Variation over Large-Scale Plateau Domain during Summer Monsoon Transition.

    NASA Astrophysics Data System (ADS)

    Shi, Lei; Smith, Eric A.

    1992-05-01

    During the summer east Asian monsoon transition period in 1979, a meteorological field experiment entitled the Qinghai-Xizang Plateau Meteorological Experiment (QXPMEX-79) was conducted over the entire Tibetan Plateau. Data collected on and around the plateau during this period, in conjunction with a medium spectral-resolution infrared radiative transfer model, are used to gain an understanding of how elevation and surface biophysical factors, which are highly variable over the large-scale plateau domain, regulate the spatial distribution of clear-sky infrared cooling during the transition phase of the summer monsoon.The spatial distribution of longwave cooling over the plateau is significantly influenced by variations in biophysical composition, topography, and elevation, the surface thermal diurnal cycle, and various climatological factors. An important factor is soil moisture. Bulk clear-sky longwave cooling rates are larger in the southeast sector of the plateau than in the north. This is because rainfall is greatest in the southeast, whereas the north is highly desertified and relative longwave radiative heating by the surface is greatest. Another important phenomenon is that the locale of a large-scale east-west-aligned spatial gradient in radiative cooling propagates northward with time. During the premonsoon period (May-June), the location of the strong spatial gradient is found in the southeastern margin of the plateau. Due to changes in surface and atmospheric conditions after the summer monsoon commences, the high gradient sector is shifted to the central Qinghai region. Furthermore, an overall decrease in longwave cooling takes place in the lower atmosphere immediately prior to the arrival of the active monsoon.The magnitude of longwave cooling is significantly affected by skin-temperature boundary conditions at plateau altitudes. If skin-temperature discontinuities across the surface-atmosphere interface are neglected, bulk cooling rates will be in

  14. Molecular Basis of Interactions Between SH3 Domain-Containing Proteins and the Proline-Rich Region of the Ubiquitin Ligase Itch.

    PubMed

    Desrochers, Guillaume; Cappadocia, Laurent; Lussier-Price, Mathieu; Ton, Anh-Tien; Ayoubi, Riham; Serohijos, Adrian; Omichinski, James G; Angers, Annie

    2017-02-24

    The ligase Itch plays major roles in signalling pathways by inducing ubiquitylation-dependent degradation of several substrates. Substrate recognition and binding is critical for the regulation of this reaction. Like closely related ligases, Itch can interact with proteins containing a PPxY motif via its WW domains. In addition to these WW domains, Itch possesses a proline-rich region (PRR) that has been shown to interact with several Src Homology 3 (SH3) domain-containing proteins. We have previously established that despite the apparent surface uniformity and conserved fold of SH3 domains, they display different binding mechanisms and affinities for their interaction with the PRR of Itch. Here, we attempt to determine the molecular bases underlying the wide range of binding properties of the Itch PRR. Using pull-down assays combined with mass spectrometry analysis, we show that the Itch PRR preferentially forms complexes with Endophilins, Amphyphisins and Pacsins, but can also target a variety of other SH3 domain-containing proteins. In addition, we map the binding sites of these proteins using a combination of PRR sub-sequences and mutants. We find that different SH3 domains target distinct proline-rich sequences overlapping significantly. We also structurally analyze these protein complexes using crystallography and molecular modelling. These structures depict the position of Itch PRR engaged in a 1:2 protein complex with β-PIX and a 1:1 complex with the other SH3 domain-containing proteins. Taken together, these results reveal the binding preferences of the Itch PRR towards its most common SH3 domain-containing partners, and demonstrate that the PRR region is sufficient for binding.

  15. Packaging of hepatitis delta virus RNA via the RNA-binding domain of hepatitis delta antigens: different roles for the small and large delta antigens.

    PubMed Central

    Wang, H W; Chen, P J; Lee, C Z; Wu, H L; Chen, D S

    1994-01-01

    Hepatitis delta virus (HDV) is composed of four specific components. The first component is envelope protein which contains hepatitis B surface antigens. The second and third components are nucleocapsid proteins, referred to as small and large hepatitis delta antigens (HDAgs). The final component is a single-stranded circular RNA molecule known as the viral genome. In order to study the mechanism of HDV RNA packaging, a four-plasmid cotransfection system in which each viral component was provided by a separate plasmid was employed. Virus-like particles released from Huh-7 cells receiving such a cotransfection were found to contain HDV RNA along with three proteins. Therefore, the four-plasmid cotransfection system could lead to successful HDV RNA packaging in vitro. The system was then used to show that the large HDAg alone was able to achieve a low level of HDV RNA packaging. Analysis of a variety of large HDAg mutants revealed that the RNA-binding domain was essential for viral RNA packaging. By increasing the incorporation of small HDAg into virus-like particles, we found a three- to fourfold enhancement of HDV RNA packaging. This effect was probably through a direct binding of HDV RNA, independent from that of large HDAg, with the small HDAg. The subsequent RNA-protein complex was packaged into particles. The results provided insight into the roles and functional domains of small and large HDAgs in HDV RNA packaging. Images PMID:8083975

  16. Characterization of lipid domains in erythrocyte membranes.

    PubMed

    Rodgers, W; Glaser, M

    1991-02-15

    Fluorescence digital imaging microscopy was used to study the lateral distribution of the lipid components in erythrocyte membranes. Intact erythrocytes labeled with phospholipids containing a fluorophore attached to one fatty acid chain showed an uneven distribution of the phospholipids in the membrane thereby demonstrating the presence of membrane domains. The enrichment of the lipotropic compound chlor-promazine in domains in intact erythrocytes also suggested that the domains are lipid-enriched regions. Similar membrane domains were present in erythrocyte ghosts. The phospholipid enrichment was increased in the domains by inducing membrane protein aggregation. Double-labeling experiments were done to determine the relative distributions of different phospholipids in the membrane. Vesicles made from extracted lipids did not show the presence of domains consistent with the conclusion that membrane proteins were responsible for creating the domains. Overall, it was found that large domains exist in the red blood cell membrane with unequal enrichment of the different phospholipid species.

  17. Crystal Structure of the C-terminal Region of Streptococcus mutans Antigen I/II and Characterization of Salivary Agglutinin Adherence Domains

    SciTech Connect

    Larson, Matthew R.; Rajashankar, Kanagalaghatta R.; Crowley, Paula J.; Kelly, Charles; Mitchell, Tim J.; Brady, L. Jeannine; Deivanayagam, Champion

    2012-05-29

    The Streptococcus mutans antigen I/II (AgI/II) is a cell surface-localized protein that adheres to salivary components and extracellular matrix molecules. Here we report the 2.5 {angstrom} resolution crystal structure of the complete C-terminal region of AgI/II. The C-terminal region is comprised of three major domains: C{sub 1}, C{sub 2}, and C{sub 3}. Each domain adopts a DE-variant IgG fold, with two {beta}-sheets whose A and F strands are linked through an intramolecular isopeptide bond. The adherence of the C-terminal AgI/II fragments to the putative tooth surface receptor salivary agglutinin (SAG), as monitored by surface plasmon resonance, indicated that the minimal region of binding was contained within the first and second DE-variant-IgG domains (C{sub 1} and C{sub 2}) of the C terminus. The minimal C-terminal region that could inhibit S. mutans adherence to SAG was also confirmed to be within the C{sub 1} and C{sub 2} domains. Competition experiments demonstrated that the C- and N-terminal regions of AgI/II adhere to distinct sites on SAG. A cleft formed at the intersection between these C{sub 1} and C{sub 2} domains bound glucose molecules from the cryo-protectant solution, revealing a putative binding site for its highly glycosylated receptor SAG. Finally, electron microscopy images confirmed the elongated structure of AgI/II and enabled building a composite tertiary model that encompasses its two distinct binding regions.

  18. Activation of G Protein-Coupled Receptor Kinase 1 Involves Interactions between Its N-Terminal Region and Its Kinase Domain

    SciTech Connect

    Huang, Chih-chin; Orban, Tivadar; Jastrzebska, Beata; Palczewski, Krzysztof; Tesmer, John J.G.

    2012-03-16

    G protein-coupled receptor kinases (GRKs) phosphorylate activated G protein-coupled receptors (GPCRs) to initiate receptor desensitization. In addition to the canonical phosphoacceptor site of the kinase domain, activated receptors bind to a distinct docking site that confers higher affinity and activates GRKs allosterically. Recent mutagenesis and structural studies support a model in which receptor docking activates a GRK by stabilizing the interaction of its 20-amino acid N-terminal region with the kinase domain. This interaction in turn stabilizes a closed, more active conformation of the enzyme. To investigate the importance of this interaction for the process of GRK activation, we first validated the functionality of the N-terminal region in rhodopsin kinase (GRK1) by site-directed mutagenesis and then introduced a disulfide bond to cross-link the N-terminal region of GRK1 with its specific binding site on the kinase domain. Characterization of the kinetic and biophysical properties of the cross-linked protein showed that disulfide bond formation greatly enhances the catalytic efficiency of the peptide phosphorylation, but receptor-dependent phosphorylation, Meta II stabilization, and inhibition of transducin activation were unaffected. These data indicate that the interaction of the N-terminal region with the kinase domain is important for GRK activation but does not dictate the affinity of GRKs for activated receptors.

  19. Potential effects of large linear pipeline construction on soil and vegetation in ecologically fragile regions.

    PubMed

    Xiao, Jun; Wang, Ya-Feng; Shi, Peng; Yang, Lei; Chen, Li-Ding

    2014-11-01

    Long-distance pipeline construction results in marked human disturbance of the regional ecosystem and brings into question the safety of pipeline construction with respect to the environment. Thus, the direct environmental impact and proper handling of such large projects have received much attention. The potential environmental effects, however, have not been fully addressed, particularly for large linear pipeline projects, and the threshold of such effects is unclear. In this study, two typical eco-fragile areas in western China, where large linear construction projects have been conducted, were chosen as the case study areas. Soil quality indices (SQI) and vegetation indices (VI), representing the most important potential effects, were used to analyze the scope of the effect of large pipeline construction on the surrounding environment. These two indices in different buffer zones along the pipeline were compared against the background values. The analysis resulted in three main findings. First, pipeline construction continues to influence the nearby eco-environment even after a 4-year recovery period. During this period, the effect on vegetation due to pipeline construction reaches 300 m beyond the working area, and is much larger in distance than the effect on soil, which is mainly confined to within 30 m either side of the pipeline, indicating that vegetation is more sensitive than soil to this type of human disturbance. However, the effect may not reach beyond 500 m from the pipeline. Second, the scope of the effect in terms of distance on vegetation may also be determined by the frequency of disturbance and the intensity of the pipeline construction. The greater the number of pipelines in an area, the higher the construction intensity and the more frequent the disturbance. Frequent disturbance may expand the effect on vegetation on both sides of the pipeline, but not on soil quality. Third, the construction may eliminate the stable, resident plant

  20. Large single domain 123 material produced by seeding with single crystal rare earth barium copper oxide single crystals

    DOEpatents

    Todt, V.; Miller, D.J.; Shi, D.; Sengupta, S.

    1998-07-07

    A method of fabricating bulk YBa{sub 2}Cu{sub 3}O{sub x} where compressed powder oxides and/or carbonates of Y and Ba and Cu present in mole ratios to form YBa{sub 2}Cu{sub 3}O{sub x} are heated in the presence of a Nd{sub 1+x}Ba{sub 2{minus}x}Cu{sub 3}O{sub y} seed crystal to a temperature sufficient to form a liquid phase in the YBa{sub 2}Cu{sub 3}O{sub x} while maintaining the seed crystal solid. The materials are slowly cooled to provide a YBa{sub 2}Cu{sub 3}O{sub x} material having a predetermined number of domains between 1 and 5. Crack-free single domain materials can be formed using either plate shaped seed crystals or cube shaped seed crystals with a pedestal of preferential orientation material. 7 figs.

  1. Peculiarities of mantle lithosphere beneath the large kimberlite pipes in different regions for Siberian craton

    NASA Astrophysics Data System (ADS)

    Ashchepkov, Igor; Logvinova, Alla; Ntaflos, Theodoros; Vladykin, Nikolai; Spetsius, Zdislav; Kostrovitsky, Sergey; Stegnitsky, Yuri; Prokopyev, Sergey

    2016-04-01

    Comparison of the structure of the mantle columns and mineralogy of the large kimberlite pipes in Yakutia from the different regions, kimberlite fields and mantle terranes in Yakutia allowed several assumptions. 1. The large kimberlite pipes possibly trace the ancient magma feeders occurred in the time of the continent growth. Commonly kimberlites and large pipes are tracing the deep faults and lineaments tracing the ancient sutures, rift zones, trans -lithospheric faults and other permeable structures, which may be parallel to the ancient continental margins. Large pipes locate at the periodic distance like volcanoes in arc settings tracing the "volcanic fronts". 2. Large pipes commonly contain the higher amounts of the sub-calcic garnets representing the dunitic associations (Stachel et al., 2008). In ophiolites dunites veins are representing the channels for the melt transfer (Kelemen et al., 2002). It is likely that ancient large magmatic arc system could have also deep seated roots represented by the (sub calcic) garnet - bearing dunitic systems. 3. Many large pipes including Udachnaya (Pokhilenko et al., 1999) and Mir (Roden et al., 2006) contain in mantle roots high amount of various pyroxenites. The most ancient pyroxenites are supplementary to the dunitic associations. But mostly they represent the materials from the re-melted eclogites and partial and hybrid melts (plume and subduction -related). They are concentrating in the traps in the lithosphere base, in the middle part of mantle section and in the basaltic trap 2.0-3.0 GPa. Pyroxenites in the lithosphere base in some cases are vary abundant but mostly they are protokimberlitic cumulates from of the latest stages of plume activity. Products of the melts crystallization from the earlier stages represent easy melting material at the lithosphere base could be the traps for the later plume melts. 5. Large pipes as a rule reveal contrast layering which is favorite for the capturing of the material from

  2. Synthesizing High-Frequency (1-25 HZ) Regional Phases at Large Distances (>1000 KM) Using Generalized Screen Propagators (GSP)

    DTIC Science & Technology

    2004-09-01

    seismology and earthquake seismology . The generalized screen propagator (GSP) is based on the one-way wave equation and the one-return approximation. The...High-Frequency (1-25 HZ) Regional Phases at Large Distances O (>1000 KM) Using Generalized Screen Propagators (GSP) SApproved for public release...DTRA 01-97-1-0004 Synthesizing High-Freguency (1-25 HZ) Regional Phases at Large Distances (1 > 1000 KM) Using Generalized Screen Propagators (GSP) 5b

  3. A Limited-Memory BFGS Algorithm Based on a Trust-Region Quadratic Model for Large-Scale Nonlinear Equations

    PubMed Central

    Li, Yong; Yuan, Gonglin; Wei, Zengxin

    2015-01-01

    In this paper, a trust-region algorithm is proposed for large-scale nonlinear equations, where the limited-memory BFGS (L-M-BFGS) update matrix is used in the trust-region subproblem to improve the effectiveness of the algorithm for large-scale problems. The global convergence of the presented method is established under suitable conditions. The numerical results of the test problems show that the method is competitive with the norm method. PMID:25950725

  4. Large stresses in the lithosphere in regions of strong Neotectonic uplift

    NASA Astrophysics Data System (ADS)

    Artyushkov, Eugene; Chekhovich, Peter

    2014-05-01

    Several mechanisms have been proposed to explain the drift of lithospheric plates: subduction pull, basal drag, ridge push and some other ones. Among them only ridge push can be quantified reliably enough as (1.5-2)×1012 Nm (Artyushkov, JGR, 1973, 78, 7675-7708; Geodynamics, Elsevier, 1983, 312 p.). Due to uncertainty of another mechanisms, estimates of the forces acting along the lithospheric layer still differ by one order of magnitude. Ridge push is only a special case of the forces produced in the gravity field by density heterogeneities in the crust and subcrustal lithosphere. These forces generally increase with the potential energy stored in the relief. This allows us to estimate what force is necessary to shorten the crust with its surface reaching a certain altitude. As follows from a large volume of data, strong shortening of the crust in folds belts usually produced a ragged topography. However, after its erosion in a few million years the crustal surface remained near to sea level and mountain building occurred after the termination of crustal shortening. Thus the present Alps were formed during the past 5 Ma after 99% of shortening in them were already over. In the Urals high mountains were formed in the late Early Permian while intense preceding shortening of the crust terminated in the middle of the Carboniferous. Using this constraint the mean force acting in the lithosphere in areas which are located near to sea level can be estimated as 3×1012 Nm. The forces produced by the above mechanism increase with the altitude of the topography. In such regions as the Tibetan Plateau, Pamir and Southern Tien-Shan they can be as large as (5-7)×1012 N/m. Depending on the boundary conditions, the forces can be compressive or tensile. Most of the present mountain ranges and high plateaus were formed due to a rapid crustal uplift during the past several million years. The main cause was infiltration of mantle fluids into the lithosphere (Artyushkov, Russian

  5. Is CD36 gene polymorphism in region encoding lipid-binding domain associated with early onset CAD?

    PubMed

    Rać, Monika; Safranow, Krzysztof; Kurzawski, Grzegorz; Krzystolik, Andrzej; Chlubek, Dariusz

    2013-11-01

    CD36 is a fatty acid translocase in striated muscle cells and cardiomyocytes. Some study suggested that alterations in CD36 gene may be associated with coronary artery disease (CAD) risk. The aim of the current study was to compare the frequency of CD36 variants in region encoding lipid-binding domain in Caucasian patients with early-onset CAD, no-CAD adult controls and neonates. The study group comprised 100 patients with early onset CAD. The genetic control groups were 306 infants and 40 no-CAD adults aged over 70years. Exons 4, 5 and 6 including fragments of flanking introns were studied using the denaturing high-performance liquid chromatography technique and direct sequencing. Changes detected in analyzed fragment of CD36: IVS3-6 T/C (rs3173798), IVS4-10 G/A (rs3211892), C311T (Thr104Ile, not described so far) in exon 5, G550A (Asp184Asn, rs138897347), C572T (Pro191Leu, rs143150225), G573A (Pro191Pro, rs5956) and A591T (Thr197Thr, rs141680676) in exon 6. No significant differences in the CD36 genotype, allele and haplotype frequencies were found between the three groups. Only borderline differences (p=0.066) were found between early onset CAD patients and newborns in the frequencies of 591T allele (2.00% vs 0.50%) and CGCGCGT haplotype (2.00% vs 0.50%) with both IVS3-6C and 591T variant alleles. In conclusion, CD36 variants: rs3173798, rs3211892, rs138897347, rs5956, rs143150225 rs141680676 and C311T do not seem to be involved in the risk of early-onset CAD in Caucasian population.

  6. Large Scale Evapotranspiration Estimates: An Important Component in Regional Water Balances to Assess Water Availability

    NASA Astrophysics Data System (ADS)

    Garatuza-Payan, J.; Yepez, E. A.; Watts, C.; Rodriguez, J. C.; Valdez-Torres, L. C.; Robles-Morua, A.

    2013-05-01

    Water security, can be defined as the reliable supply in quantity and quality of water to help sustain future populations and maintaining ecosystem health and productivity. Water security is rapidly declining in many parts of the world due to population growth, drought, climate change, salinity, pollution, land use change, over-allocation and over-utilization, among other issues. Governmental offices (such as the Comision Nacional del Agua in Mexico, CONAGUA) require and conduct studies to estimate reliable water balances at regional or continental scales in order to provide reasonable assessments of the amount of water that can be provided (from surface or ground water sources) to supply all the human needs while maintaining natural vegetation, on an operational basis and, more important, under disturbances, such as droughts. Large scale estimates of evapotranspiration (ET), a critical component of the water cycle, are needed for a better comprehension of the hydrological cycle at large scales, which, in most water balances is left as the residual. For operational purposes, such water balance estimates can not rely on ET measurements since they do not exist, should be simple and require the least ground information possible, information that is often scarce or does not exist at all. Given this limitation, the use of remotely sensed data to estimate ET could supplement the lack of ground information, particularly in remote regions In this study, a simple method, based on the Makkink equation is used to estimate ET for large areas at high spatial resolutions (1 km). The Makkink model used here is forced using three remotely sensed datasets. First, the model uses solar radiation estimates obtained from the Geostationary Operational Environmental Satellite (GOES); Second, the model uses an Enhanced Vegetation Index (EVI) obtained from the Moderate-resolution Imaging Spectroradiometer (MODIS) normalized to get an estimate for vegetation amount and land use which was

  7. Representation of spatial and temporal variability in large-domain hydrological models: case study for a mesoscale pre-Alpine basin

    NASA Astrophysics Data System (ADS)

    Melsen, Lieke; Teuling, Adriaan; Torfs, Paul; Zappa, Massimiliano; Mizukami, Naoki; Clark, Martyn; Uijlenhoet, Remko

    2016-06-01

    The transfer of parameter sets over different temporal and spatial resolutions is common practice in many large-domain hydrological modelling studies. The degree to which parameters are transferable across temporal and spatial resolutions is an indicator of how well spatial and temporal variability is represented in the models. A large degree of transferability may well indicate a poor representation of such variability in the employed models. To investigate parameter transferability over resolution in time and space we have set up a study in which the Variable Infiltration Capacity (VIC) model for the Thur basin in Switzerland was run with four different spatial resolutions (1 km × 1 km, 5 km × 5 km, 10 km × 10 km, lumped) and evaluated for three relevant temporal resolutions (hour, day, month), both applied with uniform and distributed forcing. The model was run 3150 times using the Hierarchical Latin Hypercube Sample and the best 1 % of the runs was selected as behavioural. The overlap in behavioural sets for different spatial and temporal resolutions was used as an indicator of parameter transferability. A key result from this study is that the overlap in parameter sets for different spatial resolutions was much larger than for different temporal resolutions, also when the forcing was applied in a distributed fashion. This result suggests that it is easier to transfer parameters across different spatial resolutions than across different temporal resolutions. However, the result also indicates a substantial underestimation in the spatial variability represented in the hydrological simulations, suggesting that the high spatial transferability may occur because the current generation of large-domain models has an inadequate representation of spatial variability and hydrologic connectivity. The results presented in this paper provide a strong motivation to further investigate and substantially improve the representation of spatial and temporal variability in

  8. Large-scale regionalization of water table depth in peatlands optimized for greenhouse gas emission upscaling

    NASA Astrophysics Data System (ADS)

    Bechtold, M.; Tiemeyer, B.; Laggner, A.; Leppelt, T.; Frahm, E.; Belting, S.

    2014-04-01

    Fluxes of the three main greenhouse gases (GHG) CO2, CH4 and N2O from peat and other organic soils are strongly controlled by water table depth. Information about the spatial distribution of water level is thus a crucial input parameter when upscaling GHG emissions to large scales. Here, we investigate the potential of statistical modeling for the regionalization of water levels in organic soils when data covers only a small fraction of the peatlands of the final map. Our study area is Germany. Phreatic water level data from 53 peatlands in Germany were compiled in a new dataset comprising 1094 dip wells and 7155 years of data. For each dip well, numerous possible predictor variables were determined using nationally available data sources, which included information about land cover, ditch network, protected areas, topography, peatland characteristics and climatic boundary conditions. We applied boosted regression trees to identify dependencies between predictor variables and dip well specific long-term annual mean water level (WL) as well as a transformed form of it (WLt). The latter was obtained by assuming a hypothetical GHG transfer function and is linearly related to GHG emissions. Our results demonstrate that model calibration on WLt is superior. It increases the explained variance of the water level in the sensitive range for GHG emissions and avoids model bias in subsequent GHG upscaling. The final model explained 45% of WLt variance and was built on nine predictor variables that are based on information about land cover, peatland characteristics, drainage network, topography and climatic boundary conditions. Their individual effects on WLt and the observed parameter interactions provide insights into natural and anthropogenic boundary conditions that control water levels in organic soils. Our study also demonstrates that a large fraction of the observed WLt variance cannot be explained by nationally available predictor variables and that predictors with

  9. Daily air temperature interpolated at high spatial resolution over a large mountainous region

    USGS Publications Warehouse

    Dodson, R.; Marks, D.

    1997-01-01

    Two methods are investigated for interpolating daily minimum and maximum air temperatures (Tmin and Tmax) at a 1 km spatial resolution over a large mountainous region (830 000 km2) in the U.S. Pacific Northwest. The methods were selected because of their ability to (1) account for the effect of elevation on temperature and (2) efficiently handle large volumes of data. The first method, the neutral stability algorithm (NSA), used the hydrostatic and potential temperature equations to convert measured temperatures and elevations to sea-level potential temperatures. The potential temperatures were spatially interpolated using an inverse-squared-distance algorithm and then mapped to the elevation surface of a digital elevation model (DEM). The second method, linear lapse rate adjustment (LLRA), involved the same basic procedure as the NSA, but used a constant linear lapse rate instead of the potential temperature equation. Cross-validation analyses were performed using the NSA and LLRA methods to interpolate Tmin and Tmax each day for the 1990 water year, and the methods were evaluated based on mean annual interpolation error (IE). The NSA method showed considerable bias for sites associated with vertical extrapolation. A correction based on climate station/grid cell elevation differences was developed and found to successfully remove the bias. The LLRA method was tested using 3 lapse rates, none of which produced a serious extrapolation bias. The bias-adjusted NSA and the 3 LLRA methods produced almost identical levels of accuracy (mean absolute errors between 1.2 and 1.3??C), and produced very similar temperature surfaces based on image difference statistics. In terms of accuracy, speed, and ease of implementation, LLRA was chosen as the best of the methods tested.

  10. Large Amplitude IMF Fluctuations in Corotating Interaction Regions: Ulysses at Midlatitudes

    NASA Technical Reports Server (NTRS)

    Tsurutani, Bruce T.; Ho, Christian M.; Arballo, John K.; Goldstein, Bruce E.; Balogh, Andre

    1995-01-01

    Corotating Interaction Regions (CIRs), formed by high-speed corotating streams interacting with slow speed streams, have been examined from -20 deg to -36 deg heliolatitudes. The high-speed streams emanate from a polar coronal hole that Ulysses eventually becomes fully embedded in as it travels towards the south pole. We find that the trailing portion of the CIR, from the interface surface (IF) to the reverse shock (RS), contains both large amplitude transverse fluctuations and magnitude fluctuations. Similar fluctuations have been previously noted to exist within CIRs detected in the ecliptic plane, but their existence has not been explained. The normalized magnetic field component variances within this portion of the CIR and in the trailing high-speed stream are approximately the same, indicating that the fluctuations in the CIR are compressed Alfven waves. Mirror mode structures with lower intensities are also observed in the trailing portion of the CIR, presumably generated from a local instability driven by free energy associated with compression of the high-speed solar wind plasma. The mixture of these two modes (compressed Alfven waves and mirror modes) plus other modes generated by three wave processes (wave-shock interactions) lead to a lower Alfvenicity within the trailing portion of the CfR than in the high-speed stream proper. The results presented in this paper suggest a mechanism for generation of large amplitude B(sub z) fluctuations within CIRS. Such phenomena have been noted to be responsible for the generation of moderate geomagnetic storms during the declining phase of the solar cycle.

  11. Biomechanical testing and material characterization for the rat large intestine: regional dependence of material parameters.

    PubMed

    Sokolis, Dimitrios P; Orfanidis, Ioannis K; Peroulis, Michalis

    2011-12-01

    The function of the large bowel is to absorb water from the remaining indigestible food matter and subsequently pass useless waste material from the body, but there has been only a small amount of data in the literature on its biomechanical characteristics that would facilitate our understanding of its transport function. Our study aims to fill this gap by affording comprehensive inflation/extension data of intestinal segments from distinct areas, spanning a physiologically relevant deformation range (100-130% axial stretches and 0-15 mmHg lumen pressures). These data were characterized by the Fung-type exponential model in the thick-walled setting, showing reasonable agreement, i.e. root-mean-square error ~30%. Based on optimized material parameters, i.e. a(1)regions both circumferentially (a(1) = 5.304 ± 0.952 versus proximal colon: 4.043 ± 0.643, distal colon: 1.505 ± 0.222 and rectum: 2.339 ± 0.285) and axially (a(2) = 16.639 ± 0.792 versus proximal colon: 16.580 ± 1.042, distal colon: 13.209 ± 1.185 and rectum: 12.553 ± 0.689). Our biomechanical testing and material characterization results for the large intestine of healthy young animals are expected to aid in comprehending the adaptation/remodeling that occurs with ageing, pathological conditions and surgical procedures, as well as for the development of suitable biomaterials for replacement.

  12. A refined regional modeling approach for the Corn Belt - experiences and recommendations for large-scale integrated modeling

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Nonpoint source pollution from agriculture is the main source of nitrogen and phosphorus in the stream systems of the Corn Belt region in the Midwestern U.S. This region is comprised of two large river basins, the intensely row-cropped Upper Mississippi River Basin (UMRB) and Ohio-Tennessee River B...

  13. OT2_jpineda_2: Large-scale dynamics and the formation of clouds and stars in the 30 Doradus region of the Large Magellanic Cloud

    NASA Astrophysics Data System (ADS)

    Pineda, J.

    2011-09-01

    Understanding the processes governing the formation of clouds and stars in merging systems is key for the study of how galaxies evolved in the early Universe. The 30 Doradus region in the low-metallicity Large Magellanic Cloud (LMC) is the nearest example of this process, resulting from the interaction between the LMC and the halo of the Milky Way. This makes 30 Doradus the prime laboratory to study these large-scale dynamical processes under conditions that are similar to those at early cosmological times. We propose to use Herschel to obtain a large-scale uniform sampling of this region in [CII] 158um, [NII] 122um and 205um, and [OI] 63um and 146um lines with PACS, and at selected positions in [CII] with HIFI. With this data we will derive the large-scale distribution of the density and pressure of the low-metallicity gas revealing the characteristic signatures of shocked gas. This will then be used to determine the relationships among the diffuse, "dark H2", and dense molecular gas in the 30 Doradus region. We will also derive the electron density distribution of the gas and from this the contribution from ionized gas to the observed [CII] emission. The proposed observations will allow us to study the effect of large-scale gas compression in the multiphase, low-metallicity interstellar medium of 30 Doradus. This information will be valuable for the interpretation of future observations of [CII] in high-redshift galaxies made with ALMA

  14. A new efficient 3D Discontinuous Galerkin Time Domain (DGTD) method for large and multiscale electromagnetic simulations

    NASA Astrophysics Data System (ADS)

    Tobón, Luis E.; Ren, Qiang; Liu, Qing Huo

    2015-02-01

    A new Discontinuous Galerkin Time Domain (DGTD) method for solving the 3D time dependent Maxwell's equations via the electric field intensity E and magnetic flux density B fields is proposed for the first time. It uses curl-conforming and divergence-conforming basis functions for E and B, respectively, with the same order of interpolation. In this way, higher accuracy is achieved at lower memory consumption than the conventional approach based on the field variables E and H. The centered flux and Riemann solver are both used to treat interfaces with non-conforming meshes, and both explicit Runge-Kutta method and implicit Crank-Nicholson method are implemented for time integration. Numerical examples for realistic cases will be presented to verify that the proposed method is a non-spurious and efficient DGTD scheme.

  15. Distributed Kalman filtering compared to Fourier domain preconditioned conjugate gradient for laser guide star tomography on extremely large telescopes.

    PubMed

    Gilles, Luc; Massioni, Paolo; Kulcsár, Caroline; Raynaud, Henri-François; Ellerbroek, Brent

    2013-05-01

    This paper discusses the performance and cost of two computationally efficient Fourier-based tomographic wavefront reconstruction algorithms for wide-field laser guide star (LGS) adaptive optics (AO). The first algorithm is the iterative Fourier domain preconditioned conjugate gradient (FDPCG) algorithm developed by Yang et al. [Appl. Opt.45, 5281 (2006)], combined with pseudo-open-loop control (POLC). FDPCG's computational cost is proportional to N log(N), where N denotes the dimensionality of the tomography problem. The second algorithm is the distributed Kalman filter (DKF) developed by Massioni et al. [J. Opt. Soc. Am. A28, 2298 (2011)], which is a noniterative spatially invariant controller. When implemented in the Fourier domain, DKF's cost is also proportional to N log(N). Both algorithms are capable of estimating spatial frequency components of the residual phase beyond the wavefront sensor (WFS) cutoff frequency thanks to regularization, thereby reducing WFS spatial aliasing at the expense of more computations. We present performance and cost analyses for the LGS multiconjugate AO system under design for the Thirty Meter Telescope, as well as DKF's sensitivity to uncertainties in wind profile prior information. We found that, provided the wind profile is known to better than 10% wind speed accuracy and 20 deg wind direction accuracy, DKF, despite its spatial invariance assumptions, delivers a significantly reduced wavefront error compared to the static FDPCG minimum variance estimator combined with POLC. Due to its nonsequential nature and high degree of parallelism, DKF is particularly well suited for real-time implementation on inexpensive off-the-shelf graphics processing units.

  16. Improved confinement region without large magnetohydrodynamic activity in TPE-RX reversed-field pinch plasma

    NASA Astrophysics Data System (ADS)

    Yambe, Kiyoyuki; Hirano, Yoichi; Sakakita, Hajime; Koguchi, Haruhisa

    2014-11-01

    We found that spontaneous improved confinement was brought about depending on the operating region in the Toroidal Pinch Experiment-Reversed eXperiment (TPE-RX) reversed-field pinch plasma [Y. Yagi et al., Fusion Eng. Des. 45, 421 (1999)]. Gradual decay of the toroidal magnetic field at plasma surface Btw reversal makes it possible to realize a prolonged discharge, and the poloidal beta value and energy confinement time increase in the latter half of the discharge, where reversal and pinch parameters become shallow and low, respectively. In the latter half of the discharge, the plasma current and volume-averaged toroidal magnetic field increase again, the electron density slowly decays, the electron temperature and soft X-ray radiation intensity increase, and the magnetic fluctuations are markedly reduced. In this period of improved confinement, the value of (-Btw)/Bpw, where Bpw is the poloidal magnetic field at the plasma surface, stays almost constant, which indicates that the dynamo action occurs without large magnetohydrodynamic activities.

  17. Improved confinement region without large magnetohydrodynamic activity in TPE-RX reversed-field pinch plasma

    SciTech Connect

    Yambe, Kiyoyuki; Hirano, Yoichi; Sakakita, Hajime; Koguchi, Haruhisa

    2014-11-15

    We found that spontaneous improved confinement was brought about depending on the operating region in the Toroidal Pinch Experiment-Reversed eXperiment (TPE-RX) reversed-field pinch plasma [Y. Yagi et al., Fusion Eng. Des. 45, 421 (1999)]. Gradual decay of the toroidal magnetic field at plasma surface B{sub tw} reversal makes it possible to realize a prolonged discharge, and the poloidal beta value and energy confinement time increase in the latter half of the discharge, where reversal and pinch parameters become shallow and low, respectively. In the latter half of the discharge, the plasma current and volume-averaged toroidal magnetic field 〈B{sub t}〉 increase again, the electron density slowly decays, the electron temperature and soft X-ray radiation intensity increase, and the magnetic fluctuations are markedly reduced. In this period of improved confinement, the value of (〈B{sub t}〉-B{sub tw})/B{sub pw}, where B{sub pw} is the poloidal magnetic field at the plasma surface, stays almost constant, which indicates that the dynamo action occurs without large magnetohydrodynamic activities.

  18. Seismicity trends and potential for large earthquakes in the Alaska-Aleutian region

    USGS Publications Warehouse

    Bufe, C.G.; Nishenko, S.P.; Varnes, D.J.

    1994-01-01

    The high likelihood of a gap-filling thrust earthquake in the Alaska subduction zone within this decade is indicated by two independent methods: analysis of historic earthquake recurrence data and time-to-failure analysis applied to recent decades of instrumental data. Recent (May 1993) earthquake activity in the Shumagin Islands gap is consistent with previous projections of increases in seismic release, indicating that this segment, along with the Alaska Peninsula segment, is approaching failure. Based on this pattern of accelerating seismic release, we project the occurrence of one or more M???7.3 earthquakes in the Shumagin-Alaska Peninsula region during 1994-1996. Different segments of the Alaska-Aleutian seismic zone behave differently in the decade or two preceding great earthquakes, some showing acceleration of seismic release (type "A" zones), while others show deceleration (type "D" zones). The largest Alaska-Aleutian earthquakes-in 1957, 1964, and 1965-originated in zones that exhibit type D behavior. Type A zones currently showing accelerating release are the Shumagin, Alaska Peninsula, Delarof, and Kommandorski segments. Time-to-failure analysis suggests that the large earthquakes could occur in these latter zones within the next few years. ?? 1994 Birkha??user Verlag.

  19. Large-Scale, Short-Lived Subduction of the Western Gneiss Region Ultrahigh-Pressure Terrane

    NASA Astrophysics Data System (ADS)

    Kylander-Clark, A. R.; Hacker, B. R.; Corfu, F.

    2006-12-01

    The Western Gneiss Region (WGR) of Norway includes one of Earth's giant ultrahigh-pressure (UHP) terranes. Understanding the subduction and exhumation of this >60,000 km2 area is relevant to a range of processes, including collisional orogenesis, reworking of the continents, and the global geochemical cycle. Important aspects that remain unanswered include the spatial and temporal style of subduction. Was the crust subducted as smaller slivers one at a time, or as one larger unit, all at the same time? The WGR exhibits consistent ages of ~415-400 Ma, 100+ km along strike, but no ages have been identified at an equivalent distance across strike. To address this issue we have determined the age of one of the easternmost eclogites identified in the WGR, a retrogressed eclogite from Lesja. Seven fractions of this sample were analyzed; six of them yield identical U/Pb ages, however, they are slightly discordant. The seventh fraction is anomalously young and interpreted to have suffered lead loss. A weighted-mean 206Pb/238U age of 408.0 ± 1.7 Ma is obtained from the six older fractions; an age that is within the range of U/Pb, Sm/Nd, and Lu/Hf ages from the western portion of the WGR. The similarity in ages from 100+ km north to south and 100+ km east to west indicate that large portions of the continental crust were subducted in a short-lived event, if not en masse.

  20. Characteristics of active regions associated to large solar energetic proton events

    NASA Astrophysics Data System (ADS)

    Bronarska, K.; Michalek, G.

    2017-01-01

    The relationship between properties of active regions (ARs) and solar energetic particles (SEP events, protons with energy ⩾10 MeV) is examined. For this purpose we study 84 SEP events recorded during the SOHO era (1996-2014). We compare properties of these SEP events with associated ARs, flares and CMEs. The ARs are characterized by McIntosh classification. Statistical analysis demonstrates that SEP events are more likely to be associated to the ARs having complex magnetic structures and the most energetic SEPs are ejected only from the associated ARs having a large and asymmetric penumbra. This tendency is used to estimate intensities of potential SEP events. For this purpose we express a probability of occurrence of an SEP event from a given AR which is correlated with fluxes of associated SEPs. We find that SEP events associated with ARs from eastern longitudes have to be more complex to produce SEP events at Earth. On the other hand, SEP particles originating from mid-longitudes (30 ° < longitude < 70 °) on the west side of solar disk are associated to the least complex ARs. These results could be useful for forecasting of space weather.

  1. YOUNG STELLAR OBJECTS IN THE LARGE MAGELLANIC CLOUD STAR-FORMING REGION N206

    SciTech Connect

    Romita, Krista Alexandra; Meixner, M.; Sewilo, M.; Shiao, B.; Carlson, Lynn Redding; Whitney, B.; Babler, B.; Meade, M.; Indebetouw, R.; Hora, J. L. E-mail: carlson@stsci.ed E-mail: brian@sal.wisc.ed E-mail: jhora@cfa.harvard.ed

    2010-09-20

    We present analysis of the energetic star-forming region Henize 206 (N206) located near the southern edge of the Large Magellanic Cloud (LMC) based on photometric data from the Spitzer Surveying the Agents of Galaxy Evolution (SAGE-LMC; IRAC 3.6, 4.5, 5.8, 8.0 {mu}m and MIPS 24 {mu}m), Infrared Survey Facility near-infrared survey (J, H, K{sub s}), and the Magellanic Clouds Photometric Survey (MCPS UBVI) covering a wavelength range of 0.36-24 {mu}m. Young stellar object (YSO) candidates are identified based upon their location in infrared color-magnitude space and classified by the shapes of their spectral energy distributions in comparison with a pre-computed grid of YSO models. We identify 116 YSO candidates: 102 are well characterized by the YSO models, predominately Stage I, and 14 may be multiple sources or young sources with transition disks. Careful examination of the individual sources and their surrounding environment allows us to identify a factor of {approx}14.5 more YSO candidates than have already been identified. The total mass of these well-fit YSO candidates is {approx}520 M{sub sun}. We calculate a current star formation rate of 0.27 x 10{sup -1} M{sub sun} yr{sup -1} kpc{sup -2}. The distribution of YSO candidates appears to follow shells of neutral material in the interstellar medium.

  2. Gravity Wave Disturbances in the F-Region Ionosphere Above Large Earthquakes

    NASA Astrophysics Data System (ADS)

    Bruff, Margie

    The direction of propagation, duration and wavelength of gravity waves in the ionosphere above large earthquakes were studied using data from the Super Dual Auroral Radar Network. Ground scatter data were plotted versus range and time to identify gravity waves as alternating focused and de-focused regions of radar power in wave-like patterns. The wave patterns before and after earthquakes were analyzed to determine the directions of propagation and wavelengths. Conditions were considered 48 hours before and after each identified disturbances to exclude waves from geomagnetic activity. Gravity waves were found travelling away from the epicenter before all six earthquakes for which data were available and after four of the six earthquakes. Gravity waves travelled in at least two directions away from the epicenter in all cases, and even stronger patterns were found for two earthquakes. Waves appeared, on average, 4 days before, persisting 2-3 hours, and 1-2 days after earthquakes, persisting 4-6 hours. Most wavelengths were between 200-300 km. We show a possible correlation between magnitude and depth of earthquakes and gravity wave patterns, but study of more earthquakes is required. This study provides a better understanding of the causes of ionospheric gravity wave disturbances and has potential applications for predicting earthquakes.

  3. Stability of stationary solution for the compressible viscous magnetohydrodynamic equations with large potential force in bounded domain

    NASA Astrophysics Data System (ADS)

    Li, Yeping; Yang, Xiongfeng

    2017-02-01

    In this paper, we consider the 3-D compressible viscous magnetohydrodynamic (MHD) equations with some large potential force in bounded rigid vessel. We firstly construct the non-constant stationary solutions of the compressible viscous MHD equations under suitable constitutive assumptions. Next, a critical energy identity is established to achieve a universal stability criterion of the stationary solution. In this case, the stationary solution is exponential stable for any large external potential force. Finally, we show the well-posedness of the initial boundary value problem for the compressible viscous MHD equations with the large potential force, provided that the prescribed initial data is close to the stationary solution. It implies that the set satisfying the stability criterion is not empty.

  4. Unique Piezoelectric Properties of the Monoclinic Phase in Pb(Zr,Ti)O_{3} Ceramics: Large Lattice Strain and Negligible Domain Switching.

    PubMed

    Fan, Longlong; Chen, Jun; Ren, Yang; Pan, Zhao; Zhang, Linxing; Xing, Xianran

    2016-01-15

    The origin of the excellent piezoelectric properties at the morphotropic phase boundary is generally attributed to the existence of a monoclinic phase in various piezoelectric systems. However, there exist no experimental studies that reveal the role of the monoclinic phase in the piezoelectric behavior in phase-pure ceramics. In this work, a single monoclinic phase has been identified in Pb(Zr,Ti)O_{3} ceramics at room temperature by in situ high-energy synchrotron x-ray diffraction, and its response to electric field has been characterized for the first time. Unique piezoelectric properties of the monoclinic phase in terms of large intrinsic lattice strain and negligible domain switching have been observed. The extensional strain constant d_{33} and the transverse strain constant d_{31} are calculated to be 520 and -200  pm/V, respectively. These large piezoelectric coefficients are mainly due to the large intrinsic lattice strain, with very little extrinsic contribution from domain switching. The unique properties of the monoclinic phase provide new insights into the mechanisms responsible for the piezoelectric properties at the morphotropic phase boundary.

  5. Biochemical Activities of the Wiskott-Aldrich Syndrome Homology Region 2 Domains of Sarcomere Length Short (SALS) Protein.

    PubMed

    Tóth, Mónika Ágnes; Majoros, Andrea Kinga; Vig, Andrea Teréz; Migh, Ede; Nyitrai, Miklós; Mihály, József; Bugyi, Beáta

    2016-01-08

    Drosophila melanogaster sarcomere length short (SALS) is a recently identified Wiskott-Aldrich syndrome protein homology 2 (WH2) domain protein involved in skeletal muscle thin filament regulation. SALS was shown to be important for the establishment of the proper length and organization of sarcomeric actin filaments. Here, we present the first detailed characterization of the biochemical activities of the tandem WH2 domains of SALS (SALS-WH2). Our results revealed that SALS-WH2 binds both monomeric and filamentous actin and shifts the monomer-filament equilibrium toward the monomeric actin. In addition, SALS-WH2 can bind to but fails to depolymerize phalloidin- or jasplakinolide-bound actin filaments. These interactions endow SALS-WH2 with the following two major activities in the regulation of actin dynamics: SALS-WH2 sequesters actin monomers into non-polymerizable complexes and enhances actin filament disassembly by severing, which is modulated by tropomyosin. We also show that profilin does not influence the activities of the WH2 domains of SALS in actin dynamics. In conclusion, the tandem WH2 domains of SALS are multifunctional regulators of actin dynamics. Our findings suggest that the activities of the WH2 domains do not reconstitute the presumed biological function of the full-length protein. Consequently, the interactions of the WH2 domains of SALS with actin must be tuned in the cellular context by other modules of the protein and/or sarcomeric components for its proper functioning.

  6. The Relationship between Intelligence and Multiple Domains of Religious Belief: Evidence from a Large Adult US Sample

    ERIC Educational Resources Information Center

    Lewis, Gary J.; Ritchie, Stuart J.; Bates, Timothy C.

    2011-01-01

    High levels of religiosity have been linked to lower levels of intelligence in a number of recent studies. These results have generated both controversy and theoretical interest. Here in a large sample of US adults we address several issues that restricted the generalizability of these previous results. We measured six dimensions of religiosity…

  7. Identification of an antigenic domain in the N-terminal region of avian hepatitis E virus (HEV) capsid protein that is not common to swine and human HEVs.

    PubMed

    Wang, Lizhen; Sun, Yani; Du, Taofeng; Wang, Chengbao; Xiao, Shuqi; Mu, Yang; Zhang, Gaiping; Liu, Lihong; Widén, Frederik; Hsu, Walter H; Zhao, Qin; Zhou, En-Min

    2014-12-01

    The antigenic domains located in the C-terminal 268 amino acid residues of avian hepatitis E virus (HEV) capsid protein have been characterized. This region shares common epitopes with swine and human HEVs. However, epitopes in the N-terminal 338 amino acid residues have never been reported. In this study, an antigenic domain located between amino acids 23 and 85 was identified by indirect ELISA using the truncated recombinant capsid proteins as coating antigens and anti-avian HEV chicken sera as primary antibodies. In addition, this domain did not react with anti-swine and human HEV sera. These results indicated that the N-terminal 338 amino acid residues of avian HEV capsid protein do not share common epitopes with swine and human HEVs. This finding is important for our understanding of the antigenicity of the avian HEV capsid protein. Furthermore, it has important implications in the selection of viral antigens for serological diagnosis.

  8. Quantum dots - artificial atoms, large molecules, or small pieces of bulk? Insights from time-domain ab ignition studies

    NASA Astrophysics Data System (ADS)

    Prezhdo, Oleg

    2014-03-01

    Quantum dots (QD) are quasi-zero dimensional structures with a unique combination of solid-state and atom-like properties. Unlike bulk or atomic materials, QD properties can be modified continuously by changing QD shape and size. Often, the bulk and atomic viewpoints contradict each other. The atomic view suggests strong electron-hole and charge-phonon interactions, and slow energy relaxation due to mismatch between electronic energy gaps and phonon frequencies. The bulk view advocates that the kinetic energy of quantum confinement is greater than electron-hole interactions, that charge-phonon coupling is weak, and that the relaxation through quasi-continuous bands is rapid. QDs exhibit new physical phenomena. The phonon bottleneck to electron energy relaxation and generation of multiple excitons can improve efficiencies of photovoltaic devices. Our state-of-the-art non-adiabatic molecular dynamics techniques, implemented within time-dependent density-functional-theory, allow us to model QDs at the atomistic level and in time-domain, providing a unifying description of quantum dynamics on the nanoscale.

  9. Large-scale regionalization of water table depth in peatlands optimized for greenhouse gas emission upscaling

    NASA Astrophysics Data System (ADS)

    Bechtold, M.; Tiemeyer, B.; Laggner, A.; Leppelt, T.; Frahm, E.; Belting, S.

    2014-09-01

    Fluxes of the three main greenhouse gases (GHG) CO2, CH4 and N2O from peat and other soils with high organic carbon contents are strongly controlled by water table depth. Information about the spatial distribution of water level is thus a crucial input parameter when upscaling GHG emissions to large scales. Here, we investigate the potential of statistical modeling for the regionalization of water levels in organic soils when data covers only a small fraction of the peatlands of the final map. Our study area is Germany. Phreatic water level data from 53 peatlands in Germany were compiled in a new data set comprising 1094 dip wells and 7155 years of data. For each dip well, numerous possible predictor variables were determined using nationally available data sources, which included information about land cover, ditch network, protected areas, topography, peatland characteristics and climatic boundary conditions. We applied boosted regression trees to identify dependencies between predictor variables and dip-well-specific long-term annual mean water level (WL) as well as a transformed form (WLt). The latter was obtained by assuming a hypothetical GHG transfer function and is linearly related to GHG emissions. Our results demonstrate that model calibration on WLt is superior. It increases the explained variance of the water level in the sensitive range for GHG emissions and avoids model bias in subsequent GHG upscaling. The final model explained 45% of WLt variance and was built on nine predictor variables that are based on information about land cover, peatland characteristics, drainage network, topography and climatic boundary conditions. Their individual effects on WLt and the observed parameter interactions provide insight into natural and anthropogenic boundary conditions that control water levels in organic soils. Our study also demonstrates that a large fraction of the observed WLt variance cannot be explained by nationally available predictor variables and

  10. Staphylococcus aureus protein A binding to von Willebrand factor A1 domain is mediated by conserved IgG binding regions.

    PubMed

    O'Seaghdha, Maghnus; van Schooten, Carina J; Kerrigan, Steven W; Emsley, Jonas; Silverman, Gregg J; Cox, Dermot; Lenting, Peter J; Foster, Timothy J

    2006-11-01

    Protein A (Spa) is a surface-associated protein of Staphylococcus aureus best known for its ability to bind to the Fc region of IgG. Spa also binds strongly to the Fab region of the immunoglobulins bearing V(H)3 heavy chains and to von Willebrand factor (vWF). Previous studies have suggested that the protein A-vWF interaction is important in S. aureus adherence to platelets under conditions of shear stress. We demonstrate that Spa expression is sufficient for adherence of bacteria to immobilized vWF under low fluid shear. The full length recombinant Ig-binding region of protein A, Spa-EDABC, fused to glutathione-S-transferase (GST), bound recombinant vWF in a dose-dependent and saturable fashion with half maximal binding of about 30 nm in immunosorbent assays. Full length-Spa did not bind recombinant vWF A3 domain but displayed binding to recombinant vWF domains A1 and D'-D3 (half maximal binding at 100 nm and 250 nm, respectively). Each recombinant protein A Ig-binding domain bound to the A1 domain in a similar manner to the full length-Spa molecule (half maximal binding 100 nm). Amino acid substitutions were introduced in the GST-SpaD protein at sites known to be involved in IgG Fc or in V(H)3 Fab binding. Mutants altered in residues that recognized IgG Fc but not those that recognized V(H)3 Fab had reduced binding to vWF A1 and D'-D3. This indicated that both vWF regions recognized a region on helices I and II that overlapped the IgG Fc binding site.

  11. Structural features of T cell receptor variable regions that enhance domain stability and enable expression as single-chain VαVβ fragments

    PubMed Central

    Richman, Sarah A.; Aggen, David H.; Dossett, Michelle L.; Donermeyer, David L.; Allen, Paul M.; Greenberg, Philip D.; Kranz, David M.

    2009-01-01

    The variable (V) domains of antibodies and T cell receptors (TCRs) share sequence homology and striking structural similarity. Single-chain antibody V domain constructs (scFv) are routinely expressed in a variety of heterologous systems, both for production of soluble protein as well as for in vitro engineering. In contrast, single-chain T cell receptor V domain constructs (scTCR) are prone to aggregation and misfolding and are refractory to display on phage or yeast in their wild-type form. However, through random mutagenesis and yeast display engineering, it has been possible to isolate scTCR mutants that are properly folded and displayed on the yeast surface. These displayed mutants can serve not only as a scaffold for further engineering but also as scTCR variants that exhibit favorable biophysical properties in E. coli expression. Thus, a more comprehensive understanding of the V domain mutations that allowed display would be beneficial. Our goal here was to identify generalizable patterns of important mutations that can be applied to different TCRs. We compared five different scTCRs, four from mice and one from a human, for yeast surface display. Analysis of a collection of mutants revealed four distinct regions of TCR V domains that were most important for enabling surface expression: the Vα-Vβ interface, the HV4 of Vβ, and the region of the Vα and Vβ domains normally apposed against the constant (C) domains. Consistent with the role of the V-C interface in surface display, reconstitution of this interface, by including the constant domains of each chain, allowed V domain display and αβ chain association on the yeast surface, thus providing an alternative TCR scaffold. However, the surface levels of TCR achieved with engineered scTCR mutants were superior to that of the VαCα/VβCβ constructs. Therefore, we describe further optimization of the current strategy for surface display of the single-chain format in order to facilitate yeast display

  12. Multi-Scale Associations between Vegetation Cover and Woodland Bird Communities across a Large Agricultural Region

    PubMed Central

    Ikin, Karen; Barton, Philip S.; Stirnemann, Ingrid A.; Stein, John R.; Michael, Damian; Crane, Mason; Okada, Sachiko; Lindenmayer, David B.

    2014-01-01

    Improving biodiversity conservation in fragmented agricultural landscapes has become an important global issue. Vegetation at the patch and landscape-scale is important for species occupancy and diversity, yet few previous studies have explored multi-scale associations between vegetation and community assemblages. Here, we investigated how patch and landscape-scale vegetation cover structure woodland bird communities. We asked: (1) How is the bird community associated with the vegetation structure of woodland patches and the amount of vegetation cover in the surrounding landscape? (2) Do species of conservation concern respond to woodland vegetation structure and surrounding vegetation cover differently to other species in the community? And (3) Can the relationships between the bird community and the woodland vegetation structure and surrounding vegetation cover be explained by the ecological traits of the species comprising the bird community? We studied 103 woodland patches (0.5 - 53.8 ha) over two time periods across a large (6,800 km2) agricultural region in southeastern Australia. We found that both patch vegetation and surrounding woody vegetation cover were important for structuring the bird community, and that these relationships were consistent over time. In particular, the occurrence of mistletoe within the patches and high values of woody vegetation cover within 1,000 ha and 10,000 ha were important, especially for bird species of conservation concern. We found that the majority of these species displayed similar, positive responses to patch and landscape vegetation attributes. We also found that these relationships were related to the foraging and nesting traits of the bird community. Our findings suggest that management strategies to increase both remnant vegetation quality and the cover of surrounding woody vegetation in fragmented agricultural landscapes may lead to improved conservation of bird communities. PMID:24830684

  13. Very Large Array Observations of Ammonia in High-mass Star Formation Regions

    NASA Astrophysics Data System (ADS)

    Lu, Xing; Zhang, Qizhou; Liu, Hauyu Baobab; Wang, Junzhi; Gu, Qiusheng

    2014-08-01

    We report systematic mapping observations of the NH3 (1, 1) and (2, 2) inversion lines toward 62 high-mass star-forming regions using the Very Large Array (VLA) in its D and DnC array configurations. The VLA images cover a spatial dynamic range from 40'' to 3'', allowing us to trace gas kinematics from ~1 pc scales to lsim0.1 pc scales. Based on the NH3 morphology and the infrared nebulosity on 1 pc scales, we categorize three subclasses in the sample: filaments, hot cores, and NH3-dispersed sources. The ubiquitous gas filaments found on 1 pc scales have a typical width of ~0.1 pc and often contain regularly spaced fragments along the major axis. The spacing of the fragments and the column densities is consistent with the turbulent supported fragmentation of cylinders. Several sources show multiple filaments that converge toward a center where the velocity field in the filaments is consistent with gas flows. We derive rotational temperature maps for the entire sample. For the three hot core sources, we find a projected radial temperature distribution that is best fit by power-law indices from -0.18 to -0.35. We identify 174 velocity-coherent ~0.1 pc scale dense cores from the entire sample. The mean physical properties for these cores are 1.1 km s-1 in intrinsic linewidth, 18 K in NH3 rotational temperature, 2.3 × 1015 cm-2 in NH3 gas column density, and 67 M ⊙ in molecular mass. The dense cores identified from the filamentary sources are closer to being virialized. Dense cores in the other two categories of sources appear to be dynamically unstable.

  14. Direct selection: a method for the isolation of cDNAs encoded by large genomic regions.

    PubMed Central

    Lovett, M; Kere, J; Hinton, L M

    1991-01-01

    We have developed a strategy for the rapid enrichment and identification of cDNAs encoded by large genomic regions. The basis of this "direct selection" scheme is the hybridization of an entire library of cDNAs to an immobilized genomic clone. Nonspecific hybrids are eliminated and selected cDNAs are eluted. These molecules are then amplified and are either cloned or subjected to further selection/amplification cycles. This scheme was tested using a 550-kilobase yeast artificial chromosome clone that contains the EPO gene. Using this clone and a fetal kidney cDNA library, we have achieved a 1000-fold enrichment of EPO cDNAs in one cycle of enrichment. More significantly, we have further investigated one of the "anonymous" cDNAs that was selectively enriched. We confirmed that this cDNA was encoded by the yeast artificial chromosome. Its frequency in the starting library was 1 in 1 x 10(5) cDNAs and after selection comprised 2% of the selected library. DNA sequence analysis of this cDNA and of the yeast artificial chromosome clone revealed that this gene encodes the beta 2 subunit of the human guanine nucleotide-binding regulatory proteins. Restriction mapping and hybridization data position this gene (GNB2) to within 30-70 kilobases of the EPO gene. The selective isolation and mapping of GNB2 confirms the feasibility of this direct selection strategy and suggests that it will be useful for the rapid isolation of cDNAs, including disease-related genes, across extensive portions of the human genome. Images PMID:1946378

  15. Identification and Typing of Malassezia Species by Amplified Fragment Length Polymorphism and Sequence Analyses of the Internal Transcribed Spacer and Large-Subunit Regions of Ribosomal DNA

    PubMed Central

    Gupta, Aditya K.; Boekhout, Teun; Theelen, Bart; Summerbell, Richard; Batra, Roma

    2004-01-01

    Malassezia yeasts are associated with several dermatological disorders. The conventional identification of Malassezia species by phenotypic methods is complicated and time-consuming, and the results based on culture methods are difficult to interpret. A comparative molecular approach based on the use of three molecular techniques, namely, amplified fragment length polymorphism (AFLP) analysis, sequencing of the internal transcribed spacer, and sequencing of the D1 and D2 domains of the large-subunit ribosomal DNA region, was applied for the identification of Malassezia species. All species could be correctly identified by means of these methods. The results of AFLP analysis and sequencing were in complete agreement with each other. However, some discrepancies were noted when the molecular methods were compared with the phenotypic method of identification. Specific genotypes were distinguished within a collection of Malassezia furfur isolates from Canadian sources. AFLP analysis revealed significant geographical differences between the North American and European M. furfur strains. PMID:15365020

  16. The signal for clathrin-mediated endocytosis of the paramyxovirus SV5 HN protein resides at the transmembrane domain-ectodomain boundary region.

    PubMed

    Leser, G P; Ector, K J; Ng, D T; Shaughnessy, M A; Lamb, R A

    1999-09-15

    The hemagglutinin-neuraminidase (HN) glycoprotein of the paramyxovirus SV5 is internalized from the cell surface via clathrin-coated pits. However, the cytoplasmic domain of SV5 HN does not contain a previously characterized internalization motif. A cell-surface-expressed chimeric protein (APK), consisting of the cytoplasmic tail, transmembrane (TM) domain, and 12 residues of the ectodomain of HN joined to the cytoplasmic protein pyruvate kinase is internalized, indicating that the N-terminal region of HN contains an internalization signal. Although SV5 HN is internalized at a rate similar to that of influenza virus hemagglutinin (HA) mutant Y543, which contains a degenerate tyrosine-based signal in its cytoplasmic tail, the elimination of the majority of the HN cytoplasmic tail, or substitution of the HN TM domain with leucine residues, did not affect the rate of HN internalization. The HN protein of the closely related virus, Newcastle disease virus (NDV), is not internalized from the cell surface. Working under the usual convention that the TM domain consists of the hydrophobic residues bounded by two charged residues, analysis of internalization of mutant and chimeric NDV HN molecules indicates that the first seven SV5 HN ectodomain residues are critical for internalization of HN. A glutamic acid residue (E37) that abuts this presumptive HN TM domain/ectodomain boundary is important for SV5 HN internalization.

  17. Autoinhibitory structure of the WW domain of HYPB/SETD2 regulates its interaction with the proline-rich region of huntingtin.

    PubMed

    Gao, Yong-Guang; Yang, Hui; Zhao, Jian; Jiang, Ya-Jun; Hu, Hong-Yu

    2014-03-04

    Huntington's disease (HD) is an autosomally dominant neurodegenerative disorder caused by expansion of polyglutamine (polyQ) in the huntingtin (Htt) protein. Htt yeast two-hybrid protein B (HYPB/SETD2), a histone methyltransferase, directly interacts with Htt and is involved in HD pathology. Using NMR techniques, we characterized a polyproline (polyP) stretch at the C terminus of HYPB, which directly interacts with the following WW domain and leads this domain predominantly to be in a closed conformational state. The solution structure shows that the polyP stretch extends from the back and binds to the WW core domain in a typical binding mode. This autoinhibitory structure regulates interaction between the WW domain of HYPB and the proline-rich region (PRR) of Htt, as evidenced by NMR and immunofluorescence techniques. This work provides structural and mechanistic insights into the intramolecular regulation of the WW domain in Htt-interacting partners and will be helpful for understanding the pathology of HD.

  18. Structure of the iSH2 domain of Human phosphatidylinositol 3-kinase p85 beta Subunit Reveals Conformational Plasticity in the Interhelical Turn Region

    SciTech Connect

    C Schauder; L Ma; R Krug; G Montelione; R Guan

    2011-12-31

    Phosphatidylinositol 3-kinase (PI3K) proteins actively trigger signaling pathways leading to cell growth, proliferation and survival. These proteins have multiple isoforms and consist of a catalytic p110 subunit and a regulatory p85 subunit. The iSH2 domain of the p85 {beta} isoform has been implicated in the binding of nonstructural protein 1 (NS1) of influenza A viruses. Here, the crystal structure of human p85 {beta} iSH2 determined to 3.3 {angstrom} resolution is reported. The structure reveals that this domain mainly consists of a coiled-coil motif. Comparison with the published structure of the bovine p85 {beta} iSH2 domain bound to the influenza A virus nonstructural protein 1 indicates that little or no structural change occurs upon complex formation. By comparing this human p85 {beta} iSH2 structure with the bovine p85 {beta} iSH2 domain, which shares 99% sequence identity, and by comparing the multiple conformations observed within the asymmetric unit of the bovine iSH2 structure, it was found that this coiled-coil domain exhibits a certain degree of conformational variability or 'plasticity' in the interhelical turn region. It is speculated that this plasticity of p85 {beta} iSH2 may play a role in regulating its functional and molecular-recognition properties.

  19. On the relationship between large-scale climate modes and regional synoptic patterns that drive Victorian rainfall

    NASA Astrophysics Data System (ADS)

    Verdon-Kidd, D.; Kiem, A. S.

    2008-10-01

    In this paper regional (synoptic) and large-scale climate drivers of rainfall are investigated for Victoria, Australia. A non-linear classification methodology known as self-organizing maps (SOM) is used to identify 20 key regional synoptic patterns, which are shown to capture a range of significant synoptic features known to influence the climate of the region. Rainfall distributions are assigned to each of the 20 patterns for nine rainfall stations located across Victoria, resulting in a clear distinction between wet and dry synoptic types at each station. The influence of large-scale climate modes on the frequency and timing of the regional synoptic patterns is also investigated. This analysis revealed that phase changes in the El Niño Southern Oscillation (ENSO), the Southern Annular Mode (SAM) and/or Indian Ocean Dipole (IOD) are associated with a shift in the relative frequency of wet and dry synoptic types. Importantly, these results highlight the potential to utilise the link between the regional synoptic patterns derived in this study and large-scale climate modes to improve rainfall forecasting for Victoria, both in the short- (i.e. seasonal) and long-term (i.e. decadal/multi-decadal scale). In addition, the regional and large-scale climate drivers identified in this study provide a benchmark by which the performance of Global Climate Models (GCMs) may be assessed.

  20. Mapping regions of the beta1 integrin cytoplasmic domain involved in migration and survival in primary oligodendrocyte precursors using cell-permeable homeopeptides.

    PubMed

    Buttery, P C; Mallawaarachchi, C M; Milner, R; Doherty, P; ffrench-Constant, C

    1999-05-27

    The mapping of regions within integrin cytoplasmic domains responsible for the different effects on cell behaviour is an important part of an analysis of integrin-mediated signalling. In order to facilitate this analysis in primary cells, we have used cell-permeable homeopeptides to deliver sequences mimicking parts of the integrin beta1 cytoplasmic domain into the cell. In a study using oligodendrocyte precursors, the cells that give rise to myelin-forming oligodendrocytes during CNS development, we show that these peptides can be used to manipulate beta1 integrin signalling and that the regions of the cytoplasmic domain involved in migration and survival are distinct. Peptides mimicking the N-terminal portion of the cytoplasmic domain previously implicated in binding to Focal Adhesion Kinase (FAK) induce apoptosis, while peptides mimicking more C-terminal sequences do not cause cell death. In contrast they show that the NPIY sequence, the N-terminal one of two NPXY motifs previously implicated in signalling, is involved in migration. Peptides containing this sequence promote migration while alteration of NPIY to NPIA makes the peptide inhibitory to migration. Our results show that these peptides represent a novel approach to integrin signalling that allow rapid definition of critical cytoplasmic sequences in primary cells.

  1. Time-domain analysis of sub-micron transit region GaAs Gunn diodes for use in terahertz frequency multiplication chains

    NASA Astrophysics Data System (ADS)

    Amir, F.; Farrington, N.; Mitchell, C.; Missous, M.

    2010-10-01

    Simulated RF time-domain characteristics for advanced Gunn diodes with hot electron injection and sub-micron transit region lengths for use at frequencies over 100GHz are reported. The physical models used have been developed in SILVACO and are compared to measured results. The devices measured were originally fabricated to investigate the feasibility of GaAs Gunn diode oscillators capable of operating at D-band frequencies and ultimately intended for use in high power (multi-mW) Terahertz sources (~0.6THz) when used in conjunction with novel Schottky diode frequency multiplier technology. The device models created using SILVACO are described and the DC and time-domain results presented. The simulations were used to determine the shortest transit region length capable of producing sustained oscillation. The operation of resonant disk second harmonic Gunn diode oscillators is also discussed and accurate electromagnetic models created using Ansoft High Frequency Structure Simulator presented. Novel methods for combining small-signal frequency-domain electromagnetic simulations with time-domain device simulations in order to account for the significant interactions between the diode and oscillator circuit are described.

  2. Improvement of lateral resolution of spectral domain optical coherence tomography images in out-of-focus regions with holographic data processing techniques

    SciTech Connect

    Moiseev, A A; Gelikonov, G V; Terpelov, D A; Shilyagin, P A; Gelikonov, V M

    2014-08-31

    An analogy between spectral-domain optical coherence tomography (SD OCT) data and broadband digital holography data is considered. Based on this analogy, a method for processing SD OCT data, which makes it possible to construct images with a lateral resolution in the whole investigated volume equal to the resolution in the in-focus region, is developed. Several issues concerning practical application of the proposed method are discussed. (laser biophotonics)

  3. Productive association between MHC class I and tapasin requires the tapasin transmembrane/cytosolic region and the tapasin C-terminal Ig-like domain

    PubMed Central

    Simone, Laura C.; Georgesen, Corey J.; Simone, Peter D.; Wang, Xiaojian; Solheim, Joyce C.

    2011-01-01

    The current model of antigen assembly with major histocompatibility complex (MHC) class I molecules posits that interactions between the tapasin N-terminal immunoglobulin (Ig)-like domain and the MHC class I peptide-binding groove permit tapasin to regulate antigen selection. Much less is known regarding interactions that might involve the tapasin C-terminal Ig-like domain. Additionally, the tapasin transmembrane/cytoplasmic region enables tapasin to bridge the MHC class I molecule to the transporter associated with antigen processing (TAP). In this investigation, we made use of two tapasin mutants to determine the relative contribution of the tapasin C-terminal Ig-like domain and the tapasin transmembrane/cytoplasmic region to the assembly of MHC class I molecules. Deletion of a loop within the tapasin C-terminal Ig-like domain (Δ334-342) prevented tapasin association with the MHC class I molecule Kd. Although tapasin Δ334-342 did not increase the efficiency of Kd folding, Kd surface expression was enhanced on cells expressing this mutant relative to tapasin-deficient cells. In contrast to tapasin Δ334-342, a soluble tapasin mutant lacking the transmembrane/cytoplasmic region retained the ability to bind to Kd molecules, but did not facilitate Kd surface expression. Furthermore, when soluble tapasin and tapasin Δ334-342 were co-expressed, soluble tapasin had a dominant negative effect on the folding and surface expression of not only Kd, but also Db and Kb. In addition, our molecular modeling of the MHC class I-tapasin interface revealed novel potential interactions involving tapasin residues 334-342. Together, these findings demonstrate that the tapasin C-terminal and transmembrane/cytoplasmic regions are critical to tapasin's capacity to associate effectively with the MHC class I molecule. PMID:22169163

  4. Active region 11748: Recurring X-class flares, large scale dimmings and waves.

    NASA Astrophysics Data System (ADS)

    Davey, Alisdair R.; Malanushenko, Anna; McIntosh, Scott W.

    2014-06-01

    AR 11748 was a relatively compact active region that crossed the solar disk between 05/14/2013 and 05/26/2013. Despite its size it produced a number X-class flares, and global scale eruptive events that were captured by the SDO Feature Finding Team's (FFT) Dimming Region Detector. Using the results of this module and other FFT modules, we present an analysis of the this AR region and investigate why it was so globally impactful.

  5. Impact of the internal variability on the cyclone tracks simulated by a regional climate model over the Med-CORDEX domain

    NASA Astrophysics Data System (ADS)

    Sanchez-Gomez, Emilia; Somot, Samuel

    2016-10-01

    Regional climate models (RCMs) constitute a powerful tool to study and understand climate variability and change at local scales. Nevertheless, to correctly interpret regional climate simulations, a number of uncertainties need to be considered. In this study, we investigate the so-called Internal Variability (IV) of an RCM. The IV can be defined as the degree of irreproducibility in an RCM solution observed when it is conducted by the same lateral boundary conditions (LBCs) but initialised from different initial states. The main goal of this work is to investigate how the IV affects the cyclone tracks simulated by an RCM over a Mediterranean domain. For standard variables such as sea level pressure, 2 m temperature and precipitation, our results over the Mediterranean region are consistent with studies conducted over other geographical domains: the IV is stronger at the easternmost part of the domain, where the control exerted by the LBCs is weaker; the IV shows a strong seasonal dependence, reaching larger values in summer than in winter. We show here that the IV values associated with the density of cyclone tracks are much stronger than for the other documented variables, reaching more than 50 % of the estimated total variability. Concerning the cyclone characteristics, long travelling tracks are associated to a greatest IV. Within the latter cyclone category, the fast moving cyclones seems to exhibit also larger IV values. A secondary IV maximum is observed for static cyclones with short travelling distances (thermal lows) during the warm season.

  6. Properties of RR Lyrae stars in the inner regions of the Large Magellanic Cloud

    NASA Astrophysics Data System (ADS)

    Borissova, J.; Minniti, D.; Rejkuba, M.; Alves, D.; Cook, K. H.; Freeman, K. C.

    2004-08-01

    We present the radial velocities, metallicities and the K-band magnitudes of 74 RR Lyrae stars in the inner regions of the LMC. The intermediate resolution spectra and infrared images were obtained with FORS1 at the ESO VLT and with the SOFI infrared imager at the ESO NTT. The best 43 RR Lyrae with measured velocities yield an observed velocity dispersion of σ=61± 7 km s-1. We obtain a true LMC RR Lyrae velocity dispersion of σ=53 km s-1, which is higher than the velocity dispersion of any other LMC population previously measured. This is the first empirical evidence for a kinematically hot, metal-poor halo in the LMC as discussed in Minniti et al. (\\cite{Minniti03}). Using Layden's (1994) modification of the \\Delta S method we measured the metallicity for 23 of our stars. The mean value is [Fe/H] =-1.46±0.09 dex. The absolute magnitudes MV and MK of RR Lyrae stars are linear functions of metallicity. In the V band, our data agree with the Olech et al. (\\cite{Olech03}) relation, in the K band the slope is flatter. The average apparent V luminosity of 70 RR Lyrae stars is < V> = 19.45±0.04 and the average K luminosity of 37 RR Lyrae stars is < K>=18.20±0.06. There is no obvious relation between apparent V magnitude and Log P, while the RR Lyrae K band magnitudes show a well defined linear trend with Log P. Using the Bono et al. (\\cite{Bono01}) and Bono et al. (2003) theoretical Near-Infrared Period-Luminosity-Metallicity relations we calculate the LMC distance modulus μ0 = 18.48±0.08. Based on observations collected with the Very Large Telescope and the New Technology Telescope of the European Southern Observatory within the Observing Programs 64.N-0176(B) and 70.B-0547. Tables 3, 4 and 6 are also available in electronic form at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsweb.u-strasbg.fr/cgi-bin/qcat?J/A+A/423/97

  7. Large Scale Parameter Estimation Problems in Frequency-Domain Elastodynamics Using an Error in Constitutive Equation Functional

    PubMed Central

    Banerjee, Biswanath; Walsh, Timothy F.; Aquino, Wilkins; Bonnet, Marc

    2012-01-01

    This paper presents the formulation and implementation of an Error in Constitutive Equations (ECE) method suitable for large-scale inverse identification of linear elastic material properties in the context of steady-state elastodynamics. In ECE-based methods, the inverse problem is postulated as an optimization problem in which the cost functional measures the discrepancy in the constitutive equations that connect kinematically admissible strains and dynamically admissible stresses. Furthermore, in a more recent modality of this methodology introduced by Feissel and Allix (2007), referred to as the Modified ECE (MECE), the measured data is incorporated into the formulation as a quadratic penalty term. We show that a simple and efficient continuation scheme for the penalty term, suggested by the theory of quadratic penalty methods, can significantly accelerate the convergence of the MECE algorithm. Furthermore, a (block) successive over-relaxation (SOR) technique is introduced, enabling the use of existing parallel finite element codes with minimal modification to solve the coupled system of equations that arises from the optimality conditions in MECE methods. Our numerical results demonstrate that the proposed methodology can successfully reconstruct the spatial distribution of elastic material parameters from partial and noisy measurements in as few as ten iterations in a 2D example and fifty in a 3D example. We show (through numerical experiments) that the proposed continuation scheme can improve the rate of convergence of MECE methods by at least an order of magnitude versus the alternative of using a fixed penalty parameter. Furthermore, the proposed block SOR strategy coupled with existing parallel solvers produces a computationally efficient MECE method that can be used for large scale materials identification problems, as demonstrated on a 3D example involving about 400,000 unknown moduli. Finally, our numerical results suggest that the proposed MECE

  8. A numerical approach for simulating fluid structure interaction of flexible thin shells undergoing arbitrarily large deformations in complex domains

    NASA Astrophysics Data System (ADS)

    Gilmanov, Anvar; Le, Trung Bao; Sotiropoulos, Fotis

    2015-11-01

    We present a new numerical methodology for simulating fluid-structure interaction (FSI) problems involving thin flexible bodies in an incompressible fluid. The FSI algorithm uses the Dirichlet-Neumann partitioning technique. The curvilinear immersed boundary method (CURVIB) is coupled with a rotation-free finite element (FE) model for thin shells enabling the efficient simulation of FSI problems with arbitrarily large deformation. Turbulent flow problems are handled using large-eddy simulation with the dynamic Smagorinsky model in conjunction with a wall model to reconstruct boundary conditions near immersed boundaries. The CURVIB and FE solvers are coupled together on the flexible solid-fluid interfaces where the structural nodal positions, displacements, velocities and loads are calculated and exchanged between the two solvers. Loose and strong coupling FSI schemes are employed enhanced by the Aitken acceleration technique to ensure robust coupling and fast convergence especially for low mass ratio problems. The coupled CURVIB-FE-FSI method is validated by applying it to simulate two FSI problems involving thin flexible structures: 1) vortex-induced vibrations of a cantilever mounted in the wake of a square cylinder at different mass ratios and at low Reynolds number; and 2) the more challenging high Reynolds number problem involving the oscillation of an inverted elastic flag. For both cases the computed results are in excellent agreement with previous numerical simulations and/or experiential measurements. Grid convergence tests/studies are carried out for both the cantilever and inverted flag problems, which show that the CURVIB-FE-FSI method provides their convergence. Finally, the capability of the new methodology in simulations of complex cardiovascular flows is demonstrated by applying it to simulate the FSI of a tri-leaflet, prosthetic heart valve in an anatomic aorta and under physiologic pulsatile conditions.

  9. A numerical approach for simulating fluid structure interaction of flexible thin shells undergoing arbitrarily large deformations in complex domains

    SciTech Connect

    Gilmanov, Anvar; Le, Trung Bao; Sotiropoulos, Fotis

    2015-11-01

    We present a new numerical methodology for simulating fluid–structure interaction (FSI) problems involving thin flexible bodies in an incompressible fluid. The FSI algorithm uses the Dirichlet–Neumann partitioning technique. The curvilinear immersed boundary method (CURVIB) is coupled with a rotation-free finite element (FE) model for thin shells enabling the efficient simulation of FSI problems with arbitrarily large deformation. Turbulent flow problems are handled using large-eddy simulation with the dynamic Smagorinsky model in conjunction with a wall model to reconstruct boundary conditions near immersed boundaries. The CURVIB and FE solvers are coupled together on the flexible solid–fluid interfaces where the structural nodal positions, displacements, velocities and loads are calculated and exchanged between the two solvers. Loose and strong coupling FSI schemes are employed enhanced by the Aitken acceleration technique to ensure robust coupling and fast convergence especially for low mass ratio problems. The coupled CURVIB-FE-FSI method is validated by applying it to simulate two FSI problems involving thin flexible structures: 1) vortex-induced vibrations of a cantilever mounted in the wake of a square cylinder at different mass ratios and at low Reynolds number; and 2) the more challenging high Reynolds number problem involving the oscillation of an inverted elastic flag. For both cases the computed results are in excellent agreement with previous numerical simulations and/or experiential measurements. Grid convergence tests/studies are carried out for both the cantilever and inverted flag problems, which show that the CURVIB-FE-FSI method provides their convergence. Finally, the capability of the new methodology in simulations of complex cardiovascular flows is demonstrated by applying it to simulate the FSI of a tri-leaflet, prosthetic heart valve in an anatomic aorta and under physiologic pulsatile conditions.

  10. Spatial Structure of Large-Scale Plasma Density Perturbations HF-Induced in the Ionospheric F 2 Region

    NASA Astrophysics Data System (ADS)

    Frolov, V. L.; Komrakov, G. P.; Glukhov, Ya. V.; Andreeva, E. S.; Kunitsyn, V. E.; Kurbatov, G. A.

    2016-07-01

    We consider the experimental results obtained by studying the large-scale structure of the HF-disturbed ionospheric region. The experiments were performed using the SURA heating facility. The disturbed ionospheric region was sounded by signals radiated by GPS navigation satellite beacons as well as by signals of low-orbit satellites (radio tomography). The results of the experiments show that large-scale plasma density perturbations induced at altitudes higher than the F2 layer maximum can contribute significantly to the measured variations of the total electron density and can, with a certain arrangement of the reception points, be measured by the GPS sounding method.

  11. Tethered Domains and Flexible Regions in tRNase ZL, the Long Form of tRNase Z

    PubMed Central

    Wilson, Christopher; Ramai, Daryl; Serjanov, Dmitri; Lama, Neema; Levinger, Louis; Chang, Emmanuel J.

    2013-01-01

    tRNase Z, a member of the metallo-β-lactamase family, endonucleolytically removes the pre-tRNA 3′ trailer in a step central to tRNA maturation. The short form (tRNase ZS) is the only one found in bacteria and archaebacteria and is also present in some eukaryotes. The homologous long form (tRNase ZL), exclusively found in eukaryotes, consists of related amino- and carboxy-domains, suggesting that tRNase ZL arose from a tandem duplication of tRNase ZS followed by interdependent divergence of the domains. X-ray crystallographic structures of tRNase ZS reveal a flexible arm (FA) extruded from the body of tRNase Z remote from the active site that binds tRNA far from the scissile bond. No tRNase ZL structures have been solved; alternative biophysical studies are therefore needed to illuminate its functional characteristics. Structural analyses of tRNase ZL performed by limited proteolysis, two dimensional gel electrophoresis and mass spectrometry establish stability of the amino and carboxy domains and flexibility of the FA and inter-domain tether, with implications for tRNase ZL function. PMID:23874404

  12. Exon organization of the mouse entactin gene corresponds to the structural domains of the polypeptide and has regional homology to the low-density lipoprotein receptor gene

    SciTech Connect

    Durkin, M.E.; Chung, A.E.; Wewer, U.M.

    1995-03-20

    Entactin is a widespread basement membrane protein of 150 kDa that binds to type IV collagen and laminin. The complete exon-intron structure of the mouse entactin gene has been determined from {lambda} genomic DNA clones. The gene spans at least 65 kb and contains 20 exons. The exon organization of the mouse entactin gene closely corresponds to the organization of the polypeptide into distinct structural and functional domains. The two amino-terminal globular domains are encoded by three exons each. Single exons encode the two protease-sensitive, O-glycosylated linking regions. The six EGF-like repeats and the single thyroglobulin-type repeat are each encoded by separate exons. The carboxyl-terminal half of entactin displays sequence homology to the growth factor-like region of the low-density lipoprotein receptor, and in both genes this region is encoded by eight exons. The positions of four introns are also conserved in the homologous region of the two genes. These observations suggest that the entactin gene has evolved via exon shuffling. Finally, several sequence polymorphisms useful for gene linkage analysis were found in the 3{prime} noncoding region of the last exon. 52 refs., 8 figs.

  13. A technique for extrapolating and validating forest cover across large regions - Calibrating AVHRR data with TM data

    NASA Technical Reports Server (NTRS)

    Iverson, L. R.; Cook, E. A.; Graham, R. L.

    1989-01-01

    A method is presented for extending high-resolution forest cover information across large regions. Using Landsat TM data with AVHRR data, an empirical relationship beween AVHRR spectral signatures and forest cover is developed. The resulting regression equation is applied to an AVHRR scene covering a large area centered around southern Illinois. The map is used to estimate forest cover within a geographical information system. The results are compared with U.S. Forest Service estimates, showing good agreement.

  14. The regions of the retinoblastoma protein needed for binding to adenovirus E1A or SV40 large T antigen are common sites for mutations.

    PubMed Central

    Hu, Q J; Dyson, N; Harlow, E

    1990-01-01

    The protein product of the retinoblastoma (RB) gene is thought to function in a pathway that restricts cell proliferation. Recently, transforming proteins from three different classes of DNA tumor viruses have been shown to form complexes with the RB protein. Genetic studies suggest that these interactions with the RB protein are important steps in transformation by these viruses. In order to understand better the function of the RB-viral oncoprotein complexes, we have mapped the regions of the RB protein that are necessary for these associations. Two non-contiguous regions of RB were found to be essential for complex formation with adenovirus E1A or SV40 large T antigen. These two regions are found between amino acids 393 and 572 and 646 and 772. Interestingly, these binding sites on RB overlap with the positions of naturally occurring, inactivating mutations of the RB gene. These results strongly suggest that these viral oncoproteins are targeting a protein domain that is an important site in the normal function of the RB protein. Images Fig. 1. Fig. 2. Fig. 3. Fig. 4. Fig. 5. Fig. 6. Fig. 7. Fig. 9. PMID:2138977

  15. Crystal structure of Staphylococcus aureus metallopeptidase (Sapep) reveals large domain motions between the manganese-bound and apo-states.

    PubMed

    Girish, Tavarekere S; Gopal, Balasubramanian

    2010-09-17

    Proteases belonging to the M20 family are characterized by diverse substrate specificity and participate in several metabolic pathways. The Staphylococcus aureus metallopeptidase, Sapep, is a member of the aminoacylase-I/M20 protein family. This protein is a Mn(2+)-dependent dipeptidase. The crystal structure of this protein in the Mn(2+)-bound form and in the open, metal-free state suggests that large interdomain movements could potentially regulate the activity of this enzyme. We note that the extended inactive conformation is stabilized by a disulfide bond in the vicinity of the active site. Although these cysteines, Cys(155) and Cys(178), are not active site residues, the reduced form of this enzyme is substantially more active as a dipeptidase. These findings acquire further relevance given a recent observation that this enzyme is only active in methicillin-resistant S. aureus. The structural and biochemical features of this enzyme provide a template for the design of novel methicillin-resistant S. aureus-specific therapeutics.

  16. Effect of glycosylation on an immunodominant region in the V1V2 variable domain of the HIV-1 envelope gp120 protein

    SciTech Connect

    Tian, Jianhui; Lopez, Cesar Augusto; Derdeyn, Cynthia A.; Jones, Morris S.; Pinter, Abraham; Korber, Bette Tina Marie; Gnanakaran, Sandrasegaram; Rein, Alan

    2016-10-07

    Heavy glycosylation of the envelope (Env) surface subunit, gp120, is a key adaptation of HIV-1; however, the precise effects of glycosylation on the folding, conformation and dynamics of this protein are poorly understood. Here we explore the patterns of HIV-1 Env gp120 glycosylation, and particularly the enrichment in glycosylation sites proximal to the disulfide linkages at the base of the surface-exposed variable domains. To dissect the influence of glycans on the conformation these regions, we focused on an antigenic peptide fragment from a disulfide bridge-bounded region spanning the V1 and V2 hyper-variable domains of HIV-1 gp120. We used replica exchange molecular dynamics (MD) simulations to investigate how glycosylation influences its conformation and stability. Simulations were performed with and without N-linked glycosylation at two sites that are highly conserved across HIV-1 isolates (N156 and N160); both are contacts for recognition by V1V2-targeted broadly neutralizing antibodies against HIV-1. Glycosylation stabilized the pre-existing conformations of this peptide construct, reduced its propensity to adopt other secondary structures, and provided resistance against thermal unfolding. Simulations performed in the context of the Env trimer also indicated that glycosylation reduces flexibility of the V1V2 region, and provided insight into glycan-glycan interactions in this region. These stabilizing effects were influenced by a combination of factors, including the presence of a disulfide bond between the Cysteines at 131 and 157, which increased the formation of beta-strands. Together, these results provide a mechanism for conservation of disulfide linkage proximal glycosylation adjacent to the variable domains of gp120 and begin to explain how this could be exploited to enhance the immunogenicity of those regions. Furthermore, these studies suggest that glycopeptide immunogens can be designed to stabilize the most relevant Env conformations to focus

  17. Oxidative Unfolding of the Rubredoxin Domain and the Natively Disordered N-terminal Region Regulate the Catalytic Activity of Mycobacterium tuberculosis Protein Kinase G.

    PubMed

    Wittwer, Matthias; Luo, Qi; Kaila, Ville R I; Dames, Sonja A

    2016-12-30

    Mycobacterium tuberculosis escapes killing in human macrophages by secreting protein kinase G (PknG). PknG intercepts host signaling to prevent fusion of the phagosome engulfing the mycobacteria with the lysosome and, thus, their degradation. The N-terminal NORS (no regulatory secondary structure) region of PknG (approximately residues 1-75) has been shown to play a role in PknG regulation by (auto)phosphorylation, whereas the following rubredoxin-like metal-binding motif (RD, residues ∼74-147) has been shown to interact tightly with the subsequent catalytic domain (approximately residues 148-420) to mediate its redox regulation. Deletions or mutations in NORS or the redox-sensitive RD significantly decrease PknG survival function. Based on combined NMR spectroscopy, in vitro kinase assay, and molecular dynamics simulation data, we provide novel insights into the regulatory roles of the N-terminal regions. The NORS region is indeed natively disordered and rather dynamic. Consistent with most earlier data, autophosphorylation occurs in our assays only when the NORS region is present and, thus, in the NORS region. Phosphorylation of it results only in local conformational changes and does not induce interactions with the subsequent RD. Although the reduced, metal-bound RD makes tight interactions with the following catalytic domain in the published crystal structures, it can also fold in its absence. Our data further suggest that oxidation-induced unfolding of the RD regulates substrate access to the catalytic domain and, thereby, PknG function under different redox conditions, e.g. when exposed to increased levels of reactive oxidative species in host macrophages.

  18. Effect of Glycosylation on an Immunodominant Region in the V1V2 Variable Domain of the HIV-1 Envelope gp120 Protein

    PubMed Central

    Derdeyn, Cynthia A.; Jones, Morris S.; Pinter, Abraham; Korber, Bette; Gnanakaran, S.

    2016-01-01

    Heavy glycosylation of the envelope (Env) surface subunit, gp120, is a key adaptation of HIV-1; however, the precise effects of glycosylation on the folding, conformation and dynamics of this protein are poorly understood. Here we explore the patterns of HIV-1 Env gp120 glycosylation, and particularly the enrichment in glycosylation sites proximal to the disulfide linkages at the base of the surface-exposed variable domains. To dissect the influence of glycans on the conformation these regions, we focused on an antigenic peptide fragment from a disulfide bridge-bounded region spanning the V1 and V2 hyper-variable domains of HIV-1 gp120. We used replica exchange molecular dynamics (MD) simulations to investigate how glycosylation influences its conformation and stability. Simulations were performed with and without N-linked glycosylation at two sites that are highly conserved across HIV-1 isolates (N156 and N160); both are contacts for recognition by V1V2-targeted broadly neutralizing antibodies against HIV-1. Glycosylation stabilized the pre-existing conformations of this peptide construct, reduced its propensity to adopt other secondary structures, and provided resistance against thermal unfolding. Simulations performed in the context of the Env trimer also indicated that glycosylation reduces flexibility of the V1V2 region, and provided insight into glycan-glycan interactions in this region. These stabilizing effects were influenced by a combination of factors, including the presence of a disulfide bond between the Cysteines at 131 and 157, which increased the formation of beta-strands. Together, these results provide a mechanism for conservation of disulfide linkage proximal glycosylation adjacent to the variable domains of gp120 and begin to explain how this could be exploited to enhance the immunogenicity of those regions. These studies suggest that glycopeptide immunogens can be designed to stabilize the most relevant Env conformations to focus the immune

  19. Effect of glycosylation on an immunodominant region in the V1V2 variable domain of the HIV-1 envelope gp120 protein

    DOE PAGES

    Tian, Jianhui; Lopez, Cesar Augusto; Derdeyn, Cynthia A.; ...

    2016-10-07

    Heavy glycosylation of the envelope (Env) surface subunit, gp120, is a key adaptation of HIV-1; however, the precise effects of glycosylation on the folding, conformation and dynamics of this protein are poorly understood. Here we explore the patterns of HIV-1 Env gp120 glycosylation, and particularly the enrichment in glycosylation sites proximal to the disulfide linkages at the base of the surface-exposed variable domains. To dissect the influence of glycans on the conformation these regions, we focused on an antigenic peptide fragment from a disulfide bridge-bounded region spanning the V1 and V2 hyper-variable domains of HIV-1 gp120. We used replica exchangemore » molecular dynamics (MD) simulations to investigate how glycosylation influences its conformation and stability. Simulations were performed with and without N-linked glycosylation at two sites that are highly conserved across HIV-1 isolates (N156 and N160); both are contacts for recognition by V1V2-targeted broadly neutralizing antibodies against HIV-1. Glycosylation stabilized the pre-existing conformations of this peptide construct, reduced its propensity to adopt other secondary structures, and provided resistance against thermal unfolding. Simulations performed in the context of the Env trimer also indicated that glycosylation reduces flexibility of the V1V2 region, and provided insight into glycan-glycan interactions in this region. These stabilizing effects were influenced by a combination of factors, including the presence of a disulfide bond between the Cysteines at 131 and 157, which increased the formation of beta-strands. Together, these results provide a mechanism for conservation of disulfide linkage proximal glycosylation adjacent to the variable domains of gp120 and begin to explain how this could be exploited to enhance the immunogenicity of those regions. Furthermore, these studies suggest that glycopeptide immunogens can be designed to stabilize the most relevant Env conformations to

  20. Identification and Characterization of a Large Protein Essential for Degradation of the Crystalline Region of Cellulose by Cytophaga hutchinsonii.

    PubMed

    Wang, Sen; Zhao, Dong; Bai, Xinfeng; Zhang, Weican; Lu, Xuemei

    2017-01-01

    Cytophaga hutchinsonii is a Gram-negative bacterium that can efficiently degrade crystalline cellulose by a unique mechanism different from the free cellulase or cellulosome strategy. In this study, chu_3220, encoding the hypothetical protein CHU_3220 (205 kDa), was identified by insertional mutation and gene deletion as the first gene essential for degradation of the crystalline region but not the amorphous region of cellulose by C. hutchinsonii A chu_3220 deletion mutant was defective in the degradation of crystalline cellulose and increased the degree of crystallinity of Avicel PH101 but could still degrade amorphous cellulose completely. CHU_3220 was found to be located on the outer surface of the outer membrane and could bind to cellulose. It contains 15 PbH1 domains and a C-terminal domain (CHU_C) that was proved to be critical for the localization of CHU_3220 on the cell surface and the function of CHU_3220 in crystalline cellulose degradation. Moreover, the degradation of crystalline cellulose was intact-cell dependent and inhibited by NaN3 Further study showed that chu_3220 was induced by cellulose and that the endoglucanase activity on the cell surface was significantly reduced without chu_3220 Real-time PCR revealed that the transcription of most genes encoding endoglucanases located on the cell surface was decreased in the chu_3220 deletion mutant, indicating that chu_3220 might also play a role in the regulation of the expression of some endoglucanases.

  1. Genomic shotgun array: a procedure linking large-scale DNA sequencing with regional transcript mapping.

    PubMed

    Li, Ling-Hui; Li, Jian-Chiuan; Lin, Yung-Feng; Lin, Chung-Yen; Chen, Chung-Yung; Tsai, Shih-Feng

    2004-02-11

    To facilitate transcript mapping and to investigate alterations in genomic structure and gene expression in a defined genomic target, we developed a novel microarray-based method to detect transcriptional activity of the human chromosome 4q22-24 region. Loss of heterozygosity of human 4q22-24 is frequently observed in hepatocellular carcinoma (HCC). One hundred and eighteen well-characterized genes have been identified from this region. We took previously sequenced shotgun subclones as templates to amplify overlapping sequences for the genomic segment and constructed a chromosome-region-specific microarray. Using genomic DNA fragments as probes, we detected transcriptional activity from within this region among five different tissues. The hybridization results indicate that there are new transcripts that have not yet been identified by other methods. The existence of new transcripts encoded by genes in this region was confirmed by PCR cloning or cDNA library screening. The procedure reported here allows coupling of shotgun sequencing with transcript mapping and, potentially, detailed analysis of gene expression and chromosomal copy of the genomic sequence for the putative HCC tumor suppressor gene(s) in the 4q candidate region.

  2. Blocking the large extracellular loop (LEL) domain of FcTetraspanin-3 could inhibit the infection of white spot syndrome virus (WSSV) in Chinese shrimp, Fenneropenaeus chinensis.

    PubMed

    Gui, Lang; Wang, Bing; Li, Fu-Hua; Sun, Yu-Miao; Luo, Zhan; Xiang, Jian-Hai

    2012-06-01

    Tetraspanins belong to the transmembrane 4 superfamily (TM(4)SF), which span the cell membrane 4 times and act as bridges or connectors. Increasing evidences have shown that tetraspanins play important role in virus infection. The large extracellular loop (LEL) of a tetraspanin is considered as a possible target of some virus. Tetraspanins are widely found in invertebrates, but the functional roles of most invertebrate tetraspanins have remained unknown. Recently, a tetraspanin, called FcTetraspanin-3, was cloned from the cDNA library of Chinese shrimp, Fenneropenaeus chinensis. The FcTetraspanin-3 constitutive expression in all examined tissues and the expression of the gene were highly induced in hepatopancreas, lymphoid organ and intestine by white spot syndrome virus (WSSV) challenge. In this study, we expressed and purified the recombinant peptide containing the LEL domain of FcTetraspanin-3, and produced the anti-LEL polyclone antibody. The expression of FcTetraspanin-3 was observed by real-time PCR and Western blot. Also, the localization of FcTetraspanin-3-positive cells in intestine and hepatopancreas were revealed by immunofluorescence. The results of anti-LEL antibody blocking experiments shown that the antibody can significantly reduce the mortality of shrimp challenged by WSSV. Additionally, dsRNA interference was utilized to examine the functional role of FcTetraspanin-3 in response to WSSV infection, and a sensible decrease of the viral copy number in the tetraspanin knockdown shrimp. These results suggested the blocking of LEL domain of FcTetraspanin-3 could inhibit the infection of WSSV. FcTetraspanin-3 might play an important role in response to WSSV infection, and the LEL domain of FcTetraspanin-3 might mediate the entry of WSSV.

  3. De novo, systemic, deleterious amino acid substitutions are common in large cytoskeleton-related protein coding regions

    PubMed Central

    Stoll, Rebecca J.; Thompson, Grace R.; Samy, Mohammad D.; Blanck, George

    2017-01-01

    Human mutagenesis is largely random, thus large coding regions, simply on the basis of probability, represent relatively large mutagenesis targets. Thus, we considered the possibility that large cytoskeletal-protein related coding regions (CPCRs), including extra-cellular matrix (ECM) coding regions, would have systemic nucleotide variants that are not present in common SNP databases. Presumably, such variants arose recently in development or in recent, preceding generations. Using matched breast cancer and blood-derived normal datasets from the cancer genome atlas, CPCR single nucleotide variants (SNVs) not present in the All SNPs(142) or 1000 Genomes databases were identified. Using the Protein Variation Effect Analyzer internet-based tool, it was discovered that apparent, systemic mutations (not shared among others in the analysis group) in the CPCRs, represented numerous deleterious amino acid substitutions. However, no such deleterious variants were identified among the (cancer blood-matched) variants shared by other members of the analysis group. These data indicate that private SNVs, which potentially have a medical consequence, occur de novo with significant frequency in the larger, human coding regions that collectively impact the cytoskeleton and ECM. PMID:28357075

  4. Multi-dimension and Comprehensive Assessment on the Utilizing and Sharing of Regional Large-Scale Scientific Equipment

    PubMed Central

    Li, Chen; Yongbo, Lv; Chi, Chen

    2015-01-01

    Based on the data from 30 provincial regions in China, an assessment and empirical analysis was carried out on the utilizing and sharing of the large-scale scientific equipment with a comprehensive assessment model established on the three dimensions, namely, equipment, utilization and sharing. The assessment results were interpreted in light of relevant policies. The results showed that on the whole, the overall development level in the provincial regions in eastern and central China is higher than that in western China. This is mostly because of the large gap among the different provincial regions with respect to the equipped level. But in terms of utilizing and sharing, some of the Western provincial regions, such as Ningxia, perform well, which is worthy of our attention. Policy adjustment targeting at the differentiation, elevation of the capacity of the equipment management personnel, perfection of the sharing and cooperation platform, and the promotion of the establishment of open sharing funds, are all important measures to promote the utilization and sharing of the large-scale scientific equipment and to narrow the gap among different regions. PMID:25937850

  5. The Nedd8 Non-covalent Binding Region in the Smurf HECT Domain is Critical to its Ubiquitn Ligase Function

    PubMed Central

    He, Shan; Cao, Yu; Xie, Ping; Dong, Guanglong; Zhang, Lingqiang

    2017-01-01

    Nedd8 is a ubiquitin-like protein that controls vital biological events through conjugation to target proteins. We previously identified the HECT-type ubiquitin ligase Smurf1 which controls diverse cellular processes is activated by Nedd8 through covalent neddylation. However, the effect of non-covalent binding to Nedd8 remains unknown. In this study, we demonstrate that both Smurf1 and its homologue Smurf2 carry a non-covalent Nedd8-binding site within its catalytic HECT domain. Structural analysis reveals that Smurf2 has Nedd8-binding sites within the small sub-domain of N-lobe and the C-lobe of HECT domain. Interestingly, the consensus Nedd8 binding sequence, L(X7)R(X5)F(X)ALQ is conserved in both Smurfs. Mutational studies reveal that all the five residues in the conserved sequence are required for binding to Nedd8. Functional studies suggest that mutations that disrupt Smurf interaction with Nedd8 reduce its neddylation and stabilize the protein. Furthermore, Nedd8 binding site in Smurf is shown to be necessary for its ubiquitin ligase activity towards the substrate and also the self-ubiquitylation. Finally, we show that Nedd8 binding to Smurf plays important roles in the regulation of cell migration and the BMP and TGFβ signaling pathways. PMID:28169289

  6. Large depth-high resolution full 3D imaging of the anterior segments of the eye using high speed optical frequency domain imaging

    NASA Astrophysics Data System (ADS)

    Kerbage, C.; Lim, H.; Sun, W.; Mujat, M.; de Boer, J. F.

    2007-06-01

    Three dimensional rapid large depth range imaging of the anterior segments of the human eye by an optical frequency domain imaging system is presented. The tunable source spans from 1217 to 1356 nm with an average output power of 60 mW providing a measured axial resolution of 10 μm in air based on the coherence envelope. The effective depth range is 4 mm, defined as the distance over which the sensitivity drops by 6 dB, achieved by frequency shifting the optical signal using acousto-optic modulators. The measured maximum sensitivity is 109 dB at a sample arm power of 14.7mW and A-lines rate of 43,900 per second. Images consisting of 512 depth profiles are acquired at an acquisition rate of 85 frames per second. We demonstrate an optical frequency domain imaging system capable of mapping in vivo the entire area of the human anterior segment (13.4 x 12 x 4.2 mm) in 1.4 seconds.

  7. Large Rotation of the N-terminal Domain of Hsp90 Is Important for Interaction with Some but Not All Client Proteins.

    PubMed

    Daturpalli, Soumya; Knieß, Robert A; Lee, Chung-Tien; Mayer, Matthias P

    2017-03-28

    The 90-kDa heat shock protein (Hsp90) chaperones the late folding steps of many protein kinases, transcription factors, and a diverse set of other protein clients not related in sequence and structure. Hsp90's interaction with clients appears to be coupled to a series of conformational changes. How these conformational changes contribute to its chaperone activity is currently unclear. Using crosslinking, hydrogen exchange mass spectrometry, and fluorescence experiments, we demonstrate here that the N-terminal domain of Hsp90 rotates by approximately 180° as compared to the crystal structure of yeast Hsp90 in complex with Sba1 and AMPPNP. Surprisingly, Aha1 but not Sba1 suppresses this rotation in the presence of AMPPNP but not in its absence. A minimum length of the largely unstructured linker between N-terminal and middle domain is necessary for this rotation, and interfering with the rotation strongly affects the interaction with Aha1 and the intrinsic and Aha1-stimulated ATPase activity. Surprisingly, suppression of the rotation only affects the activity of some clients and does not compromise yeast viability.

  8. An Intrinsically Disordered Region of the Acetyltransferase p300 with Similarity to Prion-Like Domains Plays a Role in Aggregation

    PubMed Central

    Kirilyuk, Alexander; Shimoji, Mika; Catania, Jason; Sahu, Geetaram; Pattabiraman, Nagarajan; Giordano, Antonio; Albanese, Christopher; Mocchetti, Italo; Toretsky, Jeffrey A.; Uversky, Vladimir N.; Avantaggiati, Maria Laura

    2012-01-01

    Several human diseases including neurodegenerative disorders and cancer are associated with abnormal accumulation and aggregation of misfolded proteins. Proteins with high tendency to aggregate include the p53 gene product, TAU and alpha synuclein. The potential toxicity of aberrantly folded proteins is limited via their transport into intracellular sub-compartments, the aggresomes, where misfolded proteins are stored or cleared via autophagy. We have identified a region of the acetyltransferase p300 that is highly disordered and displays similarities with prion-like domains. We show that this region is encoded as an alternative spliced variant independently of the acetyltransferase domain, and provides an interaction interface for various misfolded proteins, promoting their aggregation. p300 enhances aggregation of TAU and of p53 and is a component of cellular aggregates in both tissue culture cells and in alpha-synuclein positive Lewy bodies of patients affected by Parkinson disease. Down-regulation of p300 impairs aggresome formation and enhances cytotoxicity induced by misfolded protein stress. These data unravel a novel activity of p300, offer new insights into the function of disordered domains and implicate p300 in pathological aggregation that occurs in neurodegeneration and cancer. PMID:23133622

  9. Large mammals from the Upper Neopleistocene reference sections in the Tunka rift valley, southwestern Baikal Region

    NASA Astrophysics Data System (ADS)

    Shchetnikov, A. A.; Klementiev, A. M.; Filinov, I. A.; Semeney, E. Yu.

    2015-03-01

    This work presents the data on new finds of fossil macrotheriofauna in the reference sections of the Upper Neopleistocene sediments in the Tunka rift valley (southwestern Baikal Region). The osteological material of a number of Late Neopleistocene mammals including extinct species rare for the Baikal region such as Crocuta spelaea, Panthera spelaea, and Spirocerus kiakhtensis (?) was directly dated with a radiocarbon (AMS) method. The obtained 14C data (18000-35000 years) allow one to rejuvenate significantly the upper limit of the common age interval of habitat of these animals in southern part of Eastern Siberia. Cave hyena and spiral-horned antelope lived in the Tunka rift valley in the Baikal region in Late Kargino time (37-24 ka), and cave lion survived the maximum in the Sartan cryochron in the region (21-20 ka). The study of collected paleontological collections provides a basis for selection of independent Kargino (MIS 3) faunal assemblages to use them for regional biostratigraphic analysis of Pleistocene deposits. Radiocarbon age dating of samples allows one to attribute confidently all paleofaunal remains available to the second half of the Late Pleistocene.

  10. On the relationship between large-scale climate modes and regional synoptic patterns that drive Victorian rainfall

    NASA Astrophysics Data System (ADS)

    Verdon-Kidd, D. C.; Kiem, A. S.

    2009-04-01

    In this paper regional (synoptic) and large-scale climate drivers of rainfall are investigated for Victoria, Australia. A non-linear classification methodology known as self-organizing maps (SOM) is used to identify 20 key regional synoptic patterns, which are shown to capture a range of significant synoptic features known to influence the climate of the region. Rainfall distributions are assigned to each of the 20 patterns for nine rainfall stations located across Victoria, resulting in a clear distinction between wet and dry synoptic types at each station. The influence of large-scale climate modes on the frequency and timing of the regional synoptic patterns is also investigated. This analysis revealed that phase changes in the El Niño Southern Oscillation (ENSO), the Indian Ocean Dipole (IOD) and/or the Southern Annular Mode (SAM) are associated with a shift in the relative frequency of wet and dry synoptic types on an annual to inter-annual timescale. In addition, the relative frequency of synoptic types is shown to vary on a multi-decadal timescale, associated with changes in the Inter-decadal Pacific Oscillation (IPO). Importantly, these results highlight the potential to utilise the link between the regional synoptic patterns derived in this study and large-scale climate modes to improve rainfall forecasting for Victoria, both in the short- (i.e. seasonal) and long-term (i.e. decadal/multi-decadal scale). In addition, the regional and large-scale climate drivers identified in this study provide a benchmark by which the performance of Global Climate Models (GCMs) may be assessed.

  11. Very large domain wall velocities in Pt/Co/GdOx and Pt/Co/Gd trilayers with Dzyaloshinskii-Moriya interaction

    NASA Astrophysics Data System (ADS)

    Pham, Thai Ha; Vogel, J.; Sampaio, J.; Vaňatka, M.; Rojas-Sánchez, J.-C.; Bonfim, M.; Chaves, D. S.; Choueikani, F.; Ohresser, P.; Otero, E.; Thiaville, A.; Pizzini, S.

    2016-03-01

    We carried out measurements of domain wall (DW) velocities driven by magnetic-field pulses in symmetric Pt/Co/Pt and asymmetric Pt/Co/AlOx, Pt/Co/GdOx and Pt/Co/Gd trilayers with ultrathin Co layers and perpendicular magnetic anisotropy. The maximum observed velocity is much larger in the asymmetric samples, where the interfacial Dzyaloshinskii-Moriya interaction (DMI) stabilises chiral Néel walls. In quantitative agreement with analytical models, in all samples the maximum observed DW speed scales as D/Ms , where D is the strength of the DMI and Ms the spontaneous magnetisation. In Pt/Co/Gd, where the anti-parallel coupling between the magnetic moments of Gd and Co leads to a decrease of the total magnetisation, very large DW speeds (up to 700 m/s) are obtained.

  12. An STM study on nonionic fluorosurfactant zonyl FSN self-assembly on Au(111): large domains, few defects, and good stability.

    PubMed

    Tang, Yongan; Yan, Jiawei; Zhou, Xiaoshun; Fu, Yongchun; Mao, Bingwei

    2008-12-02

    Nonionic Fluorosurfactant Zonyl FSN self-assembly on Au(111) is investigated with scanning tunneling microscopy under ambient conditions. STM reveals that the FSN forms SAMs on Au(l11) with very large domain size and almost no defects. A (mean square root of 3 x mean square root of 3)R3 degree arrangement of the FSN SAM on Au(111) is observed. The SAMs show excellent chemical stability and last for at least a month in atmospheric conditions. The structure and stability of the FSN SAMs are compared with those of alkanethiols SAMs. It is expected that FSN may serve as a new kind of molecule to form SAMs for surface modification, which would benefit wider applications for various purposes.

  13. Statistical convergence and the effect of large-scale motions on turbulent Rayleigh-Bénard convection in a cylindrical domain with 6.3 aspect ratio

    NASA Astrophysics Data System (ADS)

    Sakievich, Philip; Peet, Yulia; Adrian, Ronald

    2016-11-01

    At high Rayleigh numbers in moderate aspect-ratio cylindrical domains turbulent Rayleigh-Bénard convection (RBC) exhibits coherent large-scale motions with patterns like some of those found in laminar flow. In this work we show how the patterns of the largest scales in turbulent RBC affect the bias and convergence of the flow statistics at aspect-ratio 6.3 (diameter/ height). Large scale motions influence two of the finite-time statistical mean's inherent properties: 1) the orientation of the patterns changes so slowly that it may appear almost fixed during a finite averaging time interval, thereby imbedding a preferred azimuthal direction in the sampled data; 2) they also have at least two states associated with the occurrence of up and down motions near the center of the convection cell. We will present a novel technique for triggering additional states of RBC in DNS simulations that are targeted for improving the statistical convergence of the flow. This technique gently perturbs the flow so that the new variations of the large scale patterns can be sampled. Funding through U. S. National Science Foundation Grants CBET-1335731, CMMI-1250124 and XSEDE research allocation TG-CTS150039.

  14. Inclusive electron scattering from nuclei in the quasielastic region at large momentum transfer

    NASA Astrophysics Data System (ADS)

    Fomin, Nadia

    2008-12-01

    Experiment E02-019, performed in Hall C at the Thomas Jefferson National Accelerator Facility (TJNAF), was a measurement of inclusive electron cross sections for several nuclei (^{2}H,^{3}He, ^{4}He, ^{9}Be,^{12}C, ^{63}Cu, and ^{197}Au) in the quasielastic region at high momentum transfer. In the region of low energy transfer, the cross sections were analyzed in terms of the reduced response, F(y), by examining its y-scaling behavior. The data were also examined in terms of the nuclear structure function ν W_2^A and its behavior in x and the Nachtmann variable ξ. The data show approximate scaling of ν W_2^A in ξ for all targets at all kinematics, unlike scaling in x, which is confined to the DIS regime. However, y-scaling observations are limited to the kinematic region dominated by the quasielastic response ({y<0}), where some scaling violations arising from FSIs are observed.

  15. Statistical searches for microlensing events in large, non-uniformly sampled time-domain surveys: A test using palomar transient factory data

    SciTech Connect

    Price-Whelan, Adrian M.; Agüeros, Marcel A.; Fournier, Amanda P.; Street, Rachel; Ofek, Eran O.; Covey, Kevin R.; Levitan, David; Sesar, Branimir; Laher, Russ R.; Surace, Jason

    2014-01-20

    Many photometric time-domain surveys are driven by specific goals, such as searches for supernovae or transiting exoplanets, which set the cadence with which fields are re-imaged. In the case of the Palomar Transient Factory (PTF), several sub-surveys are conducted in parallel, leading to non-uniform sampling over its ∼20,000 deg{sup 2} footprint. While the median 7.26 deg{sup 2} PTF field has been imaged ∼40 times in the R band, ∼2300 deg{sup 2} have been observed >100 times. We use PTF data to study the trade off between searching for microlensing events in a survey whose footprint is much larger than that of typical microlensing searches, but with far-from-optimal time sampling. To examine the probability that microlensing events can be recovered in these data, we test statistics used on uniformly sampled data to identify variables and transients. We find that the von Neumann ratio performs best for identifying simulated microlensing events in our data. We develop a selection method using this statistic and apply it to data from fields with >10 R-band observations, 1.1 × 10{sup 9} light curves, uncovering three candidate microlensing events. We lack simultaneous, multi-color photometry to confirm these as microlensing events. However, their number is consistent with predictions for the event rate in the PTF footprint over the survey's three years of operations, as estimated from near-field microlensing models. This work can help constrain all-sky event rate predictions and tests microlensing signal recovery in large data sets, which will be useful to future time-domain surveys, such as that planned with the Large Synoptic Survey Telescope.

  16. Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes.

    PubMed

    Upadhyay, Amit A; Fleetwood, Aaron D; Adebali, Ogun; Finn, Robert D; Zhulin, Igor B

    2016-04-01

    Cellular receptors usually contain a designated sensory domain that recognizes the signal. Per/Arnt/Sim (PAS) domains are ubiquitous sensors in thousands of species ranging from bacteria to humans. Although PAS domains were described as intracellular sensors, recent structural studies revealed PAS-like domains in extracytoplasmic regions in several transmembrane receptors. However, these structurally defined extracellular PAS-like domains do not match sequence-derived PAS domain models, and thus their distribution across the genomic landscape remains largely unknown. Here we show that structurally defined extracellular PAS-like domains belong to the Cache superfamily, which is homologous to, but distinct from the PAS superfamily. Our newly built computational models enabled identification of Cache domains in tens of thousands of signal transduction proteins including those from important pathogens and model organisms. Furthermore, we show that Cache domains comprise the dominant mode of extracellular sensing in prokaryotes.

  17. Cache domains that are homologous to, but different from PAS domains comprise the largest superfamily of extracellular sensors in prokaryotes

    DOE PAGES

    Upadhyay, Amit A.; Fleetwood, Aaron D.; Adebali, Ogun; ...

    2016-04-06

    Cellular receptors usually contain a designated sensory domain that recognizes the signal. Per/Arnt/Sim (PAS) domains are ubiquitous sensors in thousands of species ranging from bacteria to humans. Although PAS domains were described as intracellular sensors, recent structural studies revealed PAS-like domains in extracytoplasmic regions in several transmembrane receptors. However, these structurally defined extracellular PAS-like domains do not match sequence-derived PAS domain models, and thus their distribution across the genomic landscape remains largely unknown. Here we show that structurally defined extracellular PAS-like domains belong to the Cache superfamily, which is homologous to, but distinct from the PAS superfamily. Our newly builtmore » computational models enabled identification of Cache domains in tens of thousands of signal transduction proteins including those from important pathogens and model organisms.Moreover, we show that Cache domains comprise the dominant mode of extracellular sensing in prokaryotes.« less

  18. Cache domains that are homologous to, but different from PAS domains comprise the largest superfamily of extracellular sensors in prokaryotes

    SciTech Connect

    Upadhyay, Amit A.; Fleetwood, Aaron D.; Adebali, Ogun; Finn, Robert D.; Zhulin, Igor B.; Schlessinger, Avner

    2016-04-06

    Cellular receptors usually contain a designated sensory domain that recognizes the signal. Per/Arnt/Sim (PAS) domains are ubiquitous sensors in thousands of species ranging from bacteria to humans. Although PAS domains were described as intracellular sensors, recent structural studies revealed PAS-like domains in extracytoplasmic regions in several transmembrane receptors. However, these structurally defined extracellular PAS-like domains do not match sequence-derived PAS domain models, and thus their distribution across the genomic landscape remains largely unknown. Here we show that structurally defined extracellular PAS-like domains belong to the Cache superfamily, which is homologous to, but distinct from the PAS superfamily. Our newly built computational models enabled identification of Cache domains in tens of thousands of signal transduction proteins including those from important pathogens and model organisms.Moreover, we show that Cache domains comprise the dominant mode of extracellular sensing in prokaryotes.

  19. Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes

    PubMed Central

    Upadhyay, Amit A.; Fleetwood, Aaron D.; Adebali, Ogun; Finn, Robert D.; Zhulin, Igor B.

    2016-01-01

    Cellular receptors usually contain a designated sensory domain that recognizes the signal. Per/Arnt/Sim (PAS) domains are ubiquitous sensors in thousands of species ranging from bacteria to humans. Although PAS domains were described as intracellular sensors, recent structural studies revealed PAS-like domains in extracytoplasmic regions in several transmembrane receptors. However, these structurally defined extracellular PAS-like domains do not match sequence-derived PAS domain models, and thus their distribution across the genomic landscape remains largely unknown. Here we show that structurally defined extracellular PAS-like domains belong to the Cache superfamily, which is homologous to, but distinct from the PAS superfamily. Our newly built computational models enabled identification of Cache domains in tens of thousands of signal transduction proteins including those from important pathogens and model organisms. Furthermore, we show that Cache domains comprise the dominant mode of extracellular sensing in prokaryotes. PMID:27049771

  20. Nonhemolytic Streptococcus pyogenes Isolates That Lack Large Regions of the sag Operon Mediating Streptolysin S Production▿

    PubMed Central

    Yoshino, Miho; Murayama, Somay Y.; Sunaoshi, Katsuhiko; Wajima, Takeaki; Takahashi, Miki; Masaki, Junko; Kurokawa, Iku; Ubukata, Kimiko

    2010-01-01

    Among nonhemolytic Streptococcus pyogenes (group A streptococcus) strains (n = 9) isolated from patients with pharyngitis or acute otitis media, we identified three deletions in the region from the epf gene, encoding the extracellular matrix binding protein, to the sag operon, mediating streptolysin S production. PMID:20018818

  1. Simultaneous SMM flat crystal spectrometer and Very Large Array observations of solar active regions

    NASA Technical Reports Server (NTRS)

    Lang, Kenneth R.; Willson, Robert F.; Smith, Kermit L.; Strong, Keith T.

    1987-01-01

    High-resolution images of the quiescent emission from two solar active regions at 20 cm (VLA) and soft X-ray (SMM FCS) wavelengths are compared. There are regions where the X-ray coronal loops have been completely imaged at 20 cm wavelength. In other regions, the X-ray radiation was detected without detectable 20 cm radiation, and vice versa. The X-ray data were used to infer average electron temperatures of about 3-million K and average electron densities of about 2.5 x 10 to the 9th/cu cm for the X-ray emitting plasma in the two active regions. The thermal bremsstrahlung of the X-ray emitting plasma is optically thin at 20 cm wavelength. The 20 cm brightness temperatures were always less than T(e), which is consistent with optically thin bremsstrahlung. The low T(B) can be explained if a higher, cooler plasma covers the hotter X-ray emitting plasma. Thermal gyroresonance radiation must account for the intense 20 cm radiation near and above sunspots where no X-ray radiation is detected.

  2. γδTCR immunoglobulin constant region domain exchange in human αβTCRs improves TCR pairing without altering TCR gene-modified T cell function.

    PubMed

    Tao, Changli; Shao, Hongwei; Zhang, Wenfeng; Bo, Huaben; Wu, Fenglin; Shen, Han; Huang, Shulin

    2017-02-15

    The adoptive genetic transfer of T cell receptors (TCRs) has been shown to be overall feasible and offer clinical potential as a treatment for different types of cancer. However, this promising clinical approach is limited by the serious potential consequence that exogenous TCR mispairing with endogenous TCR chains may lead to the risk of self-reactivity. In the present study, domain‑exchange and three‑dimensional modeling strategies were used to create a set of chimeric TCR variants, which were used to exchange the partial or complete constant region of αβTCR with corresponding γδTCR domains. The expression, assembly and function of the chimeric TCR variants were examined in Jurkat T cells and peripheral mononuclear blood cells (PBMCs). Genetically‑encoded chimeras were fused with a pair of fluorescent proteins (ECFP/EYFP) to monitor expression and the pairing between chimeric TCRα chains and TCRβ chains. The fluorescence energy transfer based on confocal laser scanning microscopy showed that the introduction of γδTCR constant sequences into the αβTCR did not result in a global reduction of mispairing with endogenous TCR. However, the TCR harboring the immunoglobulin‑like domain of the γδTCR constant region (i.e., TCR∆IgC), showed a higher expression and preferential pairing, compared with wild‑type (wt)TCR. The function analysis showed that TCR∆IgC exhibited the same levels of interferon-γ production and cytotoxic activity, compared with wtTCR. Furthermore, these modified TCR-transduced T cells retained the classic human leukocyte antigen restriction of the original TCR. The other two chimeric TCRs, had either exchange of the cp+tm+ic domain or exchange of the whole C domain (Fig. 1). Ultimately, exchange of these domains demonstrated defective function in the transduced T cells. Taken together, these findings may provide further understanding of the γδTCR constant domain with implications for the improvement of TCR gene transfer

  3. Large-Scale Assessments of Students' Learning and Education Policy: Synthesising Evidence across World Regions

    ERIC Educational Resources Information Center

    Tobin, Mollie; Nugroho, Dita; Lietz, Petra

    2016-01-01

    This article synthesises findings from two systematic reviews that examined evidence of the link between large-scale assessments (LSAs) and education policy in economically developing countries and in countries of the Asia-Pacific. Analyses summarise evidence of assessment characteristics and policy goals of LSAs that influence education policy,…

  4. Bulk GaN alpha-particle detector with large depletion region and improved energy resolution

    NASA Astrophysics Data System (ADS)

    Xu, Qiang; Mulligan, Padhraic; Wang, Jinghui; Chuirazzi, William; Cao, Lei

    2017-03-01

    An alpha-particle detector was fabricated using a freestanding n-type bulk GaN wafer with a Au/Ni/GaN sandwich Schottky structure. Current-voltage measurements at room temperature revealed a Schottky contact with a leakage current of 7.53±0.3 nA at a reverse bias of 200 V. The detector had a large depletion depth that can capture much of the energy from 5.486 MeV alpha particles emitted from a 241Am source. The resolution of its alpha-particle energy spectrum was improved to 2.2±0.2% at 5.486 MeV under a bias of 550 V. This superior resolution was attributed to the shortening of the carrier transit time and the large energy deposition within the large depletion depth, i.e., 27 μm at -550 V, which all resulted in a more complete charge collection. A model developed using the ATLAS simulation framework from Silvaco Inc. was employed to study the charge collection process. The simulation results were found to agree closely with the experimental results. This detector will be beneficial for research at neutron scattering facilities, the International Thermonuclear Experimental Reactor, and the Large Hadron Collider, among other institutions, where the Si-based charged particle detectors could be quickly degraded in an intense radiation field.

  5. A Topographic Image Map of the Sabrina Valles Region Including Information on Large Martian Impact Craters

    NASA Astrophysics Data System (ADS)

    Gehrke, S.; Köhring, R.; Barlow, N. G.; Gwinner, K.; Scholten, F.; Lehmann, H.; Albertz, J.

    2007-03-01

    The Catalog of Large Martian Impact Craters provides detailed information on 42,283 craters >5 km; it is planned to be integrated in the Topographic Image Map Mars 1:200,000 series. Such an update is shown in a special target map, based on HRSC data.

  6. Large/giant meningiomas of posterior third ventricular region: falcotentorial or velum interpositum?

    PubMed

    Behari, Sanjay; Das, Kuntal Kanti; Kumar, Ashish; Mehrotra, Anant; Srivastava, Arun K; Sahu, Rabi N; Jaiswal, Awadhesh K

    2014-01-01

    Surgical excision of rare, large-to-giant posterior third ventricular (PTV) meningiomas [including velum-interpositum meningiomas (VIM; postero-superior venous complex displacement; without falco-tentorial attachment) and falco-tentorial meningiomas (FTM; falco-tentorial attachment; displacing major veins antero-inferiorly)] is extremely challenging. To study the management nuances in the excision of large-to-giant PTV meningiomas. Tertiary care referral center. Four patients with large (>3 cm; n = 2) and giant (>5 cm; n = 2) meningiomas (FTM = 2; VIM = 2, mean tumor size = 4.9 cm) underwent occipital transtentorial approach (OTT) for tumor excision. One also underwent a second-stage supracerebellar infratentorial (SCIT) approach. The side of approach was determined by lateral tumor extension and venous displacement (right = 3, left = 1). Near-total removal or subtotal excision (<10% remaining) with radiotherapy was performed in 2 patients each, respectively. At follow-up (mean: 14.75 months), clinical improvement without tumor recurrence/re-growth was achieved. Extent of excision was determined by position of great vein of Galen; tumor attachment to falco-tentorium or major veins; its consistency; its lateral and inferior extent; and, presence of a good tumor-neuraxial arachnoidal plane. OTT is the preferable approach for large-to-giant meningiomas as it provides a wider corridor and better delineation of tumor-neurovascular arachnoidal interface.

  7. How Large Should the QM Region Be in QM/MM Calculations? The Case of Catechol O-Methyltransferase.

    PubMed

    Kulik, Heather J; Zhang, Jianyu; Klinman, Judith P; Martínez, Todd J

    2016-11-10

    Hybrid quantum mechanical-molecular mechanical (QM/MM) simulations are widely used in studies of enzymatic catalysis. Until recently, it has been cost prohibitive to determine the asymptotic limit of key energetic and structural properties with respect to increasingly large QM regions. Leveraging recent advances in electronic structure efficiency and accuracy, we investigate catalytic properties in catechol O-methyltransferase, a prototypical methyltransferase critical to human health. Using QM regions ranging in size from reactants-only (64 atoms) to nearly one-third of the entire protein (940 atoms), we show that properties such as the activation energy approach within chemical accuracy of the large-QM asymptotic limits rather slowly, requiring approximately 500-600 atoms if the QM residues are chosen simply by distance from the substrate. This slow approach to asymptotic limit is due to charge transfer from protein residues to the reacting substrates. Our large QM/MM calculations enable identification of charge separation for fragments in the transition state as a key component of enzymatic methyl transfer rate enhancement. We introduce charge shift analysis that reveals the minimum number of protein residues (approximately 11-16 residues or 200-300 atoms for COMT) needed for quantitative agreement with large-QM simulations. The identified residues are not those that would be typically selected using criteria such as chemical intuition or proximity. These results provide a recipe for a more careful determination of QM region sizes in future QM/MM studies of enzymes.

  8. How Large Should the QM Region Be in QM/MM Calculations? The Case of Catechol O-Methyltransferase

    PubMed Central

    2016-01-01

    Hybrid quantum mechanical–molecular mechanical (QM/MM) simulations are widely used in studies of enzymatic catalysis. Until recently, it has been cost prohibitive to determine the asymptotic limit of key energetic and structural properties with respect to increasingly large QM regions. Leveraging recent advances in electronic structure efficiency and accuracy, we investigate catalytic properties in catechol O-methyltransferase, a prototypical methyltransferase critical to human health. Using QM regions ranging in size from reactants-only (64 atoms) to nearly one-third of the entire protein (940 atoms), we show that properties such as the activation energy approach within chemical accuracy of the large-QM asymptotic limits rather slowly, requiring approximately 500–600 atoms if the QM residues are chosen simply by distance from the substrate. This slow approach to asymptotic limit is due to charge transfer from protein residues to the reacting substrates. Our large QM/MM calculations enable identification of charge separation for fragments in the transition state as a key component of enzymatic methyl transfer rate enhancement. We introduce charge shift analysis that reveals the minimum number of protein residues (approximately 11–16 residues or 200–300 atoms for COMT) needed for quantitative agreement with large-QM simulations. The identified residues are not those that would be typically selected using criteria such as chemical intuition or proximity. These results provide a recipe for a more careful determination of QM region sizes in future QM/MM studies of enzymes. PMID:27704827

  9. Paring Down HIV Env: Design and Crystal Structure of a Stabilized Inner Domain of HIV-1 gp120 Displaying a Major ADCC Target of the A32 Region.

    PubMed

    Tolbert, William D; Gohain, Neelakshi; Veillette, Maxime; Chapleau, Jean-Philippe; Orlandi, Chiara; Visciano, Maria L; Ebadi, Maryam; DeVico, Anthony L; Fouts, Timothy R; Finzi, Andrés; Lewis, George K; Pazgier, Marzena

    2016-05-03

    Evidence supports a role of antibody-dependent cellular cytotoxicity (ADCC) toward transitional epitopes in the first and second constant (C1-C2) regions of gp120 (A32-like epitopes) in preventing HIV-1 infection and in vaccine-induced protection. Here, we describe the first successful attempt at isolating the inner domain (ID) of gp120 as an independent molecule that encapsulates the A32-like region within a minimal structural unit of the HIV-1 Env. Through structure-based design, we developed ID2, which consists of the ID expressed independently of the outer domain and stabilized in the CD4-bound conformation by an inter-layer disulfide bond. ID2 expresses C1-C2 epitopes in the context of CD4-triggered full-length gp120 but without any known neutralizing epitope present. Thus, ID2 represents a novel probe for the analysis and/or selective induction of antibody responses to the A32 epitope region. We also present the crystal structure of ID2 complexed with mAb A32, which defines its epitope.

  10. Essential regions in the membrane domain of bacterial complex I (NDH-1): the machinery for proton translocation.

    PubMed

    Sato, Motoaki; Torres-Bacete, Jesus; Sinha, Prem Kumar; Matsuno-Yagi, Akemi; Yagi, Takao

    2014-08-01

    The proton-translocating NADH-quinone oxidoreductase (complex I/NDH-1) is the first and largest enzyme of the respiratory chain which has a central role in cellular energy production and is implicated in many human neurodegenerative diseases and aging. It is believed that the peripheral domain of complex I/NDH-1 transfers the electron from NADH to Quinone (Q) and the redox energy couples the proton translocation in the membrane domain. To investigate the mechanism of the proton translocation, in a series of works we have systematically studied all membrane subunits in the Escherichia coli NDH-1 by site-directed mutagenesis. In this mini-review, we have summarized our strategy and results of the mutagenesis by depicting residues essential for proton translocation, along with those for subunit connection. It is suggested that clues to understanding the driving forces of proton translocation lie in the similarities and differences of the membrane subunits, highlighting the communication of essential charged residues among the subunits. A possible proton translocation mechanism with all membrane subunits operating in unison is described.

  11. Large plasma density enhancements occurring in the northern polar region during the 6 April 2000 superstorm

    NASA Astrophysics Data System (ADS)

    Horvath, Ildiko; Lovell, Brian C.

    2014-06-01

    We focus on the ionospheric response of northern high-latitude region to the 6 April 2000 superstorm and aim to investigate how the storm-enhanced density (SED) plume plasma became distributed in the regions of auroral zone and polar cap plus to study the resultant ionospheric features and their development. Multi-instrument observational results combined with model-generated, two-cell convection maps permitted identifying the high-density plasma's origin and the underlying plasma transportation processes. Results show the plasma density feature of polar cap enhancement (PCE; ~600 × 103 i+/cm3) appearing for 7 h during the main phase and characterized by increases reaching up to 6 times of the quiet time values. Meanwhile, strong westward convections (~17,500 m/s) created low plasma densities in a wider region of the dusk cell. Oppositely, small (~750 m/s) but rigorous westward drifts drove the SED plume plasma through the auroral zone, wherein plasma densities doubled. As the SED plume plasma traveled along the convection streamlines and entered the polar cap, a continuous enhancement of the tongue of ionization (TOI) developed under steady convection conditions. However, convection changes caused slow convections and flow stagnations and thus segmented the TOI feature by locally depleting the plasma in the affected regions of the auroral zone and polar cap. From the strong correspondence of polar cap potential drop and subauroral polarization stream (SAPS), we conclude that the SAPS E-field strength remained strong, and under its prolonged influence, the SED plume provided a continuous supply of downward flowing high-density plasma for the development and maintenance of PCEs.

  12. Large Eddy Simulations of the Effects of EMBr and SEN Submergence Depth on Turbulent Flow in the Mold Region of a Steel Caster

    NASA Astrophysics Data System (ADS)

    Jin, Kai; Vanka, Surya P.; Thomas, Brian G.

    2017-02-01

    Transient turbulent flow in the mold region during continuous casting of steel is related to many quality problems, such as surface defects and slag entrainment. This work applies an efficient multi-GPU based code, CUFlow, to perform large eddy simulations (LES) of the turbulent flow in a domain that includes the slide gate, SEN, and mold region. The computations were first validated by comparing the predicted surface velocity with plant measurements. Then, seven LES simulations were conducted to study the effects of casting speed, electromagnetic braking (EMBr) field strength, and submerged entry nozzle (SEN) depth on the transient flow. The results show that EMBr has an important influence on flow inside the SEN, in addition to flow in the mold. With EMBr, an "M-shaped" flow profile is seen inside the SEN. The swirling flow behavior in the SEN and ports is more symmetrical at high casting speed and with higher EMBr strength. The position of the SEN ports relative to the peak magnetic field affects the EMBr performance. The results confirm and quantify how applying EMBr greatly lowers both the magnitude and turbulent variations of the surface velocity and level profile.

  13. Large differences in regional precipitation change between a first and second 2 K of global warming

    NASA Astrophysics Data System (ADS)

    Good, Peter; Booth, Ben B. B.; Chadwick, Robin; Hawkins, Ed; Jonko, Alexandra; Lowe, Jason A.

    2016-12-01

    For adaptation and mitigation planning, stakeholders need reliable information about regional precipitation changes under different emissions scenarios and for different time periods. A significant amount of current planning effort assumes that each K of global warming produces roughly the same regional climate change. Here using 25 climate models, we compare precipitation responses with three 2 K intervals of global ensemble mean warming: a fast and a slower route to a first 2 K above pre-industrial levels, and the end-of-century difference between high-emission and mitigation scenarios. We show that, although the two routes to a first 2 K give very similar precipitation changes, a second 2 K produces quite a different response. In particular, the balance of physical mechanisms responsible for climate model uncertainty is different for a first and a second 2 K of warming. The results are consistent with a significant influence from nonlinear physical mechanisms, but aerosol and land-use effects may be important regionally.

  14. Himalayan Wintertime Climate Variability: Large-Scale Atmospheric Circulation and Regional Precipitation

    NASA Astrophysics Data System (ADS)

    Cannon, Forest Glen

    The future state of High Mountain Asia's (HMA) glaciers is of critical importance to water security throughout densely populated regions of Asia. Without understanding regional climatic influences, the prediction of terrestrial water fluxes is not possible. Glacier records in the eastern and central Himalaya (CH) yield some of the world's most rapid retreat rates. However, there are a number of steady state or positive mass-balance glaciers in the Karakoram and western Himalaya (KH) regions. The goal of this research is to investigate multi-annual variations in synoptic wintertime weather as a contributing factor to regional mass-balance trends. Winter Westerly Disturbances (WWD) are the primary climatic influence within HMA during the boreal winter. This research investigates variations and changes in WWD over the period 1979--2010 and relationships with extreme precipitation in the KH and CH using multiple datasets. It is demonstrated that extreme precipitation events occurring in the KH and CH are often spatiotemporally independent, suggesting differing behavior of WWD affecting each region. The wavelet power spectrum of 200hPa geopotential height anomalies is used to characterize the frequency and magnitude of individual disturbances and to distinguish synoptic scale variability through time. This analysis exhibits an enhancement in the strength and frequency of WWD in the KH and indicates an increase in local extreme precipitation events. In contrast, the CH is observed to experience weakening influence of these disturbances and consequently, a decrease in extreme precipitation. Additionally, peak melt season temperatures are observed to decrease (increase) in the KH (CH) during the study period. This study also investigates multi-annual variability of WWD and teleconnections with some known modes of climate variability affecting central Asia, including the Arctic Oscillation, the El Nino Southern Oscillation, and the Siberian High. Although there is clear

  15. Large Water Management Projects and Schistosomiasis Control, Dongting Lake Region, China

    PubMed Central

    Li, Yue-Sheng; Zhao, Zheng-Yuan; He, Yong-Kang; Ellis, Magda K.; McManus, Donald P.

    2007-01-01

    Construction of the Three Gorges Dam across the Yangtze River will substantially change the ecology of the Dongting Lake in southern China. In addition, the Central and Hunan Provinces’ governmental authorities have instigated a Return Land to Lake Program that will extend the Dongting Lake surface area from the current 2,681 km2 to 4,350 km2.The previous construction of embankments and the large silt deposits made by the Yangtze River and other connecting rivers have contributed to frequent disastrous flooding. As a consequence of the 2 water projects, >2 million persons and their domestic animals are being resettled. This article provides an overview of the historical background of these 2 large water management projects, the associated population movement, and their impact on future transmission and control of schistosomiasis in the Dongting Lake area. The dam will likely substantially extend the range of the snail habitats and increase schistosome transmission and schistosomiasis cases. PMID:18214167

  16. Improving a regional outreach program in a large health system using geographic information systems.

    PubMed

    Gabbert, John P; Trine, Robert M; Bintz, Marilu

    2012-06-01

    As government-insured populations grow, commercially insured populations decrease, and declining insurance reimbursements pressure cost and revenue. Health systems must strive to improve quality while lowering costs. Large medical centers with rural sites must understand their geography and how distances impede access to services, thereby affecting patient health. Without relevant data, which can be provided through the use of geographic information systems (GIS) technology, improvement is often delayed. Gundersen Lutheran Health System, a large multi-specialty system with urban and rural sites in 3 states, is developing an evaluative outreach GIS to facilitate understanding of, and response to, rural health needs. Investing in GIS technology furthers the health system's ability to deliver superior, affordable care.

  17. Large-scale shear velocity structure of the upper mantle beneath Europe and surrounding regions

    NASA Astrophysics Data System (ADS)

    Legendre, C. P.; Meier, T. M.; Lebedev, S.; Friederich, W.

    2009-12-01

    The automated multimode waveform inversion technique developed by Lebedev et al. (2005) was applied to available data of broadband stations in Europe and surrounding regions. It performs a fitting of the complete waveform starting from the S-wave onset to the surface wave. Assuming the location and focal mechanism of a considered earthquake as known, the first basic step is to consider each available seismogram separately and to find the 1D-model that can explain the filtered seismogram best. In a second step, each 1D-model serves as a linear constraint in an inversion for a 3D S-wave velocity model of the upper mantle. We collected data for the years from 1990 to 2006 from all permanent stations for which data were available via the data centers of ORFEUS, GEOFON amd IRIS, and from others that build the Virtual European Seismological Network (VEBSN). In addition, we incorporated data from temporary experiments like SVEKALAPKO, TOR and the Eifel plume project as well as permanent stations in France. Just recently we were also able to add the data recorded by the temporary broadband EGELADOS network in the southern Aegean. In this way, a huge data set of about 500000 seismograms came about from which about 60000 1D-models could be constructed. The resulting models exhibit an overwhelming structural detail in relation to the size of the region considered in the inversion. They are to our knowledge the most detailed models of shear wave velocity currently available for the European upper mantle and surroundings. Most prominent features are an extremely sharp demarcation of the East European platform from Western Europe. Narrow high velocity regions follow the Hellenic arc and the Ionian trench toward the north. Whereas high velocities are found beneath the western Alps between about 100 km to 200 km depth, the eastern Alps show a low velocity anomaly at these depths. Low velocity zones are found at depths around 150 km in the Pannonian basin, the back-arc of the

  18. Direct Binding of the PDZ Domain of Dishevelled to a Conserved Internal Sequence in the C-Terminal Region of Frizzled

    PubMed Central

    Wong, Hing-C.; Bourdelas, Audrey; Krauss, Anke; Lee, Ho-Jin; Shao, Youming; Wu, Dianqing; Mlodzik, Marek; Shi, De-Li; Zheng, Jie

    2015-01-01

    Summary The cytoplasmic protein Dishevelled (Dvl) and the associated membrane-bound receptor Frizzled (Fz) are essential in canonical and noncanonical Wnt signaling pathways. However, the molecular mechanisms underlying this signaling are not well understood. By using NMR spectroscopy, we determined that an internal sequence of Fz binds to the conventional peptide binding site in the PDZ domain of Dvl; this type of site typically binds to C-terminal binding motifs. The C-terminal region of the Dvl inhibitor Dapper (Dpr) and Frodo bound to the same site. In Xenopus, Dvl binding peptides of Fz and Dpr/Frodo inhibited canonical Wnt signaling and blocked Wnt-induced secondary axis formation in a dose-dependent manner, but did not block noncanonical Wnt signaling mediated by the DEP domain. Together, our results identify a missing molecular connection within the Wnt pathway. Differences in the binding affinity of the Dvl PDZ domain and its binding partners may be important in regulating signal transduction by Dvl. PMID:14636582

  19. Direct binding of the PDZ domain of Dishevelled to a conserved internal sequence in the C-terminal region of Frizzled.

    PubMed

    Wong, Hing-C; Bourdelas, Audrey; Krauss, Anke; Lee, Ho-Jin; Shao, Youming; Wu, Dianqing; Mlodzik, Marek; Shi, De-Li; Zheng, Jie

    2003-11-01

    The cytoplasmic protein Dishevelled (Dvl) and the associated membrane-bound receptor Frizzled (Fz) are essential in canonical and noncanonical Wnt signaling pathways. However, the molecular mechanisms underlying this signaling are not well understood. By using NMR spectroscopy, we determined that an internal sequence of Fz binds to the conventional peptide binding site in the PDZ domain of Dvl; this type of site typically binds to C-terminal binding motifs. The C-terminal region of the Dvl inhibitor Dapper (Dpr) and Frodo bound to the same site. In Xenopus, Dvl binding peptides of Fz and Dpr/Frodo inhibited canonical Wnt signaling and blocked Wnt-induced secondary axis formation in a dose-dependent manner, but did not block noncanonical Wnt signaling mediated by the DEP domain. Together, our results identify a missing molecular connection within the Wnt pathway. Differences in the binding affinity of the Dvl PDZ domain and its binding partners may be important in regulating signal transduction by Dvl.

  20. The first three domains of the insulin receptor differ structurally from the insulin-like growth factor 1 receptor in the regions governing ligand specificity

    PubMed Central

    Lou, Meizhen; Garrett, Thomas P. J.; McKern, Neil M.; Hoyne, Peter A.; Epa, V. Chandana; Bentley, John D.; Lovrecz, George O.; Cosgrove, Leah J.; Frenkel, Maurice J.; Ward, Colin W.

    2006-01-01

    The insulin receptor (IR) and the type-1 insulin-like growth factor receptor (IGF1R) are homologous multidomain proteins that bind insulin and IGF with differing specificity. Here we report the crystal structure of the first three domains (L1–CR–L2) of human IR at 2.3 Å resolution and compare it with the previously determined structure of the corresponding fragment of IGF1R. The most important differences seen between the two receptors are in the two regions governing ligand specificity. The first is at the corner of the ligand-binding surface of the L1 domain, where the side chain of F39 in IR forms part of the ligand binding surface involving the second (central) β-sheet. This is very different to the location of its counterpart in IGF1R, S35, which is not involved in ligand binding. The second major difference is in the sixth module of the CR domain, where IR contains a larger loop that protrudes further into the ligand-binding pocket. This module, which governs IGF1-binding specificity, shows negligible sequence identity, significantly more α-helix, an additional disulfide bond, and opposite electrostatic potential compared to that of the IGF1R. PMID:16894147

  1. The first three domains of the insulin receptor differ structurally from the insulin-like growth factor 1 receptor in the regions governing ligand specificity.

    PubMed

    Lou, Meizhen; Garrett, Thomas P J; McKern, Neil M; Hoyne, Peter A; Epa, V Chandana; Bentley, John D; Lovrecz, George O; Cosgrove, Leah J; Frenkel, Maurice J; Ward, Colin W

    2006-08-15

    The insulin receptor (IR) and the type-1 insulin-like growth factor receptor (IGF1R) are homologous multidomain proteins that bind insulin and IGF with differing specificity. Here we report the crystal structure of the first three domains (L1-CR-L2) of human IR at 2.3 A resolution and compare it with the previously determined structure of the corresponding fragment of IGF1R. The most important differences seen between the two receptors are in the two regions governing ligand specificity. The first is at the corner of the ligand-binding surface of the L1 domain, where the side chain of F39 in IR forms part of the ligand binding surface involving the second (central) beta-sheet. This is very different to the location of its counterpart in IGF1R, S35, which is not involved in ligand binding. The second major difference is in the sixth module of the CR domain, where IR contains a larger loop that protrudes further into the ligand-binding pocket. This module, which governs IGF1-binding specificity, shows negligible sequence identity, significantly more alpha-helix, an additional disulfide bond, and opposite electrostatic potential compared to that of the IGF1R.

  2. Distribution and origin of regional coal fracture (cleat) domains in Upper Cretaceous Fruitland Formation coal: Possible effects on coalbed stimulation and methane production

    SciTech Connect

    Laubach, S.E. ); Tremain, C.M. )

    1991-03-01

    Fracture permeability is of primary importance to producibility of coalbed methane. To evaluate controls on fracture (cleat) patterns in coal beds in the Upper Cretaceous Fruitland Formation in the San Juan basin, the authors studied fractures in the coal and adjacent sandstones in 11 cores and 90 outcrop stations along the basin margin and mapped fractures in selected areas. Cleats are perpendicular to bedding, planar, usually uniform in strike within an outcrop or core, and arranged in closely spaced subparallel sets. Face cleats are the first formed (and generally most prominent) fractures; butt cleats formed later, and most cases strike perpendicular to the face cleat. Timing of cleat development is constrained by the age of cleats relative to dated folds and the burial history of the Fruitland Formation. Where beds ar reoriented by folds, cleats remain orthogonal to bedding, indicating that they formed prior to fold development during the early Tertiary. Cleat crosscuts bedding-parallel coal compaction fabrics, indicating that cleat formed later. Cleat development was contemporaneous with orogenesis in the Cordilleran belt, in progress during late Campanian time. Patterns reflect lateral stresses associated with northeast- and southeast-directed Cordilleran orogenic movements. Domains may represent separate deformation events or contemporaneous paleostress provinces. Contrasts in cleat development in individual domains can affect hydraulic fracture treatment or cavity completion. The prevalence of strongly developed face and butt cleat in the domain-boundary region and resulting increased coal friability may increase the success of cavity completions in this areas.

  3. VERY LARGE ARRAY H I ZEEMAN OBSERVATIONS OF THE CYGNUS X REGION: DR 22 AND ON 2

    SciTech Connect

    Mayo, E. A.; Troland, T. H. E-mail: troland@pa.uky.edu

    2012-02-15

    We have used the Very Large Array to study the Zeeman effect in 21 cm H I absorption lines from two star-forming regions in the Cygnus X complex, DR 22 and ON 2. We measure the line-of-sight magnetic field toward these regions, finding B{sub los} = -84 {+-} 11 {mu}G toward the DR 22 H II region and B{sub los} < 50 {mu}G toward each of the two H II regions in ON 2. We interpret these results in terms of two different models. In one model, we assume that the H I Zeeman effect is a measure of magnetic fields in the associated molecular clouds. If so, then the DR 22 molecular cloud is magnetically subcritical, that is, magnetically dominated. The ON 2 molecular clouds are magnetically supercritical. In a second model, we assume that the H I Zeeman effect is a measure of magnetic fields in photon-dominated regions where the gas has been compressed (and the field amplified) by absorption of stellar radiation. We find that this second model, where the measured field strength has been affected by star formation, accounts well for the DR 22 H I Zeeman effect. This same model, however, overpredicts the magnetic field in ON 2. ON 2 may be a region where the magnetic field is energetically insignificant or where the field happens to lie nearly in the plane of the sky.

  4. A method for computation of inviscid three-dimensional flow over blunt bodies having large embedded subsonic regions

    NASA Technical Reports Server (NTRS)

    Weilmuenster, K. J.; Hamilton, H. H., II

    1981-01-01

    A computational technique for computing the three-dimensional inviscid flow over blunt bodies having large regions of embedded subsonic flow is detailed. Results, which were obtained using the CDC Cyber 203 vector processing computer, are presented for several analytic shapes with some comparison to experimental data. Finally, windward surface pressure computations over the first third of the Space Shuttle vehicle are compared with experimental data for angles of attack between 25 and 45 degrees.

  5. Small beetle, large-scale drivers: how regional and landscape factors affect outbreaks of the European spruce bark beetle.

    PubMed

    Seidl, Rupert; Müller, Jörg; Hothorn, Torsten; Bässler, Claus; Heurich, Marco; Kautz, Markus

    2015-10-14

    1. Unprecedented bark beetle outbreaks have been observed for a variety of forest ecosystems recently, and damage is expected to further intensify as a consequence of climate change. In Central Europe, the response of ecosystem management to increasing infestation risk has hitherto focused largely on the stand level, while the contingency of outbreak dynamics on large-scale drivers remains poorly understood. 2. To investigate how factors beyond the local scale contribute to the infestation risk from Ips typographus (Col., Scol.), we analysed drivers across seven orders of magnitude in scale (from 10(3) to 10(10) m(2)) over a 23-year period, focusing on the Bavarian Forest National Park. Time-discrete hazard modelling was used to account for local factors and temporal dependencies. Subsequently, beta regression was applied to determine the influence of regional and landscape factors, the latter characterized by means of graph theory. 3. We found that in addition to stand variables, large-scale drivers also strongly influenced bark beetle infestation risk. Outbreak waves were closely related to landscape-scale connectedness of both host and beetle populations as well as to regional bark beetle infestation levels. Furthermore, regional summer drought was identified as an important trigger for infestation pulses. Large-scale synchrony and connectivity are thus key drivers of the recently observed bark beetle outbreak in the area. 4.Synthesis and applications. Our multiscale analysis provides evidence that the risk for biotic disturbances is highly dependent on drivers beyond the control of traditional stand-scale management. This finding highlights the importance of fostering the ability to cope with and recover from disturbance. It furthermore suggests that a stronger consideration of landscape and regional processes is needed to address changing disturbance regimes in ecosystem management.

  6. Small beetle, large-scale drivers: how regional and landscape factors affect outbreaks of the European spruce bark beetle

    PubMed Central

    Seidl, Rupert; Müller, Jörg; Hothorn, Torsten; Bässler, Claus; Heurich, Marco; Kautz, Markus

    2016-01-01

    Summary 1. Unprecedented bark beetle outbreaks have been observed for a variety of forest ecosystems recently, and damage is expected to further intensify as a consequence of climate change. In Central Europe, the response of ecosystem management to increasing infestation risk has hitherto focused largely on the stand level, while the contingency of outbreak dynamics on large-scale drivers remains poorly understood. 2. To investigate how factors beyond the local scale contribute to the infestation risk from Ips typographus (Col., Scol.), we analysed drivers across seven orders of magnitude in scale (from 103 to 1010 m2) over a 23-year period, focusing on the Bavarian Forest National Park. Time-discrete hazard modelling was used to account for local factors and temporal dependencies. Subsequently, beta regression was applied to determine the influence of regional and landscape factors, the latter characterized by means of graph theory. 3. We found that in addition to stand variables, large-scale drivers also strongly influenced bark beetle infestation risk. Outbreak waves were closely related to landscape-scale connectedness of both host and beetle populations as well as to regional bark beetle infestation levels. Furthermore, regional summer drought was identified as an important trigger for infestation pulses. Large-scale synchrony and connectivity are thus key drivers of the recently observed bark beetle outbreak in the area. 4. Synthesis and applications. Our multiscale analysis provides evidence that the risk for biotic disturbances is highly dependent on drivers beyond the control of traditional stand-scale management. This finding highlights the importance of fostering the ability to cope with and recover from disturbance. It furthermore suggests that a stronger consideration of landscape and regional processes is needed to address changing disturbance regimes in ecosystem management. PMID:27041769

  7. Recurrent large earthquakes in a fault region: What can be inferred from small and intermediate events?

    NASA Astrophysics Data System (ADS)

    Zoeller, G.; Hainzl, S.; Holschneider, M.

    2008-12-01

    We present a renewal model for the recurrence of large earthquakes in a fault zone consisting of a major fault and surrounding smaller faults with Gutenberg-Richter type seismicity represented by seismic moment release drawn from a truncated power-law distribution. The recurrence times of characteristic earthquakes for the major fault are explored. It is continuously loaded (plate motion) and undergoes positive and negative fluctuations due to adjacent smaller faults, with a large number Neq of such changes between two major earthquakes. Since the distribution has a finite variance, in the limit Neq→∞ the central limit theorem implies that the recurrence times follow a Brownian passage-time (BPT) distribution. This allows to calculate individual recurrence time distributions for specific fault zones without tuning free parameters: the mean recurrence time can be estimated from geological or paleoseismic data, and the standard deviation is determined from the frequency-size distribution, namely the Richter b value, of an earthquake catalog. The approach is demonstrated for the Parkfield segment of the San Andreas fault in California as well as for a long simulation of a numerical fault model. Assuming power-law distributed earthquake magnitudes up to the size of the recurrent Parkfield event (M=6), we find a coefficient of variation that is higher than the value obtained by a direct fit of the BPT distribution to seven large earthquakes. Finally we show that uncertainties in the earthquake magnitudes, e.g. from magnitude grouping, can cause a significant bias in the results. A method to correct for the bias as well as a Baysian technique to account for evolving data are provided.

  8. Recurrent large earthquakes in a fault region: What can be inferred from small and intermediate events?

    NASA Astrophysics Data System (ADS)

    Zöller, G.; Hainzl, S.; Holschneider, M.

    2009-04-01

    We present a renewal model for the recurrence of large earthquakes in a fault zone consisting of a major fault and surrounding smaller faults with Gutenberg-Richter type seismicity represented by seismic moment release drawn from a truncated power-law distribution. The recurrence times of characteristic earthquakes for the major fault are explored. It is continuously loaded (plate motion) and undergoes positive and negative fluctuations due to adjacent smaller faults, with a large number Neq of such changes between two major earthquakes. Since the distribution has a finite variance, in the limit Neq →ž the central limit theorem implies that the recurrence times follow a Brownian passage-time (BPT) distribution. This allows to calculate individual recurrence time distributions for specific fault zones without tuning free parameters: the mean recurrence time can be estimated from geological or paleoseismic data, and the standard deviation is determined from the frequency-size distribution, namely the Richter b value, of an earthquake catalog. The approach is demonstrated for the Parkfield segment of the San Andreas fault in California as well as for a long simulation of a numerical fault model. Assuming power-law distributed earthquake magnitudes up to the size of the recurrent Parkfield event (M = 6), we find a coefficient of variation that is higher than the value obtained by a direct fit of the BPT distribution to seven large earthquakes. Finally we show that uncertainties in the earthquake magnitudes, e.g. from magnitude grouping, can cause a significant bias in the results. A method to correct for the bias as well as a Baysian technique to account for evolving data are provided.

  9. Acquisition of electroencephalographic data in a large regional hospital - Bringing the brain waves to the computer.

    NASA Technical Reports Server (NTRS)

    Low, M. D.; Baker, M.; Ferguson, R.; Frost, J. D., Jr.

    1972-01-01

    This paper describes a complete electroencephalographic acquisition and transmission system, designed to meet the needs of a large hospital with multiple critical care patient monitoring units. The system provides rapid and prolonged access to a centralized recording and computing area from remote locations within the hospital complex, and from locations in other hospitals and other cities. The system includes quick-on electrode caps, amplifier units and cable transmission for access from within the hospital, and EEG digitization and telephone transmission for access from other hospitals or cities.

  10. Large systematic trend difference between national and regional homogenized datasets and global collections

    NASA Astrophysics Data System (ADS)

    Venema, Victor

    2016-04-01

    The global land temperature trend may be biased due to remaining inhomogeneities. Well-homogenized national datasets on average clearly show more warming than global collections when averaged over the region of common coverage. For this study we have collected a dataset with more than 40 national and regional average monthly temperature series (called "national" from now on). National datasets can be better homogenized than global ones. More data is available at national weather services to serve as a reference in the detection and correction of breaks. More stations and knowledge of the local climatology can help in selecting better references that are expected to have the same climate signal. More metadata is available nationally on network-wide breaks and to determine the right date of the statistically detected breaks. Furthermore, better homogenization methods are available for regional networks. Here we compare these national datasets to the global collections BEST, CRUCY, CRUTEM4, GHCNv3 and GISS. For all datasets the country average series have been computed. A subset of 10 well-homogenized national datasets shows a clearly stronger temperature trend, which is several tenths of a degree Celsius per century larger and mostly statistically significant. These differences are seen for the entire period between 1800 and now. The differences are smallest for CRUTEM4 and CRUCY, which include homogenized data from many of our national datasets. The differences are largest for BEST and GISS. GHCN represents a middle case. We are working on better understanding these differences by comparing all datasets, which range from raw data to data homogenized by various methods and which use a range of different methods to compute the national average. We look for relationships between the methods used for homogenization and averaging and the trend differences. In an accompanying poster, we i) review the literature on trend uncertainties due to remaining inhomogeneities, ii

  11. Seismological Segmentation of Halmahera Thrust, Molucca Sea Region, based on Large Earthquake Sequences

    NASA Astrophysics Data System (ADS)

    Shiddiqi, H. A.; Widiyantoro, S.; Nugraha, A. D.; Ramdhan, M.; Wiyono, S. H.; Wandono, W.

    2015-12-01

    The Molucca Sea region in eastern Indonesia is a complex tectonic region, where the arc-arc collision between the Sangihe and Halmahera arcs takes place. Two recent largest earthquakes occurred in this area are Mw 7.5, January 2007, and Mw 7.2, November 2014, that occurred 90 km to the north from the 2007 earthquake site. Both earthquakes occurred along the Halmahera thrust, however, the aftershock of the two events occurred in separated parts of the same fault. In this study, we aim to investigate the segmentation of the seismogenic zone in Molucca Sea by using seismological analysis. We employed teleseismic double-difference relocation using P- and S-wave arrival times from the Meteorological, Climatological, and Geophysical Agency of Indonesia (BMKG) and the International Seismological Centre (ISC) catalog. We used a 3D velocity model for the Indonesian region. Our relocation result revealed that aftershocks of the two events did not overlap each other. Although they have similar focal mechanisms with NNE-SSW direction, the aftershock patterns were different. While the 2014 event aftershock distribution is consistent with the strike direction inferred from the focal mechanism, the 2007 event aftershocks occurred in NEE-SWW direction. Furthermore we analyzed the spatial variation in b-value for different time ranges. The b-value analysis also showed two separated segments of low b-value anomaly around both events for each time range. We envisage that stress regime directions and geometries of the fault are different for both aftershock clusters. For this reason we analyzed focal mechanism data and found that fault segment around the 2014 event is steeper than that related to the 2007 event. We applied focal mechanism inversion to obtain the direction of stress and fault orientation, and found different stress directions for the two segments. While the northern part segment has maximum stress with SSE direction, the stress in the southern part is rotated in SE

  12. Cross‐scale intercomparison of climate change impacts simulated by regional and global hydrological models in eleven large river basins

    SciTech Connect

    Hattermann, F. F.; Krysanova, Valentina; Gosling, Simon N.; Dankers, R.; Daggupati, P.; Donnelly, C.; Florke, M.; Huang, S.; Motovilov, Y.; Buda, S.; Yang, T.; Mueller, C.; Leng, Guoyong; Tang, Qiuhong; Portmann, F. T.; Hagemann, S.; Gerten , Dieter; Wada, Yoshihide; Masaki, Y.; Alemayehu, T.; Satoh, Yusuke; Samaniego, L.

    2017-01-01

    Ideally, the results from models operating at different scales should agree in trend direction and magnitude of impacts under climate change. However, this implies that the sensitivity of impact models designed for either scale to climate variability and change is comparable. In this study, we compare hydrological changes simulated by 9 global and 9 regional hydrological models (HM) for 11 large river basins in all continents under reference and scenario conditions. The foci are on model validation runs, sensitivity of annual discharge to climate variability in the reference period, and sensitivity of the long-term average monthly seasonal dynamics to climate change. One major result is that the global models, mostly not calibrated against observations, often show a considerable bias in mean monthly discharge, whereas regional models show a much better reproduction of reference conditions. However, the sensitivity of two HM ensembles to climate variability is in general similar. The simulated climate change impacts in terms of long-term average monthly dynamics evaluated for HM ensemble medians and spreads show that the medians are to a certain extent comparable in some cases with distinct differences in others, and the spreads related to global models are mostly notably larger. Summarizing, this implies that global HMs are useful tools when looking at large-scale impacts of climate change and variability, but whenever impacts for a specific river basin or region are of interest, e.g. for complex water management applications, the regional-scale models validated against observed discharge should be used.

  13. Quantitative analysis of spin exchange interactions to identify β strand and turn regions in Ure2 prion domain fibrils with site-directed spin labeling.

    PubMed

    Ngo, Sam; Chiang, Vicky; Guo, Zhefeng

    2012-11-01

    Amyloid formation is associated with a range of debilitating human disorders including Alzheimer's and prion diseases. The amyloid structure is essential for understanding the role of amyloids in these diseases. Amyloid formation of Ure2 protein underlies the yeast prion [URE3]. Here we use site-directed spin labeling and electron paramagnetic resonance (EPR) spectroscopy to investigate the structure of amyloid fibrils formed by the Ure2 prion domain. The Ure2 prion domain under study contains a Sup35M domain at C-terminus as a solubilization element. We introduced spin labels at every residue from positions 2-15, and every 5th residue from positions 20-80 in Ure2 prion domain. EPR spectra at most labeling sites show strong spin exchange interactions, suggesting a parallel in-register β structure. With quantitative analysis of spin exchange interactions, we show that residues 8-12 form the first β strand, followed by a turn at residues 13-14, and then the second β strand from residue 15 to at least residue 20. Comparison of the spin exchange frequency for the fibrils formed under quiescent and agitated conditions also revealed differences in the fibril structures. Currently there is a lack of techniques for in-depth structural studies of amyloid fibrils. Detailed structural information is obtained almost exclusively from solid-state NMR. The identification of β-strand and turn regions in this work suggests that quantitative analysis of spin exchange interactions in spin-labeled amyloid fibrils is a powerful approach for identifying the β-strand and turn/loop residues and for studying structural differences of different fibril polymorphs.

  14. Soft tissue reconstruction in the sacro-gluteal region after excision of a large verrucous carcinoma.

    PubMed

    Albu, E; Aldea, E A

    2013-01-01

    Verrucous carcinoma is a slow-growing malignancy which, if neglected, can seriously affect local tissues. We present the case of a 55-year-old male with a 12 9 cm nodular ulcerated lesion in the sacro-gluteal region, poorly defined, with acytologic scrape smear pozitive for squamous cell cacinoma,infiltrating on MRI both gluteal muscles. The initial radiotherapeutic treatment significantly improved local condition facilitating the radical excision of the tumor. The resulting defect, 17 14 cm in size, was covered by V-Y advancement of two fasciocutaneous triangul are flaps based on transmuscular perforators from superior and inferior gluteal arteries. The patient healed completely and the tumor didn't relapse in the past 42 months.

  15. An Unusually Large Irritation Fibroma Associated with Gingiva of Lower Left Posterior Teeth Region

    PubMed Central

    Kulkarni, Sunita; Sonule, Sonal; Rathod, Usha

    2016-01-01

    Fibroma is a benign tumor of oral cavity, with usually the tongue, gingiva, and buccal mucosa being the most common sites. Females are twice more likely to develop fibroma than males. The intraoral fibroma typically is well demarcated; and its size can vary from millimeter to few centimeters. Intraorally the growth is attached to the mucosa by means of a peduncle. Fibroma is generally slow growing, painless, smooth surface lesion and the color is slightly paler than the adjacent healthy tissue. Treatment usually requires total excision and recurrence is rare. Here we present a case of 37-year-old female patient reported to the Department of Oral Medicine and Radiology with the chief complaint of a growth in the lower left posterior teeth region 3 months earlier. PMID:28116177

  16. Noise produced by the large-scale transition region structure of turbulent jets

    NASA Technical Reports Server (NTRS)

    Hardin, J. C.

    1974-01-01

    The 'orderly' structure which has been observed recently by numerous researchers within the transition region of subsonic turbulent jets is analyzed to reveal its noise-producing potential. For the case of a circular jet, this structure is modeled as a train of toroidal vortex rings which are formed near the jet exit and propagate downstream. The noise produced by the model is evaluated from a reformulation of Lighthill's expression for the far-field acoustic density which emphasizes the importance of the vorticity within the turbulent flow field. It is shown that the noise production occurs mainly close to the jet exit and depends primarily upon temporal changes in the toroidal radii. These results suggest a new approach to noise suppression which has been substantiated experimentally.

  17. Large regional differences in incidence of arthroscopic meniscal procedures in the public and private sector in Denmark

    PubMed Central

    Hare, Kristoffer Borbjerg; Vinther, Jesper Høeg; Lohmander, L Stefan; Thorlund, Jonas Bloch

    2015-01-01

    Objectives A recent study reported a large increase in the number of meniscal procedures from 2000 to 2011 in Denmark. We examined the nation-wide distribution of meniscal procedures performed in the private and public sector in Denmark since different incentives may be present and the use of these procedures may differ from region to region. Setting We included data on all patients who underwent an arthroscopic meniscal procedure performed in the public or private sector in Denmark. Participants Data were retrieved from the Danish National Patient Register on patients who underwent arthroscopic meniscus surgery as a primary or secondary procedure in the years 2000 to 2011. Hospital identification codes enabled linkage of performed procedures to specific hospitals. Primary and secondary outcome measures Yearly incidence of meniscal procedures per 100 000 inhabitants was calculated with 95% CIs for public and private procedures for each region. Results Incidence of meniscal procedures increased at private and at public hospitals. The private sector accounted for the largest relative and absolute increase, rising from an incidence of 1 in 2000 to 98 in 2011. In 2011, the incidence of meniscal procedures was three times higher in the Capital Region than in Region Zealand. Conclusions Our study identified a large increase in the use of meniscal procedures in the public and private sector in Denmark. The increase was particularly conspicuous in the private sector as its proportion of procedures performed increased from 1% to 32%. Substantial regional differences were present in the incidence and trend over time of meniscal procedures. PMID:25712820

  18. The Pliny-Strabo trench region: A large shear zone resulting from slab tearing

    NASA Astrophysics Data System (ADS)

    Özbakır, Ali D.; Şengör, A. M. C.; Wortel, M. J. R.; Govers, R.

    2013-08-01

    The eastern part of the Hellenic subduction zone is composed of the Pliny and Strabo "trenches" that have been regarded as a zone of convergence between the subducting African lithosphere and the overriding Anatolian-Aegean plate. In the Pliny and Strabo "trenches", the oblique relative plate motion is generally thought to be accommodated by a typical strain partitioning consisting of strike-slip and convergence components. Notwithstanding the occurrence of strike-slip motion parallel with the Pliny-Strabo "trenches", trench-normal thrusting is not observed so far. Therefore, we conducted a detailed analysis to investigate the deformation mechanisms of the eastern part of the Hellenic Trench system. Our analyses of offshore faulting and mechanisms of earthquakes in the overriding Aegean lithosphere show that the region of the Pliny and Strabo "trenches" obeys the mechanics of the sinistral shear zone model of Tchalenko (1970). We propose that the trench perpendicular convergence is taken up by the Rhodes fold and thrust belt, which has been postulated off the southeast coast of Rhodes. Several regional P-wave tomography results give indications of a slow seismic anomaly under this zone, which is interpreted as a tear between the Hellenic and Cyprus subduction zones. The primary reason for such tear and its propagation is the ongoing rollback of the subducted part of the African lithosphere, also referred to as "the Aegean slab". Our work elucidates the surface expression of this tearing process in the form of the development of a shear zone between the Aegean lithosphere in the NW and the African lithosphere in the SE, the Pliny-Strabo Shear Zone.

  19. Magnetic Properties of Solar Active Regions That Govern Large Solar Flares and Eruptions

    NASA Astrophysics Data System (ADS)

    Toriumi, Shin; Schrijver, Carolus J.; Harra, Louise K.; Hudson, Hugh; Nagashima, Kaori

    2017-01-01

    Solar flares and coronal mass ejections (CMEs), especially the larger ones, emanate from active regions (ARs). With the aim of understanding the magnetic properties that govern such flares and eruptions, we systematically survey all flare events with Geostationary Orbiting Environmental Satellite levels of ≥M5.0 within 45° from disk center between 2010 May and 2016 April. These criteria lead to a total of 51 flares from 29 ARs, for which we analyze the observational data obtained by the Solar Dynamics Observatory. More than 80% of the 29 ARs are found to exhibit δ-sunspots, and at least three ARs violate Hale’s polarity rule. The flare durations are approximately proportional to the distance between the two flare ribbons, to the total magnetic flux inside the ribbons, and to the ribbon area. From our study, one of the parameters that clearly determine whether a given flare event is CME-eruptive or not is the ribbon area normalized by the sunspot area, which may indicate that the structural relationship between the flaring region and the entire AR controls CME productivity. AR characterization shows that even X-class events do not require δ-sunspots or strong-field, high-gradient polarity inversion lines. An investigation of historical observational data suggests the possibility that the largest solar ARs, with magnetic flux of 2 × 1023 Mx, might be able to produce “superflares” with energies of the order of 1034 erg. The proportionality between the flare durations and magnetic energies is consistent with stellar flare observations, suggesting a common physical background for solar and stellar flares.

  20. Functional domains in tetraspanin proteins.

    PubMed

    Stipp, Christopher S; Kolesnikova, Tatiana V; Hemler, Martin E

    2003-02-01

    Exciting new findings have emerged about the structure, function and biochemistry of tetraspanin proteins. Five distinct tetraspanin regions have now been delineated linking structural features to specific functions. Within the large extracellular loop of tetraspanins, there is a variable region that mediates specific interactions with other proteins, as well as a more highly conserved region that has been suggested to mediate homodimerization. Within the transmembrane region, the four tetraspanin transmembrane domains are probable sites of both intra- and inter-molecular interactions that are crucial during biosynthesis and assembly of the network of tetraspanin-linked membrane proteins known as the 'tetraspanin web'. In the intracellular juxtamembrane region, palmitoylation of cysteine residues also contributes to tetraspanin web assembly, and the C-terminal cytoplasmic tail region could provide specific functional links to cytoskeletal or signaling proteins.

  1. Bidirectional Modulation of Thermal and Chemical Sensitivity of TRPM8 Channels by the Initial Region of the N-terminal Domain*

    PubMed Central

    Pertusa, María; González, Alejandro; Hardy, Paulina; Madrid, Rodolfo; Viana, Félix

    2014-01-01

    TRPM8, a nonselective cation channel activated by cold, voltage, and cooling compounds such as menthol, is the principal molecular detector of cold temperatures in primary sensory neurons of the somatosensory system. The N-terminal domain of TRPM8 consists of 693 amino acids, but little is known about its contribution to channel function. Here, we identified two distinct regions within the initial N terminus of TRPM8 that contribute differentially to channel activity and proper folding and assembly. Deletion or substitution of the first 40 residues yielded channels with augmented responses to cold and menthol. The thermal threshold of activation of these mutants was shifted 2 °C to higher temperatures, and the menthol dose-response curve was displaced to lower concentrations. Site-directed mutagenesis screening revealed that single point mutations at positions Ser-26 or Ser-27 by proline caused a comparable increase in the responses to cold and menthol. Electrophysiological analysis of the S27P mutant revealed that the enhanced sensitivity to agonists is related to a leftward shift in the voltage dependence of activation, increasing the probability of channel openings at physiological membrane potentials. In addition, we found that the region encompassing positions 40–60 is a key element in the proper folding and assembly of TRPM8. Different deletions and mutations within this region rendered channels with an impaired function that are retained within the endoplasmic reticulum. Our results suggest a critical contribution of the initial region of the N-terminal domain of TRPM8 to thermal and chemical sensitivity and the proper biogenesis of this polymodal ion channel. PMID:24917670

  2. Bidirectional modulation of thermal and chemical sensitivity of TRPM8 channels by the initial region of the N-terminal domain.

    PubMed

    Pertusa, María; González, Alejandro; Hardy, Paulina; Madrid, Rodolfo; Viana, Félix

    2014-08-08

    TRPM8, a nonselective cation channel activated by cold, voltage, and cooling compounds such as menthol, is the principal molecular detector of cold temperatures in primary sensory neurons of the somatosensory system. The N-terminal domain of TRPM8 consists of 693 amino acids, but little is known about its contribution to channel function. Here, we identified two distinct regions within the initial N terminus of TRPM8 that contribute differentially to channel activity and proper folding and assembly. Deletion or substitution of the first 40 residues yielded channels with augmented responses to cold and menthol. The thermal threshold of activation of these mutants was shifted 2 °C to higher temperatures, and the menthol dose-response curve was displaced to lower concentrations. Site-directed mutagenesis screening revealed that single point mutations at positions Ser-26 or Ser-27 by proline caused a comparable increase in the responses to cold and menthol. Electrophysiological analysis of the S27P mutant revealed that the enhanced sensitivity to agonists is related to a leftward shift in the voltage dependence of activation, increasing the probability of channel openings at physiological membrane potentials. In addition, we found that the region encompassing positions 40-60 is a key element in the proper folding and assembly of TRPM8. Different deletions and mutations within this region rendered channels with an impaired function that are retained within the endoplasmic reticulum. Our results suggest a critical contribution of the initial region of the N-terminal domain of TRPM8 to thermal and chemical sensitivity and the proper biogenesis of this polymodal ion channel.

  3. Central domain of DivIB caps the C-terminal regions of the FtsL/DivIC coiled-coil rod.

    PubMed

    Masson, Soizic; Kern, Thomas; Le Gouëllec, Audrey; Giustini, Cécile; Simorre, Jean-Pierre; Callow, Philip; Vernet, Thierry; Gabel, Frank; Zapun, André

    2009-10-02

    DivIB(FtsQ), FtsL, and DivIC(FtsB) are enigmatic membrane proteins that are central to the process of bacterial cell division. DivIB(FtsQ) is dispensable in specific conditions in some species, and appears to be absent in other bacterial species. The presence of FtsL and DivIC(FtsB) appears to be conserved despite very low sequence conservation. The three proteins form a complex at the division site, FtsL and DivIC(FtsB) being associated through their extracellular coiled-coil region. We report here structural investigations by NMR, small-angle neutron and x-ray scattering, and interaction studies by surface plasmon resonance, of the complex of DivIB, FtsL, and DivIC from Streptococcus pneumoniae, using soluble truncated forms of the proteins. We found that one side of the "bean"-shaped central beta-domain of DivIB interacts with the C-terminal regions of the dimer of FtsL and DivIC. This finding is corroborated by sequence comparisons across bacterial genomes. Indeed, DivIB is absent from species with shorter FtsL and DivIC proteins that have an extracellular domain consisting only of the coiled-coil segment without C-terminal conserved regions (Campylobacterales). We propose that the main role of the interaction of DivIB with FtsL and DivIC is to help the formation, or to stabilize, the coiled-coil of the latter proteins. The coiled-coil of FtsL and DivIC, itself or with transmembrane regions, could be free to interact with other partners.

  4. Inhibitors bound to Ca(2+)-free sarcoplasmic reticulum Ca(2+)-ATPase lock its transmembrane region but not necessarily its cytosolic region, revealing the flexibility of the loops connecting transmembrane and cytosolic domains.

    PubMed

    Montigny, Cédric; Picard, Martin; Lenoir, Guillaume; Gauron, Carole; Toyoshima, Chikashi; Champeil, Philippe

    2007-12-25

    Ca2+-free crystals of sarcoplasmic reticulum Ca2+-ATPase have, up until now, been obtained in the presence of inhibitors such as thapsigargin (TG), bound to the transmembrane region of this protein. Here, we examined the consequences of such binding for the protein. We found that, after TG binding, an active site ligand such as beryllium fluoride can still bind to the ATPase and change the conformation or dynamics of the cytosolic domains (as revealed by the protection afforded against proteolysis), but it becomes unable to induce any change in the transmembrane domain (as revealed by the intrinsic fluorescence of the membranous tryptophan residues). TG also obliterates the Trp fluorescence changes normally induced by binding of MgATP or metal-free ATP, as well as those induced by binding of Mg2+ alone. In the nucleotide binding domain, the environment of Lys515 (as revealed by fluorescein isothiocyanate fluorescence after specific labeling of this residue) is significantly different in the ATPase complex with aluminum fluoride and in the ATPase complex with beryllium fluoride, and in the latter case it is modified by TG. All these facts document the flexibility of the loops connecting the transmembrane and cytosolic domains in the ATPase. In the absence of active site ligands, TG protects the ATPase from cleavage by proteinase K at Thr242-Glu243, suggesting TG-induced reduction in the mobility of these loops. 2,5-Di-tert-butyl-1,4-dihydroxybenzene or cyclopiazonic acid, inhibitors which also bind in or near the transmembrane region, also produce similar overall effects on Ca2+-free ATPase.

  5. An external loop region of domain III of dengue virus type 2 envelope protein is involved in serotype-specific binding to mosquito but not mammalian cells.

    PubMed

    Hung, Jan-Jong; Hsieh, Meng-Ti; Young, Ming-Jer; Kao, Chuan-Liang; King, Chwan-Chuen; Chang, Wen

    2004-01-01

    Dengue virus (DV) is a flavivirus and infects mammalian cells through mosquito vectors. This study investigates the roles of domain III of DV type 2 envelope protein (EIII) in DV binding to the host cell. Recombinant EIII interferes with DV infection to BHK21 and C6/36 cells by blocking dengue virion adsorption to these cells. Inhibition of EIII on BHK21 cells was broad with no serotype specificity; however, inhibition of EIII on C6/36 cells was relatively serotype specific. Soluble heparin completely blocks binding of EIII to BHK21 cells, suggesting that domain III binds mainly to cell surface heparan sulfates. This suggestion is supported by the observation that EIII binds very weakly to gro2C and sog9 mutant mammalian cell lines that lack heparan sulfate. In contrast, heparin does not block binding of EIII to mosquito cells. Furthermore, a synthetic peptide that includes amino acids (aa) 380 to 389 of EIII, IGVEPGQLKL, inhibits binding of EIII to C6/36 but not BHK21 cells. This peptide corresponds to a lateral loop region on domain III of E protein, indicating a possible role of this loop in binding to mosquito cells. In summary, these results suggest that EIII plays an important role in binding of DV type 2 to host cells. In addition, EIII interacts with heparan sulfates when binding to BHK21 cells, and a loop region containing aa 380 to 389 of EIII may participate in DV type 2 binding to C6/36 cells.

  6. An External Loop Region of Domain III of Dengue Virus Type 2 Envelope Protein Is Involved in Serotype-Specific Binding to Mosquito but Not Mammalian Cells

    PubMed Central

    Hung, Jan-Jong; Hsieh, Meng-Ti; Young, Ming-Jer; Kao, Chuan-Liang; King, Chwan-Chuen; Chang, Wen

    2004-01-01

    Dengue virus (DV) is a flavivirus and infects mammalian cells through mosquito vectors. This study investigates the roles of domain III of DV type 2 envelope protein (EIII) in DV binding to the host cell. Recombinant EIII interferes with DV infection to BHK21 and C6/36 cells by blocking dengue virion adsorption to these cells. Inhibition of EIII on BHK21 cells was broad with no serotype specificity; however, inhibition of EIII on C6/36 cells was relatively serotype specific. Soluble heparin completely blocks binding of EIII to BHK21 cells, suggesting that domain III binds mainly to cell surface heparan sulfates. This suggestion is supported by the observation that EIII binds very weakly to gro2C and sog9 mutant mammalian cell lines that lack heparan sulfate. In contrast, heparin does not block binding of EIII to mosquito cells. Furthermore, a synthetic peptide that includes amino acids (aa) 380 to 389 of EIII, IGVEPGQLKL, inhibits binding of EIII to C6/36 but not BHK21 cells. This peptide corresponds to a lateral loop region on domain III of E protein, indicating a possible role of this loop in binding to mosquito cells. In summary, these results suggest that EIII plays an important role in binding of DV type 2 to host cells. In addition, EIII interacts with heparan sulfates when binding to BHK21 cells, and a loop region containing aa 380 to 389 of EIII may participate in DV type 2 binding to C6/36 cells. PMID:14671119

  7. Specific association between the methyl-CpG-binding domain protein 2 and the hypermethylated region of the human telomerase reverse transcriptase promoter in cancer cells.

    PubMed

    Chatagnon, Amandine; Bougel, Stéphanie; Perriaud, Laury; Lachuer, Joël; Benhattar, Jean; Dante, Robert

    2009-01-01

    Human telomerase reverse transcriptase (hTERT) is expressed in most cancer cells. Paradoxically, its promoter is embedded in a hypermethylated CpG island. A short region escapes to this alteration, allowing a basal level of transcription. However, the methylation of adjacent regions may play a role in the maintenance of low hTERT expression. It is now well established that methyl-CpG binding domain proteins mediate the transcriptional silencing of hypermethylated genes. The potential involvement of these proteins in the control of hTERT expression was firstly investigated in HeLa cells. Chromatin immunoprecipitation assays showed that only methyl-CpG-binding domain protein 2 (MBD2) associated the hypermethylated hTERT promoter. In MBD2 knockdown HeLa cells, constitutively depleted in MBD2, neither methyl CpG binding protein 2 (MeCP2) nor MBD1 acted as substitutes for MBD2. MBD2 depletion by transient or constitutive RNA interference led to an upregulation of hTERT transcription that can be downregulated by expressing mouse Mbd2 protein. Our results indicate that MBD2 is specifically and directly involved in the transcriptional repression of hTERT in HeLa cells. This specific transcriptional repression was also observed in breast, liver and neuroblastoma cancer cell lines. Thus, MBD2 seems to be a general repressor of hTERT in hTERT-methylated telomerase-positive cells.

  8. Influence of ocean and atmosphere coupling in a regional climate simulation: case study on typhoons over the CORDEX Southeast Asia domain

    NASA Astrophysics Data System (ADS)

    Remedio, A. R. C.; Sein, D.; Hodges, K.; Koldunov, N.; Daniela, J.

    2015-12-01

    Coupling of ocean to the atmosphere can potentially improve climate simulations including cyclonic activities within a region heavily influenced by the ocean-atmosphere interactions. From previous studies, atmosphere-only simulations have a tendency to produce higher number of cyclones compared to observations. In this study, REMO coupled with the Max Planck Institute Ocean Model or ROM, which is a regional atmosphere coupled with a global ocean model, is used to evaluate the impact of the atmosphere-ocean interaction to the tropical climate focusing on the typhoon activities. The aim is to identify the importance of the atmosphere-ocean coupling in the CORDEX Southeast Asia domain. The model domain spans 80 E to 180E and -15 S to 40 N, with a horizontal resolution of about 50 km and 27 hybrid vertical levels. The model is driven by the ERA-Interim reanalysis and run from the period of 1980 to 2012. To compare the influence of atmosphere-ocean coupling, the atmospheric model is also run uncoupled. Results on the simulated precipitation and temperature are compared to observations as well the changes in the tropical cyclone activity. Preliminary results indicate that the warm and wet biases over the ocean in the uncoupled simulations are reduced in the coupled simulations especially during the typhoon season. The frequency of typhoon occurrences is lower compared to the uncoupled model and is comparable to observations.

  9. Structure of the Large-Scale Vortex Motions in the Ionosphere E Region

    NASA Astrophysics Data System (ADS)

    Shalimov, S. L.

    2003-11-01

    It is shown that the dissipative-centrifugal instability (DCI) revealed earlier for large-scale two-dimension vortex motions of the neutral gas in a fast-rotating atmosphere is also possible for similar motions of a weakly ionized gas in the magnetic field when one takes into account electrodynamics forces (the induction deceleration and gyroscopic force caused by the Hall current) in the absence of dissipation. In the case of a conductive atmosphere, strictly anticyclone motion at a DCI of the neutral atmosphere could be impossible or (depending on the Hall conductivity value) it could even change to a cyclone motion. Experimental results that can be considered as a confirmation of the theoretical conclusions are presented.

  10. Stochastic Inverse Modeling of Large-Scale Fractured Domains: Example of the Culebra Dolomite in the Vicinity of the WIPP Site

    NASA Astrophysics Data System (ADS)

    McKenna, S. A.; Hart, D. B.; Kanney, J. D.; Beauheim, R. L.

    2008-12-01

    The challenge described in this work is to create an ensemble of calibrated transmissivity (T) fields for the Culebra Dolomite Member of the Rustler Formation at the Waste Isolation Pilot Plant (WIPP) site in southeastern New Mexico. The T fields must individually represent 20 years of transient pumping tests and a set of steady-state head observations across a nearly 30×30 km area. A recently developed geologic conceptual model provides initial values for the T-field calibrations and provides zonation of the model domain based on classes of fracturing and presence or absence of fracture filling materials. These calibrations are completed using the pilot point method with a large (> 400) number of pilot point locations. For each pumping test, responses from between 2 and 12 observation wells at radial distances of 100s of meters to several km away from the pumping well are available. Over 1200 head and drawdown observations are used in the inverse model. Directionally focused transient responses reflect the fractured nature of the Culebra dolomite and are difficult to represent using the effective porosity conceptual model and the large cell sizes (100×100m) necessary for efficient computations within the model domain. Improved representation of the fractured nature of the Culebra is accomplished by efficient pilot point placement based on the sensitivity of the pumping - observation well pairs to perturbations in transmissivity as well as simultaneous estimation of spatially heterogeneous T, storativity, and hydraulic anisotropy fields. Simultaneous estimation of three spatially heterogeneous fields results in over 900 estimated parameters within the model. Singular value decomposition of the Jacobian matrix and adaptive regularization of the estimated parameters along with parallel computation make these calibrations numerically stable and computationally feasible. By allowing these three parameters to vary, within constraints, accurate matches to the steady

  11. The accuracy of large-area forest canopy cover estimation using Landsat in boreal region

    NASA Astrophysics Data System (ADS)

    Hadi; Korhonen, Lauri; Hovi, Aarne; Rönnholm, Petri; Rautiainen, Miina

    2016-12-01

    Large area prediction of continuous field of tree cover i.e., canopy cover (CC) using Earth observation data is of high interest in practical forestry, ecology, and climate change mitigation activities. We report the accuracy of using Landsat images for CC prediction in boreal forests validated with field reference plots (N = 250) covering large variation in latitude, forest structure, species composition, and site type. We tested two statistical models suitable for estimating CC: the beta regression (BetaReg) and random forest (RanFor). Landsat-based predictors utilized include individual bands, spectral vegetation indices (SVI), and Tasseled cap (Tass) features. Additionally, we tested an alternative model based on spectral mixture analysis (SMA). Finally, we carried out a first validation in boreal forests of the recently published Landsat Tree Cover Continuous (TCC) global product. Results showed simple BetaReg with red band reflectance provided the highest prediction accuracy (leave-site-out RMSECV 13.7%; R2CV 0.59; biasCV 0.5%). Spectral transformations into SVI and Tass did not improve accuracy. Including additional predictors did not significantly improve accuracy either. Nonlinear model RanFor did not outperform BetaReg. The alternative SMA model did not outperform the empirical models. However, empirical models cannot resolve the underestimation of high cover and overestimation of low cover. SMA prediction errors appeared less dependent on forest structure, while there seemed to be a potential for improvement by accounting for endmember variability of different tree species. Finally, using temporally concurrent observations, we showed the reasonably good accuracy of Landsat TCC product in boreal forests (RMSE 13.0%; R2 0.53; bias -2.1%), however with a tendency to underestimate high cover.

  12. Regional Expansion of Minimally Invasive Surgery for Hysterectomy: Implementation and Methodology in a Large Multispecialty Group

    PubMed Central

    Andryjowicz, Esteban; Wray, Teresa

    2011-01-01

    Introduction: Approximately 600,000 hysterectomies are performed in the US each year, making hysterectomy the second most common major operation performed in women. Several methods can be used to perform this procedure. In 2009, a Cochrane Review concluded “that vaginal hysterectomy should be performed in preference to abdominal hysterectomy, where possible. Where vaginal hysterectomy is not possible, a laparoscopic approach may avoid the need for an abdominal hysterectomy. Risks and benefits of different approaches may however be influenced by the surgeon's experience. More research is needed, particularly to examine the long-term effects of the different types of surgery.” This article reviews the steps that a large multispecialty group used to teach non-open hysterectomy methods to improve the quality of care for their patients and to decrease the number of inpatient procedures and therefore costs. The percentages of each type of hysterectomy performed yearly between 2005 and 2010 were calculated, as well as the length of stay (LOS) for each method. Methods: A structured educational intervention with both didactic and hands-on exercises was created and rolled out to 12 medical centers. All patients undergoing hysterectomy for benign conditions through the Southern California Permanente Medical Group (a large multispecialty group that provides medical care to Kaiser Permanente patients in Southern California) between 2005 and 2010 were included. This amounted to 26,055 hysterectomies for benign conditions being performed by more than 350 obstetrician/gynecologists (Ob/Gyns). Results: More than 300 Ob/Gyns took the course across 12 medical centers. On the basis of hospital discharge data, the total number of hysterectomies, types of hysterectomies, and LOS for each type were identified for each year. Between 2005 and 2010, the rate of non-open hysterectomies has increased 120% (from 38% to 78%) and the average LOS has decreased 31%. PMID:22319415

  13. A refined regional modeling approach for the Corn Belt - Experiences and recommendations for large-scale integrated modeling

    NASA Astrophysics Data System (ADS)

    Panagopoulos, Yiannis; Gassman, Philip W.; Jha, Manoj K.; Kling, Catherine L.; Campbell, Todd; Srinivasan, Raghavan; White, Michael; Arnold, Jeffrey G.

    2015-05-01

    Nonpoint source pollution from agriculture is the main source of nitrogen and phosphorus in the stream systems of the Corn Belt region in the Midwestern US. This region is comprised of two large river basins, the intensely row-cropped Upper Mississippi River Basin (UMRB) and Ohio-Tennessee River Basin (OTRB), which are considered the key contributing areas for the Northern Gulf of Mexico hypoxic zone according to the US Environmental Protection Agency. Thus, in this area it is of utmost importance to ensure that intensive agriculture for food, feed and biofuel production can coexist with a healthy water environment. To address these objectives within a river basin management context, an integrated modeling system has been constructed with the hydrologic Soil and Water Assessment Tool (SWAT) model, capable of estimating river basin responses to alternative cropping and/or management strategies. To improve modeling performance compared to previous studies and provide a spatially detailed basis for scenario development, this SWAT Corn Belt application incorporates a greatly refined subwatershed structure based on 12-digit hydrologic units or 'subwatersheds' as defined by the US Geological Service. The model setup, calibration and validation are time-demanding and challenging tasks for these large systems, given the scale intensive data requirements, and the need to ensure the reliability of flow and pollutant load predictions at multiple locations. Thus, the objectives of this study are both to comprehensively describe this large-scale modeling approach, providing estimates of pollution and crop production in the region as well as to present strengths and weaknesses of integrated modeling at such a large scale along with how it can be improved on the basis of the current modeling structure and results. The predictions were based on a semi-automatic hydrologic calibration approach for large-scale and spatially detailed modeling studies, with the use of the Sequential

  14. Structural dynamics and ssDNA binding activity of the three N-terminal domains of the large subunit of Replication Protein A from small angle X-ray scattering

    SciTech Connect

    Pretto, Dalyir I.; Tsutakawa, Susan; Brosey, Chris A.; Castillo, Amalchi; Chagot, Marie-Eve; Smith, Jarrod A.; Tainer, John A.; Chazin, Walter J.

    2010-03-11

    Replication Protein A (RPA) is the primary eukaryotic ssDNA binding protein utilized in diverse DNA transactions in the cell. RPA is a heterotrimeric protein with seven globular domains connected by flexible linkers, which enable substantial inter-domain motion that is essential to its function. Small angle X-ray scattering (SAXS) experiments on two multi-domain constructs from the N-terminus of the large subunit (RPA70) were used to examine the structural dynamics of these domains and their response to the binding of ssDNA. The SAXS data combined with molecular dynamics simulations reveal substantial interdomain flexibility for both RPA70AB (the tandem high affinity ssDNA binding domains A and B connected by a 10-residue linker) and RPA70NAB (RPA70AB extended by a 70-residue linker to the RPA70N protein interaction domain). Binding of ssDNA to RPA70NAB reduces the interdomain flexibility between the A and B domains, but has no effect on RPA70N. These studies provide the first direct measurements of changes in orientation of these three RPA domains upon binding ssDNA. The results support a model in which RPA70N remains structurally independent of RPA70AB in the DNA bound state and therefore freely available to serve as a protein recruitment module.

  15. Analysis of the promoter region and the N-propeptide domain of the human pro alpha 2(I) collagen gene.

    PubMed Central

    Dickson, L A; de Wet, W; Di Liberto, M; Weil, D; Ramirez, F

    1985-01-01

    We have located the exon coding for the start site of transcription of the human pro alpha 2(I) collagen gene. Comparison with the homologous region of other fibrillar collagen genes has confirmed the existence of a consensus sequence (CATGTCTA-n-TAGACATG) capable of forming a hairpin secondary structure possibly involved in the regulation of collagen biosynthesis. Sequence comparison of the chromosomal regions at the 5' end of the pro alpha 1(I) and pro alpha 2(I) collagen genes failed to identify unique DNA elements potentially mediating common regulatory signals. Sequencing of four exons coding for the N-terminal propeptide has determined most of its structure and it has implied the existence of smaller coding units similar to the 11 and 18 bp exons originally described in the avian gene. Images PMID:4011429

  16. Isolation of a monoclonal antibody that recognizes the origin binding domain of JCV, but not SV40, large T-antigen.

    PubMed

    Grubman, Shelley A; Shin, Jong; Phelan, Paul J; Gong, Aaron; Can, Hande; Dilworth, Ryan; Kini, Sandeep Kuntadi; Gagnon, David; Archambault, Jacques; Meinke, Gretchen; Bohm, Andrew; Jefferson, Douglas M; Bullock, Peter A

    2016-10-01

    Within immunocompromised populations, the JC polyomavirus is the cause of the often-fatal disease Progressive Multifocal Leukoencephalopathy (PML). JC virus encodes a protein, termed T-antigen (T-ag), which is essential for its replication and pathogenicity. Previous studies of JCV T-ag have, in general, used antibodies raised against SV40 T-ag. Unfortunately, SV40 T-ag is also detected in humans and therefore there have been concerns about cross-reactivity. To address this issue, we have isolated a monoclonal antibody that binds to the JCV, but not the SV40, T-ag origin-binding domain (OBD). Furthermore, the region on the surface of the JCV T-ag OBD that is recognized by the "anti-JCV OBD mAb" has been mapped. We also demonstrate that the "anti-JCV OBD mAb" will be a useful reagent for standard techniques (e.g., Westerns blots and ELISAs). Finally, we note that additional monoclonal Abs that are specific for the T-ags encoded by the other human polyomaviruses could be generated by adopting the approach described herein.

  17. Local Condensation Curve from Dropwise to Glacial Region on Large Vertical Surface

    NASA Astrophysics Data System (ADS)

    Haraguchi, Tadao; Shimada, Ryohachi; Takeyama, Toshiro

    The existence of several regimes of condensation heat transfer is well known. Regimes are given academic names as dropwise, transition, film and glacial condensation along the condensation curve showing the relationship between heat flux and surface subcooling. In case of comparatively large vertical surface, the lower part on the gravitational direction is affected by condensate from the upper part, and will be covered by water stream like a rivulet. It has no longer an existence as dropwise condition, and it is absolutely impossible that heat transfer problems under constant temperature or constant heat flux take place. The reason is why as follows, heat transfer of film condensation is some orders of magnitude less than dropwise condensation, and various regimes exist together simultaneously. In the present paper we shall try to observe the coexisting appearance of regimes in steam condensation at atmospheric pressure and make researches in the local condensation curve from top to bottom on the same surface, that is divided into eight parts in the rear side. The main results are shown as follows (1) Enhancement of heat transfer by wiping of drops appears t